From cf5923e90e341a332c1930a943de64dec7f2a364 Mon Sep 17 00:00:00 2001
From: Soeren Peters <peters@irmb.tu-bs.de>
Date: Tue, 6 Oct 2020 10:17:27 +0200
Subject: [PATCH] Remove metis 5.1.0.
---
3rdParty/metis/metis-5.1.0/CMakeLists.txt | 27 -
3rdParty/metis/metis-5.1.0/GKlib/BUILD.txt | 25 -
.../metis/metis-5.1.0/GKlib/CMakeLists.txt | 21 -
3rdParty/metis/metis-5.1.0/GKlib/GKlib.h | 84 -
.../metis/metis-5.1.0/GKlib/GKlibSystem.cmake | 129 -
3rdParty/metis/metis-5.1.0/GKlib/Makefile | 76 -
3rdParty/metis/metis-5.1.0/GKlib/b64.c | 95 -
3rdParty/metis/metis-5.1.0/GKlib/blas.c | 36 -
.../GKlib/conf/check_thread_storage.c | 5 -
3rdParty/metis/metis-5.1.0/GKlib/csr.c | 2010 ---
3rdParty/metis/metis-5.1.0/GKlib/error.c | 214 -
3rdParty/metis/metis-5.1.0/GKlib/evaluate.c | 132 -
3rdParty/metis/metis-5.1.0/GKlib/fkvkselect.c | 142 -
3rdParty/metis/metis-5.1.0/GKlib/fs.c | 225 -
3rdParty/metis/metis-5.1.0/GKlib/getopt.c | 854 --
3rdParty/metis/metis-5.1.0/GKlib/gk_arch.h | 71 -
3rdParty/metis/metis-5.1.0/GKlib/gk_defs.h | 69 -
3rdParty/metis/metis-5.1.0/GKlib/gk_externs.h | 25 -
3rdParty/metis/metis-5.1.0/GKlib/gk_getopt.h | 64 -
3rdParty/metis/metis-5.1.0/GKlib/gk_macros.h | 153 -
3rdParty/metis/metis-5.1.0/GKlib/gk_mkblas.h | 201 -
.../metis/metis-5.1.0/GKlib/gk_mkmemory.h | 142 -
.../metis/metis-5.1.0/GKlib/gk_mkpqueue.h | 437 -
.../metis/metis-5.1.0/GKlib/gk_mkpqueue2.h | 215 -
.../metis/metis-5.1.0/GKlib/gk_mkrandom.h | 123 -
3rdParty/metis/metis-5.1.0/GKlib/gk_mksort.h | 273 -
3rdParty/metis/metis-5.1.0/GKlib/gk_mkutils.h | 40 -
3rdParty/metis/metis-5.1.0/GKlib/gk_proto.h | 381 -
3rdParty/metis/metis-5.1.0/GKlib/gk_struct.h | 268 -
3rdParty/metis/metis-5.1.0/GKlib/gk_types.h | 38 -
3rdParty/metis/metis-5.1.0/GKlib/gkregex.c | 10704 ----------------
3rdParty/metis/metis-5.1.0/GKlib/gkregex.h | 556 -
3rdParty/metis/metis-5.1.0/GKlib/graph.c | 1574 ---
3rdParty/metis/metis-5.1.0/GKlib/htable.c | 247 -
3rdParty/metis/metis-5.1.0/GKlib/io.c | 384 -
3rdParty/metis/metis-5.1.0/GKlib/itemsets.c | 210 -
3rdParty/metis/metis-5.1.0/GKlib/mcore.c | 393 -
3rdParty/metis/metis-5.1.0/GKlib/memory.c | 252 -
.../metis/metis-5.1.0/GKlib/ms_inttypes.h | 301 -
3rdParty/metis/metis-5.1.0/GKlib/ms_stat.h | 22 -
3rdParty/metis/metis-5.1.0/GKlib/ms_stdint.h | 222 -
3rdParty/metis/metis-5.1.0/GKlib/omp.c | 27 -
3rdParty/metis/metis-5.1.0/GKlib/pdb.c | 460 -
3rdParty/metis/metis-5.1.0/GKlib/pqueue.c | 25 -
3rdParty/metis/metis-5.1.0/GKlib/random.c | 134 -
3rdParty/metis/metis-5.1.0/GKlib/rw.c | 103 -
3rdParty/metis/metis-5.1.0/GKlib/seq.c | 174 -
3rdParty/metis/metis-5.1.0/GKlib/sort.c | 327 -
3rdParty/metis/metis-5.1.0/GKlib/string.c | 529 -
.../metis-5.1.0/GKlib/test/CMakeLists.txt | 13 -
.../metis-5.1.0/GKlib/test/Makefile.in.old | 258 -
.../metis/metis-5.1.0/GKlib/test/Makefile.old | 39 -
3rdParty/metis/metis-5.1.0/GKlib/test/fis.c | 286 -
.../metis/metis-5.1.0/GKlib/test/gkgraph.c | 351 -
.../metis/metis-5.1.0/GKlib/test/gksort.c | 346 -
3rdParty/metis/metis-5.1.0/GKlib/test/rw.c | 307 -
.../metis/metis-5.1.0/GKlib/test/strings.c | 82 -
3rdParty/metis/metis-5.1.0/GKlib/timers.c | 52 -
3rdParty/metis/metis-5.1.0/GKlib/tokenizer.c | 77 -
3rdParty/metis/metis-5.1.0/GKlib/util.c | 108 -
.../metis/metis-5.1.0/include/CMakeLists.txt | 3 -
3rdParty/metis/metis-5.1.0/include/metis.h | 350 -
.../metis/metis-5.1.0/libmetis/CMakeLists.txt | 18 -
3rdParty/metis/metis-5.1.0/libmetis/auxapi.c | 43 -
3rdParty/metis/metis-5.1.0/libmetis/balance.c | 498 -
.../metis/metis-5.1.0/libmetis/bucketsort.c | 44 -
.../metis/metis-5.1.0/libmetis/checkgraph.c | 263 -
3rdParty/metis/metis-5.1.0/libmetis/coarsen.c | 1132 --
.../metis/metis-5.1.0/libmetis/compress.c | 229 -
3rdParty/metis/metis-5.1.0/libmetis/contig.c | 699 -
3rdParty/metis/metis-5.1.0/libmetis/debug.c | 461 -
3rdParty/metis/metis-5.1.0/libmetis/defs.h | 60 -
3rdParty/metis/metis-5.1.0/libmetis/fm.c | 543 -
3rdParty/metis/metis-5.1.0/libmetis/fortran.c | 142 -
3rdParty/metis/metis-5.1.0/libmetis/frename.c | 136 -
3rdParty/metis/metis-5.1.0/libmetis/gklib.c | 120 -
.../metis/metis-5.1.0/libmetis/gklib_defs.h | 53 -
.../metis/metis-5.1.0/libmetis/gklib_rename.h | 122 -
3rdParty/metis/metis-5.1.0/libmetis/graph.c | 274 -
.../metis/metis-5.1.0/libmetis/initpart.c | 630 -
3rdParty/metis/metis-5.1.0/libmetis/kmetis.c | 243 -
3rdParty/metis/metis-5.1.0/libmetis/kwayfm.c | 1852 ---
.../metis/metis-5.1.0/libmetis/kwayrefine.c | 672 -
3rdParty/metis/metis-5.1.0/libmetis/macros.h | 258 -
3rdParty/metis/metis-5.1.0/libmetis/mcutil.c | 330 -
3rdParty/metis/metis-5.1.0/libmetis/mesh.c | 412 -
.../metis/metis-5.1.0/libmetis/meshpart.c | 262 -
.../metis/metis-5.1.0/libmetis/metislib.h | 41 -
3rdParty/metis/metis-5.1.0/libmetis/minconn.c | 729 --
.../metis/metis-5.1.0/libmetis/mincover.c | 259 -
3rdParty/metis/metis-5.1.0/libmetis/mmd.c | 593 -
3rdParty/metis/metis-5.1.0/libmetis/ometis.c | 701 -
3rdParty/metis/metis-5.1.0/libmetis/options.c | 532 -
.../metis/metis-5.1.0/libmetis/parmetis.c | 723 --
3rdParty/metis/metis-5.1.0/libmetis/pmetis.c | 387 -
3rdParty/metis/metis-5.1.0/libmetis/proto.h | 348 -
3rdParty/metis/metis-5.1.0/libmetis/refine.c | 211 -
3rdParty/metis/metis-5.1.0/libmetis/rename.h | 266 -
.../metis/metis-5.1.0/libmetis/separator.c | 176 -
3rdParty/metis/metis-5.1.0/libmetis/sfm.c | 612 -
3rdParty/metis/metis-5.1.0/libmetis/srefine.c | 163 -
3rdParty/metis/metis-5.1.0/libmetis/stat.c | 179 -
.../metis/metis-5.1.0/libmetis/stdheaders.h | 29 -
3rdParty/metis/metis-5.1.0/libmetis/struct.h | 206 -
3rdParty/metis/metis-5.1.0/libmetis/timing.c | 63 -
3rdParty/metis/metis-5.1.0/libmetis/util.c | 138 -
3rdParty/metis/metis-5.1.0/libmetis/wspace.c | 214 -
107 files changed, 41557 deletions(-)
delete mode 100644 3rdParty/metis/metis-5.1.0/CMakeLists.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/BUILD.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/CMakeLists.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/GKlib.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/GKlibSystem.cmake
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/Makefile
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/b64.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/blas.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/conf/check_thread_storage.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/csr.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/error.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/evaluate.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/fkvkselect.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/fs.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/getopt.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_arch.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_defs.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_externs.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_getopt.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_macros.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkblas.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkmemory.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue2.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkrandom.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mksort.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_mkutils.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_proto.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_struct.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gk_types.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gkregex.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/gkregex.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/graph.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/htable.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/io.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/itemsets.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/mcore.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/memory.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/ms_inttypes.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/ms_stat.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/ms_stdint.h
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/omp.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/pdb.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/pqueue.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/random.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/rw.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/seq.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/sort.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/string.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/CMakeLists.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.in.old
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.old
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/fis.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/gkgraph.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/gksort.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/rw.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/test/strings.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/timers.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/tokenizer.c
delete mode 100644 3rdParty/metis/metis-5.1.0/GKlib/util.c
delete mode 100644 3rdParty/metis/metis-5.1.0/include/CMakeLists.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/include/metis.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/CMakeLists.txt
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/auxapi.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/balance.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/bucketsort.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/checkgraph.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/coarsen.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/compress.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/contig.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/debug.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/defs.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/fm.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/fortran.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/frename.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/gklib.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/gklib_defs.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/gklib_rename.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/graph.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/initpart.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/kmetis.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/kwayfm.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/kwayrefine.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/macros.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/mcutil.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/mesh.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/meshpart.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/metislib.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/minconn.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/mincover.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/mmd.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/ometis.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/options.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/parmetis.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/pmetis.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/proto.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/refine.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/rename.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/separator.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/sfm.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/srefine.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/stat.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/stdheaders.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/struct.h
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/timing.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/util.c
delete mode 100644 3rdParty/metis/metis-5.1.0/libmetis/wspace.c
diff --git a/3rdParty/metis/metis-5.1.0/CMakeLists.txt b/3rdParty/metis/metis-5.1.0/CMakeLists.txt
deleted file mode 100644
index 967b473ef..000000000
--- a/3rdParty/metis/metis-5.1.0/CMakeLists.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-cmake_minimum_required(VERSION 2.8)
-project(METIS)
-
-set(GKLIB_PATH "${PROJECT_SOURCE_DIR}/GKlib" CACHE PATH "path to GKlib")
-#set(SHARED FALSE CACHE BOOL "build a shared library")
-
-if(MSVC)
- set(METIS_INSTALL FALSE)
-else()
- set(METIS_INSTALL TRUE)
-endif()
-
-# Configure libmetis library.
-if(BUILD_SHARED_LIBS)
- set(METIS_LIBRARY_TYPE SHARED)
-else()
- set(METIS_LIBRARY_TYPE STATIC)
-endif()
-
-include(${GKLIB_PATH}/GKlibSystem.cmake)
-# Add include directories.
-include_directories(${GKLIB_PATH})
-include_directories(include)
-# Recursively look for CMakeLists.txt in subdirs.
-add_subdirectory("include")
-add_subdirectory("libmetis")
-#add_subdirectory("programs")
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/BUILD.txt b/3rdParty/metis/metis-5.1.0/GKlib/BUILD.txt
deleted file mode 100644
index cdb9987a9..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/BUILD.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-Building GKlib requires CMake 2.8. Once you've installed CMake run
-
- $ make
-
-This will build the GKlib library in build/<arch>/. Options can be tweaked by
-running make config. For example,
-
- $ make config openmp=ON
- $ make
-
-will build GKlib will OpenMP support if it is available.
-
-GKlib can be installed with
-
- $ make install
-
-and uninstalled with
-
- $ make uninstall
-
-You can choose the installation prefix with make config:
-
- $ make config prefix=~/local
-
-will cause GKlib to be install in the ~/local tree.
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/CMakeLists.txt b/3rdParty/metis/metis-5.1.0/GKlib/CMakeLists.txt
deleted file mode 100644
index 67b600aa6..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/CMakeLists.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-cmake_minimum_required(VERSION 2.8)
-project(GKlib)
-
-get_filename_component(abs "." ABSOLUTE)
-set(GKLIB_PATH ${abs})
-unset(abs)
-include(GKlibSystem.cmake)
-
-include_directories(".")
-add_library(GKlib STATIC ${GKlib_sources})
-if(UNIX)
- target_link_libraries(GKlib m)
-endif(UNIX)
-
-include_directories("test")
-add_subdirectory("test")
-
-install(TARGETS GKlib
- ARCHIVE DESTINATION lib
- LIBRARY DESTINATION lib)
-install(FILES ${GKlib_includes} DESTINATION include)
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/GKlib.h b/3rdParty/metis/metis-5.1.0/GKlib/GKlib.h
deleted file mode 100644
index 492c90f2e..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/GKlib.h
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * GKlib.h
- *
- * George's library of most frequently used routines
- *
- * $Id: GKlib.h 13005 2012-10-23 22:34:36Z karypis $
- *
- */
-
-#ifndef _GKLIB_H_
-#define _GKLIB_H_ 1
-
-#define GKMSPACE
-
-#if defined(_MSC_VER)
-#define __MSC__
-#endif
-#if defined(__ICC)
-#define __ICC__
-#endif
-
-
-#include "gk_arch.h" /*!< This should be here, prior to the includes */
-
-
-/*************************************************************************
-* Header file inclusion section
-**************************************************************************/
-#include <stddef.h>
-#include <stdlib.h>
-#include <stdarg.h>
-#include <stdio.h>
-#include <errno.h>
-#include <ctype.h>
-#include <math.h>
-#include <float.h>
-#include <time.h>
-#include <string.h>
-#include <limits.h>
-#include <signal.h>
-#include <setjmp.h>
-#include <assert.h>
-#include <sys/stat.h>
-
-#if defined(__WITHPCRE__)
- #include <pcreposix.h>
-#else
- #if defined(USE_GKREGEX)
- #include "gkregex.h"
- #else
- #include <regex.h>
- #endif /* defined(USE_GKREGEX) */
-#endif /* defined(__WITHPCRE__) */
-
-
-
-#if defined(__OPENMP__)
-#include <omp.h>
-#endif
-
-
-
-
-#include <gk_types.h>
-#include <gk_struct.h>
-#include <gk_externs.h>
-#include <gk_defs.h>
-#include <gk_macros.h>
-#include <gk_getopt.h>
-
-#include <gk_mksort.h>
-#include <gk_mkblas.h>
-#include <gk_mkmemory.h>
-#include <gk_mkpqueue.h>
-#include <gk_mkpqueue2.h>
-#include <gk_mkrandom.h>
-#include <gk_mkutils.h>
-
-#include <gk_proto.h>
-
-
-#endif /* GKlib.h */
-
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/GKlibSystem.cmake b/3rdParty/metis/metis-5.1.0/GKlib/GKlibSystem.cmake
deleted file mode 100644
index 86aef59c8..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/GKlibSystem.cmake
+++ /dev/null
@@ -1,129 +0,0 @@
-# Helper modules.
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-
-# Setup options.
-#option(GDB "enable use of GDB" OFF)
-#option(ASSERT "turn asserts on" OFF)
-#option(ASSERT2 "additional assertions" OFF)
-#option(DEBUG "add debugging support" OFF)
-#option(GPROF "add gprof support" OFF)
-#option(OPENMP "enable OpenMP support" OFF)
-#option(PCRE "enable PCRE support" OFF)
-#option(GKREGEX "enable GKREGEX support" OFF)
-#option(GKRAND "enable GKRAND support" OFF)
-
-# Add compiler flags.
-if(MSVC)
- set(GKlib_COPTS "/Ox")
- set(GKlib_COPTIONS "-DWIN32 -DMSC -D_CRT_SECURE_NO_DEPRECATE -DUSE_GKREGEX")
-elseif(MINGW)
- set(GKlib_COPTS "-DUSE_GKREGEX")
-else()
- set(GKlib_COPTS "-O3")
- set(GKlib_COPTIONS "-DLINUX -D_FILE_OFFSET_BITS=64")
-endif(MSVC)
-if(CYGWIN)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DCYGWIN")
-endif(CYGWIN)
-if(CMAKE_COMPILER_IS_GNUCC)
-# GCC opts.
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -std=c99 -fno-strict-aliasing")
- if(NOT MINGW)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -fPIC")
- endif(NOT MINGW)
-# GCC warnings.
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -Wall -pedantic -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas")
-elseif(${CMAKE_C_COMPILER_ID} MATCHES "Sun")
-# Sun insists on -xc99.
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -xc99")
-endif(CMAKE_COMPILER_IS_GNUCC)
-
-# Find OpenMP if it is requested.
-if(OPENMP)
- include(FindOpenMP)
- if(OPENMP_FOUND)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__OPENMP__ ${OpenMP_C_FLAGS}")
- else()
- message(WARNING "OpenMP was requested but support was not found")
- endif(OPENMP_FOUND)
-endif(OPENMP)
-
-
-# Add various definitions.
-if(GDB)
- set(GKlib_COPTS "${GKlib_COPTS} -g")
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -Werror")
-endif(GDB)
-
-
-if(DEBUG)
- set(GKlib_COPTS "-g")
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DDEBUG")
-endif(DEBUG)
-
-if(GPROF)
- set(GKlib_COPTS "-pg")
-endif(GPROF)
-
-if(NOT ASSERT)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG")
-endif(NOT ASSERT)
-
-if(NOT ASSERT2)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG2")
-endif(NOT ASSERT2)
-
-
-# Add various options
-if(PCRE)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__WITHPCRE__")
-endif(PCRE)
-
-if(GKREGEX)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKREGEX")
-endif(GKREGEX)
-
-if(GKRAND)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKRAND")
-endif(GKRAND)
-
-
-# Check for features.
-check_include_file(execinfo.h HAVE_EXECINFO_H)
-if(HAVE_EXECINFO_H)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_EXECINFO_H")
-endif(HAVE_EXECINFO_H)
-
-check_function_exists(getline HAVE_GETLINE)
-if(HAVE_GETLINE)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_GETLINE")
-endif(HAVE_GETLINE)
-
-
-# Custom check for TLS.
-if(MSVC)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=__declspec(thread)")
-else()
- # This if checks if that value is cached or not.
- if("${HAVE_THREADLOCALSTORAGE}" MATCHES "^${HAVE_THREADLOCALSTORAGE}$")
- try_compile(HAVE_THREADLOCALSTORAGE
- ${CMAKE_BINARY_DIR}
- ${GKLIB_PATH}/conf/check_thread_storage.c)
- if(HAVE_THREADLOCALSTORAGE)
- message(STATUS "checking for thread-local storage - found")
- else()
- message(STATUS "checking for thread-local storage - not found")
- endif()
- endif()
- if(NOT HAVE_THREADLOCALSTORAGE)
- set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=")
- endif()
-endif()
-
-# Finally set the official C flags.
-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GKlib_COPTIONS} ${GKlib_COPTS}")
-
-# Find GKlib sources.
-file(GLOB GKlib_sources ${GKLIB_PATH}/*.c)
-file(GLOB GKlib_includes ${GKLIB_PATH}/*.h)
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/Makefile b/3rdParty/metis/metis-5.1.0/GKlib/Makefile
deleted file mode 100644
index d17b4f44c..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/Makefile
+++ /dev/null
@@ -1,76 +0,0 @@
-# Configuration options.
-gdb = not-set
-assert = not-set
-assert2 = not-set
-debug = not-set
-gprof = not-set
-openmp = not-set
-prefix = not-set
-pcre = not-set
-gkregex = not-set
-gkrand = not-set
-
-
-# Basically proxies everything to the builddir cmake.
-cputype = $(shell uname -m | sed "s/\\ /_/g")
-systype = $(shell uname -s)
-
-BUILDDIR = build/$(systype)-$(cputype)
-
-# Process configuration options.
-CONFIG_FLAGS = -DCMAKE_VERBOSE_MAKEFILE=1
-ifneq ($(gdb), not-set)
- CONFIG_FLAGS += -DGDB=$(gdb)
-endif
-ifneq ($(assert), not-set)
- CONFIG_FLAGS += -DASSERT=$(assert)
-endif
-ifneq ($(assert2), not-set)
- CONFIG_FLAGS += -DASSERT2=$(assert2)
-endif
-ifneq ($(debug), not-set)
- CONFIG_FLAGS += -DDEBUG=$(debug)
-endif
-ifneq ($(gprof), not-set)
- CONFIG_FLAGS += -DGPROF=$(gprof)
-endif
-ifneq ($(openmp), not-set)
- CONFIG_FLAGS += -DOPENMP=$(openmp)
-endif
-ifneq ($(pcre), not-set)
- CONFIG_FLAGS += -DPCRE=$(pcre)
-endif
-ifneq ($(gkregex), not-set)
- CONFIG_FLAGS += -DGKREGEX=$(pcre)
-endif
-ifneq ($(gkrand), not-set)
- CONFIG_FLAGS += -DGKRAND=$(pcre)
-endif
-ifneq ($(prefix), not-set)
- CONFIG_FLAGS += -DCMAKE_INSTALL_PREFIX=$(prefix)
-endif
-
-define run-config
-mkdir -p $(BUILDDIR)
-cd $(BUILDDIR) && cmake $(CURDIR) $(CONFIG_FLAGS)
-endef
-
-all clean install: $(BUILDDIR)
- make -C $(BUILDDIR) $@
-
-uninstall:
- xargs rm < $(BUILDDIR)/install_manifest.txt
-
-$(BUILDDIR):
- $(run-config)
-
-config: distclean
- $(run-config)
-
-distclean:
- rm -rf $(BUILDDIR)
-
-remake:
- find . -name CMakeLists.txt -exec touch {} ';'
-
-.PHONY: config distclean all clean install uninstall remake
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/b64.c b/3rdParty/metis/metis-5.1.0/GKlib/b64.c
deleted file mode 100644
index afacd68a1..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/b64.c
+++ /dev/null
@@ -1,95 +0,0 @@
-/*!
-\file b64.c
-\brief This file contains some simple 8bit-to-6bit encoding/deconding routines
-
-Most of these routines are outdated and should be converted using glibc's equivalent
-routines.
-
-\date Started 2/22/05
-\author George
-\version\verbatim $Id: b64.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-
-\verbatim
-$Copyright$
-$License$
-\endverbatim
-
-*/
-
-
-#include "GKlib.h"
-
-#define B64OFFSET 48 /* This is the '0' number */
-
-
-/******************************************************************************
-* Encode 3 '8-bit' binary bytes as 4 '6-bit' characters
-*******************************************************************************/
-void encodeblock(unsigned char *in, unsigned char *out)
-{
- out[0] = (in[0] >> 2);
- out[1] = (((in[0] & 0x03) << 4) | (in[1] >> 4));
- out[2] = (((in[1] & 0x0f) << 2) | (in[2] >> 6));
- out[3] = (in[2] & 0x3f);
-
- out[0] += B64OFFSET;
- out[1] += B64OFFSET;
- out[2] += B64OFFSET;
- out[3] += B64OFFSET;
-
-// printf("%c %c %c %c %2x %2x %2x %2x %2x %2x %2x\n", out[0], out[1], out[2], out[3], out[0], out[1], out[2], out[3], in[0], in[1], in[2]);
-}
-
-/******************************************************************************
-* Decode 4 '6-bit' characters into 3 '8-bit' binary bytes
-*******************************************************************************/
-void decodeblock(unsigned char *in, unsigned char *out)
-{
- in[0] -= B64OFFSET;
- in[1] -= B64OFFSET;
- in[2] -= B64OFFSET;
- in[3] -= B64OFFSET;
-
- out[0] = (in[0] << 2 | in[1] >> 4);
- out[1] = (in[1] << 4 | in[2] >> 2);
- out[2] = (in[2] << 6 | in[3]);
-}
-
-
-/******************************************************************************
-* This function encodes an input array of bytes into a base64 encoding. Memory
-* for the output array is assumed to have been allocated by the calling program
-* and be sufficiently large. The output string is NULL terminated.
-*******************************************************************************/
-void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
-{
- int i, j;
-
- if (nbytes%3 != 0)
- gk_errexit(SIGERR, "GKEncodeBase64: Input buffer size should be a multiple of 3! (%d)\n", nbytes);
-
- for (j=0, i=0; i<nbytes; i+=3, j+=4)
- encodeblock(inbuffer+i, outbuffer+j);
-
-//printf("%d %d\n", nbytes, j);
- outbuffer[j] = '\0';
-}
-
-
-
-/******************************************************************************
-* This function decodes an input array of base64 characters into their actual
-* 8-bit codes. Memory * for the output array is assumed to have been allocated
-* by the calling program and be sufficiently large. The padding is discarded.
-*******************************************************************************/
-void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
-{
- int i, j;
-
- if (nbytes%4 != 0)
- gk_errexit(SIGERR, "GKDecodeBase64: Input buffer size should be a multiple of 4! (%d)\n", nbytes);
-
- for (j=0, i=0; i<nbytes; i+=4, j+=3)
- decodeblock(inbuffer+i, outbuffer+j);
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/blas.c b/3rdParty/metis/metis-5.1.0/GKlib/blas.c
deleted file mode 100644
index b65cd0264..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/blas.c
+++ /dev/null
@@ -1,36 +0,0 @@
-/*!
-\file blas.c
-\brief This file contains GKlib's implementation of BLAS-like routines
-
-The BLAS routines that are currently implemented are mostly level-one.
-They follow a naming convention of the type gk_[type][name], where
-[type] is one of c, i, f, and d, based on C's four standard scalar
-datatypes of characters, integers, floats, and doubles.
-
-These routines are implemented using a generic macro template,
-which is used for code generation.
-
-\date Started 9/28/95
-\author George
-\version\verbatim $Id: blas.c 11848 2012-04-20 13:47:37Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-
-/*************************************************************************/
-/*! Use the templates to generate BLAS routines for the scalar data types */
-/*************************************************************************/
-GK_MKBLAS(gk_c, char, int)
-GK_MKBLAS(gk_i, int, int)
-GK_MKBLAS(gk_i32, int32_t, int32_t)
-GK_MKBLAS(gk_i64, int64_t, int64_t)
-GK_MKBLAS(gk_z, ssize_t, ssize_t)
-GK_MKBLAS(gk_f, float, float)
-GK_MKBLAS(gk_d, double, double)
-GK_MKBLAS(gk_idx, gk_idx_t, gk_idx_t)
-
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/conf/check_thread_storage.c b/3rdParty/metis/metis-5.1.0/GKlib/conf/check_thread_storage.c
deleted file mode 100644
index e6e1e980e..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/conf/check_thread_storage.c
+++ /dev/null
@@ -1,5 +0,0 @@
-extern __thread int x;
-
-int main(int argc, char **argv) {
- return 0;
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/csr.c b/3rdParty/metis/metis-5.1.0/GKlib/csr.c
deleted file mode 100644
index a19d793bd..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/csr.c
+++ /dev/null
@@ -1,2010 +0,0 @@
-/*!
- * \file
- *
- * \brief Various routines with dealing with CSR matrices
- *
- * \author George Karypis
- * \version\verbatim $Id: csr.c 13437 2013-01-11 21:54:10Z karypis $ \endverbatim
- */
-
-#include <GKlib.h>
-
-#define OMPMINOPS 50000
-
-/*************************************************************************/
-/*! Allocate memory for a CSR matrix and initializes it
- \returns the allocated matrix. The various fields are set to NULL.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_Create()
-{
- gk_csr_t *mat;
-
- mat = (gk_csr_t *)gk_malloc(sizeof(gk_csr_t), "gk_csr_Create: mat");
-
- gk_csr_Init(mat);
-
- return mat;
-}
-
-
-/*************************************************************************/
-/*! Initializes the matrix
- \param mat is the matrix to be initialized.
-*/
-/*************************************************************************/
-void gk_csr_Init(gk_csr_t *mat)
-{
- memset(mat, 0, sizeof(gk_csr_t));
- mat->nrows = mat->ncols = -1;
-}
-
-
-/*************************************************************************/
-/*! Frees all the memory allocated for matrix.
- \param mat is the matrix to be freed.
-*/
-/*************************************************************************/
-void gk_csr_Free(gk_csr_t **mat)
-{
- if (*mat == NULL)
- return;
- gk_csr_FreeContents(*mat);
- gk_free((void **)mat, LTERM);
-}
-
-
-/*************************************************************************/
-/*! Frees only the memory allocated for the matrix's different fields and
- sets them to NULL.
- \param mat is the matrix whose contents will be freed.
-*/
-/*************************************************************************/
-void gk_csr_FreeContents(gk_csr_t *mat)
-{
- gk_free((void *)&mat->rowptr, &mat->rowind, &mat->rowval, &mat->rowids,
- &mat->colptr, &mat->colind, &mat->colval, &mat->colids,
- &mat->rnorms, &mat->cnorms, &mat->rsums, &mat->csums,
- &mat->rsizes, &mat->csizes, &mat->rvols, &mat->cvols,
- &mat->rwgts, &mat->cwgts,
- LTERM);
-}
-
-
-/*************************************************************************/
-/*! Returns a copy of a matrix.
- \param mat is the matrix to be duplicated.
- \returns the newly created copy of the matrix.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_Dup(gk_csr_t *mat)
-{
- gk_csr_t *nmat;
-
- nmat = gk_csr_Create();
-
- nmat->nrows = mat->nrows;
- nmat->ncols = mat->ncols;
-
- /* copy the row structure */
- if (mat->rowptr)
- nmat->rowptr = gk_zcopy(mat->nrows+1, mat->rowptr,
- gk_zmalloc(mat->nrows+1, "gk_csr_Dup: rowptr"));
- if (mat->rowids)
- nmat->rowids = gk_icopy(mat->nrows, mat->rowids,
- gk_imalloc(mat->nrows, "gk_csr_Dup: rowids"));
- if (mat->rnorms)
- nmat->rnorms = gk_fcopy(mat->nrows, mat->rnorms,
- gk_fmalloc(mat->nrows, "gk_csr_Dup: rnorms"));
- if (mat->rowind)
- nmat->rowind = gk_icopy(mat->rowptr[mat->nrows], mat->rowind,
- gk_imalloc(mat->rowptr[mat->nrows], "gk_csr_Dup: rowind"));
- if (mat->rowval)
- nmat->rowval = gk_fcopy(mat->rowptr[mat->nrows], mat->rowval,
- gk_fmalloc(mat->rowptr[mat->nrows], "gk_csr_Dup: rowval"));
-
- /* copy the col structure */
- if (mat->colptr)
- nmat->colptr = gk_zcopy(mat->ncols+1, mat->colptr,
- gk_zmalloc(mat->ncols+1, "gk_csr_Dup: colptr"));
- if (mat->colids)
- nmat->colids = gk_icopy(mat->ncols, mat->colids,
- gk_imalloc(mat->ncols, "gk_csr_Dup: colids"));
- if (mat->cnorms)
- nmat->cnorms = gk_fcopy(mat->ncols, mat->cnorms,
- gk_fmalloc(mat->ncols, "gk_csr_Dup: cnorms"));
- if (mat->colind)
- nmat->colind = gk_icopy(mat->colptr[mat->ncols], mat->colind,
- gk_imalloc(mat->colptr[mat->ncols], "gk_csr_Dup: colind"));
- if (mat->colval)
- nmat->colval = gk_fcopy(mat->colptr[mat->ncols], mat->colval,
- gk_fmalloc(mat->colptr[mat->ncols], "gk_csr_Dup: colval"));
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Returns a submatrix containint a set of consecutive rows.
- \param mat is the original matrix.
- \param rstart is the starting row.
- \param nrows is the number of rows from rstart to extract.
- \returns the row structure of the newly created submatrix.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_ExtractSubmatrix(gk_csr_t *mat, int rstart, int nrows)
-{
- ssize_t i;
- gk_csr_t *nmat;
-
- if (rstart+nrows > mat->nrows)
- return NULL;
-
- nmat = gk_csr_Create();
-
- nmat->nrows = nrows;
- nmat->ncols = mat->ncols;
-
- /* copy the row structure */
- if (mat->rowptr)
- nmat->rowptr = gk_zcopy(nrows+1, mat->rowptr+rstart,
- gk_zmalloc(nrows+1, "gk_csr_ExtractSubmatrix: rowptr"));
- for (i=nrows; i>=0; i--)
- nmat->rowptr[i] -= nmat->rowptr[0];
- ASSERT(nmat->rowptr[0] == 0);
-
- if (mat->rowids)
- nmat->rowids = gk_icopy(nrows, mat->rowids+rstart,
- gk_imalloc(nrows, "gk_csr_ExtractSubmatrix: rowids"));
- if (mat->rnorms)
- nmat->rnorms = gk_fcopy(nrows, mat->rnorms+rstart,
- gk_fmalloc(nrows, "gk_csr_ExtractSubmatrix: rnorms"));
-
- if (mat->rsums)
- nmat->rsums = gk_fcopy(nrows, mat->rsums+rstart,
- gk_fmalloc(nrows, "gk_csr_ExtractSubmatrix: rsums"));
-
- ASSERT(nmat->rowptr[nrows] == mat->rowptr[rstart+nrows]-mat->rowptr[rstart]);
- if (mat->rowind)
- nmat->rowind = gk_icopy(mat->rowptr[rstart+nrows]-mat->rowptr[rstart],
- mat->rowind+mat->rowptr[rstart],
- gk_imalloc(mat->rowptr[rstart+nrows]-mat->rowptr[rstart],
- "gk_csr_ExtractSubmatrix: rowind"));
- if (mat->rowval)
- nmat->rowval = gk_fcopy(mat->rowptr[rstart+nrows]-mat->rowptr[rstart],
- mat->rowval+mat->rowptr[rstart],
- gk_fmalloc(mat->rowptr[rstart+nrows]-mat->rowptr[rstart],
- "gk_csr_ExtractSubmatrix: rowval"));
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Returns a submatrix containing a certain set of rows.
- \param mat is the original matrix.
- \param nrows is the number of rows to extract.
- \param rind is the set of row numbers to extract.
- \returns the row structure of the newly created submatrix.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_ExtractRows(gk_csr_t *mat, int nrows, int *rind)
-{
- ssize_t i, ii, j, nnz;
- gk_csr_t *nmat;
-
- nmat = gk_csr_Create();
-
- nmat->nrows = nrows;
- nmat->ncols = mat->ncols;
-
- for (nnz=0, i=0; i<nrows; i++)
- nnz += mat->rowptr[rind[i]+1]-mat->rowptr[rind[i]];
-
- nmat->rowptr = gk_zmalloc(nmat->nrows+1, "gk_csr_ExtractPartition: rowptr");
- nmat->rowind = gk_imalloc(nnz, "gk_csr_ExtractPartition: rowind");
- nmat->rowval = gk_fmalloc(nnz, "gk_csr_ExtractPartition: rowval");
-
- nmat->rowptr[0] = 0;
- for (nnz=0, j=0, ii=0; ii<nrows; ii++) {
- i = rind[ii];
- gk_icopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowind+mat->rowptr[i], nmat->rowind+nnz);
- gk_fcopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowval+mat->rowptr[i], nmat->rowval+nnz);
- nnz += mat->rowptr[i+1]-mat->rowptr[i];
- nmat->rowptr[++j] = nnz;
- }
- ASSERT(j == nmat->nrows);
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Returns a submatrix corresponding to a specified partitioning of rows.
- \param mat is the original matrix.
- \param part is the partitioning vector of the rows.
- \param pid is the partition ID that will be extracted.
- \returns the row structure of the newly created submatrix.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_ExtractPartition(gk_csr_t *mat, int *part, int pid)
-{
- ssize_t i, j, nnz;
- gk_csr_t *nmat;
-
- nmat = gk_csr_Create();
-
- nmat->nrows = 0;
- nmat->ncols = mat->ncols;
-
- for (nnz=0, i=0; i<mat->nrows; i++) {
- if (part[i] == pid) {
- nmat->nrows++;
- nnz += mat->rowptr[i+1]-mat->rowptr[i];
- }
- }
-
- nmat->rowptr = gk_zmalloc(nmat->nrows+1, "gk_csr_ExtractPartition: rowptr");
- nmat->rowind = gk_imalloc(nnz, "gk_csr_ExtractPartition: rowind");
- nmat->rowval = gk_fmalloc(nnz, "gk_csr_ExtractPartition: rowval");
-
- nmat->rowptr[0] = 0;
- for (nnz=0, j=0, i=0; i<mat->nrows; i++) {
- if (part[i] == pid) {
- gk_icopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowind+mat->rowptr[i], nmat->rowind+nnz);
- gk_fcopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowval+mat->rowptr[i], nmat->rowval+nnz);
- nnz += mat->rowptr[i+1]-mat->rowptr[i];
- nmat->rowptr[++j] = nnz;
- }
- }
- ASSERT(j == nmat->nrows);
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Splits the matrix into multiple sub-matrices based on the provided
- color array.
- \param mat is the original matrix.
- \param color is an array of size equal to the number of non-zeros
- in the matrix (row-wise structure). The matrix is split into
- as many parts as the number of colors. For meaningfull results,
- the colors should be numbered consecutively starting from 0.
- \returns an array of matrices for each supplied color number.
-*/
-/**************************************************************************/
-gk_csr_t **gk_csr_Split(gk_csr_t *mat, int *color)
-{
- ssize_t i, j;
- int nrows, ncolors;
- ssize_t *rowptr;
- int *rowind;
- float *rowval;
- gk_csr_t **smats;
-
- nrows = mat->nrows;
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
-
- ncolors = gk_imax(rowptr[nrows], color)+1;
-
- smats = (gk_csr_t **)gk_malloc(sizeof(gk_csr_t *)*ncolors, "gk_csr_Split: smats");
- for (i=0; i<ncolors; i++) {
- smats[i] = gk_csr_Create();
- smats[i]->nrows = mat->nrows;
- smats[i]->ncols = mat->ncols;
- smats[i]->rowptr = gk_zsmalloc(nrows+1, 0, "gk_csr_Split: smats[i]->rowptr");
- }
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- smats[color[j]]->rowptr[i]++;
- }
- for (i=0; i<ncolors; i++)
- MAKECSR(j, nrows, smats[i]->rowptr);
-
- for (i=0; i<ncolors; i++) {
- smats[i]->rowind = gk_imalloc(smats[i]->rowptr[nrows], "gk_csr_Split: smats[i]->rowind");
- smats[i]->rowval = gk_fmalloc(smats[i]->rowptr[nrows], "gk_csr_Split: smats[i]->rowval");
- }
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- smats[color[j]]->rowind[smats[color[j]]->rowptr[i]] = rowind[j];
- smats[color[j]]->rowval[smats[color[j]]->rowptr[i]] = rowval[j];
- smats[color[j]]->rowptr[i]++;
- }
- }
-
- for (i=0; i<ncolors; i++)
- SHIFTCSR(j, nrows, smats[i]->rowptr);
-
- return smats;
-}
-
-
-/**************************************************************************/
-/*! Reads a CSR matrix from the supplied file and stores it the matrix's
- forward structure.
- \param filename is the file that stores the data.
- \param format is either GK_CSR_FMT_METIS, GK_CSR_FMT_CLUTO,
- GK_CSR_FMT_CSR, GK_CSR_FMT_BINROW, GK_CSR_FMT_BINCOL
- specifying the type of the input format.
- The GK_CSR_FMT_CSR does not contain a header
- line, whereas the GK_CSR_FMT_BINROW is a binary format written
- by gk_csr_Write() using the same format specifier.
- \param readvals is either 1 or 0, indicating if the CSR file contains
- values or it does not. It only applies when GK_CSR_FMT_CSR is
- used.
- \param numbering is either 1 or 0, indicating if the numbering of the
- indices start from 1 or 0, respectively. If they start from 1,
- they are automatically decreamented during input so that they
- will start from 0. It only applies when GK_CSR_FMT_CSR is
- used.
- \returns the matrix that was read.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_Read(char *filename, int format, int readvals, int numbering)
-{
- ssize_t i, k, l;
- size_t nfields, nrows, ncols, nnz, fmt, ncon;
- size_t lnlen;
- ssize_t *rowptr;
- int *rowind, ival;
- float *rowval=NULL, fval;
- int readsizes, readwgts;
- char *line=NULL, *head, *tail, fmtstr[256];
- FILE *fpin;
- gk_csr_t *mat=NULL;
-
-
- if (!gk_fexists(filename))
- gk_errexit(SIGERR, "File %s does not exist!\n", filename);
-
- if (format == GK_CSR_FMT_BINROW) {
- mat = gk_csr_Create();
-
- fpin = gk_fopen(filename, "rb", "gk_csr_Read: fpin");
- if (fread(&(mat->nrows), sizeof(int32_t), 1, fpin) != 1)
- gk_errexit(SIGERR, "Failed to read the nrows from file %s!\n", filename);
- if (fread(&(mat->ncols), sizeof(int32_t), 1, fpin) != 1)
- gk_errexit(SIGERR, "Failed to read the ncols from file %s!\n", filename);
- mat->rowptr = gk_zmalloc(mat->nrows+1, "gk_csr_Read: rowptr");
- if (fread(mat->rowptr, sizeof(ssize_t), mat->nrows+1, fpin) != mat->nrows+1)
- gk_errexit(SIGERR, "Failed to read the rowptr from file %s!\n", filename);
- mat->rowind = gk_imalloc(mat->rowptr[mat->nrows], "gk_csr_Read: rowind");
- if (fread(mat->rowind, sizeof(int32_t), mat->rowptr[mat->nrows], fpin) != mat->rowptr[mat->nrows])
- gk_errexit(SIGERR, "Failed to read the rowind from file %s!\n", filename);
- if (readvals == 1) {
- mat->rowval = gk_fmalloc(mat->rowptr[mat->nrows], "gk_csr_Read: rowval");
- if (fread(mat->rowval, sizeof(float), mat->rowptr[mat->nrows], fpin) != mat->rowptr[mat->nrows])
- gk_errexit(SIGERR, "Failed to read the rowval from file %s!\n", filename);
- }
-
- gk_fclose(fpin);
- return mat;
- }
-
- if (format == GK_CSR_FMT_BINCOL) {
- mat = gk_csr_Create();
-
- fpin = gk_fopen(filename, "rb", "gk_csr_Read: fpin");
- if (fread(&(mat->nrows), sizeof(int32_t), 1, fpin) != 1)
- gk_errexit(SIGERR, "Failed to read the nrows from file %s!\n", filename);
- if (fread(&(mat->ncols), sizeof(int32_t), 1, fpin) != 1)
- gk_errexit(SIGERR, "Failed to read the ncols from file %s!\n", filename);
- mat->colptr = gk_zmalloc(mat->ncols+1, "gk_csr_Read: colptr");
- if (fread(mat->colptr, sizeof(ssize_t), mat->ncols+1, fpin) != mat->ncols+1)
- gk_errexit(SIGERR, "Failed to read the colptr from file %s!\n", filename);
- mat->colind = gk_imalloc(mat->colptr[mat->ncols], "gk_csr_Read: colind");
- if (fread(mat->colind, sizeof(int32_t), mat->colptr[mat->ncols], fpin) != mat->colptr[mat->ncols])
- gk_errexit(SIGERR, "Failed to read the colind from file %s!\n", filename);
- if (readvals) {
- mat->colval = gk_fmalloc(mat->colptr[mat->ncols], "gk_csr_Read: colval");
- if (fread(mat->colval, sizeof(float), mat->colptr[mat->ncols], fpin) != mat->colptr[mat->ncols])
- gk_errexit(SIGERR, "Failed to read the colval from file %s!\n", filename);
- }
-
- gk_fclose(fpin);
- return mat;
- }
-
-
- if (format == GK_CSR_FMT_CLUTO) {
- fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin");
- do {
- if (gk_getline(&line, &lnlen, fpin) <= 0)
- gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename);
- } while (line[0] == '%');
-
- if (sscanf(line, "%zu %zu %zu", &nrows, &ncols, &nnz) != 3)
- gk_errexit(SIGERR, "Header line must contain 3 integers.\n");
-
- readsizes = 0;
- readwgts = 0;
- readvals = 1;
- numbering = 1;
- }
- else if (format == GK_CSR_FMT_METIS) {
- fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin");
- do {
- if (gk_getline(&line, &lnlen, fpin) <= 0)
- gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename);
- } while (line[0] == '%');
-
- fmt = ncon = 0;
- nfields = sscanf(line, "%zu %zu %zu %zu", &nrows, &nnz, &fmt, &ncon);
- if (nfields < 2)
- gk_errexit(SIGERR, "Header line must contain at least 2 integers (#vtxs and #edges).\n");
-
- ncols = nrows;
- nnz *= 2;
-
- if (fmt > 111)
- gk_errexit(SIGERR, "Cannot read this type of file format [fmt=%zu]!\n", fmt);
-
- sprintf(fmtstr, "%03zu", fmt%1000);
- readsizes = (fmtstr[0] == '1');
- readwgts = (fmtstr[1] == '1');
- readvals = (fmtstr[2] == '1');
- numbering = 1;
- ncon = (ncon == 0 ? 1 : ncon);
- }
- else {
- readsizes = 0;
- readwgts = 0;
-
- gk_getfilestats(filename, &nrows, &nnz, NULL, NULL);
-
- if (readvals == 1 && nnz%2 == 1)
- gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not even.\n", nnz, readvals);
- if (readvals == 1)
- nnz = nnz/2;
- fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin");
- }
-
- mat = gk_csr_Create();
-
- mat->nrows = nrows;
-
- rowptr = mat->rowptr = gk_zmalloc(nrows+1, "gk_csr_Read: rowptr");
- rowind = mat->rowind = gk_imalloc(nnz, "gk_csr_Read: rowind");
- if (readvals != 2)
- rowval = mat->rowval = gk_fsmalloc(nnz, 1.0, "gk_csr_Read: rowval");
-
- if (readsizes)
- mat->rsizes = gk_fsmalloc(nrows, 0.0, "gk_csr_Read: rsizes");
-
- if (readwgts)
- mat->rwgts = gk_fsmalloc(nrows*ncon, 0.0, "gk_csr_Read: rwgts");
-
- /*----------------------------------------------------------------------
- * Read the sparse matrix file
- *---------------------------------------------------------------------*/
- numbering = (numbering ? - 1 : 0);
- for (ncols=0, rowptr[0]=0, k=0, i=0; i<nrows; i++) {
- do {
- if (gk_getline(&line, &lnlen, fpin) == -1)
- gk_errexit(SIGERR, "Premature end of input file: file while reading row %d\n", i);
- } while (line[0] == '%');
-
- head = line;
- tail = NULL;
-
- /* Read vertex sizes */
- if (readsizes) {
-#ifdef __MSC__
- mat->rsizes[i] = (float)strtod(head, &tail);
-#else
- mat->rsizes[i] = strtof(head, &tail);
-#endif
- if (tail == head)
- gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1);
- if (mat->rsizes[i] < 0)
- errexit("The size for vertex %zd must be >= 0\n", i+1);
- head = tail;
- }
-
- /* Read vertex weights */
- if (readwgts) {
- for (l=0; l<ncon; l++) {
-#ifdef __MSC__
- mat->rwgts[i*ncon+l] = (float)strtod(head, &tail);
-#else
- mat->rwgts[i*ncon+l] = strtof(head, &tail);
-#endif
- if (tail == head)
- errexit("The line for vertex %zd does not have enough weights "
- "for the %d constraints.\n", i+1, ncon);
- if (mat->rwgts[i*ncon+l] < 0)
- errexit("The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l);
- head = tail;
- }
- }
-
-
- /* Read the rest of the row */
- while (1) {
- ival = (int)strtol(head, &tail, 0);
- if (tail == head)
- break;
- head = tail;
-
- if ((rowind[k] = ival + numbering) < 0)
- gk_errexit(SIGERR, "Error: Invalid column number %d at row %zd.\n", ival, i);
-
- ncols = gk_max(rowind[k], ncols);
-
- if (readvals == 1) {
-#ifdef __MSC__
- fval = (float)strtod(head, &tail);
-#else
- fval = strtof(head, &tail);
-#endif
- if (tail == head)
- gk_errexit(SIGERR, "Value could not be found for column! Row:%zd, NNZ:%zd\n", i, k);
- head = tail;
-
- rowval[k] = fval;
- }
- k++;
- }
- rowptr[i+1] = k;
- }
-
- if (format == GK_CSR_FMT_METIS) {
- ASSERT(ncols+1 == mat->nrows);
- mat->ncols = mat->nrows;
- }
- else {
- mat->ncols = ncols+1;
- }
-
- if (k != nnz)
- gk_errexit(SIGERR, "gk_csr_Read: Something wrong with the number of nonzeros in "
- "the input file. NNZ=%zd, ActualNNZ=%zd.\n", nnz, k);
-
- gk_fclose(fpin);
-
- gk_free((void **)&line, LTERM);
-
- return mat;
-}
-
-
-/**************************************************************************/
-/*! Writes the row-based structure of a matrix into a file.
- \param mat is the matrix to be written,
- \param filename is the name of the output file.
- \param format is one of: GK_CSR_FMT_CLUTO, GK_CSR_FMT_CSR,
- GK_CSR_FMT_BINROW, GK_CSR_FMT_BINCOL.
- \param writevals is either 1 or 0 indicating if the values will be
- written or not. This is only applicable when GK_CSR_FMT_CSR
- is used.
- \param numbering is either 1 or 0 indicating if the internal 0-based
- numbering will be shifted by one or not during output. This
- is only applicable when GK_CSR_FMT_CSR is used.
-*/
-/**************************************************************************/
-void gk_csr_Write(gk_csr_t *mat, char *filename, int format, int writevals, int numbering)
-{
- ssize_t i, j;
- FILE *fpout;
-
- if (format == GK_CSR_FMT_BINROW) {
- if (filename == NULL)
- gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n");
- fpout = gk_fopen(filename, "wb", "gk_csr_Write: fpout");
-
- fwrite(&(mat->nrows), sizeof(int32_t), 1, fpout);
- fwrite(&(mat->ncols), sizeof(int32_t), 1, fpout);
- fwrite(mat->rowptr, sizeof(ssize_t), mat->nrows+1, fpout);
- fwrite(mat->rowind, sizeof(int32_t), mat->rowptr[mat->nrows], fpout);
- if (writevals)
- fwrite(mat->rowval, sizeof(float), mat->rowptr[mat->nrows], fpout);
-
- gk_fclose(fpout);
- return;
- }
-
- if (format == GK_CSR_FMT_BINCOL) {
- if (filename == NULL)
- gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n");
- fpout = gk_fopen(filename, "wb", "gk_csr_Write: fpout");
-
- fwrite(&(mat->nrows), sizeof(int32_t), 1, fpout);
- fwrite(&(mat->ncols), sizeof(int32_t), 1, fpout);
- fwrite(mat->colptr, sizeof(ssize_t), mat->ncols+1, fpout);
- fwrite(mat->colind, sizeof(int32_t), mat->colptr[mat->ncols], fpout);
- if (writevals)
- fwrite(mat->colval, sizeof(float), mat->colptr[mat->ncols], fpout);
-
- gk_fclose(fpout);
- return;
- }
-
- if (filename)
- fpout = gk_fopen(filename, "w", "gk_csr_Write: fpout");
- else
- fpout = stdout;
-
- if (format == GK_CSR_FMT_CLUTO) {
- fprintf(fpout, "%d %d %zd\n", mat->nrows, mat->ncols, mat->rowptr[mat->nrows]);
- writevals = 1;
- numbering = 1;
- }
-
- for (i=0; i<mat->nrows; i++) {
- for (j=mat->rowptr[i]; j<mat->rowptr[i+1]; j++) {
- fprintf(fpout, " %d", mat->rowind[j]+(numbering ? 1 : 0));
- if (writevals)
- fprintf(fpout, " %f", mat->rowval[j]);
- }
- fprintf(fpout, "\n");
- }
- if (filename)
- gk_fclose(fpout);
-}
-
-
-/*************************************************************************/
-/*! Prunes certain rows/columns of the matrix. The prunning takes place
- by analyzing the row structure of the matrix. The prunning takes place
- by removing rows/columns but it does not affect the numbering of the
- remaining rows/columns.
-
- \param mat the matrix to be prunned,
- \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL)
- of the matrix will be prunned,
- \param minf is the minimum number of rows (columns) that a column (row) must
- be present in order to be kept,
- \param maxf is the maximum number of rows (columns) that a column (row) must
- be present at in order to be kept.
- \returns the prunned matrix consisting only of its row-based structure.
- The input matrix is not modified.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_Prune(gk_csr_t *mat, int what, int minf, int maxf)
-{
- ssize_t i, j, nnz;
- int nrows, ncols;
- ssize_t *rowptr, *nrowptr;
- int *rowind, *nrowind, *collen;
- float *rowval, *nrowval;
- gk_csr_t *nmat;
-
- nmat = gk_csr_Create();
-
- nrows = nmat->nrows = mat->nrows;
- ncols = nmat->ncols = mat->ncols;
-
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
-
- nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_Prune: nrowptr");
- nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_Prune: nrowind");
- nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_Prune: nrowval");
-
-
- switch (what) {
- case GK_CSR_COL:
- collen = gk_ismalloc(ncols, 0, "gk_csr_Prune: collen");
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- ASSERT(rowind[j] < ncols);
- collen[rowind[j]]++;
- }
- }
- for (i=0; i<ncols; i++)
- collen[i] = (collen[i] >= minf && collen[i] <= maxf ? 1 : 0);
-
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (collen[rowind[j]]) {
- nrowind[nnz] = rowind[j];
- nrowval[nnz] = rowval[j];
- nnz++;
- }
- }
- nrowptr[i+1] = nnz;
- }
- gk_free((void **)&collen, LTERM);
- break;
-
- case GK_CSR_ROW:
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- if (rowptr[i+1]-rowptr[i] >= minf && rowptr[i+1]-rowptr[i] <= maxf) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++, nnz++) {
- nrowind[nnz] = rowind[j];
- nrowval[nnz] = rowval[j];
- }
- }
- nrowptr[i+1] = nnz;
- }
- break;
-
- default:
- gk_csr_Free(&nmat);
- gk_errexit(SIGERR, "Unknown prunning type of %d\n", what);
- return NULL;
- }
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Eliminates certain entries from the rows/columns of the matrix. The
- filtering takes place by keeping only the highest weight entries whose
- sum accounts for a certain fraction of the overall weight of the
- row/column.
-
- \param mat the matrix to be prunned,
- \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL)
- of the matrix will be prunned,
- \param norm indicates the norm that will be used to aggregate the weights
- and possible values are 1 or 2,
- \param fraction is the fraction of the overall norm that will be retained
- by the kept entries.
- \returns the filtered matrix consisting only of its row-based structure.
- The input matrix is not modified.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_LowFilter(gk_csr_t *mat, int what, int norm, float fraction)
-{
- ssize_t i, j, nnz;
- int nrows, ncols, ncand, maxlen=0;
- ssize_t *rowptr, *colptr, *nrowptr;
- int *rowind, *colind, *nrowind;
- float *rowval, *colval, *nrowval, rsum, tsum;
- gk_csr_t *nmat;
- gk_fkv_t *cand;
-
- nmat = gk_csr_Create();
-
- nrows = nmat->nrows = mat->nrows;
- ncols = nmat->ncols = mat->ncols;
-
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
- colptr = mat->colptr;
- colind = mat->colind;
- colval = mat->colval;
-
- nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_LowFilter: nrowptr");
- nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_LowFilter: nrowind");
- nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_LowFilter: nrowval");
-
-
- switch (what) {
- case GK_CSR_COL:
- if (mat->colptr == NULL)
- gk_errexit(SIGERR, "Cannot filter columns when column-based structure has not been created.\n");
-
- gk_zcopy(nrows+1, rowptr, nrowptr);
-
- for (i=0; i<ncols; i++)
- maxlen = gk_max(maxlen, colptr[i+1]-colptr[i]);
-
- #pragma omp parallel private(i, j, ncand, rsum, tsum, cand)
- {
- cand = gk_fkvmalloc(maxlen, "gk_csr_LowFilter: cand");
-
- #pragma omp for schedule(static)
- for (i=0; i<ncols; i++) {
- for (tsum=0.0, ncand=0, j=colptr[i]; j<colptr[i+1]; j++, ncand++) {
- cand[ncand].val = colind[j];
- cand[ncand].key = colval[j];
- tsum += (norm == 1 ? colval[j] : colval[j]*colval[j]);
- }
- gk_fkvsortd(ncand, cand);
-
- for (rsum=0.0, j=0; j<ncand && rsum<=fraction*tsum; j++) {
- rsum += (norm == 1 ? cand[j].key : cand[j].key*cand[j].key);
- nrowind[nrowptr[cand[j].val]] = i;
- nrowval[nrowptr[cand[j].val]] = cand[j].key;
- nrowptr[cand[j].val]++;
- }
- }
-
- gk_free((void **)&cand, LTERM);
- }
-
- /* compact the nrowind/nrowval */
- for (nnz=0, i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<nrowptr[i]; j++, nnz++) {
- nrowind[nnz] = nrowind[j];
- nrowval[nnz] = nrowval[j];
- }
- nrowptr[i] = nnz;
- }
- SHIFTCSR(i, nrows, nrowptr);
-
- break;
-
- case GK_CSR_ROW:
- if (mat->rowptr == NULL)
- gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n");
-
- for (i=0; i<nrows; i++)
- maxlen = gk_max(maxlen, rowptr[i+1]-rowptr[i]);
-
- #pragma omp parallel private(i, j, ncand, rsum, tsum, cand)
- {
- cand = gk_fkvmalloc(maxlen, "gk_csr_LowFilter: cand");
-
- #pragma omp for schedule(static)
- for (i=0; i<nrows; i++) {
- for (tsum=0.0, ncand=0, j=rowptr[i]; j<rowptr[i+1]; j++, ncand++) {
- cand[ncand].val = rowind[j];
- cand[ncand].key = rowval[j];
- tsum += (norm == 1 ? rowval[j] : rowval[j]*rowval[j]);
- }
- gk_fkvsortd(ncand, cand);
-
- for (rsum=0.0, j=0; j<ncand && rsum<=fraction*tsum; j++) {
- rsum += (norm == 1 ? cand[j].key : cand[j].key*cand[j].key);
- nrowind[rowptr[i]+j] = cand[j].val;
- nrowval[rowptr[i]+j] = cand[j].key;
- }
- nrowptr[i+1] = rowptr[i]+j;
- }
-
- gk_free((void **)&cand, LTERM);
- }
-
- /* compact nrowind/nrowval */
- nrowptr[0] = nnz = 0;
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<nrowptr[i+1]; j++, nnz++) {
- nrowind[nnz] = nrowind[j];
- nrowval[nnz] = nrowval[j];
- }
- nrowptr[i+1] = nnz;
- }
-
- break;
-
- default:
- gk_csr_Free(&nmat);
- gk_errexit(SIGERR, "Unknown prunning type of %d\n", what);
- return NULL;
- }
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Eliminates certain entries from the rows/columns of the matrix. The
- filtering takes place by keeping only the highest weight top-K entries
- along each row/column and those entries whose weight is greater than
- a specified value.
-
- \param mat the matrix to be prunned,
- \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL)
- of the matrix will be prunned,
- \param topk is the number of the highest weight entries to keep.
- \param keepval is the weight of a term above which will be kept. This
- is used to select additional terms past the first topk.
- \returns the filtered matrix consisting only of its row-based structure.
- The input matrix is not modified.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_TopKPlusFilter(gk_csr_t *mat, int what, int topk, float keepval)
-{
- ssize_t i, j, k, nnz;
- int nrows, ncols, ncand;
- ssize_t *rowptr, *colptr, *nrowptr;
- int *rowind, *colind, *nrowind;
- float *rowval, *colval, *nrowval;
- gk_csr_t *nmat;
- gk_fkv_t *cand;
-
- nmat = gk_csr_Create();
-
- nrows = nmat->nrows = mat->nrows;
- ncols = nmat->ncols = mat->ncols;
-
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
- colptr = mat->colptr;
- colind = mat->colind;
- colval = mat->colval;
-
- nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_LowFilter: nrowptr");
- nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_LowFilter: nrowind");
- nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_LowFilter: nrowval");
-
-
- switch (what) {
- case GK_CSR_COL:
- if (mat->colptr == NULL)
- gk_errexit(SIGERR, "Cannot filter columns when column-based structure has not been created.\n");
-
- cand = gk_fkvmalloc(nrows, "gk_csr_LowFilter: cand");
-
- gk_zcopy(nrows+1, rowptr, nrowptr);
- for (i=0; i<ncols; i++) {
- for (ncand=0, j=colptr[i]; j<colptr[i+1]; j++, ncand++) {
- cand[ncand].val = colind[j];
- cand[ncand].key = colval[j];
- }
- gk_fkvsortd(ncand, cand);
-
- k = gk_min(topk, ncand);
- for (j=0; j<k; j++) {
- nrowind[nrowptr[cand[j].val]] = i;
- nrowval[nrowptr[cand[j].val]] = cand[j].key;
- nrowptr[cand[j].val]++;
- }
- for (; j<ncand; j++) {
- if (cand[j].key < keepval)
- break;
-
- nrowind[nrowptr[cand[j].val]] = i;
- nrowval[nrowptr[cand[j].val]] = cand[j].key;
- nrowptr[cand[j].val]++;
- }
- }
-
- /* compact the nrowind/nrowval */
- for (nnz=0, i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<nrowptr[i]; j++, nnz++) {
- nrowind[nnz] = nrowind[j];
- nrowval[nnz] = nrowval[j];
- }
- nrowptr[i] = nnz;
- }
- SHIFTCSR(i, nrows, nrowptr);
-
- gk_free((void **)&cand, LTERM);
- break;
-
- case GK_CSR_ROW:
- if (mat->rowptr == NULL)
- gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n");
-
- cand = gk_fkvmalloc(ncols, "gk_csr_LowFilter: cand");
-
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- for (ncand=0, j=rowptr[i]; j<rowptr[i+1]; j++, ncand++) {
- cand[ncand].val = rowind[j];
- cand[ncand].key = rowval[j];
- }
- gk_fkvsortd(ncand, cand);
-
- k = gk_min(topk, ncand);
- for (j=0; j<k; j++, nnz++) {
- nrowind[nnz] = cand[j].val;
- nrowval[nnz] = cand[j].key;
- }
- for (; j<ncand; j++, nnz++) {
- if (cand[j].key < keepval)
- break;
-
- nrowind[nnz] = cand[j].val;
- nrowval[nnz] = cand[j].key;
- }
- nrowptr[i+1] = nnz;
- }
-
- gk_free((void **)&cand, LTERM);
- break;
-
- default:
- gk_csr_Free(&nmat);
- gk_errexit(SIGERR, "Unknown prunning type of %d\n", what);
- return NULL;
- }
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Eliminates certain entries from the rows/columns of the matrix. The
- filtering takes place by keeping only the terms whose contribution to
- the total length of the document is greater than a user-splied multiple
- over the average.
-
- This routine assumes that the vectors are normalized to be unit length.
-
- \param mat the matrix to be prunned,
- \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL)
- of the matrix will be prunned,
- \param zscore is the multiplicative factor over the average contribution
- to the length of the document.
- \returns the filtered matrix consisting only of its row-based structure.
- The input matrix is not modified.
-*/
-/**************************************************************************/
-gk_csr_t *gk_csr_ZScoreFilter(gk_csr_t *mat, int what, float zscore)
-{
- ssize_t i, j, nnz;
- int nrows;
- ssize_t *rowptr, *nrowptr;
- int *rowind, *nrowind;
- float *rowval, *nrowval, avgwgt;
- gk_csr_t *nmat;
-
- nmat = gk_csr_Create();
-
- nmat->nrows = mat->nrows;
- nmat->ncols = mat->ncols;
-
- nrows = mat->nrows;
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
-
- nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_ZScoreFilter: nrowptr");
- nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_ZScoreFilter: nrowind");
- nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_ZScoreFilter: nrowval");
-
-
- switch (what) {
- case GK_CSR_COL:
- gk_errexit(SIGERR, "This has not been implemented yet.\n");
- break;
-
- case GK_CSR_ROW:
- if (mat->rowptr == NULL)
- gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n");
-
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- avgwgt = zscore/(rowptr[i+1]-rowptr[i]);
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] > avgwgt) {
- nrowind[nnz] = rowind[j];
- nrowval[nnz] = rowval[j];
- nnz++;
- }
- }
- nrowptr[i+1] = nnz;
- }
- break;
-
- default:
- gk_csr_Free(&nmat);
- gk_errexit(SIGERR, "Unknown prunning type of %d\n", what);
- return NULL;
- }
-
- return nmat;
-}
-
-
-/*************************************************************************/
-/*! Compacts the column-space of the matrix by removing empty columns.
- As a result of the compaction, the column numbers are renumbered.
- The compaction operation is done in place and only affects the row-based
- representation of the matrix.
- The new columns are ordered in decreasing frequency.
-
- \param mat the matrix whose empty columns will be removed.
-*/
-/**************************************************************************/
-void gk_csr_CompactColumns(gk_csr_t *mat)
-{
- ssize_t i;
- int nrows, ncols, nncols;
- ssize_t *rowptr;
- int *rowind, *colmap;
- gk_ikv_t *clens;
-
- nrows = mat->nrows;
- ncols = mat->ncols;
- rowptr = mat->rowptr;
- rowind = mat->rowind;
-
- colmap = gk_imalloc(ncols, "gk_csr_CompactColumns: colmap");
-
- clens = gk_ikvmalloc(ncols, "gk_csr_CompactColumns: clens");
- for (i=0; i<ncols; i++) {
- clens[i].key = 0;
- clens[i].val = i;
- }
-
- for (i=0; i<rowptr[nrows]; i++)
- clens[rowind[i]].key++;
- gk_ikvsortd(ncols, clens);
-
- for (nncols=0, i=0; i<ncols; i++) {
- if (clens[i].key > 0)
- colmap[clens[i].val] = nncols++;
- else
- break;
- }
-
- for (i=0; i<rowptr[nrows]; i++)
- rowind[i] = colmap[rowind[i]];
-
- mat->ncols = nncols;
-
- gk_free((void **)&colmap, &clens, LTERM);
-}
-
-
-/*************************************************************************/
-/*! Sorts the indices in increasing order
- \param mat the matrix itself,
- \param what is either GK_CSR_ROW or GK_CSR_COL indicating which set of
- indices to sort.
-*/
-/**************************************************************************/
-void gk_csr_SortIndices(gk_csr_t *mat, int what)
-{
- int n, nn=0;
- ssize_t *ptr;
- int *ind;
- float *val;
-
- switch (what) {
- case GK_CSR_ROW:
- if (!mat->rowptr)
- gk_errexit(SIGERR, "Row-based view of the matrix does not exists.\n");
-
- n = mat->nrows;
- ptr = mat->rowptr;
- ind = mat->rowind;
- val = mat->rowval;
- break;
-
- case GK_CSR_COL:
- if (!mat->colptr)
- gk_errexit(SIGERR, "Column-based view of the matrix does not exists.\n");
-
- n = mat->ncols;
- ptr = mat->colptr;
- ind = mat->colind;
- val = mat->colval;
- break;
-
- default:
- gk_errexit(SIGERR, "Invalid index type of %d.\n", what);
- return;
- }
-
- #pragma omp parallel if (n > 100)
- {
- ssize_t i, j, k;
- gk_ikv_t *cand;
- float *tval;
-
- #pragma omp single
- for (i=0; i<n; i++)
- nn = gk_max(nn, ptr[i+1]-ptr[i]);
-
- cand = gk_ikvmalloc(nn, "gk_csr_SortIndices: cand");
- tval = gk_fmalloc(nn, "gk_csr_SortIndices: tval");
-
- #pragma omp for schedule(static)
- for (i=0; i<n; i++) {
- for (k=0, j=ptr[i]; j<ptr[i+1]; j++) {
- if (j > ptr[i] && ind[j] < ind[j-1])
- k = 1; /* an inversion */
- cand[j-ptr[i]].val = j-ptr[i];
- cand[j-ptr[i]].key = ind[j];
- tval[j-ptr[i]] = val[j];
- }
- if (k) {
- gk_ikvsorti(ptr[i+1]-ptr[i], cand);
- for (j=ptr[i]; j<ptr[i+1]; j++) {
- ind[j] = cand[j-ptr[i]].key;
- val[j] = tval[cand[j-ptr[i]].val];
- }
- }
- }
-
- gk_free((void **)&cand, &tval, LTERM);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Creates a row/column index from the column/row data.
- \param mat the matrix itself,
- \param what is either GK_CSR_ROW or GK_CSR_COL indicating which index
- will be created.
-*/
-/**************************************************************************/
-void gk_csr_CreateIndex(gk_csr_t *mat, int what)
-{
- /* 'f' stands for forward, 'r' stands for reverse */
- ssize_t i, j, k, nf, nr;
- ssize_t *fptr, *rptr;
- int *find, *rind;
- float *fval, *rval;
-
- switch (what) {
- case GK_CSR_COL:
- nf = mat->nrows;
- fptr = mat->rowptr;
- find = mat->rowind;
- fval = mat->rowval;
-
- if (mat->colptr) gk_free((void **)&mat->colptr, LTERM);
- if (mat->colind) gk_free((void **)&mat->colind, LTERM);
- if (mat->colval) gk_free((void **)&mat->colval, LTERM);
-
- nr = mat->ncols;
- rptr = mat->colptr = gk_zsmalloc(nr+1, 0, "gk_csr_CreateIndex: rptr");
- rind = mat->colind = gk_imalloc(fptr[nf], "gk_csr_CreateIndex: rind");
- rval = mat->colval = (fval ? gk_fmalloc(fptr[nf], "gk_csr_CreateIndex: rval") : NULL);
- break;
- case GK_CSR_ROW:
- nf = mat->ncols;
- fptr = mat->colptr;
- find = mat->colind;
- fval = mat->colval;
-
- if (mat->rowptr) gk_free((void **)&mat->rowptr, LTERM);
- if (mat->rowind) gk_free((void **)&mat->rowind, LTERM);
- if (mat->rowval) gk_free((void **)&mat->rowval, LTERM);
-
- nr = mat->nrows;
- rptr = mat->rowptr = gk_zsmalloc(nr+1, 0, "gk_csr_CreateIndex: rptr");
- rind = mat->rowind = gk_imalloc(fptr[nf], "gk_csr_CreateIndex: rind");
- rval = mat->rowval = (fval ? gk_fmalloc(fptr[nf], "gk_csr_CreateIndex: rval") : NULL);
- break;
- default:
- gk_errexit(SIGERR, "Invalid index type of %d.\n", what);
- return;
- }
-
-
- for (i=0; i<nf; i++) {
- for (j=fptr[i]; j<fptr[i+1]; j++)
- rptr[find[j]]++;
- }
- MAKECSR(i, nr, rptr);
-
- if (rptr[nr] > 6*nr) {
- for (i=0; i<nf; i++) {
- for (j=fptr[i]; j<fptr[i+1]; j++)
- rind[rptr[find[j]]++] = i;
- }
- SHIFTCSR(i, nr, rptr);
-
- if (fval) {
- for (i=0; i<nf; i++) {
- for (j=fptr[i]; j<fptr[i+1]; j++)
- rval[rptr[find[j]]++] = fval[j];
- }
- SHIFTCSR(i, nr, rptr);
- }
- }
- else {
- if (fval) {
- for (i=0; i<nf; i++) {
- for (j=fptr[i]; j<fptr[i+1]; j++) {
- k = find[j];
- rind[rptr[k]] = i;
- rval[rptr[k]++] = fval[j];
- }
- }
- }
- else {
- for (i=0; i<nf; i++) {
- for (j=fptr[i]; j<fptr[i+1]; j++)
- rind[rptr[find[j]]++] = i;
- }
- }
- SHIFTCSR(i, nr, rptr);
- }
-}
-
-
-/*************************************************************************/
-/*! Normalizes the rows/columns of the matrix to be unit
- length.
- \param mat the matrix itself,
- \param what indicates what will be normalized and is obtained by
- specifying GK_CSR_ROW, GK_CSR_COL, GK_CSR_ROW|GK_CSR_COL.
- \param norm indicates what norm is to normalize to, 1: 1-norm, 2: 2-norm
-*/
-/**************************************************************************/
-void gk_csr_Normalize(gk_csr_t *mat, int what, int norm)
-{
- ssize_t i, j;
- int n;
- ssize_t *ptr;
- float *val, sum;
-
- if (what&GK_CSR_ROW && mat->rowval) {
- n = mat->nrows;
- ptr = mat->rowptr;
- val = mat->rowval;
-
- #pragma omp parallel if (ptr[n] > OMPMINOPS)
- {
- #pragma omp for private(j,sum) schedule(static)
- for (i=0; i<n; i++) {
- for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++){
- if (norm == 2)
- sum += val[j]*val[j];
- else if (norm == 1)
- sum += val[j]; /* assume val[j] > 0 */
- }
- if (sum > 0) {
- if (norm == 2)
- sum=1.0/sqrt(sum);
- else if (norm == 1)
- sum=1.0/sum;
- for (j=ptr[i]; j<ptr[i+1]; j++)
- val[j] *= sum;
-
- }
- }
- }
- }
-
- if (what&GK_CSR_COL && mat->colval) {
- n = mat->ncols;
- ptr = mat->colptr;
- val = mat->colval;
-
- #pragma omp parallel if (ptr[n] > OMPMINOPS)
- {
- #pragma omp for private(j,sum) schedule(static)
- for (i=0; i<n; i++) {
- for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++)
- if (norm == 2)
- sum += val[j]*val[j];
- else if (norm == 1)
- sum += val[j];
- if (sum > 0) {
- if (norm == 2)
- sum=1.0/sqrt(sum);
- else if (norm == 1)
- sum=1.0/sum;
- for (j=ptr[i]; j<ptr[i+1]; j++)
- val[j] *= sum;
- }
- }
- }
- }
-}
-
-
-/*************************************************************************/
-/*! Applies different row scaling methods.
- \param mat the matrix itself,
- \param type indicates the type of row scaling. Possible values are:
- GK_CSR_MAXTF, GK_CSR_SQRT, GK_CSR_LOG, GK_CSR_IDF, GK_CSR_MAXTF2.
-*/
-/**************************************************************************/
-void gk_csr_Scale(gk_csr_t *mat, int type)
-{
- ssize_t i, j;
- int nrows, ncols, nnzcols, bgfreq;
- ssize_t *rowptr;
- int *rowind, *collen;
- float *rowval, *cscale, maxtf;
-
- nrows = mat->nrows;
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
-
- switch (type) {
- case GK_CSR_MAXTF: /* TF' = .5 + .5*TF/MAX(TF) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j, maxtf) schedule(static)
- for (i=0; i<nrows; i++) {
- maxtf = fabs(rowval[rowptr[i]]);
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- maxtf = (maxtf < fabs(rowval[j]) ? fabs(rowval[j]) : maxtf);
-
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- rowval[j] = .5 + .5*rowval[j]/maxtf;
- }
- }
- break;
-
- case GK_CSR_MAXTF2: /* TF' = .1 + .9*TF/MAX(TF) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j, maxtf) schedule(static)
- for (i=0; i<nrows; i++) {
- maxtf = fabs(rowval[rowptr[i]]);
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- maxtf = (maxtf < fabs(rowval[j]) ? fabs(rowval[j]) : maxtf);
-
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- rowval[j] = .1 + .9*rowval[j]/maxtf;
- }
- }
- break;
-
- case GK_CSR_SQRT: /* TF' = .1+SQRT(TF) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = .1+sign(rowval[j], sqrt(fabs(rowval[j])));
- }
- }
- }
- break;
-
- case GK_CSR_POW25: /* TF' = .1+POW(TF,.25) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = .1+sign(rowval[j], sqrt(sqrt(fabs(rowval[j]))));
- }
- }
- }
- break;
-
- case GK_CSR_POW65: /* TF' = .1+POW(TF,.65) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = .1+sign(rowval[j], powf(fabs(rowval[j]), .65));
- }
- }
- }
- break;
-
- case GK_CSR_POW75: /* TF' = .1+POW(TF,.75) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = .1+sign(rowval[j], powf(fabs(rowval[j]), .75));
- }
- }
- }
- break;
-
- case GK_CSR_POW85: /* TF' = .1+POW(TF,.85) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = .1+sign(rowval[j], powf(fabs(rowval[j]), .85));
- }
- }
- }
- break;
-
- case GK_CSR_LOG: /* TF' = 1+log_2(TF) */
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- double logscale = 1.0/log(2.0);
- #pragma omp for schedule(static,32)
- for (i=0; i<rowptr[nrows]; i++) {
- if (rowval[i] != 0.0)
- rowval[i] = 1+(rowval[i]>0.0 ? log(rowval[i]) : -log(-rowval[i]))*logscale;
- }
-#ifdef XXX
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (rowval[j] != 0.0)
- rowval[j] = 1+(rowval[j]>0.0 ? log(rowval[j]) : -log(-rowval[j]))*logscale;
- //rowval[j] = 1+sign(rowval[j], log(fabs(rowval[j]))*logscale);
- }
- }
-#endif
- }
- break;
-
- case GK_CSR_IDF: /* TF' = TF*IDF */
- ncols = mat->ncols;
- cscale = gk_fmalloc(ncols, "gk_csr_Scale: cscale");
- collen = gk_ismalloc(ncols, 0, "gk_csr_Scale: collen");
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- collen[rowind[j]]++;
- }
-
- #pragma omp parallel if (ncols > OMPMINOPS)
- {
- #pragma omp for schedule(static)
- for (i=0; i<ncols; i++)
- cscale[i] = (collen[i] > 0 ? log(1.0*nrows/collen[i]) : 0.0);
- }
-
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- rowval[j] *= cscale[rowind[j]];
- }
- }
-
- gk_free((void **)&cscale, &collen, LTERM);
- break;
-
- case GK_CSR_IDF2: /* TF' = TF*IDF */
- ncols = mat->ncols;
- cscale = gk_fmalloc(ncols, "gk_csr_Scale: cscale");
- collen = gk_ismalloc(ncols, 0, "gk_csr_Scale: collen");
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- collen[rowind[j]]++;
- }
-
- nnzcols = 0;
- #pragma omp parallel if (ncols > OMPMINOPS)
- {
- #pragma omp for schedule(static) reduction(+:nnzcols)
- for (i=0; i<ncols; i++)
- nnzcols += (collen[i] > 0 ? 1 : 0);
-
- bgfreq = gk_max(10, (ssize_t)(.5*rowptr[nrows]/nnzcols));
- printf("nnz: %zd, nnzcols: %d, bgfreq: %d\n", rowptr[nrows], nnzcols, bgfreq);
-
- #pragma omp for schedule(static)
- for (i=0; i<ncols; i++)
- cscale[i] = (collen[i] > 0 ? log(1.0*(nrows+2*bgfreq)/(bgfreq+collen[i])) : 0.0);
- }
-
- #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
- {
- #pragma omp for private(j) schedule(static)
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- rowval[j] *= cscale[rowind[j]];
- }
- }
-
- gk_free((void **)&cscale, &collen, LTERM);
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown scaling type of %d\n", type);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Computes the sums of the rows/columns
- \param mat the matrix itself,
- \param what is either GK_CSR_ROW or GK_CSR_COL indicating which
- sums to compute.
-*/
-/**************************************************************************/
-void gk_csr_ComputeSums(gk_csr_t *mat, int what)
-{
- ssize_t i;
- int n;
- ssize_t *ptr;
- float *val, *sums;
-
- switch (what) {
- case GK_CSR_ROW:
- n = mat->nrows;
- ptr = mat->rowptr;
- val = mat->rowval;
-
- if (mat->rsums)
- gk_free((void **)&mat->rsums, LTERM);
-
- sums = mat->rsums = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: sums");
- break;
- case GK_CSR_COL:
- n = mat->ncols;
- ptr = mat->colptr;
- val = mat->colval;
-
- if (mat->csums)
- gk_free((void **)&mat->csums, LTERM);
-
- sums = mat->csums = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: sums");
- break;
- default:
- gk_errexit(SIGERR, "Invalid sum type of %d.\n", what);
- return;
- }
-
- #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static)
- for (i=0; i<n; i++)
- sums[i] = gk_fsum(ptr[i+1]-ptr[i], val+ptr[i], 1);
-}
-
-
-/*************************************************************************/
-/*! Computes the squared of the norms of the rows/columns
- \param mat the matrix itself,
- \param what is either GK_CSR_ROW or GK_CSR_COL indicating which
- squared norms to compute.
-*/
-/**************************************************************************/
-void gk_csr_ComputeSquaredNorms(gk_csr_t *mat, int what)
-{
- ssize_t i;
- int n;
- ssize_t *ptr;
- float *val, *norms;
-
- switch (what) {
- case GK_CSR_ROW:
- n = mat->nrows;
- ptr = mat->rowptr;
- val = mat->rowval;
-
- if (mat->rnorms) gk_free((void **)&mat->rnorms, LTERM);
-
- norms = mat->rnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms");
- break;
- case GK_CSR_COL:
- n = mat->ncols;
- ptr = mat->colptr;
- val = mat->colval;
-
- if (mat->cnorms) gk_free((void **)&mat->cnorms, LTERM);
-
- norms = mat->cnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms");
- break;
- default:
- gk_errexit(SIGERR, "Invalid norm type of %d.\n", what);
- return;
- }
-
- #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static)
- for (i=0; i<n; i++)
- norms[i] = gk_fdot(ptr[i+1]-ptr[i], val+ptr[i], 1, val+ptr[i], 1);
-}
-
-
-/*************************************************************************/
-/*! Computes the similarity between two rows/columns
-
- \param mat the matrix itself. The routine assumes that the indices
- are sorted in increasing order.
- \param i1 is the first row/column,
- \param i2 is the second row/column,
- \param what is either GK_CSR_ROW or GK_CSR_COL indicating the type of
- objects between the similarity will be computed,
- \param simtype is the type of similarity and is one of GK_CSR_COS,
- GK_CSR_JAC, GK_CSR_MIN, GK_CSR_AMIN
- \returns the similarity between the two rows/columns.
-*/
-/**************************************************************************/
-float gk_csr_ComputeSimilarity(gk_csr_t *mat, int i1, int i2, int what, int simtype)
-{
- int nind1, nind2;
- int *ind1, *ind2;
- float *val1, *val2, stat1, stat2, sim;
-
- switch (what) {
- case GK_CSR_ROW:
- if (!mat->rowptr)
- gk_errexit(SIGERR, "Row-based view of the matrix does not exists.\n");
- nind1 = mat->rowptr[i1+1]-mat->rowptr[i1];
- nind2 = mat->rowptr[i2+1]-mat->rowptr[i2];
- ind1 = mat->rowind + mat->rowptr[i1];
- ind2 = mat->rowind + mat->rowptr[i2];
- val1 = mat->rowval + mat->rowptr[i1];
- val2 = mat->rowval + mat->rowptr[i2];
- break;
-
- case GK_CSR_COL:
- if (!mat->colptr)
- gk_errexit(SIGERR, "Column-based view of the matrix does not exists.\n");
- nind1 = mat->colptr[i1+1]-mat->colptr[i1];
- nind2 = mat->colptr[i2+1]-mat->colptr[i2];
- ind1 = mat->colind + mat->colptr[i1];
- ind2 = mat->colind + mat->colptr[i2];
- val1 = mat->colval + mat->colptr[i1];
- val2 = mat->colval + mat->colptr[i2];
- break;
-
- default:
- gk_errexit(SIGERR, "Invalid index type of %d.\n", what);
- return 0.0;
- }
-
-
- switch (simtype) {
- case GK_CSR_COS:
- case GK_CSR_JAC:
- sim = stat1 = stat2 = 0.0;
- i1 = i2 = 0;
- while (i1<nind1 && i2<nind2) {
- if (i1 == nind1) {
- stat2 += val2[i2]*val2[i2];
- i2++;
- }
- else if (i2 == nind2) {
- stat1 += val1[i1]*val1[i1];
- i1++;
- }
- else if (ind1[i1] < ind2[i2]) {
- stat1 += val1[i1]*val1[i1];
- i1++;
- }
- else if (ind1[i1] > ind2[i2]) {
- stat2 += val2[i2]*val2[i2];
- i2++;
- }
- else {
- sim += val1[i1]*val2[i2];
- stat1 += val1[i1]*val1[i1];
- stat2 += val2[i2]*val2[i2];
- i1++;
- i2++;
- }
- }
- if (simtype == GK_CSR_COS)
- sim = (stat1*stat2 > 0.0 ? sim/sqrt(stat1*stat2) : 0.0);
- else
- sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0);
- break;
-
- case GK_CSR_MIN:
- sim = stat1 = stat2 = 0.0;
- i1 = i2 = 0;
- while (i1<nind1 && i2<nind2) {
- if (i1 == nind1) {
- stat2 += val2[i2];
- i2++;
- }
- else if (i2 == nind2) {
- stat1 += val1[i1];
- i1++;
- }
- else if (ind1[i1] < ind2[i2]) {
- stat1 += val1[i1];
- i1++;
- }
- else if (ind1[i1] > ind2[i2]) {
- stat2 += val2[i2];
- i2++;
- }
- else {
- sim += gk_min(val1[i1],val2[i2]);
- stat1 += val1[i1];
- stat2 += val2[i2];
- i1++;
- i2++;
- }
- }
- sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0);
-
- break;
-
- case GK_CSR_AMIN:
- sim = stat1 = stat2 = 0.0;
- i1 = i2 = 0;
- while (i1<nind1 && i2<nind2) {
- if (i1 == nind1) {
- stat2 += val2[i2];
- i2++;
- }
- else if (i2 == nind2) {
- stat1 += val1[i1];
- i1++;
- }
- else if (ind1[i1] < ind2[i2]) {
- stat1 += val1[i1];
- i1++;
- }
- else if (ind1[i1] > ind2[i2]) {
- stat2 += val2[i2];
- i2++;
- }
- else {
- sim += gk_min(val1[i1],val2[i2]);
- stat1 += val1[i1];
- stat2 += val2[i2];
- i1++;
- i2++;
- }
- }
- sim = (stat1 > 0.0 ? sim/stat1 : 0.0);
-
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown similarity measure %d\n", simtype);
- return -1;
- }
-
- return sim;
-
-}
-
-
-/*************************************************************************/
-/*! Finds the n most similar rows (neighbors) to the query using cosine
- similarity.
-
- \param mat the matrix itself
- \param nqterms is the number of columns in the query
- \param qind is the list of query columns
- \param qval is the list of correspodning query weights
- \param simtype is the type of similarity and is one of GK_CSR_COS,
- GK_CSR_JAC, GK_CSR_MIN, GK_CSR_AMIN
- \param nsim is the maximum number of requested most similar rows.
- If -1 is provided, then everything is returned unsorted.
- \param minsim is the minimum similarity of the requested most
- similar rows
- \param hits is the result set. This array should be at least
- of length nsim.
- \param i_marker is an array of size equal to the number of rows
- whose values are initialized to -1. If NULL is provided
- then this array is allocated and freed internally.
- \param i_cand is an array of size equal to the number of rows.
- If NULL is provided then this array is allocated and freed
- internally.
- \returns the number of identified most similar rows, which can be
- smaller than the requested number of nnbrs in those cases
- in which there are no sufficiently many neighbors.
-*/
-/**************************************************************************/
-int gk_csr_GetSimilarRows(gk_csr_t *mat, int nqterms, int *qind,
- float *qval, int simtype, int nsim, float minsim, gk_fkv_t *hits,
- int *i_marker, gk_fkv_t *i_cand)
-{
- ssize_t i, ii, j, k;
- int nrows, ncols, ncand;
- ssize_t *colptr;
- int *colind, *marker;
- float *colval, *rnorms, mynorm, *rsums, mysum;
- gk_fkv_t *cand;
-
- if (nqterms == 0)
- return 0;
-
- nrows = mat->nrows;
- ncols = mat->ncols;
- colptr = mat->colptr;
- colind = mat->colind;
- colval = mat->colval;
-
- marker = (i_marker ? i_marker : gk_ismalloc(nrows, -1, "gk_csr_SimilarRows: marker"));
- cand = (i_cand ? i_cand : gk_fkvmalloc(nrows, "gk_csr_SimilarRows: cand"));
-
- switch (simtype) {
- case GK_CSR_COS:
- for (ncand=0, ii=0; ii<nqterms; ii++) {
- i = qind[ii];
- if (i < ncols) {
- for (j=colptr[i]; j<colptr[i+1]; j++) {
- k = colind[j];
- if (marker[k] == -1) {
- cand[ncand].val = k;
- cand[ncand].key = 0;
- marker[k] = ncand++;
- }
- cand[marker[k]].key += colval[j]*qval[ii];
- }
- }
- }
- break;
-
- case GK_CSR_JAC:
- for (ncand=0, ii=0; ii<nqterms; ii++) {
- i = qind[ii];
- if (i < ncols) {
- for (j=colptr[i]; j<colptr[i+1]; j++) {
- k = colind[j];
- if (marker[k] == -1) {
- cand[ncand].val = k;
- cand[ncand].key = 0;
- marker[k] = ncand++;
- }
- cand[marker[k]].key += colval[j]*qval[ii];
- }
- }
- }
-
- rnorms = mat->rnorms;
- mynorm = gk_fdot(nqterms, qval, 1, qval, 1);
-
- for (i=0; i<ncand; i++)
- cand[i].key = cand[i].key/(rnorms[cand[i].val]+mynorm-cand[i].key);
- break;
-
- case GK_CSR_MIN:
- for (ncand=0, ii=0; ii<nqterms; ii++) {
- i = qind[ii];
- if (i < ncols) {
- for (j=colptr[i]; j<colptr[i+1]; j++) {
- k = colind[j];
- if (marker[k] == -1) {
- cand[ncand].val = k;
- cand[ncand].key = 0;
- marker[k] = ncand++;
- }
- cand[marker[k]].key += gk_min(colval[j], qval[ii]);
- }
- }
- }
-
- rsums = mat->rsums;
- mysum = gk_fsum(nqterms, qval, 1);
-
- for (i=0; i<ncand; i++)
- cand[i].key = cand[i].key/(rsums[cand[i].val]+mysum-cand[i].key);
- break;
-
- /* Assymetric MIN similarity */
- case GK_CSR_AMIN:
- for (ncand=0, ii=0; ii<nqterms; ii++) {
- i = qind[ii];
- if (i < ncols) {
- for (j=colptr[i]; j<colptr[i+1]; j++) {
- k = colind[j];
- if (marker[k] == -1) {
- cand[ncand].val = k;
- cand[ncand].key = 0;
- marker[k] = ncand++;
- }
- cand[marker[k]].key += gk_min(colval[j], qval[ii]);
- }
- }
- }
-
- mysum = gk_fsum(nqterms, qval, 1);
-
- for (i=0; i<ncand; i++)
- cand[i].key = cand[i].key/mysum;
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown similarity measure %d\n", simtype);
- return -1;
- }
-
- /* go and prune the hits that are bellow minsim */
- for (j=0, i=0; i<ncand; i++) {
- marker[cand[i].val] = -1;
- if (cand[i].key >= minsim)
- cand[j++] = cand[i];
- }
- ncand = j;
-
- if (nsim == -1 || nsim >= ncand) {
- nsim = ncand;
- }
- else {
- nsim = gk_min(nsim, ncand);
- gk_dfkvkselect(ncand, nsim, cand);
- gk_fkvsortd(nsim, cand);
- }
-
- gk_fkvcopy(nsim, cand, hits);
-
- if (i_marker == NULL)
- gk_free((void **)&marker, LTERM);
- if (i_cand == NULL)
- gk_free((void **)&cand, LTERM);
-
- return nsim;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/error.c b/3rdParty/metis/metis-5.1.0/GKlib/error.c
deleted file mode 100644
index e2a18cf03..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/error.c
+++ /dev/null
@@ -1,214 +0,0 @@
-/*!
-\file error.c
-\brief Various error-handling functions
-
-This file contains functions dealing with error reporting and termination
-
-\author George
-\date 1/1/2007
-\version\verbatim $Id: error.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#define _GK_ERROR_C_ /* this is needed to properly declare the gk_jub* variables
- as an extern function in GKlib.h */
-
-#include <GKlib.h>
-
-
-/* These are the jmp_buf for the graceful exit in case of severe errors.
- Multiple buffers are defined to allow for recursive invokation. */
-#define MAX_JBUFS 128
-__thread int gk_cur_jbufs=-1;
-__thread jmp_buf gk_jbufs[MAX_JBUFS];
-__thread jmp_buf gk_jbuf;
-
-typedef void (*gksighandler_t)(int);
-
-/* These are the holders of the old singal handlers for the trapped signals */
-static __thread gksighandler_t old_SIGMEM_handler; /* Custom signal */
-static __thread gksighandler_t old_SIGERR_handler; /* Custom signal */
-static __thread gksighandler_t old_SIGMEM_handlers[MAX_JBUFS]; /* Custom signal */
-static __thread gksighandler_t old_SIGERR_handlers[MAX_JBUFS]; /* Custom signal */
-
-/* The following is used to control if the gk_errexit() will actually abort or not.
- There is always a single copy of this variable */
-static int gk_exit_on_error = 1;
-
-
-/*************************************************************************/
-/*! This function sets the gk_exit_on_error variable
- */
-/*************************************************************************/
-void gk_set_exit_on_error(int value)
-{
- gk_exit_on_error = value;
-}
-
-
-
-/*************************************************************************/
-/*! This function prints an error message and exits
- */
-/*************************************************************************/
-void errexit(char *f_str,...)
-{
- va_list argp;
-
- va_start(argp, f_str);
- vfprintf(stderr, f_str, argp);
- va_end(argp);
-
- if (strlen(f_str) == 0 || f_str[strlen(f_str)-1] != '\n')
- fprintf(stderr,"\n");
- fflush(stderr);
-
- if (gk_exit_on_error)
- exit(-2);
-
- /* abort(); */
-}
-
-
-/*************************************************************************/
-/*! This function prints an error message and raises a signum signal
- */
-/*************************************************************************/
-void gk_errexit(int signum, char *f_str,...)
-{
- va_list argp;
-
- va_start(argp, f_str);
- vfprintf(stderr, f_str, argp);
- va_end(argp);
-
- fprintf(stderr,"\n");
- fflush(stderr);
-
- if (gk_exit_on_error)
- raise(signum);
-}
-
-
-/***************************************************************************/
-/*! This function sets a number of signal handlers and sets the return point
- of a longjmp
-*/
-/***************************************************************************/
-int gk_sigtrap()
-{
- if (gk_cur_jbufs+1 >= MAX_JBUFS)
- return 0;
-
- gk_cur_jbufs++;
-
- old_SIGMEM_handlers[gk_cur_jbufs] = signal(SIGMEM, gk_sigthrow);
- old_SIGERR_handlers[gk_cur_jbufs] = signal(SIGERR, gk_sigthrow);
-
- return 1;
-}
-
-
-/***************************************************************************/
-/*! This function sets the handlers for the signals to their default handlers
- */
-/***************************************************************************/
-int gk_siguntrap()
-{
- if (gk_cur_jbufs == -1)
- return 0;
-
- signal(SIGMEM, old_SIGMEM_handlers[gk_cur_jbufs]);
- signal(SIGERR, old_SIGERR_handlers[gk_cur_jbufs]);
-
- gk_cur_jbufs--;
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function is the custome signal handler, which all it does is to
- perform a longjump to the most recent saved environment
- */
-/*************************************************************************/
-void gk_sigthrow(int signum)
-{
- longjmp(gk_jbufs[gk_cur_jbufs], signum);
-}
-
-
-/***************************************************************************
-* This function sets a number of signal handlers and sets the return point
-* of a longjmp
-****************************************************************************/
-void gk_SetSignalHandlers()
-{
- old_SIGMEM_handler = signal(SIGMEM, gk_NonLocalExit_Handler);
- old_SIGERR_handler = signal(SIGERR, gk_NonLocalExit_Handler);
-}
-
-
-/***************************************************************************
-* This function sets the handlers for the signals to their default handlers
-****************************************************************************/
-void gk_UnsetSignalHandlers()
-{
- signal(SIGMEM, old_SIGMEM_handler);
- signal(SIGERR, old_SIGERR_handler);
-}
-
-
-/*************************************************************************
-* This function is the handler for SIGUSR1 that implements the cleaning up
-* process prior to a non-local exit.
-**************************************************************************/
-void gk_NonLocalExit_Handler(int signum)
-{
- longjmp(gk_jbuf, signum);
-}
-
-
-/*************************************************************************/
-/*! \brief Thread-safe implementation of strerror() */
-/**************************************************************************/
-char *gk_strerror(int errnum)
-{
-#if defined(WIN32) || defined(__MINGW32__)
- return strerror(errnum);
-#else
-#ifndef SUNOS
- static __thread char buf[1024];
-
- strerror_r(errnum, buf, 1024);
-
- buf[1023] = '\0';
- return buf;
-#else
- return strerror(errnum);
-#endif
-#endif
-}
-
-
-
-/*************************************************************************
-* This function prints a backtrace of calling functions
-**************************************************************************/
-void PrintBackTrace()
-{
-#ifdef HAVE_EXECINFO_H
- void *array[10];
- int i, size;
- char **strings;
-
- size = backtrace(array, 10);
- strings = backtrace_symbols(array, size);
-
- printf("Obtained %d stack frames.\n", size);
- for (i=0; i<size; i++) {
- printf("%s\n", strings[i]);
- }
- free(strings);
-#endif
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/evaluate.c b/3rdParty/metis/metis-5.1.0/GKlib/evaluate.c
deleted file mode 100644
index ce805ced9..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/evaluate.c
+++ /dev/null
@@ -1,132 +0,0 @@
-/*!
- \file evaluate.c
- \brief Various routines to evaluate classification performance
-
- \author George
- \date 9/23/2008
- \version\verbatim $Id: evaluate.c 13328 2012-12-31 14:57:40Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-/**********************************************************************
- * This function computes the max accuracy score of a ranked list,
- * given +1/-1 class list
- **********************************************************************/
-float ComputeAccuracy(int n, gk_fkv_t *list)
-{
- int i, P, N, TP, FN = 0;
- float bAccuracy = 0.0;
- float acc;
-
- for (P=0, i=0;i<n;i++)
- P += (list[i].val == 1? 1 : 0);
- N = n - P;
-
- TP = FN = 0;
-
- for(i=0; i<n; i++){
- if (list[i].val == 1)
- TP++;
- else
- FN++;
-
- acc = (TP + N - FN) * 100.0/ (P + N) ;
- if (acc > bAccuracy)
- bAccuracy = acc;
- }
-
- return bAccuracy;
-}
-
-
-/*****************************************************************************
- * This function computes the ROC score of a ranked list, given a +1/-1 class
- * list.
- ******************************************************************************/
-float ComputeROCn(int n, int maxN, gk_fkv_t *list)
-{
- int i, P, TP, FP, TPprev, FPprev, AUC;
- float prev;
-
- FP = TP = FPprev = TPprev = AUC = 0;
- prev = list[0].key -1;
-
- for (P=0, i=0; i<n; i++)
- P += (list[i].val == 1 ? 1 : 0);
-
- for (i=0; i<n && FP < maxN; i++) {
- if (list[i].key != prev) {
- AUC += (TP+TPprev)*(FP-FPprev)/2;
- prev = list[i].key;
- FPprev = FP;
- TPprev = TP;
- }
- if (list[i].val == 1)
- TP++;
- else {
- FP++;
- }
- }
- AUC += (TP+TPprev)*(FP-FPprev)/2;
-
- return (TP*FP > 0 ? (float)(1.0*AUC/(P*FP)) : 0.0);
-}
-
-
-/*****************************************************************************
-* This function computes the median rate of false positive for each positive
-* instance.
-******************************************************************************/
-float ComputeMedianRFP(int n, gk_fkv_t *list)
-{
- int i, P, N, TP, FP;
-
- P = N = 0;
- for (i=0; i<n; i++) {
- if (list[i].val == 1)
- P++;
- else
- N++;
- }
-
- FP = TP = 0;
- for (i=0; i<n && TP < (P+1)/2; i++) {
- if (list[i].val == 1)
- TP++;
- else
- FP++;
- }
-
- return 1.0*FP/N;
-}
-
-/*********************************************************
- * Compute the mean
- ********************************************************/
-float ComputeMean (int n, float *values)
-{
- int i;
- float mean = 0.0;
-
- for(i=0; i < n; i++)
- mean += values[i];
-
- return 1.0 * mean/ n;
-}
-
-/********************************************************
- * Compute the standard deviation
- ********************************************************/
-float ComputeStdDev(int n, float *values)
-{
- int i;
- float mean = ComputeMean(n, values);
- float stdDev = 0;
-
- for(i=0;i<n;i++){
- stdDev += (values[i] - mean)* (values[i] - mean);
- }
-
- return sqrt(1.0 * stdDev/n);
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/fkvkselect.c b/3rdParty/metis/metis-5.1.0/GKlib/fkvkselect.c
deleted file mode 100644
index b1238ce65..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/fkvkselect.c
+++ /dev/null
@@ -1,142 +0,0 @@
-/*!
-\file dfkvkselect.c
-\brief Sorts only the largest k values
-
-\date Started 7/14/00
-\author George
-\version\verbatim $Id: fkvkselect.c 10711 2011-08-31 22:23:04Z karypis $\endverbatim
-*/
-
-
-#include <GKlib.h>
-
-/* Byte-wise swap two items of size SIZE. */
-#define QSSWAP(a, b, stmp) do { stmp = (a); (a) = (b); (b) = stmp; } while (0)
-
-
-/******************************************************************************/
-/*! This function puts the 'topk' largest values in the beginning of the array */
-/*******************************************************************************/
-int gk_dfkvkselect(size_t n, int topk, gk_fkv_t *cand)
-{
- int i, j, lo, hi, mid;
- gk_fkv_t stmp;
- float pivot;
-
- if (n <= topk)
- return n; /* return if the array has fewer elements than we want */
-
- for (lo=0, hi=n-1; lo < hi;) {
- mid = lo + ((hi-lo) >> 1);
-
- /* select the median */
- if (cand[lo].key < cand[mid].key)
- mid = lo;
- if (cand[hi].key > cand[mid].key)
- mid = hi;
- else
- goto jump_over;
- if (cand[lo].key < cand[mid].key)
- mid = lo;
-
-jump_over:
- QSSWAP(cand[mid], cand[hi], stmp);
- pivot = cand[hi].key;
-
- /* the partitioning algorithm */
- for (i=lo-1, j=lo; j<hi; j++) {
- if (cand[j].key >= pivot) {
- i++;
- QSSWAP(cand[i], cand[j], stmp);
- }
- }
- i++;
- QSSWAP(cand[i], cand[hi], stmp);
-
-
- if (i > topk)
- hi = i-1;
- else if (i < topk)
- lo = i+1;
- else
- break;
- }
-
-/*
- if (cand[lo].key < cand[hi].key)
- printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key);
-
-
- for (i=topk; i<n; i++) {
- for (j=0; j<topk; j++)
- if (cand[i].key > cand[j].key)
- printf("Hmm Error: %d %d %f %f %d %d\n", i, j, cand[i].key, cand[j].key, lo, hi);
- }
-*/
-
- return topk;
-}
-
-
-/******************************************************************************/
-/*! This function puts the 'topk' smallest values in the beginning of the array */
-/*******************************************************************************/
-int gk_ifkvkselect(size_t n, int topk, gk_fkv_t *cand)
-{
- int i, j, lo, hi, mid;
- gk_fkv_t stmp;
- float pivot;
-
- if (n <= topk)
- return n; /* return if the array has fewer elements than we want */
-
- for (lo=0, hi=n-1; lo < hi;) {
- mid = lo + ((hi-lo) >> 1);
-
- /* select the median */
- if (cand[lo].key > cand[mid].key)
- mid = lo;
- if (cand[hi].key < cand[mid].key)
- mid = hi;
- else
- goto jump_over;
- if (cand[lo].key > cand[mid].key)
- mid = lo;
-
-jump_over:
- QSSWAP(cand[mid], cand[hi], stmp);
- pivot = cand[hi].key;
-
- /* the partitioning algorithm */
- for (i=lo-1, j=lo; j<hi; j++) {
- if (cand[j].key <= pivot) {
- i++;
- QSSWAP(cand[i], cand[j], stmp);
- }
- }
- i++;
- QSSWAP(cand[i], cand[hi], stmp);
-
-
- if (i > topk)
- hi = i-1;
- else if (i < topk)
- lo = i+1;
- else
- break;
- }
-
-/*
- if (cand[lo].key > cand[hi].key)
- printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key);
-
-
- for (i=topk; i<n; i++) {
- for (j=0; j<topk; j++)
- if (cand[i].key < cand[j].key)
- printf("Hmm Error: %d %d %f %f %d %d\n", i, j, cand[i].key, cand[j].key, lo, hi);
- }
-*/
-
- return topk;
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/fs.c b/3rdParty/metis/metis-5.1.0/GKlib/fs.c
deleted file mode 100644
index 35e4b97b2..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/fs.c
+++ /dev/null
@@ -1,225 +0,0 @@
-/*!
-\file fs.c
-\brief Various file-system functions.
-
-This file contains various functions that deal with interfacing with
-the filesystem in a portable way.
-
-\date Started 4/10/95
-\author George
-\version\verbatim $Id: fs.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-
-
-/*************************************************************************
-* This function checks if a file exists
-**************************************************************************/
-int gk_fexists(char *fname)
-{
- struct stat status;
-
- if (stat(fname, &status) == -1)
- return 0;
-
- return S_ISREG(status.st_mode);
-}
-
-
-/*************************************************************************
-* This function checks if a directory exists
-**************************************************************************/
-int gk_dexists(char *dirname)
-{
- struct stat status;
-
- if (stat(dirname, &status) == -1)
- return 0;
-
- return S_ISDIR(status.st_mode);
-}
-
-
-/*************************************************************************/
-/*! \brief Returns the size of the file in bytes
-
-This function returns the size of a file as a 64 bit integer. If there
-were any errors in stat'ing the file, -1 is returned.
-\note That due to the -1 return code, the maximum file size is limited to
- 63 bits (which I guess is okay for now).
-*/
-/**************************************************************************/
-intmax_t gk_getfsize(char *filename)
-{
- struct stat status;
-
- if (stat(filename, &status) == -1)
- return -1;
-
- return (intmax_t)(status.st_size);
-}
-
-
-/*************************************************************************/
-/*! This function gets some basic statistics about the file.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
- \param r_ntokens is the number of tokens in the file. If it is NULL,
- this information is not returned.
- \param r_max_nlntokens is the maximum number of tokens in any line
- in the file. If it is NULL this information is not returned.
- \param r_nbytes is the number of bytes in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens,
- size_t *r_max_nlntokens, size_t *r_nbytes)
-{
- size_t nlines=0, ntokens=0, max_nlntokens=0, nbytes=0, oldntokens=0, nread;
- int intoken=0;
- char buffer[2049], *cptr;
- FILE *fpin;
-
- fpin = gk_fopen(fname, "r", "gk_GetFileStats");
-
- while (!feof(fpin)) {
- nread = fread(buffer, sizeof(char), 2048, fpin);
- nbytes += nread;
-
- buffer[nread] = '\0'; /* There is space for this one */
- for (cptr=buffer; *cptr!='\0'; cptr++) {
- if (*cptr == '\n') {
- nlines++;
- ntokens += intoken;
- intoken = 0;
- if (max_nlntokens < ntokens-oldntokens)
- max_nlntokens = ntokens-oldntokens;
- oldntokens = ntokens;
- }
- else if (*cptr == ' ' || *cptr == '\t') {
- ntokens += intoken;
- intoken = 0;
- }
- else {
- intoken = 1;
- }
- }
- }
- ntokens += intoken;
- if (max_nlntokens < ntokens-oldntokens)
- max_nlntokens = ntokens-oldntokens;
-
- gk_fclose(fpin);
-
- if (r_nlines != NULL)
- *r_nlines = nlines;
- if (r_ntokens != NULL)
- *r_ntokens = ntokens;
- if (r_max_nlntokens != NULL)
- *r_max_nlntokens = max_nlntokens;
- if (r_nbytes != NULL)
- *r_nbytes = nbytes;
-}
-
-
-/*************************************************************************
-* This function takes in a potentially full path specification of a file
-* and just returns a string containing just the basename of the file.
-* The basename is derived from the actual filename by stripping the last
-* .ext part.
-**************************************************************************/
-char *gk_getbasename(char *path)
-{
- char *startptr, *endptr;
- char *basename;
-
- if ((startptr = strrchr(path, '/')) == NULL)
- startptr = path;
- else
- startptr = startptr+1;
-
- basename = gk_strdup(startptr);
-
- if ((endptr = strrchr(basename, '.')) != NULL)
- *endptr = '\0';
-
- return basename;
-}
-
-/*************************************************************************
-* This function takes in a potentially full path specification of a file
-* and just returns a string corresponding to its file extension. The
-* extension of a file is considered to be the string right after the
-* last '.' character.
-**************************************************************************/
-char *gk_getextname(char *path)
-{
- char *startptr;
-
- if ((startptr = strrchr(path, '.')) == NULL)
- return gk_strdup(path);
- else
- return gk_strdup(startptr+1);
-}
-
-/*************************************************************************
-* This function takes in a potentially full path specification of a file
-* and just returns a string containing just the filename.
-**************************************************************************/
-char *gk_getfilename(char *path)
-{
- char *startptr;
-
- if ((startptr = strrchr(path, '/')) == NULL)
- return gk_strdup(path);
- else
- return gk_strdup(startptr+1);
-}
-
-/*************************************************************************
-* This function takes in a potentially full path specification of a file
-* and extracts the directory path component if it exists, otherwise it
-* returns "./" as the path. The memory for it is dynamically allocated.
-**************************************************************************/
-char *getpathname(char *path)
-{
- char *endptr, *tmp;
-
- if ((endptr = strrchr(path, '/')) == NULL) {
- return gk_strdup(".");
- }
- else {
- tmp = gk_strdup(path);
- *(strrchr(tmp, '/')) = '\0';
- return tmp;
- }
-}
-
-
-
-/*************************************************************************
-* This function creates a path
-**************************************************************************/
-int gk_mkpath(char *pathname)
-{
- char tmp[2048];
-
- sprintf(tmp, "mkdir -p %s", pathname);
- return system(tmp);
-}
-
-
-/*************************************************************************
-* This function deletes a directory tree and all of its contents
-**************************************************************************/
-int gk_rmpath(char *pathname)
-{
- char tmp[2048];
-
- sprintf(tmp, "rm -r %s", pathname);
- return system(tmp);
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/getopt.c b/3rdParty/metis/metis-5.1.0/GKlib/getopt.c
deleted file mode 100644
index 437befc86..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/getopt.c
+++ /dev/null
@@ -1,854 +0,0 @@
-/*************************************************************************/
-/*! \file getopt.c
-\brief Command line parsing
-
-This file contains a implementation of GNU's Getopt facility. The purpose
-for including it here is to ensure portability across different unix- and
-windows-based systems.
-
-\warning
-The implementation provided here uses the \c gk_ prefix for all variables
-used by the standard Getopt facility to communicate with the program.
-So, do read the documentation here.
-
-\verbatim
- Copyright (C) 1987,88,89,90,91,92,93,94,95,96,98,99,2000,2001
- Free Software Foundation, Inc. This file is part of the GNU C Library.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA.
-\endverbatim
-*/
-/*************************************************************************/
-
-
-#include <GKlib.h>
-
-/*************************************************************************/
-/* Local function prototypes */
-/*************************************************************************/
-static void exchange (char **);
-static char *gk_getopt_initialize (int, char **, char *);
-static int gk_getopt_internal(int argc, char **argv, char *optstring,
- struct gk_option *longopts, int *longind, int long_only);
-
-
-
-/*************************************************************************/
-/*! \brief For communication arguments to the caller.
-
-This variable is set by getopt to point at the value of the option argument,
-for those options that accept arguments.
-*/
-/*************************************************************************/
-char *gk_optarg;
-
-
-/*************************************************************************/
-/*! \brief Index in ARGV of the next element to be scanned.
-
-This variable is set by getopt to the index of the next element of the argv
-array to be processed. Once getopt has found all of the option arguments,
-you can use this variable to determine where the remaining non-option arguments
-begin.
-*/
-/*************************************************************************/
-int gk_optind = 1;
-
-
-/*************************************************************************/
-/*! \brief Controls error reporting for unrecognized options.
-
-If the value of this variable is nonzero, then getopt prints an error
-message to the standard error stream if it encounters an unknown option
-character or an option with a missing required argument. This is the default
-behavior. If you set this variable to zero, getopt does not print any messages,
-but it still returns the character ? to indicate an error.
-*/
-/*************************************************************************/
-int gk_opterr = 1;
-
-
-/*************************************************************************/
-/*! \brief Stores unknown option characters
-
-When getopt encounters an unknown option character or an option with a
-missing required argument, it stores that option character in this
-variable. You can use this for providing your own diagnostic messages.
-*/
-/*************************************************************************/
-int gk_optopt = '?';
-
-
-/*************************************************************************/
-/*
-Records that the getopt facility has been initialized.
-*/
-/*************************************************************************/
-int gk_getopt_initialized;
-
-
-/*************************************************************************/
-/*
-The next char to be scanned in the option-element in which the last option
-character we returned was found. This allows us to pick up the scan where
-we left off.
-
-If this is zero, or a null string, it means resume the scan by advancing
-to the next ARGV-element.
-*/
-/*************************************************************************/
-static char *nextchar;
-
-
-/*************************************************************************/
-/*
-Value of POSIXLY_CORRECT environment variable.
-*/
-/*************************************************************************/
-static char *posixly_correct;
-
-
-/*************************************************************************/
-/*
-Describe how to deal with options that follow non-option ARGV-elements.
-
-If the caller did not specify anything, the default is REQUIRE_ORDER if
-the environment variable POSIXLY_CORRECT is defined, PERMUTE otherwise.
-
-REQUIRE_ORDER means don't recognize them as options; stop option processing
-when the first non-option is seen. This is what Unix does. This mode of
-operation is selected by either setting the environment variable
-POSIXLY_CORRECT, or using `+' as the first character of the list of
-option characters.
-
-PERMUTE is the default. We permute the contents of ARGV as we scan, so
-that eventually all the non-options are at the end. This allows options
-to be given in any order, even with programs that were not written to
-expect this.
-
-RETURN_IN_ORDER is an option available to programs that were written
-to expect options and other ARGV-elements in any order and that care
-about the ordering of the two. We describe each non-option ARGV-element
-as if it were the argument of an option with character code 1.
-Using `-' as the first character of the list of option characters
-selects this mode of operation.
-
-The special argument `--' forces an end of option-scanning regardless
-of the value of `ordering'. In the case of RETURN_IN_ORDER, only
-`--' can cause `getopt' to return -1 with `gk_optind' != ARGC.
-*/
-/*************************************************************************/
-static enum
-{
- REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER
-} ordering;
-
-
-
-/*************************************************************************/
-/*
-Describe the part of ARGV that contains non-options that have
-been skipped. `first_nonopt' is the index in ARGV of the first of them;
-`last_nonopt' is the index after the last of them.
-*/
-/*************************************************************************/
-static int first_nonopt;
-static int last_nonopt;
-
-
-
-
-
-/*************************************************************************/
-/*
-Handle permutation of arguments.
-
-Exchange two adjacent subsequences of ARGV.
-One subsequence is elements [first_nonopt,last_nonopt)
-which contains all the non-options that have been skipped so far.
-The other is elements [last_nonopt,gk_optind), which contains all
-the options processed since those non-options were skipped.
-
-`first_nonopt' and `last_nonopt' are relocated so that they describe
-the new indices of the non-options in ARGV after they are moved.
-*/
-/*************************************************************************/
-static void exchange (char **argv)
-{
- int bottom = first_nonopt;
- int middle = last_nonopt;
- int top = gk_optind;
- char *tem;
-
- /* Exchange the shorter segment with the far end of the longer segment.
- That puts the shorter segment into the right place.
- It leaves the longer segment in the right place overall,
- but it consists of two parts that need to be swapped next. */
-
- while (top > middle && middle > bottom) {
- if (top - middle > middle - bottom) {
- /* Bottom segment is the short one. */
- int len = middle - bottom;
- register int i;
-
- /* Swap it with the top part of the top segment. */
- for (i = 0; i < len; i++) {
- tem = argv[bottom + i];
- argv[bottom + i] = argv[top - (middle - bottom) + i];
- argv[top - (middle - bottom) + i] = tem;
- }
- /* Exclude the moved bottom segment from further swapping. */
- top -= len;
- }
- else {
- /* Top segment is the short one. */
- int len = top - middle;
- register int i;
-
- /* Swap it with the bottom part of the bottom segment. */
- for (i = 0; i < len; i++) {
- tem = argv[bottom + i];
- argv[bottom + i] = argv[middle + i];
- argv[middle + i] = tem;
- }
- /* Exclude the moved top segment from further swapping. */
- bottom += len;
- }
- }
-
- /* Update records for the slots the non-options now occupy. */
-
- first_nonopt += (gk_optind - last_nonopt);
- last_nonopt = gk_optind;
-}
-
-
-
-/*************************************************************************/
-/*
-Initialize the internal data when the first call is made.
-*/
-/*************************************************************************/
-static char *gk_getopt_initialize (int argc, char **argv, char *optstring)
-{
- /* Start processing options with ARGV-element 1 (since ARGV-element 0
- is the program name); the sequence of previously skipped
- non-option ARGV-elements is empty. */
-
- first_nonopt = last_nonopt = gk_optind;
-
- nextchar = NULL;
-
- posixly_correct = getenv("POSIXLY_CORRECT");
-
- /* Determine how to handle the ordering of options and nonoptions. */
- if (optstring[0] == '-') {
- ordering = RETURN_IN_ORDER;
- ++optstring;
- }
- else if (optstring[0] == '+') {
- ordering = REQUIRE_ORDER;
- ++optstring;
- }
- else if (posixly_correct != NULL)
- ordering = REQUIRE_ORDER;
- else
- ordering = PERMUTE;
-
- return optstring;
-}
-
-
-/*************************************************************************/
-/*
- Scan elements of ARGV (whose length is ARGC) for option characters
- given in OPTSTRING.
-
- If an element of ARGV starts with '-', and is not exactly "-" or "--",
- then it is an option element. The characters of this element
- (aside from the initial '-') are option characters. If `getopt'
- is called repeatedly, it returns successively each of the option characters
- from each of the option elements.
-
- If `getopt' finds another option character, it returns that character,
- updating `gk_optind' and `nextchar' so that the next call to `getopt' can
- resume the scan with the following option character or ARGV-element.
-
- If there are no more option characters, `getopt' returns -1.
- Then `gk_optind' is the index in ARGV of the first ARGV-element
- that is not an option. (The ARGV-elements have been permuted
- so that those that are not options now come last.)
-
- OPTSTRING is a string containing the legitimate option characters.
- If an option character is seen that is not listed in OPTSTRING,
- return '?' after printing an error message. If you set `gk_opterr' to
- zero, the error message is suppressed but we still return '?'.
-
- If a char in OPTSTRING is followed by a colon, that means it wants an arg,
- so the following text in the same ARGV-element, or the text of the following
- ARGV-element, is returned in `gk_optarg'. Two colons mean an option that
- wants an optional arg; if there is text in the current ARGV-element,
- it is returned in `gk_optarg', otherwise `gk_optarg' is set to zero.
-
- If OPTSTRING starts with `-' or `+', it requests different methods of
- handling the non-option ARGV-elements.
- See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
-
- Long-named options begin with `--' instead of `-'.
- Their names may be abbreviated as long as the abbreviation is unique
- or is an exact match for some defined option. If they have an
- argument, it follows the option name in the same ARGV-element, separated
- from the option name by a `=', or else the in next ARGV-element.
- When `getopt' finds a long-named option, it returns 0 if that option's
- `flag' field is nonzero, the value of the option's `val' field
- if the `flag' field is zero.
-
- LONGOPTS is a vector of `struct gk_option' terminated by an
- element containing a name which is zero.
-
- LONGIND returns the index in LONGOPT of the long-named option found.
- It is only valid when a long-named option has been found by the most
- recent call.
-
- If LONG_ONLY is nonzero, '-' as well as '--' can introduce
- long-named options.
-*/
-/*************************************************************************/
-static int gk_getopt_internal(int argc, char **argv, char *optstring,
- struct gk_option *longopts, int *longind, int long_only)
-{
- int print_errors = gk_opterr;
- if (optstring[0] == ':')
- print_errors = 0;
-
- if (argc < 1)
- return -1;
-
- gk_optarg = NULL;
-
- if (gk_optind == 0 || !gk_getopt_initialized) {
- if (gk_optind == 0)
- gk_optind = 1; /* Don't scan ARGV[0], the program name. */
- optstring = gk_getopt_initialize (argc, argv, optstring);
- gk_getopt_initialized = 1;
- }
-
- /* Test whether ARGV[gk_optind] points to a non-option argument.
- Either it does not have option syntax, or there is an environment flag
- from the shell indicating it is not an option. The later information
- is only used when the used in the GNU libc. */
-# define NONOPTION_P (argv[gk_optind][0] != '-' || argv[gk_optind][1] == '\0')
-
- if (nextchar == NULL || *nextchar == '\0') {
- /* Advance to the next ARGV-element. */
-
- /* Give FIRST_NONOPT & LAST_NONOPT rational values if OPTIND has been
- moved back by the user (who may also have changed the arguments). */
- if (last_nonopt > gk_optind)
- last_nonopt = gk_optind;
- if (first_nonopt > gk_optind)
- first_nonopt = gk_optind;
-
- if (ordering == PERMUTE) {
- /* If we have just processed some options following some non-options,
- exchange them so that the options come first. */
-
- if (first_nonopt != last_nonopt && last_nonopt != gk_optind)
- exchange ((char **) argv);
- else if (last_nonopt != gk_optind)
- first_nonopt = gk_optind;
-
- /* Skip any additional non-options
- and extend the range of non-options previously skipped. */
-
- while (gk_optind < argc && NONOPTION_P)
- gk_optind++;
-
- last_nonopt = gk_optind;
- }
-
- /* The special ARGV-element `--' means premature end of options.
- Skip it like a null option,
- then exchange with previous non-options as if it were an option,
- then skip everything else like a non-option. */
-
- if (gk_optind != argc && !strcmp (argv[gk_optind], "--")) {
- gk_optind++;
-
- if (first_nonopt != last_nonopt && last_nonopt != gk_optind)
- exchange ((char **) argv);
- else if (first_nonopt == last_nonopt)
- first_nonopt = gk_optind;
- last_nonopt = argc;
-
- gk_optind = argc;
- }
-
- /* If we have done all the ARGV-elements, stop the scan
- and back over any non-options that we skipped and permuted. */
-
- if (gk_optind == argc) {
- /* Set the next-arg-index to point at the non-options
- that we previously skipped, so the caller will digest them. */
- if (first_nonopt != last_nonopt)
- gk_optind = first_nonopt;
- return -1;
- }
-
- /* If we have come to a non-option and did not permute it,
- either stop the scan or describe it to the caller and pass it by. */
-
- if (NONOPTION_P) {
- if (ordering == REQUIRE_ORDER)
- return -1;
- gk_optarg = argv[gk_optind++];
- return 1;
- }
-
- /* We have found another option-ARGV-element.
- Skip the initial punctuation. */
-
- nextchar = (argv[gk_optind] + 1 + (longopts != NULL && argv[gk_optind][1] == '-'));
- }
-
- /* Decode the current option-ARGV-element. */
-
- /* Check whether the ARGV-element is a long option.
-
- If long_only and the ARGV-element has the form "-f", where f is
- a valid short option, don't consider it an abbreviated form of
- a long option that starts with f. Otherwise there would be no
- way to give the -f short option.
-
- On the other hand, if there's a long option "fubar" and
- the ARGV-element is "-fu", do consider that an abbreviation of
- the long option, just like "--fu", and not "-f" with arg "u".
-
- This distinction seems to be the most useful approach. */
-
- if (longopts != NULL && (argv[gk_optind][1] == '-' || (long_only && (argv[gk_optind][2] || !strchr(optstring, argv[gk_optind][1]))))) {
- char *nameend;
- struct gk_option *p;
- struct gk_option *pfound = NULL;
- int exact = 0;
- int ambig = 0;
- int indfound = -1;
- int option_index;
-
- for (nameend = nextchar; *nameend && *nameend != '='; nameend++)
- /* Do nothing. */ ;
-
- /* Test all long options for either exact match or abbreviated matches. */
- for (p = longopts, option_index = 0; p->name; p++, option_index++) {
- if (!strncmp (p->name, nextchar, nameend - nextchar)) {
- if ((unsigned int) (nameend - nextchar) == (unsigned int) strlen (p->name)) {
- /* Exact match found. */
- pfound = p;
- indfound = option_index;
- exact = 1;
- break;
- }
- else if (pfound == NULL) {
- /* First nonexact match found. */
- pfound = p;
- indfound = option_index;
- }
- else if (long_only || pfound->has_arg != p->has_arg || pfound->flag != p->flag || pfound->val != p->val)
- /* Second or later nonexact match found. */
- ambig = 1;
- }
- }
-
- if (ambig && !exact) {
- if (print_errors)
- fprintf(stderr, "%s: option `%s' is ambiguous\n", argv[0], argv[gk_optind]);
-
- nextchar += strlen (nextchar);
- gk_optind++;
- gk_optopt = 0;
- return '?';
- }
-
- if (pfound != NULL) {
- option_index = indfound;
- gk_optind++;
- if (*nameend) {
- /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */
- if (pfound->has_arg)
- gk_optarg = nameend + 1;
- else {
- if (print_errors) {
- if (argv[gk_optind - 1][1] == '-')
- /* --option */
- fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n", argv[0], pfound->name);
- else
- /* +option or -option */
- fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n", argv[0], argv[gk_optind - 1][0], pfound->name);
- }
-
- nextchar += strlen (nextchar);
-
- gk_optopt = pfound->val;
- return '?';
- }
- }
- else if (pfound->has_arg == 1) {
- if (gk_optind < argc)
- gk_optarg = argv[gk_optind++];
- else {
- if (print_errors)
- fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]);
- nextchar += strlen (nextchar);
- gk_optopt = pfound->val;
- return optstring[0] == ':' ? ':' : '?';
- }
- }
- nextchar += strlen (nextchar);
- if (longind != NULL)
- *longind = option_index;
- if (pfound->flag) {
- *(pfound->flag) = pfound->val;
- return 0;
- }
- return pfound->val;
- }
-
- /* Can't find it as a long option. If this is not getopt_long_only,
- or the option starts with '--' or is not a valid short
- option, then it's an error. Otherwise interpret it as a short option. */
- if (!long_only || argv[gk_optind][1] == '-' || strchr(optstring, *nextchar) == NULL) {
- if (print_errors) {
- if (argv[gk_optind][1] == '-')
- /* --option */
- fprintf(stderr, "%s: unrecognized option `--%s'\n", argv[0], nextchar);
- else
- /* +option or -option */
- fprintf(stderr, "%s: unrecognized option `%c%s'\n", argv[0], argv[gk_optind][0], nextchar);
- }
- nextchar = (char *) "";
- gk_optind++;
- gk_optopt = 0;
- return '?';
- }
- }
-
- /* Look at and handle the next short option-character. */
- {
- char c = *nextchar++;
- char *temp = strchr(optstring, c);
-
- /* Increment `gk_optind' when we start to process its last character. */
- if (*nextchar == '\0')
- ++gk_optind;
-
- if (temp == NULL || c == ':') {
- if (print_errors) {
- if (posixly_correct)
- /* 1003.2 specifies the format of this message. */
- fprintf(stderr, "%s: illegal option -- %c\n", argv[0], c);
- else
- fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
- }
- gk_optopt = c;
- return '?';
- }
-
- /* Convenience. Treat POSIX -W foo same as long option --foo */
- if (temp[0] == 'W' && temp[1] == ';') {
- char *nameend;
- struct gk_option *p;
- struct gk_option *pfound = NULL;
- int exact = 0;
- int ambig = 0;
- int indfound = 0;
- int option_index;
-
- /* This is an option that requires an argument. */
- if (*nextchar != '\0') {
- gk_optarg = nextchar;
- /* If we end this ARGV-element by taking the rest as an arg,
- we must advance to the next element now. */
- gk_optind++;
- }
- else if (gk_optind == argc) {
- if (print_errors) {
- /* 1003.2 specifies the format of this message. */
- fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c);
- }
- gk_optopt = c;
- if (optstring[0] == ':')
- c = ':';
- else
- c = '?';
- return c;
- }
- else
- /* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */
- gk_optarg = argv[gk_optind++];
-
- /* gk_optarg is now the argument, see if it's in the table of longopts. */
-
- for (nextchar = nameend = gk_optarg; *nameend && *nameend != '='; nameend++)
- /* Do nothing. */ ;
-
- /* Test all long options for either exact match or abbreviated matches. */
- for (p = longopts, option_index = 0; p->name; p++, option_index++) {
- if (!strncmp (p->name, nextchar, nameend - nextchar)) {
- if ((unsigned int) (nameend - nextchar) == strlen (p->name)) {
- /* Exact match found. */
- pfound = p;
- indfound = option_index;
- exact = 1;
- break;
- }
- else if (pfound == NULL) {
- /* First nonexact match found. */
- pfound = p;
- indfound = option_index;
- }
- else
- /* Second or later nonexact match found. */
- ambig = 1;
- }
- }
- if (ambig && !exact) {
- if (print_errors)
- fprintf(stderr, "%s: option `-W %s' is ambiguous\n", argv[0], argv[gk_optind]);
- nextchar += strlen (nextchar);
- gk_optind++;
- return '?';
- }
- if (pfound != NULL) {
- option_index = indfound;
- if (*nameend) {
- /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */
- if (pfound->has_arg)
- gk_optarg = nameend + 1;
- else {
- if (print_errors)
- fprintf(stderr, "%s: option `-W %s' doesn't allow an argument\n", argv[0], pfound->name);
-
- nextchar += strlen (nextchar);
- return '?';
- }
- }
- else if (pfound->has_arg == 1) {
- if (gk_optind < argc)
- gk_optarg = argv[gk_optind++];
- else {
- if (print_errors)
- fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]);
- nextchar += strlen (nextchar);
- return optstring[0] == ':' ? ':' : '?';
- }
- }
- nextchar += strlen (nextchar);
- if (longind != NULL)
- *longind = option_index;
- if (pfound->flag) {
- *(pfound->flag) = pfound->val;
- return 0;
- }
- return pfound->val;
- }
- nextchar = NULL;
- return 'W'; /* Let the application handle it. */
- }
-
- if (temp[1] == ':') {
- if (temp[2] == ':') {
- /* This is an option that accepts an argument optionally. */
- if (*nextchar != '\0') {
- gk_optarg = nextchar;
- gk_optind++;
- }
- else
- gk_optarg = NULL;
- nextchar = NULL;
- }
- else {
- /* This is an option that requires an argument. */
- if (*nextchar != '\0') {
- gk_optarg = nextchar;
- /* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now. */
- gk_optind++;
- }
- else if (gk_optind == argc) {
- if (print_errors) {
- /* 1003.2 specifies the format of this message. */
- fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c);
- }
- gk_optopt = c;
- if (optstring[0] == ':')
- c = ':';
- else
- c = '?';
- }
- else
- /* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */
- gk_optarg = argv[gk_optind++];
- nextchar = NULL;
- }
- }
- return c;
- }
-}
-
-
-
-/*************************************************************************/
-/*! \brief Parse command-line arguments
-
-The gk_getopt() function gets the next option argument from the argument
-list specified by the \c argv and \c argc arguments. Normally these values
-come directly from the arguments received by main().
-
-\param argc is the number of command line arguments passed to main().
-\param argv is an array of strings storing the above command line
- arguments.
-\param options is a string that specifies the option characters that
- are valid for this program. An option character in this string
- can be followed by a colon (`:') to indicate that it takes a
- required argument. If an option character is followed by two
- colons (`::'), its argument is optional; this is a GNU extension.
-
-\return
-It returns the option character for the next command line option. When no
-more option arguments are available, it returns -1. There may still be
-more non-option arguments; you must compare the external variable
-#gk_optind against the \c argc parameter to check this.
-
-\return
-If the option has an argument, gk_getopt() returns the argument by storing
-it in the variable #gk_optarg. You don't ordinarily need to copy the
-#gk_optarg string, since it is a pointer into the original \c argv array,
-not into a static area that might be overwritten.
-
-\return
-If gk_getopt() finds an option character in \c argv that was not included
-in options, or a missing option argument, it returns `?' and sets the
-external variable #gk_optopt to the actual option character.
-If the first character of options is a colon (`:'), then gk_getopt()
-returns `:' instead of `?' to indicate a missing option argument.
-In addition, if the external variable #gk_opterr is nonzero (which is
-the default), gk_getopt() prints an error message. This variable is
-set by gk_getopt() to point at the value of the option argument,
-for those options that accept arguments.
-
-
-gk_getopt() has three ways to deal with options that follow non-options
-\c argv elements. The special argument <tt>`--'</tt> forces in all cases
-the end of option scanning.
- - The default is to permute the contents of \c argv while scanning it
- so that eventually all the non-options are at the end. This allows
- options to be given in any order, even with programs that were not
- written to expect this.
- - If the options argument string begins with a hyphen (`-'), this is
- treated specially. It permits arguments that are not options to be
- returned as if they were associated with option character `\\1'.
- - POSIX demands the following behavior: The first non-option stops
- option processing. This mode is selected by either setting the
- environment variable POSIXLY_CORRECT or beginning the options
- argument string with a plus sign (`+').
-
-*/
-/*************************************************************************/
-int gk_getopt(int argc, char **argv, char *options)
-{
- return gk_getopt_internal(argc, argv, options, NULL, NULL, 0);
-}
-
-
-/*************************************************************************/
-/*! \brief Parse command-line arguments with long options
-
-This function accepts GNU-style long options as well as single-character
-options.
-
-\param argc is the number of command line arguments passed to main().
-\param argv is an array of strings storing the above command line
- arguments.
-\param options describes the short options to accept, just as it does
- in gk_getopt().
-\param long_options describes the long options to accept. See the
- defintion of ::gk_option for more information.
-\param opt_index this is a returned variable. For any long option,
- gk_getopt_long() tells you the index in the array \c long_options
- of the options definition, by storing it into <tt>*opt_index</tt>.
- You can get the name of the option with <tt>longopts[*opt_index].name</tt>.
- So you can distinguish among long options either by the values
- in their val fields or by their indices. You can also distinguish
- in this way among long options that set flags.
-
-
-\return
-When gk_getopt_long() encounters a short option, it does the same thing
-that gk_getopt() would do: it returns the character code for the option,
-and stores the options argument (if it has one) in #gk_optarg.
-
-\return
-When gk_getopt_long() encounters a long option, it takes actions based
-on the flag and val fields of the definition of that option.
-
-\return
-If flag is a null pointer, then gk_getopt_long() returns the contents
-of val to indicate which option it found. You should arrange distinct
-values in the val field for options with different meanings, so you
-can decode these values after gk_getopt_long() returns. If the long
-option is equivalent to a short option, you can use the short option's
-character code in val.
-
-\return
-If flag is not a null pointer, that means this option should just set
-a flag in the program. The flag is a variable of type int that you
-define. Put the address of the flag in the flag field. Put in the
-val field the value you would like this option to store in the flag.
-In this case, gk_getopt_long() returns 0.
-
-\return
-When a long option has an argument, gk_getopt_long() puts the argument
-value in the variable #gk_optarg before returning. When the option has
-no argument, the value in #gk_optarg is a null pointer. This is
-how you can tell whether an optional argument was supplied.
-
-\return
-When gk_getopt_long() has no more options to handle, it returns -1,
-and leaves in the variable #gk_optind the index in argv of the next
-remaining argument.
-*/
-/*************************************************************************/
-int gk_getopt_long( int argc, char **argv, char *options,
- struct gk_option *long_options, int *opt_index)
-{
- return gk_getopt_internal (argc, argv, options, long_options, opt_index, 0);
-}
-
-
-
-/*************************************************************************/
-/*! \brief Parse command-line arguments with only long options
-
-Like gk_getopt_long(), but '-' as well as '--' can indicate a long option.
-If an option that starts with '-' (not '--') doesn't match a long option,
-but does match a short option, it is parsed as a short option instead.
-*/
-/*************************************************************************/
-int gk_getopt_long_only(int argc, char **argv, char *options,
- struct gk_option *long_options, int *opt_index)
-{
- return gk_getopt_internal(argc, argv, options, long_options, opt_index, 1);
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_arch.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_arch.h
deleted file mode 100644
index 18889b64b..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_arch.h
+++ /dev/null
@@ -1,71 +0,0 @@
-/*!
-\file gk_arch.h
-\brief This file contains various architecture-specific declerations
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_arch.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_ARCH_H_
-#define _GK_ARCH_H_
-
-/*************************************************************************
-* Architecture-specific differences in header files
-**************************************************************************/
-#ifdef LINUX
-#if !defined(__USE_XOPEN)
-#define __USE_XOPEN
-#endif
-#if !defined(_XOPEN_SOURCE)
-#define _XOPEN_SOURCE 600
-#endif
-#if !defined(__USE_XOPEN2K)
-#define __USE_XOPEN2K
-#endif
-#endif
-
-
-#ifdef HAVE_EXECINFO_H
-#include <execinfo.h>
-#endif
-
-
-#ifdef __MSC__
- #include "ms_stdint.h"
- #include "ms_inttypes.h"
- #include "ms_stat.h"
-#else
-#ifndef SUNOS
- #include <stdint.h>
-#endif
- #include <inttypes.h>
- #include <sys/types.h>
- #include <sys/resource.h>
- #include <sys/time.h>
-#endif
-
-
-/*************************************************************************
-* Architecture-specific modifications
-**************************************************************************/
-#ifdef WIN32
-typedef ptrdiff_t ssize_t;
-#endif
-
-
-#ifdef SUNOS
-#define PTRDIFF_MAX INT64_MAX
-#endif
-
-//#ifdef __MSC__
-/* MSC does not have rint() function */
-//#define rint(x) ((int)((x)+0.5))
-
-/* MSC does not have INFINITY defined */
-//#ifndef INFINITY
-//#define INFINITY FLT_MAX
-//#endif
-//#endif
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_defs.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_defs.h
deleted file mode 100644
index d75e72d24..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_defs.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/*!
-\file gk_defs.h
-\brief This file contains various constants definitions
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_defs.h 12732 2012-09-24 20:54:50Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_DEFS_H_
-#define _GK_DEFS_H_
-
-
-#define LTERM (void **) 0 /* List terminator for GKfree() */
-
-/* mopt_t types */
-#define GK_MOPT_MARK 1
-#define GK_MOPT_CORE 2
-#define GK_MOPT_HEAP 3
-
-#define HTABLE_EMPTY -1
-#define HTABLE_DELETED -2
-#define HTABLE_FIRST 1
-#define HTABLE_NEXT 2
-
-/* pdb corruption bit switches */
-#define CRP_ALTLOCS 1
-#define CRP_MISSINGCA 2
-#define CRP_MISSINGBB 4
-#define CRP_MULTICHAIN 8
-#define CRP_MULTICA 16
-#define CRP_MULTIBB 32
-
-#define MAXLINELEN 300000
-
-/* GKlib signals to standard signal mapping */
-#define SIGMEM SIGABRT
-#define SIGERR SIGTERM
-
-
-/* CSR-related defines */
-#define GK_CSR_ROW 1
-#define GK_CSR_COL 2
-
-#define GK_CSR_MAXTF 1
-#define GK_CSR_SQRT 2
-#define GK_CSR_POW25 3
-#define GK_CSR_POW65 4
-#define GK_CSR_POW75 5
-#define GK_CSR_POW85 6
-#define GK_CSR_LOG 7
-#define GK_CSR_IDF 8
-#define GK_CSR_IDF2 9
-#define GK_CSR_MAXTF2 10
-
-#define GK_CSR_COS 1
-#define GK_CSR_JAC 2
-#define GK_CSR_MIN 3
-#define GK_CSR_AMIN 4
-
-#define GK_CSR_FMT_CLUTO 1
-#define GK_CSR_FMT_CSR 2
-#define GK_CSR_FMT_METIS 3
-#define GK_CSR_FMT_BINROW 4
-#define GK_CSR_FMT_BINCOL 5
-
-#define GK_GRAPH_FMT_METIS 1
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_externs.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_externs.h
deleted file mode 100644
index 2c0fdd968..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_externs.h
+++ /dev/null
@@ -1,25 +0,0 @@
-/*!
-\file gk_externs.h
-\brief This file contains definitions of external variables created by GKlib
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_externs.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_EXTERNS_H_
-#define _GK_EXTERNS_H_
-
-
-/*************************************************************************
-* Extern variable definition. Hopefully, the __thread makes them thread-safe.
-**************************************************************************/
-#ifndef _GK_ERROR_C_
-/* declared in error.c */
-extern __thread int gk_cur_jbufs;
-extern __thread jmp_buf gk_jbufs[];
-extern __thread jmp_buf gk_jbuf;
-
-#endif
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_getopt.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_getopt.h
deleted file mode 100644
index 4bb86115f..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_getopt.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*!
-\file gk_getopt.h
-\brief This file contains GNU's externs/structs/prototypes
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_getopt.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_GETOPT_H_
-#define _GK_GETOPT_H_
-
-
-/* Externals from getopt.c */
-extern char *gk_optarg;
-extern int gk_optind;
-extern int gk_opterr;
-extern int gk_optopt;
-
-
-/*! \brief The structure that stores the information about the command-line options
-
-This structure describes a single long option name for the sake of
-gk_getopt_long(). The argument <tt>long_options</tt> must be an array
-of these structures, one for each long option. Terminate the array with
-an element containing all zeros.
-*/
-struct gk_option {
- char *name; /*!< This field is the name of the option. */
- int has_arg; /*!< This field says whether the option takes an argument.
- It is an integer, and there are three legitimate values:
- no_argument, required_argument and optional_argument.
- */
- int *flag; /*!< See the discussion on ::gk_option#val */
- int val; /*!< These fields control how to report or act on the option
- when it occurs.
-
- If flag is a null pointer, then the val is a value which
- identifies this option. Often these values are chosen
- to uniquely identify particular long options.
-
- If flag is not a null pointer, it should be the address
- of an int variable which is the flag for this option.
- The value in val is the value to store in the flag to
- indicate that the option was seen. */
-};
-
-/* Names for the values of the `has_arg' field of `struct gk_option'. */
-#define no_argument 0
-#define required_argument 1
-#define optional_argument 2
-
-
-/* Function prototypes */
-extern int gk_getopt(int __argc, char **__argv, char *__shortopts);
-extern int gk_getopt_long(int __argc, char **__argv, char *__shortopts,
- struct gk_option *__longopts, int *__longind);
-extern int gk_getopt_long_only (int __argc, char **__argv,
- char *__shortopts, struct gk_option *__longopts, int *__longind);
-
-
-
-#endif
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_macros.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_macros.h
deleted file mode 100644
index d1e288bc3..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_macros.h
+++ /dev/null
@@ -1,153 +0,0 @@
-/*!
-\file gk_macros.h
-\brief This file contains various macros
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_macros.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_MACROS_H_
-#define _GK_MACROS_H_
-
-/*-------------------------------------------------------------
- * Usefull commands
- *-------------------------------------------------------------*/
-#define gk_max(a, b) ((a) >= (b) ? (a) : (b))
-#define gk_min(a, b) ((a) >= (b) ? (b) : (a))
-#define gk_max3(a, b, c) ((a) >= (b) && (a) >= (c) ? (a) : ((b) >= (a) && (b) >= (c) ? (b) : (c)))
-#define gk_SWAP(a, b, tmp) do {(tmp) = (a); (a) = (b); (b) = (tmp);} while(0)
-#define INC_DEC(a, b, val) do {(a) += (val); (b) -= (val);} while(0)
-#define sign(a, b) ((a >= 0 ? b : -b))
-
-#define ONEOVERRANDMAX (1.0/(RAND_MAX+1.0))
-#define RandomInRange(u) ((int) (ONEOVERRANDMAX*(u)*rand()))
-
-#define gk_abs(x) ((x) >= 0 ? (x) : -(x))
-
-
-/*-------------------------------------------------------------
- * Timing macros
- *-------------------------------------------------------------*/
-#define gk_clearcputimer(tmr) (tmr = 0.0)
-#define gk_startcputimer(tmr) (tmr -= gk_CPUSeconds())
-#define gk_stopcputimer(tmr) (tmr += gk_CPUSeconds())
-#define gk_getcputimer(tmr) (tmr)
-
-#define gk_clearwctimer(tmr) (tmr = 0.0)
-#define gk_startwctimer(tmr) (tmr -= gk_WClockSeconds())
-#define gk_stopwctimer(tmr) (tmr += gk_WClockSeconds())
-#define gk_getwctimer(tmr) (tmr)
-
-/*-------------------------------------------------------------
- * dbglvl handling macros
- *-------------------------------------------------------------*/
-#define IFSET(a, flag, cmd) if ((a)&(flag)) (cmd);
-
-
-/*-------------------------------------------------------------
- * gracefull library exit macro
- *-------------------------------------------------------------*/
-#define GKSETJMP() (setjmp(gk_return_to_entry))
-#define gk_sigcatch() (setjmp(gk_jbufs[gk_cur_jbufs]))
-
-
-/*-------------------------------------------------------------
- * Debuging memory leaks
- *-------------------------------------------------------------*/
-#ifdef DMALLOC
-# define MALLOC_CHECK(ptr) \
- if (malloc_verify((ptr)) == DMALLOC_VERIFY_ERROR) { \
- printf("***MALLOC_CHECK failed on line %d of file %s: " #ptr "\n", \
- __LINE__, __FILE__); \
- abort(); \
- }
-#else
-# define MALLOC_CHECK(ptr) ;
-#endif
-
-
-/*-------------------------------------------------------------
- * CSR conversion macros
- *-------------------------------------------------------------*/
-#define MAKECSR(i, n, a) \
- do { \
- for (i=1; i<n; i++) a[i] += a[i-1]; \
- for (i=n; i>0; i--) a[i] = a[i-1]; \
- a[0] = 0; \
- } while(0)
-
-#define SHIFTCSR(i, n, a) \
- do { \
- for (i=n; i>0; i--) a[i] = a[i-1]; \
- a[0] = 0; \
- } while(0)
-
-
-/*-------------------------------------------------------------
- * ASSERTS that cannot be turned off!
- *-------------------------------------------------------------*/
-#define GKASSERT(expr) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- abort(); \
- }
-
-#define GKASSERTP(expr,msg) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- printf msg ; \
- printf("\n"); \
- abort(); \
- }
-
-#define GKCUASSERT(expr) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- }
-
-#define GKCUASSERTP(expr,msg) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- printf msg ; \
- printf("\n"); \
- }
-
-/*-------------------------------------------------------------
- * Program Assertions
- *-------------------------------------------------------------*/
-#ifndef NDEBUG
-# define ASSERT(expr) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- assert(expr); \
- }
-
-# define ASSERTP(expr,msg) \
- if (!(expr)) { \
- printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
- __LINE__, __FILE__); \
- printf msg ; \
- printf("\n"); \
- assert(expr); \
- }
-#else
-# define ASSERT(expr) ;
-# define ASSERTP(expr,msg) ;
-#endif
-
-#ifndef NDEBUG2
-# define ASSERT2 ASSERT
-# define ASSERTP2 ASSERTP
-#else
-# define ASSERT2(expr) ;
-# define ASSERTP2(expr,msg) ;
-#endif
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkblas.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkblas.h
deleted file mode 100644
index 7dd96dff2..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkblas.h
+++ /dev/null
@@ -1,201 +0,0 @@
-/*!
-\file gk_mkblas.h
-\brief Templates for BLAS-like routines
-
-\date Started 3/28/07
-\author George
-\version\verbatim $Id: gk_mkblas.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_MKBLAS_H_
-#define _GK_MKBLAS_H_
-
-
-#define GK_MKBLAS(PRFX, TYPE, OUTTYPE) \
-/*************************************************************************/\
-/*! The macro for gk_?incset()-class of routines */\
-/*************************************************************************/\
-TYPE *PRFX ## incset(size_t n, TYPE baseval, TYPE *x)\
-{\
- size_t i;\
-\
- for (i=0; i<n; i++)\
- x[i] = baseval+i;\
-\
- return x;\
-}\
-\
-/*************************************************************************/\
-/*! The macro for gk_?max()-class of routines */\
-/*************************************************************************/\
-TYPE PRFX ## max(size_t n, TYPE *x)\
-{\
- size_t i, max=0; \
-\
- if (n <= 0) return (TYPE) 0;\
-\
- for (i=1; i<n; i++)\
- max = (x[i] > x[max] ? i : max);\
-\
- return x[max];\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?min()-class of routines */\
-/*************************************************************************/\
-TYPE PRFX ## min(size_t n, TYPE *x)\
-{\
- size_t i, min=0;\
-\
- if (n <= 0) return (TYPE) 0;\
-\
- for (i=1; i<n; i++)\
- min = (x[i] < x[min] ? i : min);\
-\
- return x[min];\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?argmax()-class of routines */\
-/*************************************************************************/\
-size_t PRFX ## argmax(size_t n, TYPE *x)\
-{\
- size_t i, max=0;\
-\
- for (i=1; i<n; i++)\
- max = (x[i] > x[max] ? i : max);\
-\
- return max;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?argmin()-class of routines */\
-/*************************************************************************/\
-size_t PRFX ## argmin(size_t n, TYPE *x)\
-{\
- size_t i, min=0;\
-\
- for (i=1; i<n; i++)\
- min = (x[i] < x[min] ? i : min);\
-\
- return min;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?argmax_n()-class of routines */\
-/*************************************************************************/\
-size_t PRFX ## argmax_n(size_t n, TYPE *x, size_t k)\
-{\
- size_t i, max_n;\
- PRFX ## kv_t *cand;\
-\
- cand = PRFX ## kvmalloc(n, "GK_ARGMAX_N: cand");\
-\
- for (i=0; i<n; i++) {\
- cand[i].val = i;\
- cand[i].key = x[i];\
- }\
- PRFX ## kvsortd(n, cand);\
-\
- max_n = cand[k-1].val;\
-\
- gk_free((void *)&cand, LTERM);\
-\
- return max_n;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?sum()-class of routines */\
-/**************************************************************************/\
-OUTTYPE PRFX ## sum(size_t n, TYPE *x, size_t incx)\
-{\
- size_t i;\
- OUTTYPE sum = 0;\
-\
- for (i=0; i<n; i++, x+=incx)\
- sum += (*x);\
-\
- return sum;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?scale()-class of routines */\
-/**************************************************************************/\
-TYPE *PRFX ## scale(size_t n, TYPE alpha, TYPE *x, size_t incx)\
-{\
- size_t i;\
-\
- for (i=0; i<n; i++, x+=incx)\
- (*x) *= alpha;\
-\
- return x;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?norm2()-class of routines */\
-/**************************************************************************/\
-OUTTYPE PRFX ## norm2(size_t n, TYPE *x, size_t incx)\
-{\
- size_t i;\
- OUTTYPE partial = 0;\
-\
- for (i=0; i<n; i++, x+=incx)\
- partial += (*x) * (*x);\
-\
- return (partial > 0 ? (OUTTYPE)sqrt((double)partial) : (OUTTYPE)0);\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?dot()-class of routines */\
-/**************************************************************************/\
-OUTTYPE PRFX ## dot(size_t n, TYPE *x, size_t incx, TYPE *y, size_t incy)\
-{\
- size_t i;\
- OUTTYPE partial = 0.0;\
- \
- for (i=0; i<n; i++, x+=incx, y+=incy)\
- partial += (*x) * (*y);\
-\
- return partial;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?axpy()-class of routines */\
-/**************************************************************************/\
-TYPE *PRFX ## axpy(size_t n, TYPE alpha, TYPE *x, size_t incx, TYPE *y, size_t incy)\
-{\
- size_t i;\
- TYPE *y_in = y;\
-\
- for (i=0; i<n; i++, x+=incx, y+=incy)\
- *y += alpha*(*x);\
-\
- return y_in;\
-}\
-
-
-
-#define GK_MKBLAS_PROTO(PRFX, TYPE, OUTTYPE) \
- TYPE *PRFX ## incset(size_t n, TYPE baseval, TYPE *x);\
- TYPE PRFX ## max(size_t n, TYPE *x);\
- TYPE PRFX ## min(size_t n, TYPE *x);\
- size_t PRFX ## argmax(size_t n, TYPE *x);\
- size_t PRFX ## argmin(size_t n, TYPE *x);\
- size_t PRFX ## argmax_n(size_t n, TYPE *x, size_t k);\
- OUTTYPE PRFX ## sum(size_t n, TYPE *x, size_t incx);\
- TYPE *PRFX ## scale(size_t n, TYPE alpha, TYPE *x, size_t incx);\
- OUTTYPE PRFX ## norm2(size_t n, TYPE *x, size_t incx);\
- OUTTYPE PRFX ## dot(size_t n, TYPE *x, size_t incx, TYPE *y, size_t incy);\
- TYPE *PRFX ## axpy(size_t n, TYPE alpha, TYPE *x, size_t incx, TYPE *y, size_t incy);\
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkmemory.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkmemory.h
deleted file mode 100644
index 78e216e0e..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkmemory.h
+++ /dev/null
@@ -1,142 +0,0 @@
-/*!
-\file gk_mkmemory.h
-\brief Templates for memory allocation routines
-
-\date Started 3/29/07
-\author George
-\version\verbatim $Id: gk_mkmemory.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_MKMEMORY_H_
-#define _GK_MKMEMORY_H_
-
-
-#define GK_MKALLOC(PRFX, TYPE)\
-/*************************************************************************/\
-/*! The macro for gk_?malloc()-class of routines */\
-/**************************************************************************/\
-TYPE *PRFX ## malloc(size_t n, char *msg)\
-{\
- return (TYPE *)gk_malloc(sizeof(TYPE)*n, msg);\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?realloc()-class of routines */\
-/**************************************************************************/\
-TYPE *PRFX ## realloc(TYPE *ptr, size_t n, char *msg)\
-{\
- return (TYPE *)gk_realloc((void *)ptr, sizeof(TYPE)*n, msg);\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?smalloc()-class of routines */\
-/**************************************************************************/\
-TYPE *PRFX ## smalloc(size_t n, TYPE ival, char *msg)\
-{\
- TYPE *ptr;\
-\
- ptr = (TYPE *)gk_malloc(sizeof(TYPE)*n, msg);\
- if (ptr == NULL) \
- return NULL; \
-\
- return PRFX ## set(n, ival, ptr); \
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?set()-class of routines */\
-/*************************************************************************/\
-TYPE *PRFX ## set(size_t n, TYPE val, TYPE *x)\
-{\
- size_t i;\
-\
- for (i=0; i<n; i++)\
- x[i] = val;\
-\
- return x;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?set()-class of routines */\
-/*************************************************************************/\
-TYPE *PRFX ## copy(size_t n, TYPE *a, TYPE *b)\
-{\
- return (TYPE *)memmove((void *)b, (void *)a, sizeof(TYPE)*n);\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?AllocMatrix()-class of routines */\
-/**************************************************************************/\
-TYPE **PRFX ## AllocMatrix(size_t ndim1, size_t ndim2, TYPE value, char *errmsg)\
-{\
- gk_idx_t i, j;\
- TYPE **matrix;\
-\
- matrix = (TYPE **)gk_malloc(ndim1*sizeof(TYPE *), errmsg);\
- if (matrix == NULL) \
- return NULL;\
-\
- for (i=0; i<ndim1; i++) { \
- matrix[i] = PRFX ## smalloc(ndim2, value, errmsg);\
- if (matrix[i] == NULL) { \
- for (j=0; j<i; j++) \
- gk_free((void **)&matrix[j], LTERM); \
- return NULL; \
- } \
- }\
-\
- return matrix;\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?AllocMatrix()-class of routines */\
-/**************************************************************************/\
-void PRFX ## FreeMatrix(TYPE ***r_matrix, size_t ndim1, size_t ndim2)\
-{\
- gk_idx_t i;\
- TYPE **matrix;\
-\
- if (*r_matrix == NULL) \
- return; \
-\
- matrix = *r_matrix;\
-\
- for (i=0; i<ndim1; i++) \
- gk_free((void **)&(matrix[i]), LTERM);\
-\
- gk_free((void **)r_matrix, LTERM);\
-}\
-\
-\
-/*************************************************************************/\
-/*! The macro for gk_?SetMatrix()-class of routines */\
-/**************************************************************************/\
-void PRFX ## SetMatrix(TYPE **matrix, size_t ndim1, size_t ndim2, TYPE value)\
-{\
- gk_idx_t i, j;\
-\
- for (i=0; i<ndim1; i++) {\
- for (j=0; j<ndim2; j++)\
- matrix[i][j] = value;\
- }\
-}\
-
-
-#define GK_MKALLOC_PROTO(PRFX, TYPE)\
- TYPE *PRFX ## malloc(size_t n, char *msg);\
- TYPE *PRFX ## realloc(TYPE *ptr, size_t n, char *msg);\
- TYPE *PRFX ## smalloc(size_t n, TYPE ival, char *msg);\
- TYPE *PRFX ## set(size_t n, TYPE val, TYPE *x);\
- TYPE *PRFX ## copy(size_t n, TYPE *a, TYPE *b);\
- TYPE **PRFX ## AllocMatrix(size_t ndim1, size_t ndim2, TYPE value, char *errmsg);\
- void PRFX ## FreeMatrix(TYPE ***r_matrix, size_t ndim1, size_t ndim2);\
- void PRFX ## SetMatrix(TYPE **matrix, size_t ndim1, size_t ndim2, TYPE value);\
-
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue.h
deleted file mode 100644
index 3da7d26c0..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue.h
+++ /dev/null
@@ -1,437 +0,0 @@
-/*!
-\file gk_mkpqueue.h
-\brief Templates for priority queues
-
-\date Started 4/09/07
-\author George
-\version\verbatim $Id: gk_mkpqueue.h 13005 2012-10-23 22:34:36Z karypis $ \endverbatim
-*/
-
-
-#ifndef _GK_MKPQUEUE_H
-#define _GK_MKPQUEUE_H
-
-
-#define GK_MKPQUEUE(FPRFX, PQT, KVT, KT, VT, KVMALLOC, KMAX, KEY_LT)\
-/*************************************************************************/\
-/*! This function creates and initializes a priority queue */\
-/**************************************************************************/\
-PQT *FPRFX ## Create(size_t maxnodes)\
-{\
- PQT *queue; \
-\
- queue = (PQT *)gk_malloc(sizeof(PQT), "gk_pqCreate: queue");\
- FPRFX ## Init(queue, maxnodes);\
-\
- return queue;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function initializes the data structures of the priority queue */\
-/**************************************************************************/\
-void FPRFX ## Init(PQT *queue, size_t maxnodes)\
-{\
- queue->nnodes = 0;\
- queue->maxnodes = maxnodes;\
-\
- queue->heap = KVMALLOC(maxnodes, "gk_PQInit: heap");\
- queue->locator = gk_idxsmalloc(maxnodes, -1, "gk_PQInit: locator");\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function resets the priority queue */\
-/**************************************************************************/\
-void FPRFX ## Reset(PQT *queue)\
-{\
- gk_idx_t i;\
- gk_idx_t *locator=queue->locator;\
- KVT *heap=queue->heap;\
-\
- for (i=queue->nnodes-1; i>=0; i--)\
- locator[heap[i].val] = -1;\
- queue->nnodes = 0;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function frees the internal datastructures of the priority queue */\
-/**************************************************************************/\
-void FPRFX ## Free(PQT *queue)\
-{\
- if (queue == NULL) return;\
- gk_free((void **)&queue->heap, &queue->locator, LTERM);\
- queue->maxnodes = 0;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function frees the internal datastructures of the priority queue \
- and the queue itself */\
-/**************************************************************************/\
-void FPRFX ## Destroy(PQT *queue)\
-{\
- if (queue == NULL) return;\
- FPRFX ## Free(queue);\
- gk_free((void **)&queue, LTERM);\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the length of the queue */\
-/**************************************************************************/\
-size_t FPRFX ## Length(PQT *queue)\
-{\
- return queue->nnodes;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function adds an item in the priority queue */\
-/**************************************************************************/\
-int FPRFX ## Insert(PQT *queue, VT node, KT key)\
-{\
- gk_idx_t i, j;\
- gk_idx_t *locator=queue->locator;\
- KVT *heap=queue->heap;\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- ASSERT(locator[node] == -1);\
-\
- i = queue->nnodes++;\
- while (i > 0) {\
- j = (i-1)>>1;\
- if (KEY_LT(key, heap[j].key)) {\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
- ASSERT(i >= 0);\
- heap[i].key = key;\
- heap[i].val = node;\
- locator[node] = i;\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- return 0;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function deletes an item from the priority queue */\
-/**************************************************************************/\
-int FPRFX ## Delete(PQT *queue, VT node)\
-{\
- gk_idx_t i, j, nnodes;\
- KT newkey, oldkey;\
- gk_idx_t *locator=queue->locator;\
- KVT *heap=queue->heap;\
-\
- ASSERT(locator[node] != -1);\
- ASSERT(heap[locator[node]].val == node);\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- i = locator[node];\
- locator[node] = -1;\
-\
- if (--queue->nnodes > 0 && heap[queue->nnodes].val != node) {\
- node = heap[queue->nnodes].val;\
- newkey = heap[queue->nnodes].key;\
- oldkey = heap[i].key;\
-\
- if (KEY_LT(newkey, oldkey)) { /* Filter-up */\
- while (i > 0) {\
- j = (i-1)>>1;\
- if (KEY_LT(newkey, heap[j].key)) {\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
- }\
- else { /* Filter down */\
- nnodes = queue->nnodes;\
- while ((j=(i<<1)+1) < nnodes) {\
- if (KEY_LT(heap[j].key, newkey)) {\
- if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
- j++;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\
- j++;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
- }\
-\
- heap[i].key = newkey;\
- heap[i].val = node;\
- locator[node] = i;\
- }\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- return 0;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function updates the key values associated for a particular item */ \
-/**************************************************************************/\
-void FPRFX ## Update(PQT *queue, VT node, KT newkey)\
-{\
- gk_idx_t i, j, nnodes;\
- KT oldkey;\
- gk_idx_t *locator=queue->locator;\
- KVT *heap=queue->heap;\
-\
- oldkey = heap[locator[node]].key;\
-\
- ASSERT(locator[node] != -1);\
- ASSERT(heap[locator[node]].val == node);\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- i = locator[node];\
-\
- if (KEY_LT(newkey, oldkey)) { /* Filter-up */\
- while (i > 0) {\
- j = (i-1)>>1;\
- if (KEY_LT(newkey, heap[j].key)) {\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
- }\
- else { /* Filter down */\
- nnodes = queue->nnodes;\
- while ((j=(i<<1)+1) < nnodes) {\
- if (KEY_LT(heap[j].key, newkey)) {\
- if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
- j++;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\
- j++;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
- }\
-\
- heap[i].key = newkey;\
- heap[i].val = node;\
- locator[node] = i;\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- return;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the item at the top of the queue and removes\
- it from the priority queue */\
-/**************************************************************************/\
-VT FPRFX ## GetTop(PQT *queue)\
-{\
- gk_idx_t i, j;\
- gk_idx_t *locator;\
- KVT *heap;\
- VT vtx, node;\
- KT key;\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
-\
- if (queue->nnodes == 0)\
- return -1;\
-\
- queue->nnodes--;\
-\
- heap = queue->heap;\
- locator = queue->locator;\
-\
- vtx = heap[0].val;\
- locator[vtx] = -1;\
-\
- if ((i = queue->nnodes) > 0) {\
- key = heap[i].key;\
- node = heap[i].val;\
- i = 0;\
- while ((j=2*i+1) < queue->nnodes) {\
- if (KEY_LT(heap[j].key, key)) {\
- if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
- j = j+1;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, key)) {\
- j = j+1;\
- heap[i] = heap[j];\
- locator[heap[i].val] = i;\
- i = j;\
- }\
- else\
- break;\
- }\
-\
- heap[i].key = key;\
- heap[i].val = node;\
- locator[node] = i;\
- }\
-\
- ASSERT2(FPRFX ## CheckHeap(queue));\
- return vtx;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the item at the top of the queue. The item is not\
- deleted from the queue. */\
-/**************************************************************************/\
-VT FPRFX ## SeeTopVal(PQT *queue)\
-{\
- return (queue->nnodes == 0 ? -1 : queue->heap[0].val);\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the key of the top item. The item is not\
- deleted from the queue. */\
-/**************************************************************************/\
-KT FPRFX ## SeeTopKey(PQT *queue)\
-{\
- return (queue->nnodes == 0 ? KMAX : queue->heap[0].key);\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the key of a specific item */\
-/**************************************************************************/\
-KT FPRFX ## SeeKey(PQT *queue, VT node)\
-{\
- gk_idx_t *locator;\
- KVT *heap;\
-\
- heap = queue->heap;\
- locator = queue->locator;\
-\
- return heap[locator[node]].key;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the first item in a breadth-first traversal of\
- the heap whose key is less than maxwgt. This function is here due to\
- hMETIS and is not general!*/\
-/**************************************************************************/\
-/*\
-VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts)\
-{\
- gk_idx_t i;\
-\
- if (queue->nnodes == 0)\
- return -1;\
-\
- if (maxwgt <= 1000)\
- return FPRFX ## SeeTopVal(queue);\
-\
- for (i=0; i<queue->nnodes; i++) {\
- if (queue->heap[i].key > 0) {\
- if (wgts[queue->heap[i].val] <= maxwgt)\
- return queue->heap[i].val;\
- }\
- else {\
- if (queue->heap[i/2].key <= 0)\
- break;\
- }\
- }\
-\
- return queue->heap[0].val;\
-\
-}\
-*/\
-\
-\
-/*************************************************************************/\
-/*! This functions checks the consistency of the heap */\
-/**************************************************************************/\
-int FPRFX ## CheckHeap(PQT *queue)\
-{\
- gk_idx_t i, j;\
- size_t nnodes;\
- gk_idx_t *locator;\
- KVT *heap;\
-\
- heap = queue->heap;\
- locator = queue->locator;\
- nnodes = queue->nnodes;\
-\
- if (nnodes == 0)\
- return 1;\
-\
- ASSERT(locator[heap[0].val] == 0);\
- for (i=1; i<nnodes; i++) {\
- ASSERT(locator[heap[i].val] == i);\
- ASSERT(!KEY_LT(heap[i].key, heap[(i-1)/2].key));\
- }\
- for (i=1; i<nnodes; i++)\
- ASSERT(!KEY_LT(heap[i].key, heap[0].key));\
-\
- for (j=i=0; i<queue->maxnodes; i++) {\
- if (locator[i] != -1)\
- j++;\
- }\
- ASSERTP(j == nnodes, ("%jd %jd\n", (intmax_t)j, (intmax_t)nnodes));\
-\
- return 1;\
-}\
-
-
-#define GK_MKPQUEUE_PROTO(FPRFX, PQT, KT, VT)\
- PQT * FPRFX ## Create(size_t maxnodes);\
- void FPRFX ## Init(PQT *queue, size_t maxnodes);\
- void FPRFX ## Reset(PQT *queue);\
- void FPRFX ## Free(PQT *queue);\
- void FPRFX ## Destroy(PQT *queue);\
- size_t FPRFX ## Length(PQT *queue);\
- int FPRFX ## Insert(PQT *queue, VT node, KT key);\
- int FPRFX ## Delete(PQT *queue, VT node);\
- void FPRFX ## Update(PQT *queue, VT node, KT newkey);\
- VT FPRFX ## GetTop(PQT *queue);\
- VT FPRFX ## SeeTopVal(PQT *queue);\
- KT FPRFX ## SeeTopKey(PQT *queue);\
- KT FPRFX ## SeeKey(PQT *queue, VT node);\
- VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts);\
- int FPRFX ## CheckHeap(PQT *queue);\
-
-
-/* This is how these macros are used
-GK_MKPQUEUE(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX)
-GK_MKPQUEUE_PROTO(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t)
-*/
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue2.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue2.h
deleted file mode 100644
index 10e8ee462..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkpqueue2.h
+++ /dev/null
@@ -1,215 +0,0 @@
-/*!
-\file gk_mkpqueue2.h
-\brief Templates for priority queues that do not utilize locators and as such
- they can use different types of values.
-
-\date Started 4/09/07
-\author George
-\version\verbatim $Id: gk_mkpqueue2.h 13005 2012-10-23 22:34:36Z karypis $ \endverbatim
-*/
-
-
-#ifndef _GK_MKPQUEUE2_H
-#define _GK_MKPQUEUE2_H
-
-
-#define GK_MKPQUEUE2(FPRFX, PQT, KT, VT, KMALLOC, VMALLOC, KMAX, KEY_LT)\
-/*************************************************************************/\
-/*! This function creates and initializes a priority queue */\
-/**************************************************************************/\
-PQT *FPRFX ## Create2(ssize_t maxnodes)\
-{\
- PQT *queue; \
-\
- if ((queue = (PQT *)gk_malloc(sizeof(PQT), "gk_pqCreate2: queue")) != NULL) {\
- memset(queue, 0, sizeof(PQT));\
- queue->nnodes = 0;\
- queue->maxnodes = maxnodes;\
- queue->keys = KMALLOC(maxnodes, "gk_pqCreate2: keys");\
- queue->vals = VMALLOC(maxnodes, "gk_pqCreate2: vals");\
-\
- if (queue->keys == NULL || queue->vals == NULL)\
- gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\
- }\
-\
- return queue;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function resets the priority queue */\
-/**************************************************************************/\
-void FPRFX ## Reset2(PQT *queue)\
-{\
- queue->nnodes = 0;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function frees the internal datastructures of the priority queue */\
-/**************************************************************************/\
-void FPRFX ## Destroy2(PQT **r_queue)\
-{\
- PQT *queue = *r_queue; \
- if (queue == NULL) return;\
- gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\
- *r_queue = NULL;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the length of the queue */\
-/**************************************************************************/\
-size_t FPRFX ## Length2(PQT *queue)\
-{\
- return queue->nnodes;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function adds an item in the priority queue. */\
-/**************************************************************************/\
-int FPRFX ## Insert2(PQT *queue, VT val, KT key)\
-{\
- ssize_t i, j;\
- KT *keys=queue->keys;\
- VT *vals=queue->vals;\
-\
- ASSERT2(FPRFX ## CheckHeap2(queue));\
-\
- if (queue->nnodes == queue->maxnodes) \
- return 0;\
-\
- ASSERT2(FPRFX ## CheckHeap2(queue));\
-\
- i = queue->nnodes++;\
- while (i > 0) {\
- j = (i-1)>>1;\
- if (KEY_LT(key, keys[j])) {\
- keys[i] = keys[j];\
- vals[i] = vals[j];\
- i = j;\
- }\
- else\
- break;\
- }\
- ASSERT(i >= 0);\
- keys[i] = key;\
- vals[i] = val;\
-\
- ASSERT2(FPRFX ## CheckHeap2(queue));\
-\
- return 1;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the item at the top of the queue and removes\
- it from the priority queue */\
-/**************************************************************************/\
-int FPRFX ## GetTop2(PQT *queue, VT *r_val)\
-{\
- ssize_t i, j;\
- KT key, *keys=queue->keys;\
- VT val, *vals=queue->vals;\
-\
- ASSERT2(FPRFX ## CheckHeap2(queue));\
-\
- if (queue->nnodes == 0)\
- return 0;\
-\
- queue->nnodes--;\
-\
- *r_val = vals[0];\
-\
- if ((i = queue->nnodes) > 0) {\
- key = keys[i];\
- val = vals[i];\
- i = 0;\
- while ((j=2*i+1) < queue->nnodes) {\
- if (KEY_LT(keys[j], key)) {\
- if (j+1 < queue->nnodes && KEY_LT(keys[j+1], keys[j]))\
- j = j+1;\
- keys[i] = keys[j];\
- vals[i] = vals[j];\
- i = j;\
- }\
- else if (j+1 < queue->nnodes && KEY_LT(keys[j+1], key)) {\
- j = j+1;\
- keys[i] = keys[j];\
- vals[i] = vals[j];\
- i = j;\
- }\
- else\
- break;\
- }\
-\
- keys[i] = key;\
- vals[i] = val;\
- }\
-\
- ASSERT2(FPRFX ## CheckHeap2(queue));\
-\
- return 1;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the item at the top of the queue. The item is not\
- deleted from the queue. */\
-/**************************************************************************/\
-int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val)\
-{\
- if (queue->nnodes == 0) \
- return 0;\
-\
- *r_val = queue->vals[0];\
-\
- return 1;\
-}\
-\
-\
-/*************************************************************************/\
-/*! This function returns the key of the top item. The item is not\
- deleted from the queue. */\
-/**************************************************************************/\
-KT FPRFX ## SeeTopKey2(PQT *queue)\
-{\
- return (queue->nnodes == 0 ? KMAX : queue->keys[0]);\
-}\
-\
-\
-/*************************************************************************/\
-/*! This functions checks the consistency of the heap */\
-/**************************************************************************/\
-int FPRFX ## CheckHeap2(PQT *queue)\
-{\
- ssize_t i;\
- KT *keys=queue->keys;\
-\
- if (queue->nnodes == 0)\
- return 1;\
-\
- for (i=1; i<queue->nnodes; i++) {\
- ASSERT(!KEY_LT(keys[i], keys[(i-1)/2]));\
- }\
- for (i=1; i<queue->nnodes; i++)\
- ASSERT(!KEY_LT(keys[i], keys[0]));\
-\
- return 1;\
-}\
-
-
-#define GK_MKPQUEUE2_PROTO(FPRFX, PQT, KT, VT)\
- PQT * FPRFX ## Create2(ssize_t maxnodes);\
- void FPRFX ## Reset2(PQT *queue);\
- void FPRFX ## Destroy2(PQT **r_queue);\
- size_t FPRFX ## Length2(PQT *queue);\
- int FPRFX ## Insert2(PQT *queue, VT node, KT key);\
- int FPRFX ## GetTop2(PQT *queue, VT *r_val);\
- int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val);\
- KT FPRFX ## SeeTopKey2(PQT *queue);\
- int FPRFX ## CheckHeap2(PQT *queue);\
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkrandom.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkrandom.h
deleted file mode 100644
index 68d54fa3f..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkrandom.h
+++ /dev/null
@@ -1,123 +0,0 @@
-/*!
-\file
-\brief Templates for portable random number generation
-
-\date Started 5/17/07
-\author George
-\version\verbatim $Id: gk_mkrandom.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#ifndef _GK_MKRANDOM_H
-#define _GK_MKRANDOM_H
-
-/*************************************************************************/\
-/*! The generator for the rand() related routines. \
- \params RNGT the datatype that defines the range of values over which\
- random numbers will be generated\
- \params VALT the datatype that defines the contents of the array to \
- be permuted by randArrayPermute() \
- \params FPRFX the function prefix \
-*/\
-/**************************************************************************/\
-#define GK_MKRANDOM(FPRFX, RNGT, VALT)\
-/*************************************************************************/\
-/*! Initializes the generator */ \
-/**************************************************************************/\
-void FPRFX ## srand(RNGT seed) \
-{\
- gk_randinit((uint64_t) seed);\
-}\
-\
-\
-/*************************************************************************/\
-/*! Returns a random number */ \
-/**************************************************************************/\
-RNGT FPRFX ## rand() \
-{\
- if (sizeof(RNGT) <= sizeof(int32_t)) \
- return (RNGT)gk_randint32(); \
- else \
- return (RNGT)gk_randint64(); \
-}\
-\
-\
-/*************************************************************************/\
-/*! Returns a random number between [0, max) */ \
-/**************************************************************************/\
-RNGT FPRFX ## randInRange(RNGT max) \
-{\
- return (RNGT)((FPRFX ## rand())%max); \
-}\
-\
-\
-/*************************************************************************/\
-/*! Randomly permutes the elements of an array p[]. \
- flag == 1, p[i] = i prior to permutation, \
- flag == 0, p[] is not initialized. */\
-/**************************************************************************/\
-void FPRFX ## randArrayPermute(RNGT n, VALT *p, RNGT nshuffles, int flag)\
-{\
- RNGT i, u, v;\
- VALT tmp;\
-\
- if (flag == 1) {\
- for (i=0; i<n; i++)\
- p[i] = (VALT)i;\
- }\
-\
- if (n < 10) {\
- for (i=0; i<n; i++) {\
- v = FPRFX ## randInRange(n);\
- u = FPRFX ## randInRange(n);\
- gk_SWAP(p[v], p[u], tmp);\
- }\
- }\
- else {\
- for (i=0; i<nshuffles; i++) {\
- v = FPRFX ## randInRange(n-3);\
- u = FPRFX ## randInRange(n-3);\
- /*gk_SWAP(p[v+0], p[u+0], tmp);*/\
- /*gk_SWAP(p[v+1], p[u+1], tmp);*/\
- /*gk_SWAP(p[v+2], p[u+2], tmp);*/\
- /*gk_SWAP(p[v+3], p[u+3], tmp);*/\
- gk_SWAP(p[v+0], p[u+2], tmp);\
- gk_SWAP(p[v+1], p[u+3], tmp);\
- gk_SWAP(p[v+2], p[u+0], tmp);\
- gk_SWAP(p[v+3], p[u+1], tmp);\
- }\
- }\
-}\
-\
-\
-/*************************************************************************/\
-/*! Randomly permutes the elements of an array p[]. \
- flag == 1, p[i] = i prior to permutation, \
- flag == 0, p[] is not initialized. */\
-/**************************************************************************/\
-void FPRFX ## randArrayPermuteFine(RNGT n, VALT *p, int flag)\
-{\
- RNGT i, v;\
- VALT tmp;\
-\
- if (flag == 1) {\
- for (i=0; i<n; i++)\
- p[i] = (VALT)i;\
- }\
-\
- for (i=0; i<n; i++) {\
- v = FPRFX ## randInRange(n);\
- gk_SWAP(p[i], p[v], tmp);\
- }\
-}\
-
-
-#define GK_MKRANDOM_PROTO(FPRFX, RNGT, VALT)\
- void FPRFX ## srand(RNGT seed); \
- RNGT FPRFX ## rand(); \
- RNGT FPRFX ## randInRange(RNGT max); \
- void FPRFX ## randArrayPermute(RNGT n, VALT *p, RNGT nshuffles, int flag);\
- void FPRFX ## randArrayPermuteFine(RNGT n, VALT *p, int flag);\
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mksort.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mksort.h
deleted file mode 100644
index 56ac0b11a..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mksort.h
+++ /dev/null
@@ -1,273 +0,0 @@
-/*!
-\file gk_mksort.h
-\brief Templates for the qsort routine
-
-\date Started 3/28/07
-\author George
-\version\verbatim $Id: gk_mksort.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#ifndef _GK_MKSORT_H_
-#define _GK_MKSORT_H_
-
-/* $Id: gk_mksort.h 10711 2011-08-31 22:23:04Z karypis $
- * Adopted from GNU glibc by Mjt.
- * See stdlib/qsort.c in glibc */
-
-/* Copyright (C) 1991, 1992, 1996, 1997, 1999 Free Software Foundation, Inc.
- This file is part of the GNU C Library.
- Written by Douglas C. Schmidt (schmidt@ics.uci.edu).
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-/* in-line qsort implementation. Differs from traditional qsort() routine
- * in that it is a macro, not a function, and instead of passing an address
- * of a comparision routine to the function, it is possible to inline
- * comparision routine, thus speed up sorting alot.
- *
- * Usage:
- * #include "iqsort.h"
- * #define islt(a,b) (strcmp((*a),(*b))<0)
- * char *arr[];
- * int n;
- * GKQSORT(char*, arr, n, islt);
- *
- * The "prototype" and 4 arguments are:
- * GKQSORT(TYPE,BASE,NELT,ISLT)
- * 1) type of each element, TYPE,
- * 2) address of the beginning of the array, of type TYPE*,
- * 3) number of elements in the array, and
- * 4) comparision routine.
- * Array pointer and number of elements are referenced only once.
- * This is similar to a call
- * qsort(BASE,NELT,sizeof(TYPE),ISLT)
- * with the difference in last parameter.
- * Note the islt macro/routine (it receives pointers to two elements):
- * the only condition of interest is whenever one element is less than
- * another, no other conditions (greather than, equal to etc) are tested.
- * So, for example, to define integer sort, use:
- * #define islt(a,b) ((*a)<(*b))
- * GKQSORT(int, arr, n, islt)
- *
- * The macro could be used to implement a sorting function (see examples
- * below), or to implement the sorting algorithm inline. That is, either
- * create a sorting function and use it whenever you want to sort something,
- * or use GKQSORT() macro directly instead a call to such routine. Note that
- * the macro expands to quite some code (compiled size of int qsort on x86
- * is about 700..800 bytes).
- *
- * Using this macro directly it isn't possible to implement traditional
- * qsort() routine, because the macro assumes sizeof(element) == sizeof(TYPE),
- * while qsort() allows element size to be different.
- *
- * Several ready-to-use examples:
- *
- * Sorting array of integers:
- * void int_qsort(int *arr, unsigned n) {
- * #define int_lt(a,b) ((*a)<(*b))
- * GKQSORT(int, arr, n, int_lt);
- * }
- *
- * Sorting array of string pointers:
- * void str_qsort(char *arr[], unsigned n) {
- * #define str_lt(a,b) (strcmp((*a),(*b)) < 0)
- * GKQSORT(char*, arr, n, str_lt);
- * }
- *
- * Sorting array of structures:
- *
- * struct elt {
- * int key;
- * ...
- * };
- * void elt_qsort(struct elt *arr, unsigned n) {
- * #define elt_lt(a,b) ((a)->key < (b)->key)
- * GKQSORT(struct elt, arr, n, elt_lt);
- * }
- *
- * And so on.
- */
-
-/* Swap two items pointed to by A and B using temporary buffer t. */
-#define _GKQSORT_SWAP(a, b, t) ((void)((t = *a), (*a = *b), (*b = t)))
-
-/* Discontinue quicksort algorithm when partition gets below this size.
- This particular magic number was chosen to work best on a Sun 4/260. */
-#define _GKQSORT_MAX_THRESH 4
-
-/* The next 4 #defines implement a very fast in-line stack abstraction. */
-#define _GKQSORT_STACK_SIZE (8 * sizeof(size_t))
-#define _GKQSORT_PUSH(top, low, high) (((top->_lo = (low)), (top->_hi = (high)), ++top))
-#define _GKQSORT_POP(low, high, top) ((--top, (low = top->_lo), (high = top->_hi)))
-#define _GKQSORT_STACK_NOT_EMPTY (_stack < _top)
-
-
-/* The main code starts here... */
-#define GK_MKQSORT(GKQSORT_TYPE,GKQSORT_BASE,GKQSORT_NELT,GKQSORT_LT) \
-{ \
- GKQSORT_TYPE *const _base = (GKQSORT_BASE); \
- const size_t _elems = (GKQSORT_NELT); \
- GKQSORT_TYPE _hold; \
- \
- if (_elems == 0) \
- return; \
- \
- /* Don't declare two variables of type GKQSORT_TYPE in a single \
- * statement: eg `TYPE a, b;', in case if TYPE is a pointer, \
- * expands to `type* a, b;' wich isn't what we want. \
- */ \
- \
- if (_elems > _GKQSORT_MAX_THRESH) { \
- GKQSORT_TYPE *_lo = _base; \
- GKQSORT_TYPE *_hi = _lo + _elems - 1; \
- struct { \
- GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \
- } _stack[_GKQSORT_STACK_SIZE], *_top = _stack + 1; \
- \
- while (_GKQSORT_STACK_NOT_EMPTY) { \
- GKQSORT_TYPE *_left_ptr; GKQSORT_TYPE *_right_ptr; \
- \
- /* Select median value from among LO, MID, and HI. Rearrange \
- LO and HI so the three values are sorted. This lowers the \
- probability of picking a pathological pivot value and \
- skips a comparison for both the LEFT_PTR and RIGHT_PTR in \
- the while loops. */ \
- \
- GKQSORT_TYPE *_mid = _lo + ((_hi - _lo) >> 1); \
- \
- if (GKQSORT_LT (_mid, _lo)) \
- _GKQSORT_SWAP (_mid, _lo, _hold); \
- if (GKQSORT_LT (_hi, _mid)) \
- _GKQSORT_SWAP (_mid, _hi, _hold); \
- else \
- goto _jump_over; \
- if (GKQSORT_LT (_mid, _lo)) \
- _GKQSORT_SWAP (_mid, _lo, _hold); \
- _jump_over:; \
- \
- _left_ptr = _lo + 1; \
- _right_ptr = _hi - 1; \
- \
- /* Here's the famous ``collapse the walls'' section of quicksort. \
- Gotta like those tight inner loops! They are the main reason \
- that this algorithm runs much faster than others. */ \
- do { \
- while (GKQSORT_LT (_left_ptr, _mid)) \
- ++_left_ptr; \
- \
- while (GKQSORT_LT (_mid, _right_ptr)) \
- --_right_ptr; \
- \
- if (_left_ptr < _right_ptr) { \
- _GKQSORT_SWAP (_left_ptr, _right_ptr, _hold); \
- if (_mid == _left_ptr) \
- _mid = _right_ptr; \
- else if (_mid == _right_ptr) \
- _mid = _left_ptr; \
- ++_left_ptr; \
- --_right_ptr; \
- } \
- else if (_left_ptr == _right_ptr) { \
- ++_left_ptr; \
- --_right_ptr; \
- break; \
- } \
- } while (_left_ptr <= _right_ptr); \
- \
- /* Set up pointers for next iteration. First determine whether \
- left and right partitions are below the threshold size. If so, \
- ignore one or both. Otherwise, push the larger partition's \
- bounds on the stack and continue sorting the smaller one. */ \
- \
- if (_right_ptr - _lo <= _GKQSORT_MAX_THRESH) { \
- if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \
- /* Ignore both small partitions. */ \
- _GKQSORT_POP (_lo, _hi, _top); \
- else \
- /* Ignore small left partition. */ \
- _lo = _left_ptr; \
- } \
- else if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \
- /* Ignore small right partition. */ \
- _hi = _right_ptr; \
- else if (_right_ptr - _lo > _hi - _left_ptr) { \
- /* Push larger left partition indices. */ \
- _GKQSORT_PUSH (_top, _lo, _right_ptr); \
- _lo = _left_ptr; \
- } \
- else { \
- /* Push larger right partition indices. */ \
- _GKQSORT_PUSH (_top, _left_ptr, _hi); \
- _hi = _right_ptr; \
- } \
- } \
- } \
- \
- /* Once the BASE array is partially sorted by quicksort the rest \
- is completely sorted using insertion sort, since this is efficient \
- for partitions below MAX_THRESH size. BASE points to the \
- beginning of the array to sort, and END_PTR points at the very \
- last element in the array (*not* one beyond it!). */ \
- \
- { \
- GKQSORT_TYPE *const _end_ptr = _base + _elems - 1; \
- GKQSORT_TYPE *_tmp_ptr = _base; \
- register GKQSORT_TYPE *_run_ptr; \
- GKQSORT_TYPE *_thresh; \
- \
- _thresh = _base + _GKQSORT_MAX_THRESH; \
- if (_thresh > _end_ptr) \
- _thresh = _end_ptr; \
- \
- /* Find smallest element in first threshold and place it at the \
- array's beginning. This is the smallest array element, \
- and the operation speeds up insertion sort's inner loop. */ \
- \
- for (_run_ptr = _tmp_ptr + 1; _run_ptr <= _thresh; ++_run_ptr) \
- if (GKQSORT_LT (_run_ptr, _tmp_ptr)) \
- _tmp_ptr = _run_ptr; \
- \
- if (_tmp_ptr != _base) \
- _GKQSORT_SWAP (_tmp_ptr, _base, _hold); \
- \
- /* Insertion sort, running from left-hand-side \
- * up to right-hand-side. */ \
- \
- _run_ptr = _base + 1; \
- while (++_run_ptr <= _end_ptr) { \
- _tmp_ptr = _run_ptr - 1; \
- while (GKQSORT_LT (_run_ptr, _tmp_ptr)) \
- --_tmp_ptr; \
- \
- ++_tmp_ptr; \
- if (_tmp_ptr != _run_ptr) { \
- GKQSORT_TYPE *_trav = _run_ptr + 1; \
- while (--_trav >= _run_ptr) { \
- GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \
- _hold = *_trav; \
- \
- for (_hi = _lo = _trav; --_lo >= _tmp_ptr; _hi = _lo) \
- *_hi = *_lo; \
- *_hi = _hold; \
- } \
- } \
- } \
- } \
- \
-}
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkutils.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_mkutils.h
deleted file mode 100644
index a092f2227..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_mkutils.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*!
-\file
-\brief Templates for various utility routines
-
-\date Started 5/28/07
-\author George
-\version\verbatim $Id: gk_mkutils.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_MKUTILS_H_
-#define _GK_MKUTILS_H_
-
-
-#define GK_MKARRAY2CSR(PRFX, TYPE)\
-/*************************************************************************/\
-/*! The macro for gk_?array2csr() routine */\
-/**************************************************************************/\
-void PRFX ## array2csr(TYPE n, TYPE range, TYPE *array, TYPE *ptr, TYPE *ind)\
-{\
- TYPE i;\
-\
- for (i=0; i<=range; i++)\
- ptr[i] = 0;\
-\
- for (i=0; i<n; i++)\
- ptr[array[i]]++;\
-\
- /* Compute the ptr, ind structure */\
- MAKECSR(i, range, ptr);\
- for (i=0; i<n; i++)\
- ind[ptr[array[i]]++] = i;\
- SHIFTCSR(i, range, ptr);\
-}
-
-
-#define GK_MKARRAY2CSR_PROTO(PRFX, TYPE)\
- void PRFX ## array2csr(TYPE n, TYPE range, TYPE *array, TYPE *ptr, TYPE *ind);\
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_proto.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_proto.h
deleted file mode 100644
index 2cc299d4c..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_proto.h
+++ /dev/null
@@ -1,381 +0,0 @@
-/*!
-\file gk_proto.h
-\brief This file contains function prototypes
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_proto.h 12591 2012-09-01 19:03:15Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_PROTO_H_
-#define _GK_PROTO_H_
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*-------------------------------------------------------------
- * blas.c
- *-------------------------------------------------------------*/
-GK_MKBLAS_PROTO(gk_c, char, int)
-GK_MKBLAS_PROTO(gk_i, int, int)
-GK_MKBLAS_PROTO(gk_i32, int32_t, int32_t)
-GK_MKBLAS_PROTO(gk_i64, int64_t, int64_t)
-GK_MKBLAS_PROTO(gk_z, ssize_t, ssize_t)
-GK_MKBLAS_PROTO(gk_f, float, float)
-GK_MKBLAS_PROTO(gk_d, double, double)
-GK_MKBLAS_PROTO(gk_idx, gk_idx_t, gk_idx_t)
-
-
-
-
-/*-------------------------------------------------------------
- * io.c
- *-------------------------------------------------------------*/
-FILE *gk_fopen(char *, char *, const char *);
-void gk_fclose(FILE *);
-gk_idx_t gk_getline(char **lineptr, size_t *n, FILE *stream);
-char **gk_readfile(char *fname, gk_idx_t *r_nlines);
-int32_t *gk_i32readfile(char *fname, gk_idx_t *r_nlines);
-int64_t *gk_i64readfile(char *fname, gk_idx_t *r_nlines);
-int32_t *gk_i32readfilebin(char *fname, ssize_t *r_nelmnts);
-int64_t *gk_i64readfilebin(char *fname, ssize_t *r_nelmnts);
-float *gk_freadfilebin(char *fname, ssize_t *r_nelmnts);
-size_t gk_fwritefilebin(char *fname, size_t n, float *a);
-double *gk_dreadfilebin(char *fname, ssize_t *r_nelmnts);
-
-
-
-
-/*-------------------------------------------------------------
- * fs.c
- *-------------------------------------------------------------*/
-int gk_fexists(char *);
-int gk_dexists(char *);
-intmax_t gk_getfsize(char *);
-void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens,
- size_t *r_max_nlntokens, size_t *r_nbytes);
-char *gk_getbasename(char *path);
-char *gk_getextname(char *path);
-char *gk_getfilename(char *path);
-char *gk_getpathname(char *path);
-int gk_mkpath(char *);
-int gk_rmpath(char *);
-
-
-
-/*-------------------------------------------------------------
- * memory.c
- *-------------------------------------------------------------*/
-GK_MKALLOC_PROTO(gk_c, char)
-GK_MKALLOC_PROTO(gk_i, int)
-GK_MKALLOC_PROTO(gk_i32, int32_t)
-GK_MKALLOC_PROTO(gk_i64, int64_t)
-GK_MKALLOC_PROTO(gk_z, ssize_t)
-GK_MKALLOC_PROTO(gk_f, float)
-GK_MKALLOC_PROTO(gk_d, double)
-GK_MKALLOC_PROTO(gk_idx, gk_idx_t)
-
-GK_MKALLOC_PROTO(gk_ckv, gk_ckv_t)
-GK_MKALLOC_PROTO(gk_ikv, gk_ikv_t)
-GK_MKALLOC_PROTO(gk_i32kv, gk_i32kv_t)
-GK_MKALLOC_PROTO(gk_i64kv, gk_i64kv_t)
-GK_MKALLOC_PROTO(gk_zkv, gk_zkv_t)
-GK_MKALLOC_PROTO(gk_fkv, gk_fkv_t)
-GK_MKALLOC_PROTO(gk_dkv, gk_dkv_t)
-GK_MKALLOC_PROTO(gk_skv, gk_skv_t)
-GK_MKALLOC_PROTO(gk_idxkv, gk_idxkv_t)
-
-void gk_AllocMatrix(void ***, size_t, size_t , size_t);
-void gk_FreeMatrix(void ***, size_t, size_t);
-int gk_malloc_init();
-void gk_malloc_cleanup(int showstats);
-void *gk_malloc(size_t nbytes, char *msg);
-void *gk_realloc(void *oldptr, size_t nbytes, char *msg);
-void gk_free(void **ptr1,...);
-size_t gk_GetCurMemoryUsed();
-size_t gk_GetMaxMemoryUsed();
-
-
-
-/*-------------------------------------------------------------
- * seq.c
- *-------------------------------------------------------------*/
-gk_seq_t *gk_seq_ReadGKMODPSSM(char *file_name);
-gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet);
-void gk_seq_init(gk_seq_t *seq);
-
-
-
-
-/*-------------------------------------------------------------
- * pdb.c
- *-------------------------------------------------------------*/
-char gk_threetoone(char *res);
-void gk_freepdbf(pdbf *p);
-pdbf *gk_readpdbfile(char *fname);
-void gk_writefullatom(pdbf *p, char *fname);
-void gk_writebackbone(pdbf *p, char *fname);
-void gk_writealphacarbons(pdbf *p, char *fname);
-void gk_showcorruption(pdbf *p);
-
-
-/*-------------------------------------------------------------
- * error.c
- *-------------------------------------------------------------*/
-void gk_set_exit_on_error(int value);
-void errexit(char *,...);
-void gk_errexit(int signum, char *,...);
-int gk_sigtrap();
-int gk_siguntrap();
-void gk_sigthrow(int signum);
-void gk_SetSignalHandlers();
-void gk_UnsetSignalHandlers();
-void gk_NonLocalExit_Handler(int signum);
-char *gk_strerror(int errnum);
-void PrintBackTrace();
-
-
-/*-------------------------------------------------------------
- * util.c
- *-------------------------------------------------------------*/
-void gk_RandomPermute(size_t, int *, int);
-void gk_array2csr(size_t n, size_t range, int *array, int *ptr, int *ind);
-int gk_log2(int);
-int gk_ispow2(int);
-float gk_flog2(float);
-
-
-/*-------------------------------------------------------------
- * time.c
- *-------------------------------------------------------------*/
-gk_wclock_t gk_WClockSeconds(void);
-double gk_CPUSeconds(void);
-
-/*-------------------------------------------------------------
- * string.c
- *-------------------------------------------------------------*/
-char *gk_strchr_replace(char *str, char *fromlist, char *tolist);
-int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options, char **new_str);
-char *gk_strtprune(char *, char *);
-char *gk_strhprune(char *, char *);
-char *gk_strtoupper(char *);
-char *gk_strtolower(char *);
-char *gk_strdup(char *orgstr);
-int gk_strcasecmp(char *s1, char *s2);
-int gk_strrcmp(char *s1, char *s2);
-char *gk_time2str(time_t time);
-time_t gk_str2time(char *str);
-int gk_GetStringID(gk_StringMap_t *strmap, char *key);
-
-
-
-/*-------------------------------------------------------------
- * sort.c
- *-------------------------------------------------------------*/
-void gk_csorti(size_t, char *);
-void gk_csortd(size_t, char *);
-void gk_isorti(size_t, int *);
-void gk_isortd(size_t, int *);
-void gk_fsorti(size_t, float *);
-void gk_fsortd(size_t, float *);
-void gk_dsorti(size_t, double *);
-void gk_dsortd(size_t, double *);
-void gk_idxsorti(size_t, gk_idx_t *);
-void gk_idxsortd(size_t, gk_idx_t *);
-void gk_ckvsorti(size_t, gk_ckv_t *);
-void gk_ckvsortd(size_t, gk_ckv_t *);
-void gk_ikvsorti(size_t, gk_ikv_t *);
-void gk_ikvsortd(size_t, gk_ikv_t *);
-void gk_i32kvsorti(size_t, gk_i32kv_t *);
-void gk_i32kvsortd(size_t, gk_i32kv_t *);
-void gk_i64kvsorti(size_t, gk_i64kv_t *);
-void gk_i64kvsortd(size_t, gk_i64kv_t *);
-void gk_zkvsorti(size_t, gk_zkv_t *);
-void gk_zkvsortd(size_t, gk_zkv_t *);
-void gk_fkvsorti(size_t, gk_fkv_t *);
-void gk_fkvsortd(size_t, gk_fkv_t *);
-void gk_dkvsorti(size_t, gk_dkv_t *);
-void gk_dkvsortd(size_t, gk_dkv_t *);
-void gk_skvsorti(size_t, gk_skv_t *);
-void gk_skvsortd(size_t, gk_skv_t *);
-void gk_idxkvsorti(size_t, gk_idxkv_t *);
-void gk_idxkvsortd(size_t, gk_idxkv_t *);
-
-
-/*-------------------------------------------------------------
- * Selection routines
- *-------------------------------------------------------------*/
-int gk_dfkvkselect(size_t, int, gk_fkv_t *);
-int gk_ifkvkselect(size_t, int, gk_fkv_t *);
-
-
-/*-------------------------------------------------------------
- * Priority queue
- *-------------------------------------------------------------*/
-GK_MKPQUEUE_PROTO(gk_ipq, gk_ipq_t, int, gk_idx_t)
-GK_MKPQUEUE_PROTO(gk_i32pq, gk_i32pq_t, int32_t, gk_idx_t)
-GK_MKPQUEUE_PROTO(gk_i64pq, gk_i64pq_t, int64_t, gk_idx_t)
-GK_MKPQUEUE_PROTO(gk_fpq, gk_fpq_t, float, gk_idx_t)
-GK_MKPQUEUE_PROTO(gk_dpq, gk_dpq_t, double, gk_idx_t)
-GK_MKPQUEUE_PROTO(gk_idxpq, gk_idxpq_t, gk_idx_t, gk_idx_t)
-
-
-/*-------------------------------------------------------------
- * HTable routines
- *-------------------------------------------------------------*/
-gk_HTable_t *HTable_Create(int nelements);
-void HTable_Reset(gk_HTable_t *htable);
-void HTable_Resize(gk_HTable_t *htable, int nelements);
-void HTable_Insert(gk_HTable_t *htable, int key, int val);
-void HTable_Delete(gk_HTable_t *htable, int key);
-int HTable_Search(gk_HTable_t *htable, int key);
-int HTable_GetNext(gk_HTable_t *htable, int key, int *val, int type);
-int HTable_SearchAndDelete(gk_HTable_t *htable, int key);
-void HTable_Destroy(gk_HTable_t *htable);
-int HTable_HFunction(int nelements, int key);
-
-
-/*-------------------------------------------------------------
- * Tokenizer routines
- *-------------------------------------------------------------*/
-void gk_strtokenize(char *line, char *delim, gk_Tokens_t *tokens);
-void gk_freetokenslist(gk_Tokens_t *tokens);
-
-/*-------------------------------------------------------------
- * Encoder/Decoder
- *-------------------------------------------------------------*/
-void encodeblock(unsigned char *in, unsigned char *out);
-void decodeblock(unsigned char *in, unsigned char *out);
-void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer);
-void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer);
-
-
-/*-------------------------------------------------------------
- * random.c
- *-------------------------------------------------------------*/
-GK_MKRANDOM_PROTO(gk_c, size_t, char)
-GK_MKRANDOM_PROTO(gk_i, size_t, int)
-GK_MKRANDOM_PROTO(gk_f, size_t, float)
-GK_MKRANDOM_PROTO(gk_d, size_t, double)
-GK_MKRANDOM_PROTO(gk_idx, size_t, gk_idx_t)
-GK_MKRANDOM_PROTO(gk_z, size_t, ssize_t)
-void gk_randinit(uint64_t);
-uint64_t gk_randint64(void);
-uint32_t gk_randint32(void);
-
-
-/*-------------------------------------------------------------
- * OpenMP fake functions
- *-------------------------------------------------------------*/
-#if !defined(__OPENMP__)
-void omp_set_num_threads(int num_threads);
-int omp_get_num_threads(void);
-int omp_get_max_threads(void);
-int omp_get_thread_num(void);
-int omp_get_num_procs(void);
-int omp_in_parallel(void);
-void omp_set_dynamic(int num_threads);
-int omp_get_dynamic(void);
-void omp_set_nested(int nested);
-int omp_get_nested(void);
-#endif /* __OPENMP__ */
-
-
-/*-------------------------------------------------------------
- * CSR-related functions
- *-------------------------------------------------------------*/
-gk_csr_t *gk_csr_Create();
-void gk_csr_Init(gk_csr_t *mat);
-void gk_csr_Free(gk_csr_t **mat);
-void gk_csr_FreeContents(gk_csr_t *mat);
-gk_csr_t *gk_csr_Dup(gk_csr_t *mat);
-gk_csr_t *gk_csr_ExtractSubmatrix(gk_csr_t *mat, int rstart, int nrows);
-gk_csr_t *gk_csr_ExtractRows(gk_csr_t *mat, int nrows, int *rind);
-gk_csr_t *gk_csr_ExtractPartition(gk_csr_t *mat, int *part, int pid);
-gk_csr_t **gk_csr_Split(gk_csr_t *mat, int *color);
-gk_csr_t *gk_csr_Read(char *filename, int format, int readvals, int numbering);
-void gk_csr_Write(gk_csr_t *mat, char *filename, int format, int writevals, int numbering);
-gk_csr_t *gk_csr_Prune(gk_csr_t *mat, int what, int minf, int maxf);
-gk_csr_t *gk_csr_LowFilter(gk_csr_t *mat, int what, int norm, float fraction);
-gk_csr_t *gk_csr_TopKPlusFilter(gk_csr_t *mat, int what, int topk, float keepval);
-gk_csr_t *gk_csr_ZScoreFilter(gk_csr_t *mat, int what, float zscore);
-void gk_csr_CompactColumns(gk_csr_t *mat);
-void gk_csr_SortIndices(gk_csr_t *mat, int what);
-void gk_csr_CreateIndex(gk_csr_t *mat, int what);
-void gk_csr_Normalize(gk_csr_t *mat, int what, int norm);
-void gk_csr_Scale(gk_csr_t *mat, int type);
-void gk_csr_ComputeSums(gk_csr_t *mat, int what);
-void gk_csr_ComputeSquaredNorms(gk_csr_t *mat, int what);
-float gk_csr_ComputeSimilarity(gk_csr_t *mat, int i1, int i2, int what, int simtype);
-int gk_csr_GetSimilarRows(gk_csr_t *mat, int nqterms, int *qind, float *qval,
- int simtype, int nsim, float minsim, gk_fkv_t *hits, int *_imarker,
- gk_fkv_t *i_cand);
-
-
-
-/* itemsets.c */
-void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind,
- int minfreq, int maxfreq, int minlen, int maxlen,
- void (*process_itemset)(void *stateptr, int nitems, int *itemind,
- int ntrans, int *tranind),
- void *stateptr);
-
-
-/* evaluate.c */
-float ComputeAccuracy(int n, gk_fkv_t *list);
-float ComputeROCn(int n, int maxN, gk_fkv_t *list);
-float ComputeMedianRFP(int n, gk_fkv_t *list);
-float ComputeMean (int n, float *values);
-float ComputeStdDev(int n, float *values);
-
-
-/* mcore.c */
-gk_mcore_t *gk_mcoreCreate(size_t coresize);
-gk_mcore_t *gk_gkmcoreCreate();
-void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats);
-void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats);
-void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes);
-void gk_mcorePush(gk_mcore_t *mcore);
-void gk_gkmcorePush(gk_mcore_t *mcore);
-void gk_mcorePop(gk_mcore_t *mcore);
-void gk_gkmcorePop(gk_mcore_t *mcore);
-void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr);
-void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr);
-void gk_mcoreDel(gk_mcore_t *mcore, void *ptr);
-void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr);
-
-/* rw.c */
-int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr);
-
-
-/* graph.c */
-gk_graph_t *gk_graph_Create();
-void gk_graph_Init(gk_graph_t *graph);
-void gk_graph_Free(gk_graph_t **graph);
-void gk_graph_FreeContents(gk_graph_t *graph);
-gk_graph_t *gk_graph_Read(char *filename, int format, int isfewgts,
- int isfvwgts, int isfvsizes);
-void gk_graph_Write(gk_graph_t *graph, char *filename, int format);
-gk_graph_t *gk_graph_Dup(gk_graph_t *graph);
-gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs);
-gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm);
-int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind);
-void gk_graph_ComputeBFSOrdering(gk_graph_t *graph, int v, int32_t **r_perm,
- int32_t **r_iperm);
-void gk_graph_ComputeBestFOrdering0(gk_graph_t *graph, int v, int type,
- int32_t **r_perm, int32_t **r_iperm);
-void gk_graph_ComputeBestFOrdering(gk_graph_t *graph, int v, int type,
- int32_t **r_perm, int32_t **r_iperm);
-void gk_graph_SingleSourceShortestPaths(gk_graph_t *graph, int v, void **r_sps);
-
-
-
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#endif
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_struct.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_struct.h
deleted file mode 100644
index 3ef7bbd7b..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_struct.h
+++ /dev/null
@@ -1,268 +0,0 @@
-/*!
-\file gk_struct.h
-\brief This file contains various datastructures used/provided by GKlib
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_struct.h 13005 2012-10-23 22:34:36Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_STRUCT_H_
-#define _GK_STRUCT_H_
-
-
-/********************************************************************/
-/*! Generator for gk_??KeyVal_t data structure */
-/********************************************************************/
-#define GK_MKKEYVALUE_T(NAME, KEYTYPE, VALTYPE) \
-typedef struct {\
- KEYTYPE key;\
- VALTYPE val;\
-} NAME;\
-
-/* The actual KeyVal data structures */
-GK_MKKEYVALUE_T(gk_ckv_t, char, ssize_t)
-GK_MKKEYVALUE_T(gk_ikv_t, int, ssize_t)
-GK_MKKEYVALUE_T(gk_i32kv_t, int32_t, ssize_t)
-GK_MKKEYVALUE_T(gk_i64kv_t, int64_t, ssize_t)
-GK_MKKEYVALUE_T(gk_zkv_t, ssize_t, ssize_t)
-GK_MKKEYVALUE_T(gk_fkv_t, float, ssize_t)
-GK_MKKEYVALUE_T(gk_dkv_t, double, ssize_t)
-GK_MKKEYVALUE_T(gk_skv_t, char *, ssize_t)
-GK_MKKEYVALUE_T(gk_idxkv_t, gk_idx_t, gk_idx_t)
-
-
-
-/********************************************************************/
-/*! Generator for gk_?pq_t data structure */
-/********************************************************************/
-#define GK_MKPQUEUE_T(NAME, KVTYPE)\
-typedef struct {\
- gk_idx_t nnodes;\
- gk_idx_t maxnodes;\
-\
- /* Heap version of the data structure */ \
- KVTYPE *heap;\
- gk_idx_t *locator;\
-} NAME;\
-
-GK_MKPQUEUE_T(gk_ipq_t, gk_ikv_t)
-GK_MKPQUEUE_T(gk_i32pq_t, gk_i32kv_t)
-GK_MKPQUEUE_T(gk_i64pq_t, gk_i64kv_t)
-GK_MKPQUEUE_T(gk_fpq_t, gk_fkv_t)
-GK_MKPQUEUE_T(gk_dpq_t, gk_dkv_t)
-GK_MKPQUEUE_T(gk_idxpq_t, gk_idxkv_t)
-
-
-#define GK_MKPQUEUE2_T(NAME, KTYPE, VTYPE)\
-typedef struct {\
- ssize_t nnodes;\
- ssize_t maxnodes;\
-\
- /* Heap version of the data structure */ \
- KTYPE *keys;\
- VTYPE *vals;\
-} NAME;\
-
-
-
-/*-------------------------------------------------------------
- * The following data structure stores a sparse CSR format
- *-------------------------------------------------------------*/
-typedef struct gk_csr_t {
- int32_t nrows, ncols;
- ssize_t *rowptr, *colptr;
- int32_t *rowind, *colind;
- int32_t *rowids, *colids;
- float *rowval, *colval;
- float *rnorms, *cnorms;
- float *rsums, *csums;
- float *rsizes, *csizes;
- float *rvols, *cvols;
- float *rwgts, *cwgts;
-} gk_csr_t;
-
-
-/*-------------------------------------------------------------
- * The following data structure stores a sparse graph
- *-------------------------------------------------------------*/
-typedef struct gk_graph_t {
- int32_t nvtxs; /*!< The number of vertices in the graph */
- ssize_t *xadj; /*!< The ptr-structure of the adjncy list */
- int32_t *adjncy; /*!< The adjacency list of the graph */
- int32_t *iadjwgt; /*!< The integer edge weights */
- float *fadjwgt; /*!< The floating point edge weights */
- int32_t *ivwgts; /*!< The integer vertex weights */
- float *fvwgts; /*!< The floating point vertex weights */
- int32_t *ivsizes; /*!< The integer vertex sizes */
- float *fvsizes; /*!< The floating point vertex sizes */
- int32_t *vlabels; /*!< The labels of the vertices */
-} gk_graph_t;
-
-
-/*-------------------------------------------------------------
- * The following data structure stores stores a string as a
- * pair of its allocated buffer and the buffer itself.
- *-------------------------------------------------------------*/
-typedef struct gk_str_t {
- size_t len;
- char *buf;
-} gk_str_t;
-
-
-
-
-/*-------------------------------------------------------------
-* The following data structure implements a string-2-int mapping
-* table used for parsing command-line options
-*-------------------------------------------------------------*/
-typedef struct gk_StringMap_t {
- char *name;
- int id;
-} gk_StringMap_t;
-
-
-/*------------------------------------------------------------
- * This structure implements a simple hash table
- *------------------------------------------------------------*/
-typedef struct gk_HTable_t {
- int nelements; /* The overall size of the hash-table */
- int htsize; /* The current size of the hash-table */
- gk_ikv_t *harray; /* The actual hash-table */
-} gk_HTable_t;
-
-
-/*------------------------------------------------------------
- * This structure implements a gk_Tokens_t list returned by the
- * string tokenizer
- *------------------------------------------------------------*/
-typedef struct gk_Tokens_t {
- int ntoks; /* The number of tokens in the input string */
- char *strbuf; /* The memory that stores all the entries */
- char **list; /* Pointers to the strbuf for each element */
-} gk_Tokens_t;
-
-/*------------------------------------------------------------
- * This structure implements storage for an atom in a pdb file
- *------------------------------------------------------------*/
-typedef struct atom {
- int serial;
- char *name;
- char altLoc;
- char *resname;
- char chainid;
- int rserial;
- char icode;
- char element;
- double x;
- double y;
- double z;
- double opcy;
- double tmpt;
-} atom;
-
-
-/*------------------------------------------------------------
- * This structure implements storage for a center of mass for
- * a single residue.
- *------------------------------------------------------------*/
-typedef struct center_of_mass {
- char name;
- double x;
- double y;
- double z;
-} center_of_mass;
-
-
-/*------------------------------------------------------------
- * This structure implements storage for a pdb protein
- *------------------------------------------------------------*/
-typedef struct pdbf {
- int natoms; /* Number of atoms */
- int nresidues; /* Number of residues based on coordinates */
- int ncas;
- int nbbs;
- int corruption;
- char *resSeq; /* Residue sequence based on coordinates */
- char **threeresSeq; /* three-letter residue sequence */
- atom *atoms;
- atom **bbs;
- atom **cas;
- center_of_mass *cm;
-} pdbf;
-
-
-
-/*************************************************************
-* Localization Structures for converting characters to integers
-**************************************************************/
-typedef struct gk_i2cc2i_t {
- int n;
- char *i2c;
- int *c2i;
-} gk_i2cc2i_t;
-
-
-/*******************************************************************
- *This structure implements storage of a protein sequence
- * *****************************************************************/
-typedef struct gk_seq_t {
-
- int len; /*Number of Residues */
- int *sequence; /* Stores the sequence*/
-
-
- int **pssm; /* Stores the pssm matrix */
- int **psfm; /* Stores the psfm matrix */
- char *name; /* Stores the name of the sequence */
-
- int nsymbols;
-
-
-} gk_seq_t;
-
-
-
-
-/*************************************************************************/
-/*! The following data structure stores information about a memory
- allocation operation that can either be served from gk_mcore_t or by
- a gk_malloc if not sufficient workspace memory is available. */
-/*************************************************************************/
-typedef struct gk_mop_t {
- int type;
- ssize_t nbytes;
- void *ptr;
-} gk_mop_t;
-
-
-/*************************************************************************/
-/*! The following structure stores information used by Metis */
-/*************************************************************************/
-typedef struct gk_mcore_t {
- /* Workspace information */
- size_t coresize; /*!< The amount of core memory that has been allocated */
- size_t corecpos; /*!< Index of the first free location in core */
- void *core; /*!< Pointer to the core itself */
-
- /* These are for implementing a stack-based allocation scheme using both
- core and also dynamically allocated memory */
- size_t nmops; /*!< The number of maop_t entries that have been allocated */
- size_t cmop; /*!< Index of the first free location in maops */
- gk_mop_t *mops; /*!< The array recording the maop_t operations */
-
- /* These are for keeping various statistics for wspacemalloc */
- size_t num_callocs; /*!< The number of core mallocs */
- size_t num_hallocs; /*!< The number of heap mallocs */
- size_t size_callocs; /*!< The total # of bytes in core mallocs */
- size_t size_hallocs; /*!< The total # of bytes in heap mallocs */
- size_t cur_callocs; /*!< The current # of bytes in core mallocs */
- size_t cur_hallocs; /*!< The current # of bytes in heap mallocs */
- size_t max_callocs; /*!< The maximum # of bytes in core mallocs at any given time */
- size_t max_hallocs; /*!< The maximum # of bytes in heap mallocs at any given time */
-
-} gk_mcore_t;
-
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gk_types.h b/3rdParty/metis/metis-5.1.0/GKlib/gk_types.h
deleted file mode 100644
index 57c119101..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gk_types.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*!
-\file gk_types.h
-\brief This file contains basic scalar datatype used in GKlib
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: gk_types.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#ifndef _GK_TYPES_H_
-#define _GK_TYPES_H_
-
-/*************************************************************************
-* Basic data type definitions. These definitions allow GKlib to separate
-* the following elemental types:
-* - loop iterator variables, which are set to size_t
-* - signed and unsigned int variables that can be set to any # of bits
-* - signed and unsigned long variables that can be set to any # of bits
-* - real variables, which can be set to single or double precision.
-**************************************************************************/
-/*typedef ptrdiff_t gk_idx_t; */ /* index variable */
-typedef ssize_t gk_idx_t; /* index variable */
-typedef int32_t gk_int_t; /* integer values */
-typedef uint32_t gk_uint_t; /* unsigned integer values */
-typedef int64_t gk_long_t; /* long integer values */
-typedef uint64_t gk_ulong_t; /* unsigned long integer values */
-typedef float gk_real_t; /* real type */
-typedef double gk_dreal_t; /* double precission real type */
-typedef double gk_wclock_t; /* wall-clock time */
-
-/*#define GK_IDX_MAX PTRDIFF_MAX*/
-#define GK_IDX_MAX ((SIZE_MAX>>1)-2)
-
-#define PRIGKIDX "zd"
-#define SCNGKIDX "zd"
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gkregex.c b/3rdParty/metis/metis-5.1.0/GKlib/gkregex.c
deleted file mode 100644
index 8a09caab7..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gkregex.c
+++ /dev/null
@@ -1,10704 +0,0 @@
-/* Extended regular expression matching and search library.
- Copyright (C) 2002, 2003, 2005 Free Software Foundation, Inc.
- This file is part of the GNU C Library.
- Contributed by Isamu Hasegawa <isamu@yamato.ibm.com>.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-/* this is for removing a compiler warning */
-void gkfooo() { return; }
-
-#ifdef USE_GKREGEX
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-
-#ifdef _LIBC
-/* We have to keep the namespace clean. */
-# define regfree(preg) __regfree (preg)
-# define regexec(pr, st, nm, pm, ef) __regexec (pr, st, nm, pm, ef)
-# define regcomp(preg, pattern, cflags) __regcomp (preg, pattern, cflags)
-# define regerror(errcode, preg, errbuf, errbuf_size) \
- __regerror(errcode, preg, errbuf, errbuf_size)
-# define re_set_registers(bu, re, nu, st, en) \
- __re_set_registers (bu, re, nu, st, en)
-# define re_match_2(bufp, string1, size1, string2, size2, pos, regs, stop) \
- __re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop)
-# define re_match(bufp, string, size, pos, regs) \
- __re_match (bufp, string, size, pos, regs)
-# define re_search(bufp, string, size, startpos, range, regs) \
- __re_search (bufp, string, size, startpos, range, regs)
-# define re_compile_pattern(pattern, length, bufp) \
- __re_compile_pattern (pattern, length, bufp)
-# define re_set_syntax(syntax) __re_set_syntax (syntax)
-# define re_search_2(bufp, st1, s1, st2, s2, startpos, range, regs, stop) \
- __re_search_2 (bufp, st1, s1, st2, s2, startpos, range, regs, stop)
-# define re_compile_fastmap(bufp) __re_compile_fastmap (bufp)
-
-# include "../locale/localeinfo.h"
-#endif
-
-#include "GKlib.h"
-
-
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* GKINCLUDE #include "regex_internal.h" */
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* Extended regular expression matching and search library.
- Copyright (C) 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
- This file is part of the GNU C Library.
- Contributed by Isamu Hasegawa <isamu@yamato.ibm.com>.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-#ifndef _REGEX_INTERNAL_H
-#define _REGEX_INTERNAL_H 1
-
-#include <assert.h>
-#include <ctype.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#if defined(__MINGW32_VERSION) || defined(_MSC_VER)
-#define strcasecmp stricmp
-#endif
-
-#if defined HAVE_LANGINFO_H || defined HAVE_LANGINFO_CODESET || defined _LIBC
-# include <langinfo.h>
-#endif
-#if defined HAVE_LOCALE_H || defined _LIBC
-# include <locale.h>
-#endif
-#if defined HAVE_WCHAR_H || defined _LIBC
-# include <wchar.h>
-#endif /* HAVE_WCHAR_H || _LIBC */
-#if defined HAVE_WCTYPE_H || defined _LIBC
-# include <wctype.h>
-#endif /* HAVE_WCTYPE_H || _LIBC */
-#if defined HAVE_STDBOOL_H || defined _LIBC
-# include <stdbool.h>
-#else
-typedef enum { false, true } bool;
-#endif /* HAVE_STDBOOL_H || _LIBC */
-#if defined HAVE_STDINT_H || defined _LIBC
-# include <stdint.h>
-#endif /* HAVE_STDINT_H || _LIBC */
-#if defined _LIBC
-# include <bits/libc-lock.h>
-#else
-# define __libc_lock_define(CLASS,NAME)
-# define __libc_lock_init(NAME) do { } while (0)
-# define __libc_lock_lock(NAME) do { } while (0)
-# define __libc_lock_unlock(NAME) do { } while (0)
-#endif
-
-/* In case that the system doesn't have isblank(). */
-#if !defined _LIBC && !defined HAVE_ISBLANK && !defined isblank
-# define isblank(ch) ((ch) == ' ' || (ch) == '\t')
-#endif
-
-#ifdef _LIBC
-# ifndef _RE_DEFINE_LOCALE_FUNCTIONS
-# define _RE_DEFINE_LOCALE_FUNCTIONS 1
-# include <locale/localeinfo.h>
-# include <locale/elem-hash.h>
-# include <locale/coll-lookup.h>
-# endif
-#endif
-
-/* This is for other GNU distributions with internationalized messages. */
-#if (HAVE_LIBINTL_H && ENABLE_NLS) || defined _LIBC
-# include <libintl.h>
-# ifdef _LIBC
-# undef gettext
-# define gettext(msgid) \
- INTUSE(__dcgettext) (_libc_intl_domainname, msgid, LC_MESSAGES)
-# endif
-#else
-# define gettext(msgid) (msgid)
-#endif
-
-#ifndef gettext_noop
-/* This define is so xgettext can find the internationalizable
- strings. */
-# define gettext_noop(String) String
-#endif
-
-/* For loser systems without the definition. */
-#ifndef SIZE_MAX
-# define SIZE_MAX ((size_t) -1)
-#endif
-
-#if (defined MB_CUR_MAX && HAVE_LOCALE_H && HAVE_WCTYPE_H && HAVE_WCHAR_H && HAVE_WCRTOMB && HAVE_MBRTOWC && HAVE_WCSCOLL) || _LIBC
-# define RE_ENABLE_I18N
-#endif
-
-#if __GNUC__ >= 3
-# define BE(expr, val) __builtin_expect (expr, val)
-#else
-# define BE(expr, val) (expr)
-# define inline
-#endif
-
-/* Number of single byte character. */
-#define SBC_MAX 256
-
-#define COLL_ELEM_LEN_MAX 8
-
-/* The character which represents newline. */
-#define NEWLINE_CHAR '\n'
-#define WIDE_NEWLINE_CHAR L'\n'
-
-/* Rename to standard API for using out of glibc. */
-#ifndef _LIBC
-# define __wctype wctype
-# define __iswctype iswctype
-# define __btowc btowc
-# define __mempcpy mempcpy
-# define __wcrtomb wcrtomb
-# define __regfree regfree
-# define attribute_hidden
-#endif /* not _LIBC */
-
-#ifdef __GNUC__
-# define __attribute(arg) __attribute__ (arg)
-#else
-# define __attribute(arg)
-#endif
-
-extern const char __re_error_msgid[] attribute_hidden;
-extern const size_t __re_error_msgid_idx[] attribute_hidden;
-
-/* An integer used to represent a set of bits. It must be unsigned,
- and must be at least as wide as unsigned int. */
-typedef unsigned long int bitset_word_t;
-/* All bits set in a bitset_word_t. */
-#define BITSET_WORD_MAX ULONG_MAX
-/* Number of bits in a bitset_word_t. */
-#define BITSET_WORD_BITS (sizeof (bitset_word_t) * CHAR_BIT)
-/* Number of bitset_word_t in a bit_set. */
-#define BITSET_WORDS (SBC_MAX / BITSET_WORD_BITS)
-typedef bitset_word_t bitset_t[BITSET_WORDS];
-typedef bitset_word_t *re_bitset_ptr_t;
-typedef const bitset_word_t *re_const_bitset_ptr_t;
-
-#define bitset_set(set,i) \
- (set[i / BITSET_WORD_BITS] |= (bitset_word_t) 1 << i % BITSET_WORD_BITS)
-#define bitset_clear(set,i) \
- (set[i / BITSET_WORD_BITS] &= ~((bitset_word_t) 1 << i % BITSET_WORD_BITS))
-#define bitset_contain(set,i) \
- (set[i / BITSET_WORD_BITS] & ((bitset_word_t) 1 << i % BITSET_WORD_BITS))
-#define bitset_empty(set) memset (set, '\0', sizeof (bitset_t))
-#define bitset_set_all(set) memset (set, '\xff', sizeof (bitset_t))
-#define bitset_copy(dest,src) memcpy (dest, src, sizeof (bitset_t))
-
-#define PREV_WORD_CONSTRAINT 0x0001
-#define PREV_NOTWORD_CONSTRAINT 0x0002
-#define NEXT_WORD_CONSTRAINT 0x0004
-#define NEXT_NOTWORD_CONSTRAINT 0x0008
-#define PREV_NEWLINE_CONSTRAINT 0x0010
-#define NEXT_NEWLINE_CONSTRAINT 0x0020
-#define PREV_BEGBUF_CONSTRAINT 0x0040
-#define NEXT_ENDBUF_CONSTRAINT 0x0080
-#define WORD_DELIM_CONSTRAINT 0x0100
-#define NOT_WORD_DELIM_CONSTRAINT 0x0200
-
-typedef enum
-{
- INSIDE_WORD = PREV_WORD_CONSTRAINT | NEXT_WORD_CONSTRAINT,
- WORD_FIRST = PREV_NOTWORD_CONSTRAINT | NEXT_WORD_CONSTRAINT,
- WORD_LAST = PREV_WORD_CONSTRAINT | NEXT_NOTWORD_CONSTRAINT,
- INSIDE_NOTWORD = PREV_NOTWORD_CONSTRAINT | NEXT_NOTWORD_CONSTRAINT,
- LINE_FIRST = PREV_NEWLINE_CONSTRAINT,
- LINE_LAST = NEXT_NEWLINE_CONSTRAINT,
- BUF_FIRST = PREV_BEGBUF_CONSTRAINT,
- BUF_LAST = NEXT_ENDBUF_CONSTRAINT,
- WORD_DELIM = WORD_DELIM_CONSTRAINT,
- NOT_WORD_DELIM = NOT_WORD_DELIM_CONSTRAINT
-} re_context_type;
-
-typedef struct
-{
- int alloc;
- int nelem;
- int *elems;
-} re_node_set;
-
-typedef enum
-{
- NON_TYPE = 0,
-
- /* Node type, These are used by token, node, tree. */
- CHARACTER = 1,
- END_OF_RE = 2,
- SIMPLE_BRACKET = 3,
- OP_BACK_REF = 4,
- OP_PERIOD = 5,
-#ifdef RE_ENABLE_I18N
- COMPLEX_BRACKET = 6,
- OP_UTF8_PERIOD = 7,
-#endif /* RE_ENABLE_I18N */
-
- /* We define EPSILON_BIT as a macro so that OP_OPEN_SUBEXP is used
- when the debugger shows values of this enum type. */
-#define EPSILON_BIT 8
- OP_OPEN_SUBEXP = EPSILON_BIT | 0,
- OP_CLOSE_SUBEXP = EPSILON_BIT | 1,
- OP_ALT = EPSILON_BIT | 2,
- OP_DUP_ASTERISK = EPSILON_BIT | 3,
- ANCHOR = EPSILON_BIT | 4,
-
- /* Tree type, these are used only by tree. */
- CONCAT = 16,
- SUBEXP = 17,
-
- /* Token type, these are used only by token. */
- OP_DUP_PLUS = 18,
- OP_DUP_QUESTION,
- OP_OPEN_BRACKET,
- OP_CLOSE_BRACKET,
- OP_CHARSET_RANGE,
- OP_OPEN_DUP_NUM,
- OP_CLOSE_DUP_NUM,
- OP_NON_MATCH_LIST,
- OP_OPEN_COLL_ELEM,
- OP_CLOSE_COLL_ELEM,
- OP_OPEN_EQUIV_CLASS,
- OP_CLOSE_EQUIV_CLASS,
- OP_OPEN_CHAR_CLASS,
- OP_CLOSE_CHAR_CLASS,
- OP_WORD,
- OP_NOTWORD,
- OP_SPACE,
- OP_NOTSPACE,
- BACK_SLASH
-
-} re_token_type_t;
-
-#ifdef RE_ENABLE_I18N
-typedef struct
-{
- /* Multibyte characters. */
- wchar_t *mbchars;
-
- /* Collating symbols. */
-# ifdef _LIBC
- int32_t *coll_syms;
-# endif
-
- /* Equivalence classes. */
-# ifdef _LIBC
- int32_t *equiv_classes;
-# endif
-
- /* Range expressions. */
-# ifdef _LIBC
- uint32_t *range_starts;
- uint32_t *range_ends;
-# else /* not _LIBC */
- wchar_t *range_starts;
- wchar_t *range_ends;
-# endif /* not _LIBC */
-
- /* Character classes. */
- wctype_t *char_classes;
-
- /* If this character set is the non-matching list. */
- unsigned int non_match : 1;
-
- /* # of multibyte characters. */
- int nmbchars;
-
- /* # of collating symbols. */
- int ncoll_syms;
-
- /* # of equivalence classes. */
- int nequiv_classes;
-
- /* # of range expressions. */
- int nranges;
-
- /* # of character classes. */
- int nchar_classes;
-} re_charset_t;
-#endif /* RE_ENABLE_I18N */
-
-typedef struct
-{
- union
- {
- unsigned char c; /* for CHARACTER */
- re_bitset_ptr_t sbcset; /* for SIMPLE_BRACKET */
-#ifdef RE_ENABLE_I18N
- re_charset_t *mbcset; /* for COMPLEX_BRACKET */
-#endif /* RE_ENABLE_I18N */
- int idx; /* for BACK_REF */
- re_context_type ctx_type; /* for ANCHOR */
- } opr;
-#if __GNUC__ >= 2
- re_token_type_t type : 8;
-#else
- re_token_type_t type;
-#endif
- unsigned int constraint : 10; /* context constraint */
- unsigned int duplicated : 1;
- unsigned int opt_subexp : 1;
-#ifdef RE_ENABLE_I18N
- unsigned int accept_mb : 1;
- /* These 2 bits can be moved into the union if needed (e.g. if running out
- of bits; move opr.c to opr.c.c and move the flags to opr.c.flags). */
- unsigned int mb_partial : 1;
-#endif
- unsigned int word_char : 1;
-} re_token_t;
-
-#define IS_EPSILON_NODE(type) ((type) & EPSILON_BIT)
-
-struct re_string_t
-{
- /* Indicate the raw buffer which is the original string passed as an
- argument of regexec(), re_search(), etc.. */
- const unsigned char *raw_mbs;
- /* Store the multibyte string. In case of "case insensitive mode" like
- REG_ICASE, upper cases of the string are stored, otherwise MBS points
- the same address that RAW_MBS points. */
- unsigned char *mbs;
-#ifdef RE_ENABLE_I18N
- /* Store the wide character string which is corresponding to MBS. */
- wint_t *wcs;
- int *offsets;
- mbstate_t cur_state;
-#endif
- /* Index in RAW_MBS. Each character mbs[i] corresponds to
- raw_mbs[raw_mbs_idx + i]. */
- int raw_mbs_idx;
- /* The length of the valid characters in the buffers. */
- int valid_len;
- /* The corresponding number of bytes in raw_mbs array. */
- int valid_raw_len;
- /* The length of the buffers MBS and WCS. */
- int bufs_len;
- /* The index in MBS, which is updated by re_string_fetch_byte. */
- int cur_idx;
- /* length of RAW_MBS array. */
- int raw_len;
- /* This is RAW_LEN - RAW_MBS_IDX + VALID_LEN - VALID_RAW_LEN. */
- int len;
- /* End of the buffer may be shorter than its length in the cases such
- as re_match_2, re_search_2. Then, we use STOP for end of the buffer
- instead of LEN. */
- int raw_stop;
- /* This is RAW_STOP - RAW_MBS_IDX adjusted through OFFSETS. */
- int stop;
-
- /* The context of mbs[0]. We store the context independently, since
- the context of mbs[0] may be different from raw_mbs[0], which is
- the beginning of the input string. */
- unsigned int tip_context;
- /* The translation passed as a part of an argument of re_compile_pattern. */
- RE_TRANSLATE_TYPE trans;
- /* Copy of re_dfa_t's word_char. */
- re_const_bitset_ptr_t word_char;
- /* 1 if REG_ICASE. */
- unsigned char icase;
- unsigned char is_utf8;
- unsigned char map_notascii;
- unsigned char mbs_allocated;
- unsigned char offsets_needed;
- unsigned char newline_anchor;
- unsigned char word_ops_used;
- int mb_cur_max;
-};
-typedef struct re_string_t re_string_t;
-
-
-struct re_dfa_t;
-typedef struct re_dfa_t re_dfa_t;
-
-#ifndef _LIBC
-# ifdef __i386__
-# define internal_function __attribute ((regparm (3), stdcall))
-# else
-# define internal_function
-# endif
-#endif
-
-static reg_errcode_t re_string_realloc_buffers (re_string_t *pstr,
- int new_buf_len)
- internal_function;
-#ifdef RE_ENABLE_I18N
-static void build_wcs_buffer (re_string_t *pstr) internal_function;
-static int build_wcs_upper_buffer (re_string_t *pstr) internal_function;
-#endif /* RE_ENABLE_I18N */
-static void build_upper_buffer (re_string_t *pstr) internal_function;
-static void re_string_translate_buffer (re_string_t *pstr) internal_function;
-static unsigned int re_string_context_at (const re_string_t *input, int idx,
- int eflags)
- internal_function __attribute ((pure));
-#define re_string_peek_byte(pstr, offset) \
- ((pstr)->mbs[(pstr)->cur_idx + offset])
-#define re_string_fetch_byte(pstr) \
- ((pstr)->mbs[(pstr)->cur_idx++])
-#define re_string_first_byte(pstr, idx) \
- ((idx) == (pstr)->valid_len || (pstr)->wcs[idx] != WEOF)
-#define re_string_is_single_byte_char(pstr, idx) \
- ((pstr)->wcs[idx] != WEOF && ((pstr)->valid_len == (idx) + 1 \
- || (pstr)->wcs[(idx) + 1] != WEOF))
-#define re_string_eoi(pstr) ((pstr)->stop <= (pstr)->cur_idx)
-#define re_string_cur_idx(pstr) ((pstr)->cur_idx)
-#define re_string_get_buffer(pstr) ((pstr)->mbs)
-#define re_string_length(pstr) ((pstr)->len)
-#define re_string_byte_at(pstr,idx) ((pstr)->mbs[idx])
-#define re_string_skip_bytes(pstr,idx) ((pstr)->cur_idx += (idx))
-#define re_string_set_index(pstr,idx) ((pstr)->cur_idx = (idx))
-
-#ifdef __GNUC__
-# define alloca(size) __builtin_alloca (size)
-# define HAVE_ALLOCA 1
-#elif defined(_MSC_VER)
-# include <malloc.h>
-# define alloca _alloca
-# define HAVE_ALLOCA 1
-#else
-# error No alloca()
-#endif
-
-#ifndef _LIBC
-# if HAVE_ALLOCA
-/* The OS usually guarantees only one guard page at the bottom of the stack,
- and a page size can be as small as 4096 bytes. So we cannot safely
- allocate anything larger than 4096 bytes. Also care for the possibility
- of a few compiler-allocated temporary stack slots. */
-# define __libc_use_alloca(n) ((n) < 4032)
-# else
-/* alloca is implemented with malloc, so just use malloc. */
-# define __libc_use_alloca(n) 0
-# endif
-#endif
-
-#define re_malloc(t,n) ((t *) malloc ((n) * sizeof (t)))
-#define re_realloc(p,t,n) ((t *) realloc (p, (n) * sizeof (t)))
-#define re_free(p) free (p)
-
-struct bin_tree_t
-{
- struct bin_tree_t *parent;
- struct bin_tree_t *left;
- struct bin_tree_t *right;
- struct bin_tree_t *first;
- struct bin_tree_t *next;
-
- re_token_t token;
-
- /* `node_idx' is the index in dfa->nodes, if `type' == 0.
- Otherwise `type' indicate the type of this node. */
- int node_idx;
-};
-typedef struct bin_tree_t bin_tree_t;
-
-#define BIN_TREE_STORAGE_SIZE \
- ((1024 - sizeof (void *)) / sizeof (bin_tree_t))
-
-struct bin_tree_storage_t
-{
- struct bin_tree_storage_t *next;
- bin_tree_t data[BIN_TREE_STORAGE_SIZE];
-};
-typedef struct bin_tree_storage_t bin_tree_storage_t;
-
-#define CONTEXT_WORD 1
-#define CONTEXT_NEWLINE (CONTEXT_WORD << 1)
-#define CONTEXT_BEGBUF (CONTEXT_NEWLINE << 1)
-#define CONTEXT_ENDBUF (CONTEXT_BEGBUF << 1)
-
-#define IS_WORD_CONTEXT(c) ((c) & CONTEXT_WORD)
-#define IS_NEWLINE_CONTEXT(c) ((c) & CONTEXT_NEWLINE)
-#define IS_BEGBUF_CONTEXT(c) ((c) & CONTEXT_BEGBUF)
-#define IS_ENDBUF_CONTEXT(c) ((c) & CONTEXT_ENDBUF)
-#define IS_ORDINARY_CONTEXT(c) ((c) == 0)
-
-#define IS_WORD_CHAR(ch) (isalnum (ch) || (ch) == '_')
-#define IS_NEWLINE(ch) ((ch) == NEWLINE_CHAR)
-#define IS_WIDE_WORD_CHAR(ch) (iswalnum (ch) || (ch) == L'_')
-#define IS_WIDE_NEWLINE(ch) ((ch) == WIDE_NEWLINE_CHAR)
-
-#define NOT_SATISFY_PREV_CONSTRAINT(constraint,context) \
- ((((constraint) & PREV_WORD_CONSTRAINT) && !IS_WORD_CONTEXT (context)) \
- || ((constraint & PREV_NOTWORD_CONSTRAINT) && IS_WORD_CONTEXT (context)) \
- || ((constraint & PREV_NEWLINE_CONSTRAINT) && !IS_NEWLINE_CONTEXT (context))\
- || ((constraint & PREV_BEGBUF_CONSTRAINT) && !IS_BEGBUF_CONTEXT (context)))
-
-#define NOT_SATISFY_NEXT_CONSTRAINT(constraint,context) \
- ((((constraint) & NEXT_WORD_CONSTRAINT) && !IS_WORD_CONTEXT (context)) \
- || (((constraint) & NEXT_NOTWORD_CONSTRAINT) && IS_WORD_CONTEXT (context)) \
- || (((constraint) & NEXT_NEWLINE_CONSTRAINT) && !IS_NEWLINE_CONTEXT (context)) \
- || (((constraint) & NEXT_ENDBUF_CONSTRAINT) && !IS_ENDBUF_CONTEXT (context)))
-
-struct re_dfastate_t
-{
- unsigned int hash;
- re_node_set nodes;
- re_node_set non_eps_nodes;
- re_node_set inveclosure;
- re_node_set *entrance_nodes;
- struct re_dfastate_t **trtable, **word_trtable;
- unsigned int context : 4;
- unsigned int halt : 1;
- /* If this state can accept `multi byte'.
- Note that we refer to multibyte characters, and multi character
- collating elements as `multi byte'. */
- unsigned int accept_mb : 1;
- /* If this state has backreference node(s). */
- unsigned int has_backref : 1;
- unsigned int has_constraint : 1;
-};
-typedef struct re_dfastate_t re_dfastate_t;
-
-struct re_state_table_entry
-{
- int num;
- int alloc;
- re_dfastate_t **array;
-};
-
-/* Array type used in re_sub_match_last_t and re_sub_match_top_t. */
-
-typedef struct
-{
- int next_idx;
- int alloc;
- re_dfastate_t **array;
-} state_array_t;
-
-/* Store information about the node NODE whose type is OP_CLOSE_SUBEXP. */
-
-typedef struct
-{
- int node;
- int str_idx; /* The position NODE match at. */
- state_array_t path;
-} re_sub_match_last_t;
-
-/* Store information about the node NODE whose type is OP_OPEN_SUBEXP.
- And information about the node, whose type is OP_CLOSE_SUBEXP,
- corresponding to NODE is stored in LASTS. */
-
-typedef struct
-{
- int str_idx;
- int node;
- state_array_t *path;
- int alasts; /* Allocation size of LASTS. */
- int nlasts; /* The number of LASTS. */
- re_sub_match_last_t **lasts;
-} re_sub_match_top_t;
-
-struct re_backref_cache_entry
-{
- int node;
- int str_idx;
- int subexp_from;
- int subexp_to;
- char more;
- char unused;
- unsigned short int eps_reachable_subexps_map;
-};
-
-typedef struct
-{
- /* The string object corresponding to the input string. */
- re_string_t input;
-#if defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L)
- const re_dfa_t *const dfa;
-#else
- const re_dfa_t *dfa;
-#endif
- /* EFLAGS of the argument of regexec. */
- int eflags;
- /* Where the matching ends. */
- int match_last;
- int last_node;
- /* The state log used by the matcher. */
- re_dfastate_t **state_log;
- int state_log_top;
- /* Back reference cache. */
- int nbkref_ents;
- int abkref_ents;
- struct re_backref_cache_entry *bkref_ents;
- int max_mb_elem_len;
- int nsub_tops;
- int asub_tops;
- re_sub_match_top_t **sub_tops;
-} re_match_context_t;
-
-typedef struct
-{
- re_dfastate_t **sifted_states;
- re_dfastate_t **limited_states;
- int last_node;
- int last_str_idx;
- re_node_set limits;
-} re_sift_context_t;
-
-struct re_fail_stack_ent_t
-{
- int idx;
- int node;
- regmatch_t *regs;
- re_node_set eps_via_nodes;
-};
-
-struct re_fail_stack_t
-{
- int num;
- int alloc;
- struct re_fail_stack_ent_t *stack;
-};
-
-struct re_dfa_t
-{
- re_token_t *nodes;
- size_t nodes_alloc;
- size_t nodes_len;
- int *nexts;
- int *org_indices;
- re_node_set *edests;
- re_node_set *eclosures;
- re_node_set *inveclosures;
- struct re_state_table_entry *state_table;
- re_dfastate_t *init_state;
- re_dfastate_t *init_state_word;
- re_dfastate_t *init_state_nl;
- re_dfastate_t *init_state_begbuf;
- bin_tree_t *str_tree;
- bin_tree_storage_t *str_tree_storage;
- re_bitset_ptr_t sb_char;
- int str_tree_storage_idx;
-
- /* number of subexpressions `re_nsub' is in regex_t. */
- unsigned int state_hash_mask;
- int init_node;
- int nbackref; /* The number of backreference in this dfa. */
-
- /* Bitmap expressing which backreference is used. */
- bitset_word_t used_bkref_map;
- bitset_word_t completed_bkref_map;
-
- unsigned int has_plural_match : 1;
- /* If this dfa has "multibyte node", which is a backreference or
- a node which can accept multibyte character or multi character
- collating element. */
- unsigned int has_mb_node : 1;
- unsigned int is_utf8 : 1;
- unsigned int map_notascii : 1;
- unsigned int word_ops_used : 1;
- int mb_cur_max;
- bitset_t word_char;
- reg_syntax_t syntax;
- int *subexp_map;
-#ifdef DEBUG
- char* re_str;
-#endif
- __libc_lock_define (, lock)
-};
-
-#define re_node_set_init_empty(set) memset (set, '\0', sizeof (re_node_set))
-#define re_node_set_remove(set,id) \
- (re_node_set_remove_at (set, re_node_set_contains (set, id) - 1))
-#define re_node_set_empty(p) ((p)->nelem = 0)
-#define re_node_set_free(set) re_free ((set)->elems)
-
-
-typedef enum
-{
- SB_CHAR,
- MB_CHAR,
- EQUIV_CLASS,
- COLL_SYM,
- CHAR_CLASS
-} bracket_elem_type;
-
-typedef struct
-{
- bracket_elem_type type;
- union
- {
- unsigned char ch;
- unsigned char *name;
- wchar_t wch;
- } opr;
-} bracket_elem_t;
-
-
-/* Inline functions for bitset operation. */
-static inline void
-bitset_not (bitset_t set)
-{
- int bitset_i;
- for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i)
- set[bitset_i] = ~set[bitset_i];
-}
-
-static inline void
-bitset_merge (bitset_t dest, const bitset_t src)
-{
- int bitset_i;
- for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i)
- dest[bitset_i] |= src[bitset_i];
-}
-
-static inline void
-bitset_mask (bitset_t dest, const bitset_t src)
-{
- int bitset_i;
- for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i)
- dest[bitset_i] &= src[bitset_i];
-}
-
-#ifdef RE_ENABLE_I18N
-/* Inline functions for re_string. */
-static inline int
-internal_function __attribute ((pure))
-re_string_char_size_at (const re_string_t *pstr, int idx)
-{
- int byte_idx;
- if (pstr->mb_cur_max == 1)
- return 1;
- for (byte_idx = 1; idx + byte_idx < pstr->valid_len; ++byte_idx)
- if (pstr->wcs[idx + byte_idx] != WEOF)
- break;
- return byte_idx;
-}
-
-static inline wint_t
-internal_function __attribute ((pure))
-re_string_wchar_at (const re_string_t *pstr, int idx)
-{
- if (pstr->mb_cur_max == 1)
- return (wint_t) pstr->mbs[idx];
- return (wint_t) pstr->wcs[idx];
-}
-
-static int
-internal_function __attribute ((pure))
-re_string_elem_size_at (const re_string_t *pstr, int idx)
-{
-# ifdef _LIBC
- const unsigned char *p, *extra;
- const int32_t *table, *indirect;
- int32_t tmp;
-# include <locale/weight.h>
- uint_fast32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES);
-
- if (nrules != 0)
- {
- table = (const int32_t *) _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB);
- extra = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_EXTRAMB);
- indirect = (const int32_t *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_INDIRECTMB);
- p = pstr->mbs + idx;
- tmp = findidx (&p);
- return p - pstr->mbs - idx;
- }
- else
-# endif /* _LIBC */
- return 1;
-}
-#endif /* RE_ENABLE_I18N */
-
-#endif /* _REGEX_INTERNAL_H */
-
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* GKINCLUDE #include "regex_internal.c" */
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* Extended regular expression matching and search library.
- Copyright (C) 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
- This file is part of the GNU C Library.
- Contributed by Isamu Hasegawa <isamu@yamato.ibm.com>.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-static void re_string_construct_common (const char *str, int len,
- re_string_t *pstr,
- RE_TRANSLATE_TYPE trans, int icase,
- const re_dfa_t *dfa) internal_function;
-static re_dfastate_t *create_ci_newstate (const re_dfa_t *dfa,
- const re_node_set *nodes,
- unsigned int hash) internal_function;
-static re_dfastate_t *create_cd_newstate (const re_dfa_t *dfa,
- const re_node_set *nodes,
- unsigned int context,
- unsigned int hash) internal_function;
-
-/* Functions for string operation. */
-
-/* This function allocate the buffers. It is necessary to call
- re_string_reconstruct before using the object. */
-
-static reg_errcode_t
-internal_function
-re_string_allocate (re_string_t *pstr, const char *str, int len, int init_len,
- RE_TRANSLATE_TYPE trans, int icase, const re_dfa_t *dfa)
-{
- reg_errcode_t ret;
- int init_buf_len;
-
- /* Ensure at least one character fits into the buffers. */
- if (init_len < dfa->mb_cur_max)
- init_len = dfa->mb_cur_max;
- init_buf_len = (len + 1 < init_len) ? len + 1: init_len;
- re_string_construct_common (str, len, pstr, trans, icase, dfa);
-
- ret = re_string_realloc_buffers (pstr, init_buf_len);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
-
- pstr->word_char = dfa->word_char;
- pstr->word_ops_used = dfa->word_ops_used;
- pstr->mbs = pstr->mbs_allocated ? pstr->mbs : (unsigned char *) str;
- pstr->valid_len = (pstr->mbs_allocated || dfa->mb_cur_max > 1) ? 0 : len;
- pstr->valid_raw_len = pstr->valid_len;
- return REG_NOERROR;
-}
-
-/* This function allocate the buffers, and initialize them. */
-
-static reg_errcode_t
-internal_function
-re_string_construct (re_string_t *pstr, const char *str, int len,
- RE_TRANSLATE_TYPE trans, int icase, const re_dfa_t *dfa)
-{
- reg_errcode_t ret;
- memset (pstr, '\0', sizeof (re_string_t));
- re_string_construct_common (str, len, pstr, trans, icase, dfa);
-
- if (len > 0)
- {
- ret = re_string_realloc_buffers (pstr, len + 1);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- }
- pstr->mbs = pstr->mbs_allocated ? pstr->mbs : (unsigned char *) str;
-
- if (icase)
- {
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- {
- while (1)
- {
- ret = build_wcs_upper_buffer (pstr);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- if (pstr->valid_raw_len >= len)
- break;
- if (pstr->bufs_len > pstr->valid_len + dfa->mb_cur_max)
- break;
- ret = re_string_realloc_buffers (pstr, pstr->bufs_len * 2);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- }
- }
- else
-#endif /* RE_ENABLE_I18N */
- build_upper_buffer (pstr);
- }
- else
- {
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- build_wcs_buffer (pstr);
- else
-#endif /* RE_ENABLE_I18N */
- {
- if (trans != NULL)
- re_string_translate_buffer (pstr);
- else
- {
- pstr->valid_len = pstr->bufs_len;
- pstr->valid_raw_len = pstr->bufs_len;
- }
- }
- }
-
- return REG_NOERROR;
-}
-
-/* Helper functions for re_string_allocate, and re_string_construct. */
-
-static reg_errcode_t
-internal_function
-re_string_realloc_buffers (re_string_t *pstr, int new_buf_len)
-{
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- {
- wint_t *new_wcs = re_realloc (pstr->wcs, wint_t, new_buf_len);
- if (BE (new_wcs == NULL, 0))
- return REG_ESPACE;
- pstr->wcs = new_wcs;
- if (pstr->offsets != NULL)
- {
- int *new_offsets = re_realloc (pstr->offsets, int, new_buf_len);
- if (BE (new_offsets == NULL, 0))
- return REG_ESPACE;
- pstr->offsets = new_offsets;
- }
- }
-#endif /* RE_ENABLE_I18N */
- if (pstr->mbs_allocated)
- {
- unsigned char *new_mbs = re_realloc (pstr->mbs, unsigned char,
- new_buf_len);
- if (BE (new_mbs == NULL, 0))
- return REG_ESPACE;
- pstr->mbs = new_mbs;
- }
- pstr->bufs_len = new_buf_len;
- return REG_NOERROR;
-}
-
-
-static void
-internal_function
-re_string_construct_common (const char *str, int len, re_string_t *pstr,
- RE_TRANSLATE_TYPE trans, int icase,
- const re_dfa_t *dfa)
-{
- pstr->raw_mbs = (const unsigned char *) str;
- pstr->len = len;
- pstr->raw_len = len;
- pstr->trans = trans;
- pstr->icase = icase ? 1 : 0;
- pstr->mbs_allocated = (trans != NULL || icase);
- pstr->mb_cur_max = dfa->mb_cur_max;
- pstr->is_utf8 = dfa->is_utf8;
- pstr->map_notascii = dfa->map_notascii;
- pstr->stop = pstr->len;
- pstr->raw_stop = pstr->stop;
-}
-
-#ifdef RE_ENABLE_I18N
-
-/* Build wide character buffer PSTR->WCS.
- If the byte sequence of the string are:
- <mb1>(0), <mb1>(1), <mb2>(0), <mb2>(1), <sb3>
- Then wide character buffer will be:
- <wc1> , WEOF , <wc2> , WEOF , <wc3>
- We use WEOF for padding, they indicate that the position isn't
- a first byte of a multibyte character.
-
- Note that this function assumes PSTR->VALID_LEN elements are already
- built and starts from PSTR->VALID_LEN. */
-
-static void
-internal_function
-build_wcs_buffer (re_string_t *pstr)
-{
-#ifdef _LIBC
- unsigned char buf[MB_LEN_MAX];
- assert (MB_LEN_MAX >= pstr->mb_cur_max);
-#else
- unsigned char buf[64];
-#endif
- mbstate_t prev_st;
- int byte_idx, end_idx, remain_len;
- size_t mbclen;
-
- /* Build the buffers from pstr->valid_len to either pstr->len or
- pstr->bufs_len. */
- end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len;
- for (byte_idx = pstr->valid_len; byte_idx < end_idx;)
- {
- wchar_t wc;
- const char *p;
-
- remain_len = end_idx - byte_idx;
- prev_st = pstr->cur_state;
- /* Apply the translation if we need. */
- if (BE (pstr->trans != NULL, 0))
- {
- int i, ch;
-
- for (i = 0; i < pstr->mb_cur_max && i < remain_len; ++i)
- {
- ch = pstr->raw_mbs [pstr->raw_mbs_idx + byte_idx + i];
- buf[i] = pstr->mbs[byte_idx + i] = pstr->trans[ch];
- }
- p = (const char *) buf;
- }
- else
- p = (const char *) pstr->raw_mbs + pstr->raw_mbs_idx + byte_idx;
- mbclen = mbrtowc (&wc, p, remain_len, &pstr->cur_state);
- if (BE (mbclen == (size_t) -2, 0))
- {
- /* The buffer doesn't have enough space, finish to build. */
- pstr->cur_state = prev_st;
- break;
- }
- else if (BE (mbclen == (size_t) -1 || mbclen == 0, 0))
- {
- /* We treat these cases as a singlebyte character. */
- mbclen = 1;
- wc = (wchar_t) pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx];
- if (BE (pstr->trans != NULL, 0))
- wc = pstr->trans[wc];
- pstr->cur_state = prev_st;
- }
-
- /* Write wide character and padding. */
- pstr->wcs[byte_idx++] = wc;
- /* Write paddings. */
- for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;)
- pstr->wcs[byte_idx++] = WEOF;
- }
- pstr->valid_len = byte_idx;
- pstr->valid_raw_len = byte_idx;
-}
-
-/* Build wide character buffer PSTR->WCS like build_wcs_buffer,
- but for REG_ICASE. */
-
-static reg_errcode_t
-internal_function
-build_wcs_upper_buffer (re_string_t *pstr)
-{
- mbstate_t prev_st;
- int src_idx, byte_idx, end_idx, remain_len;
- size_t mbclen;
-#ifdef _LIBC
- char buf[MB_LEN_MAX];
- assert (MB_LEN_MAX >= pstr->mb_cur_max);
-#else
- char buf[64];
-#endif
-
- byte_idx = pstr->valid_len;
- end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len;
-
- /* The following optimization assumes that ASCII characters can be
- mapped to wide characters with a simple cast. */
- if (! pstr->map_notascii && pstr->trans == NULL && !pstr->offsets_needed)
- {
- while (byte_idx < end_idx)
- {
- wchar_t wc;
-
- if (isascii (pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx])
- && mbsinit (&pstr->cur_state))
- {
- /* In case of a singlebyte character. */
- pstr->mbs[byte_idx]
- = toupper (pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx]);
- /* The next step uses the assumption that wchar_t is encoded
- ASCII-safe: all ASCII values can be converted like this. */
- pstr->wcs[byte_idx] = (wchar_t) pstr->mbs[byte_idx];
- ++byte_idx;
- continue;
- }
-
- remain_len = end_idx - byte_idx;
- prev_st = pstr->cur_state;
- mbclen = mbrtowc (&wc,
- ((const char *) pstr->raw_mbs + pstr->raw_mbs_idx
- + byte_idx), remain_len, &pstr->cur_state);
- if (BE (mbclen + 2 > 2, 1))
- {
- wchar_t wcu = wc;
- if (iswlower (wc))
- {
- size_t mbcdlen;
-
- wcu = towupper (wc);
- mbcdlen = wcrtomb (buf, wcu, &prev_st);
- if (BE (mbclen == mbcdlen, 1))
- memcpy (pstr->mbs + byte_idx, buf, mbclen);
- else
- {
- src_idx = byte_idx;
- goto offsets_needed;
- }
- }
- else
- memcpy (pstr->mbs + byte_idx,
- pstr->raw_mbs + pstr->raw_mbs_idx + byte_idx, mbclen);
- pstr->wcs[byte_idx++] = wcu;
- /* Write paddings. */
- for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;)
- pstr->wcs[byte_idx++] = WEOF;
- }
- else if (mbclen == (size_t) -1 || mbclen == 0)
- {
- /* It is an invalid character or '\0'. Just use the byte. */
- int ch = pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx];
- pstr->mbs[byte_idx] = ch;
- /* And also cast it to wide char. */
- pstr->wcs[byte_idx++] = (wchar_t) ch;
- if (BE (mbclen == (size_t) -1, 0))
- pstr->cur_state = prev_st;
- }
- else
- {
- /* The buffer doesn't have enough space, finish to build. */
- pstr->cur_state = prev_st;
- break;
- }
- }
- pstr->valid_len = byte_idx;
- pstr->valid_raw_len = byte_idx;
- return REG_NOERROR;
- }
- else
- for (src_idx = pstr->valid_raw_len; byte_idx < end_idx;)
- {
- wchar_t wc;
- const char *p;
- offsets_needed:
- remain_len = end_idx - byte_idx;
- prev_st = pstr->cur_state;
- if (BE (pstr->trans != NULL, 0))
- {
- int i, ch;
-
- for (i = 0; i < pstr->mb_cur_max && i < remain_len; ++i)
- {
- ch = pstr->raw_mbs [pstr->raw_mbs_idx + src_idx + i];
- buf[i] = pstr->trans[ch];
- }
- p = (const char *) buf;
- }
- else
- p = (const char *) pstr->raw_mbs + pstr->raw_mbs_idx + src_idx;
- mbclen = mbrtowc (&wc, p, remain_len, &pstr->cur_state);
- if (BE (mbclen + 2 > 2, 1))
- {
- wchar_t wcu = wc;
- if (iswlower (wc))
- {
- size_t mbcdlen;
-
- wcu = towupper (wc);
- mbcdlen = wcrtomb ((char *) buf, wcu, &prev_st);
- if (BE (mbclen == mbcdlen, 1))
- memcpy (pstr->mbs + byte_idx, buf, mbclen);
- else if (mbcdlen != (size_t) -1)
- {
- size_t i;
-
- if (byte_idx + mbcdlen > pstr->bufs_len)
- {
- pstr->cur_state = prev_st;
- break;
- }
-
- if (pstr->offsets == NULL)
- {
- pstr->offsets = re_malloc (int, pstr->bufs_len);
-
- if (pstr->offsets == NULL)
- return REG_ESPACE;
- }
- if (!pstr->offsets_needed)
- {
- for (i = 0; i < (size_t) byte_idx; ++i)
- pstr->offsets[i] = i;
- pstr->offsets_needed = 1;
- }
-
- memcpy (pstr->mbs + byte_idx, buf, mbcdlen);
- pstr->wcs[byte_idx] = wcu;
- pstr->offsets[byte_idx] = src_idx;
- for (i = 1; i < mbcdlen; ++i)
- {
- pstr->offsets[byte_idx + i]
- = src_idx + (i < mbclen ? i : mbclen - 1);
- pstr->wcs[byte_idx + i] = WEOF;
- }
- pstr->len += mbcdlen - mbclen;
- if (pstr->raw_stop > src_idx)
- pstr->stop += mbcdlen - mbclen;
- end_idx = (pstr->bufs_len > pstr->len)
- ? pstr->len : pstr->bufs_len;
- byte_idx += mbcdlen;
- src_idx += mbclen;
- continue;
- }
- else
- memcpy (pstr->mbs + byte_idx, p, mbclen);
- }
- else
- memcpy (pstr->mbs + byte_idx, p, mbclen);
-
- if (BE (pstr->offsets_needed != 0, 0))
- {
- size_t i;
- for (i = 0; i < mbclen; ++i)
- pstr->offsets[byte_idx + i] = src_idx + i;
- }
- src_idx += mbclen;
-
- pstr->wcs[byte_idx++] = wcu;
- /* Write paddings. */
- for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;)
- pstr->wcs[byte_idx++] = WEOF;
- }
- else if (mbclen == (size_t) -1 || mbclen == 0)
- {
- /* It is an invalid character or '\0'. Just use the byte. */
- int ch = pstr->raw_mbs[pstr->raw_mbs_idx + src_idx];
-
- if (BE (pstr->trans != NULL, 0))
- ch = pstr->trans [ch];
- pstr->mbs[byte_idx] = ch;
-
- if (BE (pstr->offsets_needed != 0, 0))
- pstr->offsets[byte_idx] = src_idx;
- ++src_idx;
-
- /* And also cast it to wide char. */
- pstr->wcs[byte_idx++] = (wchar_t) ch;
- if (BE (mbclen == (size_t) -1, 0))
- pstr->cur_state = prev_st;
- }
- else
- {
- /* The buffer doesn't have enough space, finish to build. */
- pstr->cur_state = prev_st;
- break;
- }
- }
- pstr->valid_len = byte_idx;
- pstr->valid_raw_len = src_idx;
- return REG_NOERROR;
-}
-
-/* Skip characters until the index becomes greater than NEW_RAW_IDX.
- Return the index. */
-
-static int
-internal_function
-re_string_skip_chars (re_string_t *pstr, int new_raw_idx, wint_t *last_wc)
-{
- mbstate_t prev_st;
- int rawbuf_idx;
- size_t mbclen;
- wchar_t wc = WEOF;
-
- /* Skip the characters which are not necessary to check. */
- for (rawbuf_idx = pstr->raw_mbs_idx + pstr->valid_raw_len;
- rawbuf_idx < new_raw_idx;)
- {
- int remain_len;
- remain_len = pstr->len - rawbuf_idx;
- prev_st = pstr->cur_state;
- mbclen = mbrtowc (&wc, (const char *) pstr->raw_mbs + rawbuf_idx,
- remain_len, &pstr->cur_state);
- if (BE (mbclen == (size_t) -2 || mbclen == (size_t) -1 || mbclen == 0, 0))
- {
- /* We treat these cases as a single byte character. */
- if (mbclen == 0 || remain_len == 0)
- wc = L'\0';
- else
- wc = *(unsigned char *) (pstr->raw_mbs + rawbuf_idx);
- mbclen = 1;
- pstr->cur_state = prev_st;
- }
- /* Then proceed the next character. */
- rawbuf_idx += mbclen;
- }
- *last_wc = (wint_t) wc;
- return rawbuf_idx;
-}
-#endif /* RE_ENABLE_I18N */
-
-/* Build the buffer PSTR->MBS, and apply the translation if we need.
- This function is used in case of REG_ICASE. */
-
-static void
-internal_function
-build_upper_buffer (re_string_t *pstr)
-{
- int char_idx, end_idx;
- end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len;
-
- for (char_idx = pstr->valid_len; char_idx < end_idx; ++char_idx)
- {
- int ch = pstr->raw_mbs[pstr->raw_mbs_idx + char_idx];
- if (BE (pstr->trans != NULL, 0))
- ch = pstr->trans[ch];
- if (islower (ch))
- pstr->mbs[char_idx] = toupper (ch);
- else
- pstr->mbs[char_idx] = ch;
- }
- pstr->valid_len = char_idx;
- pstr->valid_raw_len = char_idx;
-}
-
-/* Apply TRANS to the buffer in PSTR. */
-
-static void
-internal_function
-re_string_translate_buffer (re_string_t *pstr)
-{
- int buf_idx, end_idx;
- end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len;
-
- for (buf_idx = pstr->valid_len; buf_idx < end_idx; ++buf_idx)
- {
- int ch = pstr->raw_mbs[pstr->raw_mbs_idx + buf_idx];
- pstr->mbs[buf_idx] = pstr->trans[ch];
- }
-
- pstr->valid_len = buf_idx;
- pstr->valid_raw_len = buf_idx;
-}
-
-/* This function re-construct the buffers.
- Concretely, convert to wide character in case of pstr->mb_cur_max > 1,
- convert to upper case in case of REG_ICASE, apply translation. */
-
-static reg_errcode_t
-internal_function
-re_string_reconstruct (re_string_t *pstr, int idx, int eflags)
-{
- int offset = idx - pstr->raw_mbs_idx;
- if (BE (offset < 0, 0))
- {
- /* Reset buffer. */
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- memset (&pstr->cur_state, '\0', sizeof (mbstate_t));
-#endif /* RE_ENABLE_I18N */
- pstr->len = pstr->raw_len;
- pstr->stop = pstr->raw_stop;
- pstr->valid_len = 0;
- pstr->raw_mbs_idx = 0;
- pstr->valid_raw_len = 0;
- pstr->offsets_needed = 0;
- pstr->tip_context = ((eflags & REG_NOTBOL) ? CONTEXT_BEGBUF
- : CONTEXT_NEWLINE | CONTEXT_BEGBUF);
- if (!pstr->mbs_allocated)
- pstr->mbs = (unsigned char *) pstr->raw_mbs;
- offset = idx;
- }
-
- if (BE (offset != 0, 1))
- {
- /* Should the already checked characters be kept? */
- if (BE (offset < pstr->valid_raw_len, 1))
- {
- /* Yes, move them to the front of the buffer. */
-#ifdef RE_ENABLE_I18N
- if (BE (pstr->offsets_needed, 0))
- {
- int low = 0, high = pstr->valid_len, mid;
- do
- {
- mid = (high + low) / 2;
- if (pstr->offsets[mid] > offset)
- high = mid;
- else if (pstr->offsets[mid] < offset)
- low = mid + 1;
- else
- break;
- }
- while (low < high);
- if (pstr->offsets[mid] < offset)
- ++mid;
- pstr->tip_context = re_string_context_at (pstr, mid - 1,
- eflags);
- /* This can be quite complicated, so handle specially
- only the common and easy case where the character with
- different length representation of lower and upper
- case is present at or after offset. */
- if (pstr->valid_len > offset
- && mid == offset && pstr->offsets[mid] == offset)
- {
- memmove (pstr->wcs, pstr->wcs + offset,
- (pstr->valid_len - offset) * sizeof (wint_t));
- memmove (pstr->mbs, pstr->mbs + offset, pstr->valid_len - offset);
- pstr->valid_len -= offset;
- pstr->valid_raw_len -= offset;
- for (low = 0; low < pstr->valid_len; low++)
- pstr->offsets[low] = pstr->offsets[low + offset] - offset;
- }
- else
- {
- /* Otherwise, just find out how long the partial multibyte
- character at offset is and fill it with WEOF/255. */
- pstr->len = pstr->raw_len - idx + offset;
- pstr->stop = pstr->raw_stop - idx + offset;
- pstr->offsets_needed = 0;
- while (mid > 0 && pstr->offsets[mid - 1] == offset)
- --mid;
- while (mid < pstr->valid_len)
- if (pstr->wcs[mid] != WEOF)
- break;
- else
- ++mid;
- if (mid == pstr->valid_len)
- pstr->valid_len = 0;
- else
- {
- pstr->valid_len = pstr->offsets[mid] - offset;
- if (pstr->valid_len)
- {
- for (low = 0; low < pstr->valid_len; ++low)
- pstr->wcs[low] = WEOF;
- memset (pstr->mbs, 255, pstr->valid_len);
- }
- }
- pstr->valid_raw_len = pstr->valid_len;
- }
- }
- else
-#endif
- {
- pstr->tip_context = re_string_context_at (pstr, offset - 1,
- eflags);
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- memmove (pstr->wcs, pstr->wcs + offset,
- (pstr->valid_len - offset) * sizeof (wint_t));
-#endif /* RE_ENABLE_I18N */
- if (BE (pstr->mbs_allocated, 0))
- memmove (pstr->mbs, pstr->mbs + offset,
- pstr->valid_len - offset);
- pstr->valid_len -= offset;
- pstr->valid_raw_len -= offset;
-#if DEBUG
- assert (pstr->valid_len > 0);
-#endif
- }
- }
- else
- {
- /* No, skip all characters until IDX. */
- int prev_valid_len = pstr->valid_len;
-
-#ifdef RE_ENABLE_I18N
- if (BE (pstr->offsets_needed, 0))
- {
- pstr->len = pstr->raw_len - idx + offset;
- pstr->stop = pstr->raw_stop - idx + offset;
- pstr->offsets_needed = 0;
- }
-#endif
- pstr->valid_len = 0;
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- {
- int wcs_idx;
- wint_t wc = WEOF;
-
- if (pstr->is_utf8)
- {
- const unsigned char *raw, *p, *q, *end;
-
- /* Special case UTF-8. Multi-byte chars start with any
- byte other than 0x80 - 0xbf. */
- raw = pstr->raw_mbs + pstr->raw_mbs_idx;
- end = raw + (offset - pstr->mb_cur_max);
- if (end < pstr->raw_mbs)
- end = pstr->raw_mbs;
- p = raw + offset - 1;
-#ifdef _LIBC
- /* We know the wchar_t encoding is UCS4, so for the simple
- case, ASCII characters, skip the conversion step. */
- if (isascii (*p) && BE (pstr->trans == NULL, 1))
- {
- memset (&pstr->cur_state, '\0', sizeof (mbstate_t));
- /* pstr->valid_len = 0; */
- wc = (wchar_t) *p;
- }
- else
-#endif
- for (; p >= end; --p)
- if ((*p & 0xc0) != 0x80)
- {
- mbstate_t cur_state;
- wchar_t wc2;
- int mlen = raw + pstr->len - p;
- unsigned char buf[6];
- size_t mbclen;
-
- q = p;
- if (BE (pstr->trans != NULL, 0))
- {
- int i = mlen < 6 ? mlen : 6;
- while (--i >= 0)
- buf[i] = pstr->trans[p[i]];
- q = buf;
- }
- /* XXX Don't use mbrtowc, we know which conversion
- to use (UTF-8 -> UCS4). */
- memset (&cur_state, 0, sizeof (cur_state));
- mbclen = mbrtowc (&wc2, (const char *) p, mlen,
- &cur_state);
- if (raw + offset - p <= mbclen
- && mbclen < (size_t) -2)
- {
- memset (&pstr->cur_state, '\0',
- sizeof (mbstate_t));
- pstr->valid_len = mbclen - (raw + offset - p);
- wc = wc2;
- }
- break;
- }
- }
-
- if (wc == WEOF)
- pstr->valid_len = re_string_skip_chars (pstr, idx, &wc) - idx;
- if (wc == WEOF)
- pstr->tip_context
- = re_string_context_at (pstr, prev_valid_len - 1, eflags);
- else
- pstr->tip_context = ((BE (pstr->word_ops_used != 0, 0)
- && IS_WIDE_WORD_CHAR (wc))
- ? CONTEXT_WORD
- : ((IS_WIDE_NEWLINE (wc)
- && pstr->newline_anchor)
- ? CONTEXT_NEWLINE : 0));
- if (BE (pstr->valid_len, 0))
- {
- for (wcs_idx = 0; wcs_idx < pstr->valid_len; ++wcs_idx)
- pstr->wcs[wcs_idx] = WEOF;
- if (pstr->mbs_allocated)
- memset (pstr->mbs, 255, pstr->valid_len);
- }
- pstr->valid_raw_len = pstr->valid_len;
- }
- else
-#endif /* RE_ENABLE_I18N */
- {
- int c = pstr->raw_mbs[pstr->raw_mbs_idx + offset - 1];
- pstr->valid_raw_len = 0;
- if (pstr->trans)
- c = pstr->trans[c];
- pstr->tip_context = (bitset_contain (pstr->word_char, c)
- ? CONTEXT_WORD
- : ((IS_NEWLINE (c) && pstr->newline_anchor)
- ? CONTEXT_NEWLINE : 0));
- }
- }
- if (!BE (pstr->mbs_allocated, 0))
- pstr->mbs += offset;
- }
- pstr->raw_mbs_idx = idx;
- pstr->len -= offset;
- pstr->stop -= offset;
-
- /* Then build the buffers. */
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- {
- if (pstr->icase)
- {
- reg_errcode_t ret = build_wcs_upper_buffer (pstr);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- }
- else
- build_wcs_buffer (pstr);
- }
- else
-#endif /* RE_ENABLE_I18N */
- if (BE (pstr->mbs_allocated, 0))
- {
- if (pstr->icase)
- build_upper_buffer (pstr);
- else if (pstr->trans != NULL)
- re_string_translate_buffer (pstr);
- }
- else
- pstr->valid_len = pstr->len;
-
- pstr->cur_idx = 0;
- return REG_NOERROR;
-}
-
-static unsigned char
-internal_function __attribute ((pure))
-re_string_peek_byte_case (const re_string_t *pstr, int idx)
-{
- int ch, off;
-
- /* Handle the common (easiest) cases first. */
- if (BE (!pstr->mbs_allocated, 1))
- return re_string_peek_byte (pstr, idx);
-
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1
- && ! re_string_is_single_byte_char (pstr, pstr->cur_idx + idx))
- return re_string_peek_byte (pstr, idx);
-#endif
-
- off = pstr->cur_idx + idx;
-#ifdef RE_ENABLE_I18N
- if (pstr->offsets_needed)
- off = pstr->offsets[off];
-#endif
-
- ch = pstr->raw_mbs[pstr->raw_mbs_idx + off];
-
-#ifdef RE_ENABLE_I18N
- /* Ensure that e.g. for tr_TR.UTF-8 BACKSLASH DOTLESS SMALL LETTER I
- this function returns CAPITAL LETTER I instead of first byte of
- DOTLESS SMALL LETTER I. The latter would confuse the parser,
- since peek_byte_case doesn't advance cur_idx in any way. */
- if (pstr->offsets_needed && !isascii (ch))
- return re_string_peek_byte (pstr, idx);
-#endif
-
- return ch;
-}
-
-static unsigned char
-internal_function __attribute ((pure))
-re_string_fetch_byte_case (re_string_t *pstr)
-{
- if (BE (!pstr->mbs_allocated, 1))
- return re_string_fetch_byte (pstr);
-
-#ifdef RE_ENABLE_I18N
- if (pstr->offsets_needed)
- {
- int off, ch;
-
- /* For tr_TR.UTF-8 [[:islower:]] there is
- [[: CAPITAL LETTER I WITH DOT lower:]] in mbs. Skip
- in that case the whole multi-byte character and return
- the original letter. On the other side, with
- [[: DOTLESS SMALL LETTER I return [[:I, as doing
- anything else would complicate things too much. */
-
- if (!re_string_first_byte (pstr, pstr->cur_idx))
- return re_string_fetch_byte (pstr);
-
- off = pstr->offsets[pstr->cur_idx];
- ch = pstr->raw_mbs[pstr->raw_mbs_idx + off];
-
- if (! isascii (ch))
- return re_string_fetch_byte (pstr);
-
- re_string_skip_bytes (pstr,
- re_string_char_size_at (pstr, pstr->cur_idx));
- return ch;
- }
-#endif
-
- return pstr->raw_mbs[pstr->raw_mbs_idx + pstr->cur_idx++];
-}
-
-static void
-internal_function
-re_string_destruct (re_string_t *pstr)
-{
-#ifdef RE_ENABLE_I18N
- re_free (pstr->wcs);
- re_free (pstr->offsets);
-#endif /* RE_ENABLE_I18N */
- if (pstr->mbs_allocated)
- re_free (pstr->mbs);
-}
-
-/* Return the context at IDX in INPUT. */
-
-static unsigned int
-internal_function
-re_string_context_at (const re_string_t *input, int idx, int eflags)
-{
- int c;
- if (BE (idx < 0, 0))
- /* In this case, we use the value stored in input->tip_context,
- since we can't know the character in input->mbs[-1] here. */
- return input->tip_context;
- if (BE (idx == input->len, 0))
- return ((eflags & REG_NOTEOL) ? CONTEXT_ENDBUF
- : CONTEXT_NEWLINE | CONTEXT_ENDBUF);
-#ifdef RE_ENABLE_I18N
- if (input->mb_cur_max > 1)
- {
- wint_t wc;
- int wc_idx = idx;
- while(input->wcs[wc_idx] == WEOF)
- {
-#ifdef DEBUG
- /* It must not happen. */
- assert (wc_idx >= 0);
-#endif
- --wc_idx;
- if (wc_idx < 0)
- return input->tip_context;
- }
- wc = input->wcs[wc_idx];
- if (BE (input->word_ops_used != 0, 0) && IS_WIDE_WORD_CHAR (wc))
- return CONTEXT_WORD;
- return (IS_WIDE_NEWLINE (wc) && input->newline_anchor
- ? CONTEXT_NEWLINE : 0);
- }
- else
-#endif
- {
- c = re_string_byte_at (input, idx);
- if (bitset_contain (input->word_char, c))
- return CONTEXT_WORD;
- return IS_NEWLINE (c) && input->newline_anchor ? CONTEXT_NEWLINE : 0;
- }
-}
-
-/* Functions for set operation. */
-
-static reg_errcode_t
-internal_function
-re_node_set_alloc (re_node_set *set, int size)
-{
- set->alloc = size;
- set->nelem = 0;
- set->elems = re_malloc (int, size);
- if (BE (set->elems == NULL, 0))
- return REG_ESPACE;
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-re_node_set_init_1 (re_node_set *set, int elem)
-{
- set->alloc = 1;
- set->nelem = 1;
- set->elems = re_malloc (int, 1);
- if (BE (set->elems == NULL, 0))
- {
- set->alloc = set->nelem = 0;
- return REG_ESPACE;
- }
- set->elems[0] = elem;
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-re_node_set_init_2 (re_node_set *set, int elem1, int elem2)
-{
- set->alloc = 2;
- set->elems = re_malloc (int, 2);
- if (BE (set->elems == NULL, 0))
- return REG_ESPACE;
- if (elem1 == elem2)
- {
- set->nelem = 1;
- set->elems[0] = elem1;
- }
- else
- {
- set->nelem = 2;
- if (elem1 < elem2)
- {
- set->elems[0] = elem1;
- set->elems[1] = elem2;
- }
- else
- {
- set->elems[0] = elem2;
- set->elems[1] = elem1;
- }
- }
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-re_node_set_init_copy (re_node_set *dest, const re_node_set *src)
-{
- dest->nelem = src->nelem;
- if (src->nelem > 0)
- {
- dest->alloc = dest->nelem;
- dest->elems = re_malloc (int, dest->alloc);
- if (BE (dest->elems == NULL, 0))
- {
- dest->alloc = dest->nelem = 0;
- return REG_ESPACE;
- }
- memcpy (dest->elems, src->elems, src->nelem * sizeof (int));
- }
- else
- re_node_set_init_empty (dest);
- return REG_NOERROR;
-}
-
-/* Calculate the intersection of the sets SRC1 and SRC2. And merge it to
- DEST. Return value indicate the error code or REG_NOERROR if succeeded.
- Note: We assume dest->elems is NULL, when dest->alloc is 0. */
-
-static reg_errcode_t
-internal_function
-re_node_set_add_intersect (re_node_set *dest, const re_node_set *src1,
- const re_node_set *src2)
-{
- int i1, i2, is, id, delta, sbase;
- if (src1->nelem == 0 || src2->nelem == 0)
- return REG_NOERROR;
-
- /* We need dest->nelem + 2 * elems_in_intersection; this is a
- conservative estimate. */
- if (src1->nelem + src2->nelem + dest->nelem > dest->alloc)
- {
- int new_alloc = src1->nelem + src2->nelem + dest->alloc;
- int *new_elems = re_realloc (dest->elems, int, new_alloc);
- if (BE (new_elems == NULL, 0))
- return REG_ESPACE;
- dest->elems = new_elems;
- dest->alloc = new_alloc;
- }
-
- /* Find the items in the intersection of SRC1 and SRC2, and copy
- into the top of DEST those that are not already in DEST itself. */
- sbase = dest->nelem + src1->nelem + src2->nelem;
- i1 = src1->nelem - 1;
- i2 = src2->nelem - 1;
- id = dest->nelem - 1;
- for (;;)
- {
- if (src1->elems[i1] == src2->elems[i2])
- {
- /* Try to find the item in DEST. Maybe we could binary search? */
- while (id >= 0 && dest->elems[id] > src1->elems[i1])
- --id;
-
- if (id < 0 || dest->elems[id] != src1->elems[i1])
- dest->elems[--sbase] = src1->elems[i1];
-
- if (--i1 < 0 || --i2 < 0)
- break;
- }
-
- /* Lower the highest of the two items. */
- else if (src1->elems[i1] < src2->elems[i2])
- {
- if (--i2 < 0)
- break;
- }
- else
- {
- if (--i1 < 0)
- break;
- }
- }
-
- id = dest->nelem - 1;
- is = dest->nelem + src1->nelem + src2->nelem - 1;
- delta = is - sbase + 1;
-
- /* Now copy. When DELTA becomes zero, the remaining
- DEST elements are already in place; this is more or
- less the same loop that is in re_node_set_merge. */
- dest->nelem += delta;
- if (delta > 0 && id >= 0)
- for (;;)
- {
- if (dest->elems[is] > dest->elems[id])
- {
- /* Copy from the top. */
- dest->elems[id + delta--] = dest->elems[is--];
- if (delta == 0)
- break;
- }
- else
- {
- /* Slide from the bottom. */
- dest->elems[id + delta] = dest->elems[id];
- if (--id < 0)
- break;
- }
- }
-
- /* Copy remaining SRC elements. */
- memcpy (dest->elems, dest->elems + sbase, delta * sizeof (int));
-
- return REG_NOERROR;
-}
-
-/* Calculate the union set of the sets SRC1 and SRC2. And store it to
- DEST. Return value indicate the error code or REG_NOERROR if succeeded. */
-
-static reg_errcode_t
-internal_function
-re_node_set_init_union (re_node_set *dest, const re_node_set *src1,
- const re_node_set *src2)
-{
- int i1, i2, id;
- if (src1 != NULL && src1->nelem > 0 && src2 != NULL && src2->nelem > 0)
- {
- dest->alloc = src1->nelem + src2->nelem;
- dest->elems = re_malloc (int, dest->alloc);
- if (BE (dest->elems == NULL, 0))
- return REG_ESPACE;
- }
- else
- {
- if (src1 != NULL && src1->nelem > 0)
- return re_node_set_init_copy (dest, src1);
- else if (src2 != NULL && src2->nelem > 0)
- return re_node_set_init_copy (dest, src2);
- else
- re_node_set_init_empty (dest);
- return REG_NOERROR;
- }
- for (i1 = i2 = id = 0 ; i1 < src1->nelem && i2 < src2->nelem ;)
- {
- if (src1->elems[i1] > src2->elems[i2])
- {
- dest->elems[id++] = src2->elems[i2++];
- continue;
- }
- if (src1->elems[i1] == src2->elems[i2])
- ++i2;
- dest->elems[id++] = src1->elems[i1++];
- }
- if (i1 < src1->nelem)
- {
- memcpy (dest->elems + id, src1->elems + i1,
- (src1->nelem - i1) * sizeof (int));
- id += src1->nelem - i1;
- }
- else if (i2 < src2->nelem)
- {
- memcpy (dest->elems + id, src2->elems + i2,
- (src2->nelem - i2) * sizeof (int));
- id += src2->nelem - i2;
- }
- dest->nelem = id;
- return REG_NOERROR;
-}
-
-/* Calculate the union set of the sets DEST and SRC. And store it to
- DEST. Return value indicate the error code or REG_NOERROR if succeeded. */
-
-static reg_errcode_t
-internal_function
-re_node_set_merge (re_node_set *dest, const re_node_set *src)
-{
- int is, id, sbase, delta;
- if (src == NULL || src->nelem == 0)
- return REG_NOERROR;
- if (dest->alloc < 2 * src->nelem + dest->nelem)
- {
- int new_alloc = 2 * (src->nelem + dest->alloc);
- int *new_buffer = re_realloc (dest->elems, int, new_alloc);
- if (BE (new_buffer == NULL, 0))
- return REG_ESPACE;
- dest->elems = new_buffer;
- dest->alloc = new_alloc;
- }
-
- if (BE (dest->nelem == 0, 0))
- {
- dest->nelem = src->nelem;
- memcpy (dest->elems, src->elems, src->nelem * sizeof (int));
- return REG_NOERROR;
- }
-
- /* Copy into the top of DEST the items of SRC that are not
- found in DEST. Maybe we could binary search in DEST? */
- for (sbase = dest->nelem + 2 * src->nelem,
- is = src->nelem - 1, id = dest->nelem - 1; is >= 0 && id >= 0; )
- {
- if (dest->elems[id] == src->elems[is])
- is--, id--;
- else if (dest->elems[id] < src->elems[is])
- dest->elems[--sbase] = src->elems[is--];
- else /* if (dest->elems[id] > src->elems[is]) */
- --id;
- }
-
- if (is >= 0)
- {
- /* If DEST is exhausted, the remaining items of SRC must be unique. */
- sbase -= is + 1;
- memcpy (dest->elems + sbase, src->elems, (is + 1) * sizeof (int));
- }
-
- id = dest->nelem - 1;
- is = dest->nelem + 2 * src->nelem - 1;
- delta = is - sbase + 1;
- if (delta == 0)
- return REG_NOERROR;
-
- /* Now copy. When DELTA becomes zero, the remaining
- DEST elements are already in place. */
- dest->nelem += delta;
- for (;;)
- {
- if (dest->elems[is] > dest->elems[id])
- {
- /* Copy from the top. */
- dest->elems[id + delta--] = dest->elems[is--];
- if (delta == 0)
- break;
- }
- else
- {
- /* Slide from the bottom. */
- dest->elems[id + delta] = dest->elems[id];
- if (--id < 0)
- {
- /* Copy remaining SRC elements. */
- memcpy (dest->elems, dest->elems + sbase,
- delta * sizeof (int));
- break;
- }
- }
- }
-
- return REG_NOERROR;
-}
-
-/* Insert the new element ELEM to the re_node_set* SET.
- SET should not already have ELEM.
- return -1 if an error is occured, return 1 otherwise. */
-
-static int
-internal_function
-re_node_set_insert (re_node_set *set, int elem)
-{
- int idx;
- /* In case the set is empty. */
- if (set->alloc == 0)
- {
- if (BE (re_node_set_init_1 (set, elem) == REG_NOERROR, 1))
- return 1;
- else
- return -1;
- }
-
- if (BE (set->nelem, 0) == 0)
- {
- /* We already guaranteed above that set->alloc != 0. */
- set->elems[0] = elem;
- ++set->nelem;
- return 1;
- }
-
- /* Realloc if we need. */
- if (set->alloc == set->nelem)
- {
- int *new_elems;
- set->alloc = set->alloc * 2;
- new_elems = re_realloc (set->elems, int, set->alloc);
- if (BE (new_elems == NULL, 0))
- return -1;
- set->elems = new_elems;
- }
-
- /* Move the elements which follows the new element. Test the
- first element separately to skip a check in the inner loop. */
- if (elem < set->elems[0])
- {
- idx = 0;
- for (idx = set->nelem; idx > 0; idx--)
- set->elems[idx] = set->elems[idx - 1];
- }
- else
- {
- for (idx = set->nelem; set->elems[idx - 1] > elem; idx--)
- set->elems[idx] = set->elems[idx - 1];
- }
-
- /* Insert the new element. */
- set->elems[idx] = elem;
- ++set->nelem;
- return 1;
-}
-
-/* Insert the new element ELEM to the re_node_set* SET.
- SET should not already have any element greater than or equal to ELEM.
- Return -1 if an error is occured, return 1 otherwise. */
-
-static int
-internal_function
-re_node_set_insert_last (re_node_set *set, int elem)
-{
- /* Realloc if we need. */
- if (set->alloc == set->nelem)
- {
- int *new_elems;
- set->alloc = (set->alloc + 1) * 2;
- new_elems = re_realloc (set->elems, int, set->alloc);
- if (BE (new_elems == NULL, 0))
- return -1;
- set->elems = new_elems;
- }
-
- /* Insert the new element. */
- set->elems[set->nelem++] = elem;
- return 1;
-}
-
-/* Compare two node sets SET1 and SET2.
- return 1 if SET1 and SET2 are equivalent, return 0 otherwise. */
-
-static int
-internal_function __attribute ((pure))
-re_node_set_compare (const re_node_set *set1, const re_node_set *set2)
-{
- int i;
- if (set1 == NULL || set2 == NULL || set1->nelem != set2->nelem)
- return 0;
- for (i = set1->nelem ; --i >= 0 ; )
- if (set1->elems[i] != set2->elems[i])
- return 0;
- return 1;
-}
-
-/* Return (idx + 1) if SET contains the element ELEM, return 0 otherwise. */
-
-static int
-internal_function __attribute ((pure))
-re_node_set_contains (const re_node_set *set, int elem)
-{
- unsigned int idx, right, mid;
- if (set->nelem <= 0)
- return 0;
-
- /* Binary search the element. */
- idx = 0;
- right = set->nelem - 1;
- while (idx < right)
- {
- mid = (idx + right) / 2;
- if (set->elems[mid] < elem)
- idx = mid + 1;
- else
- right = mid;
- }
- return set->elems[idx] == elem ? idx + 1 : 0;
-}
-
-static void
-internal_function
-re_node_set_remove_at (re_node_set *set, int idx)
-{
- if (idx < 0 || idx >= set->nelem)
- return;
- --set->nelem;
- for (; idx < set->nelem; idx++)
- set->elems[idx] = set->elems[idx + 1];
-}
-
-
-/* Add the token TOKEN to dfa->nodes, and return the index of the token.
- Or return -1, if an error will be occured. */
-
-static int
-internal_function
-re_dfa_add_node (re_dfa_t *dfa, re_token_t token)
-{
- int type = token.type;
- if (BE (dfa->nodes_len >= dfa->nodes_alloc, 0))
- {
- size_t new_nodes_alloc = dfa->nodes_alloc * 2;
- int *new_nexts, *new_indices;
- re_node_set *new_edests, *new_eclosures;
- re_token_t *new_nodes;
-
- /* Avoid overflows. */
- if (BE (new_nodes_alloc < dfa->nodes_alloc, 0))
- return -1;
-
- new_nodes = re_realloc (dfa->nodes, re_token_t, new_nodes_alloc);
- if (BE (new_nodes == NULL, 0))
- return -1;
- dfa->nodes = new_nodes;
- new_nexts = re_realloc (dfa->nexts, int, new_nodes_alloc);
- new_indices = re_realloc (dfa->org_indices, int, new_nodes_alloc);
- new_edests = re_realloc (dfa->edests, re_node_set, new_nodes_alloc);
- new_eclosures = re_realloc (dfa->eclosures, re_node_set, new_nodes_alloc);
- if (BE (new_nexts == NULL || new_indices == NULL
- || new_edests == NULL || new_eclosures == NULL, 0))
- return -1;
- dfa->nexts = new_nexts;
- dfa->org_indices = new_indices;
- dfa->edests = new_edests;
- dfa->eclosures = new_eclosures;
- dfa->nodes_alloc = new_nodes_alloc;
- }
- dfa->nodes[dfa->nodes_len] = token;
- dfa->nodes[dfa->nodes_len].constraint = 0;
-#ifdef RE_ENABLE_I18N
- dfa->nodes[dfa->nodes_len].accept_mb =
- (type == OP_PERIOD && dfa->mb_cur_max > 1) || type == COMPLEX_BRACKET;
-#endif
- dfa->nexts[dfa->nodes_len] = -1;
- re_node_set_init_empty (dfa->edests + dfa->nodes_len);
- re_node_set_init_empty (dfa->eclosures + dfa->nodes_len);
- return dfa->nodes_len++;
-}
-
-static inline unsigned int
-internal_function
-calc_state_hash (const re_node_set *nodes, unsigned int context)
-{
- unsigned int hash = nodes->nelem + context;
- int i;
- for (i = 0 ; i < nodes->nelem ; i++)
- hash += nodes->elems[i];
- return hash;
-}
-
-/* Search for the state whose node_set is equivalent to NODES.
- Return the pointer to the state, if we found it in the DFA.
- Otherwise create the new one and return it. In case of an error
- return NULL and set the error code in ERR.
- Note: - We assume NULL as the invalid state, then it is possible that
- return value is NULL and ERR is REG_NOERROR.
- - We never return non-NULL value in case of any errors, it is for
- optimization. */
-
-static re_dfastate_t *
-internal_function
-re_acquire_state (reg_errcode_t *err, const re_dfa_t *dfa,
- const re_node_set *nodes)
-{
- unsigned int hash;
- re_dfastate_t *new_state;
- struct re_state_table_entry *spot;
- int i;
- if (BE (nodes->nelem == 0, 0))
- {
- *err = REG_NOERROR;
- return NULL;
- }
- hash = calc_state_hash (nodes, 0);
- spot = dfa->state_table + (hash & dfa->state_hash_mask);
-
- for (i = 0 ; i < spot->num ; i++)
- {
- re_dfastate_t *state = spot->array[i];
- if (hash != state->hash)
- continue;
- if (re_node_set_compare (&state->nodes, nodes))
- return state;
- }
-
- /* There are no appropriate state in the dfa, create the new one. */
- new_state = create_ci_newstate (dfa, nodes, hash);
- if (BE (new_state == NULL, 0))
- *err = REG_ESPACE;
-
- return new_state;
-}
-
-/* Search for the state whose node_set is equivalent to NODES and
- whose context is equivalent to CONTEXT.
- Return the pointer to the state, if we found it in the DFA.
- Otherwise create the new one and return it. In case of an error
- return NULL and set the error code in ERR.
- Note: - We assume NULL as the invalid state, then it is possible that
- return value is NULL and ERR is REG_NOERROR.
- - We never return non-NULL value in case of any errors, it is for
- optimization. */
-
-static re_dfastate_t *
-internal_function
-re_acquire_state_context (reg_errcode_t *err, const re_dfa_t *dfa,
- const re_node_set *nodes, unsigned int context)
-{
- unsigned int hash;
- re_dfastate_t *new_state;
- struct re_state_table_entry *spot;
- int i;
- if (nodes->nelem == 0)
- {
- *err = REG_NOERROR;
- return NULL;
- }
- hash = calc_state_hash (nodes, context);
- spot = dfa->state_table + (hash & dfa->state_hash_mask);
-
- for (i = 0 ; i < spot->num ; i++)
- {
- re_dfastate_t *state = spot->array[i];
- if (state->hash == hash
- && state->context == context
- && re_node_set_compare (state->entrance_nodes, nodes))
- return state;
- }
- /* There are no appropriate state in `dfa', create the new one. */
- new_state = create_cd_newstate (dfa, nodes, context, hash);
- if (BE (new_state == NULL, 0))
- *err = REG_ESPACE;
-
- return new_state;
-}
-
-/* Finish initialization of the new state NEWSTATE, and using its hash value
- HASH put in the appropriate bucket of DFA's state table. Return value
- indicates the error code if failed. */
-
-static reg_errcode_t
-register_state (const re_dfa_t *dfa, re_dfastate_t *newstate,
- unsigned int hash)
-{
- struct re_state_table_entry *spot;
- reg_errcode_t err;
- int i;
-
- newstate->hash = hash;
- err = re_node_set_alloc (&newstate->non_eps_nodes, newstate->nodes.nelem);
- if (BE (err != REG_NOERROR, 0))
- return REG_ESPACE;
- for (i = 0; i < newstate->nodes.nelem; i++)
- {
- int elem = newstate->nodes.elems[i];
- if (!IS_EPSILON_NODE (dfa->nodes[elem].type))
- re_node_set_insert_last (&newstate->non_eps_nodes, elem);
- }
-
- spot = dfa->state_table + (hash & dfa->state_hash_mask);
- if (BE (spot->alloc <= spot->num, 0))
- {
- int new_alloc = 2 * spot->num + 2;
- re_dfastate_t **new_array = re_realloc (spot->array, re_dfastate_t *,
- new_alloc);
- if (BE (new_array == NULL, 0))
- return REG_ESPACE;
- spot->array = new_array;
- spot->alloc = new_alloc;
- }
- spot->array[spot->num++] = newstate;
- return REG_NOERROR;
-}
-
-static void
-free_state (re_dfastate_t *state)
-{
- re_node_set_free (&state->non_eps_nodes);
- re_node_set_free (&state->inveclosure);
- if (state->entrance_nodes != &state->nodes)
- {
- re_node_set_free (state->entrance_nodes);
- re_free (state->entrance_nodes);
- }
- re_node_set_free (&state->nodes);
- re_free (state->word_trtable);
- re_free (state->trtable);
- re_free (state);
-}
-
-/* Create the new state which is independ of contexts.
- Return the new state if succeeded, otherwise return NULL. */
-
-static re_dfastate_t *
-internal_function
-create_ci_newstate (const re_dfa_t *dfa, const re_node_set *nodes,
- unsigned int hash)
-{
- int i;
- reg_errcode_t err;
- re_dfastate_t *newstate;
-
- newstate = (re_dfastate_t *) calloc (sizeof (re_dfastate_t), 1);
- if (BE (newstate == NULL, 0))
- return NULL;
- err = re_node_set_init_copy (&newstate->nodes, nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_free (newstate);
- return NULL;
- }
-
- newstate->entrance_nodes = &newstate->nodes;
- for (i = 0 ; i < nodes->nelem ; i++)
- {
- re_token_t *node = dfa->nodes + nodes->elems[i];
- re_token_type_t type = node->type;
- if (type == CHARACTER && !node->constraint)
- continue;
-#ifdef RE_ENABLE_I18N
- newstate->accept_mb |= node->accept_mb;
-#endif /* RE_ENABLE_I18N */
-
- /* If the state has the halt node, the state is a halt state. */
- if (type == END_OF_RE)
- newstate->halt = 1;
- else if (type == OP_BACK_REF)
- newstate->has_backref = 1;
- else if (type == ANCHOR || node->constraint)
- newstate->has_constraint = 1;
- }
- err = register_state (dfa, newstate, hash);
- if (BE (err != REG_NOERROR, 0))
- {
- free_state (newstate);
- newstate = NULL;
- }
- return newstate;
-}
-
-/* Create the new state which is depend on the context CONTEXT.
- Return the new state if succeeded, otherwise return NULL. */
-
-static re_dfastate_t *
-internal_function
-create_cd_newstate (const re_dfa_t *dfa, const re_node_set *nodes,
- unsigned int context, unsigned int hash)
-{
- int i, nctx_nodes = 0;
- reg_errcode_t err;
- re_dfastate_t *newstate;
-
- newstate = (re_dfastate_t *) calloc (sizeof (re_dfastate_t), 1);
- if (BE (newstate == NULL, 0))
- return NULL;
- err = re_node_set_init_copy (&newstate->nodes, nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_free (newstate);
- return NULL;
- }
-
- newstate->context = context;
- newstate->entrance_nodes = &newstate->nodes;
-
- for (i = 0 ; i < nodes->nelem ; i++)
- {
- unsigned int constraint = 0;
- re_token_t *node = dfa->nodes + nodes->elems[i];
- re_token_type_t type = node->type;
- if (node->constraint)
- constraint = node->constraint;
-
- if (type == CHARACTER && !constraint)
- continue;
-#ifdef RE_ENABLE_I18N
- newstate->accept_mb |= node->accept_mb;
-#endif /* RE_ENABLE_I18N */
-
- /* If the state has the halt node, the state is a halt state. */
- if (type == END_OF_RE)
- newstate->halt = 1;
- else if (type == OP_BACK_REF)
- newstate->has_backref = 1;
- else if (type == ANCHOR)
- constraint = node->opr.ctx_type;
-
- if (constraint)
- {
- if (newstate->entrance_nodes == &newstate->nodes)
- {
- newstate->entrance_nodes = re_malloc (re_node_set, 1);
- if (BE (newstate->entrance_nodes == NULL, 0))
- {
- free_state (newstate);
- return NULL;
- }
- re_node_set_init_copy (newstate->entrance_nodes, nodes);
- nctx_nodes = 0;
- newstate->has_constraint = 1;
- }
-
- if (NOT_SATISFY_PREV_CONSTRAINT (constraint,context))
- {
- re_node_set_remove_at (&newstate->nodes, i - nctx_nodes);
- ++nctx_nodes;
- }
- }
- }
- err = register_state (dfa, newstate, hash);
- if (BE (err != REG_NOERROR, 0))
- {
- free_state (newstate);
- newstate = NULL;
- }
- return newstate;
-}
-
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* GKINCLUDE #include "regcomp.c" */
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* Extended regular expression matching and search library.
- Copyright (C) 2002,2003,2004,2005,2006 Free Software Foundation, Inc.
- This file is part of the GNU C Library.
- Contributed by Isamu Hasegawa <isamu@yamato.ibm.com>.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-static reg_errcode_t re_compile_internal (regex_t *preg, const char * pattern,
- size_t length, reg_syntax_t syntax);
-static void re_compile_fastmap_iter (regex_t *bufp,
- const re_dfastate_t *init_state,
- char *fastmap);
-static reg_errcode_t init_dfa (re_dfa_t *dfa, size_t pat_len);
-#ifdef RE_ENABLE_I18N
-static void free_charset (re_charset_t *cset);
-#endif /* RE_ENABLE_I18N */
-static void free_workarea_compile (regex_t *preg);
-static reg_errcode_t create_initial_state (re_dfa_t *dfa);
-#ifdef RE_ENABLE_I18N
-static void optimize_utf8 (re_dfa_t *dfa);
-#endif
-static reg_errcode_t analyze (regex_t *preg);
-static reg_errcode_t preorder (bin_tree_t *root,
- reg_errcode_t (fn (void *, bin_tree_t *)),
- void *extra);
-static reg_errcode_t postorder (bin_tree_t *root,
- reg_errcode_t (fn (void *, bin_tree_t *)),
- void *extra);
-static reg_errcode_t optimize_subexps (void *extra, bin_tree_t *node);
-static reg_errcode_t lower_subexps (void *extra, bin_tree_t *node);
-static bin_tree_t *lower_subexp (reg_errcode_t *err, regex_t *preg,
- bin_tree_t *node);
-static reg_errcode_t calc_first (void *extra, bin_tree_t *node);
-static reg_errcode_t calc_next (void *extra, bin_tree_t *node);
-static reg_errcode_t link_nfa_nodes (void *extra, bin_tree_t *node);
-static int duplicate_node (re_dfa_t *dfa, int org_idx, unsigned int constraint);
-static int search_duplicated_node (const re_dfa_t *dfa, int org_node,
- unsigned int constraint);
-static reg_errcode_t calc_eclosure (re_dfa_t *dfa);
-static reg_errcode_t calc_eclosure_iter (re_node_set *new_set, re_dfa_t *dfa,
- int node, int root);
-static reg_errcode_t calc_inveclosure (re_dfa_t *dfa);
-static int fetch_number (re_string_t *input, re_token_t *token,
- reg_syntax_t syntax);
-static int peek_token (re_token_t *token, re_string_t *input,
- reg_syntax_t syntax) internal_function;
-static bin_tree_t *parse (re_string_t *regexp, regex_t *preg,
- reg_syntax_t syntax, reg_errcode_t *err);
-static bin_tree_t *parse_reg_exp (re_string_t *regexp, regex_t *preg,
- re_token_t *token, reg_syntax_t syntax,
- int nest, reg_errcode_t *err);
-static bin_tree_t *parse_branch (re_string_t *regexp, regex_t *preg,
- re_token_t *token, reg_syntax_t syntax,
- int nest, reg_errcode_t *err);
-static bin_tree_t *parse_expression (re_string_t *regexp, regex_t *preg,
- re_token_t *token, reg_syntax_t syntax,
- int nest, reg_errcode_t *err);
-static bin_tree_t *parse_sub_exp (re_string_t *regexp, regex_t *preg,
- re_token_t *token, reg_syntax_t syntax,
- int nest, reg_errcode_t *err);
-static bin_tree_t *parse_dup_op (bin_tree_t *dup_elem, re_string_t *regexp,
- re_dfa_t *dfa, re_token_t *token,
- reg_syntax_t syntax, reg_errcode_t *err);
-static bin_tree_t *parse_bracket_exp (re_string_t *regexp, re_dfa_t *dfa,
- re_token_t *token, reg_syntax_t syntax,
- reg_errcode_t *err);
-static reg_errcode_t parse_bracket_element (bracket_elem_t *elem,
- re_string_t *regexp,
- re_token_t *token, int token_len,
- re_dfa_t *dfa,
- reg_syntax_t syntax,
- int accept_hyphen);
-static reg_errcode_t parse_bracket_symbol (bracket_elem_t *elem,
- re_string_t *regexp,
- re_token_t *token);
-#ifdef RE_ENABLE_I18N
-static reg_errcode_t build_equiv_class (bitset_t sbcset,
- re_charset_t *mbcset,
- int *equiv_class_alloc,
- const unsigned char *name);
-static reg_errcode_t build_charclass (RE_TRANSLATE_TYPE trans,
- bitset_t sbcset,
- re_charset_t *mbcset,
- int *char_class_alloc,
- const unsigned char *class_name,
- reg_syntax_t syntax);
-#else /* not RE_ENABLE_I18N */
-static reg_errcode_t build_equiv_class (bitset_t sbcset,
- const unsigned char *name);
-static reg_errcode_t build_charclass (RE_TRANSLATE_TYPE trans,
- bitset_t sbcset,
- const unsigned char *class_name,
- reg_syntax_t syntax);
-#endif /* not RE_ENABLE_I18N */
-static bin_tree_t *build_charclass_op (re_dfa_t *dfa,
- RE_TRANSLATE_TYPE trans,
- const unsigned char *class_name,
- const unsigned char *extra,
- int non_match, reg_errcode_t *err);
-static bin_tree_t *create_tree (re_dfa_t *dfa,
- bin_tree_t *left, bin_tree_t *right,
- re_token_type_t type);
-static bin_tree_t *create_token_tree (re_dfa_t *dfa,
- bin_tree_t *left, bin_tree_t *right,
- const re_token_t *token);
-static bin_tree_t *duplicate_tree (const bin_tree_t *src, re_dfa_t *dfa);
-static void free_token (re_token_t *node);
-static reg_errcode_t free_tree (void *extra, bin_tree_t *node);
-static reg_errcode_t mark_opt_subexp (void *extra, bin_tree_t *node);
-
-/* This table gives an error message for each of the error codes listed
- in regex.h. Obviously the order here has to be same as there.
- POSIX doesn't require that we do anything for REG_NOERROR,
- but why not be nice? */
-
-const char __re_error_msgid[] attribute_hidden =
- {
-#define REG_NOERROR_IDX 0
- gettext_noop ("Success") /* REG_NOERROR */
- "\0"
-#define REG_NOMATCH_IDX (REG_NOERROR_IDX + sizeof "Success")
- gettext_noop ("No match") /* REG_NOMATCH */
- "\0"
-#define REG_BADPAT_IDX (REG_NOMATCH_IDX + sizeof "No match")
- gettext_noop ("Invalid regular expression") /* REG_BADPAT */
- "\0"
-#define REG_ECOLLATE_IDX (REG_BADPAT_IDX + sizeof "Invalid regular expression")
- gettext_noop ("Invalid collation character") /* REG_ECOLLATE */
- "\0"
-#define REG_ECTYPE_IDX (REG_ECOLLATE_IDX + sizeof "Invalid collation character")
- gettext_noop ("Invalid character class name") /* REG_ECTYPE */
- "\0"
-#define REG_EESCAPE_IDX (REG_ECTYPE_IDX + sizeof "Invalid character class name")
- gettext_noop ("Trailing backslash") /* REG_EESCAPE */
- "\0"
-#define REG_ESUBREG_IDX (REG_EESCAPE_IDX + sizeof "Trailing backslash")
- gettext_noop ("Invalid back reference") /* REG_ESUBREG */
- "\0"
-#define REG_EBRACK_IDX (REG_ESUBREG_IDX + sizeof "Invalid back reference")
- gettext_noop ("Unmatched [ or [^") /* REG_EBRACK */
- "\0"
-#define REG_EPAREN_IDX (REG_EBRACK_IDX + sizeof "Unmatched [ or [^")
- gettext_noop ("Unmatched ( or \\(") /* REG_EPAREN */
- "\0"
-#define REG_EBRACE_IDX (REG_EPAREN_IDX + sizeof "Unmatched ( or \\(")
- gettext_noop ("Unmatched \\{") /* REG_EBRACE */
- "\0"
-#define REG_BADBR_IDX (REG_EBRACE_IDX + sizeof "Unmatched \\{")
- gettext_noop ("Invalid content of \\{\\}") /* REG_BADBR */
- "\0"
-#define REG_ERANGE_IDX (REG_BADBR_IDX + sizeof "Invalid content of \\{\\}")
- gettext_noop ("Invalid range end") /* REG_ERANGE */
- "\0"
-#define REG_ESPACE_IDX (REG_ERANGE_IDX + sizeof "Invalid range end")
- gettext_noop ("Memory exhausted") /* REG_ESPACE */
- "\0"
-#define REG_BADRPT_IDX (REG_ESPACE_IDX + sizeof "Memory exhausted")
- gettext_noop ("Invalid preceding regular expression") /* REG_BADRPT */
- "\0"
-#define REG_EEND_IDX (REG_BADRPT_IDX + sizeof "Invalid preceding regular expression")
- gettext_noop ("Premature end of regular expression") /* REG_EEND */
- "\0"
-#define REG_ESIZE_IDX (REG_EEND_IDX + sizeof "Premature end of regular expression")
- gettext_noop ("Regular expression too big") /* REG_ESIZE */
- "\0"
-#define REG_ERPAREN_IDX (REG_ESIZE_IDX + sizeof "Regular expression too big")
- gettext_noop ("Unmatched ) or \\)") /* REG_ERPAREN */
- };
-
-const size_t __re_error_msgid_idx[] attribute_hidden =
- {
- REG_NOERROR_IDX,
- REG_NOMATCH_IDX,
- REG_BADPAT_IDX,
- REG_ECOLLATE_IDX,
- REG_ECTYPE_IDX,
- REG_EESCAPE_IDX,
- REG_ESUBREG_IDX,
- REG_EBRACK_IDX,
- REG_EPAREN_IDX,
- REG_EBRACE_IDX,
- REG_BADBR_IDX,
- REG_ERANGE_IDX,
- REG_ESPACE_IDX,
- REG_BADRPT_IDX,
- REG_EEND_IDX,
- REG_ESIZE_IDX,
- REG_ERPAREN_IDX
- };
-
-/* Entry points for GNU code. */
-
-/* re_compile_pattern is the GNU regular expression compiler: it
- compiles PATTERN (of length LENGTH) and puts the result in BUFP.
- Returns 0 if the pattern was valid, otherwise an error string.
-
- Assumes the `allocated' (and perhaps `buffer') and `translate' fields
- are set in BUFP on entry. */
-
-const char *
-re_compile_pattern (pattern, length, bufp)
- const char *pattern;
- size_t length;
- struct re_pattern_buffer *bufp;
-{
- reg_errcode_t ret;
-
- /* And GNU code determines whether or not to get register information
- by passing null for the REGS argument to re_match, etc., not by
- setting no_sub, unless RE_NO_SUB is set. */
- bufp->no_sub = !!(re_syntax_options & RE_NO_SUB);
-
- /* Match anchors at newline. */
- bufp->newline_anchor = 1;
-
- ret = re_compile_internal (bufp, pattern, length, re_syntax_options);
-
- if (!ret)
- return NULL;
- return gettext (__re_error_msgid + __re_error_msgid_idx[(int) ret]);
-}
-#ifdef _LIBC
-weak_alias (__re_compile_pattern, re_compile_pattern)
-#endif
-
-/* Set by `re_set_syntax' to the current regexp syntax to recognize. Can
- also be assigned to arbitrarily: each pattern buffer stores its own
- syntax, so it can be changed between regex compilations. */
-/* This has no initializer because initialized variables in Emacs
- become read-only after dumping. */
-reg_syntax_t re_syntax_options;
-
-
-/* Specify the precise syntax of regexps for compilation. This provides
- for compatibility for various utilities which historically have
- different, incompatible syntaxes.
-
- The argument SYNTAX is a bit mask comprised of the various bits
- defined in regex.h. We return the old syntax. */
-
-reg_syntax_t
-re_set_syntax (syntax)
- reg_syntax_t syntax;
-{
- reg_syntax_t ret = re_syntax_options;
-
- re_syntax_options = syntax;
- return ret;
-}
-#ifdef _LIBC
-weak_alias (__re_set_syntax, re_set_syntax)
-#endif
-
-int
-re_compile_fastmap (bufp)
- struct re_pattern_buffer *bufp;
-{
- re_dfa_t *dfa = (re_dfa_t *) bufp->buffer;
- char *fastmap = bufp->fastmap;
-
- memset (fastmap, '\0', sizeof (char) * SBC_MAX);
- re_compile_fastmap_iter (bufp, dfa->init_state, fastmap);
- if (dfa->init_state != dfa->init_state_word)
- re_compile_fastmap_iter (bufp, dfa->init_state_word, fastmap);
- if (dfa->init_state != dfa->init_state_nl)
- re_compile_fastmap_iter (bufp, dfa->init_state_nl, fastmap);
- if (dfa->init_state != dfa->init_state_begbuf)
- re_compile_fastmap_iter (bufp, dfa->init_state_begbuf, fastmap);
- bufp->fastmap_accurate = 1;
- return 0;
-}
-#ifdef _LIBC
-weak_alias (__re_compile_fastmap, re_compile_fastmap)
-#endif
-
-static inline void
-__attribute ((always_inline))
-re_set_fastmap (char *fastmap, int icase, int ch)
-{
- fastmap[ch] = 1;
- if (icase)
- fastmap[tolower (ch)] = 1;
-}
-
-/* Helper function for re_compile_fastmap.
- Compile fastmap for the initial_state INIT_STATE. */
-
-static void
-re_compile_fastmap_iter (regex_t *bufp, const re_dfastate_t *init_state,
- char *fastmap)
-{
- re_dfa_t *dfa = (re_dfa_t *) bufp->buffer;
- int node_cnt;
- int icase = (dfa->mb_cur_max == 1 && (bufp->syntax & RE_ICASE));
- for (node_cnt = 0; node_cnt < init_state->nodes.nelem; ++node_cnt)
- {
- int node = init_state->nodes.elems[node_cnt];
- re_token_type_t type = dfa->nodes[node].type;
-
- if (type == CHARACTER)
- {
- re_set_fastmap (fastmap, icase, dfa->nodes[node].opr.c);
-#ifdef RE_ENABLE_I18N
- if ((bufp->syntax & RE_ICASE) && dfa->mb_cur_max > 1)
- {
- unsigned char *buf = alloca (dfa->mb_cur_max), *p;
- wchar_t wc;
- mbstate_t state;
-
- p = buf;
- *p++ = dfa->nodes[node].opr.c;
- while (++node < dfa->nodes_len
- && dfa->nodes[node].type == CHARACTER
- && dfa->nodes[node].mb_partial)
- *p++ = dfa->nodes[node].opr.c;
- memset (&state, '\0', sizeof (state));
- if (mbrtowc (&wc, (const char *) buf, p - buf,
- &state) == p - buf
- && (__wcrtomb ((char *) buf, towlower (wc), &state)
- != (size_t) -1))
- re_set_fastmap (fastmap, 0, buf[0]);
- }
-#endif
- }
- else if (type == SIMPLE_BRACKET)
- {
- int i, ch;
- for (i = 0, ch = 0; i < BITSET_WORDS; ++i)
- {
- int j;
- bitset_word_t w = dfa->nodes[node].opr.sbcset[i];
- for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch)
- if (w & ((bitset_word_t) 1 << j))
- re_set_fastmap (fastmap, icase, ch);
- }
- }
-#ifdef RE_ENABLE_I18N
- else if (type == COMPLEX_BRACKET)
- {
- int i;
- re_charset_t *cset = dfa->nodes[node].opr.mbcset;
- if (cset->non_match || cset->ncoll_syms || cset->nequiv_classes
- || cset->nranges || cset->nchar_classes)
- {
-# ifdef _LIBC
- if (_NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES) != 0)
- {
- /* In this case we want to catch the bytes which are
- the first byte of any collation elements.
- e.g. In da_DK, we want to catch 'a' since "aa"
- is a valid collation element, and don't catch
- 'b' since 'b' is the only collation element
- which starts from 'b'. */
- const int32_t *table = (const int32_t *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB);
- for (i = 0; i < SBC_MAX; ++i)
- if (table[i] < 0)
- re_set_fastmap (fastmap, icase, i);
- }
-# else
- if (dfa->mb_cur_max > 1)
- for (i = 0; i < SBC_MAX; ++i)
- if (__btowc (i) == WEOF)
- re_set_fastmap (fastmap, icase, i);
-# endif /* not _LIBC */
- }
- for (i = 0; i < cset->nmbchars; ++i)
- {
- char buf[256];
- mbstate_t state;
- memset (&state, '\0', sizeof (state));
- if (__wcrtomb (buf, cset->mbchars[i], &state) != (size_t) -1)
- re_set_fastmap (fastmap, icase, *(unsigned char *) buf);
- if ((bufp->syntax & RE_ICASE) && dfa->mb_cur_max > 1)
- {
- if (__wcrtomb (buf, towlower (cset->mbchars[i]), &state)
- != (size_t) -1)
- re_set_fastmap (fastmap, 0, *(unsigned char *) buf);
- }
- }
- }
-#endif /* RE_ENABLE_I18N */
- else if (type == OP_PERIOD
-#ifdef RE_ENABLE_I18N
- || type == OP_UTF8_PERIOD
-#endif /* RE_ENABLE_I18N */
- || type == END_OF_RE)
- {
- memset (fastmap, '\1', sizeof (char) * SBC_MAX);
- if (type == END_OF_RE)
- bufp->can_be_null = 1;
- return;
- }
- }
-}
-
-/* Entry point for POSIX code. */
-/* regcomp takes a regular expression as a string and compiles it.
-
- PREG is a regex_t *. We do not expect any fields to be initialized,
- since POSIX says we shouldn't. Thus, we set
-
- `buffer' to the compiled pattern;
- `used' to the length of the compiled pattern;
- `syntax' to RE_SYNTAX_POSIX_EXTENDED if the
- REG_EXTENDED bit in CFLAGS is set; otherwise, to
- RE_SYNTAX_POSIX_BASIC;
- `newline_anchor' to REG_NEWLINE being set in CFLAGS;
- `fastmap' to an allocated space for the fastmap;
- `fastmap_accurate' to zero;
- `re_nsub' to the number of subexpressions in PATTERN.
-
- PATTERN is the address of the pattern string.
-
- CFLAGS is a series of bits which affect compilation.
-
- If REG_EXTENDED is set, we use POSIX extended syntax; otherwise, we
- use POSIX basic syntax.
-
- If REG_NEWLINE is set, then . and [^...] don't match newline.
- Also, regexec will try a match beginning after every newline.
-
- If REG_ICASE is set, then we considers upper- and lowercase
- versions of letters to be equivalent when matching.
-
- If REG_NOSUB is set, then when PREG is passed to regexec, that
- routine will report only success or failure, and nothing about the
- registers.
-
- It returns 0 if it succeeds, nonzero if it doesn't. (See regex.h for
- the return codes and their meanings.) */
-
-int
-regcomp (preg, pattern, cflags)
- regex_t *__restrict preg;
- const char *__restrict pattern;
- int cflags;
-{
- reg_errcode_t ret;
- reg_syntax_t syntax = ((cflags & REG_EXTENDED) ? RE_SYNTAX_POSIX_EXTENDED
- : RE_SYNTAX_POSIX_BASIC);
-
- preg->buffer = NULL;
- preg->allocated = 0;
- preg->used = 0;
-
- /* Try to allocate space for the fastmap. */
- preg->fastmap = re_malloc (char, SBC_MAX);
- if (BE (preg->fastmap == NULL, 0))
- return REG_ESPACE;
-
- syntax |= (cflags & REG_ICASE) ? RE_ICASE : 0;
-
- /* If REG_NEWLINE is set, newlines are treated differently. */
- if (cflags & REG_NEWLINE)
- { /* REG_NEWLINE implies neither . nor [^...] match newline. */
- syntax &= ~RE_DOT_NEWLINE;
- syntax |= RE_HAT_LISTS_NOT_NEWLINE;
- /* It also changes the matching behavior. */
- preg->newline_anchor = 1;
- }
- else
- preg->newline_anchor = 0;
- preg->no_sub = !!(cflags & REG_NOSUB);
- preg->translate = NULL;
-
- ret = re_compile_internal (preg, pattern, strlen (pattern), syntax);
-
- /* POSIX doesn't distinguish between an unmatched open-group and an
- unmatched close-group: both are REG_EPAREN. */
- if (ret == REG_ERPAREN)
- ret = REG_EPAREN;
-
- /* We have already checked preg->fastmap != NULL. */
- if (BE (ret == REG_NOERROR, 1))
- /* Compute the fastmap now, since regexec cannot modify the pattern
- buffer. This function never fails in this implementation. */
- (void) re_compile_fastmap (preg);
- else
- {
- /* Some error occurred while compiling the expression. */
- re_free (preg->fastmap);
- preg->fastmap = NULL;
- }
-
- return (int) ret;
-}
-#ifdef _LIBC
-weak_alias (__regcomp, regcomp)
-#endif
-
-/* Returns a message corresponding to an error code, ERRCODE, returned
- from either regcomp or regexec. We don't use PREG here. */
-
-/* regerror ( int errcode, preg, errbuf, errbuf_size) */
-size_t
-regerror (
- int errcode,
- const regex_t *__restrict preg,
- char *__restrict errbuf,
- size_t errbuf_size)
-{
- const char *msg;
- size_t msg_size;
-
- if (BE (errcode < 0
- || errcode >= (int) (sizeof (__re_error_msgid_idx)
- / sizeof (__re_error_msgid_idx[0])), 0))
- /* Only error codes returned by the rest of the code should be passed
- to this routine. If we are given anything else, or if other regex
- code generates an invalid error code, then the program has a bug.
- Dump core so we can fix it. */
- abort ();
-
- msg = gettext (__re_error_msgid + __re_error_msgid_idx[errcode]);
-
- msg_size = strlen (msg) + 1; /* Includes the null. */
-
- if (BE (errbuf_size != 0, 1))
- {
- if (BE (msg_size > errbuf_size, 0))
- {
-#if defined HAVE_MEMPCPY || defined _LIBC
- *((char *) __mempcpy (errbuf, msg, errbuf_size - 1)) = '\0';
-#else
- memcpy (errbuf, msg, errbuf_size - 1);
- errbuf[errbuf_size - 1] = 0;
-#endif
- }
- else
- memcpy (errbuf, msg, msg_size);
- }
-
- return msg_size;
-}
-#ifdef _LIBC
-weak_alias (__regerror, regerror)
-#endif
-
-
-#ifdef RE_ENABLE_I18N
-/* This static array is used for the map to single-byte characters when
- UTF-8 is used. Otherwise we would allocate memory just to initialize
- it the same all the time. UTF-8 is the preferred encoding so this is
- a worthwhile optimization. */
-static const bitset_t utf8_sb_map =
-{
- /* Set the first 128 bits. */
- [0 ... 0x80 / BITSET_WORD_BITS - 1] = BITSET_WORD_MAX
-};
-#endif
-
-
-static void
-free_dfa_content (re_dfa_t *dfa)
-{
- int i, j;
-
- if (dfa->nodes)
- for (i = 0; i < dfa->nodes_len; ++i)
- free_token (dfa->nodes + i);
- re_free (dfa->nexts);
- for (i = 0; i < dfa->nodes_len; ++i)
- {
- if (dfa->eclosures != NULL)
- re_node_set_free (dfa->eclosures + i);
- if (dfa->inveclosures != NULL)
- re_node_set_free (dfa->inveclosures + i);
- if (dfa->edests != NULL)
- re_node_set_free (dfa->edests + i);
- }
- re_free (dfa->edests);
- re_free (dfa->eclosures);
- re_free (dfa->inveclosures);
- re_free (dfa->nodes);
-
- if (dfa->state_table)
- for (i = 0; i <= dfa->state_hash_mask; ++i)
- {
- struct re_state_table_entry *entry = dfa->state_table + i;
- for (j = 0; j < entry->num; ++j)
- {
- re_dfastate_t *state = entry->array[j];
- free_state (state);
- }
- re_free (entry->array);
- }
- re_free (dfa->state_table);
-#ifdef RE_ENABLE_I18N
- if (dfa->sb_char != utf8_sb_map)
- re_free (dfa->sb_char);
-#endif
- re_free (dfa->subexp_map);
-#ifdef DEBUG
- re_free (dfa->re_str);
-#endif
-
- re_free (dfa);
-}
-
-
-/* Free dynamically allocated space used by PREG. */
-
-void
-regfree (preg)
- regex_t *preg;
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- if (BE (dfa != NULL, 1))
- free_dfa_content (dfa);
- preg->buffer = NULL;
- preg->allocated = 0;
-
- re_free (preg->fastmap);
- preg->fastmap = NULL;
-
- re_free (preg->translate);
- preg->translate = NULL;
-}
-#ifdef _LIBC
-weak_alias (__regfree, regfree)
-#endif
-
-/* Entry points compatible with 4.2 BSD regex library. We don't define
- them unless specifically requested. */
-
-#if defined _REGEX_RE_COMP || defined _LIBC
-
-/* BSD has one and only one pattern buffer. */
-static struct re_pattern_buffer re_comp_buf;
-
-char *
-# ifdef _LIBC
-/* Make these definitions weak in libc, so POSIX programs can redefine
- these names if they don't use our functions, and still use
- regcomp/regexec above without link errors. */
-weak_function
-# endif
-re_comp (s)
- const char *s;
-{
- reg_errcode_t ret;
- char *fastmap;
-
- if (!s)
- {
- if (!re_comp_buf.buffer)
- return gettext ("No previous regular expression");
- return 0;
- }
-
- if (re_comp_buf.buffer)
- {
- fastmap = re_comp_buf.fastmap;
- re_comp_buf.fastmap = NULL;
- __regfree (&re_comp_buf);
- memset (&re_comp_buf, '\0', sizeof (re_comp_buf));
- re_comp_buf.fastmap = fastmap;
- }
-
- if (re_comp_buf.fastmap == NULL)
- {
- re_comp_buf.fastmap = (char *) malloc (SBC_MAX);
- if (re_comp_buf.fastmap == NULL)
- return (char *) gettext (__re_error_msgid
- + __re_error_msgid_idx[(int) REG_ESPACE]);
- }
-
- /* Since `re_exec' always passes NULL for the `regs' argument, we
- don't need to initialize the pattern buffer fields which affect it. */
-
- /* Match anchors at newlines. */
- re_comp_buf.newline_anchor = 1;
-
- ret = re_compile_internal (&re_comp_buf, s, strlen (s), re_syntax_options);
-
- if (!ret)
- return NULL;
-
- /* Yes, we're discarding `const' here if !HAVE_LIBINTL. */
- return (char *) gettext (__re_error_msgid + __re_error_msgid_idx[(int) ret]);
-}
-
-#ifdef _LIBC
-libc_freeres_fn (free_mem)
-{
- __regfree (&re_comp_buf);
-}
-#endif
-
-#endif /* _REGEX_RE_COMP */
-
-/* Internal entry point.
- Compile the regular expression PATTERN, whose length is LENGTH.
- SYNTAX indicate regular expression's syntax. */
-
-static reg_errcode_t
-re_compile_internal (regex_t *preg, const char * pattern, size_t length,
- reg_syntax_t syntax)
-{
- reg_errcode_t err = REG_NOERROR;
- re_dfa_t *dfa;
- re_string_t regexp;
-
- /* Initialize the pattern buffer. */
- preg->fastmap_accurate = 0;
- preg->syntax = syntax;
- preg->not_bol = preg->not_eol = 0;
- preg->used = 0;
- preg->re_nsub = 0;
- preg->can_be_null = 0;
- preg->regs_allocated = REGS_UNALLOCATED;
-
- /* Initialize the dfa. */
- dfa = (re_dfa_t *) preg->buffer;
- if (BE (preg->allocated < sizeof (re_dfa_t), 0))
- {
- /* If zero allocated, but buffer is non-null, try to realloc
- enough space. This loses if buffer's address is bogus, but
- that is the user's responsibility. If ->buffer is NULL this
- is a simple allocation. */
- dfa = re_realloc (preg->buffer, re_dfa_t, 1);
- if (dfa == NULL)
- return REG_ESPACE;
- preg->allocated = sizeof (re_dfa_t);
- preg->buffer = (unsigned char *) dfa;
- }
- preg->used = sizeof (re_dfa_t);
-
- err = init_dfa (dfa, length);
- if (BE (err != REG_NOERROR, 0))
- {
- free_dfa_content (dfa);
- preg->buffer = NULL;
- preg->allocated = 0;
- return err;
- }
-#ifdef DEBUG
- /* Note: length+1 will not overflow since it is checked in init_dfa. */
- dfa->re_str = re_malloc (char, length + 1);
- strncpy (dfa->re_str, pattern, length + 1);
-#endif
-
- __libc_lock_init (dfa->lock);
-
- err = re_string_construct (®exp, pattern, length, preg->translate,
- syntax & RE_ICASE, dfa);
- if (BE (err != REG_NOERROR, 0))
- {
- re_compile_internal_free_return:
- free_workarea_compile (preg);
- re_string_destruct (®exp);
- free_dfa_content (dfa);
- preg->buffer = NULL;
- preg->allocated = 0;
- return err;
- }
-
- /* Parse the regular expression, and build a structure tree. */
- preg->re_nsub = 0;
- dfa->str_tree = parse (®exp, preg, syntax, &err);
- if (BE (dfa->str_tree == NULL, 0))
- goto re_compile_internal_free_return;
-
- /* Analyze the tree and create the nfa. */
- err = analyze (preg);
- if (BE (err != REG_NOERROR, 0))
- goto re_compile_internal_free_return;
-
-#ifdef RE_ENABLE_I18N
- /* If possible, do searching in single byte encoding to speed things up. */
- if (dfa->is_utf8 && !(syntax & RE_ICASE) && preg->translate == NULL)
- optimize_utf8 (dfa);
-#endif
-
- /* Then create the initial state of the dfa. */
- err = create_initial_state (dfa);
-
- /* Release work areas. */
- free_workarea_compile (preg);
- re_string_destruct (®exp);
-
- if (BE (err != REG_NOERROR, 0))
- {
- free_dfa_content (dfa);
- preg->buffer = NULL;
- preg->allocated = 0;
- }
-
- return err;
-}
-
-/* Initialize DFA. We use the length of the regular expression PAT_LEN
- as the initial length of some arrays. */
-
-static reg_errcode_t
-init_dfa (re_dfa_t *dfa, size_t pat_len)
-{
- unsigned int table_size;
-#ifndef _LIBC
- char *codeset_name;
-#endif
-
- memset (dfa, '\0', sizeof (re_dfa_t));
-
- /* Force allocation of str_tree_storage the first time. */
- dfa->str_tree_storage_idx = BIN_TREE_STORAGE_SIZE;
-
- /* Avoid overflows. */
- if (pat_len == SIZE_MAX)
- return REG_ESPACE;
-
- dfa->nodes_alloc = pat_len + 1;
- dfa->nodes = re_malloc (re_token_t, dfa->nodes_alloc);
-
- /* table_size = 2 ^ ceil(log pat_len) */
- for (table_size = 1; ; table_size <<= 1)
- if (table_size > pat_len)
- break;
-
- dfa->state_table = calloc (sizeof (struct re_state_table_entry), table_size);
- dfa->state_hash_mask = table_size - 1;
-
- dfa->mb_cur_max = MB_CUR_MAX;
-#ifdef _LIBC
- if (dfa->mb_cur_max == 6
- && strcmp (_NL_CURRENT (LC_CTYPE, _NL_CTYPE_CODESET_NAME), "UTF-8") == 0)
- dfa->is_utf8 = 1;
- dfa->map_notascii = (_NL_CURRENT_WORD (LC_CTYPE, _NL_CTYPE_MAP_TO_NONASCII)
- != 0);
-#else
-# ifdef HAVE_LANGINFO_CODESET
- codeset_name = nl_langinfo (CODESET);
-# else
- codeset_name = getenv ("LC_ALL");
- if (codeset_name == NULL || codeset_name[0] == '\0')
- codeset_name = getenv ("LC_CTYPE");
- if (codeset_name == NULL || codeset_name[0] == '\0')
- codeset_name = getenv ("LANG");
- if (codeset_name == NULL)
- codeset_name = "";
- else if (strchr (codeset_name, '.') != NULL)
- codeset_name = strchr (codeset_name, '.') + 1;
-# endif
-
- if (strcasecmp (codeset_name, "UTF-8") == 0
- || strcasecmp (codeset_name, "UTF8") == 0)
- dfa->is_utf8 = 1;
-
- /* We check exhaustively in the loop below if this charset is a
- superset of ASCII. */
- dfa->map_notascii = 0;
-#endif
-
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- {
- if (dfa->is_utf8)
- dfa->sb_char = (re_bitset_ptr_t) utf8_sb_map;
- else
- {
- int i, j, ch;
-
- dfa->sb_char = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1);
- if (BE (dfa->sb_char == NULL, 0))
- return REG_ESPACE;
-
- /* Set the bits corresponding to single byte chars. */
- for (i = 0, ch = 0; i < BITSET_WORDS; ++i)
- for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch)
- {
- wint_t wch = __btowc (ch);
- if (wch != WEOF)
- dfa->sb_char[i] |= (bitset_word_t) 1 << j;
-# ifndef _LIBC
- if (isascii (ch) && wch != ch)
- dfa->map_notascii = 1;
-# endif
- }
- }
- }
-#endif
-
- if (BE (dfa->nodes == NULL || dfa->state_table == NULL, 0))
- return REG_ESPACE;
- return REG_NOERROR;
-}
-
-/* Initialize WORD_CHAR table, which indicate which character is
- "word". In this case "word" means that it is the word construction
- character used by some operators like "\<", "\>", etc. */
-
-static void
-internal_function
-init_word_char (re_dfa_t *dfa)
-{
- int i, j, ch;
- dfa->word_ops_used = 1;
- for (i = 0, ch = 0; i < BITSET_WORDS; ++i)
- for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch)
- if (isalnum (ch) || ch == '_')
- dfa->word_char[i] |= (bitset_word_t) 1 << j;
-}
-
-/* Free the work area which are only used while compiling. */
-
-static void
-free_workarea_compile (regex_t *preg)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_storage_t *storage, *next;
- for (storage = dfa->str_tree_storage; storage; storage = next)
- {
- next = storage->next;
- re_free (storage);
- }
- dfa->str_tree_storage = NULL;
- dfa->str_tree_storage_idx = BIN_TREE_STORAGE_SIZE;
- dfa->str_tree = NULL;
- re_free (dfa->org_indices);
- dfa->org_indices = NULL;
-}
-
-/* Create initial states for all contexts. */
-
-static reg_errcode_t
-create_initial_state (re_dfa_t *dfa)
-{
- int first, i;
- reg_errcode_t err;
- re_node_set init_nodes;
-
- /* Initial states have the epsilon closure of the node which is
- the first node of the regular expression. */
- first = dfa->str_tree->first->node_idx;
- dfa->init_node = first;
- err = re_node_set_init_copy (&init_nodes, dfa->eclosures + first);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- /* The back-references which are in initial states can epsilon transit,
- since in this case all of the subexpressions can be null.
- Then we add epsilon closures of the nodes which are the next nodes of
- the back-references. */
- if (dfa->nbackref > 0)
- for (i = 0; i < init_nodes.nelem; ++i)
- {
- int node_idx = init_nodes.elems[i];
- re_token_type_t type = dfa->nodes[node_idx].type;
-
- int clexp_idx;
- if (type != OP_BACK_REF)
- continue;
- for (clexp_idx = 0; clexp_idx < init_nodes.nelem; ++clexp_idx)
- {
- re_token_t *clexp_node;
- clexp_node = dfa->nodes + init_nodes.elems[clexp_idx];
- if (clexp_node->type == OP_CLOSE_SUBEXP
- && clexp_node->opr.idx == dfa->nodes[node_idx].opr.idx)
- break;
- }
- if (clexp_idx == init_nodes.nelem)
- continue;
-
- if (type == OP_BACK_REF)
- {
- int dest_idx = dfa->edests[node_idx].elems[0];
- if (!re_node_set_contains (&init_nodes, dest_idx))
- {
- re_node_set_merge (&init_nodes, dfa->eclosures + dest_idx);
- i = 0;
- }
- }
- }
-
- /* It must be the first time to invoke acquire_state. */
- dfa->init_state = re_acquire_state_context (&err, dfa, &init_nodes, 0);
- /* We don't check ERR here, since the initial state must not be NULL. */
- if (BE (dfa->init_state == NULL, 0))
- return err;
- if (dfa->init_state->has_constraint)
- {
- dfa->init_state_word = re_acquire_state_context (&err, dfa, &init_nodes,
- CONTEXT_WORD);
- dfa->init_state_nl = re_acquire_state_context (&err, dfa, &init_nodes,
- CONTEXT_NEWLINE);
- dfa->init_state_begbuf = re_acquire_state_context (&err, dfa,
- &init_nodes,
- CONTEXT_NEWLINE
- | CONTEXT_BEGBUF);
- if (BE (dfa->init_state_word == NULL || dfa->init_state_nl == NULL
- || dfa->init_state_begbuf == NULL, 0))
- return err;
- }
- else
- dfa->init_state_word = dfa->init_state_nl
- = dfa->init_state_begbuf = dfa->init_state;
-
- re_node_set_free (&init_nodes);
- return REG_NOERROR;
-}
-
-#ifdef RE_ENABLE_I18N
-/* If it is possible to do searching in single byte encoding instead of UTF-8
- to speed things up, set dfa->mb_cur_max to 1, clear is_utf8 and change
- DFA nodes where needed. */
-
-static void
-optimize_utf8 (re_dfa_t *dfa)
-{
- int node, i, mb_chars = 0, has_period = 0;
-
- for (node = 0; node < dfa->nodes_len; ++node)
- switch (dfa->nodes[node].type)
- {
- case CHARACTER:
- if (dfa->nodes[node].opr.c >= 0x80)
- mb_chars = 1;
- break;
- case ANCHOR:
- switch (dfa->nodes[node].opr.idx)
- {
- case LINE_FIRST:
- case LINE_LAST:
- case BUF_FIRST:
- case BUF_LAST:
- break;
- default:
- /* Word anchors etc. cannot be handled. */
- return;
- }
- break;
- case OP_PERIOD:
- has_period = 1;
- break;
- case OP_BACK_REF:
- case OP_ALT:
- case END_OF_RE:
- case OP_DUP_ASTERISK:
- case OP_OPEN_SUBEXP:
- case OP_CLOSE_SUBEXP:
- break;
- case COMPLEX_BRACKET:
- return;
- case SIMPLE_BRACKET:
- /* Just double check. The non-ASCII range starts at 0x80. */
- assert (0x80 % BITSET_WORD_BITS == 0);
- for (i = 0x80 / BITSET_WORD_BITS; i < BITSET_WORDS; ++i)
- if (dfa->nodes[node].opr.sbcset[i])
- return;
- break;
- default:
- abort ();
- }
-
- if (mb_chars || has_period)
- for (node = 0; node < dfa->nodes_len; ++node)
- {
- if (dfa->nodes[node].type == CHARACTER
- && dfa->nodes[node].opr.c >= 0x80)
- dfa->nodes[node].mb_partial = 0;
- else if (dfa->nodes[node].type == OP_PERIOD)
- dfa->nodes[node].type = OP_UTF8_PERIOD;
- }
-
- /* The search can be in single byte locale. */
- dfa->mb_cur_max = 1;
- dfa->is_utf8 = 0;
- dfa->has_mb_node = dfa->nbackref > 0 || has_period;
-}
-#endif
-
-/* Analyze the structure tree, and calculate "first", "next", "edest",
- "eclosure", and "inveclosure". */
-
-static reg_errcode_t
-analyze (regex_t *preg)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- reg_errcode_t ret;
-
- /* Allocate arrays. */
- dfa->nexts = re_malloc (int, dfa->nodes_alloc);
- dfa->org_indices = re_malloc (int, dfa->nodes_alloc);
- dfa->edests = re_malloc (re_node_set, dfa->nodes_alloc);
- dfa->eclosures = re_malloc (re_node_set, dfa->nodes_alloc);
- if (BE (dfa->nexts == NULL || dfa->org_indices == NULL || dfa->edests == NULL
- || dfa->eclosures == NULL, 0))
- return REG_ESPACE;
-
- dfa->subexp_map = re_malloc (int, preg->re_nsub);
- if (dfa->subexp_map != NULL)
- {
- int i;
- for (i = 0; i < preg->re_nsub; i++)
- dfa->subexp_map[i] = i;
- preorder (dfa->str_tree, optimize_subexps, dfa);
- for (i = 0; i < preg->re_nsub; i++)
- if (dfa->subexp_map[i] != i)
- break;
- if (i == preg->re_nsub)
- {
- free (dfa->subexp_map);
- dfa->subexp_map = NULL;
- }
- }
-
- ret = postorder (dfa->str_tree, lower_subexps, preg);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- ret = postorder (dfa->str_tree, calc_first, dfa);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- preorder (dfa->str_tree, calc_next, dfa);
- ret = preorder (dfa->str_tree, link_nfa_nodes, dfa);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- ret = calc_eclosure (dfa);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
-
- /* We only need this during the prune_impossible_nodes pass in regexec.c;
- skip it if p_i_n will not run, as calc_inveclosure can be quadratic. */
- if ((!preg->no_sub && preg->re_nsub > 0 && dfa->has_plural_match)
- || dfa->nbackref)
- {
- dfa->inveclosures = re_malloc (re_node_set, dfa->nodes_len);
- if (BE (dfa->inveclosures == NULL, 0))
- return REG_ESPACE;
- ret = calc_inveclosure (dfa);
- }
-
- return ret;
-}
-
-/* Our parse trees are very unbalanced, so we cannot use a stack to
- implement parse tree visits. Instead, we use parent pointers and
- some hairy code in these two functions. */
-static reg_errcode_t
-postorder (bin_tree_t *root, reg_errcode_t (fn (void *, bin_tree_t *)),
- void *extra)
-{
- bin_tree_t *node, *prev;
-
- for (node = root; ; )
- {
- /* Descend down the tree, preferably to the left (or to the right
- if that's the only child). */
- while (node->left || node->right)
- if (node->left)
- node = node->left;
- else
- node = node->right;
-
- do
- {
- reg_errcode_t err = fn (extra, node);
- if (BE (err != REG_NOERROR, 0))
- return err;
- if (node->parent == NULL)
- return REG_NOERROR;
- prev = node;
- node = node->parent;
- }
- /* Go up while we have a node that is reached from the right. */
- while (node->right == prev || node->right == NULL);
- node = node->right;
- }
-}
-
-static reg_errcode_t
-preorder (bin_tree_t *root, reg_errcode_t (fn (void *, bin_tree_t *)),
- void *extra)
-{
- bin_tree_t *node;
-
- for (node = root; ; )
- {
- reg_errcode_t err = fn (extra, node);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- /* Go to the left node, or up and to the right. */
- if (node->left)
- node = node->left;
- else
- {
- bin_tree_t *prev = NULL;
- while (node->right == prev || node->right == NULL)
- {
- prev = node;
- node = node->parent;
- if (!node)
- return REG_NOERROR;
- }
- node = node->right;
- }
- }
-}
-
-/* Optimization pass: if a SUBEXP is entirely contained, strip it and tell
- re_search_internal to map the inner one's opr.idx to this one's. Adjust
- backreferences as well. Requires a preorder visit. */
-static reg_errcode_t
-optimize_subexps (void *extra, bin_tree_t *node)
-{
- re_dfa_t *dfa = (re_dfa_t *) extra;
-
- if (node->token.type == OP_BACK_REF && dfa->subexp_map)
- {
- int idx = node->token.opr.idx;
- node->token.opr.idx = dfa->subexp_map[idx];
- dfa->used_bkref_map |= 1 << node->token.opr.idx;
- }
-
- else if (node->token.type == SUBEXP
- && node->left && node->left->token.type == SUBEXP)
- {
- int other_idx = node->left->token.opr.idx;
-
- node->left = node->left->left;
- if (node->left)
- node->left->parent = node;
-
- dfa->subexp_map[other_idx] = dfa->subexp_map[node->token.opr.idx];
- if (other_idx < BITSET_WORD_BITS)
- dfa->used_bkref_map &= ~((bitset_word_t) 1 << other_idx);
- }
-
- return REG_NOERROR;
-}
-
-/* Lowering pass: Turn each SUBEXP node into the appropriate concatenation
- of OP_OPEN_SUBEXP, the body of the SUBEXP (if any) and OP_CLOSE_SUBEXP. */
-static reg_errcode_t
-lower_subexps (void *extra, bin_tree_t *node)
-{
- regex_t *preg = (regex_t *) extra;
- reg_errcode_t err = REG_NOERROR;
-
- if (node->left && node->left->token.type == SUBEXP)
- {
- node->left = lower_subexp (&err, preg, node->left);
- if (node->left)
- node->left->parent = node;
- }
- if (node->right && node->right->token.type == SUBEXP)
- {
- node->right = lower_subexp (&err, preg, node->right);
- if (node->right)
- node->right->parent = node;
- }
-
- return err;
-}
-
-static bin_tree_t *
-lower_subexp (reg_errcode_t *err, regex_t *preg, bin_tree_t *node)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_t *body = node->left;
- bin_tree_t *op, *cls, *tree1, *tree;
-
- if (preg->no_sub
- /* We do not optimize empty subexpressions, because otherwise we may
- have bad CONCAT nodes with NULL children. This is obviously not
- very common, so we do not lose much. An example that triggers
- this case is the sed "script" /\(\)/x. */
- && node->left != NULL
- && (node->token.opr.idx >= BITSET_WORD_BITS
- || !(dfa->used_bkref_map
- & ((bitset_word_t) 1 << node->token.opr.idx))))
- return node->left;
-
- /* Convert the SUBEXP node to the concatenation of an
- OP_OPEN_SUBEXP, the contents, and an OP_CLOSE_SUBEXP. */
- op = create_tree (dfa, NULL, NULL, OP_OPEN_SUBEXP);
- cls = create_tree (dfa, NULL, NULL, OP_CLOSE_SUBEXP);
- tree1 = body ? create_tree (dfa, body, cls, CONCAT) : cls;
- tree = create_tree (dfa, op, tree1, CONCAT);
- if (BE (tree == NULL || tree1 == NULL || op == NULL || cls == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
-
- op->token.opr.idx = cls->token.opr.idx = node->token.opr.idx;
- op->token.opt_subexp = cls->token.opt_subexp = node->token.opt_subexp;
- return tree;
-}
-
-/* Pass 1 in building the NFA: compute FIRST and create unlinked automaton
- nodes. Requires a postorder visit. */
-static reg_errcode_t
-calc_first (void *extra, bin_tree_t *node)
-{
- re_dfa_t *dfa = (re_dfa_t *) extra;
- if (node->token.type == CONCAT)
- {
- node->first = node->left->first;
- node->node_idx = node->left->node_idx;
- }
- else
- {
- node->first = node;
- node->node_idx = re_dfa_add_node (dfa, node->token);
- if (BE (node->node_idx == -1, 0))
- return REG_ESPACE;
- }
- return REG_NOERROR;
-}
-
-/* Pass 2: compute NEXT on the tree. Preorder visit. */
-static reg_errcode_t
-calc_next (void *extra, bin_tree_t *node)
-{
- switch (node->token.type)
- {
- case OP_DUP_ASTERISK:
- node->left->next = node;
- break;
- case CONCAT:
- node->left->next = node->right->first;
- node->right->next = node->next;
- break;
- default:
- if (node->left)
- node->left->next = node->next;
- if (node->right)
- node->right->next = node->next;
- break;
- }
- return REG_NOERROR;
-}
-
-/* Pass 3: link all DFA nodes to their NEXT node (any order will do). */
-static reg_errcode_t
-link_nfa_nodes (void *extra, bin_tree_t *node)
-{
- re_dfa_t *dfa = (re_dfa_t *) extra;
- int idx = node->node_idx;
- reg_errcode_t err = REG_NOERROR;
-
- switch (node->token.type)
- {
- case CONCAT:
- break;
-
- case END_OF_RE:
- assert (node->next == NULL);
- break;
-
- case OP_DUP_ASTERISK:
- case OP_ALT:
- {
- int left, right;
- dfa->has_plural_match = 1;
- if (node->left != NULL)
- left = node->left->first->node_idx;
- else
- left = node->next->node_idx;
- if (node->right != NULL)
- right = node->right->first->node_idx;
- else
- right = node->next->node_idx;
- assert (left > -1);
- assert (right > -1);
- err = re_node_set_init_2 (dfa->edests + idx, left, right);
- }
- break;
-
- case ANCHOR:
- case OP_OPEN_SUBEXP:
- case OP_CLOSE_SUBEXP:
- err = re_node_set_init_1 (dfa->edests + idx, node->next->node_idx);
- break;
-
- case OP_BACK_REF:
- dfa->nexts[idx] = node->next->node_idx;
- if (node->token.type == OP_BACK_REF)
- re_node_set_init_1 (dfa->edests + idx, dfa->nexts[idx]);
- break;
-
- default:
- assert (!IS_EPSILON_NODE (node->token.type));
- dfa->nexts[idx] = node->next->node_idx;
- break;
- }
-
- return err;
-}
-
-/* Duplicate the epsilon closure of the node ROOT_NODE.
- Note that duplicated nodes have constraint INIT_CONSTRAINT in addition
- to their own constraint. */
-
-static reg_errcode_t
-internal_function
-duplicate_node_closure (re_dfa_t *dfa, int top_org_node, int top_clone_node,
- int root_node, unsigned int init_constraint)
-{
- int org_node, clone_node, ret;
- unsigned int constraint = init_constraint;
- for (org_node = top_org_node, clone_node = top_clone_node;;)
- {
- int org_dest, clone_dest;
- if (dfa->nodes[org_node].type == OP_BACK_REF)
- {
- /* If the back reference epsilon-transit, its destination must
- also have the constraint. Then duplicate the epsilon closure
- of the destination of the back reference, and store it in
- edests of the back reference. */
- org_dest = dfa->nexts[org_node];
- re_node_set_empty (dfa->edests + clone_node);
- clone_dest = duplicate_node (dfa, org_dest, constraint);
- if (BE (clone_dest == -1, 0))
- return REG_ESPACE;
- dfa->nexts[clone_node] = dfa->nexts[org_node];
- ret = re_node_set_insert (dfa->edests + clone_node, clone_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- }
- else if (dfa->edests[org_node].nelem == 0)
- {
- /* In case of the node can't epsilon-transit, don't duplicate the
- destination and store the original destination as the
- destination of the node. */
- dfa->nexts[clone_node] = dfa->nexts[org_node];
- break;
- }
- else if (dfa->edests[org_node].nelem == 1)
- {
- /* In case of the node can epsilon-transit, and it has only one
- destination. */
- org_dest = dfa->edests[org_node].elems[0];
- re_node_set_empty (dfa->edests + clone_node);
- if (dfa->nodes[org_node].type == ANCHOR)
- {
- /* In case of the node has another constraint, append it. */
- if (org_node == root_node && clone_node != org_node)
- {
- /* ...but if the node is root_node itself, it means the
- epsilon closure have a loop, then tie it to the
- destination of the root_node. */
- ret = re_node_set_insert (dfa->edests + clone_node,
- org_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- break;
- }
- constraint |= dfa->nodes[org_node].opr.ctx_type;
- }
- clone_dest = duplicate_node (dfa, org_dest, constraint);
- if (BE (clone_dest == -1, 0))
- return REG_ESPACE;
- ret = re_node_set_insert (dfa->edests + clone_node, clone_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- }
- else /* dfa->edests[org_node].nelem == 2 */
- {
- /* In case of the node can epsilon-transit, and it has two
- destinations. In the bin_tree_t and DFA, that's '|' and '*'. */
- org_dest = dfa->edests[org_node].elems[0];
- re_node_set_empty (dfa->edests + clone_node);
- /* Search for a duplicated node which satisfies the constraint. */
- clone_dest = search_duplicated_node (dfa, org_dest, constraint);
- if (clone_dest == -1)
- {
- /* There are no such a duplicated node, create a new one. */
- reg_errcode_t err;
- clone_dest = duplicate_node (dfa, org_dest, constraint);
- if (BE (clone_dest == -1, 0))
- return REG_ESPACE;
- ret = re_node_set_insert (dfa->edests + clone_node, clone_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- err = duplicate_node_closure (dfa, org_dest, clone_dest,
- root_node, constraint);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- else
- {
- /* There are a duplicated node which satisfy the constraint,
- use it to avoid infinite loop. */
- ret = re_node_set_insert (dfa->edests + clone_node, clone_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- }
-
- org_dest = dfa->edests[org_node].elems[1];
- clone_dest = duplicate_node (dfa, org_dest, constraint);
- if (BE (clone_dest == -1, 0))
- return REG_ESPACE;
- ret = re_node_set_insert (dfa->edests + clone_node, clone_dest);
- if (BE (ret < 0, 0))
- return REG_ESPACE;
- }
- org_node = org_dest;
- clone_node = clone_dest;
- }
- return REG_NOERROR;
-}
-
-/* Search for a node which is duplicated from the node ORG_NODE, and
- satisfies the constraint CONSTRAINT. */
-
-static int
-search_duplicated_node (const re_dfa_t *dfa, int org_node,
- unsigned int constraint)
-{
- int idx;
- for (idx = dfa->nodes_len - 1; dfa->nodes[idx].duplicated && idx > 0; --idx)
- {
- if (org_node == dfa->org_indices[idx]
- && constraint == dfa->nodes[idx].constraint)
- return idx; /* Found. */
- }
- return -1; /* Not found. */
-}
-
-/* Duplicate the node whose index is ORG_IDX and set the constraint CONSTRAINT.
- Return the index of the new node, or -1 if insufficient storage is
- available. */
-
-static int
-duplicate_node (re_dfa_t *dfa, int org_idx, unsigned int constraint)
-{
- int dup_idx = re_dfa_add_node (dfa, dfa->nodes[org_idx]);
- if (BE (dup_idx != -1, 1))
- {
- dfa->nodes[dup_idx].constraint = constraint;
- if (dfa->nodes[org_idx].type == ANCHOR)
- dfa->nodes[dup_idx].constraint |= dfa->nodes[org_idx].opr.ctx_type;
- dfa->nodes[dup_idx].duplicated = 1;
-
- /* Store the index of the original node. */
- dfa->org_indices[dup_idx] = org_idx;
- }
- return dup_idx;
-}
-
-static reg_errcode_t
-calc_inveclosure (re_dfa_t *dfa)
-{
- int src, idx, ret;
- for (idx = 0; idx < dfa->nodes_len; ++idx)
- re_node_set_init_empty (dfa->inveclosures + idx);
-
- for (src = 0; src < dfa->nodes_len; ++src)
- {
- int *elems = dfa->eclosures[src].elems;
- for (idx = 0; idx < dfa->eclosures[src].nelem; ++idx)
- {
- ret = re_node_set_insert_last (dfa->inveclosures + elems[idx], src);
- if (BE (ret == -1, 0))
- return REG_ESPACE;
- }
- }
-
- return REG_NOERROR;
-}
-
-/* Calculate "eclosure" for all the node in DFA. */
-
-static reg_errcode_t
-calc_eclosure (re_dfa_t *dfa)
-{
- int node_idx, incomplete;
-#ifdef DEBUG
- assert (dfa->nodes_len > 0);
-#endif
- incomplete = 0;
- /* For each nodes, calculate epsilon closure. */
- for (node_idx = 0; ; ++node_idx)
- {
- reg_errcode_t err;
- re_node_set eclosure_elem;
- if (node_idx == dfa->nodes_len)
- {
- if (!incomplete)
- break;
- incomplete = 0;
- node_idx = 0;
- }
-
-#ifdef DEBUG
- assert (dfa->eclosures[node_idx].nelem != -1);
-#endif
-
- /* If we have already calculated, skip it. */
- if (dfa->eclosures[node_idx].nelem != 0)
- continue;
- /* Calculate epsilon closure of `node_idx'. */
- err = calc_eclosure_iter (&eclosure_elem, dfa, node_idx, 1);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- if (dfa->eclosures[node_idx].nelem == 0)
- {
- incomplete = 1;
- re_node_set_free (&eclosure_elem);
- }
- }
- return REG_NOERROR;
-}
-
-/* Calculate epsilon closure of NODE. */
-
-static reg_errcode_t
-calc_eclosure_iter (re_node_set *new_set, re_dfa_t *dfa, int node, int root)
-{
- reg_errcode_t err;
- unsigned int constraint;
- int i, incomplete;
- re_node_set eclosure;
- incomplete = 0;
- err = re_node_set_alloc (&eclosure, dfa->edests[node].nelem + 1);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- /* This indicates that we are calculating this node now.
- We reference this value to avoid infinite loop. */
- dfa->eclosures[node].nelem = -1;
-
- constraint = ((dfa->nodes[node].type == ANCHOR)
- ? dfa->nodes[node].opr.ctx_type : 0);
- /* If the current node has constraints, duplicate all nodes.
- Since they must inherit the constraints. */
- if (constraint
- && dfa->edests[node].nelem
- && !dfa->nodes[dfa->edests[node].elems[0]].duplicated)
- {
- err = duplicate_node_closure (dfa, node, node, node, constraint);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
-
- /* Expand each epsilon destination nodes. */
- if (IS_EPSILON_NODE(dfa->nodes[node].type))
- for (i = 0; i < dfa->edests[node].nelem; ++i)
- {
- re_node_set eclosure_elem;
- int edest = dfa->edests[node].elems[i];
- /* If calculating the epsilon closure of `edest' is in progress,
- return intermediate result. */
- if (dfa->eclosures[edest].nelem == -1)
- {
- incomplete = 1;
- continue;
- }
- /* If we haven't calculated the epsilon closure of `edest' yet,
- calculate now. Otherwise use calculated epsilon closure. */
- if (dfa->eclosures[edest].nelem == 0)
- {
- err = calc_eclosure_iter (&eclosure_elem, dfa, edest, 0);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- else
- eclosure_elem = dfa->eclosures[edest];
- /* Merge the epsilon closure of `edest'. */
- re_node_set_merge (&eclosure, &eclosure_elem);
- /* If the epsilon closure of `edest' is incomplete,
- the epsilon closure of this node is also incomplete. */
- if (dfa->eclosures[edest].nelem == 0)
- {
- incomplete = 1;
- re_node_set_free (&eclosure_elem);
- }
- }
-
- /* Epsilon closures include itself. */
- re_node_set_insert (&eclosure, node);
- if (incomplete && !root)
- dfa->eclosures[node].nelem = 0;
- else
- dfa->eclosures[node] = eclosure;
- *new_set = eclosure;
- return REG_NOERROR;
-}
-
-/* Functions for token which are used in the parser. */
-
-/* Fetch a token from INPUT.
- We must not use this function inside bracket expressions. */
-
-static void
-internal_function
-fetch_token (re_token_t *result, re_string_t *input, reg_syntax_t syntax)
-{
- re_string_skip_bytes (input, peek_token (result, input, syntax));
-}
-
-/* Peek a token from INPUT, and return the length of the token.
- We must not use this function inside bracket expressions. */
-
-static int
-internal_function
-peek_token (re_token_t *token, re_string_t *input, reg_syntax_t syntax)
-{
- unsigned char c;
-
- if (re_string_eoi (input))
- {
- token->type = END_OF_RE;
- return 0;
- }
-
- c = re_string_peek_byte (input, 0);
- token->opr.c = c;
-
- token->word_char = 0;
-#ifdef RE_ENABLE_I18N
- token->mb_partial = 0;
- if (input->mb_cur_max > 1 &&
- !re_string_first_byte (input, re_string_cur_idx (input)))
- {
- token->type = CHARACTER;
- token->mb_partial = 1;
- return 1;
- }
-#endif
- if (c == '\\')
- {
- unsigned char c2;
- if (re_string_cur_idx (input) + 1 >= re_string_length (input))
- {
- token->type = BACK_SLASH;
- return 1;
- }
-
- c2 = re_string_peek_byte_case (input, 1);
- token->opr.c = c2;
- token->type = CHARACTER;
-#ifdef RE_ENABLE_I18N
- if (input->mb_cur_max > 1)
- {
- wint_t wc = re_string_wchar_at (input,
- re_string_cur_idx (input) + 1);
- token->word_char = IS_WIDE_WORD_CHAR (wc) != 0;
- }
- else
-#endif
- token->word_char = IS_WORD_CHAR (c2) != 0;
-
- switch (c2)
- {
- case '|':
- if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_NO_BK_VBAR))
- token->type = OP_ALT;
- break;
- case '1': case '2': case '3': case '4': case '5':
- case '6': case '7': case '8': case '9':
- if (!(syntax & RE_NO_BK_REFS))
- {
- token->type = OP_BACK_REF;
- token->opr.idx = c2 - '1';
- }
- break;
- case '<':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = WORD_FIRST;
- }
- break;
- case '>':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = WORD_LAST;
- }
- break;
- case 'b':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = WORD_DELIM;
- }
- break;
- case 'B':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = NOT_WORD_DELIM;
- }
- break;
- case 'w':
- if (!(syntax & RE_NO_GNU_OPS))
- token->type = OP_WORD;
- break;
- case 'W':
- if (!(syntax & RE_NO_GNU_OPS))
- token->type = OP_NOTWORD;
- break;
- case 's':
- if (!(syntax & RE_NO_GNU_OPS))
- token->type = OP_SPACE;
- break;
- case 'S':
- if (!(syntax & RE_NO_GNU_OPS))
- token->type = OP_NOTSPACE;
- break;
- case '`':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = BUF_FIRST;
- }
- break;
- case '\'':
- if (!(syntax & RE_NO_GNU_OPS))
- {
- token->type = ANCHOR;
- token->opr.ctx_type = BUF_LAST;
- }
- break;
- case '(':
- if (!(syntax & RE_NO_BK_PARENS))
- token->type = OP_OPEN_SUBEXP;
- break;
- case ')':
- if (!(syntax & RE_NO_BK_PARENS))
- token->type = OP_CLOSE_SUBEXP;
- break;
- case '+':
- if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_BK_PLUS_QM))
- token->type = OP_DUP_PLUS;
- break;
- case '?':
- if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_BK_PLUS_QM))
- token->type = OP_DUP_QUESTION;
- break;
- case '{':
- if ((syntax & RE_INTERVALS) && (!(syntax & RE_NO_BK_BRACES)))
- token->type = OP_OPEN_DUP_NUM;
- break;
- case '}':
- if ((syntax & RE_INTERVALS) && (!(syntax & RE_NO_BK_BRACES)))
- token->type = OP_CLOSE_DUP_NUM;
- break;
- default:
- break;
- }
- return 2;
- }
-
- token->type = CHARACTER;
-#ifdef RE_ENABLE_I18N
- if (input->mb_cur_max > 1)
- {
- wint_t wc = re_string_wchar_at (input, re_string_cur_idx (input));
- token->word_char = IS_WIDE_WORD_CHAR (wc) != 0;
- }
- else
-#endif
- token->word_char = IS_WORD_CHAR (token->opr.c);
-
- switch (c)
- {
- case '\n':
- if (syntax & RE_NEWLINE_ALT)
- token->type = OP_ALT;
- break;
- case '|':
- if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_NO_BK_VBAR))
- token->type = OP_ALT;
- break;
- case '*':
- token->type = OP_DUP_ASTERISK;
- break;
- case '+':
- if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_BK_PLUS_QM))
- token->type = OP_DUP_PLUS;
- break;
- case '?':
- if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_BK_PLUS_QM))
- token->type = OP_DUP_QUESTION;
- break;
- case '{':
- if ((syntax & RE_INTERVALS) && (syntax & RE_NO_BK_BRACES))
- token->type = OP_OPEN_DUP_NUM;
- break;
- case '}':
- if ((syntax & RE_INTERVALS) && (syntax & RE_NO_BK_BRACES))
- token->type = OP_CLOSE_DUP_NUM;
- break;
- case '(':
- if (syntax & RE_NO_BK_PARENS)
- token->type = OP_OPEN_SUBEXP;
- break;
- case ')':
- if (syntax & RE_NO_BK_PARENS)
- token->type = OP_CLOSE_SUBEXP;
- break;
- case '[':
- token->type = OP_OPEN_BRACKET;
- break;
- case '.':
- token->type = OP_PERIOD;
- break;
- case '^':
- if (!(syntax & (RE_CONTEXT_INDEP_ANCHORS | RE_CARET_ANCHORS_HERE)) &&
- re_string_cur_idx (input) != 0)
- {
- char prev = re_string_peek_byte (input, -1);
- if (!(syntax & RE_NEWLINE_ALT) || prev != '\n')
- break;
- }
- token->type = ANCHOR;
- token->opr.ctx_type = LINE_FIRST;
- break;
- case '$':
- if (!(syntax & RE_CONTEXT_INDEP_ANCHORS) &&
- re_string_cur_idx (input) + 1 != re_string_length (input))
- {
- re_token_t next;
- re_string_skip_bytes (input, 1);
- peek_token (&next, input, syntax);
- re_string_skip_bytes (input, -1);
- if (next.type != OP_ALT && next.type != OP_CLOSE_SUBEXP)
- break;
- }
- token->type = ANCHOR;
- token->opr.ctx_type = LINE_LAST;
- break;
- default:
- break;
- }
- return 1;
-}
-
-/* Peek a token from INPUT, and return the length of the token.
- We must not use this function out of bracket expressions. */
-
-static int
-internal_function
-peek_token_bracket (re_token_t *token, re_string_t *input, reg_syntax_t syntax)
-{
- unsigned char c;
- if (re_string_eoi (input))
- {
- token->type = END_OF_RE;
- return 0;
- }
- c = re_string_peek_byte (input, 0);
- token->opr.c = c;
-
-#ifdef RE_ENABLE_I18N
- if (input->mb_cur_max > 1 &&
- !re_string_first_byte (input, re_string_cur_idx (input)))
- {
- token->type = CHARACTER;
- return 1;
- }
-#endif /* RE_ENABLE_I18N */
-
- if (c == '\\' && (syntax & RE_BACKSLASH_ESCAPE_IN_LISTS)
- && re_string_cur_idx (input) + 1 < re_string_length (input))
- {
- /* In this case, '\' escape a character. */
- unsigned char c2;
- re_string_skip_bytes (input, 1);
- c2 = re_string_peek_byte (input, 0);
- token->opr.c = c2;
- token->type = CHARACTER;
- return 1;
- }
- if (c == '[') /* '[' is a special char in a bracket exps. */
- {
- unsigned char c2;
- int token_len;
- if (re_string_cur_idx (input) + 1 < re_string_length (input))
- c2 = re_string_peek_byte (input, 1);
- else
- c2 = 0;
- token->opr.c = c2;
- token_len = 2;
- switch (c2)
- {
- case '.':
- token->type = OP_OPEN_COLL_ELEM;
- break;
- case '=':
- token->type = OP_OPEN_EQUIV_CLASS;
- break;
- case ':':
- if (syntax & RE_CHAR_CLASSES)
- {
- token->type = OP_OPEN_CHAR_CLASS;
- break;
- }
- /* else fall through. */
- default:
- token->type = CHARACTER;
- token->opr.c = c;
- token_len = 1;
- break;
- }
- return token_len;
- }
- switch (c)
- {
- case '-':
- token->type = OP_CHARSET_RANGE;
- break;
- case ']':
- token->type = OP_CLOSE_BRACKET;
- break;
- case '^':
- token->type = OP_NON_MATCH_LIST;
- break;
- default:
- token->type = CHARACTER;
- }
- return 1;
-}
-
-/* Functions for parser. */
-
-/* Entry point of the parser.
- Parse the regular expression REGEXP and return the structure tree.
- If an error is occured, ERR is set by error code, and return NULL.
- This function build the following tree, from regular expression <reg_exp>:
- CAT
- / \
- / \
- <reg_exp> EOR
-
- CAT means concatenation.
- EOR means end of regular expression. */
-
-static bin_tree_t *
-parse (re_string_t *regexp, regex_t *preg, reg_syntax_t syntax,
- reg_errcode_t *err)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_t *tree, *eor, *root;
- re_token_t current_token;
- dfa->syntax = syntax;
- fetch_token (¤t_token, regexp, syntax | RE_CARET_ANCHORS_HERE);
- tree = parse_reg_exp (regexp, preg, ¤t_token, syntax, 0, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- eor = create_tree (dfa, NULL, NULL, END_OF_RE);
- if (tree != NULL)
- root = create_tree (dfa, tree, eor, CONCAT);
- else
- root = eor;
- if (BE (eor == NULL || root == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- return root;
-}
-
-/* This function build the following tree, from regular expression
- <branch1>|<branch2>:
- ALT
- / \
- / \
- <branch1> <branch2>
-
- ALT means alternative, which represents the operator `|'. */
-
-static bin_tree_t *
-parse_reg_exp (re_string_t *regexp, regex_t *preg, re_token_t *token,
- reg_syntax_t syntax, int nest, reg_errcode_t *err)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_t *tree, *branch = NULL;
- tree = parse_branch (regexp, preg, token, syntax, nest, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
-
- while (token->type == OP_ALT)
- {
- fetch_token (token, regexp, syntax | RE_CARET_ANCHORS_HERE);
- if (token->type != OP_ALT && token->type != END_OF_RE
- && (nest == 0 || token->type != OP_CLOSE_SUBEXP))
- {
- branch = parse_branch (regexp, preg, token, syntax, nest, err);
- if (BE (*err != REG_NOERROR && branch == NULL, 0))
- return NULL;
- }
- else
- branch = NULL;
- tree = create_tree (dfa, tree, branch, OP_ALT);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- }
- return tree;
-}
-
-/* This function build the following tree, from regular expression
- <exp1><exp2>:
- CAT
- / \
- / \
- <exp1> <exp2>
-
- CAT means concatenation. */
-
-static bin_tree_t *
-parse_branch (re_string_t *regexp, regex_t *preg, re_token_t *token,
- reg_syntax_t syntax, int nest, reg_errcode_t *err)
-{
- bin_tree_t *tree, *exp;
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- tree = parse_expression (regexp, preg, token, syntax, nest, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
-
- while (token->type != OP_ALT && token->type != END_OF_RE
- && (nest == 0 || token->type != OP_CLOSE_SUBEXP))
- {
- exp = parse_expression (regexp, preg, token, syntax, nest, err);
- if (BE (*err != REG_NOERROR && exp == NULL, 0))
- {
- return NULL;
- }
- if (tree != NULL && exp != NULL)
- {
- tree = create_tree (dfa, tree, exp, CONCAT);
- if (tree == NULL)
- {
- *err = REG_ESPACE;
- return NULL;
- }
- }
- else if (tree == NULL)
- tree = exp;
- /* Otherwise exp == NULL, we don't need to create new tree. */
- }
- return tree;
-}
-
-/* This function build the following tree, from regular expression a*:
- *
- |
- a
-*/
-
-static bin_tree_t *
-parse_expression (re_string_t *regexp, regex_t *preg, re_token_t *token,
- reg_syntax_t syntax, int nest, reg_errcode_t *err)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_t *tree;
- switch (token->type)
- {
- case CHARACTER:
- tree = create_token_tree (dfa, NULL, NULL, token);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- {
- while (!re_string_eoi (regexp)
- && !re_string_first_byte (regexp, re_string_cur_idx (regexp)))
- {
- bin_tree_t *mbc_remain;
- fetch_token (token, regexp, syntax);
- mbc_remain = create_token_tree (dfa, NULL, NULL, token);
- tree = create_tree (dfa, tree, mbc_remain, CONCAT);
- if (BE (mbc_remain == NULL || tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- }
- }
-#endif
- break;
- case OP_OPEN_SUBEXP:
- tree = parse_sub_exp (regexp, preg, token, syntax, nest + 1, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- break;
- case OP_OPEN_BRACKET:
- tree = parse_bracket_exp (regexp, dfa, token, syntax, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- break;
- case OP_BACK_REF:
- if (!BE (dfa->completed_bkref_map & (1 << token->opr.idx), 1))
- {
- *err = REG_ESUBREG;
- return NULL;
- }
- dfa->used_bkref_map |= 1 << token->opr.idx;
- tree = create_token_tree (dfa, NULL, NULL, token);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- ++dfa->nbackref;
- dfa->has_mb_node = 1;
- break;
- case OP_OPEN_DUP_NUM:
- if (syntax & RE_CONTEXT_INVALID_DUP)
- {
- *err = REG_BADRPT;
- return NULL;
- }
- /* FALLTHROUGH */
- case OP_DUP_ASTERISK:
- case OP_DUP_PLUS:
- case OP_DUP_QUESTION:
- if (syntax & RE_CONTEXT_INVALID_OPS)
- {
- *err = REG_BADRPT;
- return NULL;
- }
- else if (syntax & RE_CONTEXT_INDEP_OPS)
- {
- fetch_token (token, regexp, syntax);
- return parse_expression (regexp, preg, token, syntax, nest, err);
- }
- /* else fall through */
- case OP_CLOSE_SUBEXP:
- if ((token->type == OP_CLOSE_SUBEXP) &&
- !(syntax & RE_UNMATCHED_RIGHT_PAREN_ORD))
- {
- *err = REG_ERPAREN;
- return NULL;
- }
- /* else fall through */
- case OP_CLOSE_DUP_NUM:
- /* We treat it as a normal character. */
-
- /* Then we can these characters as normal characters. */
- token->type = CHARACTER;
- /* mb_partial and word_char bits should be initialized already
- by peek_token. */
- tree = create_token_tree (dfa, NULL, NULL, token);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- break;
- case ANCHOR:
- if ((token->opr.ctx_type
- & (WORD_DELIM | NOT_WORD_DELIM | WORD_FIRST | WORD_LAST))
- && dfa->word_ops_used == 0)
- init_word_char (dfa);
- if (token->opr.ctx_type == WORD_DELIM
- || token->opr.ctx_type == NOT_WORD_DELIM)
- {
- bin_tree_t *tree_first, *tree_last;
- if (token->opr.ctx_type == WORD_DELIM)
- {
- token->opr.ctx_type = WORD_FIRST;
- tree_first = create_token_tree (dfa, NULL, NULL, token);
- token->opr.ctx_type = WORD_LAST;
- }
- else
- {
- token->opr.ctx_type = INSIDE_WORD;
- tree_first = create_token_tree (dfa, NULL, NULL, token);
- token->opr.ctx_type = INSIDE_NOTWORD;
- }
- tree_last = create_token_tree (dfa, NULL, NULL, token);
- tree = create_tree (dfa, tree_first, tree_last, OP_ALT);
- if (BE (tree_first == NULL || tree_last == NULL || tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- }
- else
- {
- tree = create_token_tree (dfa, NULL, NULL, token);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- }
- /* We must return here, since ANCHORs can't be followed
- by repetition operators.
- eg. RE"^*" is invalid or "<ANCHOR(^)><CHAR(*)>",
- it must not be "<ANCHOR(^)><REPEAT(*)>". */
- fetch_token (token, regexp, syntax);
- return tree;
- case OP_PERIOD:
- tree = create_token_tree (dfa, NULL, NULL, token);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- if (dfa->mb_cur_max > 1)
- dfa->has_mb_node = 1;
- break;
- case OP_WORD:
- case OP_NOTWORD:
- tree = build_charclass_op (dfa, regexp->trans,
- (const unsigned char *) "alnum",
- (const unsigned char *) "_",
- token->type == OP_NOTWORD, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- break;
- case OP_SPACE:
- case OP_NOTSPACE:
- tree = build_charclass_op (dfa, regexp->trans,
- (const unsigned char *) "space",
- (const unsigned char *) "",
- token->type == OP_NOTSPACE, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- break;
- case OP_ALT:
- case END_OF_RE:
- return NULL;
- case BACK_SLASH:
- *err = REG_EESCAPE;
- return NULL;
- default:
- /* Must not happen? */
-#ifdef DEBUG
- assert (0);
-#endif
- return NULL;
- }
- fetch_token (token, regexp, syntax);
-
- while (token->type == OP_DUP_ASTERISK || token->type == OP_DUP_PLUS
- || token->type == OP_DUP_QUESTION || token->type == OP_OPEN_DUP_NUM)
- {
- tree = parse_dup_op (tree, regexp, dfa, token, syntax, err);
- if (BE (*err != REG_NOERROR && tree == NULL, 0))
- return NULL;
- /* In BRE consecutive duplications are not allowed. */
- if ((syntax & RE_CONTEXT_INVALID_DUP)
- && (token->type == OP_DUP_ASTERISK
- || token->type == OP_OPEN_DUP_NUM))
- {
- *err = REG_BADRPT;
- return NULL;
- }
- }
-
- return tree;
-}
-
-/* This function build the following tree, from regular expression
- (<reg_exp>):
- SUBEXP
- |
- <reg_exp>
-*/
-
-static bin_tree_t *
-parse_sub_exp (re_string_t *regexp, regex_t *preg, re_token_t *token,
- reg_syntax_t syntax, int nest, reg_errcode_t *err)
-{
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
- bin_tree_t *tree;
- size_t cur_nsub;
- cur_nsub = preg->re_nsub++;
-
- fetch_token (token, regexp, syntax | RE_CARET_ANCHORS_HERE);
-
- /* The subexpression may be a null string. */
- if (token->type == OP_CLOSE_SUBEXP)
- tree = NULL;
- else
- {
- tree = parse_reg_exp (regexp, preg, token, syntax, nest, err);
- if (BE (*err == REG_NOERROR && token->type != OP_CLOSE_SUBEXP, 0))
- *err = REG_EPAREN;
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
- }
-
- if (cur_nsub <= '9' - '1')
- dfa->completed_bkref_map |= 1 << cur_nsub;
-
- tree = create_tree (dfa, tree, NULL, SUBEXP);
- if (BE (tree == NULL, 0))
- {
- *err = REG_ESPACE;
- return NULL;
- }
- tree->token.opr.idx = cur_nsub;
- return tree;
-}
-
-/* This function parse repetition operators like "*", "+", "{1,3}" etc. */
-
-static bin_tree_t *
-parse_dup_op (bin_tree_t *elem, re_string_t *regexp, re_dfa_t *dfa,
- re_token_t *token, reg_syntax_t syntax, reg_errcode_t *err)
-{
- bin_tree_t *tree = NULL, *old_tree = NULL;
- int i, start, end, start_idx = re_string_cur_idx (regexp);
- re_token_t start_token = *token;
-
- if (token->type == OP_OPEN_DUP_NUM)
- {
- end = 0;
- start = fetch_number (regexp, token, syntax);
- if (start == -1)
- {
- if (token->type == CHARACTER && token->opr.c == ',')
- start = 0; /* We treat "{,m}" as "{0,m}". */
- else
- {
- *err = REG_BADBR; /* <re>{} is invalid. */
- return NULL;
- }
- }
- if (BE (start != -2, 1))
- {
- /* We treat "{n}" as "{n,n}". */
- end = ((token->type == OP_CLOSE_DUP_NUM) ? start
- : ((token->type == CHARACTER && token->opr.c == ',')
- ? fetch_number (regexp, token, syntax) : -2));
- }
- if (BE (start == -2 || end == -2, 0))
- {
- /* Invalid sequence. */
- if (BE (!(syntax & RE_INVALID_INTERVAL_ORD), 0))
- {
- if (token->type == END_OF_RE)
- *err = REG_EBRACE;
- else
- *err = REG_BADBR;
-
- return NULL;
- }
-
- /* If the syntax bit is set, rollback. */
- re_string_set_index (regexp, start_idx);
- *token = start_token;
- token->type = CHARACTER;
- /* mb_partial and word_char bits should be already initialized by
- peek_token. */
- return elem;
- }
-
- if (BE (end != -1 && start > end, 0))
- {
- /* First number greater than second. */
- *err = REG_BADBR;
- return NULL;
- }
- }
- else
- {
- start = (token->type == OP_DUP_PLUS) ? 1 : 0;
- end = (token->type == OP_DUP_QUESTION) ? 1 : -1;
- }
-
- fetch_token (token, regexp, syntax);
-
- if (BE (elem == NULL, 0))
- return NULL;
- if (BE (start == 0 && end == 0, 0))
- {
- postorder (elem, free_tree, NULL);
- return NULL;
- }
-
- /* Extract "<re>{n,m}" to "<re><re>...<re><re>{0,<m-n>}". */
- if (BE (start > 0, 0))
- {
- tree = elem;
- for (i = 2; i <= start; ++i)
- {
- elem = duplicate_tree (elem, dfa);
- tree = create_tree (dfa, tree, elem, CONCAT);
- if (BE (elem == NULL || tree == NULL, 0))
- goto parse_dup_op_espace;
- }
-
- if (start == end)
- return tree;
-
- /* Duplicate ELEM before it is marked optional. */
- elem = duplicate_tree (elem, dfa);
- old_tree = tree;
- }
- else
- old_tree = NULL;
-
- if (elem->token.type == SUBEXP)
- postorder (elem, mark_opt_subexp, (void *) (long) elem->token.opr.idx);
-
- tree = create_tree (dfa, elem, NULL, (end == -1 ? OP_DUP_ASTERISK : OP_ALT));
- if (BE (tree == NULL, 0))
- goto parse_dup_op_espace;
-
- /* This loop is actually executed only when end != -1,
- to rewrite <re>{0,n} as (<re>(<re>...<re>?)?)?... We have
- already created the start+1-th copy. */
- for (i = start + 2; i <= end; ++i)
- {
- elem = duplicate_tree (elem, dfa);
- tree = create_tree (dfa, tree, elem, CONCAT);
- if (BE (elem == NULL || tree == NULL, 0))
- goto parse_dup_op_espace;
-
- tree = create_tree (dfa, tree, NULL, OP_ALT);
- if (BE (tree == NULL, 0))
- goto parse_dup_op_espace;
- }
-
- if (old_tree)
- tree = create_tree (dfa, old_tree, tree, CONCAT);
-
- return tree;
-
- parse_dup_op_espace:
- *err = REG_ESPACE;
- return NULL;
-}
-
-/* Size of the names for collating symbol/equivalence_class/character_class.
- I'm not sure, but maybe enough. */
-#define BRACKET_NAME_BUF_SIZE 32
-
-#ifndef _LIBC
- /* Local function for parse_bracket_exp only used in case of NOT _LIBC.
- Build the range expression which starts from START_ELEM, and ends
- at END_ELEM. The result are written to MBCSET and SBCSET.
- RANGE_ALLOC is the allocated size of mbcset->range_starts, and
- mbcset->range_ends, is a pointer argument sinse we may
- update it. */
-
-static reg_errcode_t
-internal_function
-# ifdef RE_ENABLE_I18N
-build_range_exp (bitset_t sbcset, re_charset_t *mbcset, int *range_alloc,
- bracket_elem_t *start_elem, bracket_elem_t *end_elem)
-# else /* not RE_ENABLE_I18N */
-build_range_exp (bitset_t sbcset, bracket_elem_t *start_elem,
- bracket_elem_t *end_elem)
-# endif /* not RE_ENABLE_I18N */
-{
- unsigned int start_ch, end_ch;
- /* Equivalence Classes and Character Classes can't be a range start/end. */
- if (BE (start_elem->type == EQUIV_CLASS || start_elem->type == CHAR_CLASS
- || end_elem->type == EQUIV_CLASS || end_elem->type == CHAR_CLASS,
- 0))
- return REG_ERANGE;
-
- /* We can handle no multi character collating elements without libc
- support. */
- if (BE ((start_elem->type == COLL_SYM
- && strlen ((char *) start_elem->opr.name) > 1)
- || (end_elem->type == COLL_SYM
- && strlen ((char *) end_elem->opr.name) > 1), 0))
- return REG_ECOLLATE;
-
-# ifdef RE_ENABLE_I18N
- {
- wchar_t wc;
- wint_t start_wc;
- wint_t end_wc;
- wchar_t cmp_buf[6] = {L'\0', L'\0', L'\0', L'\0', L'\0', L'\0'};
-
- start_ch = ((start_elem->type == SB_CHAR) ? start_elem->opr.ch
- : ((start_elem->type == COLL_SYM) ? start_elem->opr.name[0]
- : 0));
- end_ch = ((end_elem->type == SB_CHAR) ? end_elem->opr.ch
- : ((end_elem->type == COLL_SYM) ? end_elem->opr.name[0]
- : 0));
- start_wc = ((start_elem->type == SB_CHAR || start_elem->type == COLL_SYM)
- ? __btowc (start_ch) : start_elem->opr.wch);
- end_wc = ((end_elem->type == SB_CHAR || end_elem->type == COLL_SYM)
- ? __btowc (end_ch) : end_elem->opr.wch);
- if (start_wc == WEOF || end_wc == WEOF)
- return REG_ECOLLATE;
- cmp_buf[0] = start_wc;
- cmp_buf[4] = end_wc;
- if (wcscoll (cmp_buf, cmp_buf + 4) > 0)
- return REG_ERANGE;
-
- /* Got valid collation sequence values, add them as a new entry.
- However, for !_LIBC we have no collation elements: if the
- character set is single byte, the single byte character set
- that we build below suffices. parse_bracket_exp passes
- no MBCSET if dfa->mb_cur_max == 1. */
- if (mbcset)
- {
- /* Check the space of the arrays. */
- if (BE (*range_alloc == mbcset->nranges, 0))
- {
- /* There is not enough space, need realloc. */
- wchar_t *new_array_start, *new_array_end;
- int new_nranges;
-
- /* +1 in case of mbcset->nranges is 0. */
- new_nranges = 2 * mbcset->nranges + 1;
- /* Use realloc since mbcset->range_starts and mbcset->range_ends
- are NULL if *range_alloc == 0. */
- new_array_start = re_realloc (mbcset->range_starts, wchar_t,
- new_nranges);
- new_array_end = re_realloc (mbcset->range_ends, wchar_t,
- new_nranges);
-
- if (BE (new_array_start == NULL || new_array_end == NULL, 0))
- return REG_ESPACE;
-
- mbcset->range_starts = new_array_start;
- mbcset->range_ends = new_array_end;
- *range_alloc = new_nranges;
- }
-
- mbcset->range_starts[mbcset->nranges] = start_wc;
- mbcset->range_ends[mbcset->nranges++] = end_wc;
- }
-
- /* Build the table for single byte characters. */
- for (wc = 0; wc < SBC_MAX; ++wc)
- {
- cmp_buf[2] = wc;
- if (wcscoll (cmp_buf, cmp_buf + 2) <= 0
- && wcscoll (cmp_buf + 2, cmp_buf + 4) <= 0)
- bitset_set (sbcset, wc);
- }
- }
-# else /* not RE_ENABLE_I18N */
- {
- unsigned int ch;
- start_ch = ((start_elem->type == SB_CHAR ) ? start_elem->opr.ch
- : ((start_elem->type == COLL_SYM) ? start_elem->opr.name[0]
- : 0));
- end_ch = ((end_elem->type == SB_CHAR ) ? end_elem->opr.ch
- : ((end_elem->type == COLL_SYM) ? end_elem->opr.name[0]
- : 0));
- if (start_ch > end_ch)
- return REG_ERANGE;
- /* Build the table for single byte characters. */
- for (ch = 0; ch < SBC_MAX; ++ch)
- if (start_ch <= ch && ch <= end_ch)
- bitset_set (sbcset, ch);
- }
-# endif /* not RE_ENABLE_I18N */
- return REG_NOERROR;
-}
-#endif /* not _LIBC */
-
-#ifndef _LIBC
-/* Helper function for parse_bracket_exp only used in case of NOT _LIBC..
- Build the collating element which is represented by NAME.
- The result are written to MBCSET and SBCSET.
- COLL_SYM_ALLOC is the allocated size of mbcset->coll_sym, is a
- pointer argument since we may update it. */
-
-static reg_errcode_t
-internal_function
-# ifdef RE_ENABLE_I18N
-build_collating_symbol (bitset_t sbcset, re_charset_t *mbcset,
- int *coll_sym_alloc, const unsigned char *name)
-# else /* not RE_ENABLE_I18N */
-build_collating_symbol (bitset_t sbcset, const unsigned char *name)
-# endif /* not RE_ENABLE_I18N */
-{
- size_t name_len = strlen ((const char *) name);
- if (BE (name_len != 1, 0))
- return REG_ECOLLATE;
- else
- {
- bitset_set (sbcset, name[0]);
- return REG_NOERROR;
- }
-}
-#endif /* not _LIBC */
-
-/* This function parse bracket expression like "[abc]", "[a-c]",
- "[[.a-a.]]" etc. */
-
-static bin_tree_t *
-parse_bracket_exp (re_string_t *regexp, re_dfa_t *dfa, re_token_t *token,
- reg_syntax_t syntax, reg_errcode_t *err)
-{
-#ifdef _LIBC
- const unsigned char *collseqmb;
- const char *collseqwc;
- uint32_t nrules;
- int32_t table_size;
- const int32_t *symb_table;
- const unsigned char *extra;
-
- /* Local function for parse_bracket_exp used in _LIBC environement.
- Seek the collating symbol entry correspondings to NAME.
- Return the index of the symbol in the SYMB_TABLE. */
-
- auto inline int32_t
- __attribute ((always_inline))
- seek_collating_symbol_entry (name, name_len)
- const unsigned char *name;
- size_t name_len;
- {
- int32_t hash = elem_hash ((const char *) name, name_len);
- int32_t elem = hash % table_size;
- if (symb_table[2 * elem] != 0)
- {
- int32_t second = hash % (table_size - 2) + 1;
-
- do
- {
- /* First compare the hashing value. */
- if (symb_table[2 * elem] == hash
- /* Compare the length of the name. */
- && name_len == extra[symb_table[2 * elem + 1]]
- /* Compare the name. */
- && memcmp (name, &extra[symb_table[2 * elem + 1] + 1],
- name_len) == 0)
- {
- /* Yep, this is the entry. */
- break;
- }
-
- /* Next entry. */
- elem += second;
- }
- while (symb_table[2 * elem] != 0);
- }
- return elem;
- }
-
- /* Local function for parse_bracket_exp used in _LIBC environement.
- Look up the collation sequence value of BR_ELEM.
- Return the value if succeeded, UINT_MAX otherwise. */
-
- auto inline unsigned int
- __attribute ((always_inline))
- lookup_collation_sequence_value (br_elem)
- bracket_elem_t *br_elem;
- {
- if (br_elem->type == SB_CHAR)
- {
- /*
- if (MB_CUR_MAX == 1)
- */
- if (nrules == 0)
- return collseqmb[br_elem->opr.ch];
- else
- {
- wint_t wc = __btowc (br_elem->opr.ch);
- return __collseq_table_lookup (collseqwc, wc);
- }
- }
- else if (br_elem->type == MB_CHAR)
- {
- return __collseq_table_lookup (collseqwc, br_elem->opr.wch);
- }
- else if (br_elem->type == COLL_SYM)
- {
- size_t sym_name_len = strlen ((char *) br_elem->opr.name);
- if (nrules != 0)
- {
- int32_t elem, idx;
- elem = seek_collating_symbol_entry (br_elem->opr.name,
- sym_name_len);
- if (symb_table[2 * elem] != 0)
- {
- /* We found the entry. */
- idx = symb_table[2 * elem + 1];
- /* Skip the name of collating element name. */
- idx += 1 + extra[idx];
- /* Skip the byte sequence of the collating element. */
- idx += 1 + extra[idx];
- /* Adjust for the alignment. */
- idx = (idx + 3) & ~3;
- /* Skip the multibyte collation sequence value. */
- idx += sizeof (unsigned int);
- /* Skip the wide char sequence of the collating element. */
- idx += sizeof (unsigned int) *
- (1 + *(unsigned int *) (extra + idx));
- /* Return the collation sequence value. */
- return *(unsigned int *) (extra + idx);
- }
- else if (symb_table[2 * elem] == 0 && sym_name_len == 1)
- {
- /* No valid character. Match it as a single byte
- character. */
- return collseqmb[br_elem->opr.name[0]];
- }
- }
- else if (sym_name_len == 1)
- return collseqmb[br_elem->opr.name[0]];
- }
- return UINT_MAX;
- }
-
- /* Local function for parse_bracket_exp used in _LIBC environement.
- Build the range expression which starts from START_ELEM, and ends
- at END_ELEM. The result are written to MBCSET and SBCSET.
- RANGE_ALLOC is the allocated size of mbcset->range_starts, and
- mbcset->range_ends, is a pointer argument sinse we may
- update it. */
-
- auto inline reg_errcode_t
- __attribute ((always_inline))
- build_range_exp (sbcset, mbcset, range_alloc, start_elem, end_elem)
- re_charset_t *mbcset;
- int *range_alloc;
- bitset_t sbcset;
- bracket_elem_t *start_elem, *end_elem;
- {
- unsigned int ch;
- uint32_t start_collseq;
- uint32_t end_collseq;
-
- /* Equivalence Classes and Character Classes can't be a range
- start/end. */
- if (BE (start_elem->type == EQUIV_CLASS || start_elem->type == CHAR_CLASS
- || end_elem->type == EQUIV_CLASS || end_elem->type == CHAR_CLASS,
- 0))
- return REG_ERANGE;
-
- start_collseq = lookup_collation_sequence_value (start_elem);
- end_collseq = lookup_collation_sequence_value (end_elem);
- /* Check start/end collation sequence values. */
- if (BE (start_collseq == UINT_MAX || end_collseq == UINT_MAX, 0))
- return REG_ECOLLATE;
- if (BE ((syntax & RE_NO_EMPTY_RANGES) && start_collseq > end_collseq, 0))
- return REG_ERANGE;
-
- /* Got valid collation sequence values, add them as a new entry.
- However, if we have no collation elements, and the character set
- is single byte, the single byte character set that we
- build below suffices. */
- if (nrules > 0 || dfa->mb_cur_max > 1)
- {
- /* Check the space of the arrays. */
- if (BE (*range_alloc == mbcset->nranges, 0))
- {
- /* There is not enough space, need realloc. */
- uint32_t *new_array_start;
- uint32_t *new_array_end;
- int new_nranges;
-
- /* +1 in case of mbcset->nranges is 0. */
- new_nranges = 2 * mbcset->nranges + 1;
- new_array_start = re_realloc (mbcset->range_starts, uint32_t,
- new_nranges);
- new_array_end = re_realloc (mbcset->range_ends, uint32_t,
- new_nranges);
-
- if (BE (new_array_start == NULL || new_array_end == NULL, 0))
- return REG_ESPACE;
-
- mbcset->range_starts = new_array_start;
- mbcset->range_ends = new_array_end;
- *range_alloc = new_nranges;
- }
-
- mbcset->range_starts[mbcset->nranges] = start_collseq;
- mbcset->range_ends[mbcset->nranges++] = end_collseq;
- }
-
- /* Build the table for single byte characters. */
- for (ch = 0; ch < SBC_MAX; ch++)
- {
- uint32_t ch_collseq;
- /*
- if (MB_CUR_MAX == 1)
- */
- if (nrules == 0)
- ch_collseq = collseqmb[ch];
- else
- ch_collseq = __collseq_table_lookup (collseqwc, __btowc (ch));
- if (start_collseq <= ch_collseq && ch_collseq <= end_collseq)
- bitset_set (sbcset, ch);
- }
- return REG_NOERROR;
- }
-
- /* Local function for parse_bracket_exp used in _LIBC environement.
- Build the collating element which is represented by NAME.
- The result are written to MBCSET and SBCSET.
- COLL_SYM_ALLOC is the allocated size of mbcset->coll_sym, is a
- pointer argument sinse we may update it. */
-
- auto inline reg_errcode_t
- __attribute ((always_inline))
- build_collating_symbol (sbcset, mbcset, coll_sym_alloc, name)
- re_charset_t *mbcset;
- int *coll_sym_alloc;
- bitset_t sbcset;
- const unsigned char *name;
- {
- int32_t elem, idx;
- size_t name_len = strlen ((const char *) name);
- if (nrules != 0)
- {
- elem = seek_collating_symbol_entry (name, name_len);
- if (symb_table[2 * elem] != 0)
- {
- /* We found the entry. */
- idx = symb_table[2 * elem + 1];
- /* Skip the name of collating element name. */
- idx += 1 + extra[idx];
- }
- else if (symb_table[2 * elem] == 0 && name_len == 1)
- {
- /* No valid character, treat it as a normal
- character. */
- bitset_set (sbcset, name[0]);
- return REG_NOERROR;
- }
- else
- return REG_ECOLLATE;
-
- /* Got valid collation sequence, add it as a new entry. */
- /* Check the space of the arrays. */
- if (BE (*coll_sym_alloc == mbcset->ncoll_syms, 0))
- {
- /* Not enough, realloc it. */
- /* +1 in case of mbcset->ncoll_syms is 0. */
- int new_coll_sym_alloc = 2 * mbcset->ncoll_syms + 1;
- /* Use realloc since mbcset->coll_syms is NULL
- if *alloc == 0. */
- int32_t *new_coll_syms = re_realloc (mbcset->coll_syms, int32_t,
- new_coll_sym_alloc);
- if (BE (new_coll_syms == NULL, 0))
- return REG_ESPACE;
- mbcset->coll_syms = new_coll_syms;
- *coll_sym_alloc = new_coll_sym_alloc;
- }
- mbcset->coll_syms[mbcset->ncoll_syms++] = idx;
- return REG_NOERROR;
- }
- else
- {
- if (BE (name_len != 1, 0))
- return REG_ECOLLATE;
- else
- {
- bitset_set (sbcset, name[0]);
- return REG_NOERROR;
- }
- }
- }
-#endif
-
- re_token_t br_token;
- re_bitset_ptr_t sbcset;
-#ifdef RE_ENABLE_I18N
- re_charset_t *mbcset;
- int coll_sym_alloc = 0, range_alloc = 0, mbchar_alloc = 0;
- int equiv_class_alloc = 0, char_class_alloc = 0;
-#endif /* not RE_ENABLE_I18N */
- int non_match = 0;
- bin_tree_t *work_tree;
- int token_len;
- int first_round = 1;
-#ifdef _LIBC
- collseqmb = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQMB);
- nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES);
- if (nrules)
- {
- /*
- if (MB_CUR_MAX > 1)
- */
- collseqwc = _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQWC);
- table_size = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_SYMB_HASH_SIZEMB);
- symb_table = (const int32_t *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_SYMB_TABLEMB);
- extra = (const unsigned char *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_SYMB_EXTRAMB);
- }
-#endif
- sbcset = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1);
-#ifdef RE_ENABLE_I18N
- mbcset = (re_charset_t *) calloc (sizeof (re_charset_t), 1);
-#endif /* RE_ENABLE_I18N */
-#ifdef RE_ENABLE_I18N
- if (BE (sbcset == NULL || mbcset == NULL, 0))
-#else
- if (BE (sbcset == NULL, 0))
-#endif /* RE_ENABLE_I18N */
- {
- *err = REG_ESPACE;
- return NULL;
- }
-
- token_len = peek_token_bracket (token, regexp, syntax);
- if (BE (token->type == END_OF_RE, 0))
- {
- *err = REG_BADPAT;
- goto parse_bracket_exp_free_return;
- }
- if (token->type == OP_NON_MATCH_LIST)
- {
-#ifdef RE_ENABLE_I18N
- mbcset->non_match = 1;
-#endif /* not RE_ENABLE_I18N */
- non_match = 1;
- if (syntax & RE_HAT_LISTS_NOT_NEWLINE)
- bitset_set (sbcset, '\0');
- re_string_skip_bytes (regexp, token_len); /* Skip a token. */
- token_len = peek_token_bracket (token, regexp, syntax);
- if (BE (token->type == END_OF_RE, 0))
- {
- *err = REG_BADPAT;
- goto parse_bracket_exp_free_return;
- }
- }
-
- /* We treat the first ']' as a normal character. */
- if (token->type == OP_CLOSE_BRACKET)
- token->type = CHARACTER;
-
- while (1)
- {
- bracket_elem_t start_elem, end_elem;
- unsigned char start_name_buf[BRACKET_NAME_BUF_SIZE];
- unsigned char end_name_buf[BRACKET_NAME_BUF_SIZE];
- reg_errcode_t ret;
- int token_len2 = 0, is_range_exp = 0;
- re_token_t token2;
-
- start_elem.opr.name = start_name_buf;
- ret = parse_bracket_element (&start_elem, regexp, token, token_len, dfa,
- syntax, first_round);
- if (BE (ret != REG_NOERROR, 0))
- {
- *err = ret;
- goto parse_bracket_exp_free_return;
- }
- first_round = 0;
-
- /* Get information about the next token. We need it in any case. */
- token_len = peek_token_bracket (token, regexp, syntax);
-
- /* Do not check for ranges if we know they are not allowed. */
- if (start_elem.type != CHAR_CLASS && start_elem.type != EQUIV_CLASS)
- {
- if (BE (token->type == END_OF_RE, 0))
- {
- *err = REG_EBRACK;
- goto parse_bracket_exp_free_return;
- }
- if (token->type == OP_CHARSET_RANGE)
- {
- re_string_skip_bytes (regexp, token_len); /* Skip '-'. */
- token_len2 = peek_token_bracket (&token2, regexp, syntax);
- if (BE (token2.type == END_OF_RE, 0))
- {
- *err = REG_EBRACK;
- goto parse_bracket_exp_free_return;
- }
- if (token2.type == OP_CLOSE_BRACKET)
- {
- /* We treat the last '-' as a normal character. */
- re_string_skip_bytes (regexp, -token_len);
- token->type = CHARACTER;
- }
- else
- is_range_exp = 1;
- }
- }
-
- if (is_range_exp == 1)
- {
- end_elem.opr.name = end_name_buf;
- ret = parse_bracket_element (&end_elem, regexp, &token2, token_len2,
- dfa, syntax, 1);
- if (BE (ret != REG_NOERROR, 0))
- {
- *err = ret;
- goto parse_bracket_exp_free_return;
- }
-
- token_len = peek_token_bracket (token, regexp, syntax);
-
-#ifdef _LIBC
- *err = build_range_exp (sbcset, mbcset, &range_alloc,
- &start_elem, &end_elem);
-#else
-# ifdef RE_ENABLE_I18N
- *err = build_range_exp (sbcset,
- dfa->mb_cur_max > 1 ? mbcset : NULL,
- &range_alloc, &start_elem, &end_elem);
-# else
- *err = build_range_exp (sbcset, &start_elem, &end_elem);
-# endif
-#endif /* RE_ENABLE_I18N */
- if (BE (*err != REG_NOERROR, 0))
- goto parse_bracket_exp_free_return;
- }
- else
- {
- switch (start_elem.type)
- {
- case SB_CHAR:
- bitset_set (sbcset, start_elem.opr.ch);
- break;
-#ifdef RE_ENABLE_I18N
- case MB_CHAR:
- /* Check whether the array has enough space. */
- if (BE (mbchar_alloc == mbcset->nmbchars, 0))
- {
- wchar_t *new_mbchars;
- /* Not enough, realloc it. */
- /* +1 in case of mbcset->nmbchars is 0. */
- mbchar_alloc = 2 * mbcset->nmbchars + 1;
- /* Use realloc since array is NULL if *alloc == 0. */
- new_mbchars = re_realloc (mbcset->mbchars, wchar_t,
- mbchar_alloc);
- if (BE (new_mbchars == NULL, 0))
- goto parse_bracket_exp_espace;
- mbcset->mbchars = new_mbchars;
- }
- mbcset->mbchars[mbcset->nmbchars++] = start_elem.opr.wch;
- break;
-#endif /* RE_ENABLE_I18N */
- case EQUIV_CLASS:
- *err = build_equiv_class (sbcset,
-#ifdef RE_ENABLE_I18N
- mbcset, &equiv_class_alloc,
-#endif /* RE_ENABLE_I18N */
- start_elem.opr.name);
- if (BE (*err != REG_NOERROR, 0))
- goto parse_bracket_exp_free_return;
- break;
- case COLL_SYM:
- *err = build_collating_symbol (sbcset,
-#ifdef RE_ENABLE_I18N
- mbcset, &coll_sym_alloc,
-#endif /* RE_ENABLE_I18N */
- start_elem.opr.name);
- if (BE (*err != REG_NOERROR, 0))
- goto parse_bracket_exp_free_return;
- break;
- case CHAR_CLASS:
- *err = build_charclass (regexp->trans, sbcset,
-#ifdef RE_ENABLE_I18N
- mbcset, &char_class_alloc,
-#endif /* RE_ENABLE_I18N */
- start_elem.opr.name, syntax);
- if (BE (*err != REG_NOERROR, 0))
- goto parse_bracket_exp_free_return;
- break;
- default:
- assert (0);
- break;
- }
- }
- if (BE (token->type == END_OF_RE, 0))
- {
- *err = REG_EBRACK;
- goto parse_bracket_exp_free_return;
- }
- if (token->type == OP_CLOSE_BRACKET)
- break;
- }
-
- re_string_skip_bytes (regexp, token_len); /* Skip a token. */
-
- /* If it is non-matching list. */
- if (non_match)
- bitset_not (sbcset);
-
-#ifdef RE_ENABLE_I18N
- /* Ensure only single byte characters are set. */
- if (dfa->mb_cur_max > 1)
- bitset_mask (sbcset, dfa->sb_char);
-
- if (mbcset->nmbchars || mbcset->ncoll_syms || mbcset->nequiv_classes
- || mbcset->nranges || (dfa->mb_cur_max > 1 && (mbcset->nchar_classes
- || mbcset->non_match)))
- {
- bin_tree_t *mbc_tree;
- int sbc_idx;
- /* Build a tree for complex bracket. */
- dfa->has_mb_node = 1;
- br_token.type = COMPLEX_BRACKET;
- br_token.opr.mbcset = mbcset;
- mbc_tree = create_token_tree (dfa, NULL, NULL, &br_token);
- if (BE (mbc_tree == NULL, 0))
- goto parse_bracket_exp_espace;
- for (sbc_idx = 0; sbc_idx < BITSET_WORDS; ++sbc_idx)
- if (sbcset[sbc_idx])
- break;
- /* If there are no bits set in sbcset, there is no point
- of having both SIMPLE_BRACKET and COMPLEX_BRACKET. */
- if (sbc_idx < BITSET_WORDS)
- {
- /* Build a tree for simple bracket. */
- br_token.type = SIMPLE_BRACKET;
- br_token.opr.sbcset = sbcset;
- work_tree = create_token_tree (dfa, NULL, NULL, &br_token);
- if (BE (work_tree == NULL, 0))
- goto parse_bracket_exp_espace;
-
- /* Then join them by ALT node. */
- work_tree = create_tree (dfa, work_tree, mbc_tree, OP_ALT);
- if (BE (work_tree == NULL, 0))
- goto parse_bracket_exp_espace;
- }
- else
- {
- re_free (sbcset);
- work_tree = mbc_tree;
- }
- }
- else
-#endif /* not RE_ENABLE_I18N */
- {
-#ifdef RE_ENABLE_I18N
- free_charset (mbcset);
-#endif
- /* Build a tree for simple bracket. */
- br_token.type = SIMPLE_BRACKET;
- br_token.opr.sbcset = sbcset;
- work_tree = create_token_tree (dfa, NULL, NULL, &br_token);
- if (BE (work_tree == NULL, 0))
- goto parse_bracket_exp_espace;
- }
- return work_tree;
-
- parse_bracket_exp_espace:
- *err = REG_ESPACE;
- parse_bracket_exp_free_return:
- re_free (sbcset);
-#ifdef RE_ENABLE_I18N
- free_charset (mbcset);
-#endif /* RE_ENABLE_I18N */
- return NULL;
-}
-
-/* Parse an element in the bracket expression. */
-
-static reg_errcode_t
-parse_bracket_element (bracket_elem_t *elem, re_string_t *regexp,
- re_token_t *token, int token_len, re_dfa_t *dfa,
- reg_syntax_t syntax, int accept_hyphen)
-{
-#ifdef RE_ENABLE_I18N
- int cur_char_size;
- cur_char_size = re_string_char_size_at (regexp, re_string_cur_idx (regexp));
- if (cur_char_size > 1)
- {
- elem->type = MB_CHAR;
- elem->opr.wch = re_string_wchar_at (regexp, re_string_cur_idx (regexp));
- re_string_skip_bytes (regexp, cur_char_size);
- return REG_NOERROR;
- }
-#endif /* RE_ENABLE_I18N */
- re_string_skip_bytes (regexp, token_len); /* Skip a token. */
- if (token->type == OP_OPEN_COLL_ELEM || token->type == OP_OPEN_CHAR_CLASS
- || token->type == OP_OPEN_EQUIV_CLASS)
- return parse_bracket_symbol (elem, regexp, token);
- if (BE (token->type == OP_CHARSET_RANGE, 0) && !accept_hyphen)
- {
- /* A '-' must only appear as anything but a range indicator before
- the closing bracket. Everything else is an error. */
- re_token_t token2;
- (void) peek_token_bracket (&token2, regexp, syntax);
- if (token2.type != OP_CLOSE_BRACKET)
- /* The actual error value is not standardized since this whole
- case is undefined. But ERANGE makes good sense. */
- return REG_ERANGE;
- }
- elem->type = SB_CHAR;
- elem->opr.ch = token->opr.c;
- return REG_NOERROR;
-}
-
-/* Parse a bracket symbol in the bracket expression. Bracket symbols are
- such as [:<character_class>:], [.<collating_element>.], and
- [=<equivalent_class>=]. */
-
-static reg_errcode_t
-parse_bracket_symbol (bracket_elem_t *elem, re_string_t *regexp,
- re_token_t *token)
-{
- unsigned char ch, delim = token->opr.c;
- int i = 0;
- if (re_string_eoi(regexp))
- return REG_EBRACK;
- for (;; ++i)
- {
- if (i >= BRACKET_NAME_BUF_SIZE)
- return REG_EBRACK;
- if (token->type == OP_OPEN_CHAR_CLASS)
- ch = re_string_fetch_byte_case (regexp);
- else
- ch = re_string_fetch_byte (regexp);
- if (re_string_eoi(regexp))
- return REG_EBRACK;
- if (ch == delim && re_string_peek_byte (regexp, 0) == ']')
- break;
- elem->opr.name[i] = ch;
- }
- re_string_skip_bytes (regexp, 1);
- elem->opr.name[i] = '\0';
- switch (token->type)
- {
- case OP_OPEN_COLL_ELEM:
- elem->type = COLL_SYM;
- break;
- case OP_OPEN_EQUIV_CLASS:
- elem->type = EQUIV_CLASS;
- break;
- case OP_OPEN_CHAR_CLASS:
- elem->type = CHAR_CLASS;
- break;
- default:
- break;
- }
- return REG_NOERROR;
-}
-
- /* Helper function for parse_bracket_exp.
- Build the equivalence class which is represented by NAME.
- The result are written to MBCSET and SBCSET.
- EQUIV_CLASS_ALLOC is the allocated size of mbcset->equiv_classes,
- is a pointer argument sinse we may update it. */
-
-static reg_errcode_t
-#ifdef RE_ENABLE_I18N
-build_equiv_class (bitset_t sbcset, re_charset_t *mbcset,
- int *equiv_class_alloc, const unsigned char *name)
-#else /* not RE_ENABLE_I18N */
-build_equiv_class (bitset_t sbcset, const unsigned char *name)
-#endif /* not RE_ENABLE_I18N */
-{
-#ifdef _LIBC
- uint32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES);
- if (nrules != 0)
- {
- const int32_t *table, *indirect;
- const unsigned char *weights, *extra, *cp;
- unsigned char char_buf[2];
- int32_t idx1, idx2;
- unsigned int ch;
- size_t len;
- /* This #include defines a local function! */
-# include <locale/weight.h>
- /* Calculate the index for equivalence class. */
- cp = name;
- table = (const int32_t *) _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB);
- weights = (const unsigned char *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_WEIGHTMB);
- extra = (const unsigned char *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_EXTRAMB);
- indirect = (const int32_t *) _NL_CURRENT (LC_COLLATE,
- _NL_COLLATE_INDIRECTMB);
- idx1 = findidx (&cp);
- if (BE (idx1 == 0 || cp < name + strlen ((const char *) name), 0))
- /* This isn't a valid character. */
- return REG_ECOLLATE;
-
- /* Build single byte matcing table for this equivalence class. */
- char_buf[1] = (unsigned char) '\0';
- len = weights[idx1];
- for (ch = 0; ch < SBC_MAX; ++ch)
- {
- char_buf[0] = ch;
- cp = char_buf;
- idx2 = findidx (&cp);
-/*
- idx2 = table[ch];
-*/
- if (idx2 == 0)
- /* This isn't a valid character. */
- continue;
- if (len == weights[idx2])
- {
- int cnt = 0;
- while (cnt <= len &&
- weights[idx1 + 1 + cnt] == weights[idx2 + 1 + cnt])
- ++cnt;
-
- if (cnt > len)
- bitset_set (sbcset, ch);
- }
- }
- /* Check whether the array has enough space. */
- if (BE (*equiv_class_alloc == mbcset->nequiv_classes, 0))
- {
- /* Not enough, realloc it. */
- /* +1 in case of mbcset->nequiv_classes is 0. */
- int new_equiv_class_alloc = 2 * mbcset->nequiv_classes + 1;
- /* Use realloc since the array is NULL if *alloc == 0. */
- int32_t *new_equiv_classes = re_realloc (mbcset->equiv_classes,
- int32_t,
- new_equiv_class_alloc);
- if (BE (new_equiv_classes == NULL, 0))
- return REG_ESPACE;
- mbcset->equiv_classes = new_equiv_classes;
- *equiv_class_alloc = new_equiv_class_alloc;
- }
- mbcset->equiv_classes[mbcset->nequiv_classes++] = idx1;
- }
- else
-#endif /* _LIBC */
- {
- if (BE (strlen ((const char *) name) != 1, 0))
- return REG_ECOLLATE;
- bitset_set (sbcset, *name);
- }
- return REG_NOERROR;
-}
-
- /* Helper function for parse_bracket_exp.
- Build the character class which is represented by NAME.
- The result are written to MBCSET and SBCSET.
- CHAR_CLASS_ALLOC is the allocated size of mbcset->char_classes,
- is a pointer argument sinse we may update it. */
-
-static reg_errcode_t
-#ifdef RE_ENABLE_I18N
-build_charclass (RE_TRANSLATE_TYPE trans, bitset_t sbcset,
- re_charset_t *mbcset, int *char_class_alloc,
- const unsigned char *class_name, reg_syntax_t syntax)
-#else /* not RE_ENABLE_I18N */
-build_charclass (RE_TRANSLATE_TYPE trans, bitset_t sbcset,
- const unsigned char *class_name, reg_syntax_t syntax)
-#endif /* not RE_ENABLE_I18N */
-{
- int i;
- const char *name = (const char *) class_name;
-
- /* In case of REG_ICASE "upper" and "lower" match the both of
- upper and lower cases. */
- if ((syntax & RE_ICASE)
- && (strcmp (name, "upper") == 0 || strcmp (name, "lower") == 0))
- name = "alpha";
-
-#ifdef RE_ENABLE_I18N
- /* Check the space of the arrays. */
- if (BE (*char_class_alloc == mbcset->nchar_classes, 0))
- {
- /* Not enough, realloc it. */
- /* +1 in case of mbcset->nchar_classes is 0. */
- int new_char_class_alloc = 2 * mbcset->nchar_classes + 1;
- /* Use realloc since array is NULL if *alloc == 0. */
- wctype_t *new_char_classes = re_realloc (mbcset->char_classes, wctype_t,
- new_char_class_alloc);
- if (BE (new_char_classes == NULL, 0))
- return REG_ESPACE;
- mbcset->char_classes = new_char_classes;
- *char_class_alloc = new_char_class_alloc;
- }
- mbcset->char_classes[mbcset->nchar_classes++] = __wctype (name);
-#endif /* RE_ENABLE_I18N */
-
-#define BUILD_CHARCLASS_LOOP(ctype_func) \
- do { \
- if (BE (trans != NULL, 0)) \
- { \
- for (i = 0; i < SBC_MAX; ++i) \
- if (ctype_func (i)) \
- bitset_set (sbcset, trans[i]); \
- } \
- else \
- { \
- for (i = 0; i < SBC_MAX; ++i) \
- if (ctype_func (i)) \
- bitset_set (sbcset, i); \
- } \
- } while (0)
-
- if (strcmp (name, "alnum") == 0)
- BUILD_CHARCLASS_LOOP (isalnum);
- else if (strcmp (name, "cntrl") == 0)
- BUILD_CHARCLASS_LOOP (iscntrl);
- else if (strcmp (name, "lower") == 0)
- BUILD_CHARCLASS_LOOP (islower);
- else if (strcmp (name, "space") == 0)
- BUILD_CHARCLASS_LOOP (isspace);
- else if (strcmp (name, "alpha") == 0)
- BUILD_CHARCLASS_LOOP (isalpha);
- else if (strcmp (name, "digit") == 0)
- BUILD_CHARCLASS_LOOP (isdigit);
- else if (strcmp (name, "print") == 0)
- BUILD_CHARCLASS_LOOP (isprint);
- else if (strcmp (name, "upper") == 0)
- BUILD_CHARCLASS_LOOP (isupper);
- else if (strcmp (name, "blank") == 0)
- BUILD_CHARCLASS_LOOP (isblank);
- else if (strcmp (name, "graph") == 0)
- BUILD_CHARCLASS_LOOP (isgraph);
- else if (strcmp (name, "punct") == 0)
- BUILD_CHARCLASS_LOOP (ispunct);
- else if (strcmp (name, "xdigit") == 0)
- BUILD_CHARCLASS_LOOP (isxdigit);
- else
- return REG_ECTYPE;
-
- return REG_NOERROR;
-}
-
-static bin_tree_t *
-build_charclass_op (re_dfa_t *dfa, RE_TRANSLATE_TYPE trans,
- const unsigned char *class_name,
- const unsigned char *extra, int non_match,
- reg_errcode_t *err)
-{
- re_bitset_ptr_t sbcset;
-#ifdef RE_ENABLE_I18N
- re_charset_t *mbcset;
- int alloc = 0;
-#endif /* not RE_ENABLE_I18N */
- reg_errcode_t ret;
- re_token_t br_token;
- bin_tree_t *tree;
-
- sbcset = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1);
-#ifdef RE_ENABLE_I18N
- mbcset = (re_charset_t *) calloc (sizeof (re_charset_t), 1);
-#endif /* RE_ENABLE_I18N */
-
-#ifdef RE_ENABLE_I18N
- if (BE (sbcset == NULL || mbcset == NULL, 0))
-#else /* not RE_ENABLE_I18N */
- if (BE (sbcset == NULL, 0))
-#endif /* not RE_ENABLE_I18N */
- {
- *err = REG_ESPACE;
- return NULL;
- }
-
- if (non_match)
- {
-#ifdef RE_ENABLE_I18N
- /*
- if (syntax & RE_HAT_LISTS_NOT_NEWLINE)
- bitset_set(cset->sbcset, '\0');
- */
- mbcset->non_match = 1;
-#endif /* not RE_ENABLE_I18N */
- }
-
- /* We don't care the syntax in this case. */
- ret = build_charclass (trans, sbcset,
-#ifdef RE_ENABLE_I18N
- mbcset, &alloc,
-#endif /* RE_ENABLE_I18N */
- class_name, 0);
-
- if (BE (ret != REG_NOERROR, 0))
- {
- re_free (sbcset);
-#ifdef RE_ENABLE_I18N
- free_charset (mbcset);
-#endif /* RE_ENABLE_I18N */
- *err = ret;
- return NULL;
- }
- /* \w match '_' also. */
- for (; *extra; extra++)
- bitset_set (sbcset, *extra);
-
- /* If it is non-matching list. */
- if (non_match)
- bitset_not (sbcset);
-
-#ifdef RE_ENABLE_I18N
- /* Ensure only single byte characters are set. */
- if (dfa->mb_cur_max > 1)
- bitset_mask (sbcset, dfa->sb_char);
-#endif
-
- /* Build a tree for simple bracket. */
- br_token.type = SIMPLE_BRACKET;
- br_token.opr.sbcset = sbcset;
- tree = create_token_tree (dfa, NULL, NULL, &br_token);
- if (BE (tree == NULL, 0))
- goto build_word_op_espace;
-
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- {
- bin_tree_t *mbc_tree;
- /* Build a tree for complex bracket. */
- br_token.type = COMPLEX_BRACKET;
- br_token.opr.mbcset = mbcset;
- dfa->has_mb_node = 1;
- mbc_tree = create_token_tree (dfa, NULL, NULL, &br_token);
- if (BE (mbc_tree == NULL, 0))
- goto build_word_op_espace;
- /* Then join them by ALT node. */
- tree = create_tree (dfa, tree, mbc_tree, OP_ALT);
- if (BE (mbc_tree != NULL, 1))
- return tree;
- }
- else
- {
- free_charset (mbcset);
- return tree;
- }
-#else /* not RE_ENABLE_I18N */
- return tree;
-#endif /* not RE_ENABLE_I18N */
-
- build_word_op_espace:
- re_free (sbcset);
-#ifdef RE_ENABLE_I18N
- free_charset (mbcset);
-#endif /* RE_ENABLE_I18N */
- *err = REG_ESPACE;
- return NULL;
-}
-
-/* This is intended for the expressions like "a{1,3}".
- Fetch a number from `input', and return the number.
- Return -1, if the number field is empty like "{,1}".
- Return -2, If an error is occured. */
-
-static int
-fetch_number (re_string_t *input, re_token_t *token, reg_syntax_t syntax)
-{
- int num = -1;
- unsigned char c;
- while (1)
- {
- fetch_token (token, input, syntax);
- c = token->opr.c;
- if (BE (token->type == END_OF_RE, 0))
- return -2;
- if (token->type == OP_CLOSE_DUP_NUM || c == ',')
- break;
- num = ((token->type != CHARACTER || c < '0' || '9' < c || num == -2)
- ? -2 : ((num == -1) ? c - '0' : num * 10 + c - '0'));
- num = (num > RE_DUP_MAX) ? -2 : num;
- }
- return num;
-}
-
-#ifdef RE_ENABLE_I18N
-static void
-free_charset (re_charset_t *cset)
-{
- re_free (cset->mbchars);
-# ifdef _LIBC
- re_free (cset->coll_syms);
- re_free (cset->equiv_classes);
- re_free (cset->range_starts);
- re_free (cset->range_ends);
-# endif
- re_free (cset->char_classes);
- re_free (cset);
-}
-#endif /* RE_ENABLE_I18N */
-
-/* Functions for binary tree operation. */
-
-/* Create a tree node. */
-
-static bin_tree_t *
-create_tree (re_dfa_t *dfa, bin_tree_t *left, bin_tree_t *right,
- re_token_type_t type)
-{
- re_token_t t;
- t.type = type;
- return create_token_tree (dfa, left, right, &t);
-}
-
-static bin_tree_t *
-create_token_tree (re_dfa_t *dfa, bin_tree_t *left, bin_tree_t *right,
- const re_token_t *token)
-{
- bin_tree_t *tree;
- if (BE (dfa->str_tree_storage_idx == BIN_TREE_STORAGE_SIZE, 0))
- {
- bin_tree_storage_t *storage = re_malloc (bin_tree_storage_t, 1);
-
- if (storage == NULL)
- return NULL;
- storage->next = dfa->str_tree_storage;
- dfa->str_tree_storage = storage;
- dfa->str_tree_storage_idx = 0;
- }
- tree = &dfa->str_tree_storage->data[dfa->str_tree_storage_idx++];
-
- tree->parent = NULL;
- tree->left = left;
- tree->right = right;
- tree->token = *token;
- tree->token.duplicated = 0;
- tree->token.opt_subexp = 0;
- tree->first = NULL;
- tree->next = NULL;
- tree->node_idx = -1;
-
- if (left != NULL)
- left->parent = tree;
- if (right != NULL)
- right->parent = tree;
- return tree;
-}
-
-/* Mark the tree SRC as an optional subexpression.
- To be called from preorder or postorder. */
-
-static reg_errcode_t
-mark_opt_subexp (void *extra, bin_tree_t *node)
-{
- int idx = (int) (long) extra;
- if (node->token.type == SUBEXP && node->token.opr.idx == idx)
- node->token.opt_subexp = 1;
-
- return REG_NOERROR;
-}
-
-/* Free the allocated memory inside NODE. */
-
-static void
-free_token (re_token_t *node)
-{
-#ifdef RE_ENABLE_I18N
- if (node->type == COMPLEX_BRACKET && node->duplicated == 0)
- free_charset (node->opr.mbcset);
- else
-#endif /* RE_ENABLE_I18N */
- if (node->type == SIMPLE_BRACKET && node->duplicated == 0)
- re_free (node->opr.sbcset);
-}
-
-/* Worker function for tree walking. Free the allocated memory inside NODE
- and its children. */
-
-static reg_errcode_t
-free_tree (void *extra, bin_tree_t *node)
-{
- free_token (&node->token);
- return REG_NOERROR;
-}
-
-
-/* Duplicate the node SRC, and return new node. This is a preorder
- visit similar to the one implemented by the generic visitor, but
- we need more infrastructure to maintain two parallel trees --- so,
- it's easier to duplicate. */
-
-static bin_tree_t *
-duplicate_tree (const bin_tree_t *root, re_dfa_t *dfa)
-{
- const bin_tree_t *node;
- bin_tree_t *dup_root;
- bin_tree_t **p_new = &dup_root, *dup_node = root->parent;
-
- for (node = root; ; )
- {
- /* Create a new tree and link it back to the current parent. */
- *p_new = create_token_tree (dfa, NULL, NULL, &node->token);
- if (*p_new == NULL)
- return NULL;
- (*p_new)->parent = dup_node;
- (*p_new)->token.duplicated = 1;
- dup_node = *p_new;
-
- /* Go to the left node, or up and to the right. */
- if (node->left)
- {
- node = node->left;
- p_new = &dup_node->left;
- }
- else
- {
- const bin_tree_t *prev = NULL;
- while (node->right == prev || node->right == NULL)
- {
- prev = node;
- node = node->parent;
- dup_node = dup_node->parent;
- if (!node)
- return dup_root;
- }
- node = node->right;
- p_new = &dup_node->right;
- }
- }
-}
-
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-/* GKINCLUDE #include "regexec.c" */
-/******************************************************************************/
-/******************************************************************************/
-/******************************************************************************/
-static reg_errcode_t match_ctx_init (re_match_context_t *cache, int eflags,
- int n) internal_function;
-static void match_ctx_clean (re_match_context_t *mctx) internal_function;
-static void match_ctx_free (re_match_context_t *cache) internal_function;
-static reg_errcode_t match_ctx_add_entry (re_match_context_t *cache, int node,
- int str_idx, int from, int to)
- internal_function;
-static int search_cur_bkref_entry (const re_match_context_t *mctx, int str_idx)
- internal_function;
-static reg_errcode_t match_ctx_add_subtop (re_match_context_t *mctx, int node,
- int str_idx) internal_function;
-static re_sub_match_last_t * match_ctx_add_sublast (re_sub_match_top_t *subtop,
- int node, int str_idx)
- internal_function;
-static void sift_ctx_init (re_sift_context_t *sctx, re_dfastate_t **sifted_sts,
- re_dfastate_t **limited_sts, int last_node,
- int last_str_idx)
- internal_function;
-static reg_errcode_t re_search_internal (const regex_t *preg,
- const char *string, int length,
- int start, int range, int stop,
- size_t nmatch, regmatch_t pmatch[],
- int eflags) internal_function;
-static int re_search_2_stub (struct re_pattern_buffer *bufp,
- const char *string1, int length1,
- const char *string2, int length2,
- int start, int range, struct re_registers *regs,
- int stop, int ret_len) internal_function;
-static int re_search_stub (struct re_pattern_buffer *bufp,
- const char *string, int length, int start,
- int range, int stop, struct re_registers *regs,
- int ret_len) internal_function;
-static unsigned re_copy_regs (struct re_registers *regs, regmatch_t *pmatch,
- int nregs, int regs_allocated) internal_function;
-static reg_errcode_t prune_impossible_nodes (re_match_context_t *mctx)
- internal_function;
-static int check_matching (re_match_context_t *mctx, int fl_longest_match,
- int *p_match_first) internal_function;
-static int check_halt_state_context (const re_match_context_t *mctx,
- const re_dfastate_t *state, int idx)
- internal_function;
-static void update_regs (const re_dfa_t *dfa, regmatch_t *pmatch,
- regmatch_t *prev_idx_match, int cur_node,
- int cur_idx, int nmatch) internal_function;
-static reg_errcode_t push_fail_stack (struct re_fail_stack_t *fs,
- int str_idx, int dest_node, int nregs,
- regmatch_t *regs,
- re_node_set *eps_via_nodes)
- internal_function;
-static reg_errcode_t set_regs (const regex_t *preg,
- const re_match_context_t *mctx,
- size_t nmatch, regmatch_t *pmatch,
- int fl_backtrack) internal_function;
-static reg_errcode_t free_fail_stack_return (struct re_fail_stack_t *fs)
- internal_function;
-
-#ifdef RE_ENABLE_I18N
-static int sift_states_iter_mb (const re_match_context_t *mctx,
- re_sift_context_t *sctx,
- int node_idx, int str_idx, int max_str_idx)
- internal_function;
-#endif /* RE_ENABLE_I18N */
-static reg_errcode_t sift_states_backward (const re_match_context_t *mctx,
- re_sift_context_t *sctx)
- internal_function;
-static reg_errcode_t build_sifted_states (const re_match_context_t *mctx,
- re_sift_context_t *sctx, int str_idx,
- re_node_set *cur_dest)
- internal_function;
-static reg_errcode_t update_cur_sifted_state (const re_match_context_t *mctx,
- re_sift_context_t *sctx,
- int str_idx,
- re_node_set *dest_nodes)
- internal_function;
-static reg_errcode_t add_epsilon_src_nodes (const re_dfa_t *dfa,
- re_node_set *dest_nodes,
- const re_node_set *candidates)
- internal_function;
-static int check_dst_limits (const re_match_context_t *mctx,
- re_node_set *limits,
- int dst_node, int dst_idx, int src_node,
- int src_idx) internal_function;
-static int check_dst_limits_calc_pos_1 (const re_match_context_t *mctx,
- int boundaries, int subexp_idx,
- int from_node, int bkref_idx)
- internal_function;
-static int check_dst_limits_calc_pos (const re_match_context_t *mctx,
- int limit, int subexp_idx,
- int node, int str_idx,
- int bkref_idx) internal_function;
-static reg_errcode_t check_subexp_limits (const re_dfa_t *dfa,
- re_node_set *dest_nodes,
- const re_node_set *candidates,
- re_node_set *limits,
- struct re_backref_cache_entry *bkref_ents,
- int str_idx) internal_function;
-static reg_errcode_t sift_states_bkref (const re_match_context_t *mctx,
- re_sift_context_t *sctx,
- int str_idx, const re_node_set *candidates)
- internal_function;
-static reg_errcode_t merge_state_array (const re_dfa_t *dfa,
- re_dfastate_t **dst,
- re_dfastate_t **src, int num)
- internal_function;
-static re_dfastate_t *find_recover_state (reg_errcode_t *err,
- re_match_context_t *mctx) internal_function;
-static re_dfastate_t *transit_state (reg_errcode_t *err,
- re_match_context_t *mctx,
- re_dfastate_t *state) internal_function;
-static re_dfastate_t *merge_state_with_log (reg_errcode_t *err,
- re_match_context_t *mctx,
- re_dfastate_t *next_state)
- internal_function;
-static reg_errcode_t check_subexp_matching_top (re_match_context_t *mctx,
- re_node_set *cur_nodes,
- int str_idx) internal_function;
-#if 0
-static re_dfastate_t *transit_state_sb (reg_errcode_t *err,
- re_match_context_t *mctx,
- re_dfastate_t *pstate)
- internal_function;
-#endif
-#ifdef RE_ENABLE_I18N
-static reg_errcode_t transit_state_mb (re_match_context_t *mctx,
- re_dfastate_t *pstate)
- internal_function;
-#endif /* RE_ENABLE_I18N */
-static reg_errcode_t transit_state_bkref (re_match_context_t *mctx,
- const re_node_set *nodes)
- internal_function;
-static reg_errcode_t get_subexp (re_match_context_t *mctx,
- int bkref_node, int bkref_str_idx)
- internal_function;
-static reg_errcode_t get_subexp_sub (re_match_context_t *mctx,
- const re_sub_match_top_t *sub_top,
- re_sub_match_last_t *sub_last,
- int bkref_node, int bkref_str)
- internal_function;
-static int find_subexp_node (const re_dfa_t *dfa, const re_node_set *nodes,
- int subexp_idx, int type) internal_function;
-static reg_errcode_t check_arrival (re_match_context_t *mctx,
- state_array_t *path, int top_node,
- int top_str, int last_node, int last_str,
- int type) internal_function;
-static reg_errcode_t check_arrival_add_next_nodes (re_match_context_t *mctx,
- int str_idx,
- re_node_set *cur_nodes,
- re_node_set *next_nodes)
- internal_function;
-static reg_errcode_t check_arrival_expand_ecl (const re_dfa_t *dfa,
- re_node_set *cur_nodes,
- int ex_subexp, int type)
- internal_function;
-static reg_errcode_t check_arrival_expand_ecl_sub (const re_dfa_t *dfa,
- re_node_set *dst_nodes,
- int target, int ex_subexp,
- int type) internal_function;
-static reg_errcode_t expand_bkref_cache (re_match_context_t *mctx,
- re_node_set *cur_nodes, int cur_str,
- int subexp_num, int type)
- internal_function;
-static int build_trtable (const re_dfa_t *dfa,
- re_dfastate_t *state) internal_function;
-#ifdef RE_ENABLE_I18N
-static int check_node_accept_bytes (const re_dfa_t *dfa, int node_idx,
- const re_string_t *input, int idx)
- internal_function;
-# ifdef _LIBC
-static unsigned int find_collation_sequence_value (const unsigned char *mbs,
- size_t name_len)
- internal_function;
-# endif /* _LIBC */
-#endif /* RE_ENABLE_I18N */
-static int group_nodes_into_DFAstates (const re_dfa_t *dfa,
- const re_dfastate_t *state,
- re_node_set *states_node,
- bitset_t *states_ch) internal_function;
-static int check_node_accept (const re_match_context_t *mctx,
- const re_token_t *node, int idx)
- internal_function;
-static reg_errcode_t extend_buffers (re_match_context_t *mctx)
- internal_function;
-
-/* Entry point for POSIX code. */
-
-/* regexec searches for a given pattern, specified by PREG, in the
- string STRING.
-
- If NMATCH is zero or REG_NOSUB was set in the cflags argument to
- `regcomp', we ignore PMATCH. Otherwise, we assume PMATCH has at
- least NMATCH elements, and we set them to the offsets of the
- corresponding matched substrings.
-
- EFLAGS specifies `execution flags' which affect matching: if
- REG_NOTBOL is set, then ^ does not match at the beginning of the
- string; if REG_NOTEOL is set, then $ does not match at the end.
-
- We return 0 if we find a match and REG_NOMATCH if not. */
-
-int
-regexec (preg, string, nmatch, pmatch, eflags)
- const regex_t *__restrict preg;
- const char *__restrict string;
- size_t nmatch;
- regmatch_t pmatch[];
- int eflags;
-{
- reg_errcode_t err;
- int start, length;
- re_dfa_t *dfa = (re_dfa_t *) preg->buffer;
-
- if (eflags & ~(REG_NOTBOL | REG_NOTEOL | REG_STARTEND))
- return REG_BADPAT;
-
- if (eflags & REG_STARTEND)
- {
- start = pmatch[0].rm_so;
- length = pmatch[0].rm_eo;
- }
- else
- {
- start = 0;
- length = strlen (string);
- }
-
- __libc_lock_lock (dfa->lock);
- if (preg->no_sub)
- err = re_search_internal (preg, string, length, start, length - start,
- length, 0, NULL, eflags);
- else
- err = re_search_internal (preg, string, length, start, length - start,
- length, nmatch, pmatch, eflags);
- __libc_lock_unlock (dfa->lock);
- return err != REG_NOERROR;
-}
-
-#ifdef _LIBC
-# include <shlib-compat.h>
-versioned_symbol (libc, __regexec, regexec, GLIBC_2_3_4);
-
-# if SHLIB_COMPAT (libc, GLIBC_2_0, GLIBC_2_3_4)
-__typeof__ (__regexec) __compat_regexec;
-
-int
-attribute_compat_text_section
-__compat_regexec (const regex_t *__restrict preg,
- const char *__restrict string, size_t nmatch,
- regmatch_t pmatch[], int eflags)
-{
- return regexec (preg, string, nmatch, pmatch,
- eflags & (REG_NOTBOL | REG_NOTEOL));
-}
-compat_symbol (libc, __compat_regexec, regexec, GLIBC_2_0);
-# endif
-#endif
-
-/* Entry points for GNU code. */
-
-/* re_match, re_search, re_match_2, re_search_2
-
- The former two functions operate on STRING with length LENGTH,
- while the later two operate on concatenation of STRING1 and STRING2
- with lengths LENGTH1 and LENGTH2, respectively.
-
- re_match() matches the compiled pattern in BUFP against the string,
- starting at index START.
-
- re_search() first tries matching at index START, then it tries to match
- starting from index START + 1, and so on. The last start position tried
- is START + RANGE. (Thus RANGE = 0 forces re_search to operate the same
- way as re_match().)
-
- The parameter STOP of re_{match,search}_2 specifies that no match exceeding
- the first STOP characters of the concatenation of the strings should be
- concerned.
-
- If REGS is not NULL, and BUFP->no_sub is not set, the offsets of the match
- and all groups is stroed in REGS. (For the "_2" variants, the offsets are
- computed relative to the concatenation, not relative to the individual
- strings.)
-
- On success, re_match* functions return the length of the match, re_search*
- return the position of the start of the match. Return value -1 means no
- match was found and -2 indicates an internal error. */
-
-int
-re_match (bufp, string, length, start, regs)
- struct re_pattern_buffer *bufp;
- const char *string;
- int length, start;
- struct re_registers *regs;
-{
- return re_search_stub (bufp, string, length, start, 0, length, regs, 1);
-}
-#ifdef _LIBC
-weak_alias (__re_match, re_match)
-#endif
-
-int
-re_search (bufp, string, length, start, range, regs)
- struct re_pattern_buffer *bufp;
- const char *string;
- int length, start, range;
- struct re_registers *regs;
-{
- return re_search_stub (bufp, string, length, start, range, length, regs, 0);
-}
-#ifdef _LIBC
-weak_alias (__re_search, re_search)
-#endif
-
-int
-re_match_2 (bufp, string1, length1, string2, length2, start, regs, stop)
- struct re_pattern_buffer *bufp;
- const char *string1, *string2;
- int length1, length2, start, stop;
- struct re_registers *regs;
-{
- return re_search_2_stub (bufp, string1, length1, string2, length2,
- start, 0, regs, stop, 1);
-}
-#ifdef _LIBC
-weak_alias (__re_match_2, re_match_2)
-#endif
-
-int
-re_search_2 (bufp, string1, length1, string2, length2, start, range, regs, stop)
- struct re_pattern_buffer *bufp;
- const char *string1, *string2;
- int length1, length2, start, range, stop;
- struct re_registers *regs;
-{
- return re_search_2_stub (bufp, string1, length1, string2, length2,
- start, range, regs, stop, 0);
-}
-#ifdef _LIBC
-weak_alias (__re_search_2, re_search_2)
-#endif
-
-static int
-re_search_2_stub (bufp, string1, length1, string2, length2, start, range, regs,
- stop, ret_len)
- struct re_pattern_buffer *bufp;
- const char *string1, *string2;
- int length1, length2, start, range, stop, ret_len;
- struct re_registers *regs;
-{
- const char *str;
- int rval;
- int len = length1 + length2;
- int free_str = 0;
-
- if (BE (length1 < 0 || length2 < 0 || stop < 0, 0))
- return -2;
-
- /* Concatenate the strings. */
- if (length2 > 0)
- if (length1 > 0)
- {
- char *s = re_malloc (char, len);
-
- if (BE (s == NULL, 0))
- return -2;
-#ifdef _LIBC
- memcpy (__mempcpy (s, string1, length1), string2, length2);
-#else
- memcpy (s, string1, length1);
- memcpy (s + length1, string2, length2);
-#endif
- str = s;
- free_str = 1;
- }
- else
- str = string2;
- else
- str = string1;
-
- rval = re_search_stub (bufp, str, len, start, range, stop, regs,
- ret_len);
- if (free_str)
- re_free ((char *) str);
- return rval;
-}
-
-/* The parameters have the same meaning as those of re_search.
- Additional parameters:
- If RET_LEN is nonzero the length of the match is returned (re_match style);
- otherwise the position of the match is returned. */
-
-static int
-re_search_stub (bufp, string, length, start, range, stop, regs, ret_len)
- struct re_pattern_buffer *bufp;
- const char *string;
- int length, start, range, stop, ret_len;
- struct re_registers *regs;
-{
- reg_errcode_t result;
- regmatch_t *pmatch;
- int nregs, rval;
- int eflags = 0;
- re_dfa_t *dfa = (re_dfa_t *) bufp->buffer;
-
- /* Check for out-of-range. */
- if (BE (start < 0 || start > length, 0))
- return -1;
- if (BE (start + range > length, 0))
- range = length - start;
- else if (BE (start + range < 0, 0))
- range = -start;
-
- __libc_lock_lock (dfa->lock);
-
- eflags |= (bufp->not_bol) ? REG_NOTBOL : 0;
- eflags |= (bufp->not_eol) ? REG_NOTEOL : 0;
-
- /* Compile fastmap if we haven't yet. */
- if (range > 0 && bufp->fastmap != NULL && !bufp->fastmap_accurate)
- re_compile_fastmap (bufp);
-
- if (BE (bufp->no_sub, 0))
- regs = NULL;
-
- /* We need at least 1 register. */
- if (regs == NULL)
- nregs = 1;
- else if (BE (bufp->regs_allocated == REGS_FIXED &&
- regs->num_regs < bufp->re_nsub + 1, 0))
- {
- nregs = regs->num_regs;
- if (BE (nregs < 1, 0))
- {
- /* Nothing can be copied to regs. */
- regs = NULL;
- nregs = 1;
- }
- }
- else
- nregs = bufp->re_nsub + 1;
- pmatch = re_malloc (regmatch_t, nregs);
- if (BE (pmatch == NULL, 0))
- {
- rval = -2;
- goto out;
- }
-
- result = re_search_internal (bufp, string, length, start, range, stop,
- nregs, pmatch, eflags);
-
- rval = 0;
-
- /* I hope we needn't fill ther regs with -1's when no match was found. */
- if (result != REG_NOERROR)
- rval = -1;
- else if (regs != NULL)
- {
- /* If caller wants register contents data back, copy them. */
- bufp->regs_allocated = re_copy_regs (regs, pmatch, nregs,
- bufp->regs_allocated);
- if (BE (bufp->regs_allocated == REGS_UNALLOCATED, 0))
- rval = -2;
- }
-
- if (BE (rval == 0, 1))
- {
- if (ret_len)
- {
- assert (pmatch[0].rm_so == start);
- rval = pmatch[0].rm_eo - start;
- }
- else
- rval = pmatch[0].rm_so;
- }
- re_free (pmatch);
- out:
- __libc_lock_unlock (dfa->lock);
- return rval;
-}
-
-static unsigned
-re_copy_regs (regs, pmatch, nregs, regs_allocated)
- struct re_registers *regs;
- regmatch_t *pmatch;
- int nregs, regs_allocated;
-{
- int rval = REGS_REALLOCATE;
- int i;
- int need_regs = nregs + 1;
- /* We need one extra element beyond `num_regs' for the `-1' marker GNU code
- uses. */
-
- /* Have the register data arrays been allocated? */
- if (regs_allocated == REGS_UNALLOCATED)
- { /* No. So allocate them with malloc. */
- regs->start = re_malloc (regoff_t, need_regs);
- regs->end = re_malloc (regoff_t, need_regs);
- if (BE (regs->start == NULL, 0) || BE (regs->end == NULL, 0))
- return REGS_UNALLOCATED;
- regs->num_regs = need_regs;
- }
- else if (regs_allocated == REGS_REALLOCATE)
- { /* Yes. If we need more elements than were already
- allocated, reallocate them. If we need fewer, just
- leave it alone. */
- if (BE (need_regs > regs->num_regs, 0))
- {
- regoff_t *new_start = re_realloc (regs->start, regoff_t, need_regs);
- regoff_t *new_end = re_realloc (regs->end, regoff_t, need_regs);
- if (BE (new_start == NULL, 0) || BE (new_end == NULL, 0))
- return REGS_UNALLOCATED;
- regs->start = new_start;
- regs->end = new_end;
- regs->num_regs = need_regs;
- }
- }
- else
- {
- assert (regs_allocated == REGS_FIXED);
- /* This function may not be called with REGS_FIXED and nregs too big. */
- assert (regs->num_regs >= nregs);
- rval = REGS_FIXED;
- }
-
- /* Copy the regs. */
- for (i = 0; i < nregs; ++i)
- {
- regs->start[i] = pmatch[i].rm_so;
- regs->end[i] = pmatch[i].rm_eo;
- }
- for ( ; i < regs->num_regs; ++i)
- regs->start[i] = regs->end[i] = -1;
-
- return rval;
-}
-
-/* Set REGS to hold NUM_REGS registers, storing them in STARTS and
- ENDS. Subsequent matches using PATTERN_BUFFER and REGS will use
- this memory for recording register information. STARTS and ENDS
- must be allocated using the malloc library routine, and must each
- be at least NUM_REGS * sizeof (regoff_t) bytes long.
-
- If NUM_REGS == 0, then subsequent matches should allocate their own
- register data.
-
- Unless this function is called, the first search or match using
- PATTERN_BUFFER will allocate its own register data, without
- freeing the old data. */
-
-void
-re_set_registers (bufp, regs, num_regs, starts, ends)
- struct re_pattern_buffer *bufp;
- struct re_registers *regs;
- unsigned num_regs;
- regoff_t *starts, *ends;
-{
- if (num_regs)
- {
- bufp->regs_allocated = REGS_REALLOCATE;
- regs->num_regs = num_regs;
- regs->start = starts;
- regs->end = ends;
- }
- else
- {
- bufp->regs_allocated = REGS_UNALLOCATED;
- regs->num_regs = 0;
- regs->start = regs->end = (regoff_t *) 0;
- }
-}
-#ifdef _LIBC
-weak_alias (__re_set_registers, re_set_registers)
-#endif
-
-/* Entry points compatible with 4.2 BSD regex library. We don't define
- them unless specifically requested. */
-
-#if defined _REGEX_RE_COMP || defined _LIBC
-int
-# ifdef _LIBC
-weak_function
-# endif
-re_exec (s)
- const char *s;
-{
- return 0 == regexec (&re_comp_buf, s, 0, NULL, 0);
-}
-#endif /* _REGEX_RE_COMP */
-
-/* Internal entry point. */
-
-/* Searches for a compiled pattern PREG in the string STRING, whose
- length is LENGTH. NMATCH, PMATCH, and EFLAGS have the same
- mingings with regexec. START, and RANGE have the same meanings
- with re_search.
- Return REG_NOERROR if we find a match, and REG_NOMATCH if not,
- otherwise return the error code.
- Note: We assume front end functions already check ranges.
- (START + RANGE >= 0 && START + RANGE <= LENGTH) */
-
-static reg_errcode_t
-re_search_internal (preg, string, length, start, range, stop, nmatch, pmatch,
- eflags)
- const regex_t *preg;
- const char *string;
- int length, start, range, stop, eflags;
- size_t nmatch;
- regmatch_t pmatch[];
-{
- reg_errcode_t err;
- const re_dfa_t *dfa = (const re_dfa_t *) preg->buffer;
- int left_lim, right_lim, incr;
- int fl_longest_match, match_first, match_kind, match_last = -1;
- int extra_nmatch;
- int sb, ch;
-#if defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L)
- re_match_context_t mctx = { .dfa = dfa };
-#else
- re_match_context_t mctx;
-#endif
- char *fastmap = (preg->fastmap != NULL && preg->fastmap_accurate
- && range && !preg->can_be_null) ? preg->fastmap : NULL;
- RE_TRANSLATE_TYPE t = preg->translate;
-
-#if !(defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L))
- memset (&mctx, '\0', sizeof (re_match_context_t));
- mctx.dfa = dfa;
-#endif
-
- extra_nmatch = (nmatch > preg->re_nsub) ? nmatch - (preg->re_nsub + 1) : 0;
- nmatch -= extra_nmatch;
-
- /* Check if the DFA haven't been compiled. */
- if (BE (preg->used == 0 || dfa->init_state == NULL
- || dfa->init_state_word == NULL || dfa->init_state_nl == NULL
- || dfa->init_state_begbuf == NULL, 0))
- return REG_NOMATCH;
-
-#ifdef DEBUG
- /* We assume front-end functions already check them. */
- assert (start + range >= 0 && start + range <= length);
-#endif
-
- /* If initial states with non-begbuf contexts have no elements,
- the regex must be anchored. If preg->newline_anchor is set,
- we'll never use init_state_nl, so do not check it. */
- if (dfa->init_state->nodes.nelem == 0
- && dfa->init_state_word->nodes.nelem == 0
- && (dfa->init_state_nl->nodes.nelem == 0
- || !preg->newline_anchor))
- {
- if (start != 0 && start + range != 0)
- return REG_NOMATCH;
- start = range = 0;
- }
-
- /* We must check the longest matching, if nmatch > 0. */
- fl_longest_match = (nmatch != 0 || dfa->nbackref);
-
- err = re_string_allocate (&mctx.input, string, length, dfa->nodes_len + 1,
- preg->translate, preg->syntax & RE_ICASE, dfa);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- mctx.input.stop = stop;
- mctx.input.raw_stop = stop;
- mctx.input.newline_anchor = preg->newline_anchor;
-
- err = match_ctx_init (&mctx, eflags, dfa->nbackref * 2);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
-
- /* We will log all the DFA states through which the dfa pass,
- if nmatch > 1, or this dfa has "multibyte node", which is a
- back-reference or a node which can accept multibyte character or
- multi character collating element. */
- if (nmatch > 1 || dfa->has_mb_node)
- {
- mctx.state_log = re_malloc (re_dfastate_t *, mctx.input.bufs_len + 1);
- if (BE (mctx.state_log == NULL, 0))
- {
- err = REG_ESPACE;
- goto free_return;
- }
- }
- else
- mctx.state_log = NULL;
-
- match_first = start;
- mctx.input.tip_context = (eflags & REG_NOTBOL) ? CONTEXT_BEGBUF
- : CONTEXT_NEWLINE | CONTEXT_BEGBUF;
-
- /* Check incrementally whether of not the input string match. */
- incr = (range < 0) ? -1 : 1;
- left_lim = (range < 0) ? start + range : start;
- right_lim = (range < 0) ? start : start + range;
- sb = dfa->mb_cur_max == 1;
- match_kind =
- (fastmap
- ? ((sb || !(preg->syntax & RE_ICASE || t) ? 4 : 0)
- | (range >= 0 ? 2 : 0)
- | (t != NULL ? 1 : 0))
- : 8);
-
- for (;; match_first += incr)
- {
- err = REG_NOMATCH;
- if (match_first < left_lim || right_lim < match_first)
- goto free_return;
-
- /* Advance as rapidly as possible through the string, until we
- find a plausible place to start matching. This may be done
- with varying efficiency, so there are various possibilities:
- only the most common of them are specialized, in order to
- save on code size. We use a switch statement for speed. */
- switch (match_kind)
- {
- case 8:
- /* No fastmap. */
- break;
-
- case 7:
- /* Fastmap with single-byte translation, match forward. */
- while (BE (match_first < right_lim, 1)
- && !fastmap[t[(unsigned char) string[match_first]]])
- ++match_first;
- goto forward_match_found_start_or_reached_end;
-
- case 6:
- /* Fastmap without translation, match forward. */
- while (BE (match_first < right_lim, 1)
- && !fastmap[(unsigned char) string[match_first]])
- ++match_first;
-
- forward_match_found_start_or_reached_end:
- if (BE (match_first == right_lim, 0))
- {
- ch = match_first >= length
- ? 0 : (unsigned char) string[match_first];
- if (!fastmap[t ? t[ch] : ch])
- goto free_return;
- }
- break;
-
- case 4:
- case 5:
- /* Fastmap without multi-byte translation, match backwards. */
- while (match_first >= left_lim)
- {
- ch = match_first >= length
- ? 0 : (unsigned char) string[match_first];
- if (fastmap[t ? t[ch] : ch])
- break;
- --match_first;
- }
- if (match_first < left_lim)
- goto free_return;
- break;
-
- default:
- /* In this case, we can't determine easily the current byte,
- since it might be a component byte of a multibyte
- character. Then we use the constructed buffer instead. */
- for (;;)
- {
- /* If MATCH_FIRST is out of the valid range, reconstruct the
- buffers. */
- unsigned int offset = match_first - mctx.input.raw_mbs_idx;
- if (BE (offset >= (unsigned int) mctx.input.valid_raw_len, 0))
- {
- err = re_string_reconstruct (&mctx.input, match_first,
- eflags);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
-
- offset = match_first - mctx.input.raw_mbs_idx;
- }
- /* If MATCH_FIRST is out of the buffer, leave it as '\0'.
- Note that MATCH_FIRST must not be smaller than 0. */
- ch = (match_first >= length
- ? 0 : re_string_byte_at (&mctx.input, offset));
- if (fastmap[ch])
- break;
- match_first += incr;
- if (match_first < left_lim || match_first > right_lim)
- {
- err = REG_NOMATCH;
- goto free_return;
- }
- }
- break;
- }
-
- /* Reconstruct the buffers so that the matcher can assume that
- the matching starts from the beginning of the buffer. */
- err = re_string_reconstruct (&mctx.input, match_first, eflags);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
-
-#ifdef RE_ENABLE_I18N
- /* Don't consider this char as a possible match start if it part,
- yet isn't the head, of a multibyte character. */
- if (!sb && !re_string_first_byte (&mctx.input, 0))
- continue;
-#endif
-
- /* It seems to be appropriate one, then use the matcher. */
- /* We assume that the matching starts from 0. */
- mctx.state_log_top = mctx.nbkref_ents = mctx.max_mb_elem_len = 0;
- match_last = check_matching (&mctx, fl_longest_match,
- range >= 0 ? &match_first : NULL);
- if (match_last != -1)
- {
- if (BE (match_last == -2, 0))
- {
- err = REG_ESPACE;
- goto free_return;
- }
- else
- {
- mctx.match_last = match_last;
- if ((!preg->no_sub && nmatch > 1) || dfa->nbackref)
- {
- re_dfastate_t *pstate = mctx.state_log[match_last];
- mctx.last_node = check_halt_state_context (&mctx, pstate,
- match_last);
- }
- if ((!preg->no_sub && nmatch > 1 && dfa->has_plural_match)
- || dfa->nbackref)
- {
- err = prune_impossible_nodes (&mctx);
- if (err == REG_NOERROR)
- break;
- if (BE (err != REG_NOMATCH, 0))
- goto free_return;
- match_last = -1;
- }
- else
- break; /* We found a match. */
- }
- }
-
- match_ctx_clean (&mctx);
- }
-
-#ifdef DEBUG
- assert (match_last != -1);
- assert (err == REG_NOERROR);
-#endif
-
- /* Set pmatch[] if we need. */
- if (nmatch > 0)
- {
- int reg_idx;
-
- /* Initialize registers. */
- for (reg_idx = 1; reg_idx < nmatch; ++reg_idx)
- pmatch[reg_idx].rm_so = pmatch[reg_idx].rm_eo = -1;
-
- /* Set the points where matching start/end. */
- pmatch[0].rm_so = 0;
- pmatch[0].rm_eo = mctx.match_last;
-
- if (!preg->no_sub && nmatch > 1)
- {
- err = set_regs (preg, &mctx, nmatch, pmatch,
- dfa->has_plural_match && dfa->nbackref > 0);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
-
- /* At last, add the offset to the each registers, since we slided
- the buffers so that we could assume that the matching starts
- from 0. */
- for (reg_idx = 0; reg_idx < nmatch; ++reg_idx)
- if (pmatch[reg_idx].rm_so != -1)
- {
-#ifdef RE_ENABLE_I18N
- if (BE (mctx.input.offsets_needed != 0, 0))
- {
- pmatch[reg_idx].rm_so =
- (pmatch[reg_idx].rm_so == mctx.input.valid_len
- ? mctx.input.valid_raw_len
- : mctx.input.offsets[pmatch[reg_idx].rm_so]);
- pmatch[reg_idx].rm_eo =
- (pmatch[reg_idx].rm_eo == mctx.input.valid_len
- ? mctx.input.valid_raw_len
- : mctx.input.offsets[pmatch[reg_idx].rm_eo]);
- }
-#else
- assert (mctx.input.offsets_needed == 0);
-#endif
- pmatch[reg_idx].rm_so += match_first;
- pmatch[reg_idx].rm_eo += match_first;
- }
- for (reg_idx = 0; reg_idx < extra_nmatch; ++reg_idx)
- {
- pmatch[nmatch + reg_idx].rm_so = -1;
- pmatch[nmatch + reg_idx].rm_eo = -1;
- }
-
- if (dfa->subexp_map)
- for (reg_idx = 0; reg_idx + 1 < nmatch; reg_idx++)
- if (dfa->subexp_map[reg_idx] != reg_idx)
- {
- pmatch[reg_idx + 1].rm_so
- = pmatch[dfa->subexp_map[reg_idx] + 1].rm_so;
- pmatch[reg_idx + 1].rm_eo
- = pmatch[dfa->subexp_map[reg_idx] + 1].rm_eo;
- }
- }
-
- free_return:
- re_free (mctx.state_log);
- if (dfa->nbackref)
- match_ctx_free (&mctx);
- re_string_destruct (&mctx.input);
- return err;
-}
-
-static reg_errcode_t
-prune_impossible_nodes (mctx)
- re_match_context_t *mctx;
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int halt_node, match_last;
- reg_errcode_t ret;
- re_dfastate_t **sifted_states;
- re_dfastate_t **lim_states = NULL;
- re_sift_context_t sctx;
-#ifdef DEBUG
- assert (mctx->state_log != NULL);
-#endif
- match_last = mctx->match_last;
- halt_node = mctx->last_node;
- sifted_states = re_malloc (re_dfastate_t *, match_last + 1);
- if (BE (sifted_states == NULL, 0))
- {
- ret = REG_ESPACE;
- goto free_return;
- }
- if (dfa->nbackref)
- {
- lim_states = re_malloc (re_dfastate_t *, match_last + 1);
- if (BE (lim_states == NULL, 0))
- {
- ret = REG_ESPACE;
- goto free_return;
- }
- while (1)
- {
- memset (lim_states, '\0',
- sizeof (re_dfastate_t *) * (match_last + 1));
- sift_ctx_init (&sctx, sifted_states, lim_states, halt_node,
- match_last);
- ret = sift_states_backward (mctx, &sctx);
- re_node_set_free (&sctx.limits);
- if (BE (ret != REG_NOERROR, 0))
- goto free_return;
- if (sifted_states[0] != NULL || lim_states[0] != NULL)
- break;
- do
- {
- --match_last;
- if (match_last < 0)
- {
- ret = REG_NOMATCH;
- goto free_return;
- }
- } while (mctx->state_log[match_last] == NULL
- || !mctx->state_log[match_last]->halt);
- halt_node = check_halt_state_context (mctx,
- mctx->state_log[match_last],
- match_last);
- }
- ret = merge_state_array (dfa, sifted_states, lim_states,
- match_last + 1);
- re_free (lim_states);
- lim_states = NULL;
- if (BE (ret != REG_NOERROR, 0))
- goto free_return;
- }
- else
- {
- sift_ctx_init (&sctx, sifted_states, lim_states, halt_node, match_last);
- ret = sift_states_backward (mctx, &sctx);
- re_node_set_free (&sctx.limits);
- if (BE (ret != REG_NOERROR, 0))
- goto free_return;
- }
- re_free (mctx->state_log);
- mctx->state_log = sifted_states;
- sifted_states = NULL;
- mctx->last_node = halt_node;
- mctx->match_last = match_last;
- ret = REG_NOERROR;
- free_return:
- re_free (sifted_states);
- re_free (lim_states);
- return ret;
-}
-
-/* Acquire an initial state and return it.
- We must select appropriate initial state depending on the context,
- since initial states may have constraints like "\<", "^", etc.. */
-
-static inline re_dfastate_t *
-__attribute ((always_inline)) internal_function
-acquire_init_state_context (reg_errcode_t *err, const re_match_context_t *mctx,
- int idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- if (dfa->init_state->has_constraint)
- {
- unsigned int context;
- context = re_string_context_at (&mctx->input, idx - 1, mctx->eflags);
- if (IS_WORD_CONTEXT (context))
- return dfa->init_state_word;
- else if (IS_ORDINARY_CONTEXT (context))
- return dfa->init_state;
- else if (IS_BEGBUF_CONTEXT (context) && IS_NEWLINE_CONTEXT (context))
- return dfa->init_state_begbuf;
- else if (IS_NEWLINE_CONTEXT (context))
- return dfa->init_state_nl;
- else if (IS_BEGBUF_CONTEXT (context))
- {
- /* It is relatively rare case, then calculate on demand. */
- return re_acquire_state_context (err, dfa,
- dfa->init_state->entrance_nodes,
- context);
- }
- else
- /* Must not happen? */
- return dfa->init_state;
- }
- else
- return dfa->init_state;
-}
-
-/* Check whether the regular expression match input string INPUT or not,
- and return the index where the matching end, return -1 if not match,
- or return -2 in case of an error.
- FL_LONGEST_MATCH means we want the POSIX longest matching.
- If P_MATCH_FIRST is not NULL, and the match fails, it is set to the
- next place where we may want to try matching.
- Note that the matcher assume that the maching starts from the current
- index of the buffer. */
-
-static int
-internal_function
-check_matching (re_match_context_t *mctx, int fl_longest_match,
- int *p_match_first)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err;
- int match = 0;
- int match_last = -1;
- int cur_str_idx = re_string_cur_idx (&mctx->input);
- re_dfastate_t *cur_state;
- int at_init_state = p_match_first != NULL;
- int next_start_idx = cur_str_idx;
-
- err = REG_NOERROR;
- cur_state = acquire_init_state_context (&err, mctx, cur_str_idx);
- /* An initial state must not be NULL (invalid). */
- if (BE (cur_state == NULL, 0))
- {
- assert (err == REG_ESPACE);
- return -2;
- }
-
- if (mctx->state_log != NULL)
- {
- mctx->state_log[cur_str_idx] = cur_state;
-
- /* Check OP_OPEN_SUBEXP in the initial state in case that we use them
- later. E.g. Processing back references. */
- if (BE (dfa->nbackref, 0))
- {
- at_init_state = 0;
- err = check_subexp_matching_top (mctx, &cur_state->nodes, 0);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- if (cur_state->has_backref)
- {
- err = transit_state_bkref (mctx, &cur_state->nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- }
- }
-
- /* If the RE accepts NULL string. */
- if (BE (cur_state->halt, 0))
- {
- if (!cur_state->has_constraint
- || check_halt_state_context (mctx, cur_state, cur_str_idx))
- {
- if (!fl_longest_match)
- return cur_str_idx;
- else
- {
- match_last = cur_str_idx;
- match = 1;
- }
- }
- }
-
- while (!re_string_eoi (&mctx->input))
- {
- re_dfastate_t *old_state = cur_state;
- int next_char_idx = re_string_cur_idx (&mctx->input) + 1;
-
- if (BE (next_char_idx >= mctx->input.bufs_len, 0)
- || (BE (next_char_idx >= mctx->input.valid_len, 0)
- && mctx->input.valid_len < mctx->input.len))
- {
- err = extend_buffers (mctx);
- if (BE (err != REG_NOERROR, 0))
- {
- assert (err == REG_ESPACE);
- return -2;
- }
- }
-
- cur_state = transit_state (&err, mctx, cur_state);
- if (mctx->state_log != NULL)
- cur_state = merge_state_with_log (&err, mctx, cur_state);
-
- if (cur_state == NULL)
- {
- /* Reached the invalid state or an error. Try to recover a valid
- state using the state log, if available and if we have not
- already found a valid (even if not the longest) match. */
- if (BE (err != REG_NOERROR, 0))
- return -2;
-
- if (mctx->state_log == NULL
- || (match && !fl_longest_match)
- || (cur_state = find_recover_state (&err, mctx)) == NULL)
- break;
- }
-
- if (BE (at_init_state, 0))
- {
- if (old_state == cur_state)
- next_start_idx = next_char_idx;
- else
- at_init_state = 0;
- }
-
- if (cur_state->halt)
- {
- /* Reached a halt state.
- Check the halt state can satisfy the current context. */
- if (!cur_state->has_constraint
- || check_halt_state_context (mctx, cur_state,
- re_string_cur_idx (&mctx->input)))
- {
- /* We found an appropriate halt state. */
- match_last = re_string_cur_idx (&mctx->input);
- match = 1;
-
- /* We found a match, do not modify match_first below. */
- p_match_first = NULL;
- if (!fl_longest_match)
- break;
- }
- }
- }
-
- if (p_match_first)
- *p_match_first += next_start_idx;
-
- return match_last;
-}
-
-/* Check NODE match the current context. */
-
-static int
-internal_function
-check_halt_node_context (const re_dfa_t *dfa, int node, unsigned int context)
-{
- re_token_type_t type = dfa->nodes[node].type;
- unsigned int constraint = dfa->nodes[node].constraint;
- if (type != END_OF_RE)
- return 0;
- if (!constraint)
- return 1;
- if (NOT_SATISFY_NEXT_CONSTRAINT (constraint, context))
- return 0;
- return 1;
-}
-
-/* Check the halt state STATE match the current context.
- Return 0 if not match, if the node, STATE has, is a halt node and
- match the context, return the node. */
-
-static int
-internal_function
-check_halt_state_context (const re_match_context_t *mctx,
- const re_dfastate_t *state, int idx)
-{
- int i;
- unsigned int context;
-#ifdef DEBUG
- assert (state->halt);
-#endif
- context = re_string_context_at (&mctx->input, idx, mctx->eflags);
- for (i = 0; i < state->nodes.nelem; ++i)
- if (check_halt_node_context (mctx->dfa, state->nodes.elems[i], context))
- return state->nodes.elems[i];
- return 0;
-}
-
-/* Compute the next node to which "NFA" transit from NODE("NFA" is a NFA
- corresponding to the DFA).
- Return the destination node, and update EPS_VIA_NODES, return -1 in case
- of errors. */
-
-static int
-internal_function
-proceed_next_node (const re_match_context_t *mctx, int nregs, regmatch_t *regs,
- int *pidx, int node, re_node_set *eps_via_nodes,
- struct re_fail_stack_t *fs)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int i, err;
- if (IS_EPSILON_NODE (dfa->nodes[node].type))
- {
- re_node_set *cur_nodes = &mctx->state_log[*pidx]->nodes;
- re_node_set *edests = &dfa->edests[node];
- int dest_node;
- err = re_node_set_insert (eps_via_nodes, node);
- if (BE (err < 0, 0))
- return -2;
- /* Pick up a valid destination, or return -1 if none is found. */
- for (dest_node = -1, i = 0; i < edests->nelem; ++i)
- {
- int candidate = edests->elems[i];
- if (!re_node_set_contains (cur_nodes, candidate))
- continue;
- if (dest_node == -1)
- dest_node = candidate;
-
- else
- {
- /* In order to avoid infinite loop like "(a*)*", return the second
- epsilon-transition if the first was already considered. */
- if (re_node_set_contains (eps_via_nodes, dest_node))
- return candidate;
-
- /* Otherwise, push the second epsilon-transition on the fail stack. */
- else if (fs != NULL
- && push_fail_stack (fs, *pidx, candidate, nregs, regs,
- eps_via_nodes))
- return -2;
-
- /* We know we are going to exit. */
- break;
- }
- }
- return dest_node;
- }
- else
- {
- int naccepted = 0;
- re_token_type_t type = dfa->nodes[node].type;
-
-#ifdef RE_ENABLE_I18N
- if (dfa->nodes[node].accept_mb)
- naccepted = check_node_accept_bytes (dfa, node, &mctx->input, *pidx);
- else
-#endif /* RE_ENABLE_I18N */
- if (type == OP_BACK_REF)
- {
- int subexp_idx = dfa->nodes[node].opr.idx + 1;
- naccepted = regs[subexp_idx].rm_eo - regs[subexp_idx].rm_so;
- if (fs != NULL)
- {
- if (regs[subexp_idx].rm_so == -1 || regs[subexp_idx].rm_eo == -1)
- return -1;
- else if (naccepted)
- {
- char *buf = (char *) re_string_get_buffer (&mctx->input);
- if (memcmp (buf + regs[subexp_idx].rm_so, buf + *pidx,
- naccepted) != 0)
- return -1;
- }
- }
-
- if (naccepted == 0)
- {
- int dest_node;
- err = re_node_set_insert (eps_via_nodes, node);
- if (BE (err < 0, 0))
- return -2;
- dest_node = dfa->edests[node].elems[0];
- if (re_node_set_contains (&mctx->state_log[*pidx]->nodes,
- dest_node))
- return dest_node;
- }
- }
-
- if (naccepted != 0
- || check_node_accept (mctx, dfa->nodes + node, *pidx))
- {
- int dest_node = dfa->nexts[node];
- *pidx = (naccepted == 0) ? *pidx + 1 : *pidx + naccepted;
- if (fs && (*pidx > mctx->match_last || mctx->state_log[*pidx] == NULL
- || !re_node_set_contains (&mctx->state_log[*pidx]->nodes,
- dest_node)))
- return -1;
- re_node_set_empty (eps_via_nodes);
- return dest_node;
- }
- }
- return -1;
-}
-
-static reg_errcode_t
-internal_function
-push_fail_stack (struct re_fail_stack_t *fs, int str_idx, int dest_node,
- int nregs, regmatch_t *regs, re_node_set *eps_via_nodes)
-{
- reg_errcode_t err;
- int num = fs->num++;
- if (fs->num == fs->alloc)
- {
- struct re_fail_stack_ent_t *new_array;
- new_array = realloc (fs->stack, (sizeof (struct re_fail_stack_ent_t)
- * fs->alloc * 2));
- if (new_array == NULL)
- return REG_ESPACE;
- fs->alloc *= 2;
- fs->stack = new_array;
- }
- fs->stack[num].idx = str_idx;
- fs->stack[num].node = dest_node;
- fs->stack[num].regs = re_malloc (regmatch_t, nregs);
- if (fs->stack[num].regs == NULL)
- return REG_ESPACE;
- memcpy (fs->stack[num].regs, regs, sizeof (regmatch_t) * nregs);
- err = re_node_set_init_copy (&fs->stack[num].eps_via_nodes, eps_via_nodes);
- return err;
-}
-
-static int
-internal_function
-pop_fail_stack (struct re_fail_stack_t *fs, int *pidx, int nregs,
- regmatch_t *regs, re_node_set *eps_via_nodes)
-{
- int num = --fs->num;
- assert (num >= 0);
- *pidx = fs->stack[num].idx;
- memcpy (regs, fs->stack[num].regs, sizeof (regmatch_t) * nregs);
- re_node_set_free (eps_via_nodes);
- re_free (fs->stack[num].regs);
- *eps_via_nodes = fs->stack[num].eps_via_nodes;
- return fs->stack[num].node;
-}
-
-/* Set the positions where the subexpressions are starts/ends to registers
- PMATCH.
- Note: We assume that pmatch[0] is already set, and
- pmatch[i].rm_so == pmatch[i].rm_eo == -1 for 0 < i < nmatch. */
-
-static reg_errcode_t
-internal_function
-set_regs (const regex_t *preg, const re_match_context_t *mctx, size_t nmatch,
- regmatch_t *pmatch, int fl_backtrack)
-{
- const re_dfa_t *dfa = (const re_dfa_t *) preg->buffer;
- int idx, cur_node;
- re_node_set eps_via_nodes;
- struct re_fail_stack_t *fs;
- struct re_fail_stack_t fs_body = { 0, 2, NULL };
- regmatch_t *prev_idx_match;
- int prev_idx_match_malloced = 0;
-
-#ifdef DEBUG
- assert (nmatch > 1);
- assert (mctx->state_log != NULL);
-#endif
- if (fl_backtrack)
- {
- fs = &fs_body;
- fs->stack = re_malloc (struct re_fail_stack_ent_t, fs->alloc);
- if (fs->stack == NULL)
- return REG_ESPACE;
- }
- else
- fs = NULL;
-
- cur_node = dfa->init_node;
- re_node_set_init_empty (&eps_via_nodes);
-
- if (__libc_use_alloca (nmatch * sizeof (regmatch_t)))
- prev_idx_match = (regmatch_t *) alloca (nmatch * sizeof (regmatch_t));
- else
- {
- prev_idx_match = re_malloc (regmatch_t, nmatch);
- if (prev_idx_match == NULL)
- {
- free_fail_stack_return (fs);
- return REG_ESPACE;
- }
- prev_idx_match_malloced = 1;
- }
- memcpy (prev_idx_match, pmatch, sizeof (regmatch_t) * nmatch);
-
- for (idx = pmatch[0].rm_so; idx <= pmatch[0].rm_eo ;)
- {
- update_regs (dfa, pmatch, prev_idx_match, cur_node, idx, nmatch);
-
- if (idx == pmatch[0].rm_eo && cur_node == mctx->last_node)
- {
- int reg_idx;
- if (fs)
- {
- for (reg_idx = 0; reg_idx < nmatch; ++reg_idx)
- if (pmatch[reg_idx].rm_so > -1 && pmatch[reg_idx].rm_eo == -1)
- break;
- if (reg_idx == nmatch)
- {
- re_node_set_free (&eps_via_nodes);
- if (prev_idx_match_malloced)
- re_free (prev_idx_match);
- return free_fail_stack_return (fs);
- }
- cur_node = pop_fail_stack (fs, &idx, nmatch, pmatch,
- &eps_via_nodes);
- }
- else
- {
- re_node_set_free (&eps_via_nodes);
- if (prev_idx_match_malloced)
- re_free (prev_idx_match);
- return REG_NOERROR;
- }
- }
-
- /* Proceed to next node. */
- cur_node = proceed_next_node (mctx, nmatch, pmatch, &idx, cur_node,
- &eps_via_nodes, fs);
-
- if (BE (cur_node < 0, 0))
- {
- if (BE (cur_node == -2, 0))
- {
- re_node_set_free (&eps_via_nodes);
- if (prev_idx_match_malloced)
- re_free (prev_idx_match);
- free_fail_stack_return (fs);
- return REG_ESPACE;
- }
- if (fs)
- cur_node = pop_fail_stack (fs, &idx, nmatch, pmatch,
- &eps_via_nodes);
- else
- {
- re_node_set_free (&eps_via_nodes);
- if (prev_idx_match_malloced)
- re_free (prev_idx_match);
- return REG_NOMATCH;
- }
- }
- }
- re_node_set_free (&eps_via_nodes);
- if (prev_idx_match_malloced)
- re_free (prev_idx_match);
- return free_fail_stack_return (fs);
-}
-
-static reg_errcode_t
-internal_function
-free_fail_stack_return (struct re_fail_stack_t *fs)
-{
- if (fs)
- {
- int fs_idx;
- for (fs_idx = 0; fs_idx < fs->num; ++fs_idx)
- {
- re_node_set_free (&fs->stack[fs_idx].eps_via_nodes);
- re_free (fs->stack[fs_idx].regs);
- }
- re_free (fs->stack);
- }
- return REG_NOERROR;
-}
-
-static void
-internal_function
-update_regs (const re_dfa_t *dfa, regmatch_t *pmatch,
- regmatch_t *prev_idx_match, int cur_node, int cur_idx, int nmatch)
-{
- int type = dfa->nodes[cur_node].type;
- if (type == OP_OPEN_SUBEXP)
- {
- int reg_num = dfa->nodes[cur_node].opr.idx + 1;
-
- /* We are at the first node of this sub expression. */
- if (reg_num < nmatch)
- {
- pmatch[reg_num].rm_so = cur_idx;
- pmatch[reg_num].rm_eo = -1;
- }
- }
- else if (type == OP_CLOSE_SUBEXP)
- {
- int reg_num = dfa->nodes[cur_node].opr.idx + 1;
- if (reg_num < nmatch)
- {
- /* We are at the last node of this sub expression. */
- if (pmatch[reg_num].rm_so < cur_idx)
- {
- pmatch[reg_num].rm_eo = cur_idx;
- /* This is a non-empty match or we are not inside an optional
- subexpression. Accept this right away. */
- memcpy (prev_idx_match, pmatch, sizeof (regmatch_t) * nmatch);
- }
- else
- {
- if (dfa->nodes[cur_node].opt_subexp
- && prev_idx_match[reg_num].rm_so != -1)
- /* We transited through an empty match for an optional
- subexpression, like (a?)*, and this is not the subexp's
- first match. Copy back the old content of the registers
- so that matches of an inner subexpression are undone as
- well, like in ((a?))*. */
- memcpy (pmatch, prev_idx_match, sizeof (regmatch_t) * nmatch);
- else
- /* We completed a subexpression, but it may be part of
- an optional one, so do not update PREV_IDX_MATCH. */
- pmatch[reg_num].rm_eo = cur_idx;
- }
- }
- }
-}
-
-/* This function checks the STATE_LOG from the SCTX->last_str_idx to 0
- and sift the nodes in each states according to the following rules.
- Updated state_log will be wrote to STATE_LOG.
-
- Rules: We throw away the Node `a' in the STATE_LOG[STR_IDX] if...
- 1. When STR_IDX == MATCH_LAST(the last index in the state_log):
- If `a' isn't the LAST_NODE and `a' can't epsilon transit to
- the LAST_NODE, we throw away the node `a'.
- 2. When 0 <= STR_IDX < MATCH_LAST and `a' accepts
- string `s' and transit to `b':
- i. If 'b' isn't in the STATE_LOG[STR_IDX+strlen('s')], we throw
- away the node `a'.
- ii. If 'b' is in the STATE_LOG[STR_IDX+strlen('s')] but 'b' is
- thrown away, we throw away the node `a'.
- 3. When 0 <= STR_IDX < MATCH_LAST and 'a' epsilon transit to 'b':
- i. If 'b' isn't in the STATE_LOG[STR_IDX], we throw away the
- node `a'.
- ii. If 'b' is in the STATE_LOG[STR_IDX] but 'b' is thrown away,
- we throw away the node `a'. */
-
-#define STATE_NODE_CONTAINS(state,node) \
- ((state) != NULL && re_node_set_contains (&(state)->nodes, node))
-
-static reg_errcode_t
-internal_function
-sift_states_backward (const re_match_context_t *mctx, re_sift_context_t *sctx)
-{
- reg_errcode_t err;
- int null_cnt = 0;
- int str_idx = sctx->last_str_idx;
- re_node_set cur_dest;
-
-#ifdef DEBUG
- assert (mctx->state_log != NULL && mctx->state_log[str_idx] != NULL);
-#endif
-
- /* Build sifted state_log[str_idx]. It has the nodes which can epsilon
- transit to the last_node and the last_node itself. */
- err = re_node_set_init_1 (&cur_dest, sctx->last_node);
- if (BE (err != REG_NOERROR, 0))
- return err;
- err = update_cur_sifted_state (mctx, sctx, str_idx, &cur_dest);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
-
- /* Then check each states in the state_log. */
- while (str_idx > 0)
- {
- /* Update counters. */
- null_cnt = (sctx->sifted_states[str_idx] == NULL) ? null_cnt + 1 : 0;
- if (null_cnt > mctx->max_mb_elem_len)
- {
- memset (sctx->sifted_states, '\0',
- sizeof (re_dfastate_t *) * str_idx);
- re_node_set_free (&cur_dest);
- return REG_NOERROR;
- }
- re_node_set_empty (&cur_dest);
- --str_idx;
-
- if (mctx->state_log[str_idx])
- {
- err = build_sifted_states (mctx, sctx, str_idx, &cur_dest);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
-
- /* Add all the nodes which satisfy the following conditions:
- - It can epsilon transit to a node in CUR_DEST.
- - It is in CUR_SRC.
- And update state_log. */
- err = update_cur_sifted_state (mctx, sctx, str_idx, &cur_dest);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
- err = REG_NOERROR;
- free_return:
- re_node_set_free (&cur_dest);
- return err;
-}
-
-static reg_errcode_t
-internal_function
-build_sifted_states (const re_match_context_t *mctx, re_sift_context_t *sctx,
- int str_idx, re_node_set *cur_dest)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- const re_node_set *cur_src = &mctx->state_log[str_idx]->non_eps_nodes;
- int i;
-
- /* Then build the next sifted state.
- We build the next sifted state on `cur_dest', and update
- `sifted_states[str_idx]' with `cur_dest'.
- Note:
- `cur_dest' is the sifted state from `state_log[str_idx + 1]'.
- `cur_src' points the node_set of the old `state_log[str_idx]'
- (with the epsilon nodes pre-filtered out). */
- for (i = 0; i < cur_src->nelem; i++)
- {
- int prev_node = cur_src->elems[i];
- int naccepted = 0;
- int ret;
-
-#ifdef DEBUG
- re_token_type_t type = dfa->nodes[prev_node].type;
- assert (!IS_EPSILON_NODE (type));
-#endif
-#ifdef RE_ENABLE_I18N
- /* If the node may accept `multi byte'. */
- if (dfa->nodes[prev_node].accept_mb)
- naccepted = sift_states_iter_mb (mctx, sctx, prev_node,
- str_idx, sctx->last_str_idx);
-#endif /* RE_ENABLE_I18N */
-
- /* We don't check backreferences here.
- See update_cur_sifted_state(). */
- if (!naccepted
- && check_node_accept (mctx, dfa->nodes + prev_node, str_idx)
- && STATE_NODE_CONTAINS (sctx->sifted_states[str_idx + 1],
- dfa->nexts[prev_node]))
- naccepted = 1;
-
- if (naccepted == 0)
- continue;
-
- if (sctx->limits.nelem)
- {
- int to_idx = str_idx + naccepted;
- if (check_dst_limits (mctx, &sctx->limits,
- dfa->nexts[prev_node], to_idx,
- prev_node, str_idx))
- continue;
- }
- ret = re_node_set_insert (cur_dest, prev_node);
- if (BE (ret == -1, 0))
- return REG_ESPACE;
- }
-
- return REG_NOERROR;
-}
-
-/* Helper functions. */
-
-static reg_errcode_t
-internal_function
-clean_state_log_if_needed (re_match_context_t *mctx, int next_state_log_idx)
-{
- int top = mctx->state_log_top;
-
- if (next_state_log_idx >= mctx->input.bufs_len
- || (next_state_log_idx >= mctx->input.valid_len
- && mctx->input.valid_len < mctx->input.len))
- {
- reg_errcode_t err;
- err = extend_buffers (mctx);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
-
- if (top < next_state_log_idx)
- {
- memset (mctx->state_log + top + 1, '\0',
- sizeof (re_dfastate_t *) * (next_state_log_idx - top));
- mctx->state_log_top = next_state_log_idx;
- }
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-merge_state_array (const re_dfa_t *dfa, re_dfastate_t **dst,
- re_dfastate_t **src, int num)
-{
- int st_idx;
- reg_errcode_t err;
- for (st_idx = 0; st_idx < num; ++st_idx)
- {
- if (dst[st_idx] == NULL)
- dst[st_idx] = src[st_idx];
- else if (src[st_idx] != NULL)
- {
- re_node_set merged_set;
- err = re_node_set_init_union (&merged_set, &dst[st_idx]->nodes,
- &src[st_idx]->nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
- dst[st_idx] = re_acquire_state (&err, dfa, &merged_set);
- re_node_set_free (&merged_set);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- }
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-update_cur_sifted_state (const re_match_context_t *mctx,
- re_sift_context_t *sctx, int str_idx,
- re_node_set *dest_nodes)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err = REG_NOERROR;
- const re_node_set *candidates;
- candidates = ((mctx->state_log[str_idx] == NULL) ? NULL
- : &mctx->state_log[str_idx]->nodes);
-
- if (dest_nodes->nelem == 0)
- sctx->sifted_states[str_idx] = NULL;
- else
- {
- if (candidates)
- {
- /* At first, add the nodes which can epsilon transit to a node in
- DEST_NODE. */
- err = add_epsilon_src_nodes (dfa, dest_nodes, candidates);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- /* Then, check the limitations in the current sift_context. */
- if (sctx->limits.nelem)
- {
- err = check_subexp_limits (dfa, dest_nodes, candidates, &sctx->limits,
- mctx->bkref_ents, str_idx);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- }
-
- sctx->sifted_states[str_idx] = re_acquire_state (&err, dfa, dest_nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
-
- if (candidates && mctx->state_log[str_idx]->has_backref)
- {
- err = sift_states_bkref (mctx, sctx, str_idx, candidates);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-add_epsilon_src_nodes (const re_dfa_t *dfa, re_node_set *dest_nodes,
- const re_node_set *candidates)
-{
- reg_errcode_t err = REG_NOERROR;
- int i;
-
- re_dfastate_t *state = re_acquire_state (&err, dfa, dest_nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- if (!state->inveclosure.alloc)
- {
- err = re_node_set_alloc (&state->inveclosure, dest_nodes->nelem);
- if (BE (err != REG_NOERROR, 0))
- return REG_ESPACE;
- for (i = 0; i < dest_nodes->nelem; i++)
- re_node_set_merge (&state->inveclosure,
- dfa->inveclosures + dest_nodes->elems[i]);
- }
- return re_node_set_add_intersect (dest_nodes, candidates,
- &state->inveclosure);
-}
-
-static reg_errcode_t
-internal_function
-sub_epsilon_src_nodes (const re_dfa_t *dfa, int node, re_node_set *dest_nodes,
- const re_node_set *candidates)
-{
- int ecl_idx;
- reg_errcode_t err;
- re_node_set *inv_eclosure = dfa->inveclosures + node;
- re_node_set except_nodes;
- re_node_set_init_empty (&except_nodes);
- for (ecl_idx = 0; ecl_idx < inv_eclosure->nelem; ++ecl_idx)
- {
- int cur_node = inv_eclosure->elems[ecl_idx];
- if (cur_node == node)
- continue;
- if (IS_EPSILON_NODE (dfa->nodes[cur_node].type))
- {
- int edst1 = dfa->edests[cur_node].elems[0];
- int edst2 = ((dfa->edests[cur_node].nelem > 1)
- ? dfa->edests[cur_node].elems[1] : -1);
- if ((!re_node_set_contains (inv_eclosure, edst1)
- && re_node_set_contains (dest_nodes, edst1))
- || (edst2 > 0
- && !re_node_set_contains (inv_eclosure, edst2)
- && re_node_set_contains (dest_nodes, edst2)))
- {
- err = re_node_set_add_intersect (&except_nodes, candidates,
- dfa->inveclosures + cur_node);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&except_nodes);
- return err;
- }
- }
- }
- }
- for (ecl_idx = 0; ecl_idx < inv_eclosure->nelem; ++ecl_idx)
- {
- int cur_node = inv_eclosure->elems[ecl_idx];
- if (!re_node_set_contains (&except_nodes, cur_node))
- {
- int idx = re_node_set_contains (dest_nodes, cur_node) - 1;
- re_node_set_remove_at (dest_nodes, idx);
- }
- }
- re_node_set_free (&except_nodes);
- return REG_NOERROR;
-}
-
-static int
-internal_function
-check_dst_limits (const re_match_context_t *mctx, re_node_set *limits,
- int dst_node, int dst_idx, int src_node, int src_idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int lim_idx, src_pos, dst_pos;
-
- int dst_bkref_idx = search_cur_bkref_entry (mctx, dst_idx);
- int src_bkref_idx = search_cur_bkref_entry (mctx, src_idx);
- for (lim_idx = 0; lim_idx < limits->nelem; ++lim_idx)
- {
- int subexp_idx;
- struct re_backref_cache_entry *ent;
- ent = mctx->bkref_ents + limits->elems[lim_idx];
- subexp_idx = dfa->nodes[ent->node].opr.idx;
-
- dst_pos = check_dst_limits_calc_pos (mctx, limits->elems[lim_idx],
- subexp_idx, dst_node, dst_idx,
- dst_bkref_idx);
- src_pos = check_dst_limits_calc_pos (mctx, limits->elems[lim_idx],
- subexp_idx, src_node, src_idx,
- src_bkref_idx);
-
- /* In case of:
- <src> <dst> ( <subexp> )
- ( <subexp> ) <src> <dst>
- ( <subexp1> <src> <subexp2> <dst> <subexp3> ) */
- if (src_pos == dst_pos)
- continue; /* This is unrelated limitation. */
- else
- return 1;
- }
- return 0;
-}
-
-static int
-internal_function
-check_dst_limits_calc_pos_1 (const re_match_context_t *mctx, int boundaries,
- int subexp_idx, int from_node, int bkref_idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- const re_node_set *eclosures = dfa->eclosures + from_node;
- int node_idx;
-
- /* Else, we are on the boundary: examine the nodes on the epsilon
- closure. */
- for (node_idx = 0; node_idx < eclosures->nelem; ++node_idx)
- {
- int node = eclosures->elems[node_idx];
- switch (dfa->nodes[node].type)
- {
- case OP_BACK_REF:
- if (bkref_idx != -1)
- {
- struct re_backref_cache_entry *ent = mctx->bkref_ents + bkref_idx;
- do
- {
- int dst, cpos;
-
- if (ent->node != node)
- continue;
-
- if (subexp_idx < BITSET_WORD_BITS
- && !(ent->eps_reachable_subexps_map
- & ((bitset_word_t) 1 << subexp_idx)))
- continue;
-
- /* Recurse trying to reach the OP_OPEN_SUBEXP and
- OP_CLOSE_SUBEXP cases below. But, if the
- destination node is the same node as the source
- node, don't recurse because it would cause an
- infinite loop: a regex that exhibits this behavior
- is ()\1*\1* */
- dst = dfa->edests[node].elems[0];
- if (dst == from_node)
- {
- if (boundaries & 1)
- return -1;
- else /* if (boundaries & 2) */
- return 0;
- }
-
- cpos =
- check_dst_limits_calc_pos_1 (mctx, boundaries, subexp_idx,
- dst, bkref_idx);
- if (cpos == -1 /* && (boundaries & 1) */)
- return -1;
- if (cpos == 0 && (boundaries & 2))
- return 0;
-
- if (subexp_idx < BITSET_WORD_BITS)
- ent->eps_reachable_subexps_map
- &= ~((bitset_word_t) 1 << subexp_idx);
- }
- while (ent++->more);
- }
- break;
-
- case OP_OPEN_SUBEXP:
- if ((boundaries & 1) && subexp_idx == dfa->nodes[node].opr.idx)
- return -1;
- break;
-
- case OP_CLOSE_SUBEXP:
- if ((boundaries & 2) && subexp_idx == dfa->nodes[node].opr.idx)
- return 0;
- break;
-
- default:
- break;
- }
- }
-
- return (boundaries & 2) ? 1 : 0;
-}
-
-static int
-internal_function
-check_dst_limits_calc_pos (const re_match_context_t *mctx, int limit,
- int subexp_idx, int from_node, int str_idx,
- int bkref_idx)
-{
- struct re_backref_cache_entry *lim = mctx->bkref_ents + limit;
- int boundaries;
-
- /* If we are outside the range of the subexpression, return -1 or 1. */
- if (str_idx < lim->subexp_from)
- return -1;
-
- if (lim->subexp_to < str_idx)
- return 1;
-
- /* If we are within the subexpression, return 0. */
- boundaries = (str_idx == lim->subexp_from);
- boundaries |= (str_idx == lim->subexp_to) << 1;
- if (boundaries == 0)
- return 0;
-
- /* Else, examine epsilon closure. */
- return check_dst_limits_calc_pos_1 (mctx, boundaries, subexp_idx,
- from_node, bkref_idx);
-}
-
-/* Check the limitations of sub expressions LIMITS, and remove the nodes
- which are against limitations from DEST_NODES. */
-
-static reg_errcode_t
-internal_function
-check_subexp_limits (const re_dfa_t *dfa, re_node_set *dest_nodes,
- const re_node_set *candidates, re_node_set *limits,
- struct re_backref_cache_entry *bkref_ents, int str_idx)
-{
- reg_errcode_t err;
- int node_idx, lim_idx;
-
- for (lim_idx = 0; lim_idx < limits->nelem; ++lim_idx)
- {
- int subexp_idx;
- struct re_backref_cache_entry *ent;
- ent = bkref_ents + limits->elems[lim_idx];
-
- if (str_idx <= ent->subexp_from || ent->str_idx < str_idx)
- continue; /* This is unrelated limitation. */
-
- subexp_idx = dfa->nodes[ent->node].opr.idx;
- if (ent->subexp_to == str_idx)
- {
- int ops_node = -1;
- int cls_node = -1;
- for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx)
- {
- int node = dest_nodes->elems[node_idx];
- re_token_type_t type = dfa->nodes[node].type;
- if (type == OP_OPEN_SUBEXP
- && subexp_idx == dfa->nodes[node].opr.idx)
- ops_node = node;
- else if (type == OP_CLOSE_SUBEXP
- && subexp_idx == dfa->nodes[node].opr.idx)
- cls_node = node;
- }
-
- /* Check the limitation of the open subexpression. */
- /* Note that (ent->subexp_to = str_idx != ent->subexp_from). */
- if (ops_node >= 0)
- {
- err = sub_epsilon_src_nodes (dfa, ops_node, dest_nodes,
- candidates);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
-
- /* Check the limitation of the close subexpression. */
- if (cls_node >= 0)
- for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx)
- {
- int node = dest_nodes->elems[node_idx];
- if (!re_node_set_contains (dfa->inveclosures + node,
- cls_node)
- && !re_node_set_contains (dfa->eclosures + node,
- cls_node))
- {
- /* It is against this limitation.
- Remove it form the current sifted state. */
- err = sub_epsilon_src_nodes (dfa, node, dest_nodes,
- candidates);
- if (BE (err != REG_NOERROR, 0))
- return err;
- --node_idx;
- }
- }
- }
- else /* (ent->subexp_to != str_idx) */
- {
- for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx)
- {
- int node = dest_nodes->elems[node_idx];
- re_token_type_t type = dfa->nodes[node].type;
- if (type == OP_CLOSE_SUBEXP || type == OP_OPEN_SUBEXP)
- {
- if (subexp_idx != dfa->nodes[node].opr.idx)
- continue;
- /* It is against this limitation.
- Remove it form the current sifted state. */
- err = sub_epsilon_src_nodes (dfa, node, dest_nodes,
- candidates);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- }
- }
- }
- return REG_NOERROR;
-}
-
-static reg_errcode_t
-internal_function
-sift_states_bkref (const re_match_context_t *mctx, re_sift_context_t *sctx,
- int str_idx, const re_node_set *candidates)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err;
- int node_idx, node;
- re_sift_context_t local_sctx;
- int first_idx = search_cur_bkref_entry (mctx, str_idx);
-
- if (first_idx == -1)
- return REG_NOERROR;
-
- local_sctx.sifted_states = NULL; /* Mark that it hasn't been initialized. */
-
- for (node_idx = 0; node_idx < candidates->nelem; ++node_idx)
- {
- int enabled_idx;
- re_token_type_t type;
- struct re_backref_cache_entry *entry;
- node = candidates->elems[node_idx];
- type = dfa->nodes[node].type;
- /* Avoid infinite loop for the REs like "()\1+". */
- if (node == sctx->last_node && str_idx == sctx->last_str_idx)
- continue;
- if (type != OP_BACK_REF)
- continue;
-
- entry = mctx->bkref_ents + first_idx;
- enabled_idx = first_idx;
- do
- {
- int subexp_len;
- int to_idx;
- int dst_node;
- int ret;
- re_dfastate_t *cur_state;
-
- if (entry->node != node)
- continue;
- subexp_len = entry->subexp_to - entry->subexp_from;
- to_idx = str_idx + subexp_len;
- dst_node = (subexp_len ? dfa->nexts[node]
- : dfa->edests[node].elems[0]);
-
- if (to_idx > sctx->last_str_idx
- || sctx->sifted_states[to_idx] == NULL
- || !STATE_NODE_CONTAINS (sctx->sifted_states[to_idx], dst_node)
- || check_dst_limits (mctx, &sctx->limits, node,
- str_idx, dst_node, to_idx))
- continue;
-
- if (local_sctx.sifted_states == NULL)
- {
- local_sctx = *sctx;
- err = re_node_set_init_copy (&local_sctx.limits, &sctx->limits);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
- local_sctx.last_node = node;
- local_sctx.last_str_idx = str_idx;
- ret = re_node_set_insert (&local_sctx.limits, enabled_idx);
- if (BE (ret < 0, 0))
- {
- err = REG_ESPACE;
- goto free_return;
- }
- cur_state = local_sctx.sifted_states[str_idx];
- err = sift_states_backward (mctx, &local_sctx);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- if (sctx->limited_states != NULL)
- {
- err = merge_state_array (dfa, sctx->limited_states,
- local_sctx.sifted_states,
- str_idx + 1);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
- local_sctx.sifted_states[str_idx] = cur_state;
- re_node_set_remove (&local_sctx.limits, enabled_idx);
-
- /* mctx->bkref_ents may have changed, reload the pointer. */
- entry = mctx->bkref_ents + enabled_idx;
- }
- while (enabled_idx++, entry++->more);
- }
- err = REG_NOERROR;
- free_return:
- if (local_sctx.sifted_states != NULL)
- {
- re_node_set_free (&local_sctx.limits);
- }
-
- return err;
-}
-
-
-#ifdef RE_ENABLE_I18N
-static int
-internal_function
-sift_states_iter_mb (const re_match_context_t *mctx, re_sift_context_t *sctx,
- int node_idx, int str_idx, int max_str_idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int naccepted;
- /* Check the node can accept `multi byte'. */
- naccepted = check_node_accept_bytes (dfa, node_idx, &mctx->input, str_idx);
- if (naccepted > 0 && str_idx + naccepted <= max_str_idx &&
- !STATE_NODE_CONTAINS (sctx->sifted_states[str_idx + naccepted],
- dfa->nexts[node_idx]))
- /* The node can't accept the `multi byte', or the
- destination was already thrown away, then the node
- could't accept the current input `multi byte'. */
- naccepted = 0;
- /* Otherwise, it is sure that the node could accept
- `naccepted' bytes input. */
- return naccepted;
-}
-#endif /* RE_ENABLE_I18N */
-
-
-/* Functions for state transition. */
-
-/* Return the next state to which the current state STATE will transit by
- accepting the current input byte, and update STATE_LOG if necessary.
- If STATE can accept a multibyte char/collating element/back reference
- update the destination of STATE_LOG. */
-
-static re_dfastate_t *
-internal_function
-transit_state (reg_errcode_t *err, re_match_context_t *mctx,
- re_dfastate_t *state)
-{
- re_dfastate_t **trtable;
- unsigned char ch;
-
-#ifdef RE_ENABLE_I18N
- /* If the current state can accept multibyte. */
- if (BE (state->accept_mb, 0))
- {
- *err = transit_state_mb (mctx, state);
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
- }
-#endif /* RE_ENABLE_I18N */
-
- /* Then decide the next state with the single byte. */
-#if 0
- if (0)
- /* don't use transition table */
- return transit_state_sb (err, mctx, state);
-#endif
-
- /* Use transition table */
- ch = re_string_fetch_byte (&mctx->input);
- for (;;)
- {
- trtable = state->trtable;
- if (BE (trtable != NULL, 1))
- return trtable[ch];
-
- trtable = state->word_trtable;
- if (BE (trtable != NULL, 1))
- {
- unsigned int context;
- context
- = re_string_context_at (&mctx->input,
- re_string_cur_idx (&mctx->input) - 1,
- mctx->eflags);
- if (IS_WORD_CONTEXT (context))
- return trtable[ch + SBC_MAX];
- else
- return trtable[ch];
- }
-
- if (!build_trtable (mctx->dfa, state))
- {
- *err = REG_ESPACE;
- return NULL;
- }
-
- /* Retry, we now have a transition table. */
- }
-}
-
-/* Update the state_log if we need */
-re_dfastate_t *
-internal_function
-merge_state_with_log (reg_errcode_t *err, re_match_context_t *mctx,
- re_dfastate_t *next_state)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int cur_idx = re_string_cur_idx (&mctx->input);
-
- if (cur_idx > mctx->state_log_top)
- {
- mctx->state_log[cur_idx] = next_state;
- mctx->state_log_top = cur_idx;
- }
- else if (mctx->state_log[cur_idx] == 0)
- {
- mctx->state_log[cur_idx] = next_state;
- }
- else
- {
- re_dfastate_t *pstate;
- unsigned int context;
- re_node_set next_nodes, *log_nodes, *table_nodes = NULL;
- /* If (state_log[cur_idx] != 0), it implies that cur_idx is
- the destination of a multibyte char/collating element/
- back reference. Then the next state is the union set of
- these destinations and the results of the transition table. */
- pstate = mctx->state_log[cur_idx];
- log_nodes = pstate->entrance_nodes;
- if (next_state != NULL)
- {
- table_nodes = next_state->entrance_nodes;
- *err = re_node_set_init_union (&next_nodes, table_nodes,
- log_nodes);
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
- }
- else
- next_nodes = *log_nodes;
- /* Note: We already add the nodes of the initial state,
- then we don't need to add them here. */
-
- context = re_string_context_at (&mctx->input,
- re_string_cur_idx (&mctx->input) - 1,
- mctx->eflags);
- next_state = mctx->state_log[cur_idx]
- = re_acquire_state_context (err, dfa, &next_nodes, context);
- /* We don't need to check errors here, since the return value of
- this function is next_state and ERR is already set. */
-
- if (table_nodes != NULL)
- re_node_set_free (&next_nodes);
- }
-
- if (BE (dfa->nbackref, 0) && next_state != NULL)
- {
- /* Check OP_OPEN_SUBEXP in the current state in case that we use them
- later. We must check them here, since the back references in the
- next state might use them. */
- *err = check_subexp_matching_top (mctx, &next_state->nodes,
- cur_idx);
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
-
- /* If the next state has back references. */
- if (next_state->has_backref)
- {
- *err = transit_state_bkref (mctx, &next_state->nodes);
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
- next_state = mctx->state_log[cur_idx];
- }
- }
-
- return next_state;
-}
-
-/* Skip bytes in the input that correspond to part of a
- multi-byte match, then look in the log for a state
- from which to restart matching. */
-re_dfastate_t *
-internal_function
-find_recover_state (reg_errcode_t *err, re_match_context_t *mctx)
-{
- re_dfastate_t *cur_state;
- do
- {
- int max = mctx->state_log_top;
- int cur_str_idx = re_string_cur_idx (&mctx->input);
-
- do
- {
- if (++cur_str_idx > max)
- return NULL;
- re_string_skip_bytes (&mctx->input, 1);
- }
- while (mctx->state_log[cur_str_idx] == NULL);
-
- cur_state = merge_state_with_log (err, mctx, NULL);
- }
- while (*err == REG_NOERROR && cur_state == NULL);
- return cur_state;
-}
-
-/* Helper functions for transit_state. */
-
-/* From the node set CUR_NODES, pick up the nodes whose types are
- OP_OPEN_SUBEXP and which have corresponding back references in the regular
- expression. And register them to use them later for evaluating the
- correspoding back references. */
-
-static reg_errcode_t
-internal_function
-check_subexp_matching_top (re_match_context_t *mctx, re_node_set *cur_nodes,
- int str_idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int node_idx;
- reg_errcode_t err;
-
- /* TODO: This isn't efficient.
- Because there might be more than one nodes whose types are
- OP_OPEN_SUBEXP and whose index is SUBEXP_IDX, we must check all
- nodes.
- E.g. RE: (a){2} */
- for (node_idx = 0; node_idx < cur_nodes->nelem; ++node_idx)
- {
- int node = cur_nodes->elems[node_idx];
- if (dfa->nodes[node].type == OP_OPEN_SUBEXP
- && dfa->nodes[node].opr.idx < BITSET_WORD_BITS
- && (dfa->used_bkref_map
- & ((bitset_word_t) 1 << dfa->nodes[node].opr.idx)))
- {
- err = match_ctx_add_subtop (mctx, node, str_idx);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- }
- return REG_NOERROR;
-}
-
-#if 0
-/* Return the next state to which the current state STATE will transit by
- accepting the current input byte. */
-
-static re_dfastate_t *
-transit_state_sb (reg_errcode_t *err, re_match_context_t *mctx,
- re_dfastate_t *state)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- re_node_set next_nodes;
- re_dfastate_t *next_state;
- int node_cnt, cur_str_idx = re_string_cur_idx (&mctx->input);
- unsigned int context;
-
- *err = re_node_set_alloc (&next_nodes, state->nodes.nelem + 1);
- if (BE (*err != REG_NOERROR, 0))
- return NULL;
- for (node_cnt = 0; node_cnt < state->nodes.nelem; ++node_cnt)
- {
- int cur_node = state->nodes.elems[node_cnt];
- if (check_node_accept (mctx, dfa->nodes + cur_node, cur_str_idx))
- {
- *err = re_node_set_merge (&next_nodes,
- dfa->eclosures + dfa->nexts[cur_node]);
- if (BE (*err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return NULL;
- }
- }
- }
- context = re_string_context_at (&mctx->input, cur_str_idx, mctx->eflags);
- next_state = re_acquire_state_context (err, dfa, &next_nodes, context);
- /* We don't need to check errors here, since the return value of
- this function is next_state and ERR is already set. */
-
- re_node_set_free (&next_nodes);
- re_string_skip_bytes (&mctx->input, 1);
- return next_state;
-}
-#endif
-
-#ifdef RE_ENABLE_I18N
-static reg_errcode_t
-internal_function
-transit_state_mb (re_match_context_t *mctx, re_dfastate_t *pstate)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err;
- int i;
-
- for (i = 0; i < pstate->nodes.nelem; ++i)
- {
- re_node_set dest_nodes, *new_nodes;
- int cur_node_idx = pstate->nodes.elems[i];
- int naccepted, dest_idx;
- unsigned int context;
- re_dfastate_t *dest_state;
-
- if (!dfa->nodes[cur_node_idx].accept_mb)
- continue;
-
- if (dfa->nodes[cur_node_idx].constraint)
- {
- context = re_string_context_at (&mctx->input,
- re_string_cur_idx (&mctx->input),
- mctx->eflags);
- if (NOT_SATISFY_NEXT_CONSTRAINT (dfa->nodes[cur_node_idx].constraint,
- context))
- continue;
- }
-
- /* How many bytes the node can accept? */
- naccepted = check_node_accept_bytes (dfa, cur_node_idx, &mctx->input,
- re_string_cur_idx (&mctx->input));
- if (naccepted == 0)
- continue;
-
- /* The node can accepts `naccepted' bytes. */
- dest_idx = re_string_cur_idx (&mctx->input) + naccepted;
- mctx->max_mb_elem_len = ((mctx->max_mb_elem_len < naccepted) ? naccepted
- : mctx->max_mb_elem_len);
- err = clean_state_log_if_needed (mctx, dest_idx);
- if (BE (err != REG_NOERROR, 0))
- return err;
-#ifdef DEBUG
- assert (dfa->nexts[cur_node_idx] != -1);
-#endif
- new_nodes = dfa->eclosures + dfa->nexts[cur_node_idx];
-
- dest_state = mctx->state_log[dest_idx];
- if (dest_state == NULL)
- dest_nodes = *new_nodes;
- else
- {
- err = re_node_set_init_union (&dest_nodes,
- dest_state->entrance_nodes, new_nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- context = re_string_context_at (&mctx->input, dest_idx - 1,
- mctx->eflags);
- mctx->state_log[dest_idx]
- = re_acquire_state_context (&err, dfa, &dest_nodes, context);
- if (dest_state != NULL)
- re_node_set_free (&dest_nodes);
- if (BE (mctx->state_log[dest_idx] == NULL && err != REG_NOERROR, 0))
- return err;
- }
- return REG_NOERROR;
-}
-#endif /* RE_ENABLE_I18N */
-
-static reg_errcode_t
-internal_function
-transit_state_bkref (re_match_context_t *mctx, const re_node_set *nodes)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err;
- int i;
- int cur_str_idx = re_string_cur_idx (&mctx->input);
-
- for (i = 0; i < nodes->nelem; ++i)
- {
- int dest_str_idx, prev_nelem, bkc_idx;
- int node_idx = nodes->elems[i];
- unsigned int context;
- const re_token_t *node = dfa->nodes + node_idx;
- re_node_set *new_dest_nodes;
-
- /* Check whether `node' is a backreference or not. */
- if (node->type != OP_BACK_REF)
- continue;
-
- if (node->constraint)
- {
- context = re_string_context_at (&mctx->input, cur_str_idx,
- mctx->eflags);
- if (NOT_SATISFY_NEXT_CONSTRAINT (node->constraint, context))
- continue;
- }
-
- /* `node' is a backreference.
- Check the substring which the substring matched. */
- bkc_idx = mctx->nbkref_ents;
- err = get_subexp (mctx, node_idx, cur_str_idx);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
-
- /* And add the epsilon closures (which is `new_dest_nodes') of
- the backreference to appropriate state_log. */
-#ifdef DEBUG
- assert (dfa->nexts[node_idx] != -1);
-#endif
- for (; bkc_idx < mctx->nbkref_ents; ++bkc_idx)
- {
- int subexp_len;
- re_dfastate_t *dest_state;
- struct re_backref_cache_entry *bkref_ent;
- bkref_ent = mctx->bkref_ents + bkc_idx;
- if (bkref_ent->node != node_idx || bkref_ent->str_idx != cur_str_idx)
- continue;
- subexp_len = bkref_ent->subexp_to - bkref_ent->subexp_from;
- new_dest_nodes = (subexp_len == 0
- ? dfa->eclosures + dfa->edests[node_idx].elems[0]
- : dfa->eclosures + dfa->nexts[node_idx]);
- dest_str_idx = (cur_str_idx + bkref_ent->subexp_to
- - bkref_ent->subexp_from);
- context = re_string_context_at (&mctx->input, dest_str_idx - 1,
- mctx->eflags);
- dest_state = mctx->state_log[dest_str_idx];
- prev_nelem = ((mctx->state_log[cur_str_idx] == NULL) ? 0
- : mctx->state_log[cur_str_idx]->nodes.nelem);
- /* Add `new_dest_node' to state_log. */
- if (dest_state == NULL)
- {
- mctx->state_log[dest_str_idx]
- = re_acquire_state_context (&err, dfa, new_dest_nodes,
- context);
- if (BE (mctx->state_log[dest_str_idx] == NULL
- && err != REG_NOERROR, 0))
- goto free_return;
- }
- else
- {
- re_node_set dest_nodes;
- err = re_node_set_init_union (&dest_nodes,
- dest_state->entrance_nodes,
- new_dest_nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&dest_nodes);
- goto free_return;
- }
- mctx->state_log[dest_str_idx]
- = re_acquire_state_context (&err, dfa, &dest_nodes, context);
- re_node_set_free (&dest_nodes);
- if (BE (mctx->state_log[dest_str_idx] == NULL
- && err != REG_NOERROR, 0))
- goto free_return;
- }
- /* We need to check recursively if the backreference can epsilon
- transit. */
- if (subexp_len == 0
- && mctx->state_log[cur_str_idx]->nodes.nelem > prev_nelem)
- {
- err = check_subexp_matching_top (mctx, new_dest_nodes,
- cur_str_idx);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- err = transit_state_bkref (mctx, new_dest_nodes);
- if (BE (err != REG_NOERROR, 0))
- goto free_return;
- }
- }
- }
- err = REG_NOERROR;
- free_return:
- return err;
-}
-
-/* Enumerate all the candidates which the backreference BKREF_NODE can match
- at BKREF_STR_IDX, and register them by match_ctx_add_entry().
- Note that we might collect inappropriate candidates here.
- However, the cost of checking them strictly here is too high, then we
- delay these checking for prune_impossible_nodes(). */
-
-static reg_errcode_t
-internal_function
-get_subexp (re_match_context_t *mctx, int bkref_node, int bkref_str_idx)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int subexp_num, sub_top_idx;
- const char *buf = (const char *) re_string_get_buffer (&mctx->input);
- /* Return if we have already checked BKREF_NODE at BKREF_STR_IDX. */
- int cache_idx = search_cur_bkref_entry (mctx, bkref_str_idx);
- if (cache_idx != -1)
- {
- const struct re_backref_cache_entry *entry
- = mctx->bkref_ents + cache_idx;
- do
- if (entry->node == bkref_node)
- return REG_NOERROR; /* We already checked it. */
- while (entry++->more);
- }
-
- subexp_num = dfa->nodes[bkref_node].opr.idx;
-
- /* For each sub expression */
- for (sub_top_idx = 0; sub_top_idx < mctx->nsub_tops; ++sub_top_idx)
- {
- reg_errcode_t err;
- re_sub_match_top_t *sub_top = mctx->sub_tops[sub_top_idx];
- re_sub_match_last_t *sub_last;
- int sub_last_idx, sl_str, bkref_str_off;
-
- if (dfa->nodes[sub_top->node].opr.idx != subexp_num)
- continue; /* It isn't related. */
-
- sl_str = sub_top->str_idx;
- bkref_str_off = bkref_str_idx;
- /* At first, check the last node of sub expressions we already
- evaluated. */
- for (sub_last_idx = 0; sub_last_idx < sub_top->nlasts; ++sub_last_idx)
- {
- int sl_str_diff;
- sub_last = sub_top->lasts[sub_last_idx];
- sl_str_diff = sub_last->str_idx - sl_str;
- /* The matched string by the sub expression match with the substring
- at the back reference? */
- if (sl_str_diff > 0)
- {
- if (BE (bkref_str_off + sl_str_diff > mctx->input.valid_len, 0))
- {
- /* Not enough chars for a successful match. */
- if (bkref_str_off + sl_str_diff > mctx->input.len)
- break;
-
- err = clean_state_log_if_needed (mctx,
- bkref_str_off
- + sl_str_diff);
- if (BE (err != REG_NOERROR, 0))
- return err;
- buf = (const char *) re_string_get_buffer (&mctx->input);
- }
- if (memcmp (buf + bkref_str_off, buf + sl_str, sl_str_diff) != 0)
- /* We don't need to search this sub expression any more. */
- break;
- }
- bkref_str_off += sl_str_diff;
- sl_str += sl_str_diff;
- err = get_subexp_sub (mctx, sub_top, sub_last, bkref_node,
- bkref_str_idx);
-
- /* Reload buf, since the preceding call might have reallocated
- the buffer. */
- buf = (const char *) re_string_get_buffer (&mctx->input);
-
- if (err == REG_NOMATCH)
- continue;
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
-
- if (sub_last_idx < sub_top->nlasts)
- continue;
- if (sub_last_idx > 0)
- ++sl_str;
- /* Then, search for the other last nodes of the sub expression. */
- for (; sl_str <= bkref_str_idx; ++sl_str)
- {
- int cls_node, sl_str_off;
- const re_node_set *nodes;
- sl_str_off = sl_str - sub_top->str_idx;
- /* The matched string by the sub expression match with the substring
- at the back reference? */
- if (sl_str_off > 0)
- {
- if (BE (bkref_str_off >= mctx->input.valid_len, 0))
- {
- /* If we are at the end of the input, we cannot match. */
- if (bkref_str_off >= mctx->input.len)
- break;
-
- err = extend_buffers (mctx);
- if (BE (err != REG_NOERROR, 0))
- return err;
-
- buf = (const char *) re_string_get_buffer (&mctx->input);
- }
- if (buf [bkref_str_off++] != buf[sl_str - 1])
- break; /* We don't need to search this sub expression
- any more. */
- }
- if (mctx->state_log[sl_str] == NULL)
- continue;
- /* Does this state have a ')' of the sub expression? */
- nodes = &mctx->state_log[sl_str]->nodes;
- cls_node = find_subexp_node (dfa, nodes, subexp_num,
- OP_CLOSE_SUBEXP);
- if (cls_node == -1)
- continue; /* No. */
- if (sub_top->path == NULL)
- {
- sub_top->path = calloc (sizeof (state_array_t),
- sl_str - sub_top->str_idx + 1);
- if (sub_top->path == NULL)
- return REG_ESPACE;
- }
- /* Can the OP_OPEN_SUBEXP node arrive the OP_CLOSE_SUBEXP node
- in the current context? */
- err = check_arrival (mctx, sub_top->path, sub_top->node,
- sub_top->str_idx, cls_node, sl_str,
- OP_CLOSE_SUBEXP);
- if (err == REG_NOMATCH)
- continue;
- if (BE (err != REG_NOERROR, 0))
- return err;
- sub_last = match_ctx_add_sublast (sub_top, cls_node, sl_str);
- if (BE (sub_last == NULL, 0))
- return REG_ESPACE;
- err = get_subexp_sub (mctx, sub_top, sub_last, bkref_node,
- bkref_str_idx);
- if (err == REG_NOMATCH)
- continue;
- }
- }
- return REG_NOERROR;
-}
-
-/* Helper functions for get_subexp(). */
-
-/* Check SUB_LAST can arrive to the back reference BKREF_NODE at BKREF_STR.
- If it can arrive, register the sub expression expressed with SUB_TOP
- and SUB_LAST. */
-
-static reg_errcode_t
-internal_function
-get_subexp_sub (re_match_context_t *mctx, const re_sub_match_top_t *sub_top,
- re_sub_match_last_t *sub_last, int bkref_node, int bkref_str)
-{
- reg_errcode_t err;
- int to_idx;
- /* Can the subexpression arrive the back reference? */
- err = check_arrival (mctx, &sub_last->path, sub_last->node,
- sub_last->str_idx, bkref_node, bkref_str,
- OP_OPEN_SUBEXP);
- if (err != REG_NOERROR)
- return err;
- err = match_ctx_add_entry (mctx, bkref_node, bkref_str, sub_top->str_idx,
- sub_last->str_idx);
- if (BE (err != REG_NOERROR, 0))
- return err;
- to_idx = bkref_str + sub_last->str_idx - sub_top->str_idx;
- return clean_state_log_if_needed (mctx, to_idx);
-}
-
-/* Find the first node which is '(' or ')' and whose index is SUBEXP_IDX.
- Search '(' if FL_OPEN, or search ')' otherwise.
- TODO: This function isn't efficient...
- Because there might be more than one nodes whose types are
- OP_OPEN_SUBEXP and whose index is SUBEXP_IDX, we must check all
- nodes.
- E.g. RE: (a){2} */
-
-static int
-internal_function
-find_subexp_node (const re_dfa_t *dfa, const re_node_set *nodes,
- int subexp_idx, int type)
-{
- int cls_idx;
- for (cls_idx = 0; cls_idx < nodes->nelem; ++cls_idx)
- {
- int cls_node = nodes->elems[cls_idx];
- const re_token_t *node = dfa->nodes + cls_node;
- if (node->type == type
- && node->opr.idx == subexp_idx)
- return cls_node;
- }
- return -1;
-}
-
-/* Check whether the node TOP_NODE at TOP_STR can arrive to the node
- LAST_NODE at LAST_STR. We record the path onto PATH since it will be
- heavily reused.
- Return REG_NOERROR if it can arrive, or REG_NOMATCH otherwise. */
-
-static reg_errcode_t
-internal_function
-check_arrival (re_match_context_t *mctx, state_array_t *path, int top_node,
- int top_str, int last_node, int last_str, int type)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err = REG_NOERROR;
- int subexp_num, backup_cur_idx, str_idx, null_cnt;
- re_dfastate_t *cur_state = NULL;
- re_node_set *cur_nodes, next_nodes;
- re_dfastate_t **backup_state_log;
- unsigned int context;
-
- subexp_num = dfa->nodes[top_node].opr.idx;
- /* Extend the buffer if we need. */
- if (BE (path->alloc < last_str + mctx->max_mb_elem_len + 1, 0))
- {
- re_dfastate_t **new_array;
- int old_alloc = path->alloc;
- path->alloc += last_str + mctx->max_mb_elem_len + 1;
- new_array = re_realloc (path->array, re_dfastate_t *, path->alloc);
- if (BE (new_array == NULL, 0))
- {
- path->alloc = old_alloc;
- return REG_ESPACE;
- }
- path->array = new_array;
- memset (new_array + old_alloc, '\0',
- sizeof (re_dfastate_t *) * (path->alloc - old_alloc));
- }
-
- str_idx = path->next_idx ? path->next_idx : top_str;
-
- /* Temporary modify MCTX. */
- backup_state_log = mctx->state_log;
- backup_cur_idx = mctx->input.cur_idx;
- mctx->state_log = path->array;
- mctx->input.cur_idx = str_idx;
-
- /* Setup initial node set. */
- context = re_string_context_at (&mctx->input, str_idx - 1, mctx->eflags);
- if (str_idx == top_str)
- {
- err = re_node_set_init_1 (&next_nodes, top_node);
- if (BE (err != REG_NOERROR, 0))
- return err;
- err = check_arrival_expand_ecl (dfa, &next_nodes, subexp_num, type);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- }
- else
- {
- cur_state = mctx->state_log[str_idx];
- if (cur_state && cur_state->has_backref)
- {
- err = re_node_set_init_copy (&next_nodes, &cur_state->nodes);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- else
- re_node_set_init_empty (&next_nodes);
- }
- if (str_idx == top_str || (cur_state && cur_state->has_backref))
- {
- if (next_nodes.nelem)
- {
- err = expand_bkref_cache (mctx, &next_nodes, str_idx,
- subexp_num, type);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- }
- cur_state = re_acquire_state_context (&err, dfa, &next_nodes, context);
- if (BE (cur_state == NULL && err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- mctx->state_log[str_idx] = cur_state;
- }
-
- for (null_cnt = 0; str_idx < last_str && null_cnt <= mctx->max_mb_elem_len;)
- {
- re_node_set_empty (&next_nodes);
- if (mctx->state_log[str_idx + 1])
- {
- err = re_node_set_merge (&next_nodes,
- &mctx->state_log[str_idx + 1]->nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- }
- if (cur_state)
- {
- err = check_arrival_add_next_nodes (mctx, str_idx,
- &cur_state->non_eps_nodes,
- &next_nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- }
- ++str_idx;
- if (next_nodes.nelem)
- {
- err = check_arrival_expand_ecl (dfa, &next_nodes, subexp_num, type);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- err = expand_bkref_cache (mctx, &next_nodes, str_idx,
- subexp_num, type);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- }
- context = re_string_context_at (&mctx->input, str_idx - 1, mctx->eflags);
- cur_state = re_acquire_state_context (&err, dfa, &next_nodes, context);
- if (BE (cur_state == NULL && err != REG_NOERROR, 0))
- {
- re_node_set_free (&next_nodes);
- return err;
- }
- mctx->state_log[str_idx] = cur_state;
- null_cnt = cur_state == NULL ? null_cnt + 1 : 0;
- }
- re_node_set_free (&next_nodes);
- cur_nodes = (mctx->state_log[last_str] == NULL ? NULL
- : &mctx->state_log[last_str]->nodes);
- path->next_idx = str_idx;
-
- /* Fix MCTX. */
- mctx->state_log = backup_state_log;
- mctx->input.cur_idx = backup_cur_idx;
-
- /* Then check the current node set has the node LAST_NODE. */
- if (cur_nodes != NULL && re_node_set_contains (cur_nodes, last_node))
- return REG_NOERROR;
-
- return REG_NOMATCH;
-}
-
-/* Helper functions for check_arrival. */
-
-/* Calculate the destination nodes of CUR_NODES at STR_IDX, and append them
- to NEXT_NODES.
- TODO: This function is similar to the functions transit_state*(),
- however this function has many additional works.
- Can't we unify them? */
-
-static reg_errcode_t
-internal_function
-check_arrival_add_next_nodes (re_match_context_t *mctx, int str_idx,
- re_node_set *cur_nodes, re_node_set *next_nodes)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- int result;
- int cur_idx;
- reg_errcode_t err = REG_NOERROR;
- re_node_set union_set;
- re_node_set_init_empty (&union_set);
- for (cur_idx = 0; cur_idx < cur_nodes->nelem; ++cur_idx)
- {
- int naccepted = 0;
- int cur_node = cur_nodes->elems[cur_idx];
-#ifdef DEBUG
- re_token_type_t type = dfa->nodes[cur_node].type;
- assert (!IS_EPSILON_NODE (type));
-#endif
-#ifdef RE_ENABLE_I18N
- /* If the node may accept `multi byte'. */
- if (dfa->nodes[cur_node].accept_mb)
- {
- naccepted = check_node_accept_bytes (dfa, cur_node, &mctx->input,
- str_idx);
- if (naccepted > 1)
- {
- re_dfastate_t *dest_state;
- int next_node = dfa->nexts[cur_node];
- int next_idx = str_idx + naccepted;
- dest_state = mctx->state_log[next_idx];
- re_node_set_empty (&union_set);
- if (dest_state)
- {
- err = re_node_set_merge (&union_set, &dest_state->nodes);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&union_set);
- return err;
- }
- }
- result = re_node_set_insert (&union_set, next_node);
- if (BE (result < 0, 0))
- {
- re_node_set_free (&union_set);
- return REG_ESPACE;
- }
- mctx->state_log[next_idx] = re_acquire_state (&err, dfa,
- &union_set);
- if (BE (mctx->state_log[next_idx] == NULL
- && err != REG_NOERROR, 0))
- {
- re_node_set_free (&union_set);
- return err;
- }
- }
- }
-#endif /* RE_ENABLE_I18N */
- if (naccepted
- || check_node_accept (mctx, dfa->nodes + cur_node, str_idx))
- {
- result = re_node_set_insert (next_nodes, dfa->nexts[cur_node]);
- if (BE (result < 0, 0))
- {
- re_node_set_free (&union_set);
- return REG_ESPACE;
- }
- }
- }
- re_node_set_free (&union_set);
- return REG_NOERROR;
-}
-
-/* For all the nodes in CUR_NODES, add the epsilon closures of them to
- CUR_NODES, however exclude the nodes which are:
- - inside the sub expression whose number is EX_SUBEXP, if FL_OPEN.
- - out of the sub expression whose number is EX_SUBEXP, if !FL_OPEN.
-*/
-
-static reg_errcode_t
-internal_function
-check_arrival_expand_ecl (const re_dfa_t *dfa, re_node_set *cur_nodes,
- int ex_subexp, int type)
-{
- reg_errcode_t err;
- int idx, outside_node;
- re_node_set new_nodes;
-#ifdef DEBUG
- assert (cur_nodes->nelem);
-#endif
- err = re_node_set_alloc (&new_nodes, cur_nodes->nelem);
- if (BE (err != REG_NOERROR, 0))
- return err;
- /* Create a new node set NEW_NODES with the nodes which are epsilon
- closures of the node in CUR_NODES. */
-
- for (idx = 0; idx < cur_nodes->nelem; ++idx)
- {
- int cur_node = cur_nodes->elems[idx];
- const re_node_set *eclosure = dfa->eclosures + cur_node;
- outside_node = find_subexp_node (dfa, eclosure, ex_subexp, type);
- if (outside_node == -1)
- {
- /* There are no problematic nodes, just merge them. */
- err = re_node_set_merge (&new_nodes, eclosure);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&new_nodes);
- return err;
- }
- }
- else
- {
- /* There are problematic nodes, re-calculate incrementally. */
- err = check_arrival_expand_ecl_sub (dfa, &new_nodes, cur_node,
- ex_subexp, type);
- if (BE (err != REG_NOERROR, 0))
- {
- re_node_set_free (&new_nodes);
- return err;
- }
- }
- }
- re_node_set_free (cur_nodes);
- *cur_nodes = new_nodes;
- return REG_NOERROR;
-}
-
-/* Helper function for check_arrival_expand_ecl.
- Check incrementally the epsilon closure of TARGET, and if it isn't
- problematic append it to DST_NODES. */
-
-static reg_errcode_t
-internal_function
-check_arrival_expand_ecl_sub (const re_dfa_t *dfa, re_node_set *dst_nodes,
- int target, int ex_subexp, int type)
-{
- int cur_node;
- for (cur_node = target; !re_node_set_contains (dst_nodes, cur_node);)
- {
- int err;
-
- if (dfa->nodes[cur_node].type == type
- && dfa->nodes[cur_node].opr.idx == ex_subexp)
- {
- if (type == OP_CLOSE_SUBEXP)
- {
- err = re_node_set_insert (dst_nodes, cur_node);
- if (BE (err == -1, 0))
- return REG_ESPACE;
- }
- break;
- }
- err = re_node_set_insert (dst_nodes, cur_node);
- if (BE (err == -1, 0))
- return REG_ESPACE;
- if (dfa->edests[cur_node].nelem == 0)
- break;
- if (dfa->edests[cur_node].nelem == 2)
- {
- err = check_arrival_expand_ecl_sub (dfa, dst_nodes,
- dfa->edests[cur_node].elems[1],
- ex_subexp, type);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- cur_node = dfa->edests[cur_node].elems[0];
- }
- return REG_NOERROR;
-}
-
-
-/* For all the back references in the current state, calculate the
- destination of the back references by the appropriate entry
- in MCTX->BKREF_ENTS. */
-
-static reg_errcode_t
-internal_function
-expand_bkref_cache (re_match_context_t *mctx, re_node_set *cur_nodes,
- int cur_str, int subexp_num, int type)
-{
- const re_dfa_t *const dfa = mctx->dfa;
- reg_errcode_t err;
- int cache_idx_start = search_cur_bkref_entry (mctx, cur_str);
- struct re_backref_cache_entry *ent;
-
- if (cache_idx_start == -1)
- return REG_NOERROR;
-
- restart:
- ent = mctx->bkref_ents + cache_idx_start;
- do
- {
- int to_idx, next_node;
-
- /* Is this entry ENT is appropriate? */
- if (!re_node_set_contains (cur_nodes, ent->node))
- continue; /* No. */
-
- to_idx = cur_str + ent->subexp_to - ent->subexp_from;
- /* Calculate the destination of the back reference, and append it
- to MCTX->STATE_LOG. */
- if (to_idx == cur_str)
- {
- /* The backreference did epsilon transit, we must re-check all the
- node in the current state. */
- re_node_set new_dests;
- reg_errcode_t err2, err3;
- next_node = dfa->edests[ent->node].elems[0];
- if (re_node_set_contains (cur_nodes, next_node))
- continue;
- err = re_node_set_init_1 (&new_dests, next_node);
- err2 = check_arrival_expand_ecl (dfa, &new_dests, subexp_num, type);
- err3 = re_node_set_merge (cur_nodes, &new_dests);
- re_node_set_free (&new_dests);
- if (BE (err != REG_NOERROR || err2 != REG_NOERROR
- || err3 != REG_NOERROR, 0))
- {
- err = (err != REG_NOERROR ? err
- : (err2 != REG_NOERROR ? err2 : err3));
- return err;
- }
- /* TODO: It is still inefficient... */
- goto restart;
- }
- else
- {
- re_node_set union_set;
- next_node = dfa->nexts[ent->node];
- if (mctx->state_log[to_idx])
- {
- int ret;
- if (re_node_set_contains (&mctx->state_log[to_idx]->nodes,
- next_node))
- continue;
- err = re_node_set_init_copy (&union_set,
- &mctx->state_log[to_idx]->nodes);
- ret = re_node_set_insert (&union_set, next_node);
- if (BE (err != REG_NOERROR || ret < 0, 0))
- {
- re_node_set_free (&union_set);
- err = err != REG_NOERROR ? err : REG_ESPACE;
- return err;
- }
- }
- else
- {
- err = re_node_set_init_1 (&union_set, next_node);
- if (BE (err != REG_NOERROR, 0))
- return err;
- }
- mctx->state_log[to_idx] = re_acquire_state (&err, dfa, &union_set);
- re_node_set_free (&union_set);
- if (BE (mctx->state_log[to_idx] == NULL
- && err != REG_NOERROR, 0))
- return err;
- }
- }
- while (ent++->more);
- return REG_NOERROR;
-}
-
-/* Build transition table for the state.
- Return 1 if succeeded, otherwise return NULL. */
-
-static int
-internal_function
-build_trtable (const re_dfa_t *dfa, re_dfastate_t *state)
-{
- reg_errcode_t err;
- int i, j, ch, need_word_trtable = 0;
- bitset_word_t elem, mask;
- bool dests_node_malloced = false;
- bool dest_states_malloced = false;
- int ndests; /* Number of the destination states from `state'. */
- re_dfastate_t **trtable;
- re_dfastate_t **dest_states = NULL, **dest_states_word, **dest_states_nl;
- re_node_set follows, *dests_node;
- bitset_t *dests_ch;
- bitset_t acceptable;
-
- struct dests_alloc
- {
- re_node_set dests_node[SBC_MAX];
- bitset_t dests_ch[SBC_MAX];
- } *dests_alloc;
-
- /* We build DFA states which corresponds to the destination nodes
- from `state'. `dests_node[i]' represents the nodes which i-th
- destination state contains, and `dests_ch[i]' represents the
- characters which i-th destination state accepts. */
- if (__libc_use_alloca (sizeof (struct dests_alloc)))
- dests_alloc = (struct dests_alloc *) alloca (sizeof (struct dests_alloc));
- else
- {
- dests_alloc = re_malloc (struct dests_alloc, 1);
- if (BE (dests_alloc == NULL, 0))
- return 0;
- dests_node_malloced = true;
- }
- dests_node = dests_alloc->dests_node;
- dests_ch = dests_alloc->dests_ch;
-
- /* Initialize transiton table. */
- state->word_trtable = state->trtable = NULL;
-
- /* At first, group all nodes belonging to `state' into several
- destinations. */
- ndests = group_nodes_into_DFAstates (dfa, state, dests_node, dests_ch);
- if (BE (ndests <= 0, 0))
- {
- if (dests_node_malloced)
- free (dests_alloc);
- /* Return 0 in case of an error, 1 otherwise. */
- if (ndests == 0)
- {
- state->trtable = (re_dfastate_t **)
- calloc (sizeof (re_dfastate_t *), SBC_MAX);
- return 1;
- }
- return 0;
- }
-
- err = re_node_set_alloc (&follows, ndests + 1);
- if (BE (err != REG_NOERROR, 0))
- goto out_free;
-
- if (__libc_use_alloca ((sizeof (re_node_set) + sizeof (bitset_t)) * SBC_MAX
- + ndests * 3 * sizeof (re_dfastate_t *)))
- dest_states = (re_dfastate_t **)
- alloca (ndests * 3 * sizeof (re_dfastate_t *));
- else
- {
- dest_states = (re_dfastate_t **)
- malloc (ndests * 3 * sizeof (re_dfastate_t *));
- if (BE (dest_states == NULL, 0))
- {
-out_free:
- if (dest_states_malloced)
- free (dest_states);
- re_node_set_free (&follows);
- for (i = 0; i < ndests; ++i)
- re_node_set_free (dests_node + i);
- if (dests_node_malloced)
- free (dests_alloc);
- return 0;
- }
- dest_states_malloced = true;
- }
- dest_states_word = dest_states + ndests;
- dest_states_nl = dest_states_word + ndests;
- bitset_empty (acceptable);
-
- /* Then build the states for all destinations. */
- for (i = 0; i < ndests; ++i)
- {
- int next_node;
- re_node_set_empty (&follows);
- /* Merge the follows of this destination states. */
- for (j = 0; j < dests_node[i].nelem; ++j)
- {
- next_node = dfa->nexts[dests_node[i].elems[j]];
- if (next_node != -1)
- {
- err = re_node_set_merge (&follows, dfa->eclosures + next_node);
- if (BE (err != REG_NOERROR, 0))
- goto out_free;
- }
- }
- dest_states[i] = re_acquire_state_context (&err, dfa, &follows, 0);
- if (BE (dest_states[i] == NULL && err != REG_NOERROR, 0))
- goto out_free;
- /* If the new state has context constraint,
- build appropriate states for these contexts. */
- if (dest_states[i]->has_constraint)
- {
- dest_states_word[i] = re_acquire_state_context (&err, dfa, &follows,
- CONTEXT_WORD);
- if (BE (dest_states_word[i] == NULL && err != REG_NOERROR, 0))
- goto out_free;
-
- if (dest_states[i] != dest_states_word[i] && dfa->mb_cur_max > 1)
- need_word_trtable = 1;
-
- dest_states_nl[i] = re_acquire_state_context (&err, dfa, &follows,
- CONTEXT_NEWLINE);
- if (BE (dest_states_nl[i] == NULL && err != REG_NOERROR, 0))
- goto out_free;
- }
- else
- {
- dest_states_word[i] = dest_states[i];
- dest_states_nl[i] = dest_states[i];
- }
- bitset_merge (acceptable, dests_ch[i]);
- }
-
- if (!BE (need_word_trtable, 0))
- {
- /* We don't care about whether the following character is a word
- character, or we are in a single-byte character set so we can
- discern by looking at the character code: allocate a
- 256-entry transition table. */
- trtable = state->trtable =
- (re_dfastate_t **) calloc (sizeof (re_dfastate_t *), SBC_MAX);
- if (BE (trtable == NULL, 0))
- goto out_free;
-
- /* For all characters ch...: */
- for (i = 0; i < BITSET_WORDS; ++i)
- for (ch = i * BITSET_WORD_BITS, elem = acceptable[i], mask = 1;
- elem;
- mask <<= 1, elem >>= 1, ++ch)
- if (BE (elem & 1, 0))
- {
- /* There must be exactly one destination which accepts
- character ch. See group_nodes_into_DFAstates. */
- for (j = 0; (dests_ch[j][i] & mask) == 0; ++j)
- ;
-
- /* j-th destination accepts the word character ch. */
- if (dfa->word_char[i] & mask)
- trtable[ch] = dest_states_word[j];
- else
- trtable[ch] = dest_states[j];
- }
- }
- else
- {
- /* We care about whether the following character is a word
- character, and we are in a multi-byte character set: discern
- by looking at the character code: build two 256-entry
- transition tables, one starting at trtable[0] and one
- starting at trtable[SBC_MAX]. */
- trtable = state->word_trtable =
- (re_dfastate_t **) calloc (sizeof (re_dfastate_t *), 2 * SBC_MAX);
- if (BE (trtable == NULL, 0))
- goto out_free;
-
- /* For all characters ch...: */
- for (i = 0; i < BITSET_WORDS; ++i)
- for (ch = i * BITSET_WORD_BITS, elem = acceptable[i], mask = 1;
- elem;
- mask <<= 1, elem >>= 1, ++ch)
- if (BE (elem & 1, 0))
- {
- /* There must be exactly one destination which accepts
- character ch. See group_nodes_into_DFAstates. */
- for (j = 0; (dests_ch[j][i] & mask) == 0; ++j)
- ;
-
- /* j-th destination accepts the word character ch. */
- trtable[ch] = dest_states[j];
- trtable[ch + SBC_MAX] = dest_states_word[j];
- }
- }
-
- /* new line */
- if (bitset_contain (acceptable, NEWLINE_CHAR))
- {
- /* The current state accepts newline character. */
- for (j = 0; j < ndests; ++j)
- if (bitset_contain (dests_ch[j], NEWLINE_CHAR))
- {
- /* k-th destination accepts newline character. */
- trtable[NEWLINE_CHAR] = dest_states_nl[j];
- if (need_word_trtable)
- trtable[NEWLINE_CHAR + SBC_MAX] = dest_states_nl[j];
- /* There must be only one destination which accepts
- newline. See group_nodes_into_DFAstates. */
- break;
- }
- }
-
- if (dest_states_malloced)
- free (dest_states);
-
- re_node_set_free (&follows);
- for (i = 0; i < ndests; ++i)
- re_node_set_free (dests_node + i);
-
- if (dests_node_malloced)
- free (dests_alloc);
-
- return 1;
-}
-
-/* Group all nodes belonging to STATE into several destinations.
- Then for all destinations, set the nodes belonging to the destination
- to DESTS_NODE[i] and set the characters accepted by the destination
- to DEST_CH[i]. This function return the number of destinations. */
-
-static int
-internal_function
-group_nodes_into_DFAstates (const re_dfa_t *dfa, const re_dfastate_t *state,
- re_node_set *dests_node, bitset_t *dests_ch)
-{
- reg_errcode_t err;
- int result;
- int i, j, k;
- int ndests; /* Number of the destinations from `state'. */
- bitset_t accepts; /* Characters a node can accept. */
- const re_node_set *cur_nodes = &state->nodes;
- bitset_empty (accepts);
- ndests = 0;
-
- /* For all the nodes belonging to `state', */
- for (i = 0; i < cur_nodes->nelem; ++i)
- {
- re_token_t *node = &dfa->nodes[cur_nodes->elems[i]];
- re_token_type_t type = node->type;
- unsigned int constraint = node->constraint;
-
- /* Enumerate all single byte character this node can accept. */
- if (type == CHARACTER)
- bitset_set (accepts, node->opr.c);
- else if (type == SIMPLE_BRACKET)
- {
- bitset_merge (accepts, node->opr.sbcset);
- }
- else if (type == OP_PERIOD)
- {
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- bitset_merge (accepts, dfa->sb_char);
- else
-#endif
- bitset_set_all (accepts);
- if (!(dfa->syntax & RE_DOT_NEWLINE))
- bitset_clear (accepts, '\n');
- if (dfa->syntax & RE_DOT_NOT_NULL)
- bitset_clear (accepts, '\0');
- }
-#ifdef RE_ENABLE_I18N
- else if (type == OP_UTF8_PERIOD)
- {
- memset (accepts, '\xff', sizeof (bitset_t) / 2);
- if (!(dfa->syntax & RE_DOT_NEWLINE))
- bitset_clear (accepts, '\n');
- if (dfa->syntax & RE_DOT_NOT_NULL)
- bitset_clear (accepts, '\0');
- }
-#endif
- else
- continue;
-
- /* Check the `accepts' and sift the characters which are not
- match it the context. */
- if (constraint)
- {
- if (constraint & NEXT_NEWLINE_CONSTRAINT)
- {
- bool accepts_newline = bitset_contain (accepts, NEWLINE_CHAR);
- bitset_empty (accepts);
- if (accepts_newline)
- bitset_set (accepts, NEWLINE_CHAR);
- else
- continue;
- }
- if (constraint & NEXT_ENDBUF_CONSTRAINT)
- {
- bitset_empty (accepts);
- continue;
- }
-
- if (constraint & NEXT_WORD_CONSTRAINT)
- {
- bitset_word_t any_set = 0;
- if (type == CHARACTER && !node->word_char)
- {
- bitset_empty (accepts);
- continue;
- }
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- for (j = 0; j < BITSET_WORDS; ++j)
- any_set |= (accepts[j] &= (dfa->word_char[j] | ~dfa->sb_char[j]));
- else
-#endif
- for (j = 0; j < BITSET_WORDS; ++j)
- any_set |= (accepts[j] &= dfa->word_char[j]);
- if (!any_set)
- continue;
- }
- if (constraint & NEXT_NOTWORD_CONSTRAINT)
- {
- bitset_word_t any_set = 0;
- if (type == CHARACTER && node->word_char)
- {
- bitset_empty (accepts);
- continue;
- }
-#ifdef RE_ENABLE_I18N
- if (dfa->mb_cur_max > 1)
- for (j = 0; j < BITSET_WORDS; ++j)
- any_set |= (accepts[j] &= ~(dfa->word_char[j] & dfa->sb_char[j]));
- else
-#endif
- for (j = 0; j < BITSET_WORDS; ++j)
- any_set |= (accepts[j] &= ~dfa->word_char[j]);
- if (!any_set)
- continue;
- }
- }
-
- /* Then divide `accepts' into DFA states, or create a new
- state. Above, we make sure that accepts is not empty. */
- for (j = 0; j < ndests; ++j)
- {
- bitset_t intersec; /* Intersection sets, see below. */
- bitset_t remains;
- /* Flags, see below. */
- bitset_word_t has_intersec, not_subset, not_consumed;
-
- /* Optimization, skip if this state doesn't accept the character. */
- if (type == CHARACTER && !bitset_contain (dests_ch[j], node->opr.c))
- continue;
-
- /* Enumerate the intersection set of this state and `accepts'. */
- has_intersec = 0;
- for (k = 0; k < BITSET_WORDS; ++k)
- has_intersec |= intersec[k] = accepts[k] & dests_ch[j][k];
- /* And skip if the intersection set is empty. */
- if (!has_intersec)
- continue;
-
- /* Then check if this state is a subset of `accepts'. */
- not_subset = not_consumed = 0;
- for (k = 0; k < BITSET_WORDS; ++k)
- {
- not_subset |= remains[k] = ~accepts[k] & dests_ch[j][k];
- not_consumed |= accepts[k] = accepts[k] & ~dests_ch[j][k];
- }
-
- /* If this state isn't a subset of `accepts', create a
- new group state, which has the `remains'. */
- if (not_subset)
- {
- bitset_copy (dests_ch[ndests], remains);
- bitset_copy (dests_ch[j], intersec);
- err = re_node_set_init_copy (dests_node + ndests, &dests_node[j]);
- if (BE (err != REG_NOERROR, 0))
- goto error_return;
- ++ndests;
- }
-
- /* Put the position in the current group. */
- result = re_node_set_insert (&dests_node[j], cur_nodes->elems[i]);
- if (BE (result < 0, 0))
- goto error_return;
-
- /* If all characters are consumed, go to next node. */
- if (!not_consumed)
- break;
- }
- /* Some characters remain, create a new group. */
- if (j == ndests)
- {
- bitset_copy (dests_ch[ndests], accepts);
- err = re_node_set_init_1 (dests_node + ndests, cur_nodes->elems[i]);
- if (BE (err != REG_NOERROR, 0))
- goto error_return;
- ++ndests;
- bitset_empty (accepts);
- }
- }
- return ndests;
- error_return:
- for (j = 0; j < ndests; ++j)
- re_node_set_free (dests_node + j);
- return -1;
-}
-
-#ifdef RE_ENABLE_I18N
-/* Check how many bytes the node `dfa->nodes[node_idx]' accepts.
- Return the number of the bytes the node accepts.
- STR_IDX is the current index of the input string.
-
- This function handles the nodes which can accept one character, or
- one collating element like '.', '[a-z]', opposite to the other nodes
- can only accept one byte. */
-
-static int
-internal_function
-check_node_accept_bytes (const re_dfa_t *dfa, int node_idx,
- const re_string_t *input, int str_idx)
-{
- const re_token_t *node = dfa->nodes + node_idx;
- int char_len, elem_len;
- int i;
-
- if (BE (node->type == OP_UTF8_PERIOD, 0))
- {
- unsigned char c = re_string_byte_at (input, str_idx), d;
- if (BE (c < 0xc2, 1))
- return 0;
-
- if (str_idx + 2 > input->len)
- return 0;
-
- d = re_string_byte_at (input, str_idx + 1);
- if (c < 0xe0)
- return (d < 0x80 || d > 0xbf) ? 0 : 2;
- else if (c < 0xf0)
- {
- char_len = 3;
- if (c == 0xe0 && d < 0xa0)
- return 0;
- }
- else if (c < 0xf8)
- {
- char_len = 4;
- if (c == 0xf0 && d < 0x90)
- return 0;
- }
- else if (c < 0xfc)
- {
- char_len = 5;
- if (c == 0xf8 && d < 0x88)
- return 0;
- }
- else if (c < 0xfe)
- {
- char_len = 6;
- if (c == 0xfc && d < 0x84)
- return 0;
- }
- else
- return 0;
-
- if (str_idx + char_len > input->len)
- return 0;
-
- for (i = 1; i < char_len; ++i)
- {
- d = re_string_byte_at (input, str_idx + i);
- if (d < 0x80 || d > 0xbf)
- return 0;
- }
- return char_len;
- }
-
- char_len = re_string_char_size_at (input, str_idx);
- if (node->type == OP_PERIOD)
- {
- if (char_len <= 1)
- return 0;
- /* FIXME: I don't think this if is needed, as both '\n'
- and '\0' are char_len == 1. */
- /* '.' accepts any one character except the following two cases. */
- if ((!(dfa->syntax & RE_DOT_NEWLINE) &&
- re_string_byte_at (input, str_idx) == '\n') ||
- ((dfa->syntax & RE_DOT_NOT_NULL) &&
- re_string_byte_at (input, str_idx) == '\0'))
- return 0;
- return char_len;
- }
-
- elem_len = re_string_elem_size_at (input, str_idx);
- if ((elem_len <= 1 && char_len <= 1) || char_len == 0)
- return 0;
-
- if (node->type == COMPLEX_BRACKET)
- {
- const re_charset_t *cset = node->opr.mbcset;
-# ifdef _LIBC
- const unsigned char *pin
- = ((const unsigned char *) re_string_get_buffer (input) + str_idx);
- int j;
- uint32_t nrules;
-# endif /* _LIBC */
- int match_len = 0;
- wchar_t wc = ((cset->nranges || cset->nchar_classes || cset->nmbchars)
- ? re_string_wchar_at (input, str_idx) : 0);
-
- /* match with multibyte character? */
- for (i = 0; i < cset->nmbchars; ++i)
- if (wc == cset->mbchars[i])
- {
- match_len = char_len;
- goto check_node_accept_bytes_match;
- }
- /* match with character_class? */
- for (i = 0; i < cset->nchar_classes; ++i)
- {
- wctype_t wt = cset->char_classes[i];
- if (__iswctype (wc, wt))
- {
- match_len = char_len;
- goto check_node_accept_bytes_match;
- }
- }
-
-# ifdef _LIBC
- nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES);
- if (nrules != 0)
- {
- unsigned int in_collseq = 0;
- const int32_t *table, *indirect;
- const unsigned char *weights, *extra;
- const char *collseqwc;
- int32_t idx;
- /* This #include defines a local function! */
-# include <locale/weight.h>
-
- /* match with collating_symbol? */
- if (cset->ncoll_syms)
- extra = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB);
- for (i = 0; i < cset->ncoll_syms; ++i)
- {
- const unsigned char *coll_sym = extra + cset->coll_syms[i];
- /* Compare the length of input collating element and
- the length of current collating element. */
- if (*coll_sym != elem_len)
- continue;
- /* Compare each bytes. */
- for (j = 0; j < *coll_sym; j++)
- if (pin[j] != coll_sym[1 + j])
- break;
- if (j == *coll_sym)
- {
- /* Match if every bytes is equal. */
- match_len = j;
- goto check_node_accept_bytes_match;
- }
- }
-
- if (cset->nranges)
- {
- if (elem_len <= char_len)
- {
- collseqwc = _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQWC);
- in_collseq = __collseq_table_lookup (collseqwc, wc);
- }
- else
- in_collseq = find_collation_sequence_value (pin, elem_len);
- }
- /* match with range expression? */
- for (i = 0; i < cset->nranges; ++i)
- if (cset->range_starts[i] <= in_collseq
- && in_collseq <= cset->range_ends[i])
- {
- match_len = elem_len;
- goto check_node_accept_bytes_match;
- }
-
- /* match with equivalence_class? */
- if (cset->nequiv_classes)
- {
- const unsigned char *cp = pin;
- table = (const int32_t *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB);
- weights = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_WEIGHTMB);
- extra = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_EXTRAMB);
- indirect = (const int32_t *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_INDIRECTMB);
- idx = findidx (&cp);
- if (idx > 0)
- for (i = 0; i < cset->nequiv_classes; ++i)
- {
- int32_t equiv_class_idx = cset->equiv_classes[i];
- size_t weight_len = weights[idx];
- if (weight_len == weights[equiv_class_idx])
- {
- int cnt = 0;
- while (cnt <= weight_len
- && (weights[equiv_class_idx + 1 + cnt]
- == weights[idx + 1 + cnt]))
- ++cnt;
- if (cnt > weight_len)
- {
- match_len = elem_len;
- goto check_node_accept_bytes_match;
- }
- }
- }
- }
- }
- else
-# endif /* _LIBC */
- {
- /* match with range expression? */
-#if __GNUC__ >= 2
- wchar_t cmp_buf[] = {L'\0', L'\0', wc, L'\0', L'\0', L'\0'};
-#else
- wchar_t cmp_buf[] = {L'\0', L'\0', L'\0', L'\0', L'\0', L'\0'};
- cmp_buf[2] = wc;
-#endif
- for (i = 0; i < cset->nranges; ++i)
- {
- cmp_buf[0] = cset->range_starts[i];
- cmp_buf[4] = cset->range_ends[i];
- if (wcscoll (cmp_buf, cmp_buf + 2) <= 0
- && wcscoll (cmp_buf + 2, cmp_buf + 4) <= 0)
- {
- match_len = char_len;
- goto check_node_accept_bytes_match;
- }
- }
- }
- check_node_accept_bytes_match:
- if (!cset->non_match)
- return match_len;
- else
- {
- if (match_len > 0)
- return 0;
- else
- return (elem_len > char_len) ? elem_len : char_len;
- }
- }
- return 0;
-}
-
-# ifdef _LIBC
-static unsigned int
-internal_function
-find_collation_sequence_value (const unsigned char *mbs, size_t mbs_len)
-{
- uint32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES);
- if (nrules == 0)
- {
- if (mbs_len == 1)
- {
- /* No valid character. Match it as a single byte character. */
- const unsigned char *collseq = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQMB);
- return collseq[mbs[0]];
- }
- return UINT_MAX;
- }
- else
- {
- int32_t idx;
- const unsigned char *extra = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB);
- int32_t extrasize = (const unsigned char *)
- _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB + 1) - extra;
-
- for (idx = 0; idx < extrasize;)
- {
- int mbs_cnt, found = 0;
- int32_t elem_mbs_len;
- /* Skip the name of collating element name. */
- idx = idx + extra[idx] + 1;
- elem_mbs_len = extra[idx++];
- if (mbs_len == elem_mbs_len)
- {
- for (mbs_cnt = 0; mbs_cnt < elem_mbs_len; ++mbs_cnt)
- if (extra[idx + mbs_cnt] != mbs[mbs_cnt])
- break;
- if (mbs_cnt == elem_mbs_len)
- /* Found the entry. */
- found = 1;
- }
- /* Skip the byte sequence of the collating element. */
- idx += elem_mbs_len;
- /* Adjust for the alignment. */
- idx = (idx + 3) & ~3;
- /* Skip the collation sequence value. */
- idx += sizeof (uint32_t);
- /* Skip the wide char sequence of the collating element. */
- idx = idx + sizeof (uint32_t) * (extra[idx] + 1);
- /* If we found the entry, return the sequence value. */
- if (found)
- return *(uint32_t *) (extra + idx);
- /* Skip the collation sequence value. */
- idx += sizeof (uint32_t);
- }
- return UINT_MAX;
- }
-}
-# endif /* _LIBC */
-#endif /* RE_ENABLE_I18N */
-
-/* Check whether the node accepts the byte which is IDX-th
- byte of the INPUT. */
-
-static int
-internal_function
-check_node_accept (const re_match_context_t *mctx, const re_token_t *node,
- int idx)
-{
- unsigned char ch;
- ch = re_string_byte_at (&mctx->input, idx);
- switch (node->type)
- {
- case CHARACTER:
- if (node->opr.c != ch)
- return 0;
- break;
-
- case SIMPLE_BRACKET:
- if (!bitset_contain (node->opr.sbcset, ch))
- return 0;
- break;
-
-#ifdef RE_ENABLE_I18N
- case OP_UTF8_PERIOD:
- if (ch >= 0x80)
- return 0;
- /* FALLTHROUGH */
-#endif
- case OP_PERIOD:
- if ((ch == '\n' && !(mctx->dfa->syntax & RE_DOT_NEWLINE))
- || (ch == '\0' && (mctx->dfa->syntax & RE_DOT_NOT_NULL)))
- return 0;
- break;
-
- default:
- return 0;
- }
-
- if (node->constraint)
- {
- /* The node has constraints. Check whether the current context
- satisfies the constraints. */
- unsigned int context = re_string_context_at (&mctx->input, idx,
- mctx->eflags);
- if (NOT_SATISFY_NEXT_CONSTRAINT (node->constraint, context))
- return 0;
- }
-
- return 1;
-}
-
-/* Extend the buffers, if the buffers have run out. */
-
-static reg_errcode_t
-internal_function
-extend_buffers (re_match_context_t *mctx)
-{
- reg_errcode_t ret;
- re_string_t *pstr = &mctx->input;
-
- /* Double the lengthes of the buffers. */
- ret = re_string_realloc_buffers (pstr, pstr->bufs_len * 2);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
-
- if (mctx->state_log != NULL)
- {
- /* And double the length of state_log. */
- /* XXX We have no indication of the size of this buffer. If this
- allocation fail we have no indication that the state_log array
- does not have the right size. */
- re_dfastate_t **new_array = re_realloc (mctx->state_log, re_dfastate_t *,
- pstr->bufs_len + 1);
- if (BE (new_array == NULL, 0))
- return REG_ESPACE;
- mctx->state_log = new_array;
- }
-
- /* Then reconstruct the buffers. */
- if (pstr->icase)
- {
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- {
- ret = build_wcs_upper_buffer (pstr);
- if (BE (ret != REG_NOERROR, 0))
- return ret;
- }
- else
-#endif /* RE_ENABLE_I18N */
- build_upper_buffer (pstr);
- }
- else
- {
-#ifdef RE_ENABLE_I18N
- if (pstr->mb_cur_max > 1)
- build_wcs_buffer (pstr);
- else
-#endif /* RE_ENABLE_I18N */
- {
- if (pstr->trans != NULL)
- re_string_translate_buffer (pstr);
- }
- }
- return REG_NOERROR;
-}
-
-
-/* Functions for matching context. */
-
-/* Initialize MCTX. */
-
-static reg_errcode_t
-internal_function
-match_ctx_init (re_match_context_t *mctx, int eflags, int n)
-{
- mctx->eflags = eflags;
- mctx->match_last = -1;
- if (n > 0)
- {
- mctx->bkref_ents = re_malloc (struct re_backref_cache_entry, n);
- mctx->sub_tops = re_malloc (re_sub_match_top_t *, n);
- if (BE (mctx->bkref_ents == NULL || mctx->sub_tops == NULL, 0))
- return REG_ESPACE;
- }
- /* Already zero-ed by the caller.
- else
- mctx->bkref_ents = NULL;
- mctx->nbkref_ents = 0;
- mctx->nsub_tops = 0; */
- mctx->abkref_ents = n;
- mctx->max_mb_elem_len = 1;
- mctx->asub_tops = n;
- return REG_NOERROR;
-}
-
-/* Clean the entries which depend on the current input in MCTX.
- This function must be invoked when the matcher changes the start index
- of the input, or changes the input string. */
-
-static void
-internal_function
-match_ctx_clean (re_match_context_t *mctx)
-{
- int st_idx;
- for (st_idx = 0; st_idx < mctx->nsub_tops; ++st_idx)
- {
- int sl_idx;
- re_sub_match_top_t *top = mctx->sub_tops[st_idx];
- for (sl_idx = 0; sl_idx < top->nlasts; ++sl_idx)
- {
- re_sub_match_last_t *last = top->lasts[sl_idx];
- re_free (last->path.array);
- re_free (last);
- }
- re_free (top->lasts);
- if (top->path)
- {
- re_free (top->path->array);
- re_free (top->path);
- }
- free (top);
- }
-
- mctx->nsub_tops = 0;
- mctx->nbkref_ents = 0;
-}
-
-/* Free all the memory associated with MCTX. */
-
-static void
-internal_function
-match_ctx_free (re_match_context_t *mctx)
-{
- /* First, free all the memory associated with MCTX->SUB_TOPS. */
- match_ctx_clean (mctx);
- re_free (mctx->sub_tops);
- re_free (mctx->bkref_ents);
-}
-
-/* Add a new backreference entry to MCTX.
- Note that we assume that caller never call this function with duplicate
- entry, and call with STR_IDX which isn't smaller than any existing entry.
-*/
-
-static reg_errcode_t
-internal_function
-match_ctx_add_entry (re_match_context_t *mctx, int node, int str_idx, int from,
- int to)
-{
- if (mctx->nbkref_ents >= mctx->abkref_ents)
- {
- struct re_backref_cache_entry* new_entry;
- new_entry = re_realloc (mctx->bkref_ents, struct re_backref_cache_entry,
- mctx->abkref_ents * 2);
- if (BE (new_entry == NULL, 0))
- {
- re_free (mctx->bkref_ents);
- return REG_ESPACE;
- }
- mctx->bkref_ents = new_entry;
- memset (mctx->bkref_ents + mctx->nbkref_ents, '\0',
- sizeof (struct re_backref_cache_entry) * mctx->abkref_ents);
- mctx->abkref_ents *= 2;
- }
- if (mctx->nbkref_ents > 0
- && mctx->bkref_ents[mctx->nbkref_ents - 1].str_idx == str_idx)
- mctx->bkref_ents[mctx->nbkref_ents - 1].more = 1;
-
- mctx->bkref_ents[mctx->nbkref_ents].node = node;
- mctx->bkref_ents[mctx->nbkref_ents].str_idx = str_idx;
- mctx->bkref_ents[mctx->nbkref_ents].subexp_from = from;
- mctx->bkref_ents[mctx->nbkref_ents].subexp_to = to;
-
- /* This is a cache that saves negative results of check_dst_limits_calc_pos.
- If bit N is clear, means that this entry won't epsilon-transition to
- an OP_OPEN_SUBEXP or OP_CLOSE_SUBEXP for the N+1-th subexpression. If
- it is set, check_dst_limits_calc_pos_1 will recurse and try to find one
- such node.
-
- A backreference does not epsilon-transition unless it is empty, so set
- to all zeros if FROM != TO. */
- mctx->bkref_ents[mctx->nbkref_ents].eps_reachable_subexps_map
- = (from == to ? ~0 : 0);
-
- mctx->bkref_ents[mctx->nbkref_ents++].more = 0;
- if (mctx->max_mb_elem_len < to - from)
- mctx->max_mb_elem_len = to - from;
- return REG_NOERROR;
-}
-
-/* Search for the first entry which has the same str_idx, or -1 if none is
- found. Note that MCTX->BKREF_ENTS is already sorted by MCTX->STR_IDX. */
-
-static int
-internal_function
-search_cur_bkref_entry (const re_match_context_t *mctx, int str_idx)
-{
- int left, right, mid, last;
- last = right = mctx->nbkref_ents;
- for (left = 0; left < right;)
- {
- mid = (left + right) / 2;
- if (mctx->bkref_ents[mid].str_idx < str_idx)
- left = mid + 1;
- else
- right = mid;
- }
- if (left < last && mctx->bkref_ents[left].str_idx == str_idx)
- return left;
- else
- return -1;
-}
-
-/* Register the node NODE, whose type is OP_OPEN_SUBEXP, and which matches
- at STR_IDX. */
-
-static reg_errcode_t
-internal_function
-match_ctx_add_subtop (re_match_context_t *mctx, int node, int str_idx)
-{
-#ifdef DEBUG
- assert (mctx->sub_tops != NULL);
- assert (mctx->asub_tops > 0);
-#endif
- if (BE (mctx->nsub_tops == mctx->asub_tops, 0))
- {
- int new_asub_tops = mctx->asub_tops * 2;
- re_sub_match_top_t **new_array = re_realloc (mctx->sub_tops,
- re_sub_match_top_t *,
- new_asub_tops);
- if (BE (new_array == NULL, 0))
- return REG_ESPACE;
- mctx->sub_tops = new_array;
- mctx->asub_tops = new_asub_tops;
- }
- mctx->sub_tops[mctx->nsub_tops] = calloc (1, sizeof (re_sub_match_top_t));
- if (BE (mctx->sub_tops[mctx->nsub_tops] == NULL, 0))
- return REG_ESPACE;
- mctx->sub_tops[mctx->nsub_tops]->node = node;
- mctx->sub_tops[mctx->nsub_tops++]->str_idx = str_idx;
- return REG_NOERROR;
-}
-
-/* Register the node NODE, whose type is OP_CLOSE_SUBEXP, and which matches
- at STR_IDX, whose corresponding OP_OPEN_SUBEXP is SUB_TOP. */
-
-static re_sub_match_last_t *
-internal_function
-match_ctx_add_sublast (re_sub_match_top_t *subtop, int node, int str_idx)
-{
- re_sub_match_last_t *new_entry;
- if (BE (subtop->nlasts == subtop->alasts, 0))
- {
- int new_alasts = 2 * subtop->alasts + 1;
- re_sub_match_last_t **new_array = re_realloc (subtop->lasts,
- re_sub_match_last_t *,
- new_alasts);
- if (BE (new_array == NULL, 0))
- return NULL;
- subtop->lasts = new_array;
- subtop->alasts = new_alasts;
- }
- new_entry = calloc (1, sizeof (re_sub_match_last_t));
- if (BE (new_entry != NULL, 1))
- {
- subtop->lasts[subtop->nlasts] = new_entry;
- new_entry->node = node;
- new_entry->str_idx = str_idx;
- ++subtop->nlasts;
- }
- return new_entry;
-}
-
-static void
-internal_function
-sift_ctx_init (re_sift_context_t *sctx, re_dfastate_t **sifted_sts,
- re_dfastate_t **limited_sts, int last_node, int last_str_idx)
-{
- sctx->sifted_states = sifted_sts;
- sctx->limited_states = limited_sts;
- sctx->last_node = last_node;
- sctx->last_str_idx = last_str_idx;
- re_node_set_init_empty (&sctx->limits);
-}
-
-
-/* Binary backward compatibility. */
-#if _LIBC
-# include <shlib-compat.h>
-# if SHLIB_COMPAT (libc, GLIBC_2_0, GLIBC_2_3)
-link_warning (re_max_failures, "the 're_max_failures' variable is obsolete and will go away.")
-int re_max_failures = 2000;
-# endif
-#endif
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/gkregex.h b/3rdParty/metis/metis-5.1.0/GKlib/gkregex.h
deleted file mode 100644
index 807c404ec..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/gkregex.h
+++ /dev/null
@@ -1,556 +0,0 @@
-/* Definitions for data structures and routines for the regular
- expression library.
- Copyright (C) 1985,1989-93,1995-98,2000,2001,2002,2003,2005,2006
- Free Software Foundation, Inc.
- This file is part of the GNU C Library.
-
- The GNU C Library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- The GNU C Library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with the GNU C Library; if not, write to the Free
- Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- 02111-1307 USA. */
-
-#ifndef _REGEX_H
-#define _REGEX_H 1
-
-#include <sys/types.h>
-
-/* Allow the use in C++ code. */
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* The following two types have to be signed and unsigned integer type
- wide enough to hold a value of a pointer. For most ANSI compilers
- ptrdiff_t and size_t should be likely OK. Still size of these two
- types is 2 for Microsoft C. Ugh... */
-typedef long int s_reg_t;
-typedef unsigned long int active_reg_t;
-
-/* The following bits are used to determine the regexp syntax we
- recognize. The set/not-set meanings are chosen so that Emacs syntax
- remains the value 0. The bits are given in alphabetical order, and
- the definitions shifted by one from the previous bit; thus, when we
- add or remove a bit, only one other definition need change. */
-typedef unsigned long int reg_syntax_t;
-
-/* If this bit is not set, then \ inside a bracket expression is literal.
- If set, then such a \ quotes the following character. */
-#define RE_BACKSLASH_ESCAPE_IN_LISTS ((unsigned long int) 1)
-
-/* If this bit is not set, then + and ? are operators, and \+ and \? are
- literals.
- If set, then \+ and \? are operators and + and ? are literals. */
-#define RE_BK_PLUS_QM (RE_BACKSLASH_ESCAPE_IN_LISTS << 1)
-
-/* If this bit is set, then character classes are supported. They are:
- [:alpha:], [:upper:], [:lower:], [:digit:], [:alnum:], [:xdigit:],
- [:space:], [:print:], [:punct:], [:graph:], and [:cntrl:].
- If not set, then character classes are not supported. */
-#define RE_CHAR_CLASSES (RE_BK_PLUS_QM << 1)
-
-/* If this bit is set, then ^ and $ are always anchors (outside bracket
- expressions, of course).
- If this bit is not set, then it depends:
- ^ is an anchor if it is at the beginning of a regular
- expression or after an open-group or an alternation operator;
- $ is an anchor if it is at the end of a regular expression, or
- before a close-group or an alternation operator.
-
- This bit could be (re)combined with RE_CONTEXT_INDEP_OPS, because
- POSIX draft 11.2 says that * etc. in leading positions is undefined.
- We already implemented a previous draft which made those constructs
- invalid, though, so we haven't changed the code back. */
-#define RE_CONTEXT_INDEP_ANCHORS (RE_CHAR_CLASSES << 1)
-
-/* If this bit is set, then special characters are always special
- regardless of where they are in the pattern.
- If this bit is not set, then special characters are special only in
- some contexts; otherwise they are ordinary. Specifically,
- * + ? and intervals are only special when not after the beginning,
- open-group, or alternation operator. */
-#define RE_CONTEXT_INDEP_OPS (RE_CONTEXT_INDEP_ANCHORS << 1)
-
-/* If this bit is set, then *, +, ?, and { cannot be first in an re or
- immediately after an alternation or begin-group operator. */
-#define RE_CONTEXT_INVALID_OPS (RE_CONTEXT_INDEP_OPS << 1)
-
-/* If this bit is set, then . matches newline.
- If not set, then it doesn't. */
-#define RE_DOT_NEWLINE (RE_CONTEXT_INVALID_OPS << 1)
-
-/* If this bit is set, then . doesn't match NUL.
- If not set, then it does. */
-#define RE_DOT_NOT_NULL (RE_DOT_NEWLINE << 1)
-
-/* If this bit is set, nonmatching lists [^...] do not match newline.
- If not set, they do. */
-#define RE_HAT_LISTS_NOT_NEWLINE (RE_DOT_NOT_NULL << 1)
-
-/* If this bit is set, either \{...\} or {...} defines an
- interval, depending on RE_NO_BK_BRACES.
- If not set, \{, \}, {, and } are literals. */
-#define RE_INTERVALS (RE_HAT_LISTS_NOT_NEWLINE << 1)
-
-/* If this bit is set, +, ? and | aren't recognized as operators.
- If not set, they are. */
-#define RE_LIMITED_OPS (RE_INTERVALS << 1)
-
-/* If this bit is set, newline is an alternation operator.
- If not set, newline is literal. */
-#define RE_NEWLINE_ALT (RE_LIMITED_OPS << 1)
-
-/* If this bit is set, then `{...}' defines an interval, and \{ and \}
- are literals.
- If not set, then `\{...\}' defines an interval. */
-#define RE_NO_BK_BRACES (RE_NEWLINE_ALT << 1)
-
-/* If this bit is set, (...) defines a group, and \( and \) are literals.
- If not set, \(...\) defines a group, and ( and ) are literals. */
-#define RE_NO_BK_PARENS (RE_NO_BK_BRACES << 1)
-
-/* If this bit is set, then \<digit> matches <digit>.
- If not set, then \<digit> is a back-reference. */
-#define RE_NO_BK_REFS (RE_NO_BK_PARENS << 1)
-
-/* If this bit is set, then | is an alternation operator, and \| is literal.
- If not set, then \| is an alternation operator, and | is literal. */
-#define RE_NO_BK_VBAR (RE_NO_BK_REFS << 1)
-
-/* If this bit is set, then an ending range point collating higher
- than the starting range point, as in [z-a], is invalid.
- If not set, then when ending range point collates higher than the
- starting range point, the range is ignored. */
-#define RE_NO_EMPTY_RANGES (RE_NO_BK_VBAR << 1)
-
-/* If this bit is set, then an unmatched ) is ordinary.
- If not set, then an unmatched ) is invalid. */
-#define RE_UNMATCHED_RIGHT_PAREN_ORD (RE_NO_EMPTY_RANGES << 1)
-
-/* If this bit is set, succeed as soon as we match the whole pattern,
- without further backtracking. */
-#define RE_NO_POSIX_BACKTRACKING (RE_UNMATCHED_RIGHT_PAREN_ORD << 1)
-
-/* If this bit is set, do not process the GNU regex operators.
- If not set, then the GNU regex operators are recognized. */
-#define RE_NO_GNU_OPS (RE_NO_POSIX_BACKTRACKING << 1)
-
-/* If this bit is set, turn on internal regex debugging.
- If not set, and debugging was on, turn it off.
- This only works if regex.c is compiled -DDEBUG.
- We define this bit always, so that all that's needed to turn on
- debugging is to recompile regex.c; the calling code can always have
- this bit set, and it won't affect anything in the normal case. */
-#define RE_DEBUG (RE_NO_GNU_OPS << 1)
-
-/* If this bit is set, a syntactically invalid interval is treated as
- a string of ordinary characters. For example, the ERE 'a{1' is
- treated as 'a\{1'. */
-#define RE_INVALID_INTERVAL_ORD (RE_DEBUG << 1)
-
-/* If this bit is set, then ignore case when matching.
- If not set, then case is significant. */
-#define RE_ICASE (RE_INVALID_INTERVAL_ORD << 1)
-
-/* This bit is used internally like RE_CONTEXT_INDEP_ANCHORS but only
- for ^, because it is difficult to scan the regex backwards to find
- whether ^ should be special. */
-#define RE_CARET_ANCHORS_HERE (RE_ICASE << 1)
-
-/* If this bit is set, then \{ cannot be first in an bre or
- immediately after an alternation or begin-group operator. */
-#define RE_CONTEXT_INVALID_DUP (RE_CARET_ANCHORS_HERE << 1)
-
-/* If this bit is set, then no_sub will be set to 1 during
- re_compile_pattern. */
-#define RE_NO_SUB (RE_CONTEXT_INVALID_DUP << 1)
-
-/* This global variable defines the particular regexp syntax to use (for
- some interfaces). When a regexp is compiled, the syntax used is
- stored in the pattern buffer, so changing this does not affect
- already-compiled regexps. */
-extern reg_syntax_t re_syntax_options;
-
-/* Define combinations of the above bits for the standard possibilities.
- (The [[[ comments delimit what gets put into the Texinfo file, so
- don't delete them!) */
-/* [[[begin syntaxes]]] */
-#define RE_SYNTAX_EMACS 0
-
-#define RE_SYNTAX_AWK \
- (RE_BACKSLASH_ESCAPE_IN_LISTS | RE_DOT_NOT_NULL \
- | RE_NO_BK_PARENS | RE_NO_BK_REFS \
- | RE_NO_BK_VBAR | RE_NO_EMPTY_RANGES \
- | RE_DOT_NEWLINE | RE_CONTEXT_INDEP_ANCHORS \
- | RE_UNMATCHED_RIGHT_PAREN_ORD | RE_NO_GNU_OPS)
-
-#define RE_SYNTAX_GNU_AWK \
- ((RE_SYNTAX_POSIX_EXTENDED | RE_BACKSLASH_ESCAPE_IN_LISTS | RE_DEBUG) \
- & ~(RE_DOT_NOT_NULL | RE_INTERVALS | RE_CONTEXT_INDEP_OPS \
- | RE_CONTEXT_INVALID_OPS ))
-
-#define RE_SYNTAX_POSIX_AWK \
- (RE_SYNTAX_POSIX_EXTENDED | RE_BACKSLASH_ESCAPE_IN_LISTS \
- | RE_INTERVALS | RE_NO_GNU_OPS)
-
-#define RE_SYNTAX_GREP \
- (RE_BK_PLUS_QM | RE_CHAR_CLASSES \
- | RE_HAT_LISTS_NOT_NEWLINE | RE_INTERVALS \
- | RE_NEWLINE_ALT)
-
-#define RE_SYNTAX_EGREP \
- (RE_CHAR_CLASSES | RE_CONTEXT_INDEP_ANCHORS \
- | RE_CONTEXT_INDEP_OPS | RE_HAT_LISTS_NOT_NEWLINE \
- | RE_NEWLINE_ALT | RE_NO_BK_PARENS \
- | RE_NO_BK_VBAR)
-
-#define RE_SYNTAX_POSIX_EGREP \
- (RE_SYNTAX_EGREP | RE_INTERVALS | RE_NO_BK_BRACES \
- | RE_INVALID_INTERVAL_ORD)
-
-/* P1003.2/D11.2, section 4.20.7.1, lines 5078ff. */
-#define RE_SYNTAX_ED RE_SYNTAX_POSIX_BASIC
-
-#define RE_SYNTAX_SED RE_SYNTAX_POSIX_BASIC
-
-/* Syntax bits common to both basic and extended POSIX regex syntax. */
-#define _RE_SYNTAX_POSIX_COMMON \
- (RE_CHAR_CLASSES | RE_DOT_NEWLINE | RE_DOT_NOT_NULL \
- | RE_INTERVALS | RE_NO_EMPTY_RANGES)
-
-#define RE_SYNTAX_POSIX_BASIC \
- (_RE_SYNTAX_POSIX_COMMON | RE_BK_PLUS_QM | RE_CONTEXT_INVALID_DUP)
-
-/* Differs from ..._POSIX_BASIC only in that RE_BK_PLUS_QM becomes
- RE_LIMITED_OPS, i.e., \? \+ \| are not recognized. Actually, this
- isn't minimal, since other operators, such as \`, aren't disabled. */
-#define RE_SYNTAX_POSIX_MINIMAL_BASIC \
- (_RE_SYNTAX_POSIX_COMMON | RE_LIMITED_OPS)
-
-#define RE_SYNTAX_POSIX_EXTENDED \
- (_RE_SYNTAX_POSIX_COMMON | RE_CONTEXT_INDEP_ANCHORS \
- | RE_CONTEXT_INDEP_OPS | RE_NO_BK_BRACES \
- | RE_NO_BK_PARENS | RE_NO_BK_VBAR \
- | RE_CONTEXT_INVALID_OPS | RE_UNMATCHED_RIGHT_PAREN_ORD)
-
-/* Differs from ..._POSIX_EXTENDED in that RE_CONTEXT_INDEP_OPS is
- removed and RE_NO_BK_REFS is added. */
-#define RE_SYNTAX_POSIX_MINIMAL_EXTENDED \
- (_RE_SYNTAX_POSIX_COMMON | RE_CONTEXT_INDEP_ANCHORS \
- | RE_CONTEXT_INVALID_OPS | RE_NO_BK_BRACES \
- | RE_NO_BK_PARENS | RE_NO_BK_REFS \
- | RE_NO_BK_VBAR | RE_UNMATCHED_RIGHT_PAREN_ORD)
-/* [[[end syntaxes]]] */
-
-/* Maximum number of duplicates an interval can allow. Some systems
- (erroneously) define this in other header files, but we want our
- value, so remove any previous define. */
-#ifdef RE_DUP_MAX
-# undef RE_DUP_MAX
-#endif
-/* If sizeof(int) == 2, then ((1 << 15) - 1) overflows. */
-#define RE_DUP_MAX (0x7fff)
-
-
-/* POSIX `cflags' bits (i.e., information for `regcomp'). */
-
-/* If this bit is set, then use extended regular expression syntax.
- If not set, then use basic regular expression syntax. */
-#define REG_EXTENDED 1
-
-/* If this bit is set, then ignore case when matching.
- If not set, then case is significant. */
-#define REG_ICASE (REG_EXTENDED << 1)
-
-/* If this bit is set, then anchors do not match at newline
- characters in the string.
- If not set, then anchors do match at newlines. */
-#define REG_NEWLINE (REG_ICASE << 1)
-
-/* If this bit is set, then report only success or fail in regexec.
- If not set, then returns differ between not matching and errors. */
-#define REG_NOSUB (REG_NEWLINE << 1)
-
-
-/* POSIX `eflags' bits (i.e., information for regexec). */
-
-/* If this bit is set, then the beginning-of-line operator doesn't match
- the beginning of the string (presumably because it's not the
- beginning of a line).
- If not set, then the beginning-of-line operator does match the
- beginning of the string. */
-#define REG_NOTBOL 1
-
-/* Like REG_NOTBOL, except for the end-of-line. */
-#define REG_NOTEOL (1 << 1)
-
-/* Use PMATCH[0] to delimit the start and end of the search in the
- buffer. */
-#define REG_STARTEND (1 << 2)
-
-
-/* If any error codes are removed, changed, or added, update the
- `re_error_msg' table in regex.c. */
-typedef enum
-{
-#ifdef _XOPEN_SOURCE
- REG_ENOSYS = -1, /* This will never happen for this implementation. */
-#endif
-
- REG_NOERROR = 0, /* Success. */
- REG_NOMATCH, /* Didn't find a match (for regexec). */
-
- /* POSIX regcomp return error codes. (In the order listed in the
- standard.) */
- REG_BADPAT, /* Invalid pattern. */
- REG_ECOLLATE, /* Inalid collating element. */
- REG_ECTYPE, /* Invalid character class name. */
- REG_EESCAPE, /* Trailing backslash. */
- REG_ESUBREG, /* Invalid back reference. */
- REG_EBRACK, /* Unmatched left bracket. */
- REG_EPAREN, /* Parenthesis imbalance. */
- REG_EBRACE, /* Unmatched \{. */
- REG_BADBR, /* Invalid contents of \{\}. */
- REG_ERANGE, /* Invalid range end. */
- REG_ESPACE, /* Ran out of memory. */
- REG_BADRPT, /* No preceding re for repetition op. */
-
- /* Error codes we've added. */
- REG_EEND, /* Premature end. */
- REG_ESIZE, /* Compiled pattern bigger than 2^16 bytes. */
- REG_ERPAREN /* Unmatched ) or \); not returned from regcomp. */
-} reg_errcode_t;
-
-/* This data structure represents a compiled pattern. Before calling
- the pattern compiler, the fields `buffer', `allocated', `fastmap',
- `translate', and `no_sub' can be set. After the pattern has been
- compiled, the `re_nsub' field is available. All other fields are
- private to the regex routines. */
-
-#ifndef RE_TRANSLATE_TYPE
-# define RE_TRANSLATE_TYPE unsigned char *
-#endif
-
-struct re_pattern_buffer
-{
- /* Space that holds the compiled pattern. It is declared as
- `unsigned char *' because its elements are sometimes used as
- array indexes. */
- unsigned char *buffer;
-
- /* Number of bytes to which `buffer' points. */
- unsigned long int allocated;
-
- /* Number of bytes actually used in `buffer'. */
- unsigned long int used;
-
- /* Syntax setting with which the pattern was compiled. */
- reg_syntax_t syntax;
-
- /* Pointer to a fastmap, if any, otherwise zero. re_search uses the
- fastmap, if there is one, to skip over impossible starting points
- for matches. */
- char *fastmap;
-
- /* Either a translate table to apply to all characters before
- comparing them, or zero for no translation. The translation is
- applied to a pattern when it is compiled and to a string when it
- is matched. */
- RE_TRANSLATE_TYPE translate;
-
- /* Number of subexpressions found by the compiler. */
- size_t re_nsub;
-
- /* Zero if this pattern cannot match the empty string, one else.
- Well, in truth it's used only in `re_search_2', to see whether or
- not we should use the fastmap, so we don't set this absolutely
- perfectly; see `re_compile_fastmap' (the `duplicate' case). */
- unsigned can_be_null : 1;
-
- /* If REGS_UNALLOCATED, allocate space in the `regs' structure
- for `max (RE_NREGS, re_nsub + 1)' groups.
- If REGS_REALLOCATE, reallocate space if necessary.
- If REGS_FIXED, use what's there. */
-#define REGS_UNALLOCATED 0
-#define REGS_REALLOCATE 1
-#define REGS_FIXED 2
- unsigned regs_allocated : 2;
-
- /* Set to zero when `regex_compile' compiles a pattern; set to one
- by `re_compile_fastmap' if it updates the fastmap. */
- unsigned fastmap_accurate : 1;
-
- /* If set, `re_match_2' does not return information about
- subexpressions. */
- unsigned no_sub : 1;
-
- /* If set, a beginning-of-line anchor doesn't match at the beginning
- of the string. */
- unsigned not_bol : 1;
-
- /* Similarly for an end-of-line anchor. */
- unsigned not_eol : 1;
-
- /* If true, an anchor at a newline matches. */
- unsigned newline_anchor : 1;
-};
-
-typedef struct re_pattern_buffer regex_t;
-
-/* Type for byte offsets within the string. POSIX mandates this. */
-typedef int regoff_t;
-
-
-/* This is the structure we store register match data in. See
- regex.texinfo for a full description of what registers match. */
-struct re_registers
-{
- unsigned num_regs;
- regoff_t *start;
- regoff_t *end;
-};
-
-
-/* If `regs_allocated' is REGS_UNALLOCATED in the pattern buffer,
- `re_match_2' returns information about at least this many registers
- the first time a `regs' structure is passed. */
-#ifndef RE_NREGS
-# define RE_NREGS 30
-#endif
-
-
-/* POSIX specification for registers. Aside from the different names than
- `re_registers', POSIX uses an array of structures, instead of a
- structure of arrays. */
-typedef struct
-{
- regoff_t rm_so; /* Byte offset from string's start to substring's start. */
- regoff_t rm_eo; /* Byte offset from string's start to substring's end. */
-} regmatch_t;
-
-/* Declarations for routines. */
-
-/* Sets the current default syntax to SYNTAX, and return the old syntax.
- You can also simply assign to the `re_syntax_options' variable. */
-extern reg_syntax_t re_set_syntax (reg_syntax_t __syntax);
-
-/* Compile the regular expression PATTERN, with length LENGTH
- and syntax given by the global `re_syntax_options', into the buffer
- BUFFER. Return NULL if successful, and an error string if not. */
-extern const char *re_compile_pattern (const char *__pattern, size_t __length,
- struct re_pattern_buffer *__buffer);
-
-
-/* Compile a fastmap for the compiled pattern in BUFFER; used to
- accelerate searches. Return 0 if successful and -2 if was an
- internal error. */
-extern int re_compile_fastmap (struct re_pattern_buffer *__buffer);
-
-
-/* Search in the string STRING (with length LENGTH) for the pattern
- compiled into BUFFER. Start searching at position START, for RANGE
- characters. Return the starting position of the match, -1 for no
- match, or -2 for an internal error. Also return register
- information in REGS (if REGS and BUFFER->no_sub are nonzero). */
-extern int re_search (struct re_pattern_buffer *__buffer, const char *__string,
- int __length, int __start, int __range,
- struct re_registers *__regs);
-
-
-/* Like `re_search', but search in the concatenation of STRING1 and
- STRING2. Also, stop searching at index START + STOP. */
-extern int re_search_2 (struct re_pattern_buffer *__buffer,
- const char *__string1, int __length1,
- const char *__string2, int __length2, int __start,
- int __range, struct re_registers *__regs, int __stop);
-
-
-/* Like `re_search', but return how many characters in STRING the regexp
- in BUFFER matched, starting at position START. */
-extern int re_match (struct re_pattern_buffer *__buffer, const char *__string,
- int __length, int __start, struct re_registers *__regs);
-
-
-/* Relates to `re_match' as `re_search_2' relates to `re_search'. */
-extern int re_match_2 (struct re_pattern_buffer *__buffer,
- const char *__string1, int __length1,
- const char *__string2, int __length2, int __start,
- struct re_registers *__regs, int __stop);
-
-
-/* Set REGS to hold NUM_REGS registers, storing them in STARTS and
- ENDS. Subsequent matches using BUFFER and REGS will use this memory
- for recording register information. STARTS and ENDS must be
- allocated with malloc, and must each be at least `NUM_REGS * sizeof
- (regoff_t)' bytes long.
-
- If NUM_REGS == 0, then subsequent matches should allocate their own
- register data.
-
- Unless this function is called, the first search or match using
- PATTERN_BUFFER will allocate its own register data, without
- freeing the old data. */
-extern void re_set_registers (struct re_pattern_buffer *__buffer,
- struct re_registers *__regs,
- unsigned int __num_regs,
- regoff_t *__starts, regoff_t *__ends);
-
-#if defined _REGEX_RE_COMP || defined _LIBC
-# ifndef _CRAY
-/* 4.2 bsd compatibility. */
-extern char *re_comp (const char *);
-extern int re_exec (const char *);
-# endif
-#endif
-
-/* GCC 2.95 and later have "__restrict"; C99 compilers have
- "restrict", and "configure" may have defined "restrict". */
-#ifndef __restrict
-# if ! (2 < __GNUC__ || (2 == __GNUC__ && 95 <= __GNUC_MINOR__))
-# if defined restrict || 199901L <= __STDC_VERSION__
-# define __restrict restrict
-# else
-# define __restrict
-# endif
-# endif
-#endif
-/* gcc 3.1 and up support the [restrict] syntax. */
-#ifndef __restrict_arr
-# if (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1)) \
- && !defined __GNUG__
-# define __restrict_arr __restrict
-# else
-# define __restrict_arr
-# endif
-#endif
-
-/* POSIX compatibility. */
-extern int regcomp (regex_t *__restrict __preg,
- const char *__restrict __pattern,
- int __cflags);
-
-extern int regexec (const regex_t *__restrict __preg,
- const char *__restrict __string, size_t __nmatch,
- regmatch_t __pmatch[__restrict_arr],
- int __eflags);
-
-extern size_t regerror (int __errcode, const regex_t *__restrict __preg,
- char *__restrict __errbuf, size_t __errbuf_size);
-
-extern void regfree (regex_t *__preg);
-
-
-#ifdef __cplusplus
-}
-#endif /* C++ */
-
-#endif /* regex.h */
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/graph.c b/3rdParty/metis/metis-5.1.0/GKlib/graph.c
deleted file mode 100644
index 209581865..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/graph.c
+++ /dev/null
@@ -1,1574 +0,0 @@
-/*!
- * \file
- *
- * \brief Various routines with dealing with sparse graphs
- *
- * \author George Karypis
- * \version\verbatim $Id: graph.c 13328 2012-12-31 14:57:40Z karypis $ \endverbatim
- */
-
-#include <GKlib.h>
-
-#define OMPMINOPS 50000
-
-/*************************************************************************/
-/*! Allocate memory for a graph and initializes it
- \returns the allocated graph. The various fields are set to NULL.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_Create()
-{
- gk_graph_t *graph;
-
- graph = (gk_graph_t *)gk_malloc(sizeof(gk_graph_t), "gk_graph_Create: graph");
-
- gk_graph_Init(graph);
-
- return graph;
-}
-
-
-/*************************************************************************/
-/*! Initializes the graph.
- \param graph is the graph to be initialized.
-*/
-/*************************************************************************/
-void gk_graph_Init(gk_graph_t *graph)
-{
- memset(graph, 0, sizeof(gk_graph_t));
- graph->nvtxs = -1;
-}
-
-
-/*************************************************************************/
-/*! Frees all the memory allocated for a graph.
- \param graph is the graph to be freed.
-*/
-/*************************************************************************/
-void gk_graph_Free(gk_graph_t **graph)
-{
- if (*graph == NULL)
- return;
- gk_graph_FreeContents(*graph);
- gk_free((void **)graph, LTERM);
-}
-
-
-/*************************************************************************/
-/*! Frees only the memory allocated for the graph's different fields and
- sets them to NULL.
- \param graph is the graph whose contents will be freed.
-*/
-/*************************************************************************/
-void gk_graph_FreeContents(gk_graph_t *graph)
-{
- gk_free((void *)&graph->xadj, &graph->adjncy,
- &graph->iadjwgt, &graph->fadjwgt,
- &graph->ivwgts, &graph->fvwgts,
- &graph->ivsizes, &graph->fvsizes,
- &graph->vlabels,
- LTERM);
-}
-
-
-/**************************************************************************/
-/*! Reads a sparse graph from the supplied file
- \param filename is the file that stores the data.
- \param format is the graph format. The supported values are:
- GK_GRAPH_FMT_METIS.
- \param isfewgts is 1 if the edge-weights should be read as floats
- \param isfvwgts is 1 if the vertex-weights should be read as floats
- \param isfvsizes is 1 if the vertex-sizes should be read as floats
- \returns the graph that was read.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_Read(char *filename, int format, int isfewgts,
- int isfvwgts, int isfvsizes)
-{
- ssize_t i, k, l;
- size_t nfields, nvtxs, nedges, fmt, ncon, lnlen;
- int32_t ival;
- float fval;
- int readsizes=0, readwgts=0, readvals=0, numbering=0;
- char *line=NULL, *head, *tail, fmtstr[256];
- FILE *fpin=NULL;
- gk_graph_t *graph=NULL;
-
-
- if (!gk_fexists(filename))
- gk_errexit(SIGERR, "File %s does not exist!\n", filename);
-
- if (format == GK_GRAPH_FMT_METIS) {
- fpin = gk_fopen(filename, "r", "gk_graph_Read: fpin");
- do {
- if (gk_getline(&line, &lnlen, fpin) <= 0)
- gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename);
- } while (line[0] == '%');
-
- fmt = ncon = 0;
- nfields = sscanf(line, "%zu %zu %zu %zu", &nvtxs, &nedges, &fmt, &ncon);
- if (nfields < 2)
- gk_errexit(SIGERR, "Header line must contain at least 2 integers (#vtxs and #edges).\n");
-
- nedges *= 2;
-
- if (fmt > 111)
- gk_errexit(SIGERR, "Cannot read this type of file format [fmt=%zu]!\n", fmt);
-
- sprintf(fmtstr, "%03zu", fmt%1000);
- readsizes = (fmtstr[0] == '1');
- readwgts = (fmtstr[1] == '1');
- readvals = (fmtstr[2] == '1');
- numbering = 1;
- ncon = (ncon == 0 ? 1 : ncon);
- }
- else {
- gk_errexit(SIGERR, "Unrecognized format: %d\n", format);
- }
-
- graph = gk_graph_Create();
-
- graph->nvtxs = nvtxs;
-
- graph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Read: xadj");
- graph->adjncy = gk_i32malloc(nedges, "gk_graph_Read: adjncy");
- if (readvals) {
- if (isfewgts)
- graph->fadjwgt = gk_fmalloc(nedges, "gk_graph_Read: fadjwgt");
- else
- graph->iadjwgt = gk_i32malloc(nedges, "gk_graph_Read: iadjwgt");
- }
-
- if (readsizes) {
- if (isfvsizes)
- graph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Read: fvsizes");
- else
- graph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Read: ivsizes");
- }
-
- if (readwgts) {
- if (isfvwgts)
- graph->fvwgts = gk_fmalloc(nvtxs*ncon, "gk_graph_Read: fvwgts");
- else
- graph->ivwgts = gk_i32malloc(nvtxs*ncon, "gk_graph_Read: ivwgts");
- }
-
-
- /*----------------------------------------------------------------------
- * Read the sparse graph file
- *---------------------------------------------------------------------*/
- numbering = (numbering ? - 1 : 0);
- for (graph->xadj[0]=0, k=0, i=0; i<nvtxs; i++) {
- do {
- if (gk_getline(&line, &lnlen, fpin) == -1)
- gk_errexit(SIGERR, "Pregraphure end of input file: file while reading row %d\n", i);
- } while (line[0] == '%');
-
- head = line;
- tail = NULL;
-
- /* Read vertex sizes */
- if (readsizes) {
- if (isfvsizes) {
-#ifdef __MSC__
- graph->fvsizes[i] = (float)strtod(head, &tail);
-#else
- graph->fvsizes[i] = strtof(head, &tail);
-#endif
- if (tail == head)
- gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1);
- if (graph->fvsizes[i] < 0)
- gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1);
- }
- else {
- graph->ivsizes[i] = strtol(head, &tail, 0);
- if (tail == head)
- gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1);
- if (graph->ivsizes[i] < 0)
- gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1);
- }
- head = tail;
- }
-
- /* Read vertex weights */
- if (readwgts) {
- for (l=0; l<ncon; l++) {
- if (isfvwgts) {
-#ifdef __MSC__
- graph->fvwgts[i*ncon+l] = (float)strtod(head, &tail);
-#else
- graph->fvwgts[i*ncon+l] = strtof(head, &tail);
-#endif
- if (tail == head)
- gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights "
- "for the %d constraints.\n", i+1, ncon);
- if (graph->fvwgts[i*ncon+l] < 0)
- gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l);
- }
- else {
- graph->ivwgts[i*ncon+l] = strtol(head, &tail, 0);
- if (tail == head)
- gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights "
- "for the %d constraints.\n", i+1, ncon);
- if (graph->ivwgts[i*ncon+l] < 0)
- gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l);
- }
- head = tail;
- }
- }
-
-
- /* Read the rest of the row */
- while (1) {
- ival = (int)strtol(head, &tail, 0);
- if (tail == head)
- break;
- head = tail;
-
- if ((graph->adjncy[k] = ival + numbering) < 0)
- gk_errexit(SIGERR, "Error: Invalid column number %d at row %zd.\n", ival, i);
-
- if (readvals) {
- if (isfewgts) {
-#ifdef __MSC__
- fval = (float)strtod(head, &tail);
-#else
- fval = strtof(head, &tail);
-#endif
- if (tail == head)
- gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k);
-
- graph->fadjwgt[k] = fval;
- }
- else {
- ival = strtol(head, &tail, 0);
- if (tail == head)
- gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k);
-
- graph->iadjwgt[k] = ival;
- }
- head = tail;
- }
- k++;
- }
- graph->xadj[i+1] = k;
- }
-
- if (k != nedges)
- gk_errexit(SIGERR, "gk_graph_Read: Something wrong with the number of edges in "
- "the input file. nedges=%zd, Actualnedges=%zd.\n", nedges, k);
-
- gk_fclose(fpin);
-
- gk_free((void **)&line, LTERM);
-
- return graph;
-}
-
-
-/**************************************************************************/
-/*! Writes a graph into a file.
- \param graph is the graph to be written,
- \param filename is the name of the output file.
- \param format is one of GK_GRAPH_FMT_METIS specifying
- the format of the output file.
-*/
-/**************************************************************************/
-void gk_graph_Write(gk_graph_t *graph, char *filename, int format)
-{
- ssize_t i, j;
- int hasvwgts, hasvsizes, hasewgts;
- FILE *fpout;
-
- if (format != GK_GRAPH_FMT_METIS)
- gk_errexit(SIGERR, "Unknown file format. %d\n", format);
-
- if (filename)
- fpout = gk_fopen(filename, "w", "gk_graph_Write: fpout");
- else
- fpout = stdout;
-
-
- hasewgts = (graph->iadjwgt || graph->fadjwgt);
- hasvwgts = (graph->ivwgts || graph->fvwgts);
- hasvsizes = (graph->ivsizes || graph->fvsizes);
-
- /* write the header line */
- fprintf(fpout, "%d %zd", graph->nvtxs, graph->xadj[graph->nvtxs]/2);
- if (hasvwgts || hasvsizes || hasewgts)
- fprintf(fpout, " %d%d%d", hasvsizes, hasvwgts, hasewgts);
- fprintf(fpout, "\n");
-
-
- for (i=0; i<graph->nvtxs; i++) {
- if (hasvsizes) {
- if (graph->ivsizes)
- fprintf(fpout, " %d", graph->ivsizes[i]);
- else
- fprintf(fpout, " %f", graph->fvsizes[i]);
- }
-
- if (hasvwgts) {
- if (graph->ivwgts)
- fprintf(fpout, " %d", graph->ivwgts[i]);
- else
- fprintf(fpout, " %f", graph->fvwgts[i]);
- }
-
- for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++) {
- fprintf(fpout, " %d", graph->adjncy[j]+1);
- if (hasewgts) {
- if (graph->iadjwgt)
- fprintf(fpout, " %d", graph->iadjwgt[j]);
- else
- fprintf(fpout, " %f", graph->fadjwgt[j]);
- }
- }
- fprintf(fpout, "\n");
- }
- if (filename)
- gk_fclose(fpout);
-}
-
-
-/*************************************************************************/
-/*! Returns a copy of a graph.
- \param graph is the graph to be duplicated.
- \returns the newly created copy of the graph.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_Dup(gk_graph_t *graph)
-{
- gk_graph_t *ngraph;
-
- ngraph = gk_graph_Create();
-
- ngraph->nvtxs = graph->nvtxs;
-
- /* copy the adjacency structure */
- if (graph->xadj)
- ngraph->xadj = gk_zcopy(graph->nvtxs+1, graph->xadj,
- gk_zmalloc(graph->nvtxs+1, "gk_graph_Dup: xadj"));
- if (graph->ivwgts)
- ngraph->ivwgts = gk_i32copy(graph->nvtxs, graph->ivwgts,
- gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivwgts"));
- if (graph->ivsizes)
- ngraph->ivsizes = gk_i32copy(graph->nvtxs, graph->ivsizes,
- gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivsizes"));
- if (graph->vlabels)
- ngraph->vlabels = gk_i32copy(graph->nvtxs, graph->vlabels,
- gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivlabels"));
- if (graph->fvwgts)
- ngraph->fvwgts = gk_fcopy(graph->nvtxs, graph->fvwgts,
- gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvwgts"));
- if (graph->fvsizes)
- ngraph->fvsizes = gk_fcopy(graph->nvtxs, graph->fvsizes,
- gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvsizes"));
-
-
- if (graph->adjncy)
- ngraph->adjncy = gk_i32copy(graph->xadj[graph->nvtxs], graph->adjncy,
- gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: adjncy"));
- if (graph->iadjwgt)
- ngraph->iadjwgt = gk_i32copy(graph->xadj[graph->nvtxs], graph->iadjwgt,
- gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: iadjwgt"));
- if (graph->fadjwgt)
- ngraph->fadjwgt = gk_fcopy(graph->xadj[graph->nvtxs], graph->fadjwgt,
- gk_fmalloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: fadjwgt"));
-
- return ngraph;
-}
-
-
-/*************************************************************************/
-/*! Returns a subgraph containing a set of consecutive vertices.
- \param graph is the original graph.
- \param vstart is the starting vertex.
- \param nvtxs is the number of vertices from vstart to extract.
- \returns the newly created subgraph.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs)
-{
- ssize_t i;
- gk_graph_t *ngraph;
-
- if (vstart+nvtxs > graph->nvtxs)
- return NULL;
-
- ngraph = gk_graph_Create();
-
- ngraph->nvtxs = nvtxs;
-
- /* copy the adjancy structure */
- if (graph->xadj)
- ngraph->xadj = gk_zcopy(nvtxs+1, graph->xadj+vstart,
- gk_zmalloc(nvtxs+1, "gk_graph_ExtractSubgraph: xadj"));
- for (i=nvtxs; i>=0; i--)
- ngraph->xadj[i] -= ngraph->xadj[0];
- ASSERT(ngraph->xadj[0] == 0);
-
- if (graph->ivwgts)
- ngraph->ivwgts = gk_i32copy(nvtxs, graph->ivwgts+vstart,
- gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivwgts"));
- if (graph->ivsizes)
- ngraph->ivsizes = gk_i32copy(nvtxs, graph->ivsizes+vstart,
- gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivsizes"));
- if (graph->vlabels)
- ngraph->vlabels = gk_i32copy(nvtxs, graph->vlabels+vstart,
- gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: vlabels"));
-
- if (graph->fvwgts)
- ngraph->fvwgts = gk_fcopy(nvtxs, graph->fvwgts+vstart,
- gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvwgts"));
- if (graph->fvsizes)
- ngraph->fvsizes = gk_fcopy(nvtxs, graph->fvsizes+vstart,
- gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvsizes"));
-
-
- ASSERT(ngraph->xadj[nvtxs] == graph->xadj[vstart+nvtxs]-graph->xadj[vstart]);
- if (graph->adjncy)
- ngraph->adjncy = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- graph->adjncy+graph->xadj[vstart],
- gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- "gk_graph_ExtractSubgraph: adjncy"));
- if (graph->iadjwgt)
- ngraph->iadjwgt = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- graph->iadjwgt+graph->xadj[vstart],
- gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- "gk_graph_ExtractSubgraph: iadjwgt"));
- if (graph->fadjwgt)
- ngraph->fadjwgt = gk_fcopy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- graph->fadjwgt+graph->xadj[vstart],
- gk_fmalloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
- "gk_graph_ExtractSubgraph: fadjwgt"));
-
- return ngraph;
-}
-
-
-/*************************************************************************/
-/*! Returns a graph that has been reordered according to the permutation.
- \param[IN] graph is the graph to be re-ordered.
- \param[IN] perm is the new ordering of the graph's vertices
- \param[IN] iperm is the original ordering of the re-ordered graph's vertices
- \returns the newly created copy of the graph.
-
- \note Either perm or iperm can be NULL but not both.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm)
-{
- ssize_t j, jj, *xadj;
- int i, k, u, v, nvtxs;
- int freeperm=0, freeiperm=0;
- int32_t *adjncy;
- gk_graph_t *ngraph;
-
- if (perm == NULL && iperm == NULL)
- return NULL;
-
- ngraph = gk_graph_Create();
-
- ngraph->nvtxs = nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* allocate memory for the different structures that are present in graph */
- if (graph->xadj)
- ngraph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Reorder: xadj");
-
- if (graph->ivwgts)
- ngraph->ivwgts = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivwgts");
-
- if (graph->ivsizes)
- ngraph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivsizes");
-
- if (graph->vlabels)
- ngraph->vlabels = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivlabels");
-
- if (graph->fvwgts)
- ngraph->fvwgts = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvwgts");
-
- if (graph->fvsizes)
- ngraph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvsizes");
-
-
- if (graph->adjncy)
- ngraph->adjncy = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: adjncy");
-
- if (graph->iadjwgt)
- ngraph->iadjwgt = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: iadjwgt");
-
- if (graph->fadjwgt)
- ngraph->fadjwgt = gk_fmalloc(graph->xadj[nvtxs], "gk_graph_Reorder: fadjwgt");
-
-
- /* create perm/iperm if not provided */
- if (perm == NULL) {
- freeperm = 1;
- perm = gk_i32malloc(nvtxs, "gk_graph_Reorder: perm");
- for (i=0; i<nvtxs; i++)
- perm[iperm[i]] = i;
- }
- if (iperm == NULL) {
- freeiperm = 1;
- iperm = gk_i32malloc(nvtxs, "gk_graph_Reorder: iperm");
- for (i=0; i<nvtxs; i++)
- iperm[perm[i]] = i;
- }
-
- /* fill-in the information of the re-ordered graph */
- ngraph->xadj[0] = jj = 0;
- for (v=0; v<nvtxs; v++) {
- u = iperm[v];
- for (j=xadj[u]; j<xadj[u+1]; j++, jj++) {
- ngraph->adjncy[jj] = perm[adjncy[j]];
- if (graph->iadjwgt)
- ngraph->iadjwgt[jj] = graph->iadjwgt[j];
- if (graph->fadjwgt)
- ngraph->fadjwgt[jj] = graph->fadjwgt[j];
- }
- if (graph->ivwgts)
- ngraph->ivwgts[v] = graph->ivwgts[u];
- if (graph->fvwgts)
- ngraph->fvwgts[v] = graph->fvwgts[u];
- if (graph->ivsizes)
- ngraph->ivsizes[v] = graph->ivsizes[u];
- if (graph->fvsizes)
- ngraph->fvsizes[v] = graph->fvsizes[u];
- if (graph->vlabels)
- ngraph->vlabels[v] = graph->vlabels[u];
-
- ngraph->xadj[v+1] = jj;
- }
-
-
- /* free memory */
- if (freeperm)
- gk_free((void **)&perm, LTERM);
- if (freeiperm)
- gk_free((void **)&iperm, LTERM);
-
- return ngraph;
-}
-
-
-/*************************************************************************/
-/*! This function finds the connected components in a graph.
-
- \param graph is the graph structure
- \param cptr is the ptr structure of the CSR representation of the
- components. The length of this vector must be graph->nvtxs+1.
- \param cind is the indices structure of the CSR representation of
- the components. The length of this vector must be graph->nvtxs.
-
- \returns the number of components that it found.
-
- \note The cptr and cind parameters can be NULL, in which case only the
- number of connected components is returned.
-*/
-/*************************************************************************/
-int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind)
-{
- ssize_t i, ii, j, jj, k, nvtxs, first, last, ntodo, ncmps;
- ssize_t *xadj;
- int32_t *adjncy, *pos, *todo;
- int32_t mustfree_ccsr=0, mustfree_where=0;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* Deal with NULL supplied cptr/cind vectors */
- if (cptr == NULL) {
- cptr = gk_i32malloc(nvtxs+1, "gk_graph_FindComponents: cptr");
- cind = gk_i32malloc(nvtxs, "gk_graph_FindComponents: cind");
- mustfree_ccsr = 1;
- }
-
- /* The list of vertices that have not been touched yet.
- The valid entries are from [0..ntodo). */
- todo = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: todo"));
-
- /* For a vertex that has not been visited, pos[i] is the position in the
- todo list that this vertex is stored.
- If a vertex has been visited, pos[i] = -1. */
- pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: pos"));
-
-
- /* Find the connected componends */
- ncmps = -1;
- ntodo = nvtxs; /* All vertices have not been visited */
- first = last = 0; /* Point to the first and last vertices that have been touched
- but not explored.
- These vertices are stored in cind[first]...cind[last-1]. */
- while (ntodo > 0) {
- if (first == last) { /* Find another starting vertex */
- cptr[++ncmps] = first; /* Mark the end of the current CC */
-
- ASSERT(pos[todo[0]] != -1);
- i = todo[0];
-
- cind[last++] = i;
- pos[i] = -1;
- }
-
- i = cind[first++]; /* Get the first visited but unexplored vertex */
-
- /* Remove i from the todo list and put the last item in the todo
- list at the position that i was so that the todo list will be
- consequtive. The pos[] array is updated accordingly to keep track
- the location of the vertices in the todo[] list. */
- k = pos[i];
- j = todo[k] = todo[--ntodo];
- pos[j] = k;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (pos[k] != -1) {
- cind[last++] = k;
- pos[k] = -1;
- }
- }
- }
- cptr[++ncmps] = first;
-
- if (mustfree_ccsr)
- gk_free((void **)&cptr, &cind, LTERM);
-
- gk_free((void **)&pos, &todo, LTERM);
-
- return (int) ncmps;
-}
-
-
-/*************************************************************************/
-/*! This function computes a permutation of the vertices based on a
- breadth-first-traversal. It can be used for re-ordering the graph
- to reduce its bandwidth for better cache locality.
- The algorithm used is a simplified version of the method used to find
- the connected components.
-
- \param[IN] graph is the graph structure
- \param[IN] v is the starting vertex of the BFS
- \param[OUT] perm[i] stores the ID of vertex i in the re-ordered graph.
- \param[OUT] iperm[i] stores the ID of the vertex that corresponds to
- the ith vertex in the re-ordered graph.
-
- \note The perm or iperm (but not both) can be NULL, at which point,
- the corresponding arrays are not returned. Though the program
- works fine when both are NULL, doing that is not smart.
- The returned arrays should be freed with gk_free().
-*/
-/*************************************************************************/
-void gk_graph_ComputeBFSOrdering(gk_graph_t *graph, int v, int32_t **r_perm,
- int32_t **r_iperm)
-{
- ssize_t j, *xadj;
- int i, k, nvtxs, first, last;
- int32_t *adjncy, *cot, *pos;
-
- if (graph->nvtxs <= 0)
- return;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* This array will function like pos + touched of the CC method */
- pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: pos"));
-
- /* This array ([C]losed[O]pen[T]odo => cot) serves three purposes.
- Positions from [0...first) is the current iperm[] vector of the explored vertices;
- Positions from [first...last) is the OPEN list (i.e., visited vertices);
- Positions from [last...nvtxs) is the todo list. */
- cot = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: cot"));
-
-
- /* put v at the front of the todo list */
- pos[0] = cot[0] = v;
- pos[v] = cot[v] = 0;
-
- /* Find the connected componends induced by the partition */
- first = last = 0;
- while (first < nvtxs) {
- if (first == last) { /* Find another starting vertex */
- k = cot[last];
- ASSERT(pos[k] != -1);
- pos[k] = -1; /* mark node as being visited */
- last++;
- }
-
- i = cot[first++]; /* the ++ advances the explored vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- /* if a node has already been visited, its perm[] will be -1 */
- if (pos[k] != -1) {
- /* pos[k] is the location within iperm of where k resides (it is in the 'todo' part);
- It is placed in that location cot[last] (end of OPEN list) that we
- are about to overwrite and update pos[cot[last]] to reflect that. */
- cot[pos[k]] = cot[last]; /* put the head of the todo list to
- where k was in the todo list */
- pos[cot[last]] = pos[k]; /* update perm to reflect the move */
-
- cot[last++] = k; /* put node at the end of the OPEN list */
- pos[k] = -1; /* mark node as being visited */
- }
- }
- }
-
- /* time to decide what to return */
- if (r_perm != NULL) {
- /* use the 'pos' array to build the perm array */
- for (i=0; i<nvtxs; i++)
- pos[cot[i]] = i;
-
- *r_perm = pos;
- pos = NULL;
- }
-
- if (r_iperm != NULL) {
- *r_iperm = cot;
- cot = NULL;
- }
-
-
- /* cleanup memory */
- gk_free((void **)&pos, &cot, LTERM);
-
-}
-
-
-/*************************************************************************/
-/*! This function computes a permutation of the vertices based on a
- best-first-traversal. It can be used for re-ordering the graph
- to reduce its bandwidth for better cache locality.
-
- \param[IN] graph is the graph structure.
- \param[IN] v is the starting vertex of the best-first traversal.
- \param[IN] type indicates the criteria to use to measure the 'bestness'
- of a vertex.
- \param[OUT] perm[i] stores the ID of vertex i in the re-ordered graph.
- \param[OUT] iperm[i] stores the ID of the vertex that corresponds to
- the ith vertex in the re-ordered graph.
-
- \note The perm or iperm (but not both) can be NULL, at which point,
- the corresponding arrays are not returned. Though the program
- works fine when both are NULL, doing that is not smart.
- The returned arrays should be freed with gk_free().
-*/
-/*************************************************************************/
-void gk_graph_ComputeBestFOrdering0(gk_graph_t *graph, int v, int type,
- int32_t **r_perm, int32_t **r_iperm)
-{
- ssize_t j, jj, *xadj;
- int i, k, u, nvtxs;
- int32_t *adjncy, *perm, *degrees, *minIDs, *open;
- gk_i32pq_t *queue;
-
- if (graph->nvtxs <= 0)
- return;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* the degree of the vertices in the closed list */
- degrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: degrees");
-
- /* the minimum vertex ID of an open vertex to the closed list */
- minIDs = gk_i32smalloc(nvtxs, nvtxs+1, "gk_graph_ComputeBestFOrdering: minIDs");
-
- /* the open list */
- open = gk_i32malloc(nvtxs, "gk_graph_ComputeBestFOrdering: open");
-
- /* if perm[i] >= 0, then perm[i] is the order of vertex i;
- otherwise perm[i] == -1.
- */
- perm = gk_i32smalloc(nvtxs, -1, "gk_graph_ComputeBestFOrdering: perm");
-
- /* create the queue and put everything in it */
- queue = gk_i32pqCreate(nvtxs);
- for (i=0; i<nvtxs; i++)
- gk_i32pqInsert(queue, i, 0);
- gk_i32pqUpdate(queue, v, 1);
-
- open[0] = v;
-
- /* start processing the nodes */
- for (i=0; i<nvtxs; i++) {
- if ((v = gk_i32pqGetTop(queue)) == -1)
- gk_errexit(SIGERR, "The priority queue got empty ahead of time [i=%d].\n", i);
- if (perm[v] != -1)
- gk_errexit(SIGERR, "The perm[%d] has already been set.\n", v);
- perm[v] = i;
-
-
- for (j=xadj[v]; j<xadj[v+1]; j++) {
- u = adjncy[j];
- if (perm[u] == -1) {
- degrees[u]++;
- minIDs[u] = (i < minIDs[u] ? i : minIDs[u]);
-
- switch (type) {
- case 1: /* DFS */
- gk_i32pqUpdate(queue, u, 1);
- break;
- case 2: /* Max in closed degree */
- gk_i32pqUpdate(queue, u, degrees[u]);
- break;
- case 3: /* Sum of orders in closed list */
- for (k=0, jj=xadj[u]; jj<xadj[u+1]; jj++) {
- if (perm[adjncy[jj]] != -1)
- k += perm[adjncy[jj]];
- }
- gk_i32pqUpdate(queue, u, k);
- break;
- case 4: /* Sum of order-differences (w.r.t. current number) in closed
- list (updated once in a while) */
- for (k=0, jj=xadj[u]; jj<xadj[u+1]; jj++) {
- if (perm[adjncy[jj]] != -1)
- k += (i-perm[adjncy[jj]]);
- }
- gk_i32pqUpdate(queue, u, k);
- break;
- default:
- ;
- }
- }
- }
- }
-
-
- /* time to decide what to return */
- if (r_perm != NULL) {
- *r_perm = perm;
- perm = NULL;
- }
-
- if (r_iperm != NULL) {
- /* use the 'degrees' array to build the iperm array */
- for (i=0; i<nvtxs; i++)
- degrees[perm[i]] = i;
-
- *r_iperm = degrees;
- degrees = NULL;
- }
-
-
-
- /* cleanup memory */
- gk_i32pqDestroy(queue);
- gk_free((void **)&perm, °rees, &minIDs, &open, LTERM);
-
-}
-
-
-/*************************************************************************/
-/*! This function computes a permutation of the vertices based on a
- best-first-traversal. It can be used for re-ordering the graph
- to reduce its bandwidth for better cache locality.
-
- \param[IN] graph is the graph structure.
- \param[IN] v is the starting vertex of the best-first traversal.
- \param[IN] type indicates the criteria to use to measure the 'bestness'
- of a vertex.
- \param[OUT] perm[i] stores the ID of vertex i in the re-ordered graph.
- \param[OUT] iperm[i] stores the ID of the vertex that corresponds to
- the ith vertex in the re-ordered graph.
-
- \note The perm or iperm (but not both) can be NULL, at which point,
- the corresponding arrays are not returned. Though the program
- works fine when both are NULL, doing that is not smart.
- The returned arrays should be freed with gk_free().
-*/
-/*************************************************************************/
-void gk_graph_ComputeBestFOrdering(gk_graph_t *graph, int v, int type,
- int32_t **r_perm, int32_t **r_iperm)
-{
- ssize_t j, jj, *xadj;
- int i, k, u, nvtxs, nopen, ntodo;
- int32_t *adjncy, *perm, *degrees, *wdegrees, *sod, *level, *ot, *pos;
- gk_i32pq_t *queue;
-
- if (graph->nvtxs <= 0)
- return;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* the degree of the vertices in the closed list */
- degrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: degrees");
-
- /* the weighted degree of the vertices in the closed list for type==3 */
- wdegrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: wdegrees");
-
- /* the sum of differences for type==4 */
- sod = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: sod");
-
- /* the encountering level of a vertex type==5 */
- level = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: level");
-
- /* The open+todo list of vertices.
- The vertices from [0..nopen] are the open vertices.
- The vertices from [nopen..ntodo) are the todo vertices.
- */
- ot = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: ot"));
-
- /* For a vertex that has not been explored, pos[i] is the position in the ot list. */
- pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: pos"));
-
- /* if perm[i] >= 0, then perm[i] is the order of vertex i; otherwise perm[i] == -1. */
- perm = gk_i32smalloc(nvtxs, -1, "gk_graph_ComputeBestFOrdering: perm");
-
- /* create the queue and put the starting vertex in it */
- queue = gk_i32pqCreate(nvtxs);
- gk_i32pqInsert(queue, v, 1);
-
- /* put v at the front of the open list */
- pos[0] = ot[0] = v;
- pos[v] = ot[v] = 0;
- nopen = 1;
- ntodo = nvtxs;
-
- /* start processing the nodes */
- for (i=0; i<nvtxs; i++) {
- if (nopen == 0) { /* deal with non-connected graphs */
- gk_i32pqInsert(queue, ot[0], 1);
- nopen++;
- }
-
- if ((v = gk_i32pqGetTop(queue)) == -1)
- gk_errexit(SIGERR, "The priority queue got empty ahead of time [i=%d].\n", i);
-
- if (perm[v] != -1)
- gk_errexit(SIGERR, "The perm[%d] has already been set.\n", v);
- perm[v] = i;
-
- if (ot[pos[v]] != v)
- gk_errexit(SIGERR, "Something went wrong [ot[pos[%d]]!=%d.\n", v, v);
- if (pos[v] >= nopen)
- gk_errexit(SIGERR, "The position of v is not in open list. pos[%d]=%d is >=%d.\n", v, pos[v], nopen);
-
- /* remove v from the open list and re-arrange the todo part of the list */
- ot[pos[v]] = ot[nopen-1];
- pos[ot[nopen-1]] = pos[v];
- if (ntodo > nopen) {
- ot[nopen-1] = ot[ntodo-1];
- pos[ot[ntodo-1]] = nopen-1;
- }
- nopen--;
- ntodo--;
-
- for (j=xadj[v]; j<xadj[v+1]; j++) {
- u = adjncy[j];
- if (perm[u] == -1) {
- /* update ot list, if u is not in the open list by putting it at the end
- of the open list. */
- if (degrees[u] == 0) {
- ot[pos[u]] = ot[nopen];
- pos[ot[nopen]] = pos[u];
- ot[nopen] = u;
- pos[u] = nopen;
- nopen++;
-
- level[u] = level[v]+1;
- gk_i32pqInsert(queue, u, 0);
- }
-
-
- /* update the in-closed degree */
- degrees[u]++;
-
- /* update the queues based on the type */
- switch (type) {
- case 1: /* DFS */
- gk_i32pqUpdate(queue, u, 1000*(i+1)+degrees[u]);
- break;
-
- case 2: /* Max in closed degree */
- gk_i32pqUpdate(queue, u, degrees[u]);
- break;
-
- case 3: /* Sum of orders in closed list */
- wdegrees[u] += i;
- gk_i32pqUpdate(queue, u, wdegrees[u]);
- break;
-
- case 4: /* Sum of order-differences */
- /* this is handled at the end of the loop */
- ;
- break;
-
- case 5: /* BFS with in degree priority */
- gk_i32pqUpdate(queue, u, -(1000*level[u] - degrees[u]));
- break;
-
- case 6: /* Hybrid of 1+2 */
- gk_i32pqUpdate(queue, u, (i+1)*degrees[u]);
- break;
-
- default:
- ;
- }
- }
- }
-
- if (type == 4) { /* update all the vertices in the open list */
- for (j=0; j<nopen; j++) {
- u = ot[j];
- if (perm[u] != -1)
- gk_errexit(SIGERR, "For i=%d, the open list contains a closed vertex: ot[%zd]=%d, perm[%d]=%d.\n", i, j, u, u, perm[u]);
- sod[u] += degrees[u];
- if (i<1000 || i%25==0)
- gk_i32pqUpdate(queue, u, sod[u]);
- }
- }
-
- /*
- for (j=0; j<ntodo; j++) {
- if (pos[ot[j]] != j)
- gk_errexit(SIGERR, "pos[ot[%zd]] != %zd.\n", j, j);
- }
- */
-
- }
-
-
- /* time to decide what to return */
- if (r_perm != NULL) {
- *r_perm = perm;
- perm = NULL;
- }
-
- if (r_iperm != NULL) {
- /* use the 'degrees' array to build the iperm array */
- for (i=0; i<nvtxs; i++)
- degrees[perm[i]] = i;
-
- *r_iperm = degrees;
- degrees = NULL;
- }
-
-
-
- /* cleanup memory */
- gk_i32pqDestroy(queue);
- gk_free((void **)&perm, °rees, &wdegrees, &sod, &ot, &pos, &level, LTERM);
-
-}
-
-
-/*************************************************************************/
-/*! This function computes the single-source shortest path lengths from the
- root node to all the other nodes in the graph. If the graph is not
- connected then, the sortest part to the vertices in the other components
- is -1.
-
- \param[IN] graph is the graph structure.
- \param[IN] v is the root of the single-source shortest path computations.
- \param[IN] type indicates the criteria to use to measure the 'bestness'
- of a vertex.
- \param[OUT] sps[i] stores the length of the shortest path from v to vertex i.
- If no such path exists, then it is -1. Note that the returned
- array will be either an array of int32_t or an array of floats.
- The specific type is determined by the existance of non NULL
- iadjwgt and fadjwgt arrays. If both of these arrays exist, then
- priority is given to iadjwgt.
-
- \note The returned array should be freed with gk_free().
-*/
-/*************************************************************************/
-void gk_graph_SingleSourceShortestPaths(gk_graph_t *graph, int v, void **r_sps)
-{
- ssize_t *xadj;
- int i, u, nvtxs;
- int32_t *adjncy, *inqueue;
-
- if (graph->nvtxs <= 0)
- return;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- inqueue = gk_i32smalloc(nvtxs, 0, "gk_graph_SingleSourceShortestPaths: inqueue");
-
- /* determine if you will be computing using int32_t or float and proceed from there */
- if (graph->iadjwgt != NULL) {
- gk_i32pq_t *queue;
- int32_t *adjwgt;
- int32_t *sps;
-
- adjwgt = graph->iadjwgt;
-
- queue = gk_i32pqCreate(nvtxs);
- gk_i32pqInsert(queue, v, 0);
- inqueue[v] = 1;
-
- sps = gk_i32smalloc(nvtxs, -1, "gk_graph_SingleSourceShortestPaths: sps");
- sps[v] = 0;
-
- /* start processing the nodes */
- while ((v = gk_i32pqGetTop(queue)) != -1) {
- inqueue[v] = 2;
-
- /* relax the adjacent edges */
- for (i=xadj[v]; i<xadj[v+1]; i++) {
- u = adjncy[i];
- if (inqueue[u] == 2)
- continue;
-
- if (sps[u] < 0 || sps[v]+adjwgt[i] < sps[u]) {
- sps[u] = sps[v]+adjwgt[i];
-
- if (inqueue[u])
- gk_i32pqUpdate(queue, u, -sps[u]);
- else {
- gk_i32pqInsert(queue, u, -sps[u]);
- inqueue[u] = 1;
- }
- }
- }
- }
-
- *r_sps = (void *)sps;
-
- gk_i32pqDestroy(queue);
- }
- else {
- gk_fpq_t *queue;
- float *adjwgt;
- float *sps;
-
- adjwgt = graph->fadjwgt;
-
- queue = gk_fpqCreate(nvtxs);
- gk_fpqInsert(queue, v, 0);
- inqueue[v] = 1;
-
- sps = gk_fsmalloc(nvtxs, -1, "gk_graph_SingleSourceShortestPaths: sps");
- sps[v] = 0;
-
- /* start processing the nodes */
- while ((v = gk_fpqGetTop(queue)) != -1) {
- inqueue[v] = 2;
-
- /* relax the adjacent edges */
- for (i=xadj[v]; i<xadj[v+1]; i++) {
- u = adjncy[i];
- if (inqueue[u] == 2)
- continue;
-
- if (sps[u] < 0 || sps[v]+adjwgt[i] < sps[u]) {
- sps[u] = sps[v]+adjwgt[i];
-
- if (inqueue[u])
- gk_fpqUpdate(queue, u, -sps[u]);
- else {
- gk_fpqInsert(queue, u, -sps[u]);
- inqueue[u] = 1;
- }
- }
- }
- }
-
- *r_sps = (void *)sps;
-
- gk_fpqDestroy(queue);
- }
-
- gk_free((void **)&inqueue, LTERM);
-
-}
-
-
-
-#ifdef XXX
-
-/*************************************************************************/
-/*! Sorts the adjacency lists in increasing vertex order
- \param graph the graph itself,
-*/
-/**************************************************************************/
-void gk_graph_SortAdjacencies(gk_graph_t *graph)
-{
- int n, nn=0;
- ssize_t *ptr;
- int *ind;
- float *val;
-
- switch (what) {
- case GK_CSR_ROW:
- if (!graph->rowptr)
- gk_errexit(SIGERR, "Row-based view of the graphrix does not exists.\n");
-
- n = graph->nrows;
- ptr = graph->rowptr;
- ind = graph->rowind;
- val = graph->rowval;
- break;
-
- case GK_CSR_COL:
- if (!graph->colptr)
- gk_errexit(SIGERR, "Column-based view of the graphrix does not exists.\n");
-
- n = graph->ncols;
- ptr = graph->colptr;
- ind = graph->colind;
- val = graph->colval;
- break;
-
- default:
- gk_errexit(SIGERR, "Invalid index type of %d.\n", what);
- return;
- }
-
- #pragma omp parallel if (n > 100)
- {
- ssize_t i, j, k;
- gk_ikv_t *cand;
- float *tval;
-
- #pragma omp single
- for (i=0; i<n; i++)
- nn = gk_max(nn, ptr[i+1]-ptr[i]);
-
- cand = gk_ikvmalloc(nn, "gk_graph_SortIndices: cand");
- tval = gk_fmalloc(nn, "gk_graph_SortIndices: tval");
-
- #pragma omp for schedule(static)
- for (i=0; i<n; i++) {
- for (k=0, j=ptr[i]; j<ptr[i+1]; j++) {
- if (j > ptr[i] && ind[j] < ind[j-1])
- k = 1; /* an inversion */
- cand[j-ptr[i]].val = j-ptr[i];
- cand[j-ptr[i]].key = ind[j];
- tval[j-ptr[i]] = val[j];
- }
- if (k) {
- gk_ikvsorti(ptr[i+1]-ptr[i], cand);
- for (j=ptr[i]; j<ptr[i+1]; j++) {
- ind[j] = cand[j-ptr[i]].key;
- val[j] = tval[cand[j-ptr[i]].val];
- }
- }
- }
-
- gk_free((void **)&cand, &tval, LTERM);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Returns a subgraphrix containing a certain set of rows.
- \param graph is the original graphrix.
- \param nrows is the number of rows to extract.
- \param rind is the set of row numbers to extract.
- \returns the row structure of the newly created subgraphrix.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_ExtractRows(gk_graph_t *graph, int nrows, int *rind)
-{
- ssize_t i, ii, j, nnz;
- gk_graph_t *ngraph;
-
- ngraph = gk_graph_Create();
-
- ngraph->nrows = nrows;
- ngraph->ncols = graph->ncols;
-
- for (nnz=0, i=0; i<nrows; i++)
- nnz += graph->rowptr[rind[i]+1]-graph->rowptr[rind[i]];
-
- ngraph->rowptr = gk_zmalloc(ngraph->nrows+1, "gk_graph_ExtractPartition: rowptr");
- ngraph->rowind = gk_imalloc(nnz, "gk_graph_ExtractPartition: rowind");
- ngraph->rowval = gk_fmalloc(nnz, "gk_graph_ExtractPartition: rowval");
-
- ngraph->rowptr[0] = 0;
- for (nnz=0, j=0, ii=0; ii<nrows; ii++) {
- i = rind[ii];
- gk_icopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowind+graph->rowptr[i], ngraph->rowind+nnz);
- gk_fcopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowval+graph->rowptr[i], ngraph->rowval+nnz);
- nnz += graph->rowptr[i+1]-graph->rowptr[i];
- ngraph->rowptr[++j] = nnz;
- }
- ASSERT(j == ngraph->nrows);
-
- return ngraph;
-}
-
-
-/*************************************************************************/
-/*! Returns a subgraphrix corresponding to a specified partitioning of rows.
- \param graph is the original graphrix.
- \param part is the partitioning vector of the rows.
- \param pid is the partition ID that will be extracted.
- \returns the row structure of the newly created subgraphrix.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_ExtractPartition(gk_graph_t *graph, int *part, int pid)
-{
- ssize_t i, j, nnz;
- gk_graph_t *ngraph;
-
- ngraph = gk_graph_Create();
-
- ngraph->nrows = 0;
- ngraph->ncols = graph->ncols;
-
- for (nnz=0, i=0; i<graph->nrows; i++) {
- if (part[i] == pid) {
- ngraph->nrows++;
- nnz += graph->rowptr[i+1]-graph->rowptr[i];
- }
- }
-
- ngraph->rowptr = gk_zmalloc(ngraph->nrows+1, "gk_graph_ExtractPartition: rowptr");
- ngraph->rowind = gk_imalloc(nnz, "gk_graph_ExtractPartition: rowind");
- ngraph->rowval = gk_fmalloc(nnz, "gk_graph_ExtractPartition: rowval");
-
- ngraph->rowptr[0] = 0;
- for (nnz=0, j=0, i=0; i<graph->nrows; i++) {
- if (part[i] == pid) {
- gk_icopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowind+graph->rowptr[i], ngraph->rowind+nnz);
- gk_fcopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowval+graph->rowptr[i], ngraph->rowval+nnz);
- nnz += graph->rowptr[i+1]-graph->rowptr[i];
- ngraph->rowptr[++j] = nnz;
- }
- }
- ASSERT(j == ngraph->nrows);
-
- return ngraph;
-}
-
-
-/*************************************************************************/
-/*! Splits the graphrix into multiple sub-graphrices based on the provided
- color array.
- \param graph is the original graphrix.
- \param color is an array of size equal to the number of non-zeros
- in the graphrix (row-wise structure). The graphrix is split into
- as many parts as the number of colors. For meaningfull results,
- the colors should be numbered consecutively starting from 0.
- \returns an array of graphrices for each supplied color number.
-*/
-/**************************************************************************/
-gk_graph_t **gk_graph_Split(gk_graph_t *graph, int *color)
-{
- ssize_t i, j;
- int nrows, ncolors;
- ssize_t *rowptr;
- int *rowind;
- float *rowval;
- gk_graph_t **sgraphs;
-
- nrows = graph->nrows;
- rowptr = graph->rowptr;
- rowind = graph->rowind;
- rowval = graph->rowval;
-
- ncolors = gk_imax(rowptr[nrows], color)+1;
-
- sgraphs = (gk_graph_t **)gk_malloc(sizeof(gk_graph_t *)*ncolors, "gk_graph_Split: sgraphs");
- for (i=0; i<ncolors; i++) {
- sgraphs[i] = gk_graph_Create();
- sgraphs[i]->nrows = graph->nrows;
- sgraphs[i]->ncols = graph->ncols;
- sgraphs[i]->rowptr = gk_zsmalloc(nrows+1, 0, "gk_graph_Split: sgraphs[i]->rowptr");
- }
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- sgraphs[color[j]]->rowptr[i]++;
- }
- for (i=0; i<ncolors; i++)
- MAKECSR(j, nrows, sgraphs[i]->rowptr);
-
- for (i=0; i<ncolors; i++) {
- sgraphs[i]->rowind = gk_imalloc(sgraphs[i]->rowptr[nrows], "gk_graph_Split: sgraphs[i]->rowind");
- sgraphs[i]->rowval = gk_fmalloc(sgraphs[i]->rowptr[nrows], "gk_graph_Split: sgraphs[i]->rowval");
- }
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- sgraphs[color[j]]->rowind[sgraphs[color[j]]->rowptr[i]] = rowind[j];
- sgraphs[color[j]]->rowval[sgraphs[color[j]]->rowptr[i]] = rowval[j];
- sgraphs[color[j]]->rowptr[i]++;
- }
- }
-
- for (i=0; i<ncolors; i++)
- SHIFTCSR(j, nrows, sgraphs[i]->rowptr);
-
- return sgraphs;
-}
-
-
-/*************************************************************************/
-/*! Prunes certain rows/columns of the graphrix. The prunning takes place
- by analyzing the row structure of the graphrix. The prunning takes place
- by removing rows/columns but it does not affect the numbering of the
- remaining rows/columns.
-
- \param graph the graphrix to be prunned,
- \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL)
- of the graphrix will be prunned,
- \param minf is the minimum number of rows (columns) that a column (row) must
- be present in order to be kept,
- \param maxf is the maximum number of rows (columns) that a column (row) must
- be present at in order to be kept.
- \returns the prunned graphrix consisting only of its row-based structure.
- The input graphrix is not modified.
-*/
-/**************************************************************************/
-gk_graph_t *gk_graph_Prune(gk_graph_t *graph, int what, int minf, int maxf)
-{
- ssize_t i, j, nnz;
- int nrows, ncols;
- ssize_t *rowptr, *nrowptr;
- int *rowind, *nrowind, *collen;
- float *rowval, *nrowval;
- gk_graph_t *ngraph;
-
- ngraph = gk_graph_Create();
-
- nrows = ngraph->nrows = graph->nrows;
- ncols = ngraph->ncols = graph->ncols;
-
- rowptr = graph->rowptr;
- rowind = graph->rowind;
- rowval = graph->rowval;
-
- nrowptr = ngraph->rowptr = gk_zmalloc(nrows+1, "gk_graph_Prune: nrowptr");
- nrowind = ngraph->rowind = gk_imalloc(rowptr[nrows], "gk_graph_Prune: nrowind");
- nrowval = ngraph->rowval = gk_fmalloc(rowptr[nrows], "gk_graph_Prune: nrowval");
-
-
- switch (what) {
- case GK_CSR_COL:
- collen = gk_ismalloc(ncols, 0, "gk_graph_Prune: collen");
-
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- ASSERT(rowind[j] < ncols);
- collen[rowind[j]]++;
- }
- }
- for (i=0; i<ncols; i++)
- collen[i] = (collen[i] >= minf && collen[i] <= maxf ? 1 : 0);
-
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++) {
- if (collen[rowind[j]]) {
- nrowind[nnz] = rowind[j];
- nrowval[nnz] = rowval[j];
- nnz++;
- }
- }
- nrowptr[i+1] = nnz;
- }
- gk_free((void **)&collen, LTERM);
- break;
-
- case GK_CSR_ROW:
- nrowptr[0] = 0;
- for (nnz=0, i=0; i<nrows; i++) {
- if (rowptr[i+1]-rowptr[i] >= minf && rowptr[i+1]-rowptr[i] <= maxf) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++, nnz++) {
- nrowind[nnz] = rowind[j];
- nrowval[nnz] = rowval[j];
- }
- }
- nrowptr[i+1] = nnz;
- }
- break;
-
- default:
- gk_graph_Free(&ngraph);
- gk_errexit(SIGERR, "Unknown prunning type of %d\n", what);
- return NULL;
- }
-
- return ngraph;
-}
-
-
-
-/*************************************************************************/
-/*! Normalizes the rows/columns of the graphrix to be unit
- length.
- \param graph the graphrix itself,
- \param what indicates what will be normalized and is obtained by
- specifying GK_CSR_ROW, GK_CSR_COL, GK_CSR_ROW|GK_CSR_COL.
- \param norm indicates what norm is to normalize to, 1: 1-norm, 2: 2-norm
-*/
-/**************************************************************************/
-void gk_graph_Normalize(gk_graph_t *graph, int what, int norm)
-{
- ssize_t i, j;
- int n;
- ssize_t *ptr;
- float *val, sum;
-
- if (what&GK_CSR_ROW && graph->rowval) {
- n = graph->nrows;
- ptr = graph->rowptr;
- val = graph->rowval;
-
- #pragma omp parallel if (ptr[n] > OMPMINOPS)
- {
- #pragma omp for private(j,sum) schedule(static)
- for (i=0; i<n; i++) {
- for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++){
- if (norm == 2)
- sum += val[j]*val[j];
- else if (norm == 1)
- sum += val[j]; /* assume val[j] > 0 */
- }
- if (sum > 0) {
- if (norm == 2)
- sum=1.0/sqrt(sum);
- else if (norm == 1)
- sum=1.0/sum;
- for (j=ptr[i]; j<ptr[i+1]; j++)
- val[j] *= sum;
-
- }
- }
- }
- }
-
- if (what&GK_CSR_COL && graph->colval) {
- n = graph->ncols;
- ptr = graph->colptr;
- val = graph->colval;
-
- #pragma omp parallel if (ptr[n] > OMPMINOPS)
- {
- #pragma omp for private(j,sum) schedule(static)
- for (i=0; i<n; i++) {
- for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++)
- if (norm == 2)
- sum += val[j]*val[j];
- else if (norm == 1)
- sum += val[j];
- if (sum > 0) {
- if (norm == 2)
- sum=1.0/sqrt(sum);
- else if (norm == 1)
- sum=1.0/sum;
- for (j=ptr[i]; j<ptr[i+1]; j++)
- val[j] *= sum;
- }
- }
- }
- }
-}
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/htable.c b/3rdParty/metis/metis-5.1.0/GKlib/htable.c
deleted file mode 100644
index 078e11434..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/htable.c
+++ /dev/null
@@ -1,247 +0,0 @@
-/*
- * Copyright 2004, Regents of the University of Minnesota
- *
- * This file contains routines for manipulating a direct-access hash table
- *
- * Started 3/22/04
- * George
- *
- */
-
-#include <GKlib.h>
-
-/******************************************************************************
-* This function creates the hash-table
-*******************************************************************************/
-gk_HTable_t *HTable_Create(int nelements)
-{
- gk_HTable_t *htable;
-
- htable = gk_malloc(sizeof(gk_HTable_t), "HTable_Create: htable");
- htable->harray = gk_ikvmalloc(nelements, "HTable_Create: harray");
- htable->nelements = nelements;
-
- HTable_Reset(htable);
-
- return htable;
-}
-
-
-/******************************************************************************
-* This function resets the data-structures associated with the hash-table
-*******************************************************************************/
-void HTable_Reset(gk_HTable_t *htable)
-{
- int i;
-
- for (i=0; i<htable->nelements; i++)
- htable->harray[i].key = HTABLE_EMPTY;
- htable->htsize = 0;
-
-}
-
-/******************************************************************************
-* This function resizes the hash-table
-*******************************************************************************/
-void HTable_Resize(gk_HTable_t *htable, int nelements)
-{
- int i, old_nelements;
- gk_ikv_t *old_harray;
-
- old_nelements = htable->nelements;
- old_harray = htable->harray;
-
- /* prepare larger hash */
- htable->nelements = nelements;
- htable->htsize = 0;
- htable->harray = gk_ikvmalloc(nelements, "HTable_Resize: harray");
- for (i=0; i<nelements; i++)
- htable->harray[i].key = HTABLE_EMPTY;
-
- /* reassign the values */
- for (i=0; i<old_nelements; i++)
- if (old_harray[i].key != HTABLE_EMPTY)
- HTable_Insert(htable, old_harray[i].key, old_harray[i].val);
-
- /* remove old harray */
- gk_free((void **)&old_harray, LTERM);
-}
-
-
-/******************************************************************************
-* This function inserts a key-value pair in the array
-*******************************************************************************/
-void HTable_Insert(gk_HTable_t *htable, int key, int val)
-{
- int i, first;
-
- if (htable->htsize > htable->nelements/2)
- HTable_Resize(htable, 2*htable->nelements);
-
- first = HTable_HFunction(htable->nelements, key);
-
- for (i=first; i<htable->nelements; i++) {
- if (htable->harray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) {
- htable->harray[i].key = key;
- htable->harray[i].val = val;
- htable->htsize++;
- return;
- }
- }
-
- for (i=0; i<first; i++) {
- if (htable->harray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) {
- htable->harray[i].key = key;
- htable->harray[i].val = val;
- htable->htsize++;
- return;
- }
- }
-
-}
-
-
-/******************************************************************************
-* This function deletes key from the htable
-*******************************************************************************/
-void HTable_Delete(gk_HTable_t *htable, int key)
-{
- int i, first;
-
- first = HTable_HFunction(htable->nelements, key);
-
- for (i=first; i<htable->nelements; i++) {
- if (htable->harray[i].key == key) {
- htable->harray[i].key = HTABLE_DELETED;
- htable->htsize--;
- return;
- }
- }
-
- for (i=0; i<first; i++) {
- if (htable->harray[i].key == key) {
- htable->harray[i].key = HTABLE_DELETED;
- htable->htsize--;
- return;
- }
- }
-
-}
-
-
-/******************************************************************************
-* This function returns the data associated with the key in the hastable
-*******************************************************************************/
-int HTable_Search(gk_HTable_t *htable, int key)
-{
- int i, first;
-
- first = HTable_HFunction(htable->nelements, key);
-
- for (i=first; i<htable->nelements; i++) {
- if (htable->harray[i].key == key)
- return htable->harray[i].val;
- else if (htable->harray[i].key == HTABLE_EMPTY)
- return -1;
- }
-
- for (i=0; i<first; i++) {
- if (htable->harray[i].key == key)
- return htable->harray[i].val;
- else if (htable->harray[i].key == HTABLE_EMPTY)
- return -1;
- }
-
- return -1;
-}
-
-
-/******************************************************************************
-* This function returns the next key/val
-*******************************************************************************/
-int HTable_GetNext(gk_HTable_t *htable, int key, int *r_val, int type)
-{
- int i;
- static int first, last;
-
- if (type == HTABLE_FIRST)
- first = last = HTable_HFunction(htable->nelements, key);
-
- if (first > last) {
- for (i=first; i<htable->nelements; i++) {
- if (htable->harray[i].key == key) {
- *r_val = htable->harray[i].val;
- first = i+1;
- return 1;
- }
- else if (htable->harray[i].key == HTABLE_EMPTY)
- return -1;
- }
- first = 0;
- }
-
- for (i=first; i<last; i++) {
- if (htable->harray[i].key == key) {
- *r_val = htable->harray[i].val;
- first = i+1;
- return 1;
- }
- else if (htable->harray[i].key == HTABLE_EMPTY)
- return -1;
- }
-
- return -1;
-}
-
-
-/******************************************************************************
-* This function returns the data associated with the key in the hastable
-*******************************************************************************/
-int HTable_SearchAndDelete(gk_HTable_t *htable, int key)
-{
- int i, first;
-
- first = HTable_HFunction(htable->nelements, key);
-
- for (i=first; i<htable->nelements; i++) {
- if (htable->harray[i].key == key) {
- htable->harray[i].key = HTABLE_DELETED;
- htable->htsize--;
- return htable->harray[i].val;
- }
- else if (htable->harray[i].key == HTABLE_EMPTY)
- gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n");
- }
-
- for (i=0; i<first; i++) {
- if (htable->harray[i].key == key) {
- htable->harray[i].key = HTABLE_DELETED;
- htable->htsize--;
- return htable->harray[i].val;
- }
- else if (htable->harray[i].key == HTABLE_EMPTY)
- gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n");
- }
-
- return -1;
-
-}
-
-
-
-/******************************************************************************
-* This function destroys the data structures associated with the hash-table
-*******************************************************************************/
-void HTable_Destroy(gk_HTable_t *htable)
-{
- gk_free((void **)&htable->harray, &htable, LTERM);
-}
-
-
-/******************************************************************************
-* This is the hash-function. Based on multiplication
-*******************************************************************************/
-int HTable_HFunction(int nelements, int key)
-{
- return (int)(key%nelements);
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/io.c b/3rdParty/metis/metis-5.1.0/GKlib/io.c
deleted file mode 100644
index caaedcb59..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/io.c
+++ /dev/null
@@ -1,384 +0,0 @@
-/*!
-\file io.c
-\brief Various file I/O functions.
-
-This file contains various functions that perform I/O.
-
-\date Started 4/10/95
-\author George
-\version\verbatim $Id: io.c 12591 2012-09-01 19:03:15Z karypis $ \endverbatim
-*/
-
-#ifdef HAVE_GETLINE
-/* Get getline to be defined. */
-#define _GNU_SOURCE
-#include <stdio.h>
-#undef _GNU_SOURCE
-#endif
-
-#include <GKlib.h>
-
-/*************************************************************************
-* This function opens a file
-**************************************************************************/
-FILE *gk_fopen(char *fname, char *mode, const char *msg)
-{
- FILE *fp;
- char errmsg[8192];
-
- fp = fopen(fname, mode);
- if (fp != NULL)
- return fp;
-
- sprintf(errmsg,"file: %s, mode: %s, [%s]", fname, mode, msg);
- perror(errmsg);
- errexit("Failed on gk_fopen()\n");
-
- return NULL;
-}
-
-
-/*************************************************************************
-* This function closes a file
-**************************************************************************/
-void gk_fclose(FILE *fp)
-{
- fclose(fp);
-}
-
-
-/*************************************************************************/
-/*! This function is the GKlib implementation of glibc's getline()
- function.
- \returns -1 if the EOF has been reached, otherwise it returns the
- number of bytes read.
-*/
-/*************************************************************************/
-gk_idx_t gk_getline(char **lineptr, size_t *n, FILE *stream)
-{
-#ifdef HAVE_GETLINE
- return getline(lineptr, n, stream);
-#else
- size_t i;
- int ch;
-
- if (feof(stream))
- return -1;
-
- /* Initial memory allocation if *lineptr is NULL */
- if (*lineptr == NULL || *n == 0) {
- *n = 1024;
- *lineptr = gk_malloc((*n)*sizeof(char), "gk_getline: lineptr");
- }
-
- /* get into the main loop */
- i = 0;
- while ((ch = getc(stream)) != EOF) {
- (*lineptr)[i++] = (char)ch;
-
- /* reallocate memory if reached at the end of the buffer. The +1 is for '\0' */
- if (i+1 == *n) {
- *n = 2*(*n);
- *lineptr = gk_realloc(*lineptr, (*n)*sizeof(char), "gk_getline: lineptr");
- }
-
- if (ch == '\n')
- break;
- }
- (*lineptr)[i] = '\0';
-
- return (i == 0 ? -1 : i);
-#endif
-}
-
-
-/*************************************************************************/
-/*! This function reads the contents of a text file and returns it in the
- form of an array of strings.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-char **gk_readfile(char *fname, gk_idx_t *r_nlines)
-{
- size_t lnlen, nlines;
- char *line=NULL, **lines=NULL;
- FILE *fpin;
-
- gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
- if (nlines > 0) {
- lines = (char **)gk_malloc(nlines*sizeof(char *), "gk_readfile: lines");
-
- fpin = gk_fopen(fname, "r", "gk_readfile");
- nlines = 0;
- while (gk_getline(&line, &lnlen, fpin) != -1) {
- gk_strtprune(line, "\n\r");
- lines[nlines++] = gk_strdup(line);
- }
- gk_fclose(fpin);
- }
-
- gk_free((void **)&line, LTERM);
-
- if (r_nlines != NULL)
- *r_nlines = nlines;
-
- return lines;
-}
-
-
-/*************************************************************************/
-/*! This function reads the contents of a file and returns it in the
- form of an array of int32_t.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-int32_t *gk_i32readfile(char *fname, gk_idx_t *r_nlines)
-{
- size_t lnlen, nlines;
- char *line=NULL;
- int32_t *array=NULL;
- FILE *fpin;
-
- gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
- if (nlines > 0) {
- array = gk_i32malloc(nlines, "gk_i32readfile: array");
-
- fpin = gk_fopen(fname, "r", "gk_readfile");
- nlines = 0;
-
- while (gk_getline(&line, &lnlen, fpin) != -1) {
- sscanf(line, "%"SCNd32, &array[nlines++]);
- }
-
- gk_fclose(fpin);
- }
-
- gk_free((void **)&line, LTERM);
-
- if (r_nlines != NULL)
- *r_nlines = nlines;
-
- return array;
-}
-
-
-/*************************************************************************/
-/*! This function reads the contents of a file and returns it in the
- form of an array of int64_t.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-int64_t *gk_i64readfile(char *fname, gk_idx_t *r_nlines)
-{
- size_t lnlen, nlines;
- char *line=NULL;
- int64_t *array=NULL;
- FILE *fpin;
-
- gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
- if (nlines > 0) {
- array = gk_i64malloc(nlines, "gk_i64readfile: array");
-
- fpin = gk_fopen(fname, "r", "gk_readfile");
- nlines = 0;
-
- while (gk_getline(&line, &lnlen, fpin) != -1) {
- sscanf(line, "%"SCNd64, &array[nlines++]);
- }
-
- gk_fclose(fpin);
- }
-
- gk_free((void **)&line, LTERM);
-
- if (r_nlines != NULL)
- *r_nlines = nlines;
-
- return array;
-}
-
-/*************************************************************************/
-/*! This function reads the contents of a binary file and returns it in the
- form of an array of int32_t.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-int32_t *gk_i32readfilebin(char *fname, ssize_t *r_nelmnts)
-{
- ssize_t fsize, nelmnts;
- int32_t *array=NULL;
- FILE *fpin;
-
- *r_nelmnts = -1;
-
- fsize = (ssize_t) gk_getfsize(fname);
- if (fsize%sizeof(int32_t) != 0) {
- gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(int32_t).\n");
- return NULL;
- }
-
- nelmnts = fsize/sizeof(int32_t);
- array = gk_i32malloc(nelmnts, "gk_i32readfilebin: array");
-
- fpin = gk_fopen(fname, "rb", "gk_i32readfilebin");
-
- if (fread(array, sizeof(int32_t), nelmnts, fpin) != nelmnts) {
- gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
- gk_free((void **)&array, LTERM);
- return NULL;
- }
- gk_fclose(fpin);
-
- *r_nelmnts = nelmnts;
-
- return array;
-}
-
-/*************************************************************************/
-/*! This function reads the contents of a binary file and returns it in the
- form of an array of int64_t.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-int64_t *gk_i64readfilebin(char *fname, ssize_t *r_nelmnts)
-{
- ssize_t fsize, nelmnts;
- int64_t *array=NULL;
- FILE *fpin;
-
- *r_nelmnts = -1;
-
- fsize = (ssize_t) gk_getfsize(fname);
- if (fsize%sizeof(int64_t) != 0) {
- gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(int64_t).\n");
- return NULL;
- }
-
- nelmnts = fsize/sizeof(int64_t);
- array = gk_i64malloc(nelmnts, "gk_i64readfilebin: array");
-
- fpin = gk_fopen(fname, "rb", "gk_i64readfilebin");
-
- if (fread(array, sizeof(int64_t), nelmnts, fpin) != nelmnts) {
- gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
- gk_free((void **)&array, LTERM);
- return NULL;
- }
- gk_fclose(fpin);
-
- *r_nelmnts = nelmnts;
-
- return array;
-}
-
-/*************************************************************************/
-/*! This function reads the contents of a binary file and returns it in the
- form of an array of float.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-float *gk_freadfilebin(char *fname, ssize_t *r_nelmnts)
-{
- ssize_t fsize, nelmnts;
- float *array=NULL;
- FILE *fpin;
-
- *r_nelmnts = -1;
-
- fsize = (ssize_t) gk_getfsize(fname);
- if (fsize%sizeof(float) != 0) {
- gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(float).\n");
- return NULL;
- }
-
- nelmnts = fsize/sizeof(float);
- array = gk_fmalloc(nelmnts, "gk_freadfilebin: array");
-
- fpin = gk_fopen(fname, "rb", "gk_freadfilebin");
-
- if (fread(array, sizeof(float), nelmnts, fpin) != nelmnts) {
- gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
- gk_free((void **)&array, LTERM);
- return NULL;
- }
- gk_fclose(fpin);
-
- *r_nelmnts = nelmnts;
-
- return array;
-}
-
-
-/*************************************************************************/
-/*! This function writes the contents of an array into a binary file.
- \param fname is the name of the file
- \param n the number of elements in the array.
- \param a the array to be written out.
-*/
-/*************************************************************************/
-size_t gk_fwritefilebin(char *fname, size_t n, float *a)
-{
- size_t fsize;
- FILE *fp;
-
- fp = gk_fopen(fname, "wb", "gk_fwritefilebin");
-
- fsize = fwrite(a, sizeof(float), n, fp);
-
- gk_fclose(fp);
-
- return fsize;
-}
-
-
-/*************************************************************************/
-/*! This function reads the contents of a binary file and returns it in the
- form of an array of double.
- \param fname is the name of the file
- \param r_nlines is the number of lines in the file. If it is NULL,
- this information is not returned.
-*/
-/*************************************************************************/
-double *gk_dreadfilebin(char *fname, ssize_t *r_nelmnts)
-{
- ssize_t fsize, nelmnts;
- double *array=NULL;
- FILE *fpin;
-
- *r_nelmnts = -1;
-
- fsize = (ssize_t) gk_getfsize(fname);
- if (fsize%sizeof(double) != 0) {
- gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(double).\n");
- return NULL;
- }
-
- nelmnts = fsize/sizeof(double);
- array = gk_dmalloc(nelmnts, "gk_dreadfilebin: array");
-
- fpin = gk_fopen(fname, "rb", "gk_dreadfilebin");
-
- if (fread(array, sizeof(double), nelmnts, fpin) != nelmnts) {
- gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
- gk_free((void **)&array, LTERM);
- return NULL;
- }
- gk_fclose(fpin);
-
- *r_nelmnts = nelmnts;
-
- return array;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/itemsets.c b/3rdParty/metis/metis-5.1.0/GKlib/itemsets.c
deleted file mode 100644
index 65b5af40d..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/itemsets.c
+++ /dev/null
@@ -1,210 +0,0 @@
-/*!
- * \file
- * \brief Frequent/Closed itemset discovery routines
- *
- * This file contains the code for finding frequent/closed itemests. These routines
- * are implemented using a call-back mechanism to deal with the discovered itemsets.
- *
- * \date 6/13/2008
- * \author George Karypis
- * \version\verbatim $Id: itemsets.c 11075 2011-11-11 22:31:52Z karypis $ \endverbatim
- */
-
-#include <GKlib.h>
-
-/*-------------------------------------------------------------*/
-/*! Data structures for use within this module */
-/*-------------------------------------------------------------*/
-typedef struct {
- int minfreq; /* the minimum frequency of a pattern */
- int maxfreq; /* the maximum frequency of a pattern */
- int minlen; /* the minimum length of the requested pattern */
- int maxlen; /* the maximum length of the requested pattern */
- int tnitems; /* the initial range of the item space */
-
- /* the call-back function */
- void (*callback)(void *stateptr, int nitems, int *itemids, int ntrans, int *transids);
- void *stateptr; /* the user-supplied pointer to pass to the callback */
-
- /* workspace variables */
- int *rmarker;
- gk_ikv_t *cand;
-} isparams_t;
-
-
-/*-------------------------------------------------------------*/
-/*! Prototypes for this module */
-/*-------------------------------------------------------------*/
-void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat,
- int preflen, int *prefix);
-gk_csr_t *itemsets_project_matrix(isparams_t *param, gk_csr_t *mat, int cid);
-
-
-
-/*************************************************************************/
-/*! The entry point of the frequent itemset discovery code */
-/*************************************************************************/
-void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind,
- int minfreq, int maxfreq, int minlen, int maxlen,
- void (*process_itemset)(void *stateptr, int nitems, int *itemids,
- int ntrans, int *transids),
- void *stateptr)
-{
- ssize_t i;
- gk_csr_t *mat, *pmat;
- isparams_t params;
- int *pattern;
-
- /* Create the matrix */
- mat = gk_csr_Create();
- mat->nrows = ntrans;
- mat->ncols = tranind[gk_iargmax(tranptr[ntrans], tranind)]+1;
- mat->rowptr = gk_zcopy(ntrans+1, tranptr, gk_zmalloc(ntrans+1, "gk_find_frequent_itemsets: mat.rowptr"));
- mat->rowind = gk_icopy(tranptr[ntrans], tranind, gk_imalloc(tranptr[ntrans], "gk_find_frequent_itemsets: mat.rowind"));
- mat->colids = gk_iincset(mat->ncols, 0, gk_imalloc(mat->ncols, "gk_find_frequent_itemsets: mat.colids"));
-
- /* Setup the parameters */
- params.minfreq = minfreq;
- params.maxfreq = (maxfreq == -1 ? mat->nrows : maxfreq);
- params.minlen = minlen;
- params.maxlen = (maxlen == -1 ? mat->ncols : maxlen);
- params.tnitems = mat->ncols;
- params.callback = process_itemset;
- params.stateptr = stateptr;
- params.rmarker = gk_ismalloc(mat->nrows, 0, "gk_find_frequent_itemsets: rmarker");
- params.cand = gk_ikvmalloc(mat->ncols, "gk_find_frequent_itemsets: cand");
-
- /* Perform the initial projection */
- gk_csr_CreateIndex(mat, GK_CSR_COL);
- pmat = itemsets_project_matrix(¶ms, mat, -1);
- gk_csr_Free(&mat);
-
- pattern = gk_imalloc(pmat->ncols, "gk_find_frequent_itemsets: pattern");
- itemsets_find_frequent_itemsets(¶ms, pmat, 0, pattern);
-
- gk_csr_Free(&pmat);
- gk_free((void **)&pattern, ¶ms.rmarker, ¶ms.cand, LTERM);
-
-}
-
-
-
-/*************************************************************************/
-/*! The recursive routine for DFS-based frequent pattern discovery */
-/*************************************************************************/
-void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat,
- int preflen, int *prefix)
-{
- ssize_t i;
- gk_csr_t *cmat;
-
- /* Project each frequent column */
- for (i=0; i<mat->ncols; i++) {
- prefix[preflen] = mat->colids[i];
-
- if (preflen+1 >= params->minlen)
- (*params->callback)(params->stateptr, preflen+1, prefix,
- mat->colptr[i+1]-mat->colptr[i], mat->colind+mat->colptr[i]);
-
- if (preflen+1 < params->maxlen) {
- cmat = itemsets_project_matrix(params, mat, i);
- itemsets_find_frequent_itemsets(params, cmat, preflen+1, prefix);
- gk_csr_Free(&cmat);
- }
- }
-
-}
-
-
-/******************************************************************************/
-/*! This function projects a matrix w.r.t. to a particular column.
- It performs the following steps:
- - Determines the length of each column that is remaining
- - Sorts the columns in increasing length
- - Creates a column-based version of the matrix with the proper
- column ordering and renamed rowids.
- */
-/*******************************************************************************/
-gk_csr_t *itemsets_project_matrix(isparams_t *params, gk_csr_t *mat, int cid)
-{
- ssize_t i, j, k, ii, pnnz;
- int nrows, ncols, pnrows, pncols;
- ssize_t *colptr, *pcolptr;
- int *colind, *colids, *pcolind, *pcolids, *rmarker;
- gk_csr_t *pmat;
- gk_ikv_t *cand;
-
- nrows = mat->nrows;
- ncols = mat->ncols;
- colptr = mat->colptr;
- colind = mat->colind;
- colids = mat->colids;
-
- rmarker = params->rmarker;
- cand = params->cand;
-
-
- /* Allocate space for the projected matrix based on what you know thus far */
- pmat = gk_csr_Create();
- pmat->nrows = pnrows = (cid == -1 ? nrows : colptr[cid+1]-colptr[cid]);
-
-
- /* Mark the rows that will be kept and determine the prowids */
- if (cid == -1) { /* Initial projection */
- gk_iset(nrows, 1, rmarker);
- }
- else { /* The other projections */
- for (i=colptr[cid]; i<colptr[cid+1]; i++)
- rmarker[colind[i]] = 1;
- }
-
-
- /* Determine the length of each column that will be left in the projected matrix */
- for (pncols=0, pnnz=0, i=cid+1; i<ncols; i++) {
- for (k=0, j=colptr[i]; j<colptr[i+1]; j++) {
- k += rmarker[colind[j]];
- }
- if (k >= params->minfreq && k <= params->maxfreq) {
- cand[pncols].val = i;
- cand[pncols++].key = k;
- pnnz += k;
- }
- }
-
- /* Sort the columns in increasing order */
- gk_ikvsorti(pncols, cand);
-
-
- /* Allocate space for the remaining fields of the projected matrix */
- pmat->ncols = pncols;
- pmat->colids = pcolids = gk_imalloc(pncols, "itemsets_project_matrix: pcolids");
- pmat->colptr = pcolptr = gk_zmalloc(pncols+1, "itemsets_project_matrix: pcolptr");
- pmat->colind = pcolind = gk_imalloc(pnnz, "itemsets_project_matrix: pcolind");
-
-
- /* Populate the projected matrix */
- pcolptr[0] = 0;
- for (pnnz=0, ii=0; ii<pncols; ii++) {
- i = cand[ii].val;
- for (j=colptr[i]; j<colptr[i+1]; j++) {
- if (rmarker[colind[j]])
- pcolind[pnnz++] = colind[j];
- }
-
- pcolids[ii] = colids[i];
- pcolptr[ii+1] = pnnz;
- }
-
-
- /* Reset the rmarker array */
- if (cid == -1) { /* Initial projection */
- gk_iset(nrows, 0, rmarker);
- }
- else { /* The other projections */
- for (i=colptr[cid]; i<colptr[cid+1]; i++)
- rmarker[colind[i]] = 0;
- }
-
-
- return pmat;
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/mcore.c b/3rdParty/metis/metis-5.1.0/GKlib/mcore.c
deleted file mode 100644
index 6442e03a9..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/mcore.c
+++ /dev/null
@@ -1,393 +0,0 @@
-/*!
-\file
-\brief Functions dealing with creating and allocating mcores
-
-\date Started 5/30/11
-\author George
-\author Copyright 1997-2011, Regents of the University of Minnesota
-\version $Id: mcore.c 13953 2013-03-30 16:20:07Z karypis $
-*/
-
-#include <GKlib.h>
-
-
-/*************************************************************************/
-/*! This function creates an mcore
- */
-/*************************************************************************/
-gk_mcore_t *gk_mcoreCreate(size_t coresize)
-{
- gk_mcore_t *mcore;
-
- mcore = (gk_mcore_t *)gk_malloc(sizeof(gk_mcore_t), "gk_mcoreCreate: mcore");
- memset(mcore, 0, sizeof(gk_mcore_t));
-
- mcore->coresize = coresize;
- mcore->corecpos = 0;
-
- mcore->core = (coresize == 0 ? NULL : gk_malloc(mcore->coresize, "gk_mcoreCreate: core"));
-
- /* allocate the memory for keeping track of malloc ops */
- mcore->nmops = 2048;
- mcore->cmop = 0;
- mcore->mops = (gk_mop_t *)gk_malloc(mcore->nmops*sizeof(gk_mop_t), "gk_mcoreCreate: mcore->mops");
-
- return mcore;
-}
-
-
-/*************************************************************************/
-/*! This function creates an mcore. This version is used for gkmcore.
- */
-/*************************************************************************/
-gk_mcore_t *gk_gkmcoreCreate()
-{
- gk_mcore_t *mcore;
-
- if ((mcore = (gk_mcore_t *)malloc(sizeof(gk_mcore_t))) == NULL)
- return NULL;
- memset(mcore, 0, sizeof(gk_mcore_t));
-
- /* allocate the memory for keeping track of malloc ops */
- mcore->nmops = 2048;
- mcore->cmop = 0;
- if ((mcore->mops = (gk_mop_t *)malloc(mcore->nmops*sizeof(gk_mop_t))) == NULL) {
- free(mcore);
- return NULL;
- }
-
- return mcore;
-}
-
-
-/*************************************************************************/
-/*! This function destroys an mcore.
- */
-/*************************************************************************/
-void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats)
-{
- gk_mcore_t *mcore = *r_mcore;
-
- if (mcore == NULL)
- return;
-
- if (showstats)
- printf("\n gk_mcore statistics\n"
- " coresize: %12zu nmops: %12zu cmop: %6zu\n"
- " num_callocs: %12zu num_hallocs: %12zu\n"
- " size_callocs: %12zu size_hallocs: %12zu\n"
- " cur_callocs: %12zu cur_hallocs: %12zu\n"
- " max_callocs: %12zu max_hallocs: %12zu\n",
- mcore->coresize, mcore->nmops, mcore->cmop,
- mcore->num_callocs, mcore->num_hallocs,
- mcore->size_callocs, mcore->size_hallocs,
- mcore->cur_callocs, mcore->cur_hallocs,
- mcore->max_callocs, mcore->max_hallocs);
-
- if (mcore->cur_callocs != 0 || mcore->cur_hallocs != 0 || mcore->cmop != 0) {
- printf("***Warning: mcore memory was not fully freed when destroyed.\n"
- " cur_callocs: %6zu cur_hallocs: %6zu cmop: %6zu\n",
- mcore->cur_callocs, mcore->cur_hallocs, mcore->cmop);
- }
-
- gk_free((void **)&mcore->core, &mcore->mops, &mcore, LTERM);
-
- *r_mcore = NULL;
-}
-
-
-/*************************************************************************/
-/*! This function destroys an mcore. This version is for gkmcore.
- */
-/*************************************************************************/
-void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats)
-{
- gk_mcore_t *mcore = *r_mcore;
-
- if (mcore == NULL)
- return;
-
- if (showstats)
- printf("\n gk_mcore statistics\n"
- " nmops: %12zu cmop: %6zu\n"
- " num_hallocs: %12zu\n"
- " size_hallocs: %12zu\n"
- " cur_hallocs: %12zu\n"
- " max_hallocs: %12zu\n",
- mcore->nmops, mcore->cmop,
- mcore->num_hallocs,
- mcore->size_hallocs,
- mcore->cur_hallocs,
- mcore->max_hallocs);
-
- if (mcore->cur_hallocs != 0 || mcore->cmop != 0) {
- printf("***Warning: mcore memory was not fully freed when destroyed.\n"
- " cur_hallocs: %6zu cmop: %6zu\n",
- mcore->cur_hallocs, mcore->cmop);
- }
-
- free(mcore->mops);
- free(mcore);
-
- *r_mcore = NULL;
-}
-
-
-/*************************************************************************/
-/*! This function allocate space from the core/heap
- */
-/*************************************************************************/
-void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes)
-{
- void *ptr;
-
- /* pad to make pointers 8-byte aligned */
- nbytes += (nbytes%8 == 0 ? 0 : 8 - nbytes%8);
-
- if (mcore->corecpos + nbytes < mcore->coresize) {
- /* service this request from the core */
- ptr = ((char *)mcore->core)+mcore->corecpos;
- mcore->corecpos += nbytes;
-
- gk_mcoreAdd(mcore, GK_MOPT_CORE, nbytes, ptr);
- }
- else {
- /* service this request from the heap */
- ptr = gk_malloc(nbytes, "gk_mcoremalloc: ptr");
-
- gk_mcoreAdd(mcore, GK_MOPT_HEAP, nbytes, ptr);
- }
-
- /*
- printf("MCMALLOC: %zu %d %8zu\n", mcore->cmop-1,
- mcore->mops[mcore->cmop-1].type, mcore->mops[mcore->cmop-1].nbytes);
- */
-
- return ptr;
-}
-
-
-/*************************************************************************/
-/*! This function sets a marker in the stack of malloc ops to be used
- subsequently for freeing purposes
- */
-/*************************************************************************/
-void gk_mcorePush(gk_mcore_t *mcore)
-{
- gk_mcoreAdd(mcore, GK_MOPT_MARK, 0, NULL);
- /* printf("MCPPUSH: %zu\n", mcore->cmop-1); */
-}
-
-
-/*************************************************************************/
-/*! This function sets a marker in the stack of malloc ops to be used
- subsequently for freeing purposes. This is the gkmcore version.
- */
-/*************************************************************************/
-void gk_gkmcorePush(gk_mcore_t *mcore)
-{
- gk_gkmcoreAdd(mcore, GK_MOPT_MARK, 0, NULL);
- /* printf("MCPPUSH: %zu\n", mcore->cmop-1); */
-}
-
-
-/*************************************************************************/
-/*! This function frees all mops since the last push
- */
-/*************************************************************************/
-void gk_mcorePop(gk_mcore_t *mcore)
-{
- while (mcore->cmop > 0) {
- mcore->cmop--;
- switch (mcore->mops[mcore->cmop].type) {
- case GK_MOPT_MARK: /* push marker */
- goto DONE;
- break;
-
- case GK_MOPT_CORE: /* core free */
- if (mcore->corecpos < mcore->mops[mcore->cmop].nbytes)
- errexit("Internal Error: wspace's core is about to be over-freed [%zu, %zu, %zd]\n",
- mcore->coresize, mcore->corecpos, mcore->mops[mcore->cmop].nbytes);
-
- mcore->corecpos -= mcore->mops[mcore->cmop].nbytes;
- mcore->cur_callocs -= mcore->mops[mcore->cmop].nbytes;
- break;
-
- case GK_MOPT_HEAP: /* heap free */
- gk_free((void **)&mcore->mops[mcore->cmop].ptr, LTERM);
- mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes;
- break;
-
- default:
- gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type);
- }
- }
-
-DONE:
- ;
- /*printf("MCPPOP: %zu\n", mcore->cmop); */
-}
-
-
-/*************************************************************************/
-/*! This function frees all mops since the last push. This version is
- for poping the gkmcore and it uses free instead of gk_free.
- */
-/*************************************************************************/
-void gk_gkmcorePop(gk_mcore_t *mcore)
-{
- while (mcore->cmop > 0) {
- mcore->cmop--;
- switch (mcore->mops[mcore->cmop].type) {
- case GK_MOPT_MARK: /* push marker */
- goto DONE;
- break;
-
- case GK_MOPT_HEAP: /* heap free */
- free(mcore->mops[mcore->cmop].ptr);
- mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes;
- break;
-
- default:
- gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type);
- }
- }
-
-DONE:
- ;
-}
-
-
-/*************************************************************************/
-/*! Adds a memory allocation at the end of the list.
- */
-/*************************************************************************/
-void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr)
-{
- if (mcore->cmop == mcore->nmops) {
- mcore->nmops *= 2;
- mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t));
- if (mcore->mops == NULL)
- gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n");
- }
-
- mcore->mops[mcore->cmop].type = type;
- mcore->mops[mcore->cmop].nbytes = nbytes;
- mcore->mops[mcore->cmop].ptr = ptr;
- mcore->cmop++;
-
- switch (type) {
- case GK_MOPT_MARK:
- break;
-
- case GK_MOPT_CORE:
- mcore->num_callocs++;
- mcore->size_callocs += nbytes;
- mcore->cur_callocs += nbytes;
- if (mcore->max_callocs < mcore->cur_callocs)
- mcore->max_callocs = mcore->cur_callocs;
- break;
-
- case GK_MOPT_HEAP:
- mcore->num_hallocs++;
- mcore->size_hallocs += nbytes;
- mcore->cur_hallocs += nbytes;
- if (mcore->max_hallocs < mcore->cur_hallocs)
- mcore->max_hallocs = mcore->cur_hallocs;
- break;
- default:
- gk_errexit(SIGMEM, "Incorrect mcore type operation.\n");
- }
-}
-
-
-/*************************************************************************/
-/*! Adds a memory allocation at the end of the list. This is the gkmcore
- version.
- */
-/*************************************************************************/
-void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr)
-{
- if (mcore->cmop == mcore->nmops) {
- mcore->nmops *= 2;
- mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t));
- if (mcore->mops == NULL)
- gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n");
- }
-
- mcore->mops[mcore->cmop].type = type;
- mcore->mops[mcore->cmop].nbytes = nbytes;
- mcore->mops[mcore->cmop].ptr = ptr;
- mcore->cmop++;
-
- switch (type) {
- case GK_MOPT_MARK:
- break;
-
- case GK_MOPT_HEAP:
- mcore->num_hallocs++;
- mcore->size_hallocs += nbytes;
- mcore->cur_hallocs += nbytes;
- if (mcore->max_hallocs < mcore->cur_hallocs)
- mcore->max_hallocs = mcore->cur_hallocs;
- break;
- default:
- gk_errexit(SIGMEM, "Incorrect mcore type operation.\n");
- }
-}
-
-
-/*************************************************************************/
-/*! This function deletes the mop associated with the supplied pointer.
- The mop has to be a heap allocation, otherwise it fails violently.
- */
-/*************************************************************************/
-void gk_mcoreDel(gk_mcore_t *mcore, void *ptr)
-{
- int i;
-
- for (i=mcore->cmop-1; i>=0; i--) {
- if (mcore->mops[i].type == GK_MOPT_MARK)
- gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr);
-
- if (mcore->mops[i].ptr == ptr) {
- if (mcore->mops[i].type != GK_MOPT_HEAP)
- gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n");
-
- mcore->cur_hallocs -= mcore->mops[i].nbytes;
- mcore->mops[i] = mcore->mops[--mcore->cmop];
- return;
- }
- }
-
- gk_errexit(SIGMEM, "mcoreDel should never have been here!\n");
-}
-
-
-/*************************************************************************/
-/*! This function deletes the mop associated with the supplied pointer.
- The mop has to be a heap allocation, otherwise it fails violently.
- This is the gkmcore version.
- */
-/*************************************************************************/
-void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr)
-{
- int i;
-
- for (i=mcore->cmop-1; i>=0; i--) {
- if (mcore->mops[i].type == GK_MOPT_MARK)
- gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr);
-
- if (mcore->mops[i].ptr == ptr) {
- if (mcore->mops[i].type != GK_MOPT_HEAP)
- gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n");
-
- mcore->cur_hallocs -= mcore->mops[i].nbytes;
- mcore->mops[i] = mcore->mops[--mcore->cmop];
- return;
- }
- }
-
- gk_errexit(SIGMEM, "gkmcoreDel should never have been here!\n");
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/memory.c b/3rdParty/metis/metis-5.1.0/GKlib/memory.c
deleted file mode 100644
index cdd00fa79..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/memory.c
+++ /dev/null
@@ -1,252 +0,0 @@
-/*!
-\file memory.c
-\brief This file contains various allocation routines
-
-The allocation routines included are for 1D and 2D arrays of the
-most datatypes that GKlib support. Many of these routines are
-defined with the help of the macros in gk_memory.h. These macros
-can be used to define other memory allocation routines.
-
-\date Started 4/3/2007
-\author George
-\version\verbatim $Id: memory.c 10783 2011-09-21 23:19:56Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-/* This is for the global mcore that tracks all heap allocations */
-static __thread gk_mcore_t *gkmcore = NULL;
-
-
-/*************************************************************************/
-/*! Define the set of memory allocation routines for each data type */
-/**************************************************************************/
-GK_MKALLOC(gk_c, char)
-GK_MKALLOC(gk_i, int)
-GK_MKALLOC(gk_i32, int32_t)
-GK_MKALLOC(gk_i64, int64_t)
-GK_MKALLOC(gk_z, ssize_t)
-GK_MKALLOC(gk_f, float)
-GK_MKALLOC(gk_d, double)
-GK_MKALLOC(gk_idx, gk_idx_t)
-
-GK_MKALLOC(gk_ckv, gk_ckv_t)
-GK_MKALLOC(gk_ikv, gk_ikv_t)
-GK_MKALLOC(gk_i32kv, gk_i32kv_t)
-GK_MKALLOC(gk_i64kv, gk_i64kv_t)
-GK_MKALLOC(gk_zkv, gk_zkv_t)
-GK_MKALLOC(gk_fkv, gk_fkv_t)
-GK_MKALLOC(gk_dkv, gk_dkv_t)
-GK_MKALLOC(gk_skv, gk_skv_t)
-GK_MKALLOC(gk_idxkv, gk_idxkv_t)
-
-
-
-
-
-
-/*************************************************************************/
-/*! This function allocates a two-dimensional matrix.
- */
-/*************************************************************************/
-void gk_AllocMatrix(void ***r_matrix, size_t elmlen, size_t ndim1, size_t ndim2)
-{
- gk_idx_t i, j;
- void **matrix;
-
- *r_matrix = NULL;
-
- if ((matrix = (void **)gk_malloc(ndim1*sizeof(void *), "gk_AllocMatrix: matrix")) == NULL)
- return;
-
- for (i=0; i<ndim1; i++) {
- if ((matrix[i] = (void *)gk_malloc(ndim2*elmlen, "gk_AllocMatrix: matrix[i]")) == NULL) {
- for (j=0; j<i; j++)
- gk_free((void **)&matrix[j], LTERM);
- return;
- }
- }
-
- *r_matrix = matrix;
-}
-
-
-/*************************************************************************/
-/*! This function frees a two-dimensional matrix.
- */
-/*************************************************************************/
-void gk_FreeMatrix(void ***r_matrix, size_t ndim1, size_t ndim2)
-{
- gk_idx_t i;
- void **matrix;
-
- if ((matrix = *r_matrix) == NULL)
- return;
-
- for (i=0; i<ndim1; i++)
- gk_free((void **)&matrix[i], LTERM);
-
- gk_free((void **)r_matrix, LTERM);
-
-}
-
-
-/*************************************************************************/
-/*! This function initializes tracking of heap allocations.
-*/
-/*************************************************************************/
-int gk_malloc_init()
-{
- if (gkmcore == NULL)
- gkmcore = gk_gkmcoreCreate();
-
- if (gkmcore == NULL)
- return 0;
-
- gk_gkmcorePush(gkmcore);
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function frees the memory that has been allocated since the
- last call to gk_malloc_init().
-*/
-/*************************************************************************/
-void gk_malloc_cleanup(int showstats)
-{
- if (gkmcore != NULL) {
- gk_gkmcorePop(gkmcore);
- if (gkmcore->cmop == 0) {
- gk_gkmcoreDestroy(&gkmcore, showstats);
- gkmcore = NULL;
- }
- }
-}
-
-
-/*************************************************************************/
-/*! This function is my wrapper around malloc that provides the following
- enhancements over malloc:
- * It always allocates one byte of memory, even if 0 bytes are requested.
- This is to ensure that checks of returned values do not lead to NULL
- due to 0 bytes requested.
- * It zeros-out the memory that is allocated. This is for a quick init
- of the underlying datastructures.
-*/
-/**************************************************************************/
-void *gk_malloc(size_t nbytes, char *msg)
-{
- void *ptr=NULL;
-
- if (nbytes == 0)
- nbytes++; /* Force mallocs to actually allocate some memory */
-
- ptr = (void *)malloc(nbytes);
-
- if (ptr == NULL) {
- fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed());
- fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed());
- gk_errexit(SIGMEM, "***Memory allocation failed for %s. Requested size: %zu bytes",
- msg, nbytes);
- return NULL;
- }
-
- /* add this memory allocation */
- if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr);
-
- /* zero-out the allocated space */
-#ifndef NDEBUG
- memset(ptr, 0, nbytes);
-#endif
-
- return ptr;
-}
-
-
-/*************************************************************************
-* This function is my wrapper around realloc
-**************************************************************************/
-void *gk_realloc(void *oldptr, size_t nbytes, char *msg)
-{
- void *ptr=NULL;
-
- if (nbytes == 0)
- nbytes++; /* Force mallocs to actually allocate some memory */
-
- /* remove this memory de-allocation */
- if (gkmcore != NULL && oldptr != NULL) gk_gkmcoreDel(gkmcore, oldptr);
-
- ptr = (void *)realloc(oldptr, nbytes);
-
- if (ptr == NULL) {
- fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed());
- fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed());
- gk_errexit(SIGMEM, "***Memory realloc failed for %s. " "Requested size: %zu bytes",
- msg, nbytes);
- return NULL;
- }
-
- /* add this memory allocation */
- if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr);
-
- return ptr;
-}
-
-
-/*************************************************************************
-* This function is my wrapper around free, allows multiple pointers
-**************************************************************************/
-void gk_free(void **ptr1,...)
-{
- va_list plist;
- void **ptr;
-
- if (*ptr1 != NULL) {
- free(*ptr1);
-
- /* remove this memory de-allocation */
- if (gkmcore != NULL) gk_gkmcoreDel(gkmcore, *ptr1);
- }
- *ptr1 = NULL;
-
- va_start(plist, ptr1);
- while ((ptr = va_arg(plist, void **)) != LTERM) {
- if (*ptr != NULL) {
- free(*ptr);
-
- /* remove this memory de-allocation */
- if (gkmcore != NULL) gk_gkmcoreDel(gkmcore, *ptr);
- }
- *ptr = NULL;
- }
- va_end(plist);
-}
-
-
-/*************************************************************************
-* This function returns the current ammount of dynamically allocated
-* memory that is used by the system
-**************************************************************************/
-size_t gk_GetCurMemoryUsed()
-{
- if (gkmcore == NULL)
- return 0;
- else
- return gkmcore->cur_hallocs;
-}
-
-
-/*************************************************************************
-* This function returns the maximum ammount of dynamically allocated
-* memory that was used by the system
-**************************************************************************/
-size_t gk_GetMaxMemoryUsed()
-{
- if (gkmcore == NULL)
- return 0;
- else
- return gkmcore->max_hallocs;
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/ms_inttypes.h b/3rdParty/metis/metis-5.1.0/GKlib/ms_inttypes.h
deleted file mode 100644
index e26204b7f..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/ms_inttypes.h
+++ /dev/null
@@ -1,301 +0,0 @@
-// ISO C9x compliant inttypes.h for Microsoft Visual Studio
-// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
-//
-// Copyright (c) 2006 Alexander Chemeris
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-// 1. Redistributions of source code must retain the above copyright notice,
-// this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. The name of the author may be used to endorse or promote products
-// derived from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-///////////////////////////////////////////////////////////////////////////////
-
-#ifndef _MSC_VER // [
-#error "Use this header only with Microsoft Visual C++ compilers!"
-#endif // _MSC_VER ]
-
-#ifndef _MSC_INTTYPES_H_ // [
-#define _MSC_INTTYPES_H_
-
-#if _MSC_VER > 1000
-#pragma once
-#endif
-
-#include "ms_stdint.h"
-
-// 7.8 Format conversion of integer types
-
-typedef struct {
- intmax_t quot;
- intmax_t rem;
-} imaxdiv_t;
-
-// 7.8.1 Macros for format specifiers
-
-// The fprintf macros for signed integers are:
-#define PRId8 "d"
-#define PRIi8 "i"
-#define PRIdLEAST8 "d"
-#define PRIiLEAST8 "i"
-#define PRIdFAST8 "d"
-#define PRIiFAST8 "i"
-
-#define PRId16 "hd"
-#define PRIi16 "hi"
-#define PRIdLEAST16 "hd"
-#define PRIiLEAST16 "hi"
-#define PRIdFAST16 "hd"
-#define PRIiFAST16 "hi"
-
-#define PRId32 "I32d"
-#define PRIi32 "I32i"
-#define PRIdLEAST32 "I32d"
-#define PRIiLEAST32 "I32i"
-#define PRIdFAST32 "I32d"
-#define PRIiFAST32 "I32i"
-
-#define PRId64 "I64d"
-#define PRIi64 "I64i"
-#define PRIdLEAST64 "I64d"
-#define PRIiLEAST64 "I64i"
-#define PRIdFAST64 "I64d"
-#define PRIiFAST64 "I64i"
-
-#define PRIdMAX "I64d"
-#define PRIiMAX "I64i"
-
-#define PRIdPTR "Id"
-#define PRIiPTR "Ii"
-
-// The fprintf macros for unsigned integers are:
-#define PRIo8 "o"
-#define PRIu8 "u"
-#define PRIx8 "x"
-#define PRIX8 "X"
-#define PRIoLEAST8 "o"
-#define PRIuLEAST8 "u"
-#define PRIxLEAST8 "x"
-#define PRIXLEAST8 "X"
-#define PRIoFAST8 "o"
-#define PRIuFAST8 "u"
-#define PRIxFAST8 "x"
-#define PRIXFAST8 "X"
-
-#define PRIo16 "ho"
-#define PRIu16 "hu"
-#define PRIx16 "hx"
-#define PRIX16 "hX"
-#define PRIoLEAST16 "ho"
-#define PRIuLEAST16 "hu"
-#define PRIxLEAST16 "hx"
-#define PRIXLEAST16 "hX"
-#define PRIoFAST16 "ho"
-#define PRIuFAST16 "hu"
-#define PRIxFAST16 "hx"
-#define PRIXFAST16 "hX"
-
-#define PRIo32 "I32o"
-#define PRIu32 "I32u"
-#define PRIx32 "I32x"
-#define PRIX32 "I32X"
-#define PRIoLEAST32 "I32o"
-#define PRIuLEAST32 "I32u"
-#define PRIxLEAST32 "I32x"
-#define PRIXLEAST32 "I32X"
-#define PRIoFAST32 "I32o"
-#define PRIuFAST32 "I32u"
-#define PRIxFAST32 "I32x"
-#define PRIXFAST32 "I32X"
-
-#define PRIo64 "I64o"
-#define PRIu64 "I64u"
-#define PRIx64 "I64x"
-#define PRIX64 "I64X"
-#define PRIoLEAST64 "I64o"
-#define PRIuLEAST64 "I64u"
-#define PRIxLEAST64 "I64x"
-#define PRIXLEAST64 "I64X"
-#define PRIoFAST64 "I64o"
-#define PRIuFAST64 "I64u"
-#define PRIxFAST64 "I64x"
-#define PRIXFAST64 "I64X"
-
-#define PRIoMAX "I64o"
-#define PRIuMAX "I64u"
-#define PRIxMAX "I64x"
-#define PRIXMAX "I64X"
-
-#define PRIoPTR "Io"
-#define PRIuPTR "Iu"
-#define PRIxPTR "Ix"
-#define PRIXPTR "IX"
-
-// The fscanf macros for signed integers are:
-#define SCNd8 "d"
-#define SCNi8 "i"
-#define SCNdLEAST8 "d"
-#define SCNiLEAST8 "i"
-#define SCNdFAST8 "d"
-#define SCNiFAST8 "i"
-
-#define SCNd16 "hd"
-#define SCNi16 "hi"
-#define SCNdLEAST16 "hd"
-#define SCNiLEAST16 "hi"
-#define SCNdFAST16 "hd"
-#define SCNiFAST16 "hi"
-
-#define SCNd32 "ld"
-#define SCNi32 "li"
-#define SCNdLEAST32 "ld"
-#define SCNiLEAST32 "li"
-#define SCNdFAST32 "ld"
-#define SCNiFAST32 "li"
-
-#define SCNd64 "I64d"
-#define SCNi64 "I64i"
-#define SCNdLEAST64 "I64d"
-#define SCNiLEAST64 "I64i"
-#define SCNdFAST64 "I64d"
-#define SCNiFAST64 "I64i"
-
-#define SCNdMAX "I64d"
-#define SCNiMAX "I64i"
-
-#ifdef _WIN64 // [
-# define SCNdPTR "I64d"
-# define SCNiPTR "I64i"
-#else // _WIN64 ][
-# define SCNdPTR "ld"
-# define SCNiPTR "li"
-#endif // _WIN64 ]
-
-// The fscanf macros for unsigned integers are:
-#define SCNo8 "o"
-#define SCNu8 "u"
-#define SCNx8 "x"
-#define SCNX8 "X"
-#define SCNoLEAST8 "o"
-#define SCNuLEAST8 "u"
-#define SCNxLEAST8 "x"
-#define SCNXLEAST8 "X"
-#define SCNoFAST8 "o"
-#define SCNuFAST8 "u"
-#define SCNxFAST8 "x"
-#define SCNXFAST8 "X"
-
-#define SCNo16 "ho"
-#define SCNu16 "hu"
-#define SCNx16 "hx"
-#define SCNX16 "hX"
-#define SCNoLEAST16 "ho"
-#define SCNuLEAST16 "hu"
-#define SCNxLEAST16 "hx"
-#define SCNXLEAST16 "hX"
-#define SCNoFAST16 "ho"
-#define SCNuFAST16 "hu"
-#define SCNxFAST16 "hx"
-#define SCNXFAST16 "hX"
-
-#define SCNo32 "lo"
-#define SCNu32 "lu"
-#define SCNx32 "lx"
-#define SCNX32 "lX"
-#define SCNoLEAST32 "lo"
-#define SCNuLEAST32 "lu"
-#define SCNxLEAST32 "lx"
-#define SCNXLEAST32 "lX"
-#define SCNoFAST32 "lo"
-#define SCNuFAST32 "lu"
-#define SCNxFAST32 "lx"
-#define SCNXFAST32 "lX"
-
-#define SCNo64 "I64o"
-#define SCNu64 "I64u"
-#define SCNx64 "I64x"
-#define SCNX64 "I64X"
-#define SCNoLEAST64 "I64o"
-#define SCNuLEAST64 "I64u"
-#define SCNxLEAST64 "I64x"
-#define SCNXLEAST64 "I64X"
-#define SCNoFAST64 "I64o"
-#define SCNuFAST64 "I64u"
-#define SCNxFAST64 "I64x"
-#define SCNXFAST64 "I64X"
-
-#define SCNoMAX "I64o"
-#define SCNuMAX "I64u"
-#define SCNxMAX "I64x"
-#define SCNXMAX "I64X"
-
-#ifdef _WIN64 // [
-# define SCNoPTR "I64o"
-# define SCNuPTR "I64u"
-# define SCNxPTR "I64x"
-# define SCNXPTR "I64X"
-#else // _WIN64 ][
-# define SCNoPTR "lo"
-# define SCNuPTR "lu"
-# define SCNxPTR "lx"
-# define SCNXPTR "lX"
-#endif // _WIN64 ]
-
-// 7.8.2 Functions for greatest-width integer types
-
-// 7.8.2.1 The imaxabs function
-#define imaxabs _abs64
-
-// 7.8.2.2 The imaxdiv function
-
-// This is modified version of div() function from Microsoft's div.c found
-// in %MSVC.NET%\crt\src\div.c
-#ifdef STATIC_IMAXDIV // [
-static
-#else // STATIC_IMAXDIV ][
-_inline
-#endif // STATIC_IMAXDIV ]
-imaxdiv_t __cdecl imaxdiv(intmax_t numer, intmax_t denom)
-{
- imaxdiv_t result;
-
- result.quot = numer / denom;
- result.rem = numer % denom;
-
- if (numer < 0 && result.rem > 0) {
- // did division wrong; must fix up
- ++result.quot;
- result.rem -= denom;
- }
-
- return result;
-}
-
-// 7.8.2.3 The strtoimax and strtoumax functions
-#define strtoimax _strtoi64
-#define strtoumax _strtoui64
-
-// 7.8.2.4 The wcstoimax and wcstoumax functions
-#define wcstoimax _wcstoi64
-#define wcstoumax _wcstoui64
-
-
-#endif // _MSC_INTTYPES_H_ ]
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/ms_stat.h b/3rdParty/metis/metis-5.1.0/GKlib/ms_stat.h
deleted file mode 100644
index a1ef6faf7..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/ms_stat.h
+++ /dev/null
@@ -1,22 +0,0 @@
-#ifndef _MSC_VER // [
-#error "Use this header only with Microsoft Visual C++ compilers!"
-#endif // _MSC_VER ]
-
-#ifndef _MS_STAT_H_
-#define _MS_STAT_H_
-
-#if _MSC_VER > 1000
-#pragma once
-#endif
-
-#include <sys/stat.h>
-/* Test macros for file types. */
-
-#define __S_ISTYPE(mode, mask) (((mode) & S_IFMT) == (mask))
-
-#define S_ISDIR(mode) __S_ISTYPE((mode), S_IFDIR)
-#define S_ISCHR(mode) __S_ISTYPE((mode), S_IFCHR)
-#define S_ISBLK(mode) __S_ISTYPE((mode), S_IFBLK)
-#define S_ISREG(mode) __S_ISTYPE((mode), S_IFREG)
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/ms_stdint.h b/3rdParty/metis/metis-5.1.0/GKlib/ms_stdint.h
deleted file mode 100644
index 7e200dc6f..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/ms_stdint.h
+++ /dev/null
@@ -1,222 +0,0 @@
-// ISO C9x compliant stdint.h for Microsoft Visual Studio
-// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
-//
-// Copyright (c) 2006 Alexander Chemeris
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-// 1. Redistributions of source code must retain the above copyright notice,
-// this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. The name of the author may be used to endorse or promote products
-// derived from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-///////////////////////////////////////////////////////////////////////////////
-
-#ifndef _MSC_VER // [
-#error "Use this header only with Microsoft Visual C++ compilers!"
-#endif // _MSC_VER ]
-
-#ifndef _MSC_STDINT_H_ // [
-#define _MSC_STDINT_H_
-
-#if _MSC_VER > 1000
-#pragma once
-#endif
-
-#include <limits.h>
-
-// For Visual Studio 6 in C++ mode wrap <wchar.h> include with 'extern "C++" {}'
-// or compiler give many errors like this:
-// error C2733: second C linkage of overloaded function 'wmemchr' not allowed
-#if (_MSC_VER < 1300) && defined(__cplusplus)
- extern "C++" {
-#endif
-# include <wchar.h>
-#if (_MSC_VER < 1300) && defined(__cplusplus)
- }
-#endif
-
-// 7.18.1 Integer types
-
-// 7.18.1.1 Exact-width integer types
-typedef __int8 int8_t;
-typedef __int16 int16_t;
-typedef __int32 int32_t;
-typedef __int64 int64_t;
-typedef unsigned __int8 uint8_t;
-typedef unsigned __int16 uint16_t;
-typedef unsigned __int32 uint32_t;
-typedef unsigned __int64 uint64_t;
-
-// 7.18.1.2 Minimum-width integer types
-typedef int8_t int_least8_t;
-typedef int16_t int_least16_t;
-typedef int32_t int_least32_t;
-typedef int64_t int_least64_t;
-typedef uint8_t uint_least8_t;
-typedef uint16_t uint_least16_t;
-typedef uint32_t uint_least32_t;
-typedef uint64_t uint_least64_t;
-
-// 7.18.1.3 Fastest minimum-width integer types
-typedef int8_t int_fast8_t;
-typedef int16_t int_fast16_t;
-typedef int32_t int_fast32_t;
-typedef int64_t int_fast64_t;
-typedef uint8_t uint_fast8_t;
-typedef uint16_t uint_fast16_t;
-typedef uint32_t uint_fast32_t;
-typedef uint64_t uint_fast64_t;
-
-// 7.18.1.4 Integer types capable of holding object pointers
-#ifdef _WIN64 // [
- typedef __int64 intptr_t;
- typedef unsigned __int64 uintptr_t;
-#else // _WIN64 ][
- typedef int intptr_t;
- typedef unsigned int uintptr_t;
-#endif // _WIN64 ]
-
-// 7.18.1.5 Greatest-width integer types
-typedef int64_t intmax_t;
-typedef uint64_t uintmax_t;
-
-
-// 7.18.2 Limits of specified-width integer types
-
-#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259
-
-// 7.18.2.1 Limits of exact-width integer types
-#define INT8_MIN ((int8_t)_I8_MIN)
-#define INT8_MAX _I8_MAX
-#define INT16_MIN ((int16_t)_I16_MIN)
-#define INT16_MAX _I16_MAX
-#define INT32_MIN ((int32_t)_I32_MIN)
-#define INT32_MAX _I32_MAX
-#define INT64_MIN ((int64_t)_I64_MIN)
-#define INT64_MAX _I64_MAX
-#define UINT8_MAX _UI8_MAX
-#define UINT16_MAX _UI16_MAX
-#define UINT32_MAX _UI32_MAX
-#define UINT64_MAX _UI64_MAX
-
-// 7.18.2.2 Limits of minimum-width integer types
-#define INT_LEAST8_MIN INT8_MIN
-#define INT_LEAST8_MAX INT8_MAX
-#define INT_LEAST16_MIN INT16_MIN
-#define INT_LEAST16_MAX INT16_MAX
-#define INT_LEAST32_MIN INT32_MIN
-#define INT_LEAST32_MAX INT32_MAX
-#define INT_LEAST64_MIN INT64_MIN
-#define INT_LEAST64_MAX INT64_MAX
-#define UINT_LEAST8_MAX UINT8_MAX
-#define UINT_LEAST16_MAX UINT16_MAX
-#define UINT_LEAST32_MAX UINT32_MAX
-#define UINT_LEAST64_MAX UINT64_MAX
-
-// 7.18.2.3 Limits of fastest minimum-width integer types
-#define INT_FAST8_MIN INT8_MIN
-#define INT_FAST8_MAX INT8_MAX
-#define INT_FAST16_MIN INT16_MIN
-#define INT_FAST16_MAX INT16_MAX
-#define INT_FAST32_MIN INT32_MIN
-#define INT_FAST32_MAX INT32_MAX
-#define INT_FAST64_MIN INT64_MIN
-#define INT_FAST64_MAX INT64_MAX
-#define UINT_FAST8_MAX UINT8_MAX
-#define UINT_FAST16_MAX UINT16_MAX
-#define UINT_FAST32_MAX UINT32_MAX
-#define UINT_FAST64_MAX UINT64_MAX
-
-// 7.18.2.4 Limits of integer types capable of holding object pointers
-#ifdef _WIN64 // [
-# define INTPTR_MIN INT64_MIN
-# define INTPTR_MAX INT64_MAX
-# define UINTPTR_MAX UINT64_MAX
-#else // _WIN64 ][
-# define INTPTR_MIN INT32_MIN
-# define INTPTR_MAX INT32_MAX
-# define UINTPTR_MAX UINT32_MAX
-#endif // _WIN64 ]
-
-// 7.18.2.5 Limits of greatest-width integer types
-#define INTMAX_MIN INT64_MIN
-#define INTMAX_MAX INT64_MAX
-#define UINTMAX_MAX UINT64_MAX
-
-// 7.18.3 Limits of other integer types
-
-#ifdef _WIN64 // [
-# define PTRDIFF_MIN _I64_MIN
-# define PTRDIFF_MAX _I64_MAX
-#else // _WIN64 ][
-# define PTRDIFF_MIN _I32_MIN
-# define PTRDIFF_MAX _I32_MAX
-#endif // _WIN64 ]
-
-#define SIG_ATOMIC_MIN INT_MIN
-#define SIG_ATOMIC_MAX INT_MAX
-
-#ifndef SIZE_MAX // [
-# ifdef _WIN64 // [
-# define SIZE_MAX _UI64_MAX
-# else // _WIN64 ][
-# define SIZE_MAX _UI32_MAX
-# endif // _WIN64 ]
-#endif // SIZE_MAX ]
-
-// WCHAR_MIN and WCHAR_MAX are also defined in <wchar.h>
-#ifndef WCHAR_MIN // [
-# define WCHAR_MIN 0
-#endif // WCHAR_MIN ]
-#ifndef WCHAR_MAX // [
-# define WCHAR_MAX _UI16_MAX
-#endif // WCHAR_MAX ]
-
-#define WINT_MIN 0
-#define WINT_MAX _UI16_MAX
-
-#endif // __STDC_LIMIT_MACROS ]
-
-
-// 7.18.4 Limits of other integer types
-
-#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260
-
-// 7.18.4.1 Macros for minimum-width integer constants
-
-#define INT8_C(val) val##i8
-#define INT16_C(val) val##i16
-#define INT32_C(val) val##i32
-#define INT64_C(val) val##i64
-
-#define UINT8_C(val) val##ui8
-#define UINT16_C(val) val##ui16
-#define UINT32_C(val) val##ui32
-#define UINT64_C(val) val##ui64
-
-// 7.18.4.2 Macros for greatest-width integer constants
-#define INTMAX_C INT64_C
-#define UINTMAX_C UINT64_C
-
-#endif // __STDC_CONSTANT_MACROS ]
-
-
-#endif // _MSC_STDINT_H_ ]
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/omp.c b/3rdParty/metis/metis-5.1.0/GKlib/omp.c
deleted file mode 100644
index bdd543acf..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/omp.c
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * omp.c
- *
- * This file contains "fake" implementations of OpenMP's runtime libraries
- *
- */
-
-#include <GKlib.h>
-
-#ifdef GK_NOOPENMP /* remove those for now */
-#if !defined(_OPENMP)
-void omp_set_num_threads(int num_threads) { return; }
-int omp_get_num_threads(void) { return 1; }
-int omp_get_max_threads(void) { return 1; }
-int omp_get_thread_num(void) { return 0; }
-int omp_get_num_procs(void) { return 1; }
-int omp_in_parallel(void) { return 0; }
-void omp_set_dynamic(int num_threads) { return; }
-int omp_get_dynamic(void) { return 0; }
-void omp_set_nested(int nested) { return; }
-int omp_get_nested(void) { return 0; }
-#endif
-#endif
-
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/pdb.c b/3rdParty/metis/metis-5.1.0/GKlib/pdb.c
deleted file mode 100644
index b4d222653..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/pdb.c
+++ /dev/null
@@ -1,460 +0,0 @@
-/************************************************************************/
-/*! \file pdb.c
-
-\brief Functions for parsing pdb files.
-
-Pdb reader (parser). Loads arrays of pointers for easy backbone access.
-
-\date Started 10/20/06
-\author Kevin
-\version $Id: pdb.c 10711 2011-08-31 22:23:04Z karypis $
-*/
-/************************************************************************/
-#include <GKlib.h>
-
-/************************************************************************/
-/*! \brief Converts three-letter amino acid codes to one-leter codes.
-
-This function takes a three letter \c * and converts it to a single \c
-
-\param res is the three-letter code to be converted.
-\returns A \c representing the amino acid.
-*/
-/************************************************************************/
-char gk_threetoone(char *res) { /* {{{ */
- /* make sure the matching works */
- res[0] = toupper(res[0]);
- res[1] = toupper(res[1]);
- res[2] = toupper(res[2]);
- if(strcmp(res,"ALA") == 0) {
- return 'A';
- }
- else if(strcmp(res,"CYS") == 0) {
- return 'C';
- }
- else if(strcmp(res,"ASP") == 0) {
- return 'D';
- }
- else if(strcmp(res,"GLU") == 0) {
- return 'E';
- }
- else if(strcmp(res,"PHE") == 0) {
- return 'F';
- }
- else if(strcmp(res,"GLY") == 0) {
- return 'G';
- }
- else if(strcmp(res,"HIS") == 0) {
- return 'H';
- }
- else if(strcmp(res,"ILE") == 0) {
- return 'I';
- }
- else if(strcmp(res,"LYS") == 0) {
- return 'K';
- }
- else if(strcmp(res,"LEU") == 0) {
- return 'L';
- }
- else if(strcmp(res,"MET") == 0) {
- return 'M';
- }
- else if(strcmp(res,"ASN") == 0) {
- return 'N';
- }
- else if(strcmp(res,"PRO") == 0) {
- return 'P';
- }
- else if(strcmp(res,"GLN") == 0) {
- return 'Q';
- }
- else if(strcmp(res,"ARG") == 0) {
- return 'R';
- }
- else if(strcmp(res,"SER") == 0) {
- return 'S';
- }
- else if(strcmp(res,"THR") == 0) {
- return 'T';
- }
- else if(strcmp(res,"SCY") == 0) {
- return 'U';
- }
- else if(strcmp(res,"VAL") == 0) {
- return 'V';
- }
- else if(strcmp(res,"TRP") == 0) {
- return 'W';
- }
- else if(strcmp(res,"TYR") == 0) {
- return 'Y';
- }
- else {
- return 'X';
- }
-} /* }}} */
-
-/************************************************************************/
-/*! \brief Frees the memory of a pdbf structure.
-
-This function takes a pdbf pointer and frees all the memory below it.
-
-\param p is the pdbf structure to be freed.
-*/
-/************************************************************************/
-void gk_freepdbf(pdbf *p) { /* {{{ */
- int i;
- if(p != NULL) {
- gk_free((void **)&p->resSeq, LTERM);
- for(i=0; i<p->natoms; i++) {
- gk_free((void **)&p->atoms[i].name, &p->atoms[i].resname, LTERM);
- }
- for(i=0; i<p->nresidues; i++) {
- gk_free((void *)&p->threeresSeq[i], LTERM);
- }
- /* this may look like it's wrong, but it's just a 1-d array of pointers, and
- the pointers themselves are freed above */
- gk_free((void **)&p->bbs, &p->cas, &p->atoms, &p->cm, &p->threeresSeq, LTERM);
- }
- gk_free((void **)&p, LTERM);
-} /* }}} */
-
-/************************************************************************/
-/*! \brief Reads a pdb file into a pdbf structure
-
-This function allocates a pdbf structure and reads the file fname into
-that structure.
-
-\param fname is the file name to be read
-\returns A filled pdbf structure.
-*/
-/************************************************************************/
-pdbf *gk_readpdbfile(char *fname) { /* {{{ */
- int i=0, res=0;
- char linetype[6];
- int aserial;
- char aname[5] = " \0";
- char altLoc = ' ';
- char rname[4] = " \0";
- char chainid = ' ';
- char oldchainid = ' ';
- int rserial;
- int oldRserial = -37;
- char icode = ' ';
- char element = ' ';
- double x;
- double y;
- double z;
- double avgx;
- double avgy;
- double avgz;
- double opcy;
- double tmpt;
- char line[MAXLINELEN];
- int corruption=0;
- int nresatoms;
-
- int atoms=0, residues=0, cas=0, bbs=0, firstres=1;
- pdbf *toFill = gk_malloc(sizeof(pdbf),"fillme");
- FILE *FPIN;
-
- FPIN = gk_fopen(fname,"r",fname);
- while(fgets(line, 256, FPIN)) {
- sscanf(line,"%s ",linetype);
- /* It seems the only reliable parts are through temperature, so we only use these parts */
- /* if(strstr(linetype, "ATOM") != NULL || strstr(linetype, "HETATM") != NULL) { */
- if(strstr(linetype, "ATOM") != NULL) {
- sscanf(line, "%6s%5d%*1c%4c%1c%3c%*1c%1c%4d%1c%*3c%8lf%8lf%8lf%6lf%6lf %c\n",
- linetype,&aserial,aname,&altLoc,rname,&chainid,&rserial,&icode,&x,&y,&z,&opcy,&tmpt,&element);
- sscanf(linetype, " %s ",linetype);
- sscanf(aname, " %s ",aname);
- sscanf(rname, " %s ",rname);
- if(altLoc != ' ') {
- corruption = corruption|CRP_ALTLOCS;
- }
-
- if(firstres == 1) {
- oldRserial = rserial;
- oldchainid = chainid;
- residues++;
- firstres = 0;
- }
- if(oldRserial != rserial) {
- residues++;
- oldRserial = rserial;
- }
- if(oldchainid != chainid) {
- corruption = corruption|CRP_MULTICHAIN;
- }
- oldchainid = chainid;
- atoms++;
- if(strcmp(aname,"CA") == 0) {
- cas++;
- }
- if(strcmp(aname,"N") == 0 || strcmp(aname,"CA") == 0 ||
- strcmp(aname,"C") == 0 || strcmp(aname,"O") == 0) {
- bbs++;
- }
- }
- else if(strstr(linetype, "ENDMDL") != NULL || strstr(linetype, "END") != NULL || strstr(linetype, "TER") != NULL) {
- break;
- }
- }
- fclose(FPIN);
-
- /* printf("File has coordinates for %d atoms in %d residues\n",atoms,residues); */
- toFill->natoms = atoms;
- toFill->ncas = cas;
- toFill->nbbs = bbs;
- toFill->nresidues = residues;
- toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq");
- toFill->threeresSeq = (char **)gk_malloc (residues*sizeof(char *),"residue seq");
- toFill->atoms = (atom *) gk_malloc (atoms*sizeof(atom), "atoms");
- toFill->bbs = (atom **)gk_malloc ( bbs*sizeof(atom *),"bbs");
- toFill->cas = (atom **)gk_malloc ( cas*sizeof(atom *),"cas");
- toFill->cm = (center_of_mass *)gk_malloc(residues*sizeof(center_of_mass),"center of mass");
- res=0; firstres=1; cas=0; bbs=0; i=0;
- avgx = 0.0; avgy = 0.0; avgz = 0.0;
- nresatoms = 0;
-
- FPIN = gk_fopen(fname,"r",fname);
- while(fgets(line, 256, FPIN)) {
- sscanf(line,"%s ",linetype);
- /* It seems the only reliable parts are through temperature, so we only use these parts */
- /* if(strstr(linetype, "ATOM") != NULL || strstr(linetype, "HETATM") != NULL) { */
- if(strstr(linetype, "ATOM") != NULL ) {
-
- /* to ensure our memory doesn't get corrupted by the biologists, we only read this far */
- sscanf(line, "%6s%5d%*1c%4c%1c%3c%*1c%1c%4d%1c%*3c%8lf%8lf%8lf%6lf%6lf %c\n",
- linetype,&aserial,aname,&altLoc,rname,&chainid,&rserial,&icode,&x,&y,&z,&opcy,&tmpt,&element);
- sscanf(aname, "%s",aname);
- sscanf(rname, "%s",rname);
-
- if(firstres == 1) {
- toFill->resSeq[res] = gk_threetoone(rname);
- toFill->threeresSeq[res] = gk_strdup(rname);
- oldRserial = rserial;
- res++;
- firstres = 0;
- }
- if(oldRserial != rserial) {
- /* we're changing residues. store the center of mass from the last one & reset */
- toFill->cm[res-1].x = avgx/nresatoms;
- toFill->cm[res-1].y = avgy/nresatoms;
- toFill->cm[res-1].z = avgz/nresatoms;
- avgx = 0.0; avgy = 0.0; avgz = 0.0;
- nresatoms = 0;
- toFill->cm[res-1].name = toFill->resSeq[res-1];
-
- toFill->threeresSeq[res] = gk_strdup(rname);
- toFill->resSeq[res] = gk_threetoone(rname);
- res++;
- oldRserial = rserial;
- }
- avgx += x;
- avgy += y;
- avgz += z;
- nresatoms++;
-
- toFill->atoms[i].x = x;
- toFill->atoms[i].y = y;
- toFill->atoms[i].z = z;
- toFill->atoms[i].opcy = opcy;
- toFill->atoms[i].tmpt = tmpt;
- toFill->atoms[i].element = element;
- toFill->atoms[i].serial = aserial;
- toFill->atoms[i].chainid = chainid;
- toFill->atoms[i].altLoc = altLoc;
- toFill->atoms[i].rserial = rserial;
- toFill->atoms[i].icode = icode;
- toFill->atoms[i].name = gk_strdup(aname);
- toFill->atoms[i].resname = gk_strdup(rname);
- /* Set up pointers for the backbone and c-alpha shortcuts */
- if(strcmp(aname,"CA") == 0) {
- toFill->cas[cas] = &(toFill->atoms[i]);
- cas++;
- }
- if(strcmp(aname,"N") == 0 || strcmp(aname,"CA") == 0 || strcmp(aname,"C") == 0 || strcmp(aname,"O") == 0) {
- toFill->bbs[bbs] = &(toFill->atoms[i]);
- bbs++;
- }
- i++;
- }
- else if(strstr(linetype, "ENDMDL") != NULL || strstr(linetype, "END") != NULL || strstr(linetype, "TER") != NULL) {
- break;
- }
- }
- /* get that last average */
- toFill->cm[res-1].x = avgx/nresatoms;
- toFill->cm[res-1].y = avgy/nresatoms;
- toFill->cm[res-1].z = avgz/nresatoms;
- /* Begin test code */
- if(cas != residues) {
- printf("Number of residues and CA coordinates differs by %d (!)\n",residues-cas);
- if(cas < residues) {
- corruption = corruption|CRP_MISSINGCA;
- }
- else if(cas > residues) {
- corruption = corruption|CRP_MULTICA;
- }
- }
- if(bbs < residues*4) {
- corruption = corruption|CRP_MISSINGBB;
- }
- else if(bbs > residues*4) {
- corruption = corruption|CRP_MULTIBB;
- }
- fclose(FPIN);
- toFill->corruption = corruption;
- /* if(corruption == 0)
- printf("File was clean!\n"); */
- return(toFill);
-} /* }}} */
-
-/************************************************************************/
-/*! \brief Writes the sequence of residues from a pdb file.
-
-This function takes a pdbf structure and a filename, and writes out
-the amino acid sequence according to the atomic coordinates. The output
-is in fasta format.
-
-
-\param p is the pdbf structure with the sequence of interest
-\param fname is the file name to be written
-*/
-/************************************************************************/
-void gk_writefastafrompdb(pdbf *pb, char *fname) {
- int i;
- FILE *FPOUT;
-
- FPOUT = gk_fopen(fname,"w",fname);
- fprintf(FPOUT,"> %s\n",fname);
-
- for(i=0; i<pb->nresidues; i++)
- fprintf(FPOUT,"%c",pb->resSeq[i]);
-
- fprintf(FPOUT,"\n");
- fclose(FPOUT);
-}
-
-/************************************************************************/
-/*! \brief Writes all centers of mass in pdb-format to file fname.
-
-This function takes a pdbf structure and writes out the calculated
-mass center information to file fname as though each one was a c-alpha.
-
-\param p is the pdbf structure to write out
-\param fname is the file name to be written
-*/
-/************************************************************************/
-void gk_writecentersofmass(pdbf *p, char *fname) {
- int i;
- FILE *FPIN;
- FPIN = gk_fopen(fname,"w",fname);
- for(i=0; i<p->nresidues; i++) {
- fprintf(FPIN,"%-6s%5d %4s%1c%3s %1c%4d%1c %8.3lf%8.3lf%8.3lf%6.2f%6.2f\n",
- "ATOM ",i,"CA",' ',p->threeresSeq[i],' ',i,' ',p->cm[i].x,p->cm[i].y,p->cm[i].z,1.0,-37.0);
- }
- fclose(FPIN);
-}
-
-/************************************************************************/
-/*! \brief Writes all atoms in p in pdb-format to file fname.
-
-This function takes a pdbf structure and writes out all the atom
-information to file fname.
-
-\param p is the pdbf structure to write out
-\param fname is the file name to be written
-*/
-/************************************************************************/
-void gk_writefullatom(pdbf *p, char *fname) {
- int i;
- FILE *FPIN;
- FPIN = gk_fopen(fname,"w",fname);
- for(i=0; i<p->natoms; i++) {
- fprintf(FPIN,"%-6s%5d %4s%1c%3s %1c%4d%1c %8.3lf%8.3lf%8.3lf%6.2f%6.2f\n",
- "ATOM ",p->atoms[i].serial,p->atoms[i].name,p->atoms[i].altLoc,p->atoms[i].resname,p->atoms[i].chainid,p->atoms[i].rserial,p->atoms[i].icode,p->atoms[i].x,p->atoms[i].y,p->atoms[i].z,p->atoms[i].opcy,p->atoms[i].tmpt);
- }
- fclose(FPIN);
-}
-
-/************************************************************************/
-/*! \brief Writes out all the backbone atoms of a structure in pdb format
-
-This function takes a pdbf structure p and writes only the backbone atoms
-to a filename fname.
-
-\param p is the pdb structure to write out.
-\param fname is the file name to be written.
-*/
-/************************************************************************/
-void gk_writebackbone(pdbf *p, char *fname) {
- int i;
- FILE *FPIN;
- FPIN = gk_fopen(fname,"w",fname);
- for(i=0; i<p->nbbs; i++) {
- fprintf(FPIN,"%-6s%5d %4s%1c%3s %1c%4d%1c %8.3lf%8.3lf%8.3lf%6.2f%6.2f\n",
- "ATOM ",p->bbs[i]->serial,p->bbs[i]->name,p->bbs[i]->altLoc,p->bbs[i]->resname,p->bbs[i]->chainid,p->bbs[i]->rserial,p->bbs[i]->icode,p->bbs[i]->x,p->bbs[i]->y,p->bbs[i]->z,p->bbs[i]->opcy,p->bbs[i]->tmpt);
- }
- fclose(FPIN);
-}
-
-/************************************************************************/
-/*! \brief Writes out all the alpha carbon atoms of a structure
-
-This function takes a pdbf structure p and writes only the alpha carbon
-atoms to a filename fname.
-
-\param p is the pdb structure to write out.
-\param fname is the file name to be written.
-*/
-/************************************************************************/
-void gk_writealphacarbons(pdbf *p, char *fname) {
- int i;
- FILE *FPIN;
- FPIN = gk_fopen(fname,"w",fname);
- for(i=0; i<p->ncas; i++) {
- fprintf(FPIN,"%-6s%5d %4s%1c%3s %1c%4d%1c %8.3lf%8.3lf%8.3lf%6.2f%6.2f\n",
- "ATOM ",p->cas[i]->serial,p->cas[i]->name,p->cas[i]->altLoc,p->cas[i]->resname,p->cas[i]->chainid,p->cas[i]->rserial,p->cas[i]->icode,p->cas[i]->x,p->cas[i]->y,p->cas[i]->z,p->cas[i]->opcy,p->cas[i]->tmpt);
- }
- fclose(FPIN);
-}
-
-/************************************************************************/
-/*! \brief Decodes the corruption bitswitch and prints any problems
-
-Due to the totally unreliable nature of the pdb format, reading a pdb
-file stores a corruption bitswitch, and this function decodes that switch
-and prints the result on stdout.
-
-\param p is the pdb structure to write out.
-\param fname is the file name to be written.
-*/
-/************************************************************************/
-void gk_showcorruption(pdbf *p) {
- int corruption = p->corruption;
- if(corruption&CRP_ALTLOCS)
- printf("Multiple coordinate sets for at least one atom\n");
- if(corruption&CRP_MISSINGCA)
- printf("Missing coordiantes for at least one CA atom\n");
- if(corruption&CRP_MISSINGBB)
- printf("Missing coordiantes for at least one backbone atom (N,CA,C,O)\n");
- if(corruption&CRP_MULTICHAIN)
- printf("File contains coordinates for multiple chains\n");
- if(corruption&CRP_MULTICA)
- printf("Multiple CA atoms found for the same residue (could be alternate locators)\n");
- if(corruption&CRP_MULTICA)
- printf("Multiple copies of backbone atoms found for the same residue (could be alternate locators)\n");
-}
- /* sscanf(line, "%6s%5d%*1c%4s%1c%3s%*1c%1c%4d%1c%*3c%8lf%8lf%8lf%6lf%6lf%*6c%4s%2s%2s\n",
- linetype,&aserial,aname,&altLoc,rname,&chainid,&rserial,&icode,&x,&y,&z,&opcy,&tmpt,segId,element,charge);
- printf(".%s.%s.%s.\n",segId,element,charge);
- printf("%-6s%5d%-1s%-4s%1c%3s%1s%1c%4d%1c%3s%8.3lf%8.3lf%8.3lf%6.2f%6.2f%6s%4s%2s%2s\n",
- linetype,aserial," ",aname,altLoc,rname," ",chainid,rserial,icode," ",x,y,z,opcy,tmpt," ",segId,element,charge); */
-
- /* and we could probably get away with this using astral files, */
- /* sscanf(line, "%6s%5d%*1c%4s%1c%3s%*1c%1c%4d%1c%*3c%8lf%8lf%8lf%6lf%6lf%*6c%6s\n",
- linetype,&aserial,aname,&altLoc,rname,&chainid,&rserial,&icode,&x,&y,&z,&opcy,&tmpt,element);
- printf("%-6s%5d%-1s%-4s%1c%3s%1s%1c%4d%1c%3s%8.3lf%8.3lf%8.3lf%6.2f%6.2f%6s%6s\n",
- linetype,aserial," ",aname,altLoc,rname," ",chainid,rserial,icode," ",x,y,z,opcy,tmpt," ",element); */
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/pqueue.c b/3rdParty/metis/metis-5.1.0/GKlib/pqueue.c
deleted file mode 100644
index 2fb8515d2..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/pqueue.c
+++ /dev/null
@@ -1,25 +0,0 @@
-/*!
-\file pqueue.c
-\brief This file implements various max-priority queues.
-
-The priority queues are generated using the GK_MKPQUEUE macro.
-
-\date Started 3/27/2007
-\author George
-\version\verbatim $Id: pqueue.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-/*************************************************************************/
-/*! Create the various max priority queues */
-/*************************************************************************/
-#define key_gt(a, b) ((a) > (b))
-GK_MKPQUEUE(gk_ipq, gk_ipq_t, gk_ikv_t, int, gk_idx_t, gk_ikvmalloc, INT_MAX, key_gt)
-GK_MKPQUEUE(gk_i32pq, gk_i32pq_t, gk_i32kv_t, int32_t, gk_idx_t, gk_i32kvmalloc, INT32_MAX, key_gt)
-GK_MKPQUEUE(gk_i64pq, gk_i64pq_t, gk_i64kv_t, int64_t, gk_idx_t, gk_i64kvmalloc, INT64_MAX, key_gt)
-GK_MKPQUEUE(gk_fpq, gk_fpq_t, gk_fkv_t, float, gk_idx_t, gk_fkvmalloc, FLT_MAX, key_gt)
-GK_MKPQUEUE(gk_dpq, gk_dpq_t, gk_dkv_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX, key_gt)
-GK_MKPQUEUE(gk_idxpq, gk_idxpq_t, gk_idxkv_t, gk_idx_t, gk_idx_t, gk_idxkvmalloc, GK_IDX_MAX, key_gt)
-#undef key_gt
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/random.c b/3rdParty/metis/metis-5.1.0/GKlib/random.c
deleted file mode 100644
index d18e7188b..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/random.c
+++ /dev/null
@@ -1,134 +0,0 @@
-/*!
-\file
-\brief Various routines for providing portable 32 and 64 bit random number
- generators.
-
-\date Started 5/17/2007
-\author George
-\version\verbatim $Id: random.c 11793 2012-04-04 21:03:02Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-/*************************************************************************/
-/*! Create the various random number functions */
-/*************************************************************************/
-GK_MKRANDOM(gk_c, size_t, char)
-GK_MKRANDOM(gk_i, size_t, int)
-GK_MKRANDOM(gk_f, size_t, float)
-GK_MKRANDOM(gk_d, size_t, double)
-GK_MKRANDOM(gk_idx, size_t, gk_idx_t)
-GK_MKRANDOM(gk_z, size_t, ssize_t)
-
-
-
-/*************************************************************************/
-/*! GKlib's built in random number generator for portability across
- different architectures */
-/*************************************************************************/
-#ifdef USE_GKRAND
-/*
- A C-program for MT19937-64 (2004/9/29 version).
- Coded by Takuji Nishimura and Makoto Matsumoto.
-
- This is a 64-bit version of Mersenne Twister pseudorandom number
- generator.
-
- Before using, initialize the state by using init_genrand64(seed)
- or init_by_array64(init_key, key_length).
-
- Copyright (C) 2004, Makoto Matsumoto and Takuji Nishimura,
- All rights reserved.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#define NN 312
-#define MM 156
-#define MATRIX_A 0xB5026F5AA96619E9ULL
-#define UM 0xFFFFFFFF80000000ULL /* Most significant 33 bits */
-#define LM 0x7FFFFFFFULL /* Least significant 31 bits */
-
-
-/* The array for the state vector */
-static uint64_t mt[NN];
-/* mti==NN+1 means mt[NN] is not initialized */
-static int mti=NN+1;
-#endif /* USE_GKRAND */
-
-/* initializes mt[NN] with a seed */
-void gk_randinit(uint64_t seed)
-{
-#ifdef USE_GKRAND
- mt[0] = seed;
- for (mti=1; mti<NN; mti++)
- mt[mti] = (6364136223846793005ULL * (mt[mti-1] ^ (mt[mti-1] >> 62)) + mti);
-#else
- srand((unsigned int) seed);
-#endif
-}
-
-
-/* generates a random number on [0, 2^64-1]-interval */
-uint64_t gk_randint64(void)
-{
-#ifdef USE_GKRAND
- int i;
- unsigned long long x;
- static uint64_t mag01[2]={0ULL, MATRIX_A};
-
- if (mti >= NN) { /* generate NN words at one time */
- /* if init_genrand64() has not been called, */
- /* a default initial seed is used */
- if (mti == NN+1)
- gk_randinit(5489ULL);
-
- for (i=0; i<NN-MM; i++) {
- x = (mt[i]&UM)|(mt[i+1]&LM);
- mt[i] = mt[i+MM] ^ (x>>1) ^ mag01[(int)(x&1ULL)];
- }
- for (; i<NN-1; i++) {
- x = (mt[i]&UM)|(mt[i+1]&LM);
- mt[i] = mt[i+(MM-NN)] ^ (x>>1) ^ mag01[(int)(x&1ULL)];
- }
- x = (mt[NN-1]&UM)|(mt[0]&LM);
- mt[NN-1] = mt[MM-1] ^ (x>>1) ^ mag01[(int)(x&1ULL)];
-
- mti = 0;
- }
-
- x = mt[mti++];
-
- x ^= (x >> 29) & 0x5555555555555555ULL;
- x ^= (x << 17) & 0x71D67FFFEDA60000ULL;
- x ^= (x << 37) & 0xFFF7EEE000000000ULL;
- x ^= (x >> 43);
-
- return x & 0x7FFFFFFFFFFFFFFF;
-#else
- return (uint64_t)(((uint64_t) rand()) << 32 | ((uint64_t) rand()));
-#endif
-}
-
-/* generates a random number on [0, 2^32-1]-interval */
-uint32_t gk_randint32(void)
-{
-#ifdef USE_GKRAND
- return (uint32_t)(gk_randint64() & 0x7FFFFFFF);
-#else
- return (uint32_t)rand();
-#endif
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/rw.c b/3rdParty/metis/metis-5.1.0/GKlib/rw.c
deleted file mode 100644
index 7cd4391a0..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/rw.c
+++ /dev/null
@@ -1,103 +0,0 @@
-/*!
- * \file
- *
- * \brief Various routines that perform random-walk based operations
- on graphs stored as gk_csr_t matrices.
- *
- * \author George Karypis
- * \version\verbatim $Id: rw.c 11078 2011-11-12 00:20:44Z karypis $ \endverbatim
- */
-
-#include <GKlib.h>
-
-
-/*************************************************************************/
-/*! Computes the (personalized) page-rank of the vertices in a graph.
-
- \param mat is the matrix storing the graph.
- \param lamda is the restart probability.
- \param eps is the error tolerance for convergance.
- \param max_niter is the maximum number of allowed iterations.
- \param pr on entry stores the restart distribution of the vertices.
- This allows for the computation of personalized page-rank scores
- by appropriately setting that parameter.
- On return, pr stores the computed page ranks.
-
- \returns the number of iterations that were performed.
-*/
-/**************************************************************************/
-int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr)
-{
- ssize_t i, j, k, iter, nrows;
- double *rscale, *prold, *prnew, *prtmp;
- double fromsinks, error;
- ssize_t *rowptr;
- int *rowind;
- float *rowval;
-
- nrows = mat->nrows;
- rowptr = mat->rowptr;
- rowind = mat->rowind;
- rowval = mat->rowval;
-
- prold = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prnew");
- prnew = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prold");
- rscale = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: rscale");
-
- /* compute the scaling factors to get adjacency weights into transition
- probabilities */
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- rscale[i] += rowval[j];
- if (rscale[i] > 0)
- rscale[i] = 1.0/rscale[i];
- }
-
- /* the restart distribution is the initial pr scores */
- for (i=0; i<nrows; i++)
- prnew[i] = pr[i];
-
- /* get into the PR iteration */
- for (iter=0; iter<max_niter; iter++) {
- gk_SWAP(prnew, prold, prtmp);
- gk_dset(nrows, 0.0, prnew);
-
- /* determine the total current PR score of the sinks so that you
- can distribute them to all nodes according to the restart
- distribution. */
- for (fromsinks=0.0, i=0; i<nrows; i++) {
- if (rscale[i] == 0)
- fromsinks += prold[i];
- }
-
- /* push random-walk scores to the outlinks */
- for (i=0; i<nrows; i++) {
- for (j=rowptr[i]; j<rowptr[i+1]; j++)
- prnew[rowind[j]] += prold[i]*rscale[i]*rowval[j];
- }
-
- /* apply the restart conditions */
- for (i=0; i<nrows; i++) {
- prnew[i] = lamda*(fromsinks*pr[i]+prnew[i]) + (1.0-lamda)*pr[i];
- }
-
- /* compute the error */
- for (error=0.0, i=0; i<nrows; i++)
- error = (fabs(prnew[i]-prold[i]) > error ? fabs(prnew[i]-prold[i]) : error);
-
- //printf("nrm1: %le maxfabserr: %le\n", gk_dsum(nrows, prnew, 1), error);
-
- if (error < eps)
- break;
- }
-
- /* store the computed pr scores into pr for output */
- for (i=0; i<nrows; i++)
- pr[i] = prnew[i];
-
- gk_free((void **)&prnew, &prold, &rscale, LTERM);
-
- return (int)(iter+1);
-
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/seq.c b/3rdParty/metis/metis-5.1.0/GKlib/seq.c
deleted file mode 100644
index f267a3ea0..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/seq.c
+++ /dev/null
@@ -1,174 +0,0 @@
-/*
- *
- * Sequence handler library by Huzefa Rangwala
- * Date : 03.01.2007
- *
- *
- *
- */
-
-
-#include <GKlib.h>
-
-
-
-
-/*********************************************************/
-/* ! \brief Initializes the <tt>gk_seq_t</tt> variable
-
-
-
-
-\param A pointer to gk_seq_t itself
-\returns null
-*/
-/***********************************************************************/
-
-void gk_seq_init(gk_seq_t *seq)
-{
-
- seq->len = 0;
- seq->sequence = NULL;
-
- seq->pssm = NULL;
- seq->psfm = NULL;
-
- seq->name = NULL;
-
-}
-
-/***********************************************************************/
-/*! \brief This function creates the localizations for the various sequences
-
-\param string i.e amino acids, nucleotides, sequences
-\returns gk_i2cc2i_t variable
-*/
-/*********************************************************************/
-
-gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet)
-{
-
-
- int nsymbols;
- gk_idx_t i;
- gk_i2cc2i_t *t;
-
- nsymbols = strlen(alphabet);
- t = gk_malloc(sizeof(gk_i2cc2i_t),"gk_i2c_create_common");
- t->n = nsymbols;
- t->i2c = gk_cmalloc(256, "gk_i2c_create_common");
- t->c2i = gk_imalloc(256, "gk_i2c_create_common");
-
-
- gk_cset(256, -1, t->i2c);
- gk_iset(256, -1, t->c2i);
-
- for(i=0;i<nsymbols;i++){
- t->i2c[i] = alphabet[i];
- t->c2i[(int)alphabet[i]] = i;
- }
-
- return t;
-
-}
-
-
-/*********************************************************************/
-/*! \brief This function reads a pssm in the format of gkmod pssm
-
-\param file_name is the name of the pssm file
-\returns gk_seq_t
-*/
-/********************************************************************/
-gk_seq_t *gk_seq_ReadGKMODPSSM(char *filename)
-{
- gk_seq_t *seq;
- gk_idx_t i, j, ii;
- size_t ntokens, nbytes, len;
- FILE *fpin;
-
-
- gk_Tokens_t tokens;
- static char *AAORDER = "ARNDCQEGHILKMFPSTWYVBZX*";
- static int PSSMWIDTH = 20;
- char *header, line[MAXLINELEN];
- gk_i2cc2i_t *converter;
-
- header = gk_cmalloc(PSSMWIDTH, "gk_seq_ReadGKMODPSSM: header");
-
- converter = gk_i2cc2i_create_common(AAORDER);
-
- gk_getfilestats(filename, &len, &ntokens, NULL, &nbytes);
- len --;
-
- seq = gk_malloc(sizeof(gk_seq_t),"gk_seq_ReadGKMODPSSM");
- gk_seq_init(seq);
-
- seq->len = len;
- seq->sequence = gk_imalloc(len, "gk_seq_ReadGKMODPSSM");
- seq->pssm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM");
- seq->psfm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM");
-
- seq->nsymbols = PSSMWIDTH;
- seq->name = gk_getbasename(filename);
-
- fpin = gk_fopen(filename,"r","gk_seq_ReadGKMODPSSM");
-
-
- /* Read the header line */
- if (fgets(line, MAXLINELEN-1, fpin) == NULL)
- errexit("Unexpected end of file: %s\n", filename);
- gk_strtoupper(line);
- gk_strtokenize(line, " \t\n", &tokens);
-
- for (i=0; i<PSSMWIDTH; i++)
- header[i] = tokens.list[i][0];
-
- gk_freetokenslist(&tokens);
-
-
- /* Read the rest of the lines */
- for (i=0, ii=0; ii<len; ii++) {
- if (fgets(line, MAXLINELEN-1, fpin) == NULL)
- errexit("Unexpected end of file: %s\n", filename);
- gk_strtoupper(line);
- gk_strtokenize(line, " \t\n", &tokens);
-
- seq->sequence[i] = converter->c2i[(int)tokens.list[1][0]];
-
- for (j=0; j<PSSMWIDTH; j++) {
- seq->pssm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+j]);
- seq->psfm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+PSSMWIDTH+j]);
- }
-
-
-
- gk_freetokenslist(&tokens);
- i++;
- }
-
- seq->len = i; /* Reset the length if certain characters were skipped */
-
- gk_free((void **)&header, LTERM);
- gk_fclose(fpin);
-
- return seq;
-}
-
-
-/**************************************************************************/
-/*! \brief This function frees the memory allocated to the seq structure.
-
-\param gk_seq_t
-\returns nothing
-*/
-/**************************************************************************/
-void gk_seq_free(gk_seq_t *seq)
-{
- gk_iFreeMatrix(&seq->pssm, seq->len, seq->nsymbols);
- gk_iFreeMatrix(&seq->psfm, seq->len, seq->nsymbols);
- gk_free((void **)&seq->name, &seq->sequence, LTERM);
- //gk_free((void **)&seq, LTERM);
- gk_free((void **) &seq, LTERM);
-
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/sort.c b/3rdParty/metis/metis-5.1.0/GKlib/sort.c
deleted file mode 100644
index bde30f5a5..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/sort.c
+++ /dev/null
@@ -1,327 +0,0 @@
-/*!
-\file sort.c
-\brief This file contains GKlib's various sorting routines
-
-These routines are implemented using the GKSORT macro that is defined
-in gk_qsort.h and is based on GNU's GLIBC qsort() implementation.
-
-Additional sorting routines can be created using the same way that
-these routines where defined.
-
-\date Started 4/4/07
-\author George
-\version\verbatim $Id: sort.c 10796 2011-09-23 21:33:09Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-
-/*************************************************************************/
-/*! Sorts an array of chars in increasing order */
-/*************************************************************************/
-void gk_csorti(size_t n, char *base)
-{
-#define char_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(char, base, n, char_lt);
-#undef char_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of chars in decreasing order */
-/*************************************************************************/
-void gk_csortd(size_t n, char *base)
-{
-#define char_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(char, base, n, char_gt);
-#undef char_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of integers in increasing order */
-/*************************************************************************/
-void gk_isorti(size_t n, int *base)
-{
-#define int_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(int, base, n, int_lt);
-#undef int_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of integers in decreasing order */
-/*************************************************************************/
-void gk_isortd(size_t n, int *base)
-{
-#define int_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(int, base, n, int_gt);
-#undef int_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of floats in increasing order */
-/*************************************************************************/
-void gk_fsorti(size_t n, float *base)
-{
-#define float_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(float, base, n, float_lt);
-#undef float_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of floats in decreasing order */
-/*************************************************************************/
-void gk_fsortd(size_t n, float *base)
-{
-#define float_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(float, base, n, float_gt);
-#undef float_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of doubles in increasing order */
-/*************************************************************************/
-void gk_dsorti(size_t n, double *base)
-{
-#define double_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(double, base, n, double_lt);
-#undef double_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of doubles in decreasing order */
-/*************************************************************************/
-void gk_dsortd(size_t n, double *base)
-{
-#define double_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(double, base, n, double_gt);
-#undef double_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_idx_t in increasing order */
-/*************************************************************************/
-void gk_idxsorti(size_t n, gk_idx_t *base)
-{
-#define idx_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(gk_idx_t, base, n, idx_lt);
-#undef idx_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_idx_t in decreasing order */
-/*************************************************************************/
-void gk_idxsortd(size_t n, gk_idx_t *base)
-{
-#define idx_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(gk_idx_t, base, n, idx_gt);
-#undef idx_gt
-}
-
-
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_ckv_t in increasing order */
-/*************************************************************************/
-void gk_ckvsorti(size_t n, gk_ckv_t *base)
-{
-#define ckey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_ckv_t, base, n, ckey_lt);
-#undef ckey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_ckv_t in decreasing order */
-/*************************************************************************/
-void gk_ckvsortd(size_t n, gk_ckv_t *base)
-{
-#define ckey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_ckv_t, base, n, ckey_gt);
-#undef ckey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_ikv_t in increasing order */
-/*************************************************************************/
-void gk_ikvsorti(size_t n, gk_ikv_t *base)
-{
-#define ikey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_ikv_t, base, n, ikey_lt);
-#undef ikey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_ikv_t in decreasing order */
-/*************************************************************************/
-void gk_ikvsortd(size_t n, gk_ikv_t *base)
-{
-#define ikey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_ikv_t, base, n, ikey_gt);
-#undef ikey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_i32kv_t in increasing order */
-/*************************************************************************/
-void gk_i32kvsorti(size_t n, gk_i32kv_t *base)
-{
-#define ikey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_i32kv_t, base, n, ikey_lt);
-#undef ikey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_i32kv_t in decreasing order */
-/*************************************************************************/
-void gk_i32kvsortd(size_t n, gk_i32kv_t *base)
-{
-#define ikey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_i32kv_t, base, n, ikey_gt);
-#undef ikey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_i64kv_t in increasing order */
-/*************************************************************************/
-void gk_i64kvsorti(size_t n, gk_i64kv_t *base)
-{
-#define ikey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_i64kv_t, base, n, ikey_lt);
-#undef ikey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_i64kv_t in decreasing order */
-/*************************************************************************/
-void gk_i64kvsortd(size_t n, gk_i64kv_t *base)
-{
-#define ikey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_i64kv_t, base, n, ikey_gt);
-#undef ikey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_zkv_t in increasing order */
-/*************************************************************************/
-void gk_zkvsorti(size_t n, gk_zkv_t *base)
-{
-#define zkey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_zkv_t, base, n, zkey_lt);
-#undef zkey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_zkv_t in decreasing order */
-/*************************************************************************/
-void gk_zkvsortd(size_t n, gk_zkv_t *base)
-{
-#define zkey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_zkv_t, base, n, zkey_gt);
-#undef zkey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_fkv_t in increasing order */
-/*************************************************************************/
-void gk_fkvsorti(size_t n, gk_fkv_t *base)
-{
-#define fkey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_fkv_t, base, n, fkey_lt);
-#undef fkey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_fkv_t in decreasing order */
-/*************************************************************************/
-void gk_fkvsortd(size_t n, gk_fkv_t *base)
-{
-#define fkey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_fkv_t, base, n, fkey_gt);
-#undef fkey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_dkv_t in increasing order */
-/*************************************************************************/
-void gk_dkvsorti(size_t n, gk_dkv_t *base)
-{
-#define dkey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_dkv_t, base, n, dkey_lt);
-#undef dkey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_fkv_t in decreasing order */
-/*************************************************************************/
-void gk_dkvsortd(size_t n, gk_dkv_t *base)
-{
-#define dkey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_dkv_t, base, n, dkey_gt);
-#undef dkey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_skv_t in increasing order */
-/*************************************************************************/
-void gk_skvsorti(size_t n, gk_skv_t *base)
-{
-#define skey_lt(a, b) (strcmp((a)->key, (b)->key) < 0)
- GK_MKQSORT(gk_skv_t, base, n, skey_lt);
-#undef skey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_skv_t in decreasing order */
-/*************************************************************************/
-void gk_skvsortd(size_t n, gk_skv_t *base)
-{
-#define skey_gt(a, b) (strcmp((a)->key, (b)->key) > 0)
- GK_MKQSORT(gk_skv_t, base, n, skey_gt);
-#undef skey_gt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_idxkv_t in increasing order */
-/*************************************************************************/
-void gk_idxkvsorti(size_t n, gk_idxkv_t *base)
-{
-#define idxkey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(gk_idxkv_t, base, n, idxkey_lt);
-#undef idxkey_lt
-}
-
-
-/*************************************************************************/
-/*! Sorts an array of gk_idxkv_t in decreasing order */
-/*************************************************************************/
-void gk_idxkvsortd(size_t n, gk_idxkv_t *base)
-{
-#define idxkey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(gk_idxkv_t, base, n, idxkey_gt);
-#undef idxkey_gt
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/string.c b/3rdParty/metis/metis-5.1.0/GKlib/string.c
deleted file mode 100644
index 5d28452ba..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/string.c
+++ /dev/null
@@ -1,529 +0,0 @@
-/************************************************************************/
-/*! \file
-
-\brief Functions for manipulating strings.
-
-Various functions for manipulating strings. Some of these functions
-provide new functionality, whereas others are drop-in replacements
-of standard functions (but with enhanced functionality).
-
-\date Started 11/1/99
-\author George
-\version $Id: string.c 10711 2011-08-31 22:23:04Z karypis $
-*/
-/************************************************************************/
-
-#include <GKlib.h>
-
-
-
-/************************************************************************/
-/*! \brief Replaces certain characters in a string.
-
-This function takes a string and replaces all the characters in the
-\c fromlist with the corresponding characters from the \c tolist.
-That is, each occurence of <tt>fromlist[i]</tt> is replaced by
-<tt>tolist[i]</tt>.
-If the \c tolist is shorter than \c fromlist, then the corresponding
-characters are deleted. The modifications on \c str are done in place.
-It tries to provide a functionality similar to Perl's \b tr// function.
-
-\param str is the string whose characters will be replaced.
-\param fromlist is the set of characters to be replaced.
-\param tolist is the set of replacement characters .
-\returns A pointer to \c str itself.
-*/
-/************************************************************************/
-char *gk_strchr_replace(char *str, char *fromlist, char *tolist)
-{
- gk_idx_t i, j, k;
- size_t len, fromlen, tolen;
-
- len = strlen(str);
- fromlen = strlen(fromlist);
- tolen = strlen(tolist);
-
- for (i=j=0; i<len; i++) {
- for (k=0; k<fromlen; k++) {
- if (str[i] == fromlist[k]) {
- if (k < tolen)
- str[j++] = tolist[k];
- break;
- }
- }
- if (k == fromlen)
- str[j++] = str[i];
- }
- str[j] = '\0';
-
- return str;
-}
-
-
-
-/************************************************************************/
-/*! \brief Regex-based search-and-replace function
-
-This function is a C implementation of Perl's <tt> s//</tt> regular-expression
-based substitution function.
-
-\param str
- is the input string on which the operation will be performed.
-\param pattern
- is the regular expression for the pattern to be matched for substitution.
-\param replacement
- is the replacement string, in which the possible captured pattern substrings
- are referred to as $1, $2, ..., $9. The entire matched pattern is refered
- to as $0.
-\param options
- is a string specified options for the substitution operation. Currently the
- <tt>"i"</tt> (case insensitive) and <tt>"g"</tt> (global substitution) are
- supported.
-\param new_str
- is a reference to a pointer that will store a pointer to the newly created
- string that results from the substitutions. This string is allocated via
- gk_malloc() and needs to be freed using gk_free(). The string is returned
- even if no substitutions were performed.
-\returns
- If successful, it returns 1 + the number of substitutions that were performed.
- Thus, if no substitutions were performed, the returned value will be 1.
- Otherwise it returns 0. In case of error, a meaningful error message is
- returned in <tt>newstr</tt>, which also needs to be freed afterwards.
-*/
-/************************************************************************/
-int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options,
- char **new_str)
-{
- gk_idx_t i;
- int j, rc, flags, global, nmatches;
- size_t len, rlen, nlen, offset, noffset;
- regex_t re;
- regmatch_t matches[10];
-
-
- /* Parse the options */
- flags = REG_EXTENDED;
- if (strchr(options, 'i') != NULL)
- flags = flags | REG_ICASE;
- global = (strchr(options, 'g') != NULL ? 1 : 0);
-
-
- /* Compile the regex */
- if ((rc = regcomp(&re, pattern, flags)) != 0) {
- len = regerror(rc, &re, NULL, 0);
- *new_str = gk_cmalloc(len, "gk_strstr_replace: new_str");
- regerror(rc, &re, *new_str, len);
- return 0;
- }
-
- /* Prepare the output string */
- len = strlen(str);
- nlen = 2*len;
- noffset = 0;
- *new_str = gk_cmalloc(nlen+1, "gk_strstr_replace: new_str");
-
-
- /* Get into the matching-replacing loop */
- rlen = strlen(replacement);
- offset = 0;
- nmatches = 0;
- do {
- rc = regexec(&re, str+offset, 10, matches, 0);
-
- if (rc == REG_ESPACE) {
- gk_free((void **)new_str, LTERM);
- *new_str = gk_strdup("regexec ran out of memory.");
- regfree(&re);
- return 0;
- }
- else if (rc == REG_NOMATCH) {
- if (nlen-noffset < len-offset) {
- nlen += (len-offset) - (nlen-noffset);
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
- strcpy(*new_str+noffset, str+offset);
- noffset += (len-offset);
- break;
- }
- else { /* A match was found! */
- nmatches++;
-
- /* Copy the left unmatched portion of the string */
- if (matches[0].rm_so > 0) {
- if (nlen-noffset < matches[0].rm_so) {
- nlen += matches[0].rm_so - (nlen-noffset);
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
- strncpy(*new_str+noffset, str+offset, matches[0].rm_so);
- noffset += matches[0].rm_so;
- }
-
- /* Go and append the replacement string */
- for (i=0; i<rlen; i++) {
- switch (replacement[i]) {
- case '\\':
- if (i+1 < rlen) {
- if (nlen-noffset < 1) {
- nlen += nlen + 1;
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
- *new_str[noffset++] = replacement[++i];
- }
- else {
- gk_free((void **)new_str, LTERM);
- *new_str = gk_strdup("Error in replacement string. Missing character following '\'.");
- regfree(&re);
- return 0;
- }
- break;
-
- case '$':
- if (i+1 < rlen) {
- j = (int)(replacement[++i] - '0');
- if (j < 0 || j > 9) {
- gk_free((void **)new_str, LTERM);
- *new_str = gk_strdup("Error in captured subexpression specification.");
- regfree(&re);
- return 0;
- }
-
- if (nlen-noffset < matches[j].rm_eo-matches[j].rm_so) {
- nlen += nlen + (matches[j].rm_eo-matches[j].rm_so);
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
-
- strncpy(*new_str+noffset, str+offset+matches[j].rm_so, matches[j].rm_eo);
- noffset += matches[j].rm_eo-matches[j].rm_so;
- }
- else {
- gk_free((void **)new_str, LTERM);
- *new_str = gk_strdup("Error in replacement string. Missing subexpression number folloing '$'.");
- regfree(&re);
- return 0;
- }
- break;
-
- default:
- if (nlen-noffset < 1) {
- nlen += nlen + 1;
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
- (*new_str)[noffset++] = replacement[i];
- }
- }
-
- /* Update the offset of str for the next match */
- offset += matches[0].rm_eo;
-
- if (!global) {
- /* Copy the right portion of the string if no 'g' option */
- if (nlen-noffset < len-offset) {
- nlen += (len-offset) - (nlen-noffset);
- *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str");
- }
- strcpy(*new_str+noffset, str+offset);
- noffset += (len-offset);
- }
- }
- } while (global);
-
- (*new_str)[noffset] = '\0';
-
- regfree(&re);
- return nmatches + 1;
-
-}
-
-
-
-/************************************************************************/
-/*! \brief Prunes characters from the end of the string.
-
-This function removes any trailing characters that are included in the
-\c rmlist. The trimming stops at the last character (i.e., first character
-from the end) that is not in \c rmlist.
-This function can be used to removed trailing spaces, newlines, etc.
-This is a distructive operation as it modifies the string.
-
-\param str is the string that will be trimmed.
-\param rmlist contains the set of characters that will be removed.
-\returns A pointer to \c str itself.
-\sa gk_strhprune()
-*/
-/*************************************************************************/
-char *gk_strtprune(char *str, char *rmlist)
-{
- gk_idx_t i, j;
- size_t len;
-
- len = strlen(rmlist);
-
- for (i=strlen(str)-1; i>=0; i--) {
- for (j=0; j<len; j++) {
- if (str[i] == rmlist[j])
- break;
- }
- if (j == len)
- break;
- }
-
- str[i+1] = '\0';
-
- return str;
-}
-
-
-/************************************************************************/
-/*! \brief Prunes characters from the beginning of the string.
-
-This function removes any starting characters that are included in the
-\c rmlist. The trimming stops at the first character that is not in
-\c rmlist.
-This function can be used to removed leading spaces, tabs, etc.
-This is a distructive operation as it modifies the string.
-
-\param str is the string that will be trimmed.
-\param rmlist contains the set of characters that will be removed.
-\returns A pointer to \c str itself.
-\sa gk_strtprune()
-*/
-/*************************************************************************/
-char *gk_strhprune(char *str, char *rmlist)
-{
- gk_idx_t i, j;
- size_t len;
-
- len = strlen(rmlist);
-
- for (i=0; str[i]; i++) {
- for (j=0; j<len; j++) {
- if (str[i] == rmlist[j])
- break;
- }
- if (j == len)
- break;
- }
-
- if (i>0) { /* If something needs to be removed */
- for (j=0; str[i]; i++, j++)
- str[j] = str[i];
- str[j] = '\0';
- }
-
- return str;
-}
-
-
-/************************************************************************/
-/*! \brief Converts a string to upper case.
-
-This function converts a string to upper case. This operation modifies the
-string itself.
-
-\param str is the string whose case will be changed.
-\returns A pointer to \c str itself.
-\sa gk_strtolower()
-*/
-/*************************************************************************/
-char *gk_strtoupper(char *str)
-{
- int i;
-
- for (i=0; str[i]!='\0'; str[i]=toupper(str[i]), i++);
- return str;
-}
-
-
-/************************************************************************/
-/*! \brief Converts a string to lower case.
-
-This function converts a string to lower case. This operation modifies the
-string itself.
-
-\param str is the string whose case will be changed.
-\returns A pointer to \c str itself.
-\sa gk_strtoupper()
-*/
-/*************************************************************************/
-char *gk_strtolower(char *str)
-{
- int i;
-
- for (i=0; str[i]!='\0'; str[i]=tolower(str[i]), i++);
- return str;
-}
-
-
-/************************************************************************/
-/*! \brief Duplicates a string
-
-This function is a replacement for C's standard <em>strdup()</em> function.
-The key differences between the two are that gk_strdup():
- - uses the dynamic memory allocation routines of \e GKlib.
- - it correctly handles NULL input strings.
-
-The string that is returned must be freed by gk_free().
-
-\param orgstr is the string that will be duplicated.
-\returns A pointer to the newly created string.
-\sa gk_free()
-*/
-/*************************************************************************/
-char *gk_strdup(char *orgstr)
-{
- int len;
- char *str=NULL;
-
- if (orgstr != NULL) {
- len = strlen(orgstr)+1;
- str = gk_malloc(len*sizeof(char), "gk_strdup: str");
- strcpy(str, orgstr);
- }
-
- return str;
-}
-
-
-/************************************************************************/
-/*! \brief Case insensitive string comparison.
-
-This function compares two strings for equality by ignoring the case of the
-strings.
-
-\warning This function is \b not equivalent to a case-insensitive
- <em>strcmp()</em> function, as it does not return ordering
- information.
-
-\todo Remove the above warning.
-
-\param s1 is the first string to be compared.
-\param s2 is the second string to be compared.
-\retval 1 if the strings are identical,
-\retval 0 otherwise.
-*/
-/*************************************************************************/
-int gk_strcasecmp(char *s1, char *s2)
-{
- int i=0;
-
- if (strlen(s1) != strlen(s2))
- return 0;
-
- while (s1[i] != '\0') {
- if (tolower(s1[i]) != tolower(s2[i]))
- return 0;
- i++;
- }
-
- return 1;
-}
-
-
-/************************************************************************/
-/*! \brief Compare two strings in revere order
-
-This function is similar to strcmp but it performs the comparison as
-if the two strings were reversed.
-
-\param s1 is the first string to be compared.
-\param s2 is the second string to be compared.
-\retval -1, 0, 1, if the s1 < s2, s1 == s2, or s1 > s2.
-*/
-/*************************************************************************/
-int gk_strrcmp(char *s1, char *s2)
-{
- int i1 = strlen(s1)-1;
- int i2 = strlen(s2)-1;
-
- while ((i1 >= 0) && (i2 >= 0)) {
- if (s1[i1] != s2[i2])
- return (s1[i1] - s2[i2]);
- i1--;
- i2--;
- }
-
- /* i1 == -1 and/or i2 == -1 */
-
- if (i1 < i2)
- return -1;
- if (i1 > i2)
- return 1;
- return 0;
-}
-
-
-
-/************************************************************************/
-/*! \brief Converts a time_t time into a string
-
-This function takes a time_t-specified time and returns a string-formated
-representation of the corresponding time. The format of the string is
-<em>mm/dd/yyyy hh:mm:ss</em>, in which the hours are in military time.
-
-\param time is the time to be converted.
-\return It returns a pointer to a statically allocated string that is
- over-written in successive calls of this function. If the
- conversion failed, it returns NULL.
-
-*/
-/*************************************************************************/
-char *gk_time2str(time_t time)
-{
- static char datestr[128];
- struct tm *tm;
-
- tm = localtime(&time);
-
- if (strftime(datestr, 128, "%m/%d/%Y %H:%M:%S", tm) == 0)
- return NULL;
- else
- return datestr;
-}
-
-
-
-#if !defined(WIN32) && !defined(__MINGW32__)
-/************************************************************************/
-/*! \brief Converts a date/time string into its equivalent time_t value
-
-This function takes date and/or time specification and converts it in
-the equivalent time_t representation. The conversion is done using the
-strptime() function. The format that gk_str2time() understands is
-<em>mm/dd/yyyy hh:mm:ss</em>, in which the hours are in military time.
-
-\param str is the date/time string to be converted.
-\return If the conversion was successful it returns the time, otherwise
- it returns -1.
-*/
-/*************************************************************************/
-time_t gk_str2time(char *str)
-{
- struct tm time;
- time_t rtime;
-
- memset(&time, '\0', sizeof(time));
-
- if (strptime(str, "%m/%d/%Y %H:%M:%S", &time) == NULL)
- return -1;
-
- rtime = mktime(&time);
- return (rtime < 0 ? 0 : rtime);
-}
-#endif
-
-
-/*************************************************************************
-* This function returns the ID of a particular string based on the
-* supplied StringMap array
-**************************************************************************/
-int gk_GetStringID(gk_StringMap_t *strmap, char *key)
-{
- int i;
-
- for (i=0; strmap[i].name; i++) {
- if (gk_strcasecmp(key, strmap[i].name))
- return strmap[i].id;
- }
-
- return -1;
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/CMakeLists.txt b/3rdParty/metis/metis-5.1.0/GKlib/test/CMakeLists.txt
deleted file mode 100644
index 372b0e2f4..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-# Where the header files reside
-#include_directories(../)
-
-# Build program.
-add_executable(strings strings.c)
-add_executable(gksort gksort.c)
-add_executable(fis fis.c)
-add_executable(rw rw.c)
-add_executable(gkgraph gkgraph.c)
-foreach(prog strings gksort fis rw gkgraph)
- target_link_libraries(${prog} GKlib)
-endforeach(prog)
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.in.old b/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.in.old
deleted file mode 100644
index cac4f523a..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.in.old
+++ /dev/null
@@ -1,258 +0,0 @@
-#*************************************************************************
-# Global flags
-#*************************************************************************
-gdb = yes
-debug = no
-memdbg = no
-openmp = no
-x86compiler = gcc
-
-VERNUM = 0.1.0
-
-
-
-#*************************************************************************
-# System-specific compilation flags
-#*************************************************************************
-# Get some basic information about the system that you are working on
-cputype = $(shell uname -m | sed "s/\\ /_/g")
-systype = $(shell uname)
-ifeq ($(findstring CYGWIN, $(systype)),CYGWIN)
-# systype = CYGWIN
- systype = MSWIN
- cputype = x86
-endif
-
-
-GKLIBINCDIR = $(HOME)/work/algorithms/GKlib/trunk/
-GKLIBBUILDDIR = $(HOME)/work/algorithms/GKlib/builds/$(systype)-$(cputype)
-
-
-ifeq ($(systype),MSWIN)
- #-------------------------------------------------------------------
- # These defs are very much Visual Studio Specific
- #-------------------------------------------------------------------
- #Compiler information
- CC = cl
- OPTFLAGS = /Ox
- COPTIONS = -DWIN32 -DMSC -D_CRT_SECURE_NO_DEPRECATE
-
- #Compile input/output file specification
- SOURCEFILE = /c $<
- OUTPUTFILE = /Fo$@
-
- #Output specification for executables
- EXEOUTPUTFILE = /Fe$@ # This option is when cl is used for linking
- #EXEOUTPUTFILE = /OUT:$@ # This option is used when link is used for linking
-
- #Linker information
- LDOPTIONS = /MT
- #LD = /cygdrive/c/Program\ Files/Microsoft\ Visual\ Studio\ 8/VC/BIN/link
- LD = cl
- MERGEMANIFEST =
-
- #Library creation information
- AR = lib /OUT:$@
- RANLIB =
-
- ifeq ($(openmp),yes)
- COPTIONS += -D__OPENMP__ /openmp
- LDOPTIONS += /openmp
- MERGEMANIFEST = vc_mt -manifest $@.manifest -outputresource:$@\;1
- endif
-
- #Library information
- ifeq ($(cputype),i386)
- LIBPLOTDIR = ../Libplot/Win32
- else
- LIBPLOTDIR = ../Libplot/Win64
- endif
- LIBS = $(LIBPLOTDIR)/libplot.lib $(BUILDDIR)/libcluto.lib $(GKLIBBUILDDIR)/libGKlib.lib
-
- # Standard file extensions
- OBJEXT = .obj
- LIBEXT = .lib
- EXEEXT = .exe
-else
- ifeq ($(systype),Linux)
- ifeq ($(x86compiler),gcc)
- #Compiler information
- CC = gcc
- OPTFLAGS = -O6
- COPTIONS = -DLINUX -D_FILE_OFFSET_BITS=64 -pedantic -std=c99 -pthread
-
- #Linker information
- LDOPTIONS =
- LD = gcc
-
- MERGEMANIFEST =
-
- #Library creation information
- AR = ar rv
- RANLIB = ar -ts
- else
- #Compiler information
- CC = icc
- OPTFLAGS = -O3
- COPTIONS = -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99
-
- #Linker information
- LDOPTIONS =
- LD = icc
-
- #Library creation information
- AR = ar rv
- RANLIB = ar -ts
-
- ifeq ($(openmp),yes)
- COPTIONS += -D__OPENMP__ -openmp -openmp-report2
- LDOPTIONS += -openmp
- endif
- endif
-
- #Library information
- ifeq ($(cputype),x86_64)
- LIBPLOTDIR = ../Libplot/Linux64
- else
- LIBPLOTDIR = ../Libplot/Linux32
- endif
- endif
-
-
- ifeq ($(systype),SunOS)
- #Compiler information
- CC = /opt/SUNWspro/bin/cc
- OPTFLAGS = -xO4
- COPTIONS =-DSUNOS
-
- #Linker information
- LDOPTIONS =
- LD = /opt/SUNWspro/bin/cc
-
-
- #Library creation information
- AR = ar rv
- RANLIB = ar -ts
-
- #Library information
- LIBPLOTDIR = ../Libplot/SunOS
- endif
-
-
- ifeq ($(systype),Darwin)
- #Compiler information
- CC = gcc
- OPTFLAGS = -O6
- COPTIONS = -DDARWIN -D_FILE_OFFSET_BITS=64 -pedantic -std=c99
-
- #Linker information
- LDOPTIONS = -fvisibility=default
- LD = gcc
-
- #Library creation information
- AR = ar rv
- RANLIB = ar -ts
-
- #Library information
- ifeq ($(cputype),i386)
- LIBPLOTDIR = ../Libplot/Darwini386
- else
- LIBPLOTDIR = ../Libplot/DarwinPPC
- endif
- endif
-
- ifeq ($(systype),CYGWIN)
- #Compiler information
- CC = gcc
- OPTFLAGS = -O6
- COPTIONS = -DCYGWIN -DWIN32 -D_FILE_OFFSET_BITS=64 -Wall -std=c99 -pedantic -mno-cygwin
-
- #Linker information
- LDOPTIONS = -mno-cygwin
- LD = gcc
-
- #Library creation information
- AR = ar crv
- RANLIB = ar -ts
-
- #Library information
- LIBPLOTDIR = ../Libplot/CYGWIN
- endif
-
-
- #-------------------------------------------------------------------
- # These defs are common among the GNU/GCC based systems
- #-------------------------------------------------------------------
- #Compile input/output file specification
- SOURCEFILE = -c $<
- OUTPUTFILE = -o $@
-
- #Output specification for executables
- EXEOUTPUTFILE = -o $@
-
- #Library creation information
- AR = ar crv $@
- RANLIB = ar -ts $@
-
- #Libraries needed for linking
- LIBSDIR = -L$(BUILDDIR) -L$(GKLIBBUILDDIR) -L$(HOME)/local/lib
- LIBS = -lGKlib -lpcreposix -lpcre -lz -lm
-
- # Standard file extensions
- OBJEXT = .o
- LIBEXT = .a
- EXEEXT =
-endif
-
-
-#**************************************************************************
-DMALLOCINC =
-DMALLOCFLAGS =
-DEBUGFLAGS =
-
-ifeq ($(dmalloc),yes)
- DMALLOCINC = -I$(HOME)/local/include
- DMALLOCFLAGS = -DDMALLOC
- OPTFLAGS = -g
-endif
-
-ifeq ($(debug),yes)
- DEBUGFLAGS = -DDEBUG
- OPTFLAGS = -g
-endif
-
-ifeq ($(gdb),yes)
- OPTFLAGS += -g
-endif
-#**************************************************************************
-
-
-#**************************************************************************
-# Create the build directory if it does not exist
-#**************************************************************************
-ifeq ($(systype),Darwin)
- BINDIR = $(HOME)
-else
- BINDIR = $(HOME)/work/bin/$(systype)-$(cputype)
- $(shell mkdir -p $(BINDIR))
-endif
-
-ifeq ($(openmp),no)
- BUILDDIR = ./builds/$(systype)-$(cputype)
-else
- BUILDDIR = ./builds/$(systype)-$(cputype)-openmp
-endif
-
-LIBBUILDDIR = $(BUILDDIR)/lib
-PRGBUILDDIR = $(BUILDDIR)/prg
-$(shell mkdir -p $(BUILDDIR))
-$(shell mkdir -p $(LIBBUILDDIR))
-$(shell mkdir -p $(PRGBUILDDIR))
-
-
-
-
-INCLUDES = -I./ -I$(GKLIBINCDIR) -I$(LIBPLOTDIR) -I$(HOME)/local/include
-CFLAGS = $(COPTIONS) $(OPTFLAGS) $(DEBUGFLAGS) $(INCLUDES)
-
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.old b/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.old
deleted file mode 100644
index 1ca357eef..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/Makefile.old
+++ /dev/null
@@ -1,39 +0,0 @@
-include Makefile.in
-
-STRINGSOBJS = $(PRGBUILDDIR)/strings$(OBJEXT)
-GKSORTOBJS = $(PRGBUILDDIR)/gksort$(OBJEXT)
-FISOBJS = $(PRGBUILDDIR)/fis$(OBJEXT)
-
-HEADERS = $(wildcard $(GKLIBINCDIR)/*.h)
-
-
-default: $(BUILDDIR)/strings$(EXEEXT) $(BUILDDIR)/gksort$(EXEEXT) $(BUILDDIR)/fis$(EXEEXT)
-
-
-$(BUILDDIR)/strings$(EXEEXT): $(STRINGSOBJS) $(GKLIBBUILDDIR)/libGKlib.a
- $(LD) $(LDOPTIONS) $(EXEOUTPUTFILE) $(STRINGSOBJS) $(LIBSDIR) $(LIBS) ; $(MERGEMANIFEST)
- chmod 744 $@
-
-$(BUILDDIR)/gksort$(EXEEXT): $(GKSORTOBJS) $(GKLIBBUILDDIR)/libGKlib.a
- $(LD) $(LDOPTIONS) $(EXEOUTPUTFILE) $(GKSORTOBJS) $(LIBSDIR) $(LIBS) ; $(MERGEMANIFEST)
- chmod 744 $@
-
-$(BUILDDIR)/fis$(EXEEXT): $(FISOBJS) $(GKLIBBUILDDIR)/libGKlib.a
- $(LD) $(LDOPTIONS) $(EXEOUTPUTFILE) $(FISOBJS) $(LIBSDIR) $(LIBS) ; $(MERGEMANIFEST)
- chmod 744 $@
-
-
-clean:
- rm -rf $(PRGBUILDDIR)
-
-realclean:
- rm -rf $(PRGBUILDDIR) ;\
- rm -rf $(BUILDDIR) ;
-
-
-$(STRINGSOBJS) : $(HEADERS) Makefile.in Makefile $(GKLIBBUILDDIR)/libGKlib.a
-
-
-$(PRGBUILDDIR)/%$(OBJEXT) : %.c
- $(CC) $(CFLAGS) $(SOURCEFILE) $(OUTPUTFILE)
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/fis.c b/3rdParty/metis/metis-5.1.0/GKlib/test/fis.c
deleted file mode 100644
index 084a4b6a1..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/fis.c
+++ /dev/null
@@ -1,286 +0,0 @@
-/*!
-\file
-\brief A simple frequent itemset discovery program to test GKlib's routines
-
-\date 6/12/2008
-\author George
-\version \verbatim $Id: fis.c 11075 2011-11-11 22:31:52Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-/*************************************************************************/
-/*! Data structures for the code */
-/*************************************************************************/
-typedef struct {
- ssize_t minlen, maxlen;
- ssize_t minfreq, maxfreq;
- char *filename;
- int silent;
- ssize_t nitemsets;
- char *clabelfile;
- char **clabels;
-} params_t;
-
-/*************************************************************************/
-/*! Constants */
-/*************************************************************************/
-#define CMD_MINLEN 1
-#define CMD_MAXLEN 2
-#define CMD_MINFREQ 3
-#define CMD_MAXFREQ 4
-#define CMD_SILENT 5
-#define CMD_CLABELFILE 6
-#define CMD_HELP 10
-
-
-/*************************************************************************/
-/*! Local variables */
-/*************************************************************************/
-static struct gk_option long_options[] = {
- {"minlen", 1, 0, CMD_MINLEN},
- {"maxlen", 1, 0, CMD_MAXLEN},
- {"minfreq", 1, 0, CMD_MINFREQ},
- {"maxfreq", 1, 0, CMD_MAXFREQ},
- {"silent", 0, 0, CMD_SILENT},
- {"clabels", 1, 0, CMD_CLABELFILE},
- {"help", 0, 0, CMD_HELP},
- {0, 0, 0, 0}
-};
-
-
-/*-------------------------------------------------------------------*/
-/* Mini help */
-/*-------------------------------------------------------------------*/
-static char helpstr[][100] = {
-" ",
-"Usage: fis [options] <mat-file>",
-" ",
-" Required parameters",
-" mat-file",
-" The name of the file storing the transactions. The file is in ",
-" Cluto's .mat format.",
-" ",
-" Optional parameters",
-" -minlen=int",
-" Specifies the minimum length of the patterns. [default: 1]",
-" ",
-" -maxlen=int",
-" Specifies the maximum length of the patterns. [default: none]",
-" ",
-" -minfreq=int",
-" Specifies the minimum frequency of the patterns. [default: 10]",
-" ",
-" -maxfreq=int",
-" Specifies the maximum frequency of the patterns. [default: none]",
-" ",
-" -silent",
-" Does not print the discovered itemsets.",
-" ",
-" -clabels=filename",
-" Specifies the name of the file that stores the column labels.",
-" ",
-" -help",
-" Prints this message.",
-""
-};
-
-static char shorthelpstr[][100] = {
-" ",
-" Usage: fis [options] <mat-file>",
-" use 'fis -help' for a summary of the options.",
-""
-};
-
-
-
-/*************************************************************************/
-/*! Function prototypes */
-/*************************************************************************/
-void print_init_info(params_t *params, gk_csr_t *mat);
-void print_final_info(params_t *params);
-params_t *parse_cmdline(int argc, char *argv[]);
-void print_an_itemset(void *stateptr, int nitems, int *itemind,
- int ntrans, int *tranind);
-
-
-/*************************************************************************/
-/*! the entry point */
-/**************************************************************************/
-int main(int argc, char *argv[])
-{
- ssize_t i;
- char line[8192];
- FILE *fpin;
- params_t *params;
- gk_csr_t *mat;
-
- params = parse_cmdline(argc, argv);
- params->nitemsets = 0;
-
- /* read the data */
- mat = gk_csr_Read(params->filename, GK_CSR_FMT_CLUTO, 1, 1);
- gk_csr_CreateIndex(mat, GK_CSR_COL);
-
- /* read the column labels */
- params->clabels = (char **)gk_malloc(mat->ncols*sizeof(char *), "main: clabels");
- if (params->clabelfile == NULL) {
- for (i=0; i<mat->ncols; i++) {
- sprintf(line, "%zd", i);
- params->clabels[i] = gk_strdup(line);
- }
- }
- else {
- fpin = gk_fopen(params->clabelfile, "r", "main: fpin");
- for (i=0; i<mat->ncols; i++) {
- if (fgets(line, 8192, fpin) == NULL)
- errexit("Failed on fgets.\n");
- params->clabels[i] = gk_strdup(gk_strtprune(line, " \n\t"));
- }
- gk_fclose(fpin);
- }
-
-
- print_init_info(params, mat);
-
- gk_find_frequent_itemsets(mat->nrows, mat->rowptr, mat->rowind,
- params->minfreq, params->maxfreq, params->minlen, params->maxlen,
- &print_an_itemset, (void *)params);
-
- printf("Total itemsets found: %zd\n", params->nitemsets);
-
- print_final_info(params);
-}
-
-
-
-/*************************************************************************/
-/*! This function prints run parameters */
-/*************************************************************************/
-void print_init_info(params_t *params, gk_csr_t *mat)
-{
- printf("*******************************************************************************\n");
- printf(" fis\n\n");
- printf("Matrix Information ---------------------------------------------------------\n");
- printf(" input file=%s, [%d, %d, %zd]\n",
- params->filename, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]);
-
- printf("\n");
- printf("Options --------------------------------------------------------------------\n");
- printf(" minlen=%zd, maxlen=%zd, minfeq=%zd, maxfreq=%zd\n",
- params->minlen, params->maxlen, params->minfreq, params->maxfreq);
-
- printf("\n");
- printf("Finding patterns... -----------------------------------------------------\n");
-}
-
-
-/*************************************************************************/
-/*! This function prints final statistics */
-/*************************************************************************/
-void print_final_info(params_t *params)
-{
- printf("\n");
- printf("Memory Usage Information -----------------------------------------------------\n");
- printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed());
- printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed());
- printf("********************************************************************************\n");
-}
-
-
-/*************************************************************************/
-/*! This is the entry point of the command-line argument parser */
-/*************************************************************************/
-params_t *parse_cmdline(int argc, char *argv[])
-{
- int i;
- int c, option_index;
- params_t *params;
-
- params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params");
-
- /* initialize the params data structure */
- params->minlen = 1;
- params->maxlen = -1;
- params->minfreq = 10;
- params->maxfreq = -1;
- params->silent = 0;
- params->filename = NULL;
- params->clabelfile = NULL;
-
-
- /* Parse the command line arguments */
- while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) {
- switch (c) {
- case CMD_MINLEN:
- if (gk_optarg) params->minlen = atoi(gk_optarg);
- break;
- case CMD_MAXLEN:
- if (gk_optarg) params->maxlen = atoi(gk_optarg);
- break;
- case CMD_MINFREQ:
- if (gk_optarg) params->minfreq = atoi(gk_optarg);
- break;
- case CMD_MAXFREQ:
- if (gk_optarg) params->maxfreq = atoi(gk_optarg);
- break;
-
- case CMD_SILENT:
- params->silent = 1;
- break;
-
- case CMD_CLABELFILE:
- if (gk_optarg) params->clabelfile = gk_strdup(gk_optarg);
- break;
-
- case CMD_HELP:
- for (i=0; strlen(helpstr[i]) > 0; i++)
- printf("%s\n", helpstr[i]);
- exit(0);
- break;
- case '?':
- default:
- printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]);
- exit(0);
- }
- }
-
- if (argc-gk_optind != 1) {
- printf("Unrecognized parameters.");
- for (i=0; strlen(shorthelpstr[i]) > 0; i++)
- printf("%s\n", shorthelpstr[i]);
- exit(0);
- }
-
- params->filename = gk_strdup(argv[gk_optind++]);
-
- if (!gk_fexists(params->filename))
- errexit("input file %s does not exist.\n", params->filename);
-
- return params;
-}
-
-
-
-/*************************************************************************/
-/*! This is the callback function for the itemset discovery routine */
-/*************************************************************************/
-void print_an_itemset(void *stateptr, int nitems, int *itemids, int ntrans,
- int *transids)
-{
- ssize_t i;
- params_t *params;
-
- params = (params_t *)stateptr;
- params->nitemsets++;
-
- if (!params->silent) {
- printf("%4zd %4d %4d => ", params->nitemsets, nitems, ntrans);
- for (i=0; i<nitems; i++)
- printf(" %s", params->clabels[itemids[i]]);
- printf("\n");
- for (i=0; i<ntrans; i++)
- printf(" %d\n", transids[i]);
- printf("\n");
- }
-}
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/gkgraph.c b/3rdParty/metis/metis-5.1.0/GKlib/test/gkgraph.c
deleted file mode 100644
index 233620d9b..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/gkgraph.c
+++ /dev/null
@@ -1,351 +0,0 @@
-/*!
-\file
-\brief A simple frequent itemset discovery program to test GKlib's routines
-
-\date 6/12/2008
-\author George
-\version \verbatim $Id: gkgraph.c 11408 2012-01-25 15:05:58Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-/*************************************************************************/
-/*! Data structures for the code */
-/*************************************************************************/
-typedef struct {
- int type;
- int niter;
- float eps;
- float lamda;
-
- char *infile;
- char *outfile;
-} params_t;
-
-/*************************************************************************/
-/*! Constants */
-/*************************************************************************/
-#define CMD_NITER 1
-#define CMD_EPS 2
-#define CMD_LAMDA 3
-#define CMD_TYPE 4
-#define CMD_HELP 10
-
-
-/*************************************************************************/
-/*! Local variables */
-/*************************************************************************/
-static struct gk_option long_options[] = {
- {"type", 1, 0, CMD_TYPE},
- {"niter", 1, 0, CMD_NITER},
- {"lamda", 1, 0, CMD_LAMDA},
- {"eps", 1, 0, CMD_EPS},
- {"help", 0, 0, CMD_HELP},
- {0, 0, 0, 0}
-};
-
-
-/*-------------------------------------------------------------------*/
-/* Mini help */
-/*-------------------------------------------------------------------*/
-static char helpstr[][100] = {
-" ",
-"Usage: gkgraph [options] <graph-file> [<out-file>]",
-" ",
-" Required parameters",
-" graph-file",
-" The name of the file storing the graph. The file is in ",
-" Metis' graph format.",
-" ",
-" Optional parameters",
-" -niter=int",
-" Specifies the maximum number of iterations. [default: 100]",
-" ",
-" -lamda=float",
-" Specifies the follow-the-adjacent-links probability. [default: 0.80]",
-" ",
-" -eps=float",
-" Specifies the error tollerance. [default: 1e-10]",
-" ",
-" -help",
-" Prints this message.",
-""
-};
-
-static char shorthelpstr[][100] = {
-" ",
-" Usage: gkgraph [options] <graph-file> [<out-file>]",
-" use 'gkgraph -help' for a summary of the options.",
-""
-};
-
-
-
-/*************************************************************************/
-/*! Function prototypes */
-/*************************************************************************/
-double compute_compactness(params_t *params, gk_graph_t *graph, int32_t *perm);
-void reorder_centroid(params_t *params, gk_graph_t *graph, int32_t *perm);
-void print_init_info(params_t *params, gk_graph_t *graph);
-void print_final_info(params_t *params);
-params_t *parse_cmdline(int argc, char *argv[]);
-
-
-/*************************************************************************/
-/*! the entry point */
-/**************************************************************************/
-int main(int argc, char *argv[])
-{
- ssize_t i, j, v;
- params_t *params;
- gk_graph_t *graph, *pgraph;
- int32_t *perm;
-
- /* get command-line options */
- params = parse_cmdline(argc, argv);
-
- /* read the data */
- graph = gk_graph_Read(params->infile, GK_GRAPH_FMT_METIS, 0, 0, 0);
-
- /* display some basic stats */
- print_init_info(params, graph);
-
-
- /* determine the initial compactness of the graph */
- printf("Initial compactness: %le\n", compute_compactness(params, graph, NULL));
-
- /* compute the BFS ordering and re-order the graph */
- //for (i=0; i<params->niter; i++) {
- for (i=0; i<1; i++) {
- v = RandomInRange(graph->nvtxs);
- gk_graph_ComputeBFSOrdering(graph, v, &perm, NULL);
- printf("BFS from %8d. Compactness: %le\n",
- (int) v, compute_compactness(params, graph, perm));
-
- pgraph = gk_graph_Reorder(graph, perm, NULL);
- gk_graph_Write(pgraph, "bfs.metis", GK_GRAPH_FMT_METIS);
- gk_graph_Free(&pgraph);
-
- gk_graph_ComputeBestFOrdering(graph, v, params->type, &perm, NULL);
- printf("BestF from %8d. Compactness: %le\n",
- (int) v, compute_compactness(params, graph, perm));
-
- pgraph = gk_graph_Reorder(graph, perm, NULL);
- gk_graph_Write(pgraph, "bestf.metis", GK_GRAPH_FMT_METIS);
- gk_graph_Free(&pgraph);
-
-#ifdef XXX
- for (j=0; j<params->niter; j++) {
- reorder_centroid(params, graph, perm);
- printf("\tAfter centroid; Compactness: %le\n",
- compute_compactness(params, graph, perm));
- }
-
- pgraph = gk_graph_Reorder(graph, perm, NULL);
- gk_graph_Write(pgraph, "centroid.metis", GK_GRAPH_FMT_METIS);
- gk_graph_Free(&pgraph);
-#endif
- gk_free((void **)&perm, LTERM);
- }
-
- gk_graph_Free(&graph);
- //gk_graph_Free(&pgraph);
-
- print_final_info(params);
-}
-
-
-
-
-/*************************************************************************/
-/*! This function computes the compactness of the graph's adjacency list */
-/*************************************************************************/
-double compute_compactness(params_t *params, gk_graph_t *graph, int32_t *perm)
-{
- int i, v, u, nvtxs;
- ssize_t j, *xadj;
- int32_t *adjncy;
- double compactness=0.0;
- int *freq;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- freq = gk_ismalloc(nvtxs, 0, "compute_compactness: freq");
-
- for (i=0; i<nvtxs; i++) {
- v = (perm == NULL ? i : perm[i]);
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- u = (perm == NULL ? adjncy[j] : perm[adjncy[j]]);
- compactness += fabs(v-u);
- freq[gk_abs(v-u)]++;
- }
- }
-
- /*
- for (i=0; i<nvtxs; i++) {
- if (freq[i] > 0)
- printf("%7d %6d\n", i, freq[i]);
- }
- */
- printf("\tnsmall: %d\n", freq[1]+freq[2]+freq[3]);
-
- return compactness/xadj[nvtxs];
-}
-
-
-/*************************************************************************/
-/*! This function uses a centroid-based approach to refine the ordering */
-/*************************************************************************/
-void reorder_centroid(params_t *params, gk_graph_t *graph, int32_t *perm)
-{
- int i, v, u, nvtxs;
- ssize_t j, *xadj;
- int32_t *adjncy;
- gk_fkv_t *cand;
- double displacement;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- cand = gk_fkvmalloc(nvtxs, "reorder_centroid: cand");
-
- for (i=0; i<nvtxs; i++) {
- v = perm[i];
- displacement = 0.0;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- u = perm[adjncy[j]];
- displacement += u-v;
- //displacement += sign(u-v, sqrt(fabs(u-v)));
- }
-
- cand[i].val = i;
- cand[i].key = v + displacement*params->lamda/(xadj[i+1]-xadj[i]);
- }
-
- /* sort them based on the target position in increasing order */
- gk_fkvsorti(nvtxs, cand);
-
-
- /* derive the permutation from the ordered list */
- gk_i32set(nvtxs, -1, perm);
- for (i=0; i<nvtxs; i++) {
- if (perm[cand[i].val] != -1)
- errexit("Resetting perm[%d] = %d\n", cand[i].val, perm[cand[i].val]);
- perm[cand[i].val] = i;
- }
-
- gk_free((void **)&cand, LTERM);
-}
-
-
-
-
-
-
-
-
-/*************************************************************************/
-/*! This function prints run parameters */
-/*************************************************************************/
-void print_init_info(params_t *params, gk_graph_t *graph)
-{
- printf("*******************************************************************************\n");
- printf(" gkgraph\n\n");
- printf("Graph Information ----------------------------------------------------------\n");
- printf(" input file=%s, [%d, %zd]\n",
- params->infile, graph->nvtxs, graph->xadj[graph->nvtxs]);
-
- printf("\n");
- printf("Options --------------------------------------------------------------------\n");
- printf(" type=%d, niter=%d, lamda=%f, eps=%e\n",
- params->type, params->niter, params->lamda, params->eps);
-
- printf("\n");
- printf("Working... -----------------------------------------------------------------\n");
-}
-
-
-/*************************************************************************/
-/*! This function prints final statistics */
-/*************************************************************************/
-void print_final_info(params_t *params)
-{
- printf("\n");
- printf("Memory Usage Information -----------------------------------------------------\n");
- printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed());
- printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed());
- printf("********************************************************************************\n");
-}
-
-
-/*************************************************************************/
-/*! This is the entry point of the command-line argument parser */
-/*************************************************************************/
-params_t *parse_cmdline(int argc, char *argv[])
-{
- int i;
- int c, option_index;
- params_t *params;
-
- params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params");
-
- /* initialize the params data structure */
- params->type = 1;
- params->niter = 1;
- params->eps = 1e-10;
- params->lamda = 0.20;
- params->infile = NULL;
-
-
- /* Parse the command line arguments */
- while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) {
- switch (c) {
- case CMD_TYPE:
- if (gk_optarg) params->type = atoi(gk_optarg);
- break;
- case CMD_NITER:
- if (gk_optarg) params->niter = atoi(gk_optarg);
- break;
- case CMD_EPS:
- if (gk_optarg) params->eps = atof(gk_optarg);
- break;
- case CMD_LAMDA:
- if (gk_optarg) params->lamda = atof(gk_optarg);
- break;
-
- case CMD_HELP:
- for (i=0; strlen(helpstr[i]) > 0; i++)
- printf("%s\n", helpstr[i]);
- exit(0);
- break;
- case '?':
- default:
- printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]);
- exit(0);
- }
- }
-
- if (argc-gk_optind != 1) {
- printf("Unrecognized parameters.");
- for (i=0; strlen(shorthelpstr[i]) > 0; i++)
- printf("%s\n", shorthelpstr[i]);
- exit(0);
- }
-
- params->infile = gk_strdup(argv[gk_optind++]);
-
- if (argc-gk_optind > 0)
- params->outfile = gk_strdup(argv[gk_optind++]);
- else
- params->outfile = gk_strdup("gkgraph.out");
-
- if (!gk_fexists(params->infile))
- errexit("input file %s does not exist.\n", params->infile);
-
- return params;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/gksort.c b/3rdParty/metis/metis-5.1.0/GKlib/test/gksort.c
deleted file mode 100644
index 65438368f..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/gksort.c
+++ /dev/null
@@ -1,346 +0,0 @@
-/*!
-\file gksort.c
-\brief Testing module for the various sorting routines in GKlib
-
-\date Started 4/4/2007
-\author George
-\version\verbatim $Id: gksort.c 11058 2011-11-10 00:02:50Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-#define N 10000
-
-/*************************************************************************/
-/*! Testing module for gk_?isort() routine */
-/*************************************************************************/
-void test_isort()
-{
- gk_idx_t i;
- int array[N];
-
- /* test the increasing sort */
- printf("Testing iisort...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432);
-
- gk_isorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] > array[i+1])
- printf("gk_isorti error at index %jd [%d %d]\n", (intmax_t)i, array[i], array[i+1]);
- }
-
-
- /* test the decreasing sort */
- printf("Testing disort...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432);
-
- gk_isortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] < array[i+1])
- printf("gk_isortd error at index %jd [%d %d]\n", (intmax_t)i, array[i], array[i+1]);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Testing module for gk_?fsort() routine */
-/*************************************************************************/
-void test_fsort()
-{
- gk_idx_t i;
- float array[N];
-
- /* test the increasing sort */
- printf("Testing ifsort...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432)/(1.0+RandomInRange(645323));
-
- gk_fsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] > array[i+1])
- printf("gk_fsorti error at index %jd [%f %f]\n", (intmax_t)i, array[i], array[i+1]);
- }
-
-
- /* test the decreasing sort */
- printf("Testing dfsort...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432)/(1.0+RandomInRange(645323));
-
- gk_fsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] < array[i+1])
- printf("gk_fsortd error at index %jd [%f %f]\n", (intmax_t)i, array[i], array[i+1]);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Testing module for gk_?idxsort() routine */
-/*************************************************************************/
-void test_idxsort()
-{
- gk_idx_t i;
- gk_idx_t array[N];
-
- /* test the increasing sort */
- printf("Testing idxsorti...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432);
-
- gk_idxsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] > array[i+1])
- printf("gk_idxsorti error at index %zd [%zd %zd]\n", (ssize_t)i, (ssize_t)array[i], (ssize_t)array[i+1]);
- }
-
-
- /* test the decreasing sort */
- printf("Testing idxsortd...\n");
- for (i=0; i<N; i++)
- array[i] = RandomInRange(123432);
-
- gk_idxsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i] < array[i+1])
- printf("gk_idxsortd error at index %zd [%zd %zd]\n", (ssize_t)i, (ssize_t)array[i], (ssize_t)array[i+1]);
- }
-
-}
-
-
-
-/*************************************************************************/
-/*! Testing module for gk_?ikvsort() routine */
-/*************************************************************************/
-void test_ikvsort()
-{
- gk_idx_t i;
- gk_ikv_t array[N];
-
- /* test the increasing sort */
- printf("Testing ikvsorti...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432);
- array[i].val = i;
- }
-
- gk_ikvsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key > array[i+1].key)
- printf("gk_ikvsorti error at index %jd [%d %d] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-
- /* test the decreasing sort */
- printf("Testing ikvsortd...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432);
- array[i].val = i;
- }
-
- gk_ikvsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key < array[i+1].key)
- printf("gk_ikvsortd error at index %jd [%d %d] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-}
-
-
-
-/*************************************************************************/
-/*! Testing module for gk_?fkvsort() routine */
-/*************************************************************************/
-void test_fkvsort()
-{
- gk_idx_t i;
- gk_fkv_t array[N];
-
- /* test the increasing sort */
- printf("Testing fkvsorti...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323));
- array[i].val = i;
- }
-
- gk_fkvsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key > array[i+1].key)
- printf("gk_fkvsorti error at index %jd [%f %f] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-
- /* test the decreasing sort */
- printf("Testing fkvsortd...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323));
- array[i].val = i;
- }
-
- gk_fkvsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key < array[i+1].key)
- printf("gk_fkvsortd error at index %jd [%f %f] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Testing module for gk_?dkvsort() routine */
-/*************************************************************************/
-void test_dkvsort()
-{
- gk_idx_t i;
- gk_dkv_t array[N];
-
- /* test the increasing sort */
- printf("Testing dkvsorti...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323));
- array[i].val = i;
- }
-
- gk_dkvsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key > array[i+1].key)
- printf("gk_dkvsorti error at index %jd [%lf %lf] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-
- /* test the decreasing sort */
- printf("Testing dkvsortd...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323));
- array[i].val = i;
- }
-
- gk_dkvsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key < array[i+1].key)
- printf("gk_dkvsortd error at index %jd [%lf %lf] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Testing module for gk_?skvsort() routine */
-/*************************************************************************/
-void test_skvsort()
-{
- gk_idx_t i;
- gk_skv_t array[N];
- char line[256];
-
- /* test the increasing sort */
- printf("Testing skvsorti...\n");
- for (i=0; i<N; i++) {
- sprintf(line, "%d", RandomInRange(123432));
- array[i].key = gk_strdup(line);
- array[i].val = i;
- }
-
- gk_skvsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (strcmp(array[i].key, array[i+1].key) > 0)
- printf("gk_skvsorti error at index %jd [%s %s] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-
- /* test the decreasing sort */
- printf("Testing skvsortd...\n");
- for (i=0; i<N; i++) {
- sprintf(line, "%d", RandomInRange(123432));
- array[i].key = gk_strdup(line);
- array[i].val = i;
- }
-
- gk_skvsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- /*printf("%s\n", array[i].key);*/
- if (strcmp(array[i].key, array[i+1].key) < 0)
- printf("gk_skvsortd error at index %jd [%s %s] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val);
- }
-
-}
-
-
-/*************************************************************************/
-/*! Testing module for gk_?idxkvsort() routine */
-/*************************************************************************/
-void test_idxkvsort()
-{
- gk_idx_t i;
- gk_idxkv_t array[N];
-
- /* test the increasing sort */
- printf("Testing idxkvsorti...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432);
- array[i].val = i;
- }
-
- gk_idxkvsorti(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key > array[i+1].key)
- printf("gk_idxkvsorti error at index %zd [%zd %zd] [%zd %zd]\n",
- (ssize_t)i, (ssize_t)array[i].key, (ssize_t)array[i+1].key,
- (ssize_t)array[i].val, (ssize_t)array[i+1].val);
- }
-
-
- /* test the decreasing sort */
- printf("Testing idxkvsortd...\n");
- for (i=0; i<N; i++) {
- array[i].key = RandomInRange(123432);
- array[i].val = i;
- }
-
- gk_idxkvsortd(N, array);
-
- for (i=0; i<N-1; i++) {
- if (array[i].key < array[i+1].key)
- printf("gk_idxkvsortd error at index %zd [%zd %zd] [%zd %zd]\n",
- (ssize_t)i, (ssize_t)array[i].key, (ssize_t)array[i+1].key,
- (ssize_t)array[i].val, (ssize_t)array[i+1].val);
- }
-
-}
-
-
-
-
-int main()
-{
- test_isort();
- test_fsort();
- test_idxsort();
-
- test_ikvsort();
- test_fkvsort();
- test_dkvsort();
- test_skvsort();
- test_idxkvsort();
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/rw.c b/3rdParty/metis/metis-5.1.0/GKlib/test/rw.c
deleted file mode 100644
index e338f89dd..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/rw.c
+++ /dev/null
@@ -1,307 +0,0 @@
-/*!
-\file
-\brief A simple frequent itemset discovery program to test GKlib's routines
-
-\date 6/12/2008
-\author George
-\version \verbatim $Id: rw.c 11387 2012-01-21 23:36:23Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-/*************************************************************************/
-/*! Data structures for the code */
-/*************************************************************************/
-typedef struct {
- int niter;
- int ntvs;
- int ppr;
- float eps;
- float lamda;
- char *infile;
- char *outfile;
-} params_t;
-
-/*************************************************************************/
-/*! Constants */
-/*************************************************************************/
-#define CMD_NITER 1
-#define CMD_EPS 2
-#define CMD_LAMDA 3
-#define CMD_PPR 4
-#define CMD_NTVS 5
-#define CMD_HELP 10
-
-
-/*************************************************************************/
-/*! Local variables */
-/*************************************************************************/
-static struct gk_option long_options[] = {
- {"niter", 1, 0, CMD_NITER},
- {"lamda", 1, 0, CMD_LAMDA},
- {"eps", 1, 0, CMD_EPS},
- {"ppr", 1, 0, CMD_PPR},
- {"ntvs", 1, 0, CMD_NTVS},
- {"help", 0, 0, CMD_HELP},
- {0, 0, 0, 0}
-};
-
-
-/*-------------------------------------------------------------------*/
-/* Mini help */
-/*-------------------------------------------------------------------*/
-static char helpstr[][100] = {
-" ",
-"Usage: rw [options] <graph-file> <out-file>",
-" ",
-" Required parameters",
-" graph-file",
-" The name of the file storing the transactions. The file is in ",
-" Metis' graph format.",
-" ",
-" Optional parameters",
-" -niter=int",
-" Specifies the maximum number of iterations. [default: 100]",
-" ",
-" -lamda=float",
-" Specifies the follow-the-adjacent-links probability. [default: 0.80]",
-" ",
-" -eps=float",
-" Specifies the error tollerance. [default: 1e-10]",
-" ",
-" -ppr=int",
-" Specifies the source of the personalized PR. [default: -1]",
-" ",
-" -ntvs=int",
-" Specifies the number of test-vectors to compute. [default: -1]",
-" ",
-" -help",
-" Prints this message.",
-""
-};
-
-static char shorthelpstr[][100] = {
-" ",
-" Usage: rw [options] <graph-file> <out-file>",
-" use 'rw -help' for a summary of the options.",
-""
-};
-
-
-
-/*************************************************************************/
-/*! Function prototypes */
-/*************************************************************************/
-void print_init_info(params_t *params, gk_csr_t *mat);
-void print_final_info(params_t *params);
-params_t *parse_cmdline(int argc, char *argv[]);
-
-
-/*************************************************************************/
-/*! the entry point */
-/**************************************************************************/
-int main(int argc, char *argv[])
-{
- ssize_t i, j, niter;
- params_t *params;
- gk_csr_t *mat;
- FILE *fpout;
-
- /* get command-line options */
- params = parse_cmdline(argc, argv);
-
- /* read the data */
- mat = gk_csr_Read(params->infile, GK_CSR_FMT_METIS, 1, 1);
-
- /* display some basic stats */
- print_init_info(params, mat);
-
-
-
- if (params->ntvs != -1) {
- /* compute the pr for different randomly generated restart-distribution vectors */
- float **prs;
-
- prs = gk_fAllocMatrix(params->ntvs, mat->nrows, 0.0, "main: prs");
-
- /* generate the random restart vectors */
- for (j=0; j<params->ntvs; j++) {
- for (i=0; i<mat->nrows; i++)
- prs[j][i] = RandomInRange(931);
- gk_fscale(mat->nrows, 1.0/gk_fsum(mat->nrows, prs[j], 1), prs[j], 1);
-
- niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, prs[j]);
- printf("tvs#: %zd; niters: %zd\n", j, niter);
- }
-
- /* output the computed pr scores */
- fpout = gk_fopen(params->outfile, "w", "main: outfile");
- for (i=0; i<mat->nrows; i++) {
- for (j=0; j<params->ntvs; j++)
- fprintf(fpout, "%.4e ", prs[j][i]);
- fprintf(fpout, "\n");
- }
- gk_fclose(fpout);
-
- gk_fFreeMatrix(&prs, params->ntvs, mat->nrows);
- }
- else if (params->ppr != -1) {
- /* compute the personalized pr from the specified vertex */
- float *pr;
-
- pr = gk_fsmalloc(mat->nrows, 0.0, "main: pr");
-
- pr[params->ppr-1] = 1.0;
-
- niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr);
- printf("ppr: %d; niters: %zd\n", params->ppr, niter);
-
- /* output the computed pr scores */
- fpout = gk_fopen(params->outfile, "w", "main: outfile");
- for (i=0; i<mat->nrows; i++)
- fprintf(fpout, "%.4e\n", pr[i]);
- gk_fclose(fpout);
-
- gk_free((void **)&pr, LTERM);
- }
- else {
- /* compute the standard pr */
- int jmax;
- float diff, maxdiff;
- float *pr;
-
- pr = gk_fsmalloc(mat->nrows, 1.0/mat->nrows, "main: pr");
-
- niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr);
- printf("pr; niters: %zd\n", niter);
-
- /* output the computed pr scores */
- fpout = gk_fopen(params->outfile, "w", "main: outfile");
- for (i=0; i<mat->nrows; i++) {
- for (jmax=i, maxdiff=0.0, j=mat->rowptr[i]; j<mat->rowptr[i+1]; j++) {
- if ((diff = fabs(pr[i]-pr[mat->rowind[j]])) > maxdiff) {
- maxdiff = diff;
- jmax = mat->rowind[j];
- }
- }
- fprintf(fpout, "%.4e %10zd %.4e %10d\n", pr[i],
- mat->rowptr[i+1]-mat->rowptr[i], maxdiff, jmax+1);
- }
- gk_fclose(fpout);
-
- gk_free((void **)&pr, LTERM);
- }
-
- gk_csr_Free(&mat);
-
- /* display some final stats */
- print_final_info(params);
-}
-
-
-
-/*************************************************************************/
-/*! This function prints run parameters */
-/*************************************************************************/
-void print_init_info(params_t *params, gk_csr_t *mat)
-{
- printf("*******************************************************************************\n");
- printf(" fis\n\n");
- printf("Matrix Information ---------------------------------------------------------\n");
- printf(" input file=%s, [%d, %d, %zd]\n",
- params->infile, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]);
-
- printf("\n");
- printf("Options --------------------------------------------------------------------\n");
- printf(" niter=%d, ntvs=%d, ppr=%d, lamda=%f, eps=%e\n",
- params->niter, params->ntvs, params->ppr, params->lamda, params->eps);
-
- printf("\n");
- printf("Performing random walks... ----------------------------------------------\n");
-}
-
-
-/*************************************************************************/
-/*! This function prints final statistics */
-/*************************************************************************/
-void print_final_info(params_t *params)
-{
- printf("\n");
- printf("Memory Usage Information -----------------------------------------------------\n");
- printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed());
- printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed());
- printf("********************************************************************************\n");
-}
-
-
-/*************************************************************************/
-/*! This is the entry point of the command-line argument parser */
-/*************************************************************************/
-params_t *parse_cmdline(int argc, char *argv[])
-{
- int i;
- int c, option_index;
- params_t *params;
-
- params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params");
-
- /* initialize the params data structure */
- params->niter = 100;
- params->ppr = -1;
- params->ntvs = -1;
- params->eps = 1e-10;
- params->lamda = 0.80;
- params->infile = NULL;
- params->outfile = NULL;
-
-
- /* Parse the command line arguments */
- while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) {
- switch (c) {
- case CMD_NITER:
- if (gk_optarg) params->niter = atoi(gk_optarg);
- break;
- case CMD_NTVS:
- if (gk_optarg) params->ntvs = atoi(gk_optarg);
- break;
- case CMD_PPR:
- if (gk_optarg) params->ppr = atoi(gk_optarg);
- break;
- case CMD_EPS:
- if (gk_optarg) params->eps = atof(gk_optarg);
- break;
- case CMD_LAMDA:
- if (gk_optarg) params->lamda = atof(gk_optarg);
- break;
-
- case CMD_HELP:
- for (i=0; strlen(helpstr[i]) > 0; i++)
- printf("%s\n", helpstr[i]);
- exit(0);
- break;
- case '?':
- default:
- printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]);
- exit(0);
- }
- }
-
- if (argc-gk_optind != 2) {
- printf("Unrecognized parameters.");
- for (i=0; strlen(shorthelpstr[i]) > 0; i++)
- printf("%s\n", shorthelpstr[i]);
- exit(0);
- }
-
- params->infile = gk_strdup(argv[gk_optind++]);
- params->outfile = gk_strdup(argv[gk_optind++]);
-
- if (!gk_fexists(params->infile))
- errexit("input file %s does not exist.\n", params->infile);
-
- if (params->ppr != -1 && params->ntvs != -1)
- errexit("Only one of the -ppr and -ntvs options can be specified.\n");
-
- return params;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/test/strings.c b/3rdParty/metis/metis-5.1.0/GKlib/test/strings.c
deleted file mode 100644
index b241d3ff0..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/test/strings.c
+++ /dev/null
@@ -1,82 +0,0 @@
-/*!
-\file strings.c
-\brief Testing module for the string functions in GKlib
-
-\date Started 3/5/2007
-\author George
-\version\verbatim $Id: strings.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-/*************************************************************************/
-/*! Testing module for gk_strstr_replace() */
-/*************************************************************************/
-void test_strstr_replace()
-{
- char *new_str;
- int rc;
-
- rc = gk_strstr_replace("This is a simple string", "s", "S", "", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
-
- rc = gk_strstr_replace("This is a simple string", "s", "S", "g", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
-
- rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "g", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
-
- rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "ig", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
- rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w(\\w+)\\w\\b", "$1", "ig", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
- rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w+\\b", "word", "ig", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
- rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4",
- "(http://www\\.cs\\.umn\\.edu/)(.*)-T(\\d+)", "$1$2-P$3", "g", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
- rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4",
- "(\\d+)", "number:$1", "ig", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
-
- rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4",
- "(http://www\\.cs\\.umn\\.edu/)", "[$1]", "g", &new_str);
- printf("%d, %s.\n", rc, new_str);
- gk_free((void **)&new_str, LTERM);
-
-
-
-}
-
-
-
-int main()
-{
- test_strstr_replace();
-
-/*
- {
- int i;
- for (i=0; i<1000; i++)
- printf("%d\n", RandomInRange(3));
- }
-*/
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/timers.c b/3rdParty/metis/metis-5.1.0/GKlib/timers.c
deleted file mode 100644
index bb8f29620..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/timers.c
+++ /dev/null
@@ -1,52 +0,0 @@
-/*!
-\file timers.c
-\brief Various timing functions
-
-\date Started 4/12/2007
-\author George
-\version\verbatim $Id: timers.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-
-
-
-/*************************************************************************
-* This function returns the CPU seconds
-**************************************************************************/
-double gk_WClockSeconds(void)
-{
-#ifdef __GNUC__
- struct timeval ctime;
-
- gettimeofday(&ctime, NULL);
-
- return (double)ctime.tv_sec + (double).000001*ctime.tv_usec;
-#else
- return (double)time(NULL);
-#endif
-}
-
-
-/*************************************************************************
-* This function returns the CPU seconds
-**************************************************************************/
-double gk_CPUSeconds(void)
-{
-//#ifdef __OPENMP__
-#ifdef __OPENMPXXXX__
- return omp_get_wtime();
-#else
- #if defined(WIN32) || defined(__MINGW32__)
- return((double) clock()/CLOCKS_PER_SEC);
- #else
- struct rusage r;
-
- getrusage(RUSAGE_SELF, &r);
- return ((r.ru_utime.tv_sec + r.ru_stime.tv_sec) + 1.0e-6*(r.ru_utime.tv_usec + r.ru_stime.tv_usec));
- #endif
-#endif
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/tokenizer.c b/3rdParty/metis/metis-5.1.0/GKlib/tokenizer.c
deleted file mode 100644
index 5efd262db..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/tokenizer.c
+++ /dev/null
@@ -1,77 +0,0 @@
-/*!
-\file tokenizer.c
-\brief String tokenization routines
-
-This file contains various routines for splitting an input string into
-tokens and returning them in form of a list. The goal is to mimic perl's
-split function.
-
-\date Started 11/23/04
-\author George
-\version\verbatim $Id: tokenizer.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-
-/************************************************************************
-* This function tokenizes a string based on the user-supplied delimiters
-* list. The resulting tokens are returned into an array of strings.
-*************************************************************************/
-void gk_strtokenize(char *str, char *delim, gk_Tokens_t *tokens)
-{
- int i, ntoks, slen;
-
- tokens->strbuf = gk_strdup(str);
-
- slen = strlen(str);
- str = tokens->strbuf;
-
- /* Scan once to determine the number of tokens */
- for (ntoks=0, i=0; i<slen;) {
- /* Consume all the consecutive characters from the delimiters list */
- while (i<slen && strchr(delim, str[i]))
- i++;
-
- if (i == slen)
- break;
-
- ntoks++;
-
- /* Consume all the consecutive characters from the token */
- while (i<slen && !strchr(delim, str[i]))
- i++;
- }
-
-
- tokens->ntoks = ntoks;
- tokens->list = (char **)gk_malloc(ntoks*sizeof(char *), "strtokenize: tokens->list");
-
-
- /* Scan a second time to mark and link the tokens */
- for (ntoks=0, i=0; i<slen;) {
- /* Consume all the consecutive characters from the delimiters list */
- while (i<slen && strchr(delim, str[i]))
- str[i++] = '\0';
-
- if (i == slen)
- break;
-
- tokens->list[ntoks++] = str+i;
-
- /* Consume all the consecutive characters from the token */
- while (i<slen && !strchr(delim, str[i]))
- i++;
- }
-}
-
-
-/************************************************************************
-* This function frees the memory associated with a gk_Tokens_t
-*************************************************************************/
-void gk_freetokenslist(gk_Tokens_t *tokens)
-{
- gk_free((void *)&tokens->list, &tokens->strbuf, LTERM);
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/GKlib/util.c b/3rdParty/metis/metis-5.1.0/GKlib/util.c
deleted file mode 100644
index e75d68b51..000000000
--- a/3rdParty/metis/metis-5.1.0/GKlib/util.c
+++ /dev/null
@@ -1,108 +0,0 @@
-/*!
-\file util.c
-\brief Various utility routines
-
-\date Started 4/12/2007
-\author George
-\version\verbatim $Id: util.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-
-
-/*************************************************************************
-* This file randomly permutes the contents of an array.
-* flag == 0, don't initialize perm
-* flag == 1, set p[i] = i
-**************************************************************************/
-void gk_RandomPermute(size_t n, int *p, int flag)
-{
- gk_idx_t i, u, v;
- int tmp;
-
- if (flag == 1) {
- for (i=0; i<n; i++)
- p[i] = i;
- }
-
- for (i=0; i<n/2; i++) {
- v = RandomInRange(n);
- u = RandomInRange(n);
- gk_SWAP(p[v], p[u], tmp);
- }
-}
-
-
-/************************************************************************/
-/*!
-\brief Converts an element-based set membership into a CSR-format set-based
- membership.
-
-For example, it takes an array such as part[] that stores where each
-element belongs to and returns a pair of arrays (pptr[], pind[]) that
-store in CSF format the list of elements belonging in each partition.
-
-\param n
- the number of elements in the array (e.g., # of vertices)
-\param range
- the cardinality of the set (e.g., # of partitions)
-\param array
- the array that stores the per-element set membership
-\param ptr
- the array that will store the starting indices in ind for
- the elements of each set. This is filled by the routine and
- its size should be at least range+1.
-\param ind
- the array that stores consecutively which elements belong to
- each set. The size of this array should be n.
-*/
-/************************************************************************/
-void gk_array2csr(size_t n, size_t range, int *array, int *ptr, int *ind)
-{
- gk_idx_t i;
-
- gk_iset(range+1, 0, ptr);
-
- for (i=0; i<n; i++)
- ptr[array[i]]++;
-
- /* Compute the ptr, ind structure */
- MAKECSR(i, range, ptr);
- for (i=0; i<n; i++)
- ind[ptr[array[i]]++] = i;
- SHIFTCSR(i, range, ptr);
-}
-
-
-
-/*************************************************************************
-* This function returns the log2(x)
-**************************************************************************/
-int gk_log2(int a)
-{
- gk_idx_t i;
-
- for (i=1; a > 1; i++, a = a>>1);
- return i-1;
-}
-
-
-/*************************************************************************
-* This function checks if the argument is a power of 2
-**************************************************************************/
-int gk_ispow2(int a)
-{
- return (a == (1<<gk_log2(a)));
-}
-
-
-/*************************************************************************
-* This function returns the log2(x)
-**************************************************************************/
-float gk_flog2(float a)
-{
- return log(a)/log(2.0);
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/include/CMakeLists.txt b/3rdParty/metis/metis-5.1.0/include/CMakeLists.txt
deleted file mode 100644
index 9515a51b6..000000000
--- a/3rdParty/metis/metis-5.1.0/include/CMakeLists.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-if(METIS_INSTALL)
- install(FILES metis.h DESTINATION include)
-endif()
diff --git a/3rdParty/metis/metis-5.1.0/include/metis.h b/3rdParty/metis/metis-5.1.0/include/metis.h
deleted file mode 100644
index dc5406ae5..000000000
--- a/3rdParty/metis/metis-5.1.0/include/metis.h
+++ /dev/null
@@ -1,350 +0,0 @@
-/*!
-\file metis.h
-\brief This file contains function prototypes and constant definitions for METIS
- *
-\author George
-\date Started 8/9/02
-\version\verbatim $Id$\endverbatim
-*/
-
-#ifndef _METIS_H_
-#define _METIS_H_
-
-/****************************************************************************
-* A set of defines that can be modified by the user
-*****************************************************************************/
-
-/*--------------------------------------------------------------------------
- Specifies the width of the elementary data type that will hold information
- about vertices and their adjacency lists.
-
- Possible values:
- 32 : Use 32 bit signed integers
- 64 : Use 64 bit signed integers
-
- A width of 64 should be specified if the number of vertices or the total
- number of edges in the graph exceed the limits of a 32 bit signed integer
- i.e., 2^31-1.
- Proper use of 64 bit integers requires that the c99 standard datatypes
- int32_t and int64_t are supported by the compiler.
- GCC does provides these definitions in stdint.h, but it may require some
- modifications on other architectures.
---------------------------------------------------------------------------*/
-#define IDXTYPEWIDTH 32
-
-
-/*--------------------------------------------------------------------------
- Specifies the data type that will hold floating-point style information.
-
- Possible values:
- 32 : single precission floating point (float)
- 64 : double precission floating point (double)
---------------------------------------------------------------------------*/
-#define REALTYPEWIDTH 32
-
-
-
-/****************************************************************************
-* In principle, nothing needs to be changed beyond this point, unless the
-* int32_t and int64_t cannot be found in the normal places.
-*****************************************************************************/
-
-/* Uniform definitions for various compilers */
-#if defined(_MSC_VER)
- #define COMPILER_MSC
-#endif
-#if defined(__ICC)
- #define COMPILER_ICC
-#endif
-#if defined(__GNUC__)
- #define COMPILER_GCC
-#endif
-
-/* Include c99 int definitions and need constants. When building the library,
- * these are already defined by GKlib; hence the test for _GKLIB_H_ */
-#ifndef _GKLIB_H_
-#ifdef COMPILER_MSC
-#include <limits.h>
-
-typedef __int32 int32_t;
-typedef __int64 int64_t;
-#define PRId32 "I32d"
-#define PRId64 "I64d"
-#define SCNd32 "ld"
-#define SCNd64 "I64d"
-#define INT32_MIN ((int32_t)_I32_MIN)
-#define INT32_MAX _I32_MAX
-#define INT64_MIN ((int64_t)_I64_MIN)
-#define INT64_MAX _I64_MAX
-#else
-#include <inttypes.h>
-#endif
-#endif
-
-
-/*------------------------------------------------------------------------
-* Setup the basic datatypes
-*-------------------------------------------------------------------------*/
-#if IDXTYPEWIDTH == 32
- typedef int32_t idx_t;
-
- #define IDX_MAX INT32_MAX
- #define IDX_MIN INT32_MIN
-
- #define SCIDX SCNd32
- #define PRIDX PRId32
-
- #define strtoidx strtol
- #define iabs abs
-#elif IDXTYPEWIDTH == 64
- typedef int64_t idx_t;
-
- #define IDX_MAX INT64_MAX
- #define IDX_MIN INT64_MIN
-
- #define SCIDX SCNd64
- #define PRIDX PRId64
-
-#ifdef COMPILER_MSC
- #define strtoidx _strtoi64
-#else
- #define strtoidx strtoll
-#endif
- #define iabs labs
-#else
- #error "Incorrect user-supplied value fo IDXTYPEWIDTH"
-#endif
-
-
-#if REALTYPEWIDTH == 32
- typedef float real_t;
-
- #define SCREAL "f"
- #define PRREAL "f"
- #define REAL_MAX FLT_MAX
- #define REAL_MIN FLT_MIN
- #define REAL_EPSILON FLT_EPSILON
-
- #define rabs fabsf
- #define REALEQ(x,y) ((rabs((x)-(y)) <= FLT_EPSILON))
-
-#ifdef COMPILER_MSC
- #define strtoreal (float)strtod
-#else
- #define strtoreal strtof
-#endif
-#elif REALTYPEWIDTH == 64
- typedef double real_t;
-
- #define SCREAL "lf"
- #define PRREAL "lf"
- #define REAL_MAX DBL_MAX
- #define REAL_MIN DBL_MIN
- #define REAL_EPSILON DBL_EPSILON
-
- #define rabs fabs
- #define REALEQ(x,y) ((rabs((x)-(y)) <= DBL_EPSILON))
-
- #define strtoreal strtod
-#else
- #error "Incorrect user-supplied value for REALTYPEWIDTH"
-#endif
-
-
-/*------------------------------------------------------------------------
-* Constant definitions
-*-------------------------------------------------------------------------*/
-/* Metis's version number */
-#define METIS_VER_MAJOR 5
-#define METIS_VER_MINOR 1
-#define METIS_VER_SUBMINOR 0
-
-/* The maximum length of the options[] array */
-#define METIS_NOPTIONS 40
-
-
-
-/*------------------------------------------------------------------------
-* Function prototypes
-*-------------------------------------------------------------------------*/
-
-#ifdef _WINDLL
-#define METIS_API(type) __declspec(dllexport) type __cdecl
-#elif defined(__cdecl)
-#define METIS_API(type) type __cdecl
-#else
-#define METIS_API(type) type
-#endif
-
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-METIS_API(int) METIS_PartGraphRecursive(idx_t *nvtxs, idx_t *ncon, idx_t *xadj,
- idx_t *adjncy, idx_t *vwgt, idx_t *vsize, idx_t *adjwgt,
- idx_t *nparts, real_t *tpwgts, real_t *ubvec, idx_t *options,
- idx_t *edgecut, idx_t *part);
-
-METIS_API(int) METIS_PartGraphKway(idx_t *nvtxs, idx_t *ncon, idx_t *xadj,
- idx_t *adjncy, idx_t *vwgt, idx_t *vsize, idx_t *adjwgt,
- idx_t *nparts, real_t *tpwgts, real_t *ubvec, idx_t *options,
- idx_t *edgecut, idx_t *part);
-
-METIS_API(int) METIS_MeshToDual(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *ncommon, idx_t *numflag, idx_t **r_xadj, idx_t **r_adjncy);
-
-METIS_API(int) METIS_MeshToNodal(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *numflag, idx_t **r_xadj, idx_t **r_adjncy);
-
-METIS_API(int) METIS_PartMeshNodal(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *vwgt, idx_t *vsize, idx_t *nparts, real_t *tpwgts,
- idx_t *options, idx_t *objval, idx_t *epart, idx_t *npart);
-
-METIS_API(int) METIS_PartMeshDual(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *vwgt, idx_t *vsize, idx_t *ncommon, idx_t *nparts,
- real_t *tpwgts, idx_t *options, idx_t *objval, idx_t *epart,
- idx_t *npart);
-
-METIS_API(int) METIS_NodeND(idx_t *nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t *options, idx_t *perm, idx_t *iperm);
-
-METIS_API(int) METIS_Free(void *ptr);
-
-METIS_API(int) METIS_SetDefaultOptions(idx_t *options);
-
-
-/* These functions are used by ParMETIS */
-
-METIS_API(int) METIS_NodeNDP(idx_t nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t npes, idx_t *options, idx_t *perm, idx_t *iperm,
- idx_t *sizes);
-
-METIS_API(int) METIS_ComputeVertexSeparator(idx_t *nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *options, idx_t *sepsize, idx_t *part);
-
-METIS_API(int) METIS_NodeRefine(idx_t nvtxs, idx_t *xadj, idx_t *vwgt, idx_t *adjncy,
- idx_t *where, idx_t *hmarker, real_t ubfactor);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-
-
-/*------------------------------------------------------------------------
-* Enum type definitions
-*-------------------------------------------------------------------------*/
-/*! Return codes */
-typedef enum {
- METIS_OK = 1, /*!< Returned normally */
- METIS_ERROR_INPUT = -2, /*!< Returned due to erroneous inputs and/or options */
- METIS_ERROR_MEMORY = -3, /*!< Returned due to insufficient memory */
- METIS_ERROR = -4 /*!< Some other errors */
-} rstatus_et;
-
-
-/*! Operation type codes */
-typedef enum {
- METIS_OP_PMETIS,
- METIS_OP_KMETIS,
- METIS_OP_OMETIS
-} moptype_et;
-
-
-/*! Options codes (i.e., options[]) */
-typedef enum {
- METIS_OPTION_PTYPE,
- METIS_OPTION_OBJTYPE,
- METIS_OPTION_CTYPE,
- METIS_OPTION_IPTYPE,
- METIS_OPTION_RTYPE,
- METIS_OPTION_DBGLVL,
- METIS_OPTION_NITER,
- METIS_OPTION_NCUTS,
- METIS_OPTION_SEED,
- METIS_OPTION_NO2HOP,
- METIS_OPTION_MINCONN,
- METIS_OPTION_CONTIG,
- METIS_OPTION_COMPRESS,
- METIS_OPTION_CCORDER,
- METIS_OPTION_PFACTOR,
- METIS_OPTION_NSEPS,
- METIS_OPTION_UFACTOR,
- METIS_OPTION_NUMBERING,
-
- /* Used for command-line parameter purposes */
- METIS_OPTION_HELP,
- METIS_OPTION_TPWGTS,
- METIS_OPTION_NCOMMON,
- METIS_OPTION_NOOUTPUT,
- METIS_OPTION_BALANCE,
- METIS_OPTION_GTYPE,
- METIS_OPTION_UBVEC
-} moptions_et;
-
-
-/*! Partitioning Schemes */
-typedef enum {
- METIS_PTYPE_RB,
- METIS_PTYPE_KWAY
-} mptype_et;
-
-/*! Graph types for meshes */
-typedef enum {
- METIS_GTYPE_DUAL,
- METIS_GTYPE_NODAL
-} mgtype_et;
-
-/*! Coarsening Schemes */
-typedef enum {
- METIS_CTYPE_RM,
- METIS_CTYPE_SHEM
-} mctype_et;
-
-/*! Initial partitioning schemes */
-typedef enum {
- METIS_IPTYPE_GROW,
- METIS_IPTYPE_RANDOM,
- METIS_IPTYPE_EDGE,
- METIS_IPTYPE_NODE,
- METIS_IPTYPE_METISRB
-} miptype_et;
-
-
-/*! Refinement schemes */
-typedef enum {
- METIS_RTYPE_FM,
- METIS_RTYPE_GREEDY,
- METIS_RTYPE_SEP2SIDED,
- METIS_RTYPE_SEP1SIDED
-} mrtype_et;
-
-
-/*! Debug Levels */
-typedef enum {
- METIS_DBG_INFO = 1, /*!< Shows various diagnostic messages */
- METIS_DBG_TIME = 2, /*!< Perform timing analysis */
- METIS_DBG_COARSEN = 4, /*!< Show the coarsening progress */
- METIS_DBG_REFINE = 8, /*!< Show the refinement progress */
- METIS_DBG_IPART = 16, /*!< Show info on initial partitioning */
- METIS_DBG_MOVEINFO = 32, /*!< Show info on vertex moves during refinement */
- METIS_DBG_SEPINFO = 64, /*!< Show info on vertex moves during sep refinement */
- METIS_DBG_CONNINFO = 128, /*!< Show info on minimization of subdomain connectivity */
- METIS_DBG_CONTIGINFO = 256, /*!< Show info on elimination of connected components */
- METIS_DBG_MEMORY = 2048, /*!< Show info related to wspace allocation */
-} mdbglvl_et;
-
-
-/* Types of objectives */
-typedef enum {
- METIS_OBJTYPE_CUT,
- METIS_OBJTYPE_VOL,
- METIS_OBJTYPE_NODE
-} mobjtype_et;
-
-
-
-#endif /* _METIS_H_ */
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/CMakeLists.txt b/3rdParty/metis/metis-5.1.0/libmetis/CMakeLists.txt
deleted file mode 100644
index bbe23b67c..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/CMakeLists.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-# Add this directory for internal users.
-include_directories(.)
-# Find sources.
-file(GLOB metis_sources *.c)
-# Build libmetis.
-add_library(metis ${METIS_LIBRARY_TYPE} ${GKlib_sources} ${metis_sources})
-groupTarget(metis ${thirdPartyFolder})
-
-if(UNIX)
- target_link_libraries(metis m)
-endif()
-
-if(METIS_INSTALL)
- install(TARGETS metis
- LIBRARY DESTINATION lib
- RUNTIME DESTINATION lib
- ARCHIVE DESTINATION lib)
-endif()
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/auxapi.c b/3rdParty/metis/metis-5.1.0/libmetis/auxapi.c
deleted file mode 100644
index 8976b4ba4..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/auxapi.c
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
-\file
-\brief This file contains various helper API routines for using METIS.
-
-\date Started 5/12/2011
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version\verbatim $Id: auxapi.c 10409 2011-06-25 16:58:34Z karypis $ \endverbatim
-*/
-
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function free memory that was allocated by METIS and retuned
- to the application.
-
- \param ptr points to the memory that was previously allocated by
- METIS.
-*/
-/*************************************************************************/
-int METIS_Free(void *ptr)
-{
- if (ptr != NULL) free(ptr);
- return METIS_OK;
-}
-
-
-/*************************************************************************/
-/*! This function sets the default values for the options.
-
- \param options points to an array of size at least METIS_NOPTIONS.
-*/
-/*************************************************************************/
-int METIS_SetDefaultOptions(idx_t *options)
-{
- iset(METIS_NOPTIONS, -1, options);
-
- return METIS_OK;
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/balance.c b/3rdParty/metis/metis-5.1.0/libmetis/balance.c
deleted file mode 100644
index 3fb0e6e56..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/balance.c
+++ /dev/null
@@ -1,498 +0,0 @@
-/*!
-\file
-\brief Functions for the edge-based balancing
-
-\date Started 7/23/97
-\author George
-\author Copyright 1997-2011, Regents of the University of Minnesota
-\version\verbatim $Id: balance.c 10187 2011-06-13 13:46:57Z karypis $ \endverbatim
-*/
-
-#include "metislib.h"
-
-/*************************************************************************
-* This function is the entry poidx_t of the bisection balancing algorithms.
-**************************************************************************/
-void Balance2Way(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts)
-{
- if (ComputeLoadImbalanceDiff(graph, 2, ctrl->pijbm, ctrl->ubfactors) <= 0)
- return;
-
- if (graph->ncon == 1) {
- /* return right away if the balance is OK */
- if (iabs(ntpwgts[0]*graph->tvwgt[0]-graph->pwgts[0]) < 3*graph->tvwgt[0]/graph->nvtxs)
- return;
-
- if (graph->nbnd > 0)
- Bnd2WayBalance(ctrl, graph, ntpwgts);
- else
- General2WayBalance(ctrl, graph, ntpwgts);
- }
- else {
- McGeneral2WayBalance(ctrl, graph, ntpwgts);
- }
-}
-
-
-/*************************************************************************
-* This function balances two partitions by moving boundary nodes
-* from the domain that is overweight to the one that is underweight.
-**************************************************************************/
-void Bnd2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts)
-{
- idx_t i, ii, j, k, kwgt, nvtxs, nbnd, nswaps, from, to, pass, me, tmp;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where, *id, *ed, *bndptr, *bndind, *pwgts;
- idx_t *moved, *perm;
- rpq_t *queue;
- idx_t higain, mincut, mindiff;
- idx_t tpwgts[2];
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
- pwgts = graph->pwgts;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- moved = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
-
- /* Determine from which domain you will be moving data */
- tpwgts[0] = graph->tvwgt[0]*ntpwgts[0];
- tpwgts[1] = graph->tvwgt[0] - tpwgts[0];
- mindiff = iabs(tpwgts[0]-pwgts[0]);
- from = (pwgts[0] < tpwgts[0] ? 1 : 0);
- to = (from+1)%2;
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions: [%6"PRIDX" %6"PRIDX"] T[%6"PRIDX" %6"PRIDX"], Nv-Nb[%6"PRIDX" %6"PRIDX"]. ICut: %6"PRIDX" [B]\n",
- pwgts[0], pwgts[1], tpwgts[0], tpwgts[1], graph->nvtxs, graph->nbnd,
- graph->mincut));
-
- queue = rpqCreate(nvtxs);
-
- iset(nvtxs, -1, moved);
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERT(CheckBnd(graph));
-
- /* Insert the boundary nodes of the proper partition whose size is OK in the priority queue */
- nbnd = graph->nbnd;
- irandArrayPermute(nbnd, perm, nbnd/5, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = perm[ii];
- ASSERT(ed[bndind[i]] > 0 || id[bndind[i]] == 0);
- ASSERT(bndptr[bndind[i]] != -1);
- if (where[bndind[i]] == from && vwgt[bndind[i]] <= mindiff)
- rpqInsert(queue, bndind[i], ed[bndind[i]]-id[bndind[i]]);
- }
-
- mincut = graph->mincut;
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if ((higain = rpqGetTop(queue)) == -1)
- break;
- ASSERT(bndptr[higain] != -1);
-
- if (pwgts[to]+vwgt[higain] > tpwgts[to])
- break;
-
- mincut -= (ed[higain]-id[higain]);
- INC_DEC(pwgts[to], pwgts[from], vwgt[higain]);
-
- where[higain] = to;
- moved[higain] = nswaps;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" from %"PRIDX". [%3"PRIDX" %3"PRIDX"] %5"PRIDX" [%4"PRIDX" %4"PRIDX"]\n", higain, from, ed[higain]-id[higain], vwgt[higain], mincut, pwgts[0], pwgts[1]));
-
- /**************************************************************
- * Update the id[i]/ed[i] values of the affected nodes
- ***************************************************************/
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
-
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- /* Update its boundary information and queue position */
- if (bndptr[k] != -1) { /* If k was a boundary vertex */
- if (ed[k] == 0) { /* Not a boundary vertex any more */
- BNDDelete(nbnd, bndind, bndptr, k);
- if (moved[k] == -1 && where[k] == from && vwgt[k] <= mindiff) /* Remove it if in the queues */
- rpqDelete(queue, k);
- }
- else { /* If it has not been moved, update its position in the queue */
- if (moved[k] == -1 && where[k] == from && vwgt[k] <= mindiff)
- rpqUpdate(queue, k, ed[k]-id[k]);
- }
- }
- else {
- if (ed[k] > 0) { /* It will now become a boundary vertex */
- BNDInsert(nbnd, bndind, bndptr, k);
- if (moved[k] == -1 && where[k] == from && vwgt[k] <= mindiff)
- rpqInsert(queue, k, ed[k]-id[k]);
- }
- }
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum cut: %6"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", mincut, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************
-* This function balances two partitions by moving the highest gain
-* (including negative gain) vertices to the other domain.
-* It is used only when tha unbalance is due to non contigous
-* subdomains. That is, the are no boundary vertices.
-* It moves vertices from the domain that is overweight to the one that
-* is underweight.
-**************************************************************************/
-void General2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts)
-{
- idx_t i, ii, j, k, kwgt, nvtxs, nbnd, nswaps, from, to, pass, me, tmp;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where, *id, *ed, *bndptr, *bndind, *pwgts;
- idx_t *moved, *perm;
- rpq_t *queue;
- idx_t higain, mincut, mindiff;
- idx_t tpwgts[2];
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
- pwgts = graph->pwgts;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- moved = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
-
- /* Determine from which domain you will be moving data */
- tpwgts[0] = graph->tvwgt[0]*ntpwgts[0];
- tpwgts[1] = graph->tvwgt[0] - tpwgts[0];
- mindiff = iabs(tpwgts[0]-pwgts[0]);
- from = (pwgts[0] < tpwgts[0] ? 1 : 0);
- to = (from+1)%2;
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions: [%6"PRIDX" %6"PRIDX"] T[%6"PRIDX" %6"PRIDX"], Nv-Nb[%6"PRIDX" %6"PRIDX"]. ICut: %6"PRIDX" [B]\n",
- pwgts[0], pwgts[1], tpwgts[0], tpwgts[1], graph->nvtxs, graph->nbnd, graph->mincut));
-
- queue = rpqCreate(nvtxs);
-
- iset(nvtxs, -1, moved);
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERT(CheckBnd(graph));
-
- /* Insert the nodes of the proper partition whose size is OK in the priority queue */
- irandArrayPermute(nvtxs, perm, nvtxs/5, 1);
- for (ii=0; ii<nvtxs; ii++) {
- i = perm[ii];
- if (where[i] == from && vwgt[i] <= mindiff)
- rpqInsert(queue, i, ed[i]-id[i]);
- }
-
- mincut = graph->mincut;
- nbnd = graph->nbnd;
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if ((higain = rpqGetTop(queue)) == -1)
- break;
-
- if (pwgts[to]+vwgt[higain] > tpwgts[to])
- break;
-
- mincut -= (ed[higain]-id[higain]);
- INC_DEC(pwgts[to], pwgts[from], vwgt[higain]);
-
- where[higain] = to;
- moved[higain] = nswaps;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" from %"PRIDX". [%3"PRIDX" %3"PRIDX"] %5"PRIDX" [%4"PRIDX" %4"PRIDX"]\n", higain, from, ed[higain]-id[higain], vwgt[higain], mincut, pwgts[0], pwgts[1]));
-
- /**************************************************************
- * Update the id[i]/ed[i] values of the affected nodes
- ***************************************************************/
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && bndptr[higain] != -1 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
- if (ed[higain] > 0 && bndptr[higain] == -1)
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- /* Update the queue position */
- if (moved[k] == -1 && where[k] == from && vwgt[k] <= mindiff)
- rpqUpdate(queue, k, ed[k]-id[k]);
-
- /* Update its boundary information */
- if (ed[k] == 0 && bndptr[k] != -1)
- BNDDelete(nbnd, bndind, bndptr, k);
- else if (ed[k] > 0 && bndptr[k] == -1)
- BNDInsert(nbnd, bndind, bndptr, k);
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum cut: %6"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", mincut, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************
-* This function performs an edge-based FM refinement
-**************************************************************************/
-void McGeneral2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts)
-{
- idx_t i, ii, j, k, l, kwgt, nvtxs, ncon, nbnd, nswaps, from, to, pass,
- me, limit, tmp, cnum;
- idx_t *xadj, *adjncy, *vwgt, *adjwgt, *where, *pwgts, *id, *ed, *bndptr, *bndind;
- idx_t *moved, *swaps, *perm, *qnum, *qsizes;
- idx_t higain, mincut, newcut, mincutorder;
- real_t *invtvwgt, *minbalv, *newbalv, minbal, newbal;
- rpq_t **queues;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- invtvwgt = graph->invtvwgt;
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
- pwgts = graph->pwgts;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- moved = iwspacemalloc(ctrl, nvtxs);
- swaps = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
- qnum = iwspacemalloc(ctrl, nvtxs);
- newbalv = rwspacemalloc(ctrl, ncon);
- minbalv = rwspacemalloc(ctrl, ncon);
- qsizes = iwspacemalloc(ctrl, 2*ncon);
-
- limit = gk_min(gk_max(0.01*nvtxs, 15), 100);
-
- /* Initialize the queues */
- queues = (rpq_t **)wspacemalloc(ctrl, 2*ncon*sizeof(rpq_t *));
- for (i=0; i<2*ncon; i++) {
- queues[i] = rpqCreate(nvtxs);
- qsizes[i] = 0;
- }
-
- for (i=0; i<nvtxs; i++) {
- qnum[i] = iargmax_nrm(ncon, vwgt+i*ncon, invtvwgt);
- qsizes[2*qnum[i]+where[i]]++;
- }
-
-
- /* for the empty queues, move into them vertices from other queues */
- for (from=0; from<2; from++) {
- for (j=0; j<ncon; j++) {
- if (qsizes[2*j+from] == 0) {
- for (i=0; i<nvtxs; i++) {
- if (where[i] != from)
- continue;
-
- k = iargmax2_nrm(ncon, vwgt+i*ncon, invtvwgt);
- if (k == j &&
- qsizes[2*qnum[i]+from] > qsizes[2*j+from] &&
- vwgt[i*ncon+qnum[i]]*invtvwgt[qnum[i]] < 1.3*vwgt[i*ncon+j]*invtvwgt[j]) {
- qsizes[2*qnum[i]+from]--;
- qsizes[2*j+from]++;
- qnum[i] = j;
- }
- }
- }
- }
- }
-
-
- minbal = ComputeLoadImbalanceDiffVec(graph, 2, ctrl->pijbm, ctrl->ubfactors, minbalv);
- ASSERT(minbal > 0.0);
-
- newcut = mincut = graph->mincut;
- mincutorder = -1;
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("Parts: [");
- for (l=0; l<ncon; l++)
- printf("(%6"PRIDX" %6"PRIDX" %.3"PRREAL" %.3"PRREAL") ",
- pwgts[l], pwgts[ncon+l], ntpwgts[l], ntpwgts[ncon+l]);
- printf("] Nv-Nb[%5"PRIDX", %5"PRIDX"]. ICut: %6"PRIDX", LB: %+.3"PRREAL" [B]\n",
- graph->nvtxs, graph->nbnd, graph->mincut, minbal);
- }
-
- iset(nvtxs, -1, moved);
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERT(CheckBnd(graph));
-
- /* Insert all nodes in the priority queues */
- nbnd = graph->nbnd;
- irandArrayPermute(nvtxs, perm, nvtxs/10, 1);
- for (ii=0; ii<nvtxs; ii++) {
- i = perm[ii];
- rpqInsert(queues[2*qnum[i]+where[i]], i, ed[i]-id[i]);
- }
-
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if (minbal <= 0.0)
- break;
-
- SelectQueue(graph, ctrl->pijbm, ctrl->ubfactors, queues, &from, &cnum);
- to = (from+1)%2;
-
- if (from == -1 || (higain = rpqGetTop(queues[2*cnum+from])) == -1)
- break;
-
- newcut -= (ed[higain]-id[higain]);
-
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+from*ncon, 1);
- newbal = ComputeLoadImbalanceDiffVec(graph, 2, ctrl->pijbm, ctrl->ubfactors, newbalv);
-
- if (newbal < minbal || (newbal == minbal &&
- (newcut < mincut ||
- (newcut == mincut && BetterBalance2Way(ncon, minbalv, newbalv))))) {
- mincut = newcut;
- minbal = newbal;
- mincutorder = nswaps;
- rcopy(ncon, newbalv, minbalv);
- }
- else if (nswaps-mincutorder > limit) { /* We hit the limit, undo last move */
- newcut += (ed[higain]-id[higain]);
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+from*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- break;
- }
-
- where[higain] = to;
- moved[higain] = nswaps;
- swaps[nswaps] = higain;
-
- if (ctrl->dbglvl&METIS_DBG_MOVEINFO) {
- printf("Moved %6"PRIDX" from %"PRIDX"(%"PRIDX"). Gain: %5"PRIDX", "
- "Cut: %5"PRIDX", NPwgts: ", higain, from, cnum, ed[higain]-id[higain], newcut);
- for (l=0; l<ncon; l++)
- printf("(%6"PRIDX", %6"PRIDX") ", pwgts[l], pwgts[ncon+l]);
- printf(", %+.3"PRREAL" LB: %+.3"PRREAL"\n", minbal, newbal);
- }
-
-
- /**************************************************************
- * Update the id[i]/ed[i] values of the affected nodes
- ***************************************************************/
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && bndptr[higain] != -1 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
- if (ed[higain] > 0 && bndptr[higain] == -1)
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- /* Update the queue position */
- if (moved[k] == -1)
- rpqUpdate(queues[2*qnum[k]+where[k]], k, ed[k]-id[k]);
-
- /* Update its boundary information */
- if (ed[k] == 0 && bndptr[k] != -1)
- BNDDelete(nbnd, bndind, bndptr, k);
- else if (ed[k] > 0 && bndptr[k] == -1)
- BNDInsert(nbnd, bndind, bndptr, k);
- }
- }
-
-
-
- /****************************************************************
- * Roll back computations
- *****************************************************************/
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- to = where[higain] = (where[higain]+1)%2;
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && bndptr[higain] != -1 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
- else if (ed[higain] > 0 && bndptr[higain] == -1)
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+((to+1)%2)*ncon, 1);
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- if (bndptr[k] != -1 && ed[k] == 0)
- BNDDelete(nbnd, bndind, bndptr, k);
- if (bndptr[k] == -1 && ed[k] > 0)
- BNDInsert(nbnd, bndind, bndptr, k);
- }
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("\tMincut: %6"PRIDX" at %5"PRIDX", NBND: %6"PRIDX", NPwgts: [",
- mincut, mincutorder, nbnd);
- for (l=0; l<ncon; l++)
- printf("(%6"PRIDX", %6"PRIDX") ", pwgts[l], pwgts[ncon+l]);
- printf("], LB: %.3"PRREAL"\n", ComputeLoadImbalance(graph, 2, ctrl->pijbm));
- }
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
-
- for (i=0; i<2*ncon; i++)
- rpqDestroy(queues[i]);
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/bucketsort.c b/3rdParty/metis/metis-5.1.0/libmetis/bucketsort.c
deleted file mode 100644
index e126d02a6..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/bucketsort.c
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * bucketsort.c
- *
- * This file contains code that implement a variety of counting sorting
- * algorithms
- *
- * Started 7/25/97
- * George
- *
- */
-
-#include "metislib.h"
-
-
-
-/*************************************************************************
-* This function uses simple counting sort to return a permutation array
-* corresponding to the sorted order. The keys are arsumed to start from
-* 0 and they are positive. This sorting is used during matching.
-**************************************************************************/
-void BucketSortKeysInc(ctrl_t *ctrl, idx_t n, idx_t max, idx_t *keys,
- idx_t *tperm, idx_t *perm)
-{
- idx_t i, ii;
- idx_t *counts;
-
- WCOREPUSH;
-
- counts = iset(max+2, 0, iwspacemalloc(ctrl, max+2));
-
- for (i=0; i<n; i++)
- counts[keys[i]]++;
- MAKECSR(i, max+1, counts);
-
- for (ii=0; ii<n; ii++) {
- i = tperm[ii];
- perm[counts[keys[i]]++] = i;
- }
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/checkgraph.c b/3rdParty/metis/metis-5.1.0/libmetis/checkgraph.c
deleted file mode 100644
index 852634614..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/checkgraph.c
+++ /dev/null
@@ -1,263 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * checkgraph.c
- *
- * This file contains routines related to I/O
- *
- * Started 8/28/94
- * George
- *
- */
-
-#include "metislib.h"
-
-
-
-/*************************************************************************/
-/*! This function checks if a graph is valid. A valid graph must satisfy
- the following constraints:
- - It should contain no self-edges.
- - It should be undirected; i.e., (u,v) and (v,u) should be present.
- - The adjacency list should not contain multiple edges to the same
- other vertex.
-
- \param graph is the graph to be checked, whose numbering starts from 0.
- \param numflag is 0 if error reporting will be done using 0 as the
- numbering, or 1 if the reporting should be done using 1.
- \param verbose is 1 the identified errors will be displayed, or 0, if
- it should run silently.
-*/
-/*************************************************************************/
-int CheckGraph(graph_t *graph, int numflag, int verbose)
-{
- idx_t i, j, k, l;
- idx_t nvtxs, err=0;
- idx_t minedge, maxedge, minewgt, maxewgt;
- idx_t *xadj, *adjncy, *adjwgt, *htable;
-
- numflag = (numflag == 0 ? 0 : 1); /* make sure that numflag is 0 or 1 */
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- ASSERT(adjwgt != NULL);
-
- htable = ismalloc(nvtxs, 0, "htable");
-
- minedge = maxedge = adjncy[0];
- minewgt = maxewgt = adjwgt[0];
-
- for (i=0; i<nvtxs; i++) {
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
-
- minedge = (k < minedge) ? k : minedge;
- maxedge = (k > maxedge) ? k : maxedge;
- minewgt = (adjwgt[j] < minewgt) ? adjwgt[j] : minewgt;
- maxewgt = (adjwgt[j] > maxewgt) ? adjwgt[j] : maxewgt;
-
- if (i == k) {
- if (verbose)
- printf("Vertex %"PRIDX" contains a self-loop "
- "(i.e., diagonal entry in the matrix)!\n", i+numflag);
- err++;
- }
- else {
- for (l=xadj[k]; l<xadj[k+1]; l++) {
- if (adjncy[l] == i) {
- if (adjwgt[l] != adjwgt[j]) {
- if (verbose)
- printf("Edges (u:%"PRIDX" v:%"PRIDX" wgt:%"PRIDX") and "
- "(v:%"PRIDX" u:%"PRIDX" wgt:%"PRIDX") "
- "do not have the same weight!\n",
- i+numflag, k+numflag, adjwgt[j],
- k+numflag, i+numflag, adjwgt[l]);
- err++;
- }
- break;
- }
- }
- if (l == xadj[k+1]) {
- if (verbose)
- printf("Missing edge: (%"PRIDX" %"PRIDX")!\n", k+numflag, i+numflag);
- err++;
- }
- }
-
- if (htable[k] == 0) {
- htable[k]++;
- }
- else {
- if (verbose)
- printf("Edge %"PRIDX" from vertex %"PRIDX" is repeated %"PRIDX" times\n",
- k+numflag, i+numflag, htable[k]++);
- err++;
- }
- }
-
- for (j=xadj[i]; j<xadj[i+1]; j++)
- htable[adjncy[j]] = 0;
- }
-
-
- if (err > 0 && verbose) {
- printf("A total of %"PRIDX" errors exist in the input file. "
- "Correct them, and run again!\n", err);
- }
-
- gk_free((void **)&htable, LTERM);
-
- return (err == 0 ? 1 : 0);
-}
-
-
-/*************************************************************************/
-/*! This function performs a quick check of the weights of the graph */
-/*************************************************************************/
-int CheckInputGraphWeights(idx_t nvtxs, idx_t ncon, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *vsize, idx_t *adjwgt)
-{
- idx_t i;
-
- if (ncon <= 0) {
- printf("Input Error: ncon must be >= 1.\n");
- return 0;
- }
-
- if (vwgt) {
- for (i=ncon*nvtxs; i>=0; i--) {
- if (vwgt[i] < 0) {
- printf("Input Error: negative vertex weight(s).\n");
- return 0;
- }
- }
- }
- if (vsize) {
- for (i=nvtxs; i>=0; i--) {
- if (vsize[i] < 0) {
- printf("Input Error: negative vertex sizes(s).\n");
- return 0;
- }
- }
- }
- if (adjwgt) {
- for (i=xadj[nvtxs]-1; i>=0; i--) {
- if (adjwgt[i] < 0) {
- printf("Input Error: non-positive edge weight(s).\n");
- return 0;
- }
- }
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function creates a graph whose topology is consistent with
- Metis' requirements that:
- - There are no self-edges.
- - It is undirected; i.e., (u,v) and (v,u) should be present and of the
- same weight.
- - The adjacency list should not contain multiple edges to the same
- other vertex.
-
- Any of the above errors are fixed by performing the following operations:
- - Self-edges are removed.
- - The undirected graph is formed by the union of edges.
- - One of the duplicate edges is selected.
-
- The routine does not change the provided vertex weights.
-*/
-/*************************************************************************/
-graph_t *FixGraph(graph_t *graph)
-{
- idx_t i, j, k, l, nvtxs, nedges;
- idx_t *xadj, *adjncy, *adjwgt;
- idx_t *nxadj, *nadjncy, *nadjwgt;
- graph_t *ngraph;
- uvw_t *edges;
-
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- ASSERT(adjwgt != NULL);
-
- ngraph = CreateGraph();
-
- ngraph->nvtxs = nvtxs;
-
- /* deal with vertex weights/sizes */
- ngraph->ncon = graph->ncon;
- ngraph->vwgt = icopy(nvtxs*graph->ncon, graph->vwgt,
- imalloc(nvtxs*graph->ncon, "FixGraph: vwgt"));
-
- ngraph->vsize = ismalloc(nvtxs, 1, "FixGraph: vsize");
- if (graph->vsize)
- icopy(nvtxs, graph->vsize, ngraph->vsize);
-
- /* fix graph by sorting the "superset" of edges */
- edges = (uvw_t *)gk_malloc(sizeof(uvw_t)*2*xadj[nvtxs], "FixGraph: edges");
-
- for (nedges=0, i=0; i<nvtxs; i++) {
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- /* keep only the upper-trianglular part of the adjacency matrix */
- if (i < adjncy[j]) {
- edges[nedges].u = i;
- edges[nedges].v = adjncy[j];
- edges[nedges].w = adjwgt[j];
- nedges++;
- }
- else if (i > adjncy[j]) {
- edges[nedges].u = adjncy[j];
- edges[nedges].v = i;
- edges[nedges].w = adjwgt[j];
- nedges++;
- }
- }
- }
-
- uvwsorti(nedges, edges);
-
-
- /* keep the unique subset */
- for (k=0, i=1; i<nedges; i++) {
- if (edges[k].v != edges[i].v || edges[k].u != edges[i].u) {
- edges[++k] = edges[i];
- }
- }
- nedges = k+1;
-
- /* allocate memory for the fixed graph */
- nxadj = ngraph->xadj = ismalloc(nvtxs+1, 0, "FixGraph: nxadj");
- nadjncy = ngraph->adjncy = imalloc(2*nedges, "FixGraph: nadjncy");
- nadjwgt = ngraph->adjwgt = imalloc(2*nedges, "FixGraph: nadjwgt");
-
- /* create the adjacency list of the fixed graph from the upper-triangular
- part of the adjacency matrix */
- for (k=0; k<nedges; k++) {
- nxadj[edges[k].u]++;
- nxadj[edges[k].v]++;
- }
- MAKECSR(i, nvtxs, nxadj);
-
- for (k=0; k<nedges; k++) {
- nadjncy[nxadj[edges[k].u]] = edges[k].v;
- nadjncy[nxadj[edges[k].v]] = edges[k].u;
- nadjwgt[nxadj[edges[k].u]] = edges[k].w;
- nadjwgt[nxadj[edges[k].v]] = edges[k].w;
- nxadj[edges[k].u]++;
- nxadj[edges[k].v]++;
- }
- SHIFTCSR(i, nvtxs, nxadj);
-
- gk_free((void **)&edges, LTERM);
-
- return ngraph;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/coarsen.c b/3rdParty/metis/metis-5.1.0/libmetis/coarsen.c
deleted file mode 100644
index 165344e6e..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/coarsen.c
+++ /dev/null
@@ -1,1132 +0,0 @@
-/*!
-\file
-\brief Functions for computing matchings during graph coarsening
-
-\date Started 7/23/97
-\author George
-\author Copyright 1997-2011, Regents of the University of Minnesota
-\version\verbatim $Id: coarsen.c 13936 2013-03-30 03:59:09Z karypis $ \endverbatim
-*/
-
-
-#include "metislib.h"
-
-#define UNMATCHEDFOR2HOP 0.10 /* The fraction of unmatched vertices that triggers 2-hop */
-
-
-/*************************************************************************/
-/*! This function takes a graph and creates a sequence of coarser graphs.
- It implements the coarsening phase of the multilevel paradigm.
- */
-/*************************************************************************/
-graph_t *CoarsenGraph(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, eqewgts, level=0;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->CoarsenTmr));
-
- /* determine if the weights on the edges are all the same */
- for (eqewgts=1, i=1; i<graph->nedges; i++) {
- if (graph->adjwgt[0] != graph->adjwgt[i]) {
- eqewgts = 0;
- break;
- }
- }
-
- /* set the maximum allowed coarsest vertex weight */
- for (i=0; i<graph->ncon; i++)
- ctrl->maxvwgt[i] = 1.5*graph->tvwgt[i]/ctrl->CoarsenTo;
-
- do {
- IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, PrintCGraphStats(ctrl, graph));
-
- /* allocate memory for cmap, if it has not already been done due to
- multiple cuts */
- if (graph->cmap == NULL)
- graph->cmap = imalloc(graph->nvtxs, "CoarsenGraph: graph->cmap");
-
- /* determine which matching scheme you will use */
- switch (ctrl->ctype) {
- case METIS_CTYPE_RM:
- Match_RM(ctrl, graph);
- break;
- case METIS_CTYPE_SHEM:
- if (eqewgts || graph->nedges == 0)
- Match_RM(ctrl, graph);
- else
- Match_SHEM(ctrl, graph);
- break;
- default:
- gk_errexit(SIGERR, "Unknown ctype: %d\n", ctrl->ctype);
- }
-
- graph = graph->coarser;
- eqewgts = 0;
- level++;
-
- ASSERT(CheckGraph(graph, 0, 1));
-
- } while (graph->nvtxs > ctrl->CoarsenTo &&
- graph->nvtxs < COARSEN_FRACTION*graph->finer->nvtxs &&
- graph->nedges > graph->nvtxs/2);
-
- IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, PrintCGraphStats(ctrl, graph));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->CoarsenTmr));
-
- return graph;
-}
-
-
-/*************************************************************************/
-/*! This function takes a graph and creates a sequence of nlevels coarser
- graphs, where nlevels is an input parameter.
- */
-/*************************************************************************/
-graph_t *CoarsenGraphNlevels(ctrl_t *ctrl, graph_t *graph, idx_t nlevels)
-{
- idx_t i, eqewgts, level;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->CoarsenTmr));
-
- /* determine if the weights on the edges are all the same */
- for (eqewgts=1, i=1; i<graph->nedges; i++) {
- if (graph->adjwgt[0] != graph->adjwgt[i]) {
- eqewgts = 0;
- break;
- }
- }
-
- /* set the maximum allowed coarsest vertex weight */
- for (i=0; i<graph->ncon; i++)
- ctrl->maxvwgt[i] = 1.5*graph->tvwgt[i]/ctrl->CoarsenTo;
-
- for (level=0; level<nlevels; level++) {
- IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, PrintCGraphStats(ctrl, graph));
-
- /* allocate memory for cmap, if it has not already been done due to
- multiple cuts */
- if (graph->cmap == NULL)
- graph->cmap = imalloc(graph->nvtxs, "CoarsenGraph: graph->cmap");
-
- /* determine which matching scheme you will use */
- switch (ctrl->ctype) {
- case METIS_CTYPE_RM:
- Match_RM(ctrl, graph);
- break;
- case METIS_CTYPE_SHEM:
- if (eqewgts || graph->nedges == 0)
- Match_RM(ctrl, graph);
- else
- Match_SHEM(ctrl, graph);
- break;
- default:
- gk_errexit(SIGERR, "Unknown ctype: %d\n", ctrl->ctype);
- }
-
- graph = graph->coarser;
- eqewgts = 0;
-
- ASSERT(CheckGraph(graph, 0, 1));
-
- if (graph->nvtxs < ctrl->CoarsenTo ||
- graph->nvtxs > COARSEN_FRACTION*graph->finer->nvtxs ||
- graph->nedges < graph->nvtxs/2)
- break;
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, PrintCGraphStats(ctrl, graph));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->CoarsenTmr));
-
- return graph;
-}
-
-
-/*************************************************************************/
-/*! This function finds a matching by randomly selecting one of the
- unmatched adjacent vertices.
- */
-/**************************************************************************/
-idx_t Match_RM(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, pi, ii, j, jj, jjinc, k, nvtxs, ncon, cnvtxs, maxidx, last_unmatched;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *maxvwgt;
- idx_t *match, *cmap, *perm;
- size_t nunmatched=0;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->MatchTmr));
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- cmap = graph->cmap;
-
- maxvwgt = ctrl->maxvwgt;
-
- match = iset(nvtxs, UNMATCHED, iwspacemalloc(ctrl, nvtxs));
- perm = iwspacemalloc(ctrl, nvtxs);
-
- irandArrayPermute(nvtxs, perm, nvtxs/8, 1);
-
- for (cnvtxs=0, last_unmatched=0, pi=0; pi<nvtxs; pi++) {
- i = perm[pi];
-
- if (match[i] == UNMATCHED) { /* Unmatched */
- maxidx = i;
-
- if ((ncon == 1 ? vwgt[i] < maxvwgt[0] : ivecle(ncon, vwgt+i*ncon, maxvwgt))) {
- /* Deal with island vertices. Find a non-island and match it with.
- The matching ignores ctrl->maxvwgt requirements */
- if (xadj[i] == xadj[i+1]) {
- last_unmatched = gk_max(pi, last_unmatched)+1;
- for (; last_unmatched<nvtxs; last_unmatched++) {
- j = perm[last_unmatched];
- if (match[j] == UNMATCHED) {
- maxidx = j;
- break;
- }
- }
- }
- else {
- /* Find a random matching, subject to maxvwgt constraints */
- if (ncon == 1) {
- /* single constraint version */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (match[k] == UNMATCHED && vwgt[i]+vwgt[k] <= maxvwgt[0]) {
- maxidx = k;
- break;
- }
- }
-
- /* If it did not match, record for a 2-hop matching. */
- if (maxidx == i && 3*vwgt[i] < maxvwgt[0]) {
- nunmatched++;
- maxidx = UNMATCHED;
- }
- }
- else {
- /* multi-constraint version */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (match[k] == UNMATCHED &&
- ivecaxpylez(ncon, 1, vwgt+i*ncon, vwgt+k*ncon, maxvwgt)) {
- maxidx = k;
- break;
- }
- }
-
- /* If it did not match, record for a 2-hop matching. */
- if (maxidx == i && ivecaxpylez(ncon, 2, vwgt+i*ncon, vwgt+i*ncon, maxvwgt)) {
- nunmatched++;
- maxidx = UNMATCHED;
- }
- }
- }
- }
-
- if (maxidx != UNMATCHED) {
- cmap[i] = cmap[maxidx] = cnvtxs++;
- match[i] = maxidx;
- match[maxidx] = i;
- }
- }
- }
-
- //printf("nunmatched: %zu\n", nunmatched);
-
- /* see if a 2-hop matching is required/allowed */
- if (!ctrl->no2hop && nunmatched > UNMATCHEDFOR2HOP*nvtxs)
- cnvtxs = Match_2Hop(ctrl, graph, perm, match, cnvtxs, nunmatched);
-
-
- /* match the final unmatched vertices with themselves and reorder the vertices
- of the coarse graph for memory-friendly contraction */
- for (cnvtxs=0, i=0; i<nvtxs; i++) {
- if (match[i] == UNMATCHED) {
- match[i] = i;
- cmap[i] = cnvtxs++;
- }
- else {
- if (i <= match[i])
- cmap[i] = cmap[match[i]] = cnvtxs++;
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->MatchTmr));
-
- CreateCoarseGraph(ctrl, graph, cnvtxs, match);
-
- WCOREPOP;
-
- return cnvtxs;
-}
-
-
-/**************************************************************************/
-/*! This function finds a matching using the HEM heuristic. The vertices
- are visited based on increasing degree to ensure that all vertices are
- given a chance to match with something.
- */
-/**************************************************************************/
-idx_t Match_SHEM(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, pi, ii, j, jj, jjinc, k, nvtxs, ncon, cnvtxs, maxidx, maxwgt,
- last_unmatched, avgdegree;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *maxvwgt;
- idx_t *match, *cmap, *degrees, *perm, *tperm;
- size_t nunmatched=0;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->MatchTmr));
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- cmap = graph->cmap;
-
- maxvwgt = ctrl->maxvwgt;
-
- match = iset(nvtxs, UNMATCHED, iwspacemalloc(ctrl, nvtxs));
- perm = iwspacemalloc(ctrl, nvtxs);
- tperm = iwspacemalloc(ctrl, nvtxs);
- degrees = iwspacemalloc(ctrl, nvtxs);
-
- irandArrayPermute(nvtxs, tperm, nvtxs/8, 1);
-
- avgdegree = 0.7*(xadj[nvtxs]/nvtxs);
- for (i=0; i<nvtxs; i++)
- degrees[i] = (xadj[i+1]-xadj[i] > avgdegree ? avgdegree : xadj[i+1]-xadj[i]);
- BucketSortKeysInc(ctrl, nvtxs, avgdegree, degrees, tperm, perm);
-
- for (cnvtxs=0, last_unmatched=0, pi=0; pi<nvtxs; pi++) {
- i = perm[pi];
-
- if (match[i] == UNMATCHED) { /* Unmatched */
- maxidx = i;
- maxwgt = -1;
-
- if ((ncon == 1 ? vwgt[i] < maxvwgt[0] : ivecle(ncon, vwgt+i*ncon, maxvwgt))) {
- /* Deal with island vertices. Find a non-island and match it with.
- The matching ignores ctrl->maxvwgt requirements */
- if (xadj[i] == xadj[i+1]) {
- last_unmatched = gk_max(pi, last_unmatched)+1;
- for (; last_unmatched<nvtxs; last_unmatched++) {
- j = perm[last_unmatched];
- if (match[j] == UNMATCHED) {
- maxidx = j;
- break;
- }
- }
- }
- else {
- /* Find a heavy-edge matching, subject to maxvwgt constraints */
- if (ncon == 1) {
- /* single constraint version */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (match[k] == UNMATCHED &&
- maxwgt < adjwgt[j] && vwgt[i]+vwgt[k] <= maxvwgt[0]) {
- maxidx = k;
- maxwgt = adjwgt[j];
- }
- }
-
- /* If it did not match, record for a 2-hop matching. */
- if (maxidx == i && 3*vwgt[i] < maxvwgt[0]) {
- nunmatched++;
- maxidx = UNMATCHED;
- }
- }
- else {
- /* multi-constraint version */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (match[k] == UNMATCHED &&
- ivecaxpylez(ncon, 1, vwgt+i*ncon, vwgt+k*ncon, maxvwgt) &&
- (maxwgt < adjwgt[j] ||
- (maxwgt == adjwgt[j] &&
- BetterVBalance(ncon, graph->invtvwgt, vwgt+i*ncon,
- vwgt+maxidx*ncon, vwgt+k*ncon)))) {
- maxidx = k;
- maxwgt = adjwgt[j];
- }
- }
-
- /* If it did not match, record for a 2-hop matching. */
- if (maxidx == i && ivecaxpylez(ncon, 2, vwgt+i*ncon, vwgt+i*ncon, maxvwgt)) {
- nunmatched++;
- maxidx = UNMATCHED;
- }
- }
- }
- }
-
- if (maxidx != UNMATCHED) {
- cmap[i] = cmap[maxidx] = cnvtxs++;
- match[i] = maxidx;
- match[maxidx] = i;
- }
- }
- }
-
- //printf("nunmatched: %zu\n", nunmatched);
-
- /* see if a 2-hop matching is required/allowed */
- if (!ctrl->no2hop && nunmatched > UNMATCHEDFOR2HOP*nvtxs)
- cnvtxs = Match_2Hop(ctrl, graph, perm, match, cnvtxs, nunmatched);
-
-
- /* match the final unmatched vertices with themselves and reorder the vertices
- of the coarse graph for memory-friendly contraction */
- for (cnvtxs=0, i=0; i<nvtxs; i++) {
- if (match[i] == UNMATCHED) {
- match[i] = i;
- cmap[i] = cnvtxs++;
- }
- else {
- if (i <= match[i])
- cmap[i] = cmap[match[i]] = cnvtxs++;
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->MatchTmr));
-
- CreateCoarseGraph(ctrl, graph, cnvtxs, match);
-
- WCOREPOP;
-
- return cnvtxs;
-}
-
-
-/*************************************************************************/
-/*! This function matches the unmatched vertices using a 2-hop matching
- that involves vertices that are two hops away from each other. */
-/**************************************************************************/
-idx_t Match_2Hop(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t nunmatched)
-{
-
- cnvtxs = Match_2HopAny(ctrl, graph, perm, match, cnvtxs, &nunmatched, 2);
- cnvtxs = Match_2HopAll(ctrl, graph, perm, match, cnvtxs, &nunmatched, 64);
- if (nunmatched > 1.5*UNMATCHEDFOR2HOP*graph->nvtxs)
- cnvtxs = Match_2HopAny(ctrl, graph, perm, match, cnvtxs, &nunmatched, 3);
- if (nunmatched > 2.0*UNMATCHEDFOR2HOP*graph->nvtxs)
- cnvtxs = Match_2HopAny(ctrl, graph, perm, match, cnvtxs, &nunmatched, graph->nvtxs);
-
- return cnvtxs;
-}
-
-
-/*************************************************************************/
-/*! This function matches the unmatched vertices whose degree is less than
- maxdegree using a 2-hop matching that involves vertices that are two
- hops away from each other.
- The requirement of the 2-hop matching is a simple non-empty overlap
- between the adjancency lists of the vertices. */
-/**************************************************************************/
-idx_t Match_2HopAny(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t *r_nunmatched, size_t maxdegree)
-{
- idx_t i, pi, ii, j, jj, k, nvtxs;
- idx_t *xadj, *adjncy, *colptr, *rowind;
- idx_t *cmap;
- size_t nunmatched;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->Aux3Tmr));
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- cmap = graph->cmap;
-
- nunmatched = *r_nunmatched;
-
- /*IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, printf("IN: nunmatched: %zu\t", * nunmatched)); */
-
- /* create the inverted index */
- WCOREPUSH;
- colptr = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs+1));
- for (i=0; i<nvtxs; i++) {
- if (match[i] == UNMATCHED && xadj[i+1]-xadj[i] < maxdegree) {
- for (j=xadj[i]; j<xadj[i+1]; j++)
- colptr[adjncy[j]]++;
- }
- }
- MAKECSR(i, nvtxs, colptr);
-
- rowind = iwspacemalloc(ctrl, colptr[nvtxs]);
- for (pi=0; pi<nvtxs; pi++) {
- i = perm[pi];
- if (match[i] == UNMATCHED && xadj[i+1]-xadj[i] < maxdegree) {
- for (j=xadj[i]; j<xadj[i+1]; j++)
- rowind[colptr[adjncy[j]]++] = i;
- }
- }
- SHIFTCSR(i, nvtxs, colptr);
-
- /* compute matchings by going down the inverted index */
- for (pi=0; pi<nvtxs; pi++) {
- i = perm[pi];
- if (colptr[i+1]-colptr[i] < 2)
- continue;
-
- for (jj=colptr[i+1], j=colptr[i]; j<jj; j++) {
- if (match[rowind[j]] == UNMATCHED) {
- for (jj--; jj>j; jj--) {
- if (match[rowind[jj]] == UNMATCHED) {
- cmap[rowind[j]] = cmap[rowind[jj]] = cnvtxs++;
- match[rowind[j]] = rowind[jj];
- match[rowind[jj]] = rowind[j];
- nunmatched -= 2;
- break;
- }
- }
- }
- }
- }
- WCOREPOP;
-
- /* IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, printf("OUT: nunmatched: %zu\n", nunmatched)); */
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->Aux3Tmr));
-
- *r_nunmatched = nunmatched;
- return cnvtxs;
-}
-
-
-/*************************************************************************/
-/*! This function matches the unmatched vertices whose degree is less than
- maxdegree using a 2-hop matching that involves vertices that are two
- hops away from each other.
- The requirement of the 2-hop matching is that of identical adjacency
- lists.
- */
-/**************************************************************************/
-idx_t Match_2HopAll(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t *r_nunmatched, size_t maxdegree)
-{
- idx_t i, pi, pk, ii, j, jj, k, nvtxs, mask, idegree;
- idx_t *xadj, *adjncy;
- idx_t *cmap, *mark;
- ikv_t *keys;
- size_t nunmatched, ncand;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->Aux3Tmr));
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- cmap = graph->cmap;
-
- nunmatched = *r_nunmatched;
- mask = IDX_MAX/maxdegree;
-
- /*IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, printf("IN: nunmatched: %zu\t", nunmatched)); */
-
- WCOREPUSH;
-
- /* collapse vertices with identical adjancency lists */
- keys = ikvwspacemalloc(ctrl, nunmatched);
- for (ncand=0, pi=0; pi<nvtxs; pi++) {
- i = perm[pi];
- idegree = xadj[i+1]-xadj[i];
- if (match[i] == UNMATCHED && idegree > 1 && idegree < maxdegree) {
- for (k=0, j=xadj[i]; j<xadj[i+1]; j++)
- k += adjncy[j]%mask;
- keys[ncand].val = i;
- keys[ncand].key = (k%mask)*maxdegree + idegree;
- ncand++;
- }
- }
- ikvsorti(ncand, keys);
-
- mark = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- for (pi=0; pi<ncand; pi++) {
- i = keys[pi].val;
- if (match[i] != UNMATCHED)
- continue;
-
- for (j=xadj[i]; j<xadj[i+1]; j++)
- mark[adjncy[j]] = i;
-
- for (pk=pi+1; pk<ncand; pk++) {
- k = keys[pk].val;
- if (match[k] != UNMATCHED)
- continue;
-
- if (keys[pi].key != keys[pk].key)
- break;
- if (xadj[i+1]-xadj[i] != xadj[k+1]-xadj[k])
- break;
-
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- if (mark[adjncy[jj]] != i)
- break;
- }
- if (jj == xadj[k+1]) {
- cmap[i] = cmap[k] = cnvtxs++;
- match[i] = k;
- match[k] = i;
- nunmatched -= 2;
- break;
- }
- }
- }
- WCOREPOP;
-
- /*IFSET(ctrl->dbglvl, METIS_DBG_COARSEN, printf("OUT: ncand: %zu, nunmatched: %zu\n", ncand, nunmatched)); */
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->Aux3Tmr));
-
- *r_nunmatched = nunmatched;
- return cnvtxs;
-}
-
-
-/*************************************************************************/
-/*! This function prints various stats for each graph during coarsening
- */
-/*************************************************************************/
-void PrintCGraphStats(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i;
-
- printf("%10"PRIDX" %10"PRIDX" %10"PRIDX" [%"PRIDX"] [",
- graph->nvtxs, graph->nedges, isum(graph->nedges, graph->adjwgt, 1), ctrl->CoarsenTo);
-
- for (i=0; i<graph->ncon; i++)
- printf(" %8"PRIDX":%8"PRIDX, ctrl->maxvwgt[i], graph->tvwgt[i]);
- printf(" ]\n");
-}
-
-
-/*************************************************************************/
-/*! This function creates the coarser graph. It uses a simple hash-table
- for identifying the adjacent vertices that get collapsed to the same
- node. The hash-table can have conflicts, which are handled via a
- linear scan.
- */
-/*************************************************************************/
-void CreateCoarseGraph(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match)
-{
- idx_t j, jj, k, kk, l, m, istart, iend, nvtxs, nedges, ncon, cnedges,
- v, u, mask, dovsize;
- idx_t *xadj, *vwgt, *vsize, *adjncy, *adjwgt;
- idx_t *cmap, *htable;
- idx_t *cxadj, *cvwgt, *cvsize, *cadjncy, *cadjwgt;
- graph_t *cgraph;
-
- dovsize = (ctrl->objtype == METIS_OBJTYPE_VOL ? 1 : 0);
-
- /* Check if the mask-version of the code is a good choice */
- mask = HTLENGTH;
- if (cnvtxs < 2*mask || graph->nedges/graph->nvtxs > mask/20) {
- CreateCoarseGraphNoMask(ctrl, graph, cnvtxs, match);
- return;
- }
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- for (v=0; v<nvtxs; v++) {
- if (xadj[v+1]-xadj[v] > (mask>>3)) {
- CreateCoarseGraphNoMask(ctrl, graph, cnvtxs, match);
- return;
- }
- }
-
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ContractTmr));
-
- ncon = graph->ncon;
- vwgt = graph->vwgt;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- cmap = graph->cmap;
-
- /* Initialize the coarser graph */
- cgraph = SetupCoarseGraph(graph, cnvtxs, dovsize);
- cxadj = cgraph->xadj;
- cvwgt = cgraph->vwgt;
- cvsize = cgraph->vsize;
- cadjncy = cgraph->adjncy;
- cadjwgt = cgraph->adjwgt;
-
- htable = iset(gk_min(cnvtxs+1, mask+1), -1, iwspacemalloc(ctrl, mask+1));
-
- cxadj[0] = cnvtxs = cnedges = 0;
- for (v=0; v<nvtxs; v++) {
- if ((u = match[v]) < v)
- continue;
-
- ASSERT(cmap[v] == cnvtxs);
- ASSERT(cmap[match[v]] == cnvtxs);
-
- if (ncon == 1)
- cvwgt[cnvtxs] = vwgt[v];
- else
- icopy(ncon, vwgt+v*ncon, cvwgt+cnvtxs*ncon);
-
- if (dovsize)
- cvsize[cnvtxs] = vsize[v];
-
- nedges = 0;
-
- istart = xadj[v];
- iend = xadj[v+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- kk = k&mask;
- if ((m = htable[kk]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[kk] = nedges++;
- }
- else if (cadjncy[m] == k) {
- cadjwgt[m] += adjwgt[j];
- }
- else {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == k) {
- cadjwgt[jj] += adjwgt[j];
- break;
- }
- }
- if (jj == nedges) {
- cadjncy[nedges] = k;
- cadjwgt[nedges++] = adjwgt[j];
- }
- }
- }
-
- if (v != u) {
- if (ncon == 1)
- cvwgt[cnvtxs] += vwgt[u];
- else
- iaxpy(ncon, 1, vwgt+u*ncon, 1, cvwgt+cnvtxs*ncon, 1);
-
- if (dovsize)
- cvsize[cnvtxs] += vsize[u];
-
- istart = xadj[u];
- iend = xadj[u+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- kk = k&mask;
- if ((m = htable[kk]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[kk] = nedges++;
- }
- else if (cadjncy[m] == k) {
- cadjwgt[m] += adjwgt[j];
- }
- else {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == k) {
- cadjwgt[jj] += adjwgt[j];
- break;
- }
- }
- if (jj == nedges) {
- cadjncy[nedges] = k;
- cadjwgt[nedges++] = adjwgt[j];
- }
- }
- }
-
- /* Remove the contracted adjacency weight */
- jj = htable[cnvtxs&mask];
- if (jj >= 0 && cadjncy[jj] != cnvtxs) {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == cnvtxs)
- break;
- }
- }
- /* This 2nd check is needed for non-adjacent matchings */
- if (jj >= 0 && jj < nedges && cadjncy[jj] == cnvtxs) {
- cadjncy[jj] = cadjncy[--nedges];
- cadjwgt[jj] = cadjwgt[nedges];
- }
- }
-
- /* Zero out the htable */
- for (j=0; j<nedges; j++)
- htable[cadjncy[j]&mask] = -1;
- htable[cnvtxs&mask] = -1;
-
- cnedges += nedges;
- cxadj[++cnvtxs] = cnedges;
- cadjncy += nedges;
- cadjwgt += nedges;
- }
-
- cgraph->nedges = cnedges;
-
- for (j=0; j<ncon; j++) {
- cgraph->tvwgt[j] = isum(cgraph->nvtxs, cgraph->vwgt+j, ncon);
- cgraph->invtvwgt[j] = 1.0/(cgraph->tvwgt[j] > 0 ? cgraph->tvwgt[j] : 1);
- }
-
-
- ReAdjustMemory(ctrl, graph, cgraph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ContractTmr));
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function creates the coarser graph. It uses a full-size array
- (htable) for identifying the adjacent vertices that get collapsed to
- the same node.
- */
-/*************************************************************************/
-void CreateCoarseGraphNoMask(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match)
-{
- idx_t j, k, m, istart, iend, nvtxs, nedges, ncon, cnedges, v, u, dovsize;
- idx_t *xadj, *vwgt, *vsize, *adjncy, *adjwgt;
- idx_t *cmap, *htable;
- idx_t *cxadj, *cvwgt, *cvsize, *cadjncy, *cadjwgt;
- graph_t *cgraph;
-
- WCOREPUSH;
-
- dovsize = (ctrl->objtype == METIS_OBJTYPE_VOL ? 1 : 0);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ContractTmr));
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- cmap = graph->cmap;
-
-
- /* Initialize the coarser graph */
- cgraph = SetupCoarseGraph(graph, cnvtxs, dovsize);
- cxadj = cgraph->xadj;
- cvwgt = cgraph->vwgt;
- cvsize = cgraph->vsize;
- cadjncy = cgraph->adjncy;
- cadjwgt = cgraph->adjwgt;
-
- htable = iset(cnvtxs, -1, iwspacemalloc(ctrl, cnvtxs));
-
- cxadj[0] = cnvtxs = cnedges = 0;
- for (v=0; v<nvtxs; v++) {
- if ((u = match[v]) < v)
- continue;
-
- ASSERT(cmap[v] == cnvtxs);
- ASSERT(cmap[match[v]] == cnvtxs);
-
- if (ncon == 1)
- cvwgt[cnvtxs] = vwgt[v];
- else
- icopy(ncon, vwgt+v*ncon, cvwgt+cnvtxs*ncon);
-
- if (dovsize)
- cvsize[cnvtxs] = vsize[v];
-
- nedges = 0;
-
- istart = xadj[v];
- iend = xadj[v+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- if ((m = htable[k]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[k] = nedges++;
- }
- else {
- cadjwgt[m] += adjwgt[j];
- }
- }
-
- if (v != u) {
- if (ncon == 1)
- cvwgt[cnvtxs] += vwgt[u];
- else
- iaxpy(ncon, 1, vwgt+u*ncon, 1, cvwgt+cnvtxs*ncon, 1);
-
- if (dovsize)
- cvsize[cnvtxs] += vsize[u];
-
- istart = xadj[u];
- iend = xadj[u+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- if ((m = htable[k]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[k] = nedges++;
- }
- else {
- cadjwgt[m] += adjwgt[j];
- }
- }
-
- /* Remove the contracted adjacency weight */
- if ((j = htable[cnvtxs]) != -1) {
- ASSERT(cadjncy[j] == cnvtxs);
- cadjncy[j] = cadjncy[--nedges];
- cadjwgt[j] = cadjwgt[nedges];
- htable[cnvtxs] = -1;
- }
- }
-
- /* Zero out the htable */
- for (j=0; j<nedges; j++)
- htable[cadjncy[j]] = -1;
-
- cnedges += nedges;
- cxadj[++cnvtxs] = cnedges;
- cadjncy += nedges;
- cadjwgt += nedges;
- }
-
- cgraph->nedges = cnedges;
-
- for (j=0; j<ncon; j++) {
- cgraph->tvwgt[j] = isum(cgraph->nvtxs, cgraph->vwgt+j, ncon);
- cgraph->invtvwgt[j] = 1.0/(cgraph->tvwgt[j] > 0 ? cgraph->tvwgt[j] : 1);
- }
-
- ReAdjustMemory(ctrl, graph, cgraph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ContractTmr));
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function creates the coarser graph. It uses a simple hash-table
- for identifying the adjacent vertices that get collapsed to the same
- node. The hash-table can have conflicts, which are handled via a
- linear scan. It relies on the perm[] array to visit the vertices in
- increasing cnvtxs order.
- */
-/*************************************************************************/
-void CreateCoarseGraphPerm(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match, idx_t *perm)
-{
- idx_t i, j, jj, k, kk, l, m, istart, iend, nvtxs, nedges, ncon, cnedges,
- v, u, mask, dovsize;
- idx_t *xadj, *vwgt, *vsize, *adjncy, *adjwgt;
- idx_t *cmap, *htable;
- idx_t *cxadj, *cvwgt, *cvsize, *cadjncy, *cadjwgt;
- graph_t *cgraph;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ContractTmr));
-
- dovsize = (ctrl->objtype == METIS_OBJTYPE_VOL ? 1 : 0);
-
- mask = HTLENGTH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- cmap = graph->cmap;
-
- /* Initialize the coarser graph */
- cgraph = SetupCoarseGraph(graph, cnvtxs, dovsize);
- cxadj = cgraph->xadj;
- cvwgt = cgraph->vwgt;
- cvsize = cgraph->vsize;
- cadjncy = cgraph->adjncy;
- cadjwgt = cgraph->adjwgt;
-
- htable = iset(mask+1, -1, iwspacemalloc(ctrl, mask+1));
-
- cxadj[0] = cnvtxs = cnedges = 0;
- for (i=0; i<nvtxs; i++) {
- v = perm[i];
- if (cmap[v] != cnvtxs)
- continue;
-
- u = match[v];
- if (ncon == 1)
- cvwgt[cnvtxs] = vwgt[v];
- else
- icopy(ncon, vwgt+v*ncon, cvwgt+cnvtxs*ncon);
-
- if (dovsize)
- cvsize[cnvtxs] = vsize[v];
-
- nedges = 0;
-
- istart = xadj[v];
- iend = xadj[v+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- kk = k&mask;
- if ((m = htable[kk]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[kk] = nedges++;
- }
- else if (cadjncy[m] == k) {
- cadjwgt[m] += adjwgt[j];
- }
- else {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == k) {
- cadjwgt[jj] += adjwgt[j];
- break;
- }
- }
- if (jj == nedges) {
- cadjncy[nedges] = k;
- cadjwgt[nedges++] = adjwgt[j];
- }
- }
- }
-
- if (v != u) {
- if (ncon == 1)
- cvwgt[cnvtxs] += vwgt[u];
- else
- iaxpy(ncon, 1, vwgt+u*ncon, 1, cvwgt+cnvtxs*ncon, 1);
-
- if (dovsize)
- cvsize[cnvtxs] += vsize[u];
-
- istart = xadj[u];
- iend = xadj[u+1];
- for (j=istart; j<iend; j++) {
- k = cmap[adjncy[j]];
- kk = k&mask;
- if ((m = htable[kk]) == -1) {
- cadjncy[nedges] = k;
- cadjwgt[nedges] = adjwgt[j];
- htable[kk] = nedges++;
- }
- else if (cadjncy[m] == k) {
- cadjwgt[m] += adjwgt[j];
- }
- else {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == k) {
- cadjwgt[jj] += adjwgt[j];
- break;
- }
- }
- if (jj == nedges) {
- cadjncy[nedges] = k;
- cadjwgt[nedges++] = adjwgt[j];
- }
- }
- }
-
- /* Remove the contracted adjacency weight */
- jj = htable[cnvtxs&mask];
- if (jj >= 0 && cadjncy[jj] != cnvtxs) {
- for (jj=0; jj<nedges; jj++) {
- if (cadjncy[jj] == cnvtxs)
- break;
- }
- }
- if (jj >= 0 && cadjncy[jj] == cnvtxs) { /* This 2nd check is needed for non-adjacent matchings */
- cadjncy[jj] = cadjncy[--nedges];
- cadjwgt[jj] = cadjwgt[nedges];
- }
- }
-
- for (j=0; j<nedges; j++)
- htable[cadjncy[j]&mask] = -1; /* Zero out the htable */
- htable[cnvtxs&mask] = -1;
-
- cnedges += nedges;
- cxadj[++cnvtxs] = cnedges;
- cadjncy += nedges;
- cadjwgt += nedges;
- }
-
- cgraph->nedges = cnedges;
-
- for (i=0; i<ncon; i++) {
- cgraph->tvwgt[i] = isum(cgraph->nvtxs, cgraph->vwgt+i, ncon);
- cgraph->invtvwgt[i] = 1.0/(cgraph->tvwgt[i] > 0 ? cgraph->tvwgt[i] : 1);
- }
-
-
- ReAdjustMemory(ctrl, graph, cgraph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ContractTmr));
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! Setup the various arrays for the coarse graph
- */
-/*************************************************************************/
-graph_t *SetupCoarseGraph(graph_t *graph, idx_t cnvtxs, idx_t dovsize)
-{
- graph_t *cgraph;
-
- cgraph = CreateGraph();
-
- cgraph->nvtxs = cnvtxs;
- cgraph->ncon = graph->ncon;
-
- cgraph->finer = graph;
- graph->coarser = cgraph;
-
-
- /* Allocate memory for the coarser graph */
- cgraph->xadj = imalloc(cnvtxs+1, "SetupCoarseGraph: xadj");
- cgraph->adjncy = imalloc(graph->nedges, "SetupCoarseGraph: adjncy");
- cgraph->adjwgt = imalloc(graph->nedges, "SetupCoarseGraph: adjwgt");
- cgraph->vwgt = imalloc(cgraph->ncon*cnvtxs, "SetupCoarseGraph: vwgt");
- cgraph->tvwgt = imalloc(cgraph->ncon, "SetupCoarseGraph: tvwgt");
- cgraph->invtvwgt = rmalloc(cgraph->ncon, "SetupCoarseGraph: invtvwgt");
-
- if (dovsize)
- cgraph->vsize = imalloc(cnvtxs, "SetupCoarseGraph: vsize");
-
- return cgraph;
-}
-
-
-/*************************************************************************/
-/*! This function re-adjusts the amount of memory that was allocated if
- it will lead to significant savings
- */
-/*************************************************************************/
-void ReAdjustMemory(ctrl_t *ctrl, graph_t *graph, graph_t *cgraph)
-{
- if (cgraph->nedges > 10000 && cgraph->nedges < 0.9*graph->nedges) {
- cgraph->adjncy = irealloc(cgraph->adjncy, cgraph->nedges, "ReAdjustMemory: adjncy");
- cgraph->adjwgt = irealloc(cgraph->adjwgt, cgraph->nedges, "ReAdjustMemory: adjwgt");
- }
-}
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/compress.c b/3rdParty/metis/metis-5.1.0/libmetis/compress.c
deleted file mode 100644
index d72472b25..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/compress.c
+++ /dev/null
@@ -1,229 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * compress.c
- *
- * This file contains code for compressing nodes with identical adjacency
- * structure and for prunning dense columns
- *
- * Started 9/17/97
- * George
- */
-
-#include "metislib.h"
-
-/*************************************************************************/
-/*! This function compresses a graph by merging identical vertices
- The compression should lead to at least 10% reduction.
-
- The compressed graph that is generated has its adjwgts set to 1.
-
- \returns 1 if compression was performed, otherwise it returns 0.
-
-*/
-/**************************************************************************/
-graph_t *CompressGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *cptr, idx_t *cind)
-{
- idx_t i, ii, iii, j, jj, k, l, cnvtxs, cnedges;
- idx_t *cxadj, *cadjncy, *cvwgt, *mark, *map;
- ikv_t *keys;
- graph_t *graph=NULL;
-
- mark = ismalloc(nvtxs, -1, "CompressGraph: mark");
- map = ismalloc(nvtxs, -1, "CompressGraph: map");
- keys = ikvmalloc(nvtxs, "CompressGraph: keys");
-
- /* Compute a key for each adjacency list */
- for (i=0; i<nvtxs; i++) {
- k = 0;
- for (j=xadj[i]; j<xadj[i+1]; j++)
- k += adjncy[j];
- keys[i].key = k+i; /* Add the diagonal entry as well */
- keys[i].val = i;
- }
-
- ikvsorti(nvtxs, keys);
-
- l = cptr[0] = 0;
- for (cnvtxs=i=0; i<nvtxs; i++) {
- ii = keys[i].val;
- if (map[ii] == -1) {
- mark[ii] = i; /* Add the diagonal entry */
- for (j=xadj[ii]; j<xadj[ii+1]; j++)
- mark[adjncy[j]] = i;
-
- map[ii] = cnvtxs;
- cind[l++] = ii;
-
- for (j=i+1; j<nvtxs; j++) {
- iii = keys[j].val;
-
- if (keys[i].key != keys[j].key || xadj[ii+1]-xadj[ii] != xadj[iii+1]-xadj[iii])
- break; /* Break if keys or degrees are different */
-
- if (map[iii] == -1) { /* Do a comparison if iii has not been mapped */
- for (jj=xadj[iii]; jj<xadj[iii+1]; jj++) {
- if (mark[adjncy[jj]] != i)
- break;
- }
-
- if (jj == xadj[iii+1]) { /* Identical adjacency structure */
- map[iii] = cnvtxs;
- cind[l++] = iii;
- }
- }
- }
-
- cptr[++cnvtxs] = l;
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_INFO,
- printf(" Compression: reduction in # of vertices: %"PRIDX".\n", nvtxs-cnvtxs));
-
-
- if (cnvtxs < COMPRESSION_FRACTION*nvtxs) {
- /* Sufficient compression is possible, so go ahead and create the
- compressed graph */
-
- graph = CreateGraph();
-
- cnedges = 0;
- for (i=0; i<cnvtxs; i++) {
- ii = cind[cptr[i]];
- cnedges += xadj[ii+1]-xadj[ii];
- }
-
- /* Allocate memory for the compressed graph */
- cxadj = graph->xadj = imalloc(cnvtxs+1, "CompressGraph: xadj");
- cvwgt = graph->vwgt = ismalloc(cnvtxs, 0, "CompressGraph: vwgt");
- cadjncy = graph->adjncy = imalloc(cnedges, "CompressGraph: adjncy");
- graph->adjwgt = ismalloc(cnedges, 1, "CompressGraph: adjwgt");
-
- /* Now go and compress the graph */
- iset(nvtxs, -1, mark);
- l = cxadj[0] = 0;
- for (i=0; i<cnvtxs; i++) {
- mark[i] = i; /* Remove any dioganal entries in the compressed graph */
- for (j=cptr[i]; j<cptr[i+1]; j++) {
- ii = cind[j];
-
- /* accumulate the vertex weights of the consistuent vertices */
- cvwgt[i] += (vwgt == NULL ? 1 : vwgt[ii]);
-
- /* generate the combined adjancency list */
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++) {
- k = map[adjncy[jj]];
- if (mark[k] != i) {
- mark[k] = i;
- cadjncy[l++] = k;
- }
- }
- }
- cxadj[i+1] = l;
- }
-
- graph->nvtxs = cnvtxs;
- graph->nedges = l;
- graph->ncon = 1;
-
- SetupGraph_tvwgt(graph);
- SetupGraph_label(graph);
- }
-
- gk_free((void **)&keys, &map, &mark, LTERM);
-
- return graph;
-
-}
-
-
-
-/*************************************************************************/
-/*! This function prunes all the vertices in a graph with degree greater
- than factor*average.
-
- \returns the number of vertices that were prunned.
-*/
-/*************************************************************************/
-graph_t *PruneGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *iperm, real_t factor)
-{
- idx_t i, j, k, l, nlarge, pnvtxs, pnedges;
- idx_t *pxadj, *padjncy, *padjwgt, *pvwgt;
- idx_t *perm;
- graph_t *graph=NULL;
-
- perm = imalloc(nvtxs, "PruneGraph: perm");
-
- factor = factor*xadj[nvtxs]/nvtxs;
-
- pnvtxs = pnedges = nlarge = 0;
- for (i=0; i<nvtxs; i++) {
- if (xadj[i+1]-xadj[i] < factor) {
- perm[i] = pnvtxs;
- iperm[pnvtxs++] = i;
- pnedges += xadj[i+1]-xadj[i];
- }
- else {
- perm[i] = nvtxs - ++nlarge;
- iperm[nvtxs-nlarge] = i;
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_INFO,
- printf(" Pruned %"PRIDX" of %"PRIDX" vertices.\n", nlarge, nvtxs));
-
-
- if (nlarge > 0 && nlarge < nvtxs) {
- /* Prunning is possible, so go ahead and create the prunned graph */
- graph = CreateGraph();
-
- /* Allocate memory for the prunned graph*/
- pxadj = graph->xadj = imalloc(pnvtxs+1, "PruneGraph: xadj");
- pvwgt = graph->vwgt = imalloc(pnvtxs, "PruneGraph: vwgt");
- padjncy = graph->adjncy = imalloc(pnedges, "PruneGraph: adjncy");
- graph->adjwgt = ismalloc(pnedges, 1, "PruneGraph: adjwgt");
-
- pxadj[0] = pnedges = l = 0;
- for (i=0; i<nvtxs; i++) {
- if (xadj[i+1]-xadj[i] < factor) {
- pvwgt[l] = (vwgt == NULL ? 1 : vwgt[i]);
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = perm[adjncy[j]];
- if (k < pnvtxs)
- padjncy[pnedges++] = k;
- }
- pxadj[++l] = pnedges;
- }
- }
-
- graph->nvtxs = pnvtxs;
- graph->nedges = pnedges;
- graph->ncon = 1;
-
- SetupGraph_tvwgt(graph);
- SetupGraph_label(graph);
- }
- else if (nlarge > 0 && nlarge == nvtxs) {
- IFSET(ctrl->dbglvl, METIS_DBG_INFO,
- printf(" Pruning is ignored as it removes all vertices.\n"));
- nlarge = 0;
- }
-
-
- gk_free((void **)&perm, LTERM);
-
- return graph;
-}
-
-
-
-
-
-
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/contig.c b/3rdParty/metis/metis-5.1.0/libmetis/contig.c
deleted file mode 100644
index 3f45902db..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/contig.c
+++ /dev/null
@@ -1,699 +0,0 @@
-/*!
-\file
-\brief Functions that deal with eliminating disconnected partitions
-
-\date Started 7/15/98
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version $Id: contig.c 10513 2011-07-07 22:06:03Z karypis $
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function finds the connected components induced by the
- partitioning vector.
-
- \param graph is the graph structure
- \param where is the partitioning vector. If this is NULL, then the
- entire graph is treated to belong into a single partition.
- \param cptr is the ptr structure of the CSR representation of the
- components. The length of this vector must be graph->nvtxs+1.
- \param cind is the indices structure of the CSR representation of
- the components. The length of this vector must be graph->nvtxs.
-
- \returns the number of components that it found.
-
- \note The cptr and cind parameters can be NULL, in which case only the
- number of connected components is returned.
-*/
-/*************************************************************************/
-idx_t FindPartitionInducedComponents(graph_t *graph, idx_t *where,
- idx_t *cptr, idx_t *cind)
-{
- idx_t i, ii, j, jj, k, me=0, nvtxs, first, last, nleft, ncmps;
- idx_t *xadj, *adjncy;
- idx_t *touched, *perm, *todo;
- idx_t mustfree_ccsr=0, mustfree_where=0;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* Deal with NULL supplied cptr/cind vectors */
- if (cptr == NULL) {
- cptr = imalloc(nvtxs+1, "FindPartitionInducedComponents: cptr");
- cind = imalloc(nvtxs, "FindPartitionInducedComponents: cind");
- mustfree_ccsr = 1;
- }
-
- /* Deal with NULL supplied where vector */
- if (where == NULL) {
- where = ismalloc(nvtxs, 0, "FindPartitionInducedComponents: where");
- mustfree_where = 1;
- }
-
- /* Allocate memory required for the BFS traversal */
- perm = iincset(nvtxs, 0, imalloc(nvtxs, "FindPartitionInducedComponents: perm"));
- todo = iincset(nvtxs, 0, imalloc(nvtxs, "FindPartitionInducedComponents: todo"));
- touched = ismalloc(nvtxs, 0, "FindPartitionInducedComponents: touched");
-
-
- /* Find the connected componends induced by the partition */
- ncmps = -1;
- first = last = 0;
- nleft = nvtxs;
- while (nleft > 0) {
- if (first == last) { /* Find another starting vertex */
- cptr[++ncmps] = first;
- ASSERT(touched[todo[0]] == 0);
- i = todo[0];
- cind[last++] = i;
- touched[i] = 1;
- me = where[i];
- }
-
- i = cind[first++];
- k = perm[i];
- j = todo[k] = todo[--nleft];
- perm[j] = k;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (where[k] == me && !touched[k]) {
- cind[last++] = k;
- touched[k] = 1;
- }
- }
- }
- cptr[++ncmps] = first;
-
- if (mustfree_ccsr)
- gk_free((void **)&cptr, &cind, LTERM);
- if (mustfree_where)
- gk_free((void **)&where, LTERM);
-
- gk_free((void **)&perm, &todo, &touched, LTERM);
-
- return ncmps;
-}
-
-
-/*************************************************************************/
-/*! This function computes a permutation of the vertices based on a
- breadth-first-traversal. It can be used for re-ordering the graph
- to reduce its bandwidth for better cache locality.
-
- \param ctrl is the control structure
- \param graph is the graph structure
- \param perm is the array that upon completion, perm[i] will store
- the ID of the vertex that corresponds to the ith vertex in the
- re-ordered graph.
-*/
-/*************************************************************************/
-void ComputeBFSOrdering(ctrl_t *ctrl, graph_t *graph, idx_t *bfsperm)
-{
- idx_t i, j, k, nvtxs, first, last;
- idx_t *xadj, *adjncy, *perm;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* Allocate memory required for the BFS traversal */
- perm = iincset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
-
- iincset(nvtxs, 0, bfsperm); /* this array will also store the vertices
- still to be processed */
-
- /* Find the connected componends induced by the partition */
- first = last = 0;
- while (first < nvtxs) {
- if (first == last) { /* Find another starting vertex */
- k = bfsperm[last];
- ASSERT(perm[k] != -1);
- perm[k] = -1; /* mark node as being visited */
- last++;
- }
-
- i = bfsperm[first++];
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- /* if a node has been already been visited, its perm[] will be -1 */
- if (perm[k] != -1) {
- /* perm[k] is the location within bfsperm of where k resides;
- put in that location bfsperm[last] that we are about to
- overwrite and update perm[bfsperm[last]] to reflect that. */
- bfsperm[perm[k]] = bfsperm[last];
- perm[bfsperm[last]] = perm[k];
-
- bfsperm[last++] = k; /* put node at the end of the "queue" */
- perm[k] = -1; /* mark node as being visited */
- }
- }
- }
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function checks whether a graph is contiguous or not.
- */
-/**************************************************************************/
-idx_t IsConnected(graph_t *graph, idx_t report)
-{
- idx_t ncmps;
-
- ncmps = FindPartitionInducedComponents(graph, NULL, NULL, NULL);
-
- if (ncmps != 1 && report)
- printf("The graph is not connected. It has %"PRIDX" connected components.\n", ncmps);
-
- return (ncmps == 1);
-}
-
-
-/*************************************************************************/
-/*! This function checks whether or not partition pid is contigous
- */
-/*************************************************************************/
-idx_t IsConnectedSubdomain(ctrl_t *ctrl, graph_t *graph, idx_t pid, idx_t report)
-{
- idx_t i, j, k, nvtxs, first, last, nleft, ncmps, wgt;
- idx_t *xadj, *adjncy, *where, *touched, *queue;
- idx_t *cptr;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
-
- touched = ismalloc(nvtxs, 0, "IsConnected: touched");
- queue = imalloc(nvtxs, "IsConnected: queue");
- cptr = imalloc(nvtxs+1, "IsConnected: cptr");
-
- nleft = 0;
- for (i=0; i<nvtxs; i++) {
- if (where[i] == pid)
- nleft++;
- }
-
- for (i=0; i<nvtxs; i++) {
- if (where[i] == pid)
- break;
- }
-
- touched[i] = 1;
- queue[0] = i;
- first = 0; last = 1;
-
- cptr[0] = 0; /* This actually points to queue */
- ncmps = 0;
- while (first != nleft) {
- if (first == last) { /* Find another starting vertex */
- cptr[++ncmps] = first;
- for (i=0; i<nvtxs; i++) {
- if (where[i] == pid && !touched[i])
- break;
- }
- queue[last++] = i;
- touched[i] = 1;
- }
-
- i = queue[first++];
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (where[k] == pid && !touched[k]) {
- queue[last++] = k;
- touched[k] = 1;
- }
- }
- }
- cptr[++ncmps] = first;
-
- if (ncmps > 1 && report) {
- printf("The graph has %"PRIDX" connected components in partition %"PRIDX":\t", ncmps, pid);
- for (i=0; i<ncmps; i++) {
- wgt = 0;
- for (j=cptr[i]; j<cptr[i+1]; j++)
- wgt += graph->vwgt[queue[j]];
- printf("[%5"PRIDX" %5"PRIDX"] ", cptr[i+1]-cptr[i], wgt);
- /*
- if (cptr[i+1]-cptr[i] == 1)
- printf("[%"PRIDX" %"PRIDX"] ", queue[cptr[i]], xadj[queue[cptr[i]]+1]-xadj[queue[cptr[i]]]);
- */
- }
- printf("\n");
- }
-
- gk_free((void **)&touched, &queue, &cptr, LTERM);
-
- return (ncmps == 1 ? 1 : 0);
-}
-
-
-/*************************************************************************/
-/*! This function identifies the number of connected components in a graph
- that result after removing the vertices that belong to the vertex
- separator (i.e., graph->where[i] == 2).
- The connected component memberships are returned in the CSR-style
- pair of arrays cptr, cind.
-*/
-/**************************************************************************/
-idx_t FindSepInducedComponents(ctrl_t *ctrl, graph_t *graph, idx_t *cptr,
- idx_t *cind)
-{
- idx_t i, j, k, nvtxs, first, last, nleft, ncmps, wgt;
- idx_t *xadj, *adjncy, *where, *touched, *queue;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
-
- touched = ismalloc(nvtxs, 0, "IsConnected: queue");
-
- for (i=0; i<graph->nbnd; i++)
- touched[graph->bndind[i]] = 1;
-
- queue = cind;
-
- nleft = 0;
- for (i=0; i<nvtxs; i++) {
- if (where[i] != 2)
- nleft++;
- }
-
- for (i=0; i<nvtxs; i++) {
- if (where[i] != 2)
- break;
- }
-
- touched[i] = 1;
- queue[0] = i;
- first = 0;
- last = 1;
- cptr[0] = 0; /* This actually points to queue */
- ncmps = 0;
-
- while (first != nleft) {
- if (first == last) { /* Find another starting vertex */
- cptr[++ncmps] = first;
- for (i=0; i<nvtxs; i++) {
- if (!touched[i])
- break;
- }
- queue[last++] = i;
- touched[i] = 1;
- }
-
- i = queue[first++];
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (!touched[k]) {
- queue[last++] = k;
- touched[k] = 1;
- }
- }
- }
- cptr[++ncmps] = first;
-
- gk_free((void **)&touched, LTERM);
-
- return ncmps;
-}
-
-
-/*************************************************************************/
-/*! This function finds all the connected components induced by the
- partitioning vector in graph->where and tries to push them around to
- remove some of them. */
-/*************************************************************************/
-void EliminateComponents(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, jj, k, me, nparts, nvtxs, ncon, ncmps, other,
- ncand, target;
- idx_t *xadj, *adjncy, *vwgt, *adjwgt, *where, *pwgts;
- idx_t *cptr, *cind, *cpvec, *pcptr, *pcind, *cwhere;
- idx_t cid, bestcid, *cwgt, *bestcwgt;
- idx_t ntodo, oldntodo, *todo;
- rkv_t *cand;
- real_t *tpwgts;
- idx_t *vmarker=NULL, *pmarker=NULL, *modind=NULL; /* volume specific work arrays */
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
- adjwgt = (ctrl->objtype == METIS_OBJTYPE_VOL ? NULL : graph->adjwgt);
-
- where = graph->where;
- pwgts = graph->pwgts;
-
- nparts = ctrl->nparts;
- tpwgts = ctrl->tpwgts;
-
- cptr = iwspacemalloc(ctrl, nvtxs+1);
- cind = iwspacemalloc(ctrl, nvtxs);
-
- ncmps = FindPartitionInducedComponents(graph, where, cptr, cind);
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONTIGINFO,
- printf("I found %"PRIDX" components, for this %"PRIDX"-way partition\n",
- ncmps, nparts));
-
- /* There are more components than partitions */
- if (ncmps > nparts) {
- cwgt = iwspacemalloc(ctrl, ncon);
- bestcwgt = iwspacemalloc(ctrl, ncon);
- cpvec = iwspacemalloc(ctrl, nparts);
- pcptr = iset(nparts+1, 0, iwspacemalloc(ctrl, nparts+1));
- pcind = iwspacemalloc(ctrl, ncmps);
- cwhere = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- todo = iwspacemalloc(ctrl, ncmps);
- cand = (rkv_t *)wspacemalloc(ctrl, nparts*sizeof(rkv_t));
-
- if (ctrl->objtype == METIS_OBJTYPE_VOL) {
- /* Vol-refinement specific working arrays */
- modind = iwspacemalloc(ctrl, nvtxs);
- vmarker = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- pmarker = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
- }
-
-
- /* Get a CSR representation of the components-2-partitions mapping */
- for (i=0; i<ncmps; i++)
- pcptr[where[cind[cptr[i]]]]++;
- MAKECSR(i, nparts, pcptr);
- for (i=0; i<ncmps; i++)
- pcind[pcptr[where[cind[cptr[i]]]]++] = i;
- SHIFTCSR(i, nparts, pcptr);
-
- /* Assign the heaviest component of each partition to its original partition */
- for (ntodo=0, i=0; i<nparts; i++) {
- if (pcptr[i+1]-pcptr[i] == 1)
- bestcid = pcind[pcptr[i]];
- else {
- for (bestcid=-1, j=pcptr[i]; j<pcptr[i+1]; j++) {
- cid = pcind[j];
- iset(ncon, 0, cwgt);
- for (ii=cptr[cid]; ii<cptr[cid+1]; ii++)
- iaxpy(ncon, 1, vwgt+cind[ii]*ncon, 1, cwgt, 1);
- if (bestcid == -1 || isum(ncon, bestcwgt, 1) < isum(ncon, cwgt, 1)) {
- bestcid = cid;
- icopy(ncon, cwgt, bestcwgt);
- }
- }
- /* Keep track of those that need to be dealt with */
- for (j=pcptr[i]; j<pcptr[i+1]; j++) {
- if (pcind[j] != bestcid)
- todo[ntodo++] = pcind[j];
- }
- }
-
- for (j=cptr[bestcid]; j<cptr[bestcid+1]; j++) {
- ASSERT(where[cind[j]] == i);
- cwhere[cind[j]] = i;
- }
- }
-
-
- while (ntodo > 0) {
- oldntodo = ntodo;
- for (i=0; i<ntodo; i++) {
- cid = todo[i];
- me = where[cind[cptr[cid]]]; /* Get the domain of this component */
-
- /* Determine the weight of the block to be moved */
- iset(ncon, 0, cwgt);
- for (j=cptr[cid]; j<cptr[cid+1]; j++)
- iaxpy(ncon, 1, vwgt+cind[j]*ncon, 1, cwgt, 1);
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONTIGINFO,
- printf("Trying to move %"PRIDX" [%"PRIDX"] from %"PRIDX"\n",
- cid, isum(ncon, cwgt, 1), me));
-
- /* Determine the connectivity */
- iset(nparts, 0, cpvec);
- for (j=cptr[cid]; j<cptr[cid+1]; j++) {
- ii = cind[j];
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++)
- if (cwhere[adjncy[jj]] != -1)
- cpvec[cwhere[adjncy[jj]]] += (adjwgt ? adjwgt[jj] : 1);
- }
-
- /* Put the neighbors into a cand[] array for sorting */
- for (ncand=0, j=0; j<nparts; j++) {
- if (cpvec[j] > 0) {
- cand[ncand].key = cpvec[j];
- cand[ncand++].val = j;
- }
- }
- if (ncand == 0)
- continue;
-
- rkvsortd(ncand, cand);
-
- /* Limit the moves to only the top candidates, which are defined as
- those with connectivity at least 50% of the best.
- This applies only when ncon=1, as for multi-constraint, balancing
- will be hard. */
- if (ncon == 1) {
- for (j=1; j<ncand; j++) {
- if (cand[j].key < .5*cand[0].key)
- break;
- }
- ncand = j;
- }
-
- /* Now among those, select the one with the best balance */
- target = cand[0].val;
- for (j=1; j<ncand; j++) {
- if (BetterBalanceKWay(ncon, cwgt, ctrl->ubfactors,
- 1, pwgts+target*ncon, ctrl->pijbm+target*ncon,
- 1, pwgts+cand[j].val*ncon, ctrl->pijbm+cand[j].val*ncon))
- target = cand[j].val;
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONTIGINFO,
- printf("\tMoving it to %"PRIDX" [%"PRIDX"] [%"PRIDX"]\n", target, cpvec[target], ncand));
-
- /* Note that as a result of a previous movement, a connected component may
- now will like to stay to its original partition */
- if (target != me) {
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- MoveGroupContigForCut(ctrl, graph, target, cid, cptr, cind);
- break;
-
- case METIS_OBJTYPE_VOL:
- MoveGroupContigForVol(ctrl, graph, target, cid, cptr, cind,
- vmarker, pmarker, modind);
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype %d\n", ctrl->objtype);
- }
- }
-
- /* Update the cwhere vector */
- for (j=cptr[cid]; j<cptr[cid+1]; j++)
- cwhere[cind[j]] = target;
-
- todo[i] = todo[--ntodo];
- }
- if (oldntodo == ntodo) {
- IFSET(ctrl->dbglvl, METIS_DBG_CONTIGINFO, printf("Stopped at ntodo: %"PRIDX"\n", ntodo));
- break;
- }
- }
-
- for (i=0; i<nvtxs; i++)
- ASSERT(where[i] == cwhere[i]);
-
- }
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function moves a collection of vertices and updates their rinfo
- */
-/*************************************************************************/
-void MoveGroupContigForCut(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t gid,
- idx_t *ptr, idx_t *ind)
-{
- idx_t i, ii, iii, j, jj, k, l, nvtxs, nbnd, from, me;
- idx_t *xadj, *adjncy, *adjwgt, *where, *bndptr, *bndind;
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- nbnd = graph->nbnd;
-
- for (iii=ptr[gid]; iii<ptr[gid+1]; iii++) {
- i = ind[iii];
- from = where[i];
-
- myrinfo = graph->ckrinfo+i;
- if (myrinfo->inbr == -1) {
- myrinfo->inbr = cnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- myrinfo->nnbrs = 0;
- }
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- /* find the location of 'to' in myrinfo or create it if it is not there */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == to)
- break;
- }
- if (k == myrinfo->nnbrs) {
- mynbrs[k].pid = to;
- mynbrs[k].ed = 0;
- myrinfo->nnbrs++;
- }
-
- graph->mincut -= mynbrs[k].ed-myrinfo->id;
-
- /* Update ID/ED and BND related information for the moved vertex */
- iaxpy(graph->ncon, 1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+to*graph->ncon, 1);
- iaxpy(graph->ncon, -1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+from*graph->ncon, 1);
- UpdateMovedVertexInfoAndBND(i, from, k, to, myrinfo, mynbrs, where, nbnd,
- bndptr, bndind, BNDTYPE_REFINE);
-
- /* Update the degrees of adjacent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- me = where[ii];
- myrinfo = graph->ckrinfo+ii;
-
- UpdateAdjacentVertexInfoAndBND(ctrl, ii, xadj[ii+1]-xadj[ii], me,
- from, to, myrinfo, adjwgt[j], nbnd, bndptr, bndind, BNDTYPE_REFINE);
- }
-
- ASSERT(CheckRInfo(ctrl, graph->ckrinfo+i));
- }
-
- graph->nbnd = nbnd;
-}
-
-
-/*************************************************************************/
-/*! This function moves a collection of vertices and updates their rinfo
- */
-/*************************************************************************/
-void MoveGroupContigForVol(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t gid,
- idx_t *ptr, idx_t *ind, idx_t *vmarker, idx_t *pmarker,
- idx_t *modind)
-{
- idx_t i, ii, iii, j, jj, k, l, nvtxs, from, me, other, xgain;
- idx_t *xadj, *vsize, *adjncy, *where;
- vkrinfo_t *myrinfo, *orinfo;
- vnbr_t *mynbrs, *onbrs;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- where = graph->where;
-
- for (iii=ptr[gid]; iii<ptr[gid+1]; iii++) {
- i = ind[iii];
- from = where[i];
-
- myrinfo = graph->vkrinfo+i;
- if (myrinfo->inbr == -1) {
- myrinfo->inbr = vnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- myrinfo->nnbrs = 0;
- }
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- xgain = (myrinfo->nid == 0 && myrinfo->ned > 0 ? vsize[i] : 0);
-
- /* find the location of 'to' in myrinfo or create it if it is not there */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == to)
- break;
- }
- if (k == myrinfo->nnbrs) {
- if (myrinfo->nid > 0)
- xgain -= vsize[i];
-
- /* determine the volume gain resulting from that move */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
- ASSERT(other != to)
-
- if (from == other) {
- /* Same subdomain vertex: Decrease the gain if 'to' is a new neighbor. */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == to)
- break;
- }
- if (l == orinfo->nnbrs)
- xgain -= vsize[ii];
- }
- else {
- /* Remote vertex: increase if 'to' is a new subdomain */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == to)
- break;
- }
- if (l == orinfo->nnbrs)
- xgain -= vsize[ii];
-
- /* Remote vertex: decrease if i is the only connection to 'from' */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == from && onbrs[l].ned == 1) {
- xgain += vsize[ii];
- break;
- }
- }
- }
- }
- graph->minvol -= xgain;
- graph->mincut -= -myrinfo->nid;
- }
- else {
- graph->minvol -= (xgain + mynbrs[k].gv);
- graph->mincut -= mynbrs[k].ned-myrinfo->nid;
- }
-
-
- /* Update where and pwgts */
- where[i] = to;
- iaxpy(graph->ncon, 1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+to*graph->ncon, 1);
- iaxpy(graph->ncon, -1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+from*graph->ncon, 1);
-
- /* Update the id/ed/gains/bnd of potentially affected nodes */
- KWayVolUpdate(ctrl, graph, i, from, to, NULL, NULL, NULL, NULL,
- NULL, BNDTYPE_REFINE, vmarker, pmarker, modind);
-
- /*CheckKWayVolPartitionParams(ctrl, graph);*/
- }
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERTP(ComputeVolume(graph, where) == graph->minvol,
- ("%"PRIDX" %"PRIDX"\n", ComputeVolume(graph, where), graph->minvol));
-
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/debug.c b/3rdParty/metis/metis-5.1.0/libmetis/debug.c
deleted file mode 100644
index e188135da..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/debug.c
+++ /dev/null
@@ -1,461 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * debug.c
- *
- * This file contains code that performs self debuging
- *
- * Started 7/24/97
- * George
- *
- */
-
-#include "metislib.h"
-
-
-
-/*************************************************************************/
-/*! This function computes the total edgecut
- */
-/*************************************************************************/
-idx_t ComputeCut(graph_t *graph, idx_t *where)
-{
- idx_t i, j, cut;
-
- if (graph->adjwgt == NULL) {
- for (cut=0, i=0; i<graph->nvtxs; i++) {
- for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++)
- if (where[i] != where[graph->adjncy[j]])
- cut++;
- }
- }
- else {
- for (cut=0, i=0; i<graph->nvtxs; i++) {
- for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++)
- if (where[i] != where[graph->adjncy[j]])
- cut += graph->adjwgt[j];
- }
- }
-
- return cut/2;
-}
-
-
-/*************************************************************************/
-/*! This function computes the total volume
- */
-/*************************************************************************/
-idx_t ComputeVolume(graph_t *graph, idx_t *where)
-{
- idx_t i, j, k, me, nvtxs, nparts, totalv;
- idx_t *xadj, *adjncy, *vsize, *marker;
-
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vsize = graph->vsize;
-
- nparts = where[iargmax(nvtxs, where)]+1;
- marker = ismalloc(nparts, -1, "ComputeVolume: marker");
-
- totalv = 0;
-
- for (i=0; i<nvtxs; i++) {
- marker[where[i]] = i;
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = where[adjncy[j]];
- if (marker[k] != i) {
- marker[k] = i;
- totalv += (vsize ? vsize[i] : 1);
- }
- }
- }
-
- gk_free((void **)&marker, LTERM);
-
- return totalv;
-}
-
-
-/*************************************************************************/
-/*! This function computes the cut given the graph and a where vector
- */
-/*************************************************************************/
-idx_t ComputeMaxCut(graph_t *graph, idx_t nparts, idx_t *where)
-{
- idx_t i, j, maxcut;
- idx_t *cuts;
-
- cuts = ismalloc(nparts, 0, "ComputeMaxCut: cuts");
-
- if (graph->adjwgt == NULL) {
- for (i=0; i<graph->nvtxs; i++) {
- for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++)
- if (where[i] != where[graph->adjncy[j]])
- cuts[where[i]]++;
- }
- }
- else {
- for (i=0; i<graph->nvtxs; i++) {
- for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++)
- if (where[i] != where[graph->adjncy[j]])
- cuts[where[i]] += graph->adjwgt[j];
- }
- }
-
- maxcut = cuts[iargmax(nparts, cuts)];
-
- printf("%zu => %"PRIDX"\n", iargmax(nparts, cuts), maxcut);
-
- gk_free((void **)&cuts, LTERM);
-
- return maxcut;
-}
-
-
-/*************************************************************************/
-/*! This function checks whether or not the boundary information is correct
- */
-/*************************************************************************/
-idx_t CheckBnd(graph_t *graph)
-{
- idx_t i, j, nvtxs, nbnd;
- idx_t *xadj, *adjncy, *where, *bndptr, *bndind;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- for (nbnd=0, i=0; i<nvtxs; i++) {
- if (xadj[i+1]-xadj[i] == 0)
- nbnd++; /* Islands are considered to be boundary vertices */
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (where[i] != where[adjncy[j]]) {
- nbnd++;
- ASSERT(bndptr[i] != -1);
- ASSERT(bndind[bndptr[i]] == i);
- break;
- }
- }
- }
-
- ASSERTP(nbnd == graph->nbnd, ("%"PRIDX" %"PRIDX"\n", nbnd, graph->nbnd));
-
- return 1;
-}
-
-
-
-/*************************************************************************/
-/*! This function checks whether or not the boundary information is correct
- */
-/*************************************************************************/
-idx_t CheckBnd2(graph_t *graph)
-{
- idx_t i, j, nvtxs, nbnd, id, ed;
- idx_t *xadj, *adjncy, *where, *bndptr, *bndind;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- for (nbnd=0, i=0; i<nvtxs; i++) {
- id = ed = 0;
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (where[i] != where[adjncy[j]])
- ed += graph->adjwgt[j];
- else
- id += graph->adjwgt[j];
- }
- if (ed - id >= 0 && xadj[i] < xadj[i+1]) {
- nbnd++;
- ASSERTP(bndptr[i] != -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", i, id, ed));
- ASSERT(bndind[bndptr[i]] == i);
- }
- }
-
- ASSERTP(nbnd == graph->nbnd, ("%"PRIDX" %"PRIDX"\n", nbnd, graph->nbnd));
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function checks whether or not the boundary information is correct
- */
-/*************************************************************************/
-idx_t CheckNodeBnd(graph_t *graph, idx_t onbnd)
-{
- idx_t i, j, nvtxs, nbnd;
- idx_t *xadj, *adjncy, *where, *bndptr, *bndind;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- for (nbnd=0, i=0; i<nvtxs; i++) {
- if (where[i] == 2)
- nbnd++;
- }
-
- ASSERTP(nbnd == onbnd, ("%"PRIDX" %"PRIDX"\n", nbnd, onbnd));
-
- for (i=0; i<nvtxs; i++) {
- if (where[i] != 2) {
- ASSERTP(bndptr[i] == -1, ("%"PRIDX" %"PRIDX"\n", i, bndptr[i]));
- }
- else {
- ASSERTP(bndptr[i] != -1, ("%"PRIDX" %"PRIDX"\n", i, bndptr[i]));
- }
- }
-
- return 1;
-}
-
-
-
-/*************************************************************************/
-/*! This function checks whether or not the rinfo of a vertex is consistent
- */
-/*************************************************************************/
-idx_t CheckRInfo(ctrl_t *ctrl, ckrinfo_t *rinfo)
-{
- idx_t i, j;
- cnbr_t *nbrs;
-
- nbrs = ctrl->cnbrpool + rinfo->inbr;
-
- for (i=0; i<rinfo->nnbrs; i++) {
- for (j=i+1; j<rinfo->nnbrs; j++)
- ASSERTP(nbrs[i].pid != nbrs[j].pid,
- ("%"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"\n",
- i, j, nbrs[i].pid, nbrs[j].pid));
- }
-
- return 1;
-}
-
-
-
-/*************************************************************************/
-/*! This function checks the correctness of the NodeFM data structures
- */
-/*************************************************************************/
-idx_t CheckNodePartitionParams(graph_t *graph)
-{
- idx_t i, j, k, l, nvtxs, me, other;
- idx_t *xadj, *adjncy, *adjwgt, *vwgt, *where;
- idx_t edegrees[2], pwgts[3];
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- where = graph->where;
-
- /*------------------------------------------------------------
- / Compute now the separator external degrees
- /------------------------------------------------------------*/
- pwgts[0] = pwgts[1] = pwgts[2] = 0;
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- pwgts[me] += vwgt[i];
-
- if (me == 2) { /* If it is on the separator do some computations */
- edegrees[0] = edegrees[1] = 0;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- other = where[adjncy[j]];
- if (other != 2)
- edegrees[other] += vwgt[adjncy[j]];
- }
- if (edegrees[0] != graph->nrinfo[i].edegrees[0] ||
- edegrees[1] != graph->nrinfo[i].edegrees[1]) {
- printf("Something wrong with edegrees: %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"\n",
- i, edegrees[0], edegrees[1],
- graph->nrinfo[i].edegrees[0], graph->nrinfo[i].edegrees[1]);
- return 0;
- }
- }
- }
-
- if (pwgts[0] != graph->pwgts[0] ||
- pwgts[1] != graph->pwgts[1] ||
- pwgts[2] != graph->pwgts[2]) {
- printf("Something wrong with part-weights: %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"\n", pwgts[0], pwgts[1], pwgts[2], graph->pwgts[0], graph->pwgts[1], graph->pwgts[2]);
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function checks if the separator is indeed a separator
- */
-/*************************************************************************/
-idx_t IsSeparable(graph_t *graph)
-{
- idx_t i, j, nvtxs, other;
- idx_t *xadj, *adjncy, *where;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- where = graph->where;
-
- for (i=0; i<nvtxs; i++) {
- if (where[i] == 2)
- continue;
- other = (where[i]+1)%2;
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ASSERTP(where[adjncy[j]] != other,
- ("%"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"\n",
- i, where[i], adjncy[j], where[adjncy[j]], xadj[i+1]-xadj[i],
- xadj[adjncy[j]+1]-xadj[adjncy[j]]));
- }
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function recomputes the vrinfo fields and checks them against
- those in the graph->vrinfo structure */
-/*************************************************************************/
-void CheckKWayVolPartitionParams(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, k, kk, l, nvtxs, nbnd, mincut, minvol, me, other, pid;
- idx_t *xadj, *vsize, *adjncy, *pwgts, *where, *bndind, *bndptr;
- vkrinfo_t *rinfo, *myrinfo, *orinfo, tmprinfo;
- vnbr_t *mynbrs, *onbrs, *tmpnbrs;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- where = graph->where;
- rinfo = graph->vkrinfo;
-
- tmpnbrs = (vnbr_t *)wspacemalloc(ctrl, ctrl->nparts*sizeof(vnbr_t));
-
- /*------------------------------------------------------------
- / Compute now the iv/ev degrees
- /------------------------------------------------------------*/
- for (i=0; i<nvtxs; i++) {
- me = where[i];
-
- myrinfo = rinfo+i;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- for (k=0; k<myrinfo->nnbrs; k++)
- tmpnbrs[k] = mynbrs[k];
-
- tmprinfo.nnbrs = myrinfo->nnbrs;
- tmprinfo.nid = myrinfo->nid;
- tmprinfo.ned = myrinfo->ned;
-
- myrinfo = &tmprinfo;
- mynbrs = tmpnbrs;
-
- for (k=0; k<myrinfo->nnbrs; k++)
- mynbrs[k].gv = 0;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = rinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- if (me == other) {
- /* Find which domains 'i' is connected and 'ii' is not and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- pid = mynbrs[k].pid;
- for (kk=0; kk<orinfo->nnbrs; kk++) {
- if (onbrs[kk].pid == pid)
- break;
- }
- if (kk == orinfo->nnbrs)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- else {
- /* Find the orinfo[me].ed and see if I'm the only connection */
- for (k=0; k<orinfo->nnbrs; k++) {
- if (onbrs[k].pid == me)
- break;
- }
-
- if (onbrs[k].ned == 1) { /* I'm the only connection of 'ii' in 'me' */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == other) {
- mynbrs[k].gv += vsize[ii];
- break;
- }
- }
-
- /* Increase the gains for all the common domains between 'i' and 'ii' */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if ((pid = mynbrs[k].pid) == other)
- continue;
- for (kk=0; kk<orinfo->nnbrs; kk++) {
- if (onbrs[kk].pid == pid) {
- mynbrs[k].gv += vsize[ii];
- break;
- }
- }
- }
-
- }
- else {
- /* Find which domains 'i' is connected and 'ii' is not and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if ((pid = mynbrs[k].pid) == other)
- continue;
- for (kk=0; kk<orinfo->nnbrs; kk++) {
- if (onbrs[kk].pid == pid)
- break;
- }
- if (kk == orinfo->nnbrs)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- }
- }
-
- myrinfo = rinfo+i;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- for (k=0; k<myrinfo->nnbrs; k++) {
- pid = mynbrs[k].pid;
- for (kk=0; kk<tmprinfo.nnbrs; kk++) {
- if (tmpnbrs[kk].pid == pid) {
- if (tmpnbrs[kk].gv != mynbrs[k].gv)
- printf("[%8"PRIDX" %8"PRIDX" %8"PRIDX" %+8"PRIDX" %+8"PRIDX"]\n",
- i, where[i], pid, mynbrs[k].gv, tmpnbrs[kk].gv);
- break;
- }
- }
- }
-
- }
-
- WCOREPOP;
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/defs.h b/3rdParty/metis/metis-5.1.0/libmetis/defs.h
deleted file mode 100644
index 196117838..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/defs.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * defs.h
- *
- * This file contains constant definitions
- *
- * Started 8/27/94
- * George
- *
- * $Id: defs.h 13933 2013-03-29 22:20:46Z karypis $
- *
- */
-
-#ifndef _LIBMETIS_DEFS_H_
-#define _LIBMETIS_DEFS_H_
-
-#define METISTITLE "METIS 5.0 Copyright 1998-13, Regents of the University of Minnesota\n"
-#define MAXLINE 1280000
-
-#define LTERM (void **) 0 /* List terminator for gk_free() */
-
-#define HTLENGTH ((1<<11)-1)
-
-#define INIT_MAXNAD 200 /* Initial number of maximum number of
- adjacent domains. This number will be
- adjusted as required. */
-
-/* Types of boundaries */
-#define BNDTYPE_REFINE 1 /* Used for k-way refinement-purposes */
-#define BNDTYPE_BALANCE 2 /* Used for k-way balancing purposes */
-
-/* Mode of optimization */
-#define OMODE_REFINE 1 /* Optimize the objective function */
-#define OMODE_BALANCE 2 /* Balance the subdomains */
-
-/* Types of vertex statues in the priority queue */
-#define VPQSTATUS_PRESENT 1 /* The vertex is in the queue */
-#define VPQSTATUS_EXTRACTED 2 /* The vertex has been extracted from the queue */
-#define VPQSTATUS_NOTPRESENT 3 /* The vertex is not present in the queue and
- has not been extracted before */
-
-#define UNMATCHED -1
-
-#define LARGENIPARTS 7 /* Number of random initial partitions */
-#define SMALLNIPARTS 5 /* Number of random initial partitions */
-
-#define COARSEN_FRACTION 0.85 /* Node reduction between succesive coarsening levels */
-
-#define COMPRESSION_FRACTION 0.85
-
-#define MMDSWITCH 120
-
-/* Default ufactors for the various operational modes */
-#define PMETIS_DEFAULT_UFACTOR 1
-#define MCPMETIS_DEFAULT_UFACTOR 10
-#define KMETIS_DEFAULT_UFACTOR 30
-#define OMETIS_DEFAULT_UFACTOR 200
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/fm.c b/3rdParty/metis/metis-5.1.0/libmetis/fm.c
deleted file mode 100644
index 7f5ea6b01..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/fm.c
+++ /dev/null
@@ -1,543 +0,0 @@
-/*!
-\file
-\brief Functions for the edge-based FM refinement
-
-\date Started 7/23/97
-\author George
-\author Copyright 1997-2011, Regents of the University of Minnesota
-\version\verbatim $Id: fm.c 10187 2011-06-13 13:46:57Z karypis $ \endverbatim
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************
-* This function performs an edge-based FM refinement
-**************************************************************************/
-void FM_2WayRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter)
-{
- if (graph->ncon == 1)
- FM_2WayCutRefine(ctrl, graph, ntpwgts, niter);
- else
- FM_Mc2WayCutRefine(ctrl, graph, ntpwgts, niter);
-}
-
-
-/*************************************************************************/
-/*! This function performs a cut-focused FM refinement */
-/*************************************************************************/
-void FM_2WayCutRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter)
-{
- idx_t i, ii, j, k, kwgt, nvtxs, nbnd, nswaps, from, to, pass, me, limit, tmp;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where, *id, *ed, *bndptr, *bndind, *pwgts;
- idx_t *moved, *swaps, *perm;
- rpq_t *queues[2];
- idx_t higain, mincut, mindiff, origdiff, initcut, newcut, mincutorder, avgvwgt;
- idx_t tpwgts[2];
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
- pwgts = graph->pwgts;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- moved = iwspacemalloc(ctrl, nvtxs);
- swaps = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
-
- tpwgts[0] = graph->tvwgt[0]*ntpwgts[0];
- tpwgts[1] = graph->tvwgt[0]-tpwgts[0];
-
- limit = gk_min(gk_max(0.01*nvtxs, 15), 100);
- avgvwgt = gk_min((pwgts[0]+pwgts[1])/20, 2*(pwgts[0]+pwgts[1])/nvtxs);
-
- queues[0] = rpqCreate(nvtxs);
- queues[1] = rpqCreate(nvtxs);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- Print2WayRefineStats(ctrl, graph, ntpwgts, 0, -2));
-
- origdiff = iabs(tpwgts[0]-pwgts[0]);
- iset(nvtxs, -1, moved);
- for (pass=0; pass<niter; pass++) { /* Do a number of passes */
- rpqReset(queues[0]);
- rpqReset(queues[1]);
-
- mincutorder = -1;
- newcut = mincut = initcut = graph->mincut;
- mindiff = iabs(tpwgts[0]-pwgts[0]);
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERT(CheckBnd(graph));
-
- /* Insert boundary nodes in the priority queues */
- nbnd = graph->nbnd;
- irandArrayPermute(nbnd, perm, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = perm[ii];
- ASSERT(ed[bndind[i]] > 0 || id[bndind[i]] == 0);
- ASSERT(bndptr[bndind[i]] != -1);
- rpqInsert(queues[where[bndind[i]]], bndind[i], ed[bndind[i]]-id[bndind[i]]);
- }
-
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- from = (tpwgts[0]-pwgts[0] < tpwgts[1]-pwgts[1] ? 0 : 1);
- to = (from+1)%2;
-
- if ((higain = rpqGetTop(queues[from])) == -1)
- break;
- ASSERT(bndptr[higain] != -1);
-
- newcut -= (ed[higain]-id[higain]);
- INC_DEC(pwgts[to], pwgts[from], vwgt[higain]);
-
- if ((newcut < mincut && iabs(tpwgts[0]-pwgts[0]) <= origdiff+avgvwgt) ||
- (newcut == mincut && iabs(tpwgts[0]-pwgts[0]) < mindiff)) {
- mincut = newcut;
- mindiff = iabs(tpwgts[0]-pwgts[0]);
- mincutorder = nswaps;
- }
- else if (nswaps-mincutorder > limit) { /* We hit the limit, undo last move */
- newcut += (ed[higain]-id[higain]);
- INC_DEC(pwgts[from], pwgts[to], vwgt[higain]);
- break;
- }
-
- where[higain] = to;
- moved[higain] = nswaps;
- swaps[nswaps] = higain;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" from %"PRIDX". [%3"PRIDX" %3"PRIDX"] %5"PRIDX" [%4"PRIDX" %4"PRIDX"]\n", higain, from, ed[higain]-id[higain], vwgt[higain], newcut, pwgts[0], pwgts[1]));
-
- /**************************************************************
- * Update the id[i]/ed[i] values of the affected nodes
- ***************************************************************/
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
-
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- /* Update its boundary information and queue position */
- if (bndptr[k] != -1) { /* If k was a boundary vertex */
- if (ed[k] == 0) { /* Not a boundary vertex any more */
- BNDDelete(nbnd, bndind, bndptr, k);
- if (moved[k] == -1) /* Remove it if in the queues */
- rpqDelete(queues[where[k]], k);
- }
- else { /* If it has not been moved, update its position in the queue */
- if (moved[k] == -1)
- rpqUpdate(queues[where[k]], k, ed[k]-id[k]);
- }
- }
- else {
- if (ed[k] > 0) { /* It will now become a boundary vertex */
- BNDInsert(nbnd, bndind, bndptr, k);
- if (moved[k] == -1)
- rpqInsert(queues[where[k]], k, ed[k]-id[k]);
- }
- }
- }
-
- }
-
-
- /****************************************************************
- * Roll back computations
- *****************************************************************/
- for (i=0; i<nswaps; i++)
- moved[swaps[i]] = -1; /* reset moved array */
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- to = where[higain] = (where[higain]+1)%2;
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && bndptr[higain] != -1 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
- else if (ed[higain] > 0 && bndptr[higain] == -1)
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- INC_DEC(pwgts[to], pwgts[(to+1)%2], vwgt[higain]);
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- if (bndptr[k] != -1 && ed[k] == 0)
- BNDDelete(nbnd, bndind, bndptr, k);
- if (bndptr[k] == -1 && ed[k] > 0)
- BNDInsert(nbnd, bndind, bndptr, k);
- }
- }
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- Print2WayRefineStats(ctrl, graph, ntpwgts, 0, mincutorder));
-
- if (mincutorder <= 0 || mincut == initcut)
- break;
- }
-
- rpqDestroy(queues[0]);
- rpqDestroy(queues[1]);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function performs a cut-focused multi-constraint FM refinement */
-/*************************************************************************/
-void FM_Mc2WayCutRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter)
-{
- idx_t i, ii, j, k, l, kwgt, nvtxs, ncon, nbnd, nswaps, from, to, pass,
- me, limit, tmp, cnum;
- idx_t *xadj, *adjncy, *vwgt, *adjwgt, *pwgts, *where, *id, *ed,
- *bndptr, *bndind;
- idx_t *moved, *swaps, *perm, *qnum;
- idx_t higain, mincut, initcut, newcut, mincutorder;
- real_t *invtvwgt, *ubfactors, *minbalv, *newbalv;
- real_t origbal, minbal, newbal, rgain, ffactor;
- rpq_t **queues;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- invtvwgt = graph->invtvwgt;
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
- pwgts = graph->pwgts;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- moved = iwspacemalloc(ctrl, nvtxs);
- swaps = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
- qnum = iwspacemalloc(ctrl, nvtxs);
- ubfactors = rwspacemalloc(ctrl, ncon);
- newbalv = rwspacemalloc(ctrl, ncon);
- minbalv = rwspacemalloc(ctrl, ncon);
-
- limit = gk_min(gk_max(0.01*nvtxs, 25), 150);
-
-
- /* Determine a fudge factor to allow the refinement routines to get out
- of tight balancing constraints. */
- ffactor = .5/gk_max(20, nvtxs);
-
- /* Initialize the queues */
- queues = (rpq_t **)wspacemalloc(ctrl, 2*ncon*sizeof(rpq_t *));
- for (i=0; i<2*ncon; i++)
- queues[i] = rpqCreate(nvtxs);
- for (i=0; i<nvtxs; i++)
- qnum[i] = iargmax_nrm(ncon, vwgt+i*ncon, invtvwgt);
-
- /* Determine the unbalance tolerance for each constraint. The tolerance is
- equal to the maximum of the original load imbalance and the user-supplied
- allowed tolerance. The rationale behind this approach is to allow the
- refinement routine to improve the cut, without having to worry about fixing
- load imbalance problems. The load imbalance is addressed by the balancing
- routines. */
- origbal = ComputeLoadImbalanceDiffVec(graph, 2, ctrl->pijbm, ctrl->ubfactors, ubfactors);
- for (i=0; i<ncon; i++)
- ubfactors[i] = (ubfactors[i] > 0 ? ctrl->ubfactors[i]+ubfactors[i] : ctrl->ubfactors[i]);
-
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- Print2WayRefineStats(ctrl, graph, ntpwgts, origbal, -2));
-
- iset(nvtxs, -1, moved);
- for (pass=0; pass<niter; pass++) { /* Do a number of passes */
- for (i=0; i<2*ncon; i++)
- rpqReset(queues[i]);
-
- mincutorder = -1;
- newcut = mincut = initcut = graph->mincut;
-
- minbal = ComputeLoadImbalanceDiffVec(graph, 2, ctrl->pijbm, ubfactors, minbalv);
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERT(CheckBnd(graph));
-
- /* Insert boundary nodes in the priority queues */
- nbnd = graph->nbnd;
- irandArrayPermute(nbnd, perm, nbnd/5, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[perm[ii]];
- ASSERT(ed[i] > 0 || id[i] == 0);
- ASSERT(bndptr[i] != -1);
- //rgain = 1.0*(ed[i]-id[i])/sqrt(vwgt[i*ncon+qnum[i]]+1);
- //rgain = (ed[i]-id[i] > 0 ? 1.0*(ed[i]-id[i])/sqrt(vwgt[i*ncon+qnum[i]]+1) : ed[i]-id[i]);
- rgain = ed[i]-id[i];
- rpqInsert(queues[2*qnum[i]+where[i]], i, rgain);
- }
-
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- SelectQueue(graph, ctrl->pijbm, ubfactors, queues, &from, &cnum);
-
- to = (from+1)%2;
-
- if (from == -1 || (higain = rpqGetTop(queues[2*cnum+from])) == -1)
- break;
- ASSERT(bndptr[higain] != -1);
-
- newcut -= (ed[higain]-id[higain]);
-
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+from*ncon, 1);
- newbal = ComputeLoadImbalanceDiffVec(graph, 2, ctrl->pijbm, ubfactors, newbalv);
-
- if ((newcut < mincut && newbal <= ffactor) ||
- (newcut == mincut && (newbal < minbal ||
- (newbal == minbal && BetterBalance2Way(ncon, minbalv, newbalv))))) {
- mincut = newcut;
- minbal = newbal;
- mincutorder = nswaps;
- rcopy(ncon, newbalv, minbalv);
- }
- else if (nswaps-mincutorder > limit) { /* We hit the limit, undo last move */
- newcut += (ed[higain]-id[higain]);
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+from*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- break;
- }
-
- where[higain] = to;
- moved[higain] = nswaps;
- swaps[nswaps] = higain;
-
- if (ctrl->dbglvl&METIS_DBG_MOVEINFO) {
- printf("Moved%6"PRIDX" from %"PRIDX"(%"PRIDX") Gain:%5"PRIDX", "
- "Cut:%5"PRIDX", NPwgts:", higain, from, cnum, ed[higain]-id[higain], newcut);
- for (l=0; l<ncon; l++)
- printf("(%.3"PRREAL" %.3"PRREAL")", pwgts[l]*invtvwgt[l], pwgts[ncon+l]*invtvwgt[l]);
- printf(" %+.3"PRREAL" LB: %.3"PRREAL"(%+.3"PRREAL")\n",
- minbal, ComputeLoadImbalance(graph, 2, ctrl->pijbm), newbal);
- }
-
-
- /**************************************************************
- * Update the id[i]/ed[i] values of the affected nodes
- ***************************************************************/
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
-
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- /* Update its boundary information and queue position */
- if (bndptr[k] != -1) { /* If k was a boundary vertex */
- if (ed[k] == 0) { /* Not a boundary vertex any more */
- BNDDelete(nbnd, bndind, bndptr, k);
- if (moved[k] == -1) /* Remove it if in the queues */
- rpqDelete(queues[2*qnum[k]+where[k]], k);
- }
- else { /* If it has not been moved, update its position in the queue */
- if (moved[k] == -1) {
- //rgain = 1.0*(ed[k]-id[k])/sqrt(vwgt[k*ncon+qnum[k]]+1);
- //rgain = (ed[k]-id[k] > 0 ?
- // 1.0*(ed[k]-id[k])/sqrt(vwgt[k*ncon+qnum[k]]+1) : ed[k]-id[k]);
- rgain = ed[k]-id[k];
- rpqUpdate(queues[2*qnum[k]+where[k]], k, rgain);
- }
- }
- }
- else {
- if (ed[k] > 0) { /* It will now become a boundary vertex */
- BNDInsert(nbnd, bndind, bndptr, k);
- if (moved[k] == -1) {
- //rgain = 1.0*(ed[k]-id[k])/sqrt(vwgt[k*ncon+qnum[k]]+1);
- //rgain = (ed[k]-id[k] > 0 ?
- // 1.0*(ed[k]-id[k])/sqrt(vwgt[k*ncon+qnum[k]]+1) : ed[k]-id[k]);
- rgain = ed[k]-id[k];
- rpqInsert(queues[2*qnum[k]+where[k]], k, rgain);
- }
- }
- }
- }
-
- }
-
-
- /****************************************************************
- * Roll back computations
- *****************************************************************/
- for (i=0; i<nswaps; i++)
- moved[swaps[i]] = -1; /* reset moved array */
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- to = where[higain] = (where[higain]+1)%2;
- SWAP(id[higain], ed[higain], tmp);
- if (ed[higain] == 0 && bndptr[higain] != -1 && xadj[higain] < xadj[higain+1])
- BNDDelete(nbnd, bndind, bndptr, higain);
- else if (ed[higain] > 0 && bndptr[higain] == -1)
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- iaxpy(ncon, 1, vwgt+higain*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+higain*ncon, 1, pwgts+((to+1)%2)*ncon, 1);
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- kwgt = (to == where[k] ? adjwgt[j] : -adjwgt[j]);
- INC_DEC(id[k], ed[k], kwgt);
-
- if (bndptr[k] != -1 && ed[k] == 0)
- BNDDelete(nbnd, bndind, bndptr, k);
- if (bndptr[k] == -1 && ed[k] > 0)
- BNDInsert(nbnd, bndind, bndptr, k);
- }
- }
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- Print2WayRefineStats(ctrl, graph, ntpwgts, minbal, mincutorder));
-
- if (mincutorder <= 0 || mincut == initcut)
- break;
- }
-
- for (i=0; i<2*ncon; i++)
- rpqDestroy(queues[i]);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function selects the partition number and the queue from which
- we will move vertices out. */
-/*************************************************************************/
-void SelectQueue(graph_t *graph, real_t *pijbm, real_t *ubfactors,
- rpq_t **queues, idx_t *from, idx_t *cnum)
-{
- idx_t ncon, i, part;
- real_t max, tmp;
-
- ncon = graph->ncon;
-
- *from = -1;
- *cnum = -1;
-
- /* First determine the side and the queue, irrespective of the presence of nodes.
- The side & queue is determined based on the most violated balancing constraint. */
- for (max=0.0, part=0; part<2; part++) {
- for (i=0; i<ncon; i++) {
- tmp = graph->pwgts[part*ncon+i]*pijbm[part*ncon+i] - ubfactors[i];
- /* the '=' in the test bellow is to ensure that under tight constraints
- the partition that is at the max is selected */
- if (tmp >= max) {
- max = tmp;
- *from = part;
- *cnum = i;
- }
- }
- }
-
-
- if (*from != -1) {
- /* in case the desired queue is empty, select a queue from the same side */
- if (rpqLength(queues[2*(*cnum)+(*from)]) == 0) {
- for (i=0; i<ncon; i++) {
- if (rpqLength(queues[2*i+(*from)]) > 0) {
- max = graph->pwgts[(*from)*ncon+i]*pijbm[(*from)*ncon+i] - ubfactors[i];
- *cnum = i;
- break;
- }
- }
-
- for (i++; i<ncon; i++) {
- tmp = graph->pwgts[(*from)*ncon+i]*pijbm[(*from)*ncon+i] - ubfactors[i];
- if (tmp > max && rpqLength(queues[2*i+(*from)]) > 0) {
- max = tmp;
- *cnum = i;
- }
- }
- }
-
- /*
- printf("Selected1 %"PRIDX"(%"PRIDX") -> %"PRIDX" [%5"PRREAL"]\n",
- *from, *cnum, rpqLength(queues[2*(*cnum)+(*from)]), max);
- */
- }
- else {
- /* the partitioning does not violate balancing constraints, in which case select
- a queue based on cut criteria */
- for (part=0; part<2; part++) {
- for (i=0; i<ncon; i++) {
- if (rpqLength(queues[2*i+part]) > 0 &&
- (*from == -1 || rpqSeeTopKey(queues[2*i+part]) > max)) {
- max = rpqSeeTopKey(queues[2*i+part]);
- *from = part;
- *cnum = i;
- }
- }
- }
- /*
- printf("Selected2 %"PRIDX"(%"PRIDX") -> %"PRIDX"\n",
- *from, *cnum, rpqLength(queues[2*(*cnum)+(*from)]), max);
- */
- }
-}
-
-
-/*************************************************************************/
-/*! Prints statistics about the refinement */
-/*************************************************************************/
-void Print2WayRefineStats(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- real_t deltabal, idx_t mincutorder)
-{
- int i;
-
- if (mincutorder == -2) {
- printf("Parts: ");
- printf("Nv-Nb[%5"PRIDX" %5"PRIDX"] ICut: %6"PRIDX,
- graph->nvtxs, graph->nbnd, graph->mincut);
- printf(" [");
- for (i=0; i<graph->ncon; i++)
- printf("(%.3"PRREAL" %.3"PRREAL" T:%.3"PRREAL" %.3"PRREAL")",
- graph->pwgts[i]*graph->invtvwgt[i],
- graph->pwgts[graph->ncon+i]*graph->invtvwgt[i],
- ntpwgts[i], ntpwgts[graph->ncon+i]);
- printf("] LB: %.3"PRREAL"(%+.3"PRREAL")\n",
- ComputeLoadImbalance(graph, 2, ctrl->pijbm), deltabal);
- }
- else {
- printf("\tMincut: %6"PRIDX" at %5"PRIDX" NBND %6"PRIDX" NPwgts: [",
- graph->mincut, mincutorder, graph->nbnd);
- for (i=0; i<graph->ncon; i++)
- printf("(%.3"PRREAL" %.3"PRREAL")",
- graph->pwgts[i]*graph->invtvwgt[i], graph->pwgts[graph->ncon+i]*graph->invtvwgt[i]);
- printf("] LB: %.3"PRREAL"(%+.3"PRREAL")\n",
- ComputeLoadImbalance(graph, 2, ctrl->pijbm), deltabal);
- }
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/fortran.c b/3rdParty/metis/metis-5.1.0/libmetis/fortran.c
deleted file mode 100644
index 5c3ed9029..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/fortran.c
+++ /dev/null
@@ -1,142 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * fortran.c
- *
- * This file contains code for the fortran to C interface
- *
- * Started 8/19/97
- * George
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 0 instead of 1 */
-/*************************************************************************/
-void Change2CNumbering(idx_t nvtxs, idx_t *xadj, idx_t *adjncy)
-{
- idx_t i;
-
- for (i=0; i<=nvtxs; i++)
- xadj[i]--;
-
- for (i=0; i<xadj[nvtxs]; i++)
- adjncy[i]--;
-}
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 1 instead of 0 */
-/*************************************************************************/
-void Change2FNumbering(idx_t nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vector)
-{
- idx_t i;
-
- for (i=0; i<nvtxs; i++)
- vector[i]++;
-
- for (i=0; i<xadj[nvtxs]; i++)
- adjncy[i]++;
-
- for (i=0; i<=nvtxs; i++)
- xadj[i]++;
-}
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 1 instead of 0 */
-/*************************************************************************/
-void Change2FNumbering2(idx_t nvtxs, idx_t *xadj, idx_t *adjncy)
-{
- idx_t i, nedges;
-
- nedges = xadj[nvtxs];
- for (i=0; i<nedges; i++)
- adjncy[i]++;
-
- for (i=0; i<=nvtxs; i++)
- xadj[i]++;
-}
-
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 1 instead of 0 */
-/*************************************************************************/
-void Change2FNumberingOrder(idx_t nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *v1, idx_t *v2)
-{
- idx_t i, nedges;
-
- for (i=0; i<nvtxs; i++) {
- v1[i]++;
- v2[i]++;
- }
-
- nedges = xadj[nvtxs];
- for (i=0; i<nedges; i++)
- adjncy[i]++;
-
- for (i=0; i<=nvtxs; i++)
- xadj[i]++;
-
-}
-
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 0 instead of 1 */
-/*************************************************************************/
-void ChangeMesh2CNumbering(idx_t n, idx_t *ptr, idx_t *ind)
-{
- idx_t i;
-
- for (i=0; i<=n; i++)
- ptr[i]--;
- for (i=0; i<ptr[n]; i++)
- ind[i]--;
-}
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 1 instead of 0 */
-/*************************************************************************/
-void ChangeMesh2FNumbering(idx_t n, idx_t *ptr, idx_t *ind, idx_t nvtxs,
- idx_t *xadj, idx_t *adjncy)
-{
- idx_t i;
-
- for (i=0; i<ptr[n]; i++)
- ind[i]++;
- for (i=0; i<=n; i++)
- ptr[i]++;
-
- for (i=0; i<xadj[nvtxs]; i++)
- adjncy[i]++;
- for (i=0; i<=nvtxs; i++)
- xadj[i]++;
-}
-
-
-/*************************************************************************/
-/*! This function changes the numbering to start from 1 instead of 0 */
-/*************************************************************************/
-void ChangeMesh2FNumbering2(idx_t ne, idx_t nn, idx_t *ptr, idx_t *ind,
- idx_t *epart, idx_t *npart)
-{
- idx_t i;
-
- for (i=0; i<ptr[ne]; i++)
- ind[i]++;
- for (i=0; i<=ne; i++)
- ptr[i]++;
-
- for (i=0; i<ne; i++)
- epart[i]++;
-
- for (i=0; i<nn; i++)
- npart[i]++;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/frename.c b/3rdParty/metis/metis-5.1.0/libmetis/frename.c
deleted file mode 100644
index 3d43c3ade..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/frename.c
+++ /dev/null
@@ -1,136 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * Frename.c
- *
- * THis file contains some renaming routines to deal with different Fortran compilers
- *
- * Started 9/15/97
- * George
- *
- */
-
-
-#include "metislib.h"
-
-#define FRENAME(name, dargs, cargs, name1, name2, name3, name4) \
- int name1 dargs { return name cargs; } \
- int name2 dargs { return name cargs; } \
- int name3 dargs { return name cargs; } \
- int name4 dargs { return name cargs; }
-
-
-FRENAME(
- METIS_PartGraphRecursive,
- (idx_t *nvtxs, idx_t *ncon, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t *vsize, idx_t *adjwgt, idx_t *nparts, real_t *tpwgts,
- real_t *ubvec, idx_t *options, idx_t *edgecut, idx_t *part),
- (nvtxs, ncon, xadj, adjncy, vwgt,
- vsize, adjwgt, nparts, tpwgts,
- ubvec, options, edgecut, part),
- METIS_PARTGRAPHRECURSIVE,
- metis_partgraphrecursive,
- metis_partgraphrecursive_,
- metis_partgraphrecursive__
-)
-
-
-FRENAME(
- METIS_PartGraphKway,
- (idx_t *nvtxs, idx_t *ncon, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t *vsize, idx_t *adjwgt, idx_t *nparts, real_t *tpwgts,
- real_t *ubvec, idx_t *options, idx_t *edgecut, idx_t *part),
- (nvtxs, ncon, xadj, adjncy, vwgt,
- vsize, adjwgt, nparts, tpwgts,
- ubvec, options, edgecut, part),
- METIS_PARTGRAPHKWAY,
- metis_partgraphkway,
- metis_partgraphkway_,
- metis_partgraphkway__
-)
-
-FRENAME(
- METIS_MeshToDual,
- (idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind, idx_t *ncommon, idx_t *numflag,
- idx_t **r_xadj, idx_t **r_adjncy),
- (ne, nn, eptr, eind, ncommon, numflag, r_xadj, r_adjncy),
- METIS_MESHTODUAL,
- metis_meshtodual,
- metis_meshtodual_,
- metis_meshtodual__
-)
-
-
-FRENAME(
- METIS_MeshToNodal,
- (idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind, idx_t *numflag, idx_t **r_xadj,
- idx_t **r_adjncy),
- (ne, nn, eptr, eind, numflag, r_xadj, r_adjncy),
- METIS_MESHTONODAL,
- metis_meshtonodal,
- metis_meshtonodal_,
- metis_meshtonodal__
-)
-
-
-FRENAME(
- METIS_PartMeshNodal,
- (idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind, idx_t *vwgt, idx_t *vsize,
- idx_t *nparts, real_t *tpwgts, idx_t *options, idx_t *objval, idx_t *epart,
- idx_t *npart),
- (ne, nn, eptr, eind, vwgt, vsize, nparts, tpwgts, options, objval, epart, npart),
- METIS_PARTMESHNODAL,
- metis_partmeshnodal,
- metis_partmeshnodal_,
- metis_partmeshnodal__
-)
-
-
-FRENAME(
- METIS_PartMeshDual,
- (idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind, idx_t *vwgt, idx_t *vsize,
- idx_t *ncommon, idx_t *nparts, real_t *tpwgts, idx_t *options, idx_t *objval,
- idx_t *epart, idx_t *npart),
- (ne, nn, eptr, eind, vwgt, vsize, ncommon, nparts, tpwgts, options, objval, epart, npart),
- METIS_PARTMESHDUAL,
- metis_partmeshdual,
- metis_partmeshdual_,
- metis_partmeshdual__
-)
-
-
-FRENAME(
- METIS_NodeND,
- (idx_t *nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vwgt, idx_t *options, idx_t *perm,
- idx_t *iperm),
- (nvtxs, xadj, adjncy, vwgt, options, perm, iperm),
- METIS_NODEND,
- metis_nodend,
- metis_nodend_,
- metis_nodend__
-)
-
-
-FRENAME(
- METIS_Free,
- (void *ptr),
- (ptr),
- METIS_FREE,
- metis_free,
- metis_free_,
- metis_free__
-)
-
-
-FRENAME(
- METIS_SetDefaultOptions,
- (idx_t *options),
- (options),
- METIS_SETDEFAULTOPTIONS,
- metis_setdefaultoptions,
- metis_setdefaultoptions_,
- metis_setdefaultoptions__
-)
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/gklib.c b/3rdParty/metis/metis-5.1.0/libmetis/gklib.c
deleted file mode 100644
index 4e17eac42..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/gklib.c
+++ /dev/null
@@ -1,120 +0,0 @@
-/*!
-\file gklib.c
-\brief Various helper routines generated using GKlib's templates
-
-\date Started 4/12/2007
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version\verbatim $Id: gklib.c 10395 2011-06-23 23:28:06Z karypis $ \endverbatim
-*/
-
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! BLAS routines */
-/*************************************************************************/
-GK_MKBLAS(i, idx_t, idx_t)
-GK_MKBLAS(r, real_t, real_t)
-
-/*************************************************************************/
-/*! Memory allocation routines */
-/*************************************************************************/
-GK_MKALLOC(i, idx_t)
-GK_MKALLOC(r, real_t)
-GK_MKALLOC(ikv, ikv_t)
-GK_MKALLOC(rkv, rkv_t)
-
-/*************************************************************************/
-/*! Priority queues routines */
-/*************************************************************************/
-#define key_gt(a, b) ((a) > (b))
-GK_MKPQUEUE(ipq, ipq_t, ikv_t, idx_t, idx_t, ikvmalloc, IDX_MAX, key_gt)
-GK_MKPQUEUE(rpq, rpq_t, rkv_t, real_t, idx_t, rkvmalloc, REAL_MAX, key_gt)
-#undef key_gt
-
-/*************************************************************************/
-/*! Random number generation routines */
-/*************************************************************************/
-GK_MKRANDOM(i, idx_t, idx_t)
-
-/*************************************************************************/
-/*! Utility routines */
-/*************************************************************************/
-GK_MKARRAY2CSR(i, idx_t)
-
-/*************************************************************************/
-/*! Sorting routines */
-/*************************************************************************/
-void isorti(size_t n, idx_t *base)
-{
-#define i_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(idx_t, base, n, i_lt);
-#undef i_lt
-}
-
-void isortd(size_t n, idx_t *base)
-{
-#define i_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(idx_t, base, n, i_gt);
-#undef i_gt
-}
-
-void rsorti(size_t n, real_t *base)
-{
-#define r_lt(a, b) ((*a) < (*b))
- GK_MKQSORT(real_t, base, n, r_lt);
-#undef r_lt
-}
-
-void rsortd(size_t n, real_t *base)
-{
-#define r_gt(a, b) ((*a) > (*b))
- GK_MKQSORT(real_t, base, n, r_gt);
-#undef r_gt
-}
-
-void ikvsorti(size_t n, ikv_t *base)
-{
-#define ikey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(ikv_t, base, n, ikey_lt);
-#undef ikey_lt
-}
-
-/* Sorts based both on key and val */
-void ikvsortii(size_t n, ikv_t *base)
-{
-#define ikeyval_lt(a, b) ((a)->key < (b)->key || ((a)->key == (b)->key && (a)->val < (b)->val))
- GK_MKQSORT(ikv_t, base, n, ikeyval_lt);
-#undef ikeyval_lt
-}
-
-void ikvsortd(size_t n, ikv_t *base)
-{
-#define ikey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(ikv_t, base, n, ikey_gt);
-#undef ikey_gt
-}
-
-void rkvsorti(size_t n, rkv_t *base)
-{
-#define rkey_lt(a, b) ((a)->key < (b)->key)
- GK_MKQSORT(rkv_t, base, n, rkey_lt);
-#undef rkey_lt
-}
-
-void rkvsortd(size_t n, rkv_t *base)
-{
-#define rkey_gt(a, b) ((a)->key > (b)->key)
- GK_MKQSORT(rkv_t, base, n, rkey_gt);
-#undef rkey_gt
-}
-
-void uvwsorti(size_t n, uvw_t *base)
-{
-#define uvwkey_lt(a, b) ((a)->u < (b)->u || ((a)->u == (b)->u && (a)->v < (b)->v))
- GK_MKQSORT(uvw_t, base, n, uvwkey_lt);
-#undef uvwkey_lt
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/gklib_defs.h b/3rdParty/metis/metis-5.1.0/libmetis/gklib_defs.h
deleted file mode 100644
index dfac5ca67..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/gklib_defs.h
+++ /dev/null
@@ -1,53 +0,0 @@
-/*!
-\file
-\brief Data structures and prototypes for GKlib integration
-
-\date Started 12/23/2008
-\author George
-\version\verbatim $Id: gklib_defs.h 10395 2011-06-23 23:28:06Z karypis $ \endverbatim
-*/
-
-#ifndef _LIBMETIS_GKLIB_H_
-#define _LIBMETIS_GKLIB_H_
-
-#include "gklib_rename.h"
-
-/*************************************************************************/
-/*! Stores a weighted edge */
-/*************************************************************************/
-typedef struct {
- idx_t u, v, w; /*!< Edge (u,v) with weight w */
-} uvw_t;
-
-/*************************************************************************
-* Define various data structure using GKlib's templates.
-**************************************************************************/
-GK_MKKEYVALUE_T(ikv_t, idx_t, idx_t)
-GK_MKKEYVALUE_T(rkv_t, real_t, idx_t)
-GK_MKPQUEUE_T(ipq_t, ikv_t)
-GK_MKPQUEUE_T(rpq_t, rkv_t)
-
-
-/* gklib.c */
-GK_MKBLAS_PROTO(i, idx_t, idx_t)
-GK_MKBLAS_PROTO(r, real_t, real_t)
-GK_MKALLOC_PROTO(i, idx_t)
-GK_MKALLOC_PROTO(r, real_t)
-GK_MKALLOC_PROTO(ikv, ikv_t)
-GK_MKALLOC_PROTO(rkv, rkv_t)
-GK_MKPQUEUE_PROTO(ipq, ipq_t, idx_t, idx_t)
-GK_MKPQUEUE_PROTO(rpq, rpq_t, real_t, idx_t)
-GK_MKRANDOM_PROTO(i, idx_t, idx_t)
-GK_MKARRAY2CSR_PROTO(i, idx_t)
-void isorti(size_t n, idx_t *base);
-void isortd(size_t n, idx_t *base);
-void rsorti(size_t n, real_t *base);
-void rsortd(size_t n, real_t *base);
-void ikvsorti(size_t n, ikv_t *base);
-void ikvsortii(size_t n, ikv_t *base);
-void ikvsortd(size_t n, ikv_t *base);
-void rkvsorti(size_t n, rkv_t *base);
-void rkvsortd(size_t n, rkv_t *base);
-void uvwsorti(size_t n, uvw_t *base);
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/gklib_rename.h b/3rdParty/metis/metis-5.1.0/libmetis/gklib_rename.h
deleted file mode 100644
index 78dc8b39e..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/gklib_rename.h
+++ /dev/null
@@ -1,122 +0,0 @@
-/*!
-\file
-
- * Copyright 1997, Regents of the University of Minnesota
- *
- * This file contains header files
- *
- * Started 10/2/97
- * George
- *
- * $Id: gklib_rename.h 10395 2011-06-23 23:28:06Z karypis $
- *
- */
-
-
-#ifndef _LIBMETIS_GKLIB_RENAME_H_
-#define _LIBMETIS_GKLIB_RENAME_H_
-
-/* gklib.c - generated from the .o files using the ./utils/listundescapedsumbols.csh */
-#define iAllocMatrix libmetis__iAllocMatrix
-#define iFreeMatrix libmetis__iFreeMatrix
-#define iSetMatrix libmetis__iSetMatrix
-#define iargmax libmetis__iargmax
-#define iargmax_n libmetis__iargmax_n
-#define iargmin libmetis__iargmin
-#define iarray2csr libmetis__iarray2csr
-#define iaxpy libmetis__iaxpy
-#define icopy libmetis__icopy
-#define idot libmetis__idot
-#define iincset libmetis__iincset
-#define ikvAllocMatrix libmetis__ikvAllocMatrix
-#define ikvFreeMatrix libmetis__ikvFreeMatrix
-#define ikvSetMatrix libmetis__ikvSetMatrix
-#define ikvcopy libmetis__ikvcopy
-#define ikvmalloc libmetis__ikvmalloc
-#define ikvrealloc libmetis__ikvrealloc
-#define ikvset libmetis__ikvset
-#define ikvsmalloc libmetis__ikvsmalloc
-#define ikvsortd libmetis__ikvsortd
-#define ikvsorti libmetis__ikvsorti
-#define ikvsortii libmetis__ikvsortii
-#define imalloc libmetis__imalloc
-#define imax libmetis__imax
-#define imin libmetis__imin
-#define inorm2 libmetis__inorm2
-#define ipqCheckHeap libmetis__ipqCheckHeap
-#define ipqCreate libmetis__ipqCreate
-#define ipqDelete libmetis__ipqDelete
-#define ipqDestroy libmetis__ipqDestroy
-#define ipqFree libmetis__ipqFree
-#define ipqGetTop libmetis__ipqGetTop
-#define ipqInit libmetis__ipqInit
-#define ipqInsert libmetis__ipqInsert
-#define ipqLength libmetis__ipqLength
-#define ipqReset libmetis__ipqReset
-#define ipqSeeKey libmetis__ipqSeeKey
-#define ipqSeeTopKey libmetis__ipqSeeTopKey
-#define ipqSeeTopVal libmetis__ipqSeeTopVal
-#define ipqUpdate libmetis__ipqUpdate
-#define isrand libmetis__isrand
-#define irand libmetis__irand
-#define irandArrayPermute libmetis__irandArrayPermute
-#define irandArrayPermuteFine libmetis__irandArrayPermuteFine
-#define irandInRange libmetis__irandInRange
-#define irealloc libmetis__irealloc
-#define iscale libmetis__iscale
-#define iset libmetis__iset
-#define ismalloc libmetis__ismalloc
-#define isortd libmetis__isortd
-#define isorti libmetis__isorti
-#define isrand libmetis__isrand
-#define isum libmetis__isum
-#define rAllocMatrix libmetis__rAllocMatrix
-#define rFreeMatrix libmetis__rFreeMatrix
-#define rSetMatrix libmetis__rSetMatrix
-#define rargmax libmetis__rargmax
-#define rargmax_n libmetis__rargmax_n
-#define rargmin libmetis__rargmin
-#define raxpy libmetis__raxpy
-#define rcopy libmetis__rcopy
-#define rdot libmetis__rdot
-#define rincset libmetis__rincset
-#define rkvAllocMatrix libmetis__rkvAllocMatrix
-#define rkvFreeMatrix libmetis__rkvFreeMatrix
-#define rkvSetMatrix libmetis__rkvSetMatrix
-#define rkvcopy libmetis__rkvcopy
-#define rkvmalloc libmetis__rkvmalloc
-#define rkvrealloc libmetis__rkvrealloc
-#define rkvset libmetis__rkvset
-#define rkvsmalloc libmetis__rkvsmalloc
-#define rkvsortd libmetis__rkvsortd
-#define rkvsorti libmetis__rkvsorti
-#define rmalloc libmetis__rmalloc
-#define rmax libmetis__rmax
-#define rmin libmetis__rmin
-#define rnorm2 libmetis__rnorm2
-#define rpqCheckHeap libmetis__rpqCheckHeap
-#define rpqCreate libmetis__rpqCreate
-#define rpqDelete libmetis__rpqDelete
-#define rpqDestroy libmetis__rpqDestroy
-#define rpqFree libmetis__rpqFree
-#define rpqGetTop libmetis__rpqGetTop
-#define rpqInit libmetis__rpqInit
-#define rpqInsert libmetis__rpqInsert
-#define rpqLength libmetis__rpqLength
-#define rpqReset libmetis__rpqReset
-#define rpqSeeKey libmetis__rpqSeeKey
-#define rpqSeeTopKey libmetis__rpqSeeTopKey
-#define rpqSeeTopVal libmetis__rpqSeeTopVal
-#define rpqUpdate libmetis__rpqUpdate
-#define rrealloc libmetis__rrealloc
-#define rscale libmetis__rscale
-#define rset libmetis__rset
-#define rsmalloc libmetis__rsmalloc
-#define rsortd libmetis__rsortd
-#define rsorti libmetis__rsorti
-#define rsum libmetis__rsum
-#define uvwsorti libmetis__uvwsorti
-
-#endif
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/graph.c b/3rdParty/metis/metis-5.1.0/libmetis/graph.c
deleted file mode 100644
index 37f7d09dc..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/graph.c
+++ /dev/null
@@ -1,274 +0,0 @@
-/**
-\file
-\brief Functions that deal with setting up the graphs for METIS.
-
-\date Started 7/25/1997
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version\verbatim $Id: graph.c 10513 2011-07-07 22:06:03Z karypis $ \endverbatim
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function sets up the graph from the user input */
-/*************************************************************************/
-graph_t *SetupGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t ncon, idx_t *xadj,
- idx_t *adjncy, idx_t *vwgt, idx_t *vsize, idx_t *adjwgt)
-{
- idx_t i, j, k, sum;
- real_t *nvwgt;
- graph_t *graph;
-
- /* allocate the graph and fill in the fields */
- graph = CreateGraph();
-
- graph->nvtxs = nvtxs;
- graph->nedges = xadj[nvtxs];
- graph->ncon = ncon;
-
- graph->xadj = xadj;
- graph->free_xadj = 0;
-
- graph->adjncy = adjncy;
- graph->free_adjncy = 0;
-
-
- /* setup the vertex weights */
- if (vwgt) {
- graph->vwgt = vwgt;
- graph->free_vwgt = 0;
- }
- else {
- vwgt = graph->vwgt = ismalloc(ncon*nvtxs, 1, "SetupGraph: vwgt");
- }
-
- graph->tvwgt = imalloc(ncon, "SetupGraph: tvwgts");
- graph->invtvwgt = rmalloc(ncon, "SetupGraph: invtvwgts");
- for (i=0; i<ncon; i++) {
- graph->tvwgt[i] = isum(nvtxs, vwgt+i, ncon);
- graph->invtvwgt[i] = 1.0/(graph->tvwgt[i] > 0 ? graph->tvwgt[i] : 1);
- }
-
-
- if (ctrl->objtype == METIS_OBJTYPE_VOL) {
- /* Setup the vsize */
- if (vsize) {
- graph->vsize = vsize;
- graph->free_vsize = 0;
- }
- else {
- vsize = graph->vsize = ismalloc(nvtxs, 1, "SetupGraph: vsize");
- }
-
- /* Allocate memory for edge weights and initialize them to the sum of the vsize */
- adjwgt = graph->adjwgt = imalloc(graph->nedges, "SetupGraph: adjwgt");
- for (i=0; i<nvtxs; i++) {
- for (j=xadj[i]; j<xadj[i+1]; j++)
- adjwgt[j] = 1+vsize[i]+vsize[adjncy[j]];
- }
- }
- else { /* For edgecut minimization */
- /* setup the edge weights */
- if (adjwgt) {
- graph->adjwgt = adjwgt;
- graph->free_adjwgt = 0;
- }
- else {
- adjwgt = graph->adjwgt = ismalloc(graph->nedges, 1, "SetupGraph: adjwgt");
- }
- }
-
-
- /* setup various derived info */
- SetupGraph_tvwgt(graph);
-
- if (ctrl->optype == METIS_OP_PMETIS || ctrl->optype == METIS_OP_OMETIS)
- SetupGraph_label(graph);
-
- ASSERT(CheckGraph(graph, ctrl->numflag, 1));
-
- return graph;
-}
-
-
-/*************************************************************************/
-/*! Set's up the tvwgt/invtvwgt info */
-/*************************************************************************/
-void SetupGraph_tvwgt(graph_t *graph)
-{
- idx_t i;
-
- if (graph->tvwgt == NULL)
- graph->tvwgt = imalloc(graph->ncon, "SetupGraph_tvwgt: tvwgt");
- if (graph->invtvwgt == NULL)
- graph->invtvwgt = rmalloc(graph->ncon, "SetupGraph_tvwgt: invtvwgt");
-
- for (i=0; i<graph->ncon; i++) {
- graph->tvwgt[i] = isum(graph->nvtxs, graph->vwgt+i, graph->ncon);
- graph->invtvwgt[i] = 1.0/(graph->tvwgt[i] > 0 ? graph->tvwgt[i] : 1);
- }
-}
-
-
-/*************************************************************************/
-/*! Set's up the label info */
-/*************************************************************************/
-void SetupGraph_label(graph_t *graph)
-{
- idx_t i;
-
- if (graph->label == NULL)
- graph->label = imalloc(graph->nvtxs, "SetupGraph_label: label");
-
- for (i=0; i<graph->nvtxs; i++)
- graph->label[i] = i;
-}
-
-
-/*************************************************************************/
-/*! Setup the various arrays for the splitted graph */
-/*************************************************************************/
-graph_t *SetupSplitGraph(graph_t *graph, idx_t snvtxs, idx_t snedges)
-{
- graph_t *sgraph;
-
- sgraph = CreateGraph();
-
- sgraph->nvtxs = snvtxs;
- sgraph->nedges = snedges;
- sgraph->ncon = graph->ncon;
-
- /* Allocate memory for the splitted graph */
- sgraph->xadj = imalloc(snvtxs+1, "SetupSplitGraph: xadj");
- sgraph->vwgt = imalloc(sgraph->ncon*snvtxs, "SetupSplitGraph: vwgt");
- sgraph->adjncy = imalloc(snedges, "SetupSplitGraph: adjncy");
- sgraph->adjwgt = imalloc(snedges, "SetupSplitGraph: adjwgt");
- sgraph->label = imalloc(snvtxs, "SetupSplitGraph: label");
- sgraph->tvwgt = imalloc(sgraph->ncon, "SetupSplitGraph: tvwgt");
- sgraph->invtvwgt = rmalloc(sgraph->ncon, "SetupSplitGraph: invtvwgt");
-
- if (graph->vsize)
- sgraph->vsize = imalloc(snvtxs, "SetupSplitGraph: vsize");
-
- return sgraph;
-}
-
-
-/*************************************************************************/
-/*! This function creates and initializes a graph_t data structure */
-/*************************************************************************/
-graph_t *CreateGraph(void)
-{
- graph_t *graph;
-
- graph = (graph_t *)gk_malloc(sizeof(graph_t), "CreateGraph: graph");
-
- InitGraph(graph);
-
- return graph;
-}
-
-
-/*************************************************************************/
-/*! This function initializes a graph_t data structure */
-/*************************************************************************/
-void InitGraph(graph_t *graph)
-{
- memset((void *)graph, 0, sizeof(graph_t));
-
- /* graph size constants */
- graph->nvtxs = -1;
- graph->nedges = -1;
- graph->ncon = -1;
- graph->mincut = -1;
- graph->minvol = -1;
- graph->nbnd = -1;
-
- /* memory for the graph structure */
- graph->xadj = NULL;
- graph->vwgt = NULL;
- graph->vsize = NULL;
- graph->adjncy = NULL;
- graph->adjwgt = NULL;
- graph->label = NULL;
- graph->cmap = NULL;
- graph->tvwgt = NULL;
- graph->invtvwgt = NULL;
-
- /* by default these are set to true, but the can be explicitly changed afterwards */
- graph->free_xadj = 1;
- graph->free_vwgt = 1;
- graph->free_vsize = 1;
- graph->free_adjncy = 1;
- graph->free_adjwgt = 1;
-
-
- /* memory for the partition/refinement structure */
- graph->where = NULL;
- graph->pwgts = NULL;
- graph->id = NULL;
- graph->ed = NULL;
- graph->bndptr = NULL;
- graph->bndind = NULL;
- graph->nrinfo = NULL;
- graph->ckrinfo = NULL;
- graph->vkrinfo = NULL;
-
- /* linked-list structure */
- graph->coarser = NULL;
- graph->finer = NULL;
-}
-
-
-/*************************************************************************/
-/*! This function frees the refinement/partition memory stored in a graph */
-/*************************************************************************/
-void FreeRData(graph_t *graph)
-{
-
- /* The following is for the -minconn and -contig to work properly in
- the vol-refinement routines */
- if ((void *)graph->ckrinfo == (void *)graph->vkrinfo)
- graph->ckrinfo = NULL;
-
-
- /* free partition/refinement structure */
- gk_free((void **)&graph->where, &graph->pwgts, &graph->id, &graph->ed,
- &graph->bndptr, &graph->bndind, &graph->nrinfo, &graph->ckrinfo,
- &graph->vkrinfo, LTERM);
-}
-
-
-/*************************************************************************/
-/*! This function deallocates any memory stored in a graph */
-/*************************************************************************/
-void FreeGraph(graph_t **r_graph)
-{
- graph_t *graph;
-
- graph = *r_graph;
-
- /* free graph structure */
- if (graph->free_xadj)
- gk_free((void **)&graph->xadj, LTERM);
- if (graph->free_vwgt)
- gk_free((void **)&graph->vwgt, LTERM);
- if (graph->free_vsize)
- gk_free((void **)&graph->vsize, LTERM);
- if (graph->free_adjncy)
- gk_free((void **)&graph->adjncy, LTERM);
- if (graph->free_adjwgt)
- gk_free((void **)&graph->adjwgt, LTERM);
-
- /* free partition/refinement structure */
- FreeRData(graph);
-
- gk_free((void **)&graph->tvwgt, &graph->invtvwgt, &graph->label,
- &graph->cmap, &graph, LTERM);
-
- *r_graph = NULL;
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/initpart.c b/3rdParty/metis/metis-5.1.0/libmetis/initpart.c
deleted file mode 100644
index 2f6c81b72..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/initpart.c
+++ /dev/null
@@ -1,630 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * initpart.c
- *
- * This file contains code that performs the initial partition of the
- * coarsest graph
- *
- * Started 7/23/97
- * George
- *
- */
-
-#include "metislib.h"
-
-/*************************************************************************/
-/*! This function computes the initial bisection of the coarsest graph */
-/*************************************************************************/
-void Init2WayPartition(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- mdbglvl_et dbglvl;
-
- ASSERT(graph->tvwgt[0] >= 0);
-
- dbglvl = ctrl->dbglvl;
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE, ctrl->dbglvl -= METIS_DBG_REFINE);
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO, ctrl->dbglvl -= METIS_DBG_MOVEINFO);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->InitPartTmr));
-
- switch (ctrl->iptype) {
- case METIS_IPTYPE_RANDOM:
- if (graph->ncon == 1)
- RandomBisection(ctrl, graph, ntpwgts, niparts);
- else
- McRandomBisection(ctrl, graph, ntpwgts, niparts);
- break;
-
- case METIS_IPTYPE_GROW:
- if (graph->nedges == 0)
- if (graph->ncon == 1)
- RandomBisection(ctrl, graph, ntpwgts, niparts);
- else
- McRandomBisection(ctrl, graph, ntpwgts, niparts);
- else
- if (graph->ncon == 1)
- GrowBisection(ctrl, graph, ntpwgts, niparts);
- else
- McGrowBisection(ctrl, graph, ntpwgts, niparts);
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown initial partition type: %d\n", ctrl->iptype);
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_IPART, printf("Initial Cut: %"PRIDX"\n", graph->mincut));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->InitPartTmr));
- ctrl->dbglvl = dbglvl;
-
-}
-
-
-/*************************************************************************/
-/*! This function computes the initial separator of the coarsest graph */
-/*************************************************************************/
-void InitSeparator(ctrl_t *ctrl, graph_t *graph, idx_t niparts)
-{
- real_t ntpwgts[2] = {0.5, 0.5};
- mdbglvl_et dbglvl;
-
- dbglvl = ctrl->dbglvl;
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE, ctrl->dbglvl -= METIS_DBG_REFINE);
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO, ctrl->dbglvl -= METIS_DBG_MOVEINFO);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->InitPartTmr));
-
- /* this is required for the cut-based part of the refinement */
- Setup2WayBalMultipliers(ctrl, graph, ntpwgts);
-
- switch (ctrl->iptype) {
- case METIS_IPTYPE_EDGE:
- if (graph->nedges == 0)
- RandomBisection(ctrl, graph, ntpwgts, niparts);
- else
- GrowBisection(ctrl, graph, ntpwgts, niparts);
-
- Compute2WayPartitionParams(ctrl, graph);
- ConstructSeparator(ctrl, graph);
- break;
-
- case METIS_IPTYPE_NODE:
- GrowBisectionNode(ctrl, graph, ntpwgts, niparts);
- break;
-
- default:
- gk_errexit(SIGERR, "Unkown iptype of %"PRIDX"\n", ctrl->iptype);
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_IPART, printf("Initial Sep: %"PRIDX"\n", graph->mincut));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->InitPartTmr));
-
- ctrl->dbglvl = dbglvl;
-
-}
-
-
-/*************************************************************************/
-/*! This function computes a bisection of a graph by randomly assigning
- the vertices followed by a bisection refinement.
- The resulting partition is returned in graph->where.
-*/
-/*************************************************************************/
-void RandomBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, ii, j, k, nvtxs, pwgts[2], zeromaxpwgt, from, me,
- bestcut=0, icut, mincut, inbfs;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where;
- idx_t *perm, *bestwhere;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- Allocate2WayPartitionMemory(ctrl, graph);
- where = graph->where;
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
-
- zeromaxpwgt = ctrl->ubfactors[0]*graph->tvwgt[0]*ntpwgts[0];
-
- for (inbfs=0; inbfs<niparts; inbfs++) {
- iset(nvtxs, 1, where);
-
- if (inbfs > 0) {
- irandArrayPermute(nvtxs, perm, nvtxs/2, 1);
- pwgts[1] = graph->tvwgt[0];
- pwgts[0] = 0;
-
- for (ii=0; ii<nvtxs; ii++) {
- i = perm[ii];
- if (pwgts[0]+vwgt[i] < zeromaxpwgt) {
- where[i] = 0;
- pwgts[0] += vwgt[i];
- pwgts[1] -= vwgt[i];
- if (pwgts[0] > zeromaxpwgt)
- break;
- }
- }
- }
-
- /* Do some partition refinement */
- Compute2WayPartitionParams(ctrl, graph);
- /* printf("IPART: %3"PRIDX" [%5"PRIDX" %5"PRIDX"] [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n", graph->nvtxs, pwgts[0], pwgts[1], graph->pwgts[0], graph->pwgts[1], graph->mincut); */
-
- Balance2Way(ctrl, graph, ntpwgts);
- /* printf("BPART: [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n", graph->pwgts[0], graph->pwgts[1], graph->mincut); */
-
- FM_2WayRefine(ctrl, graph, ntpwgts, 4);
- /* printf("RPART: [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n", graph->pwgts[0], graph->pwgts[1], graph->mincut); */
-
- if (inbfs==0 || bestcut > graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- if (bestcut == 0)
- break;
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function takes a graph and produces a bisection by using a region
- growing algorithm. The resulting bisection is refined using FM.
- The resulting partition is returned in graph->where.
-*/
-/*************************************************************************/
-void GrowBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, j, k, nvtxs, drain, nleft, first, last,
- pwgts[2], oneminpwgt, onemaxpwgt,
- from, me, bestcut=0, icut, mincut, inbfs;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where;
- idx_t *queue, *touched, *gain, *bestwhere;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- Allocate2WayPartitionMemory(ctrl, graph);
- where = graph->where;
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
- queue = iwspacemalloc(ctrl, nvtxs);
- touched = iwspacemalloc(ctrl, nvtxs);
-
- onemaxpwgt = ctrl->ubfactors[0]*graph->tvwgt[0]*ntpwgts[1];
- oneminpwgt = (1.0/ctrl->ubfactors[0])*graph->tvwgt[0]*ntpwgts[1];
-
- for (inbfs=0; inbfs<niparts; inbfs++) {
- iset(nvtxs, 1, where);
-
- iset(nvtxs, 0, touched);
-
- pwgts[1] = graph->tvwgt[0];
- pwgts[0] = 0;
-
-
- queue[0] = irandInRange(nvtxs);
- touched[queue[0]] = 1;
- first = 0;
- last = 1;
- nleft = nvtxs-1;
- drain = 0;
-
- /* Start the BFS from queue to get a partition */
- for (;;) {
- if (first == last) { /* Empty. Disconnected graph! */
- if (nleft == 0 || drain)
- break;
-
- k = irandInRange(nleft);
- for (i=0; i<nvtxs; i++) {
- if (touched[i] == 0) {
- if (k == 0)
- break;
- else
- k--;
- }
- }
-
- queue[0] = i;
- touched[i] = 1;
- first = 0;
- last = 1;
- nleft--;
- }
-
- i = queue[first++];
- if (pwgts[0] > 0 && pwgts[1]-vwgt[i] < oneminpwgt) {
- drain = 1;
- continue;
- }
-
- where[i] = 0;
- INC_DEC(pwgts[0], pwgts[1], vwgt[i]);
- if (pwgts[1] <= onemaxpwgt)
- break;
-
- drain = 0;
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (touched[k] == 0) {
- queue[last++] = k;
- touched[k] = 1;
- nleft--;
- }
- }
- }
-
- /* Check to see if we hit any bad limiting cases */
- if (pwgts[1] == 0)
- where[irandInRange(nvtxs)] = 1;
- if (pwgts[0] == 0)
- where[irandInRange(nvtxs)] = 0;
-
- /*************************************************************
- * Do some partition refinement
- **************************************************************/
- Compute2WayPartitionParams(ctrl, graph);
- /*
- printf("IPART: %3"PRIDX" [%5"PRIDX" %5"PRIDX"] [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n",
- graph->nvtxs, pwgts[0], pwgts[1], graph->pwgts[0], graph->pwgts[1], graph->mincut);
- */
-
- Balance2Way(ctrl, graph, ntpwgts);
- /*
- printf("BPART: [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n", graph->pwgts[0],
- graph->pwgts[1], graph->mincut);
- */
-
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
- /*
- printf("RPART: [%5"PRIDX" %5"PRIDX"] %5"PRIDX"\n", graph->pwgts[0],
- graph->pwgts[1], graph->mincut);
- */
-
- if (inbfs == 0 || bestcut > graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- if (bestcut == 0)
- break;
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function takes a multi-constraint graph and computes a bisection
- by randomly assigning the vertices and then refining it. The resulting
- partition is returned in graph->where.
-*/
-/**************************************************************************/
-void McRandomBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, ii, j, k, nvtxs, ncon, from, bestcut=0, mincut, inbfs, qnum;
- idx_t *bestwhere, *where, *perm, *counts;
- idx_t *vwgt;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- vwgt = graph->vwgt;
-
- Allocate2WayPartitionMemory(ctrl, graph);
- where = graph->where;
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
- perm = iwspacemalloc(ctrl, nvtxs);
- counts = iwspacemalloc(ctrl, ncon);
-
- for (inbfs=0; inbfs<2*niparts; inbfs++) {
- irandArrayPermute(nvtxs, perm, nvtxs/2, 1);
- iset(ncon, 0, counts);
-
- /* partition by spliting the queues randomly */
- for (ii=0; ii<nvtxs; ii++) {
- i = perm[ii];
- qnum = iargmax(ncon, vwgt+i*ncon);
- where[i] = (counts[qnum]++)%2;
- }
-
- Compute2WayPartitionParams(ctrl, graph);
-
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
- Balance2Way(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
- Balance2Way(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
-
- if (inbfs == 0 || bestcut >= graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- if (bestcut == 0)
- break;
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function takes a multi-constraint graph and produces a bisection
- by using a region growing algorithm. The resulting partition is
- returned in graph->where.
-*/
-/*************************************************************************/
-void McGrowBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, j, k, nvtxs, ncon, from, bestcut=0, mincut, inbfs;
- idx_t *bestwhere, *where;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
-
- Allocate2WayPartitionMemory(ctrl, graph);
- where = graph->where;
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
-
- for (inbfs=0; inbfs<2*niparts; inbfs++) {
- iset(nvtxs, 1, where);
- where[irandInRange(nvtxs)] = 0;
-
- Compute2WayPartitionParams(ctrl, graph);
-
- Balance2Way(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
- Balance2Way(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
-
- if (inbfs == 0 || bestcut >= graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- if (bestcut == 0)
- break;
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/* This function takes a graph and produces a tri-section into left, right,
- and separator using a region growing algorithm. The resulting separator
- is refined using node FM.
- The resulting partition is returned in graph->where.
-*/
-/**************************************************************************/
-void GrowBisectionNode(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, j, k, nvtxs, drain, nleft, first, last, pwgts[2], oneminpwgt,
- onemaxpwgt, from, me, bestcut=0, icut, mincut, inbfs;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *where, *bndind;
- idx_t *queue, *touched, *gain, *bestwhere;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
- queue = iwspacemalloc(ctrl, nvtxs);
- touched = iwspacemalloc(ctrl, nvtxs);
-
- onemaxpwgt = ctrl->ubfactors[0]*graph->tvwgt[0]*0.5;
- oneminpwgt = (1.0/ctrl->ubfactors[0])*graph->tvwgt[0]*0.5;
-
-
- /* Allocate refinement memory. Allocate sufficient memory for both edge and node */
- graph->pwgts = imalloc(3, "GrowBisectionNode: pwgts");
- graph->where = imalloc(nvtxs, "GrowBisectionNode: where");
- graph->bndptr = imalloc(nvtxs, "GrowBisectionNode: bndptr");
- graph->bndind = imalloc(nvtxs, "GrowBisectionNode: bndind");
- graph->id = imalloc(nvtxs, "GrowBisectionNode: id");
- graph->ed = imalloc(nvtxs, "GrowBisectionNode: ed");
- graph->nrinfo = (nrinfo_t *)gk_malloc(nvtxs*sizeof(nrinfo_t), "GrowBisectionNode: nrinfo");
-
- where = graph->where;
- bndind = graph->bndind;
-
- for (inbfs=0; inbfs<niparts; inbfs++) {
- iset(nvtxs, 1, where);
- iset(nvtxs, 0, touched);
-
- pwgts[1] = graph->tvwgt[0];
- pwgts[0] = 0;
-
- queue[0] = irandInRange(nvtxs);
- touched[queue[0]] = 1;
- first = 0; last = 1;
- nleft = nvtxs-1;
- drain = 0;
-
- /* Start the BFS from queue to get a partition */
- for (;;) {
- if (first == last) { /* Empty. Disconnected graph! */
- if (nleft == 0 || drain)
- break;
-
- k = irandInRange(nleft);
- for (i=0; i<nvtxs; i++) { /* select the kth untouched vertex */
- if (touched[i] == 0) {
- if (k == 0)
- break;
- else
- k--;
- }
- }
-
- queue[0] = i;
- touched[i] = 1;
- first = 0;
- last = 1;
- nleft--;
- }
-
- i = queue[first++];
- if (pwgts[1]-vwgt[i] < oneminpwgt) {
- drain = 1;
- continue;
- }
-
- where[i] = 0;
- INC_DEC(pwgts[0], pwgts[1], vwgt[i]);
- if (pwgts[1] <= onemaxpwgt)
- break;
-
- drain = 0;
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (touched[k] == 0) {
- queue[last++] = k;
- touched[k] = 1;
- nleft--;
- }
- }
- }
-
- /*************************************************************
- * Do some partition refinement
- **************************************************************/
- Compute2WayPartitionParams(ctrl, graph);
- Balance2Way(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, 4);
-
- /* Construct and refine the vertex separator */
- for (i=0; i<graph->nbnd; i++) {
- j = bndind[i];
- if (xadj[j+1]-xadj[j] > 0) /* ignore islands */
- where[j] = 2;
- }
-
- Compute2WayNodePartitionParams(ctrl, graph);
- FM_2WayNodeRefine2Sided(ctrl, graph, 1);
- FM_2WayNodeRefine1Sided(ctrl, graph, 4);
-
- /*
- printf("ISep: [%"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"] %"PRIDX"\n",
- inbfs, graph->pwgts[0], graph->pwgts[1], graph->pwgts[2], bestcut);
- */
-
- if (inbfs == 0 || bestcut > graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/* This function takes a graph and produces a tri-section into left, right,
- and separator using a region growing algorithm. The resulting separator
- is refined using node FM.
- The resulting partition is returned in graph->where.
-*/
-/**************************************************************************/
-void GrowBisectionNode2(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- idx_t niparts)
-{
- idx_t i, j, k, nvtxs, bestcut=0, mincut, inbfs;
- idx_t *xadj, *where, *bndind, *bestwhere;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
-
- /* Allocate refinement memory. Allocate sufficient memory for both edge and node */
- graph->pwgts = imalloc(3, "GrowBisectionNode: pwgts");
- graph->where = imalloc(nvtxs, "GrowBisectionNode: where");
- graph->bndptr = imalloc(nvtxs, "GrowBisectionNode: bndptr");
- graph->bndind = imalloc(nvtxs, "GrowBisectionNode: bndind");
- graph->id = imalloc(nvtxs, "GrowBisectionNode: id");
- graph->ed = imalloc(nvtxs, "GrowBisectionNode: ed");
- graph->nrinfo = (nrinfo_t *)gk_malloc(nvtxs*sizeof(nrinfo_t), "GrowBisectionNode: nrinfo");
-
- bestwhere = iwspacemalloc(ctrl, nvtxs);
-
- where = graph->where;
- bndind = graph->bndind;
-
- for (inbfs=0; inbfs<niparts; inbfs++) {
- iset(nvtxs, 1, where);
- if (inbfs > 0)
- where[irandInRange(nvtxs)] = 0;
-
- Compute2WayPartitionParams(ctrl, graph);
- General2WayBalance(ctrl, graph, ntpwgts);
- FM_2WayRefine(ctrl, graph, ntpwgts, ctrl->niter);
-
- /* Construct and refine the vertex separator */
- for (i=0; i<graph->nbnd; i++) {
- j = bndind[i];
- if (xadj[j+1]-xadj[j] > 0) /* ignore islands */
- where[j] = 2;
- }
-
- Compute2WayNodePartitionParams(ctrl, graph);
- FM_2WayNodeRefine2Sided(ctrl, graph, 4);
-
- /*
- printf("ISep: [%"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"] %"PRIDX"\n",
- inbfs, graph->pwgts[0], graph->pwgts[1], graph->pwgts[2], bestcut);
- */
-
- if (inbfs == 0 || bestcut > graph->mincut) {
- bestcut = graph->mincut;
- icopy(nvtxs, where, bestwhere);
- }
- }
-
- graph->mincut = bestcut;
- icopy(nvtxs, bestwhere, where);
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/kmetis.c b/3rdParty/metis/metis-5.1.0/libmetis/kmetis.c
deleted file mode 100644
index cb6d1afb3..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/kmetis.c
+++ /dev/null
@@ -1,243 +0,0 @@
-/*!
-\file
-\brief The top-level routines for multilevel k-way partitioning that minimizes
- the edge cut.
-
-\date Started 7/28/1997
-\author George
-\author Copyright 1997-2011, Regents of the University of Minnesota
-\version\verbatim $Id: kmetis.c 13905 2013-03-25 13:21:20Z karypis $ \endverbatim
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point for MCKMETIS */
-/*************************************************************************/
-int METIS_PartGraphKway(idx_t *nvtxs, idx_t *ncon, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *vsize, idx_t *adjwgt, idx_t *nparts,
- real_t *tpwgts, real_t *ubvec, idx_t *options, idx_t *objval,
- idx_t *part)
-{
- int sigrval=0, renumber=0;
- graph_t *graph;
- ctrl_t *ctrl;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
-
- /* set up the run parameters */
- ctrl = SetupCtrl(METIS_OP_KMETIS, options, *ncon, *nparts, tpwgts, ubvec);
- if (!ctrl) {
- gk_siguntrap();
- return METIS_ERROR_INPUT;
- }
-
- /* if required, change the numbering to 0 */
- if (ctrl->numflag == 1) {
- Change2CNumbering(*nvtxs, xadj, adjncy);
- renumber = 1;
- }
-
- /* set up the graph */
- graph = SetupGraph(ctrl, *nvtxs, *ncon, xadj, adjncy, vwgt, vsize, adjwgt);
-
- /* set up multipliers for making balance computations easier */
- SetupKWayBalMultipliers(ctrl, graph);
-
- /* set various run parameters that depend on the graph */
- ctrl->CoarsenTo = gk_max((*nvtxs)/(20*gk_log2(*nparts)), 30*(*nparts));
- ctrl->nIparts = (ctrl->CoarsenTo == 30*(*nparts) ? 4 : 5);
-
- /* take care contiguity requests for disconnected graphs */
- if (ctrl->contig && !IsConnected(graph, 0))
- gk_errexit(SIGERR, "METIS Error: A contiguous partition is requested for a non-contiguous input graph.\n");
-
- /* allocate workspace memory */
- AllocateWorkSpace(ctrl, graph);
-
- /* start the partitioning */
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, InitTimers(ctrl));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->TotalTmr));
-
- *objval = MlevelKWayPartitioning(ctrl, graph, part);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->TotalTmr));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, PrintTimers(ctrl));
-
- /* clean up */
- FreeCtrl(&ctrl);
-
-SIGTHROW:
- /* if required, change the numbering back to 1 */
- if (renumber)
- Change2FNumbering(*nvtxs, xadj, adjncy, part);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- return metis_rcode(sigrval);
-}
-
-
-/*************************************************************************/
-/*! This function computes a k-way partitioning of a graph that minimizes
- the specified objective function.
-
- \param ctrl is the control structure
- \param graph is the graph to be partitioned
- \param part is the vector that on return will store the partitioning
-
- \returns the objective value of the partitoning. The partitioning
- itself is stored in the part vector.
-*/
-/*************************************************************************/
-idx_t MlevelKWayPartitioning(ctrl_t *ctrl, graph_t *graph, idx_t *part)
-{
- idx_t i, j, objval=0, curobj=0, bestobj=0;
- real_t curbal=0.0, bestbal=0.0;
- graph_t *cgraph;
- int status;
-
-
- for (i=0; i<ctrl->ncuts; i++) {
- cgraph = CoarsenGraph(ctrl, graph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->InitPartTmr));
- AllocateKWayPartitionMemory(ctrl, cgraph);
-
- /* Release the work space */
- FreeWorkSpace(ctrl);
-
- /* Compute the initial partitioning */
- InitKWayPartitioning(ctrl, cgraph);
-
- /* Re-allocate the work space */
- AllocateWorkSpace(ctrl, graph);
- AllocateRefinementWorkSpace(ctrl, 2*cgraph->nedges);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->InitPartTmr));
- IFSET(ctrl->dbglvl, METIS_DBG_IPART,
- printf("Initial %"PRIDX"-way partitioning cut: %"PRIDX"\n", ctrl->nparts, objval));
-
- RefineKWay(ctrl, graph, cgraph);
-
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- curobj = graph->mincut;
- break;
-
- case METIS_OBJTYPE_VOL:
- curobj = graph->minvol;
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype: %d\n", ctrl->objtype);
- }
-
- curbal = ComputeLoadImbalanceDiff(graph, ctrl->nparts, ctrl->pijbm, ctrl->ubfactors);
-
- if (i == 0
- || (curbal <= 0.0005 && bestobj > curobj)
- || (bestbal > 0.0005 && curbal < bestbal)) {
- icopy(graph->nvtxs, graph->where, part);
- bestobj = curobj;
- bestbal = curbal;
- }
-
- FreeRData(graph);
-
- if (bestobj == 0)
- break;
- }
-
- FreeGraph(&graph);
-
- return bestobj;
-}
-
-
-/*************************************************************************/
-/*! This function computes the initial k-way partitioning using PMETIS
-*/
-/*************************************************************************/
-void InitKWayPartitioning(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ntrials, options[METIS_NOPTIONS], curobj=0, bestobj=0;
- idx_t *bestwhere=NULL;
- real_t *ubvec=NULL;
- int status;
-
- METIS_SetDefaultOptions(options);
- options[METIS_OPTION_NITER] = 10;
- options[METIS_OPTION_OBJTYPE] = METIS_OBJTYPE_CUT;
- options[METIS_OPTION_NO2HOP] = ctrl->no2hop;
-
-
- ubvec = rmalloc(graph->ncon, "InitKWayPartitioning: ubvec");
- for (i=0; i<graph->ncon; i++)
- ubvec[i] = (real_t)pow(ctrl->ubfactors[i], 1.0/log(ctrl->nparts));
-
-
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- case METIS_OBJTYPE_VOL:
- options[METIS_OPTION_NCUTS] = ctrl->nIparts;
- status = METIS_PartGraphRecursive(&graph->nvtxs, &graph->ncon,
- graph->xadj, graph->adjncy, graph->vwgt, graph->vsize,
- graph->adjwgt, &ctrl->nparts, ctrl->tpwgts, ubvec,
- options, &curobj, graph->where);
-
- if (status != METIS_OK)
- gk_errexit(SIGERR, "Failed during initial partitioning\n");
-
- break;
-
-#ifdef XXX /* This does not seem to help */
- case METIS_OBJTYPE_VOL:
- bestwhere = imalloc(graph->nvtxs, "InitKWayPartitioning: bestwhere");
- options[METIS_OPTION_NCUTS] = 2;
-
- ntrials = (ctrl->nIparts+1)/2;
- for (i=0; i<ntrials; i++) {
- status = METIS_PartGraphRecursive(&graph->nvtxs, &graph->ncon,
- graph->xadj, graph->adjncy, graph->vwgt, graph->vsize,
- graph->adjwgt, &ctrl->nparts, ctrl->tpwgts, ubvec,
- options, &curobj, graph->where);
- if (status != METIS_OK)
- gk_errexit(SIGERR, "Failed during initial partitioning\n");
-
- curobj = ComputeVolume(graph, graph->where);
-
- if (i == 0 || bestobj > curobj) {
- bestobj = curobj;
- if (i < ntrials-1)
- icopy(graph->nvtxs, graph->where, bestwhere);
- }
-
- if (bestobj == 0)
- break;
- }
- if (bestobj != curobj)
- icopy(graph->nvtxs, bestwhere, graph->where);
-
- break;
-#endif
-
- default:
- gk_errexit(SIGERR, "Unknown objtype: %d\n", ctrl->objtype);
- }
-
- gk_free((void **)&ubvec, &bestwhere, LTERM);
-
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/kwayfm.c b/3rdParty/metis/metis-5.1.0/libmetis/kwayfm.c
deleted file mode 100644
index dedfd3909..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/kwayfm.c
+++ /dev/null
@@ -1,1852 +0,0 @@
-/*!
-\file
-\brief Routines for k-way refinement
-
-\date Started 7/28/97
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version $Id: kwayfm.c 10567 2011-07-13 16:17:07Z karypis $
-*/
-
-#include "metislib.h"
-
-
-
-/*************************************************************************/
-/* Top-level routine for k-way partitioning refinement. This routine just
- calls the appropriate refinement routine based on the objectives and
- constraints. */
-/*************************************************************************/
-void Greedy_KWayOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode)
-{
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- if (graph->ncon == 1)
- Greedy_KWayCutOptimize(ctrl, graph, niter, ffactor, omode);
- else
- Greedy_McKWayCutOptimize(ctrl, graph, niter, ffactor, omode);
- break;
-
- case METIS_OBJTYPE_VOL:
- if (graph->ncon == 1)
- Greedy_KWayVolOptimize(ctrl, graph, niter, ffactor, omode);
- else
- Greedy_McKWayVolOptimize(ctrl, graph, niter, ffactor, omode);
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-}
-
-
-/*************************************************************************/
-/*! K-way partitioning optimization in which the vertices are visited in
- decreasing ed/sqrt(nnbrs)-id order. Note this is just an
- approximation, as the ed is often split across different subdomains
- and the sqrt(nnbrs) is just a crude approximation.
-
- \param graph is the graph that is being refined.
- \param niter is the number of refinement iterations.
- \param ffactor is the \em fudge-factor for allowing positive gain moves
- to violate the max-pwgt constraint.
- \param omode is the type of optimization that will performed among
- OMODE_REFINE and OMODE_BALANCE
-
-
-*/
-/**************************************************************************/
-void Greedy_KWayCutOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode)
-{
- /* Common variables to all types of kway-refinement/balancing routines */
- idx_t i, ii, iii, j, k, l, pass, nvtxs, nparts, gain;
- idx_t from, me, to, oldcut, vwgt;
- idx_t *xadj, *adjncy, *adjwgt;
- idx_t *where, *pwgts, *perm, *bndptr, *bndind, *minwgt, *maxwgt, *itpwgts;
- idx_t nmoved, nupd, *vstatus, *updptr, *updind;
- idx_t maxndoms, *safetos=NULL, *nads=NULL, *doms=NULL, **adids=NULL, **adwgts=NULL;
- idx_t *bfslvl=NULL, *bfsind=NULL, *bfsmrk=NULL;
- idx_t bndtype = (omode == OMODE_REFINE ? BNDTYPE_REFINE : BNDTYPE_BALANCE);
-
- /* Edgecut-specific/different variables */
- idx_t nbnd, oldnnbrs;
- rpq_t *queue;
- real_t rgain;
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- WCOREPUSH;
-
- /* Link the graph fields */
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
-
- where = graph->where;
- pwgts = graph->pwgts;
-
- nparts = ctrl->nparts;
-
- /* Setup the weight intervals of the various subdomains */
- minwgt = iwspacemalloc(ctrl, nparts);
- maxwgt = iwspacemalloc(ctrl, nparts);
- itpwgts = iwspacemalloc(ctrl, nparts);
-
- for (i=0; i<nparts; i++) {
- itpwgts[i] = ctrl->tpwgts[i]*graph->tvwgt[0];
- maxwgt[i] = ctrl->tpwgts[i]*graph->tvwgt[0]*ctrl->ubfactors[0];
- minwgt[i] = ctrl->tpwgts[i]*graph->tvwgt[0]*(1.0/ctrl->ubfactors[0]);
- }
-
- perm = iwspacemalloc(ctrl, nvtxs);
-
-
- /* This stores the valid target subdomains. It is used when ctrl->minconn to
- control the subdomains to which moves are allowed to be made.
- When ctrl->minconn is false, the default values of 2 allow all moves to
- go through and it does not interfere with the zero-gain move selection. */
- safetos = iset(nparts, 2, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->minconn) {
- ComputeSubDomainGraph(ctrl, graph);
-
- nads = ctrl->nads;
- adids = ctrl->adids;
- adwgts = ctrl->adwgts;
- doms = iset(nparts, 0, ctrl->pvec1);
- }
-
-
- /* Setup updptr, updind like boundary info to keep track of the vertices whose
- vstatus's need to be reset at the end of the inner iteration */
- vstatus = iset(nvtxs, VPQSTATUS_NOTPRESENT, iwspacemalloc(ctrl, nvtxs));
- updptr = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- updind = iwspacemalloc(ctrl, nvtxs);
-
- if (ctrl->contig) {
- /* The arrays that will be used for limited check of articulation points */
- bfslvl = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- bfsind = iwspacemalloc(ctrl, nvtxs);
- bfsmrk = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("%s: [%6"PRIDX" %6"PRIDX"]-[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL","
- " Nv-Nb[%6"PRIDX" %6"PRIDX"], Cut: %6"PRIDX,
- (omode == OMODE_REFINE ? "GRC" : "GBC"),
- pwgts[iargmin(nparts, pwgts)], imax(nparts, pwgts), minwgt[0], maxwgt[0],
- ComputeLoadImbalance(graph, nparts, ctrl->pijbm),
- graph->nvtxs, graph->nbnd, graph->mincut);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- queue = rpqCreate(nvtxs);
-
- /*=====================================================================
- * The top-level refinement loop
- *======================================================================*/
- for (pass=0; pass<niter; pass++) {
- ASSERT(ComputeCut(graph, where) == graph->mincut);
-
- if (omode == OMODE_BALANCE) {
- /* Check to see if things are out of balance, given the tolerance */
- for (i=0; i<nparts; i++) {
- if (pwgts[i] > maxwgt[i])
- break;
- }
- if (i == nparts) /* Things are balanced. Return right away */
- break;
- }
-
- oldcut = graph->mincut;
- nbnd = graph->nbnd;
- nupd = 0;
-
- if (ctrl->minconn)
- maxndoms = imax(nparts, nads);
-
- /* Insert the boundary vertices in the priority queue */
- irandArrayPermute(nbnd, perm, nbnd/4, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[perm[ii]];
- rgain = (graph->ckrinfo[i].nnbrs > 0 ?
- 1.0*graph->ckrinfo[i].ed/sqrt(graph->ckrinfo[i].nnbrs) : 0.0)
- - graph->ckrinfo[i].id;
- rpqInsert(queue, i, rgain);
- vstatus[i] = VPQSTATUS_PRESENT;
- ListInsert(nupd, updind, updptr, i);
- }
-
- /* Start extracting vertices from the queue and try to move them */
- for (nmoved=0, iii=0;;iii++) {
- if ((i = rpqGetTop(queue)) == -1)
- break;
- vstatus[i] = VPQSTATUS_EXTRACTED;
-
- myrinfo = graph->ckrinfo+i;
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- from = where[i];
- vwgt = graph->vwgt[i];
-
- /* Prevent moves that make 'from' domain underbalanced */
- if (omode == OMODE_REFINE) {
- if (myrinfo->id > 0 && pwgts[from]-vwgt < minwgt[from])
- continue;
- }
- else { /* OMODE_BALANCE */
- if (pwgts[from]-vwgt < minwgt[from])
- continue;
- }
-
- if (ctrl->contig && IsArticulationNode(i, xadj, adjncy, where, bfslvl, bfsind, bfsmrk))
- continue;
-
- if (ctrl->minconn)
- SelectSafeTargetSubdomains(myrinfo, mynbrs, nads, adids, maxndoms, safetos, doms);
-
- /* Find the most promising subdomain to move to */
- if (omode == OMODE_REFINE) {
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- gain = mynbrs[k].ed-myrinfo->id;
- if (gain >= 0 && pwgts[to]+vwgt <= maxwgt[to]+ffactor*gain)
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- gain = mynbrs[j].ed-myrinfo->id;
- if ((mynbrs[j].ed > mynbrs[k].ed && pwgts[to]+vwgt <= maxwgt[to]+ffactor*gain)
- ||
- (mynbrs[j].ed == mynbrs[k].ed &&
- itpwgts[mynbrs[k].pid]*pwgts[to] < itpwgts[to]*pwgts[mynbrs[k].pid]))
- k = j;
- }
-
- to = mynbrs[k].pid;
-
- gain = mynbrs[k].ed-myrinfo->id;
- if (!(gain > 0
- || (gain == 0
- && (pwgts[from] >= maxwgt[from]
- || itpwgts[to]*pwgts[from] > itpwgts[from]*(pwgts[to]+vwgt)
- || (iii%2 == 0 && safetos[to] == 2)
- )
- )
- )
- )
- continue;
- }
- else { /* OMODE_BALANCE */
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- if (pwgts[to]+vwgt <= maxwgt[to] ||
- itpwgts[from]*(pwgts[to]+vwgt) <= itpwgts[to]*pwgts[from])
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- if (itpwgts[mynbrs[k].pid]*pwgts[to] < itpwgts[to]*pwgts[mynbrs[k].pid])
- k = j;
- }
-
- to = mynbrs[k].pid;
-
- if (pwgts[from] < maxwgt[from] && pwgts[to] > minwgt[to] &&
- mynbrs[k].ed-myrinfo->id < 0)
- continue;
- }
-
-
-
- /*=====================================================================
- * If we got here, we can now move the vertex from 'from' to 'to'
- *======================================================================*/
- graph->mincut -= mynbrs[k].ed-myrinfo->id;
- nmoved++;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("\t\tMoving %6"PRIDX" to %3"PRIDX". Gain: %4"PRIDX". Cut: %6"PRIDX"\n",
- i, to, mynbrs[k].ed-myrinfo->id, graph->mincut));
-
- /* Update the subdomain connectivity information */
- if (ctrl->minconn) {
- /* take care of i's move itself */
- UpdateEdgeSubDomainGraph(ctrl, from, to, myrinfo->id-mynbrs[k].ed, &maxndoms);
-
- /* take care of the adjancent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- me = where[adjncy[j]];
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -adjwgt[j], &maxndoms);
- UpdateEdgeSubDomainGraph(ctrl, to, me, adjwgt[j], &maxndoms);
- }
- }
- }
-
- /* Update ID/ED and BND related information for the moved vertex */
- INC_DEC(pwgts[to], pwgts[from], vwgt);
- UpdateMovedVertexInfoAndBND(i, from, k, to, myrinfo, mynbrs, where, nbnd,
- bndptr, bndind, bndtype);
-
- /* Update the degrees of adjacent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- me = where[ii];
- myrinfo = graph->ckrinfo+ii;
-
- oldnnbrs = myrinfo->nnbrs;
-
- UpdateAdjacentVertexInfoAndBND(ctrl, ii, xadj[ii+1]-xadj[ii], me,
- from, to, myrinfo, adjwgt[j], nbnd, bndptr, bndind, bndtype);
-
- UpdateQueueInfo(queue, vstatus, ii, me, from, to, myrinfo, oldnnbrs,
- nupd, updptr, updind, bndtype);
-
- ASSERT(myrinfo->nnbrs <= xadj[ii+1]-xadj[ii]);
- }
- }
-
- graph->nbnd = nbnd;
-
- /* Reset the vstatus and associated data structures */
- for (i=0; i<nupd; i++) {
- ASSERT(updptr[updind[i]] != -1);
- ASSERT(vstatus[updind[i]] != VPQSTATUS_NOTPRESENT);
- vstatus[updind[i]] = VPQSTATUS_NOTPRESENT;
- updptr[updind[i]] = -1;
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("\t[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL", Nb: %6"PRIDX"."
- " Nmoves: %5"PRIDX", Cut: %6"PRIDX", Vol: %6"PRIDX,
- pwgts[iargmin(nparts, pwgts)], imax(nparts, pwgts),
- ComputeLoadImbalance(graph, nparts, ctrl->pijbm),
- graph->nbnd, nmoved, graph->mincut, ComputeVolume(graph, where));
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- if (nmoved == 0 || (omode == OMODE_REFINE && graph->mincut == oldcut))
- break;
- }
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! K-way refinement that minimizes the communication volume. This is a
- greedy routine and the vertices are visited in decreasing gv order.
-
- \param graph is the graph that is being refined.
- \param niter is the number of refinement iterations.
- \param ffactor is the \em fudge-factor for allowing positive gain moves
- to violate the max-pwgt constraint.
-
-*/
-/**************************************************************************/
-void Greedy_KWayVolOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode)
-{
- /* Common variables to all types of kway-refinement/balancing routines */
- idx_t i, ii, iii, j, k, l, pass, nvtxs, nparts, gain;
- idx_t from, me, to, oldcut, vwgt;
- idx_t *xadj, *adjncy;
- idx_t *where, *pwgts, *perm, *bndptr, *bndind, *minwgt, *maxwgt, *itpwgts;
- idx_t nmoved, nupd, *vstatus, *updptr, *updind;
- idx_t maxndoms, *safetos=NULL, *nads=NULL, *doms=NULL, **adids=NULL, **adwgts=NULL;
- idx_t *bfslvl=NULL, *bfsind=NULL, *bfsmrk=NULL;
- idx_t bndtype = (omode == OMODE_REFINE ? BNDTYPE_REFINE : BNDTYPE_BALANCE);
-
- /* Volume-specific/different variables */
- ipq_t *queue;
- idx_t oldvol, xgain;
- idx_t *vmarker, *pmarker, *modind;
- vkrinfo_t *myrinfo;
- vnbr_t *mynbrs;
-
- WCOREPUSH;
-
- /* Link the graph fields */
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
- where = graph->where;
- pwgts = graph->pwgts;
-
- nparts = ctrl->nparts;
-
- /* Setup the weight intervals of the various subdomains */
- minwgt = iwspacemalloc(ctrl, nparts);
- maxwgt = iwspacemalloc(ctrl, nparts);
- itpwgts = iwspacemalloc(ctrl, nparts);
-
- for (i=0; i<nparts; i++) {
- itpwgts[i] = ctrl->tpwgts[i]*graph->tvwgt[0];
- maxwgt[i] = ctrl->tpwgts[i]*graph->tvwgt[0]*ctrl->ubfactors[0];
- minwgt[i] = ctrl->tpwgts[i]*graph->tvwgt[0]*(1.0/ctrl->ubfactors[0]);
- }
-
- perm = iwspacemalloc(ctrl, nvtxs);
-
-
- /* This stores the valid target subdomains. It is used when ctrl->minconn to
- control the subdomains to which moves are allowed to be made.
- When ctrl->minconn is false, the default values of 2 allow all moves to
- go through and it does not interfere with the zero-gain move selection. */
- safetos = iset(nparts, 2, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->minconn) {
- ComputeSubDomainGraph(ctrl, graph);
-
- nads = ctrl->nads;
- adids = ctrl->adids;
- adwgts = ctrl->adwgts;
- doms = iset(nparts, 0, ctrl->pvec1);
- }
-
-
- /* Setup updptr, updind like boundary info to keep track of the vertices whose
- vstatus's need to be reset at the end of the inner iteration */
- vstatus = iset(nvtxs, VPQSTATUS_NOTPRESENT, iwspacemalloc(ctrl, nvtxs));
- updptr = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- updind = iwspacemalloc(ctrl, nvtxs);
-
- if (ctrl->contig) {
- /* The arrays that will be used for limited check of articulation points */
- bfslvl = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- bfsind = iwspacemalloc(ctrl, nvtxs);
- bfsmrk = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- }
-
- /* Vol-refinement specific working arrays */
- modind = iwspacemalloc(ctrl, nvtxs);
- vmarker = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- pmarker = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("%s: [%6"PRIDX" %6"PRIDX"]-[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL
- ", Nv-Nb[%6"PRIDX" %6"PRIDX"], Cut: %5"PRIDX", Vol: %5"PRIDX,
- (omode == OMODE_REFINE ? "GRV" : "GBV"),
- pwgts[iargmin(nparts, pwgts)], imax(nparts, pwgts), minwgt[0], maxwgt[0],
- ComputeLoadImbalance(graph, nparts, ctrl->pijbm),
- graph->nvtxs, graph->nbnd, graph->mincut, graph->minvol);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- queue = ipqCreate(nvtxs);
-
-
- /*=====================================================================
- * The top-level refinement loop
- *======================================================================*/
- for (pass=0; pass<niter; pass++) {
- ASSERT(ComputeVolume(graph, where) == graph->minvol);
-
- if (omode == OMODE_BALANCE) {
- /* Check to see if things are out of balance, given the tolerance */
- for (i=0; i<nparts; i++) {
- if (pwgts[i] > maxwgt[i])
- break;
- }
- if (i == nparts) /* Things are balanced. Return right away */
- break;
- }
-
- oldcut = graph->mincut;
- oldvol = graph->minvol;
- nupd = 0;
-
- if (ctrl->minconn)
- maxndoms = imax(nparts, nads);
-
- /* Insert the boundary vertices in the priority queue */
- irandArrayPermute(graph->nbnd, perm, graph->nbnd/4, 1);
- for (ii=0; ii<graph->nbnd; ii++) {
- i = bndind[perm[ii]];
- ipqInsert(queue, i, graph->vkrinfo[i].gv);
- vstatus[i] = VPQSTATUS_PRESENT;
- ListInsert(nupd, updind, updptr, i);
- }
-
- /* Start extracting vertices from the queue and try to move them */
- for (nmoved=0, iii=0;;iii++) {
- if ((i = ipqGetTop(queue)) == -1)
- break;
- vstatus[i] = VPQSTATUS_EXTRACTED;
-
- myrinfo = graph->vkrinfo+i;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- from = where[i];
- vwgt = graph->vwgt[i];
-
- /* Prevent moves that make 'from' domain underbalanced */
- if (omode == OMODE_REFINE) {
- if (myrinfo->nid > 0 && pwgts[from]-vwgt < minwgt[from])
- continue;
- }
- else { /* OMODE_BALANCE */
- if (pwgts[from]-vwgt < minwgt[from])
- continue;
- }
-
- if (ctrl->contig && IsArticulationNode(i, xadj, adjncy, where, bfslvl, bfsind, bfsmrk))
- continue;
-
- if (ctrl->minconn)
- SelectSafeTargetSubdomains(myrinfo, mynbrs, nads, adids, maxndoms, safetos, doms);
-
- xgain = (myrinfo->nid == 0 && myrinfo->ned > 0 ? graph->vsize[i] : 0);
-
- /* Find the most promising subdomain to move to */
- if (omode == OMODE_REFINE) {
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- gain = mynbrs[k].gv + xgain;
- if (gain >= 0 && pwgts[to]+vwgt <= maxwgt[to]+ffactor*gain)
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- gain = mynbrs[j].gv + xgain;
- if ((mynbrs[j].gv > mynbrs[k].gv &&
- pwgts[to]+vwgt <= maxwgt[to]+ffactor*gain)
- ||
- (mynbrs[j].gv == mynbrs[k].gv &&
- mynbrs[j].ned > mynbrs[k].ned &&
- pwgts[to]+vwgt <= maxwgt[to])
- ||
- (mynbrs[j].gv == mynbrs[k].gv &&
- mynbrs[j].ned == mynbrs[k].ned &&
- itpwgts[mynbrs[k].pid]*pwgts[to] < itpwgts[to]*pwgts[mynbrs[k].pid])
- )
- k = j;
- }
- to = mynbrs[k].pid;
-
- ASSERT(xgain+mynbrs[k].gv >= 0);
-
- j = 0;
- if (xgain+mynbrs[k].gv > 0 || mynbrs[k].ned-myrinfo->nid > 0)
- j = 1;
- else if (mynbrs[k].ned-myrinfo->nid == 0) {
- if ((iii%2 == 0 && safetos[to] == 2) ||
- pwgts[from] >= maxwgt[from] ||
- itpwgts[from]*(pwgts[to]+vwgt) < itpwgts[to]*pwgts[from])
- j = 1;
- }
- if (j == 0)
- continue;
- }
- else { /* OMODE_BALANCE */
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- if (pwgts[to]+vwgt <= maxwgt[to] ||
- itpwgts[from]*(pwgts[to]+vwgt) <= itpwgts[to]*pwgts[from])
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- if (itpwgts[mynbrs[k].pid]*pwgts[to] < itpwgts[to]*pwgts[mynbrs[k].pid])
- k = j;
- }
- to = mynbrs[k].pid;
-
- if (pwgts[from] < maxwgt[from] && pwgts[to] > minwgt[to] &&
- (xgain+mynbrs[k].gv < 0 ||
- (xgain+mynbrs[k].gv == 0 && mynbrs[k].ned-myrinfo->nid < 0))
- )
- continue;
- }
-
-
- /*=====================================================================
- * If we got here, we can now move the vertex from 'from' to 'to'
- *======================================================================*/
- INC_DEC(pwgts[to], pwgts[from], vwgt);
- graph->mincut -= mynbrs[k].ned-myrinfo->nid;
- graph->minvol -= (xgain+mynbrs[k].gv);
- where[i] = to;
- nmoved++;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("\t\tMoving %6"PRIDX" from %3"PRIDX" to %3"PRIDX". "
- "Gain: [%4"PRIDX" %4"PRIDX"]. Cut: %6"PRIDX", Vol: %6"PRIDX"\n",
- i, from, to, xgain+mynbrs[k].gv, mynbrs[k].ned-myrinfo->nid,
- graph->mincut, graph->minvol));
-
- /* Update the subdomain connectivity information */
- if (ctrl->minconn) {
- /* take care of i's move itself */
- UpdateEdgeSubDomainGraph(ctrl, from, to, myrinfo->nid-mynbrs[k].ned, &maxndoms);
-
- /* take care of the adjancent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- me = where[adjncy[j]];
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -1, &maxndoms);
- UpdateEdgeSubDomainGraph(ctrl, to, me, 1, &maxndoms);
- }
- }
- }
-
- /* Update the id/ed/gains/bnd/queue of potentially affected nodes */
- KWayVolUpdate(ctrl, graph, i, from, to, queue, vstatus, &nupd, updptr,
- updind, bndtype, vmarker, pmarker, modind);
-
- /*CheckKWayVolPartitionParams(ctrl, graph); */
- }
-
-
- /* Reset the vstatus and associated data structures */
- for (i=0; i<nupd; i++) {
- ASSERT(updptr[updind[i]] != -1);
- ASSERT(vstatus[updind[i]] != VPQSTATUS_NOTPRESENT);
- vstatus[updind[i]] = VPQSTATUS_NOTPRESENT;
- updptr[updind[i]] = -1;
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("\t[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL", Nb: %6"PRIDX"."
- " Nmoves: %5"PRIDX", Cut: %6"PRIDX", Vol: %6"PRIDX,
- pwgts[iargmin(nparts, pwgts)], imax(nparts, pwgts),
- ComputeLoadImbalance(graph, nparts, ctrl->pijbm),
- graph->nbnd, nmoved, graph->mincut, graph->minvol);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- if (nmoved == 0 ||
- (omode == OMODE_REFINE && graph->minvol == oldvol && graph->mincut == oldcut))
- break;
- }
-
- ipqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! K-way partitioning optimization in which the vertices are visited in
- decreasing ed/sqrt(nnbrs)-id order. Note this is just an
- approximation, as the ed is often split across different subdomains
- and the sqrt(nnbrs) is just a crude approximation.
-
- \param graph is the graph that is being refined.
- \param niter is the number of refinement iterations.
- \param ffactor is the \em fudge-factor for allowing positive gain moves
- to violate the max-pwgt constraint.
- \param omode is the type of optimization that will performed among
- OMODE_REFINE and OMODE_BALANCE
-
-
-*/
-/**************************************************************************/
-void Greedy_McKWayCutOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode)
-{
- /* Common variables to all types of kway-refinement/balancing routines */
- idx_t i, ii, iii, j, k, l, pass, nvtxs, ncon, nparts, gain;
- idx_t from, me, to, cto, oldcut;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt;
- idx_t *where, *pwgts, *perm, *bndptr, *bndind, *minwgt, *maxwgt;
- idx_t nmoved, nupd, *vstatus, *updptr, *updind;
- idx_t maxndoms, *safetos=NULL, *nads=NULL, *doms=NULL, **adids=NULL, **adwgts=NULL;
- idx_t *bfslvl=NULL, *bfsind=NULL, *bfsmrk=NULL;
- idx_t bndtype = (omode == OMODE_REFINE ? BNDTYPE_REFINE : BNDTYPE_BALANCE);
- real_t *ubfactors, *pijbm;
- real_t origbal;
-
- /* Edgecut-specific/different variables */
- idx_t nbnd, oldnnbrs;
- rpq_t *queue;
- real_t rgain;
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- WCOREPUSH;
-
- /* Link the graph fields */
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
-
- where = graph->where;
- pwgts = graph->pwgts;
-
- nparts = ctrl->nparts;
- pijbm = ctrl->pijbm;
-
-
- /* Determine the ubfactors. The method used is different based on omode.
- When OMODE_BALANCE, the ubfactors are those supplied by the user.
- When OMODE_REFINE, the ubfactors are the max of the current partition
- and the user-specified ones. */
- ubfactors = rwspacemalloc(ctrl, ncon);
- ComputeLoadImbalanceVec(graph, nparts, pijbm, ubfactors);
- origbal = rvecmaxdiff(ncon, ubfactors, ctrl->ubfactors);
- if (omode == OMODE_BALANCE) {
- rcopy(ncon, ctrl->ubfactors, ubfactors);
- }
- else {
- for (i=0; i<ncon; i++)
- ubfactors[i] = (ubfactors[i] > ctrl->ubfactors[i] ? ubfactors[i] : ctrl->ubfactors[i]);
- }
-
-
- /* Setup the weight intervals of the various subdomains */
- minwgt = iwspacemalloc(ctrl, nparts*ncon);
- maxwgt = iwspacemalloc(ctrl, nparts*ncon);
-
- for (i=0; i<nparts; i++) {
- for (j=0; j<ncon; j++) {
- maxwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*ubfactors[j];
- /*minwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*(.9/ubfactors[j]);*/
- minwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*.2;
- }
- }
-
- perm = iwspacemalloc(ctrl, nvtxs);
-
-
- /* This stores the valid target subdomains. It is used when ctrl->minconn to
- control the subdomains to which moves are allowed to be made.
- When ctrl->minconn is false, the default values of 2 allow all moves to
- go through and it does not interfere with the zero-gain move selection. */
- safetos = iset(nparts, 2, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->minconn) {
- ComputeSubDomainGraph(ctrl, graph);
-
- nads = ctrl->nads;
- adids = ctrl->adids;
- adwgts = ctrl->adwgts;
- doms = iset(nparts, 0, ctrl->pvec1);
- }
-
-
- /* Setup updptr, updind like boundary info to keep track of the vertices whose
- vstatus's need to be reset at the end of the inner iteration */
- vstatus = iset(nvtxs, VPQSTATUS_NOTPRESENT, iwspacemalloc(ctrl, nvtxs));
- updptr = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- updind = iwspacemalloc(ctrl, nvtxs);
-
- if (ctrl->contig) {
- /* The arrays that will be used for limited check of articulation points */
- bfslvl = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- bfsind = iwspacemalloc(ctrl, nvtxs);
- bfsmrk = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("%s: [%6"PRIDX" %6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL"(%.3"PRREAL"),"
- " Nv-Nb[%6"PRIDX" %6"PRIDX"], Cut: %6"PRIDX", (%"PRIDX")",
- (omode == OMODE_REFINE ? "GRC" : "GBC"),
- imin(nparts*ncon, pwgts), imax(nparts*ncon, pwgts), imax(nparts*ncon, maxwgt),
- ComputeLoadImbalance(graph, nparts, pijbm), origbal,
- graph->nvtxs, graph->nbnd, graph->mincut, niter);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- queue = rpqCreate(nvtxs);
-
-
- /*=====================================================================
- * The top-level refinement loop
- *======================================================================*/
- for (pass=0; pass<niter; pass++) {
- ASSERT(ComputeCut(graph, where) == graph->mincut);
-
- /* In balancing mode, exit as soon as balance is reached */
- if (omode == OMODE_BALANCE && IsBalanced(ctrl, graph, 0))
- break;
-
- oldcut = graph->mincut;
- nbnd = graph->nbnd;
- nupd = 0;
-
- if (ctrl->minconn)
- maxndoms = imax(nparts, nads);
-
- /* Insert the boundary vertices in the priority queue */
- irandArrayPermute(nbnd, perm, nbnd/4, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[perm[ii]];
- rgain = (graph->ckrinfo[i].nnbrs > 0 ?
- 1.0*graph->ckrinfo[i].ed/sqrt(graph->ckrinfo[i].nnbrs) : 0.0)
- - graph->ckrinfo[i].id;
- rpqInsert(queue, i, rgain);
- vstatus[i] = VPQSTATUS_PRESENT;
- ListInsert(nupd, updind, updptr, i);
- }
-
- /* Start extracting vertices from the queue and try to move them */
- for (nmoved=0, iii=0;;iii++) {
- if ((i = rpqGetTop(queue)) == -1)
- break;
- vstatus[i] = VPQSTATUS_EXTRACTED;
-
- myrinfo = graph->ckrinfo+i;
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- from = where[i];
-
- /* Prevent moves that make 'from' domain underbalanced */
- if (omode == OMODE_REFINE) {
- if (myrinfo->id > 0 &&
- !ivecaxpygez(ncon, -1, vwgt+i*ncon, pwgts+from*ncon, minwgt+from*ncon))
- continue;
- }
- else { /* OMODE_BALANCE */
- if (!ivecaxpygez(ncon, -1, vwgt+i*ncon, pwgts+from*ncon, minwgt+from*ncon))
- continue;
- }
-
- if (ctrl->contig && IsArticulationNode(i, xadj, adjncy, where, bfslvl, bfsind, bfsmrk))
- continue;
-
- if (ctrl->minconn)
- SelectSafeTargetSubdomains(myrinfo, mynbrs, nads, adids, maxndoms, safetos, doms);
-
- /* Find the most promising subdomain to move to */
- if (omode == OMODE_REFINE) {
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- gain = mynbrs[k].ed-myrinfo->id;
- if (gain >= 0 && ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon))
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- cto = to;
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- if ((mynbrs[j].ed > mynbrs[k].ed &&
- ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon))
- ||
- (mynbrs[j].ed == mynbrs[k].ed &&
- BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- 1, pwgts+cto*ncon, pijbm+cto*ncon,
- 1, pwgts+to*ncon, pijbm+to*ncon))) {
- k = j;
- cto = to;
- }
- }
- to = cto;
-
- gain = mynbrs[k].ed-myrinfo->id;
- if (!(gain > 0
- || (gain == 0
- && (BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon)
- || (iii%2 == 0 && safetos[to] == 2)
- )
- )
- )
- )
- continue;
- }
- else { /* OMODE_BALANCE */
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- if (ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon) ||
- BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon))
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- cto = to;
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- if (BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- 1, pwgts+cto*ncon, pijbm+cto*ncon,
- 1, pwgts+to*ncon, pijbm+to*ncon)) {
- k = j;
- cto = to;
- }
- }
- to = cto;
-
- if (mynbrs[k].ed-myrinfo->id < 0 &&
- !BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon))
- continue;
- }
-
-
-
- /*=====================================================================
- * If we got here, we can now move the vertex from 'from' to 'to'
- *======================================================================*/
- graph->mincut -= mynbrs[k].ed-myrinfo->id;
- nmoved++;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("\t\tMoving %6"PRIDX" to %3"PRIDX". Gain: %4"PRIDX". Cut: %6"PRIDX"\n",
- i, to, mynbrs[k].ed-myrinfo->id, graph->mincut));
-
- /* Update the subdomain connectivity information */
- if (ctrl->minconn) {
- /* take care of i's move itself */
- UpdateEdgeSubDomainGraph(ctrl, from, to, myrinfo->id-mynbrs[k].ed, &maxndoms);
-
- /* take care of the adjancent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- me = where[adjncy[j]];
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -adjwgt[j], &maxndoms);
- UpdateEdgeSubDomainGraph(ctrl, to, me, adjwgt[j], &maxndoms);
- }
- }
- }
-
- /* Update ID/ED and BND related information for the moved vertex */
- iaxpy(ncon, 1, vwgt+i*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+i*ncon, 1, pwgts+from*ncon, 1);
- UpdateMovedVertexInfoAndBND(i, from, k, to, myrinfo, mynbrs, where,
- nbnd, bndptr, bndind, bndtype);
-
- /* Update the degrees of adjacent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- me = where[ii];
- myrinfo = graph->ckrinfo+ii;
-
- oldnnbrs = myrinfo->nnbrs;
-
- UpdateAdjacentVertexInfoAndBND(ctrl, ii, xadj[ii+1]-xadj[ii], me,
- from, to, myrinfo, adjwgt[j], nbnd, bndptr, bndind, bndtype);
-
- UpdateQueueInfo(queue, vstatus, ii, me, from, to, myrinfo, oldnnbrs,
- nupd, updptr, updind, bndtype);
-
- ASSERT(myrinfo->nnbrs <= xadj[ii+1]-xadj[ii]);
- }
- }
-
- graph->nbnd = nbnd;
-
- /* Reset the vstatus and associated data structures */
- for (i=0; i<nupd; i++) {
- ASSERT(updptr[updind[i]] != -1);
- ASSERT(vstatus[updind[i]] != VPQSTATUS_NOTPRESENT);
- vstatus[updind[i]] = VPQSTATUS_NOTPRESENT;
- updptr[updind[i]] = -1;
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("\t[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL", Nb: %6"PRIDX"."
- " Nmoves: %5"PRIDX", Cut: %6"PRIDX", Vol: %6"PRIDX,
- imin(nparts*ncon, pwgts), imax(nparts*ncon, pwgts),
- ComputeLoadImbalance(graph, nparts, pijbm),
- graph->nbnd, nmoved, graph->mincut, ComputeVolume(graph, where));
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- if (nmoved == 0 || (omode == OMODE_REFINE && graph->mincut == oldcut))
- break;
- }
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! K-way refinement that minimizes the communication volume. This is a
- greedy routine and the vertices are visited in decreasing gv order.
-
- \param graph is the graph that is being refined.
- \param niter is the number of refinement iterations.
- \param ffactor is the \em fudge-factor for allowing positive gain moves
- to violate the max-pwgt constraint.
-
-*/
-/**************************************************************************/
-void Greedy_McKWayVolOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode)
-{
- /* Common variables to all types of kway-refinement/balancing routines */
- idx_t i, ii, iii, j, k, l, pass, nvtxs, ncon, nparts, gain;
- idx_t from, me, to, cto, oldcut;
- idx_t *xadj, *vwgt, *adjncy;
- idx_t *where, *pwgts, *perm, *bndptr, *bndind, *minwgt, *maxwgt;
- idx_t nmoved, nupd, *vstatus, *updptr, *updind;
- idx_t maxndoms, *safetos=NULL, *nads=NULL, *doms=NULL, **adids=NULL, **adwgts=NULL;
- idx_t *bfslvl=NULL, *bfsind=NULL, *bfsmrk=NULL;
- idx_t bndtype = (omode == OMODE_REFINE ? BNDTYPE_REFINE : BNDTYPE_BALANCE);
- real_t *ubfactors, *pijbm;
- real_t origbal;
-
- /* Volume-specific/different variables */
- ipq_t *queue;
- idx_t oldvol, xgain;
- idx_t *vmarker, *pmarker, *modind;
- vkrinfo_t *myrinfo;
- vnbr_t *mynbrs;
-
- WCOREPUSH;
-
- /* Link the graph fields */
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
- where = graph->where;
- pwgts = graph->pwgts;
-
- nparts = ctrl->nparts;
- pijbm = ctrl->pijbm;
-
-
- /* Determine the ubfactors. The method used is different based on omode.
- When OMODE_BALANCE, the ubfactors are those supplied by the user.
- When OMODE_REFINE, the ubfactors are the max of the current partition
- and the user-specified ones. */
- ubfactors = rwspacemalloc(ctrl, ncon);
- ComputeLoadImbalanceVec(graph, nparts, pijbm, ubfactors);
- origbal = rvecmaxdiff(ncon, ubfactors, ctrl->ubfactors);
- if (omode == OMODE_BALANCE) {
- rcopy(ncon, ctrl->ubfactors, ubfactors);
- }
- else {
- for (i=0; i<ncon; i++)
- ubfactors[i] = (ubfactors[i] > ctrl->ubfactors[i] ? ubfactors[i] : ctrl->ubfactors[i]);
- }
-
-
- /* Setup the weight intervals of the various subdomains */
- minwgt = iwspacemalloc(ctrl, nparts*ncon);
- maxwgt = iwspacemalloc(ctrl, nparts*ncon);
-
- for (i=0; i<nparts; i++) {
- for (j=0; j<ncon; j++) {
- maxwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*ubfactors[j];
- /*minwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*(.9/ubfactors[j]); */
- minwgt[i*ncon+j] = ctrl->tpwgts[i*ncon+j]*graph->tvwgt[j]*.2;
- }
- }
-
- perm = iwspacemalloc(ctrl, nvtxs);
-
-
- /* This stores the valid target subdomains. It is used when ctrl->minconn to
- control the subdomains to which moves are allowed to be made.
- When ctrl->minconn is false, the default values of 2 allow all moves to
- go through and it does not interfere with the zero-gain move selection. */
- safetos = iset(nparts, 2, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->minconn) {
- ComputeSubDomainGraph(ctrl, graph);
-
- nads = ctrl->nads;
- adids = ctrl->adids;
- adwgts = ctrl->adwgts;
- doms = iset(nparts, 0, ctrl->pvec1);
- }
-
-
- /* Setup updptr, updind like boundary info to keep track of the vertices whose
- vstatus's need to be reset at the end of the inner iteration */
- vstatus = iset(nvtxs, VPQSTATUS_NOTPRESENT, iwspacemalloc(ctrl, nvtxs));
- updptr = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- updind = iwspacemalloc(ctrl, nvtxs);
-
- if (ctrl->contig) {
- /* The arrays that will be used for limited check of articulation points */
- bfslvl = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- bfsind = iwspacemalloc(ctrl, nvtxs);
- bfsmrk = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- }
-
- /* Vol-refinement specific working arrays */
- modind = iwspacemalloc(ctrl, nvtxs);
- vmarker = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- pmarker = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("%s: [%6"PRIDX" %6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL"(%.3"PRREAL"),"
- ", Nv-Nb[%6"PRIDX" %6"PRIDX"], Cut: %5"PRIDX", Vol: %5"PRIDX", (%"PRIDX")",
- (omode == OMODE_REFINE ? "GRV" : "GBV"),
- imin(nparts*ncon, pwgts), imax(nparts*ncon, pwgts), imax(nparts*ncon, maxwgt),
- ComputeLoadImbalance(graph, nparts, pijbm), origbal,
- graph->nvtxs, graph->nbnd, graph->mincut, graph->minvol, niter);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- queue = ipqCreate(nvtxs);
-
-
- /*=====================================================================
- * The top-level refinement loop
- *======================================================================*/
- for (pass=0; pass<niter; pass++) {
- ASSERT(ComputeVolume(graph, where) == graph->minvol);
-
- /* In balancing mode, exit as soon as balance is reached */
- if (omode == OMODE_BALANCE && IsBalanced(ctrl, graph, 0))
- break;
-
- oldcut = graph->mincut;
- oldvol = graph->minvol;
- nupd = 0;
-
- if (ctrl->minconn)
- maxndoms = imax(nparts, nads);
-
- /* Insert the boundary vertices in the priority queue */
- irandArrayPermute(graph->nbnd, perm, graph->nbnd/4, 1);
- for (ii=0; ii<graph->nbnd; ii++) {
- i = bndind[perm[ii]];
- ipqInsert(queue, i, graph->vkrinfo[i].gv);
- vstatus[i] = VPQSTATUS_PRESENT;
- ListInsert(nupd, updind, updptr, i);
- }
-
- /* Start extracting vertices from the queue and try to move them */
- for (nmoved=0, iii=0;;iii++) {
- if ((i = ipqGetTop(queue)) == -1)
- break;
- vstatus[i] = VPQSTATUS_EXTRACTED;
-
- myrinfo = graph->vkrinfo+i;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- from = where[i];
-
- /* Prevent moves that make 'from' domain underbalanced */
- if (omode == OMODE_REFINE) {
- if (myrinfo->nid > 0 &&
- !ivecaxpygez(ncon, -1, vwgt+i*ncon, pwgts+from*ncon, minwgt+from*ncon))
- continue;
- }
- else { /* OMODE_BALANCE */
- if (!ivecaxpygez(ncon, -1, vwgt+i*ncon, pwgts+from*ncon, minwgt+from*ncon))
- continue;
- }
-
- if (ctrl->contig && IsArticulationNode(i, xadj, adjncy, where, bfslvl, bfsind, bfsmrk))
- continue;
-
- if (ctrl->minconn)
- SelectSafeTargetSubdomains(myrinfo, mynbrs, nads, adids, maxndoms, safetos, doms);
-
- xgain = (myrinfo->nid == 0 && myrinfo->ned > 0 ? graph->vsize[i] : 0);
-
- /* Find the most promising subdomain to move to */
- if (omode == OMODE_REFINE) {
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- gain = mynbrs[k].gv + xgain;
- if (gain >= 0 && ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon))
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- cto = to;
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- gain = mynbrs[j].gv + xgain;
- if ((mynbrs[j].gv > mynbrs[k].gv &&
- ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon))
- ||
- (mynbrs[j].gv == mynbrs[k].gv &&
- mynbrs[j].ned > mynbrs[k].ned &&
- ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon))
- ||
- (mynbrs[j].gv == mynbrs[k].gv &&
- mynbrs[j].ned == mynbrs[k].ned &&
- BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- 1, pwgts+cto*ncon, pijbm+cto*ncon,
- 1, pwgts+to*ncon, pijbm+to*ncon))) {
- k = j;
- cto = to;
- }
- }
- to = cto;
-
- j = 0;
- if (xgain+mynbrs[k].gv > 0 || mynbrs[k].ned-myrinfo->nid > 0)
- j = 1;
- else if (mynbrs[k].ned-myrinfo->nid == 0) {
- if ((iii%2 == 0 && safetos[to] == 2) ||
- BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon))
- j = 1;
- }
- if (j == 0)
- continue;
- }
- else { /* OMODE_BALANCE */
- for (k=myrinfo->nnbrs-1; k>=0; k--) {
- if (!safetos[to=mynbrs[k].pid])
- continue;
- if (ivecaxpylez(ncon, 1, vwgt+i*ncon, pwgts+to*ncon, maxwgt+to*ncon) ||
- BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon))
- break;
- }
- if (k < 0)
- continue; /* break out if you did not find a candidate */
-
- cto = to;
- for (j=k-1; j>=0; j--) {
- if (!safetos[to=mynbrs[j].pid])
- continue;
- if (BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- 1, pwgts+cto*ncon, pijbm+cto*ncon,
- 1, pwgts+to*ncon, pijbm+to*ncon)) {
- k = j;
- cto = to;
- }
- }
- to = cto;
-
- if ((xgain+mynbrs[k].gv < 0 ||
- (xgain+mynbrs[k].gv == 0 && mynbrs[k].ned-myrinfo->nid < 0))
- &&
- !BetterBalanceKWay(ncon, vwgt+i*ncon, ubfactors,
- -1, pwgts+from*ncon, pijbm+from*ncon,
- +1, pwgts+to*ncon, pijbm+to*ncon))
- continue;
- }
-
-
- /*=====================================================================
- * If we got here, we can now move the vertex from 'from' to 'to'
- *======================================================================*/
- graph->mincut -= mynbrs[k].ned-myrinfo->nid;
- graph->minvol -= (xgain+mynbrs[k].gv);
- where[i] = to;
- nmoved++;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("\t\tMoving %6"PRIDX" from %3"PRIDX" to %3"PRIDX". "
- "Gain: [%4"PRIDX" %4"PRIDX"]. Cut: %6"PRIDX", Vol: %6"PRIDX"\n",
- i, from, to, xgain+mynbrs[k].gv, mynbrs[k].ned-myrinfo->nid,
- graph->mincut, graph->minvol));
-
- /* Update the subdomain connectivity information */
- if (ctrl->minconn) {
- /* take care of i's move itself */
- UpdateEdgeSubDomainGraph(ctrl, from, to, myrinfo->nid-mynbrs[k].ned, &maxndoms);
-
- /* take care of the adjancent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- me = where[adjncy[j]];
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -1, &maxndoms);
- UpdateEdgeSubDomainGraph(ctrl, to, me, 1, &maxndoms);
- }
- }
- }
-
- /* Update pwgts */
- iaxpy(ncon, 1, vwgt+i*ncon, 1, pwgts+to*ncon, 1);
- iaxpy(ncon, -1, vwgt+i*ncon, 1, pwgts+from*ncon, 1);
-
- /* Update the id/ed/gains/bnd/queue of potentially affected nodes */
- KWayVolUpdate(ctrl, graph, i, from, to, queue, vstatus, &nupd, updptr,
- updind, bndtype, vmarker, pmarker, modind);
-
- /*CheckKWayVolPartitionParams(ctrl, graph); */
- }
-
-
- /* Reset the vstatus and associated data structures */
- for (i=0; i<nupd; i++) {
- ASSERT(updptr[updind[i]] != -1);
- ASSERT(vstatus[updind[i]] != VPQSTATUS_NOTPRESENT);
- vstatus[updind[i]] = VPQSTATUS_NOTPRESENT;
- updptr[updind[i]] = -1;
- }
-
- if (ctrl->dbglvl&METIS_DBG_REFINE) {
- printf("\t[%6"PRIDX" %6"PRIDX"], Bal: %5.3"PRREAL", Nb: %6"PRIDX"."
- " Nmoves: %5"PRIDX", Cut: %6"PRIDX", Vol: %6"PRIDX,
- imin(nparts*ncon, pwgts), imax(nparts*ncon, pwgts),
- ComputeLoadImbalance(graph, nparts, pijbm),
- graph->nbnd, nmoved, graph->mincut, graph->minvol);
- if (ctrl->minconn)
- printf(", Doms: [%3"PRIDX" %4"PRIDX"]", imax(nparts, nads), isum(nparts, nads,1));
- printf("\n");
- }
-
- if (nmoved == 0 ||
- (omode == OMODE_REFINE && graph->minvol == oldvol && graph->mincut == oldcut))
- break;
- }
-
- ipqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function performs an approximate articulation vertex test.
- It assumes that the bfslvl, bfsind, and bfsmrk arrays are initialized
- appropriately. */
-/*************************************************************************/
-idx_t IsArticulationNode(idx_t i, idx_t *xadj, idx_t *adjncy, idx_t *where,
- idx_t *bfslvl, idx_t *bfsind, idx_t *bfsmrk)
-{
- idx_t ii, j, k=0, head, tail, nhits, tnhits, from, BFSDEPTH=5;
-
- from = where[i];
-
- /* Determine if the vertex is safe to move from a contiguity standpoint */
- for (tnhits=0, j=xadj[i]; j<xadj[i+1]; j++) {
- if (where[adjncy[j]] == from) {
- ASSERT(bfsmrk[adjncy[j]] == 0);
- ASSERT(bfslvl[adjncy[j]] == 0);
- bfsmrk[k=adjncy[j]] = 1;
- tnhits++;
- }
- }
-
- /* Easy cases */
- if (tnhits == 0)
- return 0;
- if (tnhits == 1) {
- bfsmrk[k] = 0;
- return 0;
- }
-
- ASSERT(bfslvl[i] == 0);
- bfslvl[i] = 1;
-
- bfsind[0] = k; /* That was the last one from the previous loop */
- bfslvl[k] = 1;
- bfsmrk[k] = 0;
- head = 0;
- tail = 1;
-
- /* Do a limited BFS traversal to see if you can get to all the other nodes */
- for (nhits=1; head<tail; ) {
- ii = bfsind[head++];
- for (j=xadj[ii]; j<xadj[ii+1]; j++) {
- if (where[k=adjncy[j]] == from) {
- if (bfsmrk[k]) {
- bfsmrk[k] = 0;
- if (++nhits == tnhits)
- break;
- }
- if (bfslvl[k] == 0 && bfslvl[ii] < BFSDEPTH) {
- bfsind[tail++] = k;
- bfslvl[k] = bfslvl[ii]+1;
- }
- }
- }
- if (nhits == tnhits)
- break;
- }
-
- /* Reset the various BFS related arrays */
- bfslvl[i] = 0;
- for (j=0; j<tail; j++)
- bfslvl[bfsind[j]] = 0;
-
-
- /* Reset the bfsmrk array for the next vertex when has not already being cleared */
- if (nhits < tnhits) {
- for (j=xadj[i]; j<xadj[i+1]; j++)
- if (where[adjncy[j]] == from)
- bfsmrk[adjncy[j]] = 0;
- }
-
- return (nhits != tnhits);
-}
-
-
-/*************************************************************************/
-/*!
- This function updates the edge and volume gains due to a vertex movement.
- v from 'from' to 'to'.
-
- \param ctrl is the control structure.
- \param graph is the graph being partitioned.
- \param v is the vertex that is moving.
- \param from is the original partition of v.
- \param to is the new partition of v.
- \param queue is the priority queue. If the queue is NULL, no priority-queue
- related updates are performed.
- \param vstatus is an array that marks the status of the vertex in terms
- of the priority queue. If queue is NULL, this parameter is ignored.
- \param r_nqupd is the number of vertices that have been inserted/removed
- from the queue. If queue is NULL, this parameter is ignored.
- \param updptr stores the index of each vertex in updind. If queue is NULL,
- this parameter is ignored.
- \param updind is the list of vertices that have been inserted/removed from
- the queue. If queue is NULL, this parameter is ignored.
- \param vmarker is of size nvtxs and is used internally as a temporary array.
- On entry and return all of its entries are 0.
- \param pmarker is of sie nparts and is used internally as a temporary marking
- array. On entry and return all of its entries are -1.
- \param modind is an array of size nvtxs and is used to keep track of the
- list of vertices whose gains need to be updated.
-*/
-/*************************************************************************/
-void KWayVolUpdate(ctrl_t *ctrl, graph_t *graph, idx_t v, idx_t from,
- idx_t to, ipq_t *queue, idx_t *vstatus, idx_t *r_nupd, idx_t *updptr,
- idx_t *updind, idx_t bndtype, idx_t *vmarker, idx_t *pmarker,
- idx_t *modind)
-{
- idx_t i, ii, iii, j, jj, k, kk, l, u, nmod, other, me, myidx;
- idx_t *xadj, *vsize, *adjncy, *where;
- vkrinfo_t *myrinfo, *orinfo;
- vnbr_t *mynbrs, *onbrs;
-
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vsize = graph->vsize;
- where = graph->where;
-
- myrinfo = graph->vkrinfo+v;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
-
- /*======================================================================
- * Remove the contributions on the gain made by 'v'.
- *=====================================================================*/
- for (k=0; k<myrinfo->nnbrs; k++)
- pmarker[mynbrs[k].pid] = k;
- pmarker[from] = k;
-
- myidx = pmarker[to]; /* Keep track of the index in mynbrs of the 'to' domain */
-
- for (j=xadj[v]; j<xadj[v+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- if (other == from) {
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] == -1)
- onbrs[k].gv += vsize[v];
- }
- }
- else {
- ASSERT(pmarker[other] != -1);
-
- if (mynbrs[pmarker[other]].ned > 1) {
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] == -1)
- onbrs[k].gv += vsize[v];
- }
- }
- else { /* There is only one connection */
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] != -1)
- onbrs[k].gv -= vsize[v];
- }
- }
- }
- }
-
- for (k=0; k<myrinfo->nnbrs; k++)
- pmarker[mynbrs[k].pid] = -1;
- pmarker[from] = -1;
-
-
- /*======================================================================
- * Update the id/ed of vertex 'v'
- *=====================================================================*/
- if (myidx == -1) {
- myidx = myrinfo->nnbrs++;
- ASSERT(myidx < xadj[v+1]-xadj[v]);
- mynbrs[myidx].ned = 0;
- }
- myrinfo->ned += myrinfo->nid-mynbrs[myidx].ned;
- SWAP(myrinfo->nid, mynbrs[myidx].ned, j);
- if (mynbrs[myidx].ned == 0)
- mynbrs[myidx] = mynbrs[--myrinfo->nnbrs];
- else
- mynbrs[myidx].pid = from;
-
-
- /*======================================================================
- * Update the degrees of adjacent vertices and their volume gains
- *=====================================================================*/
- vmarker[v] = 1;
- modind[0] = v;
- nmod = 1;
- for (j=xadj[v]; j<xadj[v+1]; j++) {
- ii = adjncy[j];
- me = where[ii];
-
- if (!vmarker[ii]) { /* The marking is done for boundary and max gv calculations */
- vmarker[ii] = 2;
- modind[nmod++] = ii;
- }
-
- myrinfo = graph->vkrinfo+ii;
- if (myrinfo->inbr == -1)
- myrinfo->inbr = vnbrpoolGetNext(ctrl, xadj[ii+1]-xadj[ii]+1);
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- if (me == from) {
- INC_DEC(myrinfo->ned, myrinfo->nid, 1);
- }
- else if (me == to) {
- INC_DEC(myrinfo->nid, myrinfo->ned, 1);
- }
-
- /* Remove the edgeweight from the 'pid == from' entry of the vertex */
- if (me != from) {
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == from) {
- if (mynbrs[k].ned == 1) {
- mynbrs[k] = mynbrs[--myrinfo->nnbrs];
- vmarker[ii] = 1; /* You do a complete .gv calculation */
-
- /* All vertices adjacent to 'ii' need to be updated */
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++) {
- u = adjncy[jj];
- other = where[u];
- orinfo = graph->vkrinfo+u;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- for (kk=0; kk<orinfo->nnbrs; kk++) {
- if (onbrs[kk].pid == from) {
- onbrs[kk].gv -= vsize[ii];
- if (!vmarker[u]) { /* Need to update boundary etc */
- vmarker[u] = 2;
- modind[nmod++] = u;
- }
- break;
- }
- }
- }
- }
- else {
- mynbrs[k].ned--;
-
- /* Update the gv due to single 'ii' connection to 'from' */
- if (mynbrs[k].ned == 1) {
- /* find the vertex 'u' that 'ii' was connected into 'from' */
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++) {
- u = adjncy[jj];
- other = where[u];
-
- if (other == from) {
- orinfo = graph->vkrinfo+u;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- /* The following is correct because domains in common
- between ii and u will lead to a reduction over the
- previous gain, whereas domains only in u but not in
- ii, will lead to no change as opposed to the earlier
- increase */
- for (kk=0; kk<orinfo->nnbrs; kk++)
- onbrs[kk].gv += vsize[ii];
-
- if (!vmarker[u]) { /* Need to update boundary etc */
- vmarker[u] = 2;
- modind[nmod++] = u;
- }
- break;
- }
- }
- }
- }
- break;
- }
- }
- }
-
-
- /* Add the edgeweight to the 'pid == to' entry of the vertex */
- if (me != to) {
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == to) {
- mynbrs[k].ned++;
-
- /* Update the gv due to non-single 'ii' connection to 'to' */
- if (mynbrs[k].ned == 2) {
- /* find the vertex 'u' that 'ii' was connected into 'to' */
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++) {
- u = adjncy[jj];
- other = where[u];
-
- if (u != v && other == to) {
- orinfo = graph->vkrinfo+u;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
- for (kk=0; kk<orinfo->nnbrs; kk++)
- onbrs[kk].gv -= vsize[ii];
-
- if (!vmarker[u]) { /* Need to update boundary etc */
- vmarker[u] = 2;
- modind[nmod++] = u;
- }
- break;
- }
- }
- }
- break;
- }
- }
-
- if (k == myrinfo->nnbrs) {
- mynbrs[myrinfo->nnbrs].pid = to;
- mynbrs[myrinfo->nnbrs++].ned = 1;
- vmarker[ii] = 1; /* You do a complete .gv calculation */
-
- /* All vertices adjacent to 'ii' need to be updated */
- for (jj=xadj[ii]; jj<xadj[ii+1]; jj++) {
- u = adjncy[jj];
- other = where[u];
- orinfo = graph->vkrinfo+u;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- for (kk=0; kk<orinfo->nnbrs; kk++) {
- if (onbrs[kk].pid == to) {
- onbrs[kk].gv += vsize[ii];
- if (!vmarker[u]) { /* Need to update boundary etc */
- vmarker[u] = 2;
- modind[nmod++] = u;
- }
- break;
- }
- }
- }
- }
- }
-
- ASSERT(myrinfo->nnbrs <= xadj[ii+1]-xadj[ii]);
- }
-
-
- /*======================================================================
- * Add the contributions on the volume gain due to 'v'
- *=====================================================================*/
- myrinfo = graph->vkrinfo+v;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
- for (k=0; k<myrinfo->nnbrs; k++)
- pmarker[mynbrs[k].pid] = k;
- pmarker[to] = k;
-
- for (j=xadj[v]; j<xadj[v+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- if (other == to) {
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] == -1)
- onbrs[k].gv -= vsize[v];
- }
- }
- else {
- ASSERT(pmarker[other] != -1);
-
- if (mynbrs[pmarker[other]].ned > 1) {
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] == -1)
- onbrs[k].gv -= vsize[v];
- }
- }
- else { /* There is only one connection */
- for (k=0; k<orinfo->nnbrs; k++) {
- if (pmarker[onbrs[k].pid] != -1)
- onbrs[k].gv += vsize[v];
- }
- }
- }
- }
- for (k=0; k<myrinfo->nnbrs; k++)
- pmarker[mynbrs[k].pid] = -1;
- pmarker[to] = -1;
-
-
- /*======================================================================
- * Recompute the volume information of the 'hard' nodes, and update the
- * max volume gain for all the modified vertices and the priority queue
- *=====================================================================*/
- for (iii=0; iii<nmod; iii++) {
- i = modind[iii];
- me = where[i];
-
- myrinfo = graph->vkrinfo+i;
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- if (vmarker[i] == 1) { /* Only complete gain updates go through */
- for (k=0; k<myrinfo->nnbrs; k++)
- mynbrs[k].gv = 0;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- for (kk=0; kk<orinfo->nnbrs; kk++)
- pmarker[onbrs[kk].pid] = kk;
- pmarker[other] = 1;
-
- if (me == other) {
- /* Find which domains 'i' is connected and 'ii' is not and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (pmarker[mynbrs[k].pid] == -1)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- else {
- ASSERT(pmarker[me] != -1);
-
- /* I'm the only connection of 'ii' in 'me' */
- if (onbrs[pmarker[me]].ned == 1) {
- /* Increase the gains for all the common domains between 'i' and 'ii' */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (pmarker[mynbrs[k].pid] != -1)
- mynbrs[k].gv += vsize[ii];
- }
- }
- else {
- /* Find which domains 'i' is connected and 'ii' is not and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (pmarker[mynbrs[k].pid] == -1)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- }
-
- for (kk=0; kk<orinfo->nnbrs; kk++)
- pmarker[onbrs[kk].pid] = -1;
- pmarker[other] = -1;
-
- }
- }
-
- /* Compute the overall gv for that node */
- myrinfo->gv = IDX_MIN;
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].gv > myrinfo->gv)
- myrinfo->gv = mynbrs[k].gv;
- }
-
- /* Add the xtra gain due to id == 0 */
- if (myrinfo->ned > 0 && myrinfo->nid == 0)
- myrinfo->gv += vsize[i];
-
-
- /*======================================================================
- * Maintain a consistent boundary
- *=====================================================================*/
- if (bndtype == BNDTYPE_REFINE) {
- if (myrinfo->gv >= 0 && graph->bndptr[i] == -1)
- BNDInsert(graph->nbnd, graph->bndind, graph->bndptr, i);
-
- if (myrinfo->gv < 0 && graph->bndptr[i] != -1)
- BNDDelete(graph->nbnd, graph->bndind, graph->bndptr, i);
- }
- else {
- if (myrinfo->ned > 0 && graph->bndptr[i] == -1)
- BNDInsert(graph->nbnd, graph->bndind, graph->bndptr, i);
-
- if (myrinfo->ned == 0 && graph->bndptr[i] != -1)
- BNDDelete(graph->nbnd, graph->bndind, graph->bndptr, i);
- }
-
-
- /*======================================================================
- * Update the priority queue appropriately (if allowed)
- *=====================================================================*/
- if (queue != NULL) {
- if (vstatus[i] != VPQSTATUS_EXTRACTED) {
- if (graph->bndptr[i] != -1) { /* In-boundary vertex */
- if (vstatus[i] == VPQSTATUS_PRESENT) {
- ipqUpdate(queue, i, myrinfo->gv);
- }
- else {
- ipqInsert(queue, i, myrinfo->gv);
- vstatus[i] = VPQSTATUS_PRESENT;
- ListInsert(*r_nupd, updind, updptr, i);
- }
- }
- else { /* Off-boundary vertex */
- if (vstatus[i] == VPQSTATUS_PRESENT) {
- ipqDelete(queue, i);
- vstatus[i] = VPQSTATUS_NOTPRESENT;
- ListDelete(*r_nupd, updind, updptr, i);
- }
- }
- }
- }
-
- vmarker[i] = 0;
- }
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/kwayrefine.c b/3rdParty/metis/metis-5.1.0/libmetis/kwayrefine.c
deleted file mode 100644
index 0e3c6dbd2..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/kwayrefine.c
+++ /dev/null
@@ -1,672 +0,0 @@
-/*!
-\file
-\brief Driving routines for multilevel k-way refinement
-
-\date Started 7/28/1997
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version $Id: kwayrefine.c 10737 2011-09-13 13:37:25Z karypis $
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point of cut-based refinement */
-/*************************************************************************/
-void RefineKWay(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph)
-{
- idx_t i, nlevels, contig=ctrl->contig;
- graph_t *ptr;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->UncoarsenTmr));
-
- /* Determine how many levels are there */
- for (ptr=graph, nlevels=0; ptr!=orggraph; ptr=ptr->finer, nlevels++);
-
- /* Compute the parameters of the coarsest graph */
- ComputeKWayPartitionParams(ctrl, graph);
-
- /* Try to minimize the sub-domain connectivity */
- if (ctrl->minconn)
- EliminateSubDomainEdges(ctrl, graph);
-
- /* Deal with contiguity constraints at the beginning */
- if (contig && FindPartitionInducedComponents(graph, graph->where, NULL, NULL) > ctrl->nparts) {
- EliminateComponents(ctrl, graph);
-
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_BALANCE);
- Greedy_KWayOptimize(ctrl, graph, 5, 0, OMODE_BALANCE);
-
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_REFINE);
- Greedy_KWayOptimize(ctrl, graph, ctrl->niter, 0, OMODE_REFINE);
-
- ctrl->contig = 0;
- }
-
- /* Refine each successively finer graph */
- for (i=0; ;i++) {
- if (ctrl->minconn && i == nlevels/2)
- EliminateSubDomainEdges(ctrl, graph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->RefTmr));
-
- if (2*i >= nlevels && !IsBalanced(ctrl, graph, .02)) {
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_BALANCE);
- Greedy_KWayOptimize(ctrl, graph, 1, 0, OMODE_BALANCE);
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_REFINE);
- }
-
- Greedy_KWayOptimize(ctrl, graph, ctrl->niter, 5.0, OMODE_REFINE);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->RefTmr));
-
- /* Deal with contiguity constraints in the middle */
- if (contig && i == nlevels/2) {
- if (FindPartitionInducedComponents(graph, graph->where, NULL, NULL) > ctrl->nparts) {
- EliminateComponents(ctrl, graph);
-
- if (!IsBalanced(ctrl, graph, .02)) {
- ctrl->contig = 1;
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_BALANCE);
- Greedy_KWayOptimize(ctrl, graph, 5, 0, OMODE_BALANCE);
-
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_REFINE);
- Greedy_KWayOptimize(ctrl, graph, ctrl->niter, 0, OMODE_REFINE);
- ctrl->contig = 0;
- }
- }
- }
-
- if (graph == orggraph)
- break;
-
- graph = graph->finer;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ProjectTmr));
- ASSERT(graph->vwgt != NULL);
-
- ProjectKWayPartition(ctrl, graph);
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ProjectTmr));
- }
-
- /* Deal with contiguity requirement at the end */
- ctrl->contig = contig;
- if (contig && FindPartitionInducedComponents(graph, graph->where, NULL, NULL) > ctrl->nparts)
- EliminateComponents(ctrl, graph);
-
- if (!IsBalanced(ctrl, graph, 0.0)) {
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_BALANCE);
- Greedy_KWayOptimize(ctrl, graph, 10, 0, OMODE_BALANCE);
-
- ComputeKWayBoundary(ctrl, graph, BNDTYPE_REFINE);
- Greedy_KWayOptimize(ctrl, graph, ctrl->niter, 0, OMODE_REFINE);
- }
-
- if (ctrl->contig)
- ASSERT(FindPartitionInducedComponents(graph, graph->where, NULL, NULL) == ctrl->nparts);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->UncoarsenTmr));
-}
-
-
-/*************************************************************************/
-/*! This function allocates memory for the k-way cut-based refinement */
-/*************************************************************************/
-void AllocateKWayPartitionMemory(ctrl_t *ctrl, graph_t *graph)
-{
-
- graph->pwgts = imalloc(ctrl->nparts*graph->ncon, "AllocateKWayPartitionMemory: pwgts");
- graph->where = imalloc(graph->nvtxs, "AllocateKWayPartitionMemory: where");
- graph->bndptr = imalloc(graph->nvtxs, "AllocateKWayPartitionMemory: bndptr");
- graph->bndind = imalloc(graph->nvtxs, "AllocateKWayPartitionMemory: bndind");
-
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- graph->ckrinfo = (ckrinfo_t *)gk_malloc(graph->nvtxs*sizeof(ckrinfo_t),
- "AllocateKWayPartitionMemory: ckrinfo");
- break;
-
- case METIS_OBJTYPE_VOL:
- graph->vkrinfo = (vkrinfo_t *)gk_malloc(graph->nvtxs*sizeof(vkrinfo_t),
- "AllocateKWayVolPartitionMemory: vkrinfo");
-
- /* This is to let the cut-based -minconn and -contig large-scale graph
- changes to go through */
- graph->ckrinfo = (ckrinfo_t *)graph->vkrinfo;
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
-}
-
-
-/*************************************************************************/
-/*! This function computes the initial id/ed for cut-based partitioning */
-/**************************************************************************/
-void ComputeKWayPartitionParams(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, k, l, nvtxs, ncon, nparts, nbnd, mincut, me, other;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *pwgts, *where, *bndind, *bndptr;
-
- nparts = ctrl->nparts;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- pwgts = iset(nparts*ncon, 0, graph->pwgts);
- bndind = graph->bndind;
- bndptr = iset(nvtxs, -1, graph->bndptr);
-
- nbnd = mincut = 0;
-
- /* Compute pwgts */
- if (ncon == 1) {
- for (i=0; i<nvtxs; i++) {
- ASSERT(where[i] >= 0 && where[i] < nparts);
- pwgts[where[i]] += vwgt[i];
- }
- }
- else {
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- for (j=0; j<ncon; j++)
- pwgts[me*ncon+j] += vwgt[i*ncon+j];
- }
- }
-
- /* Compute the required info for refinement */
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- {
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- memset(graph->ckrinfo, 0, sizeof(ckrinfo_t)*nvtxs);
- cnbrpoolReset(ctrl);
-
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- myrinfo = graph->ckrinfo+i;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (me == where[adjncy[j]])
- myrinfo->id += adjwgt[j];
- else
- myrinfo->ed += adjwgt[j];
- }
-
- /* Time to compute the particular external degrees */
- if (myrinfo->ed > 0) {
- mincut += myrinfo->ed;
-
- myrinfo->inbr = cnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- other = where[adjncy[j]];
- if (me != other) {
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == other) {
- mynbrs[k].ed += adjwgt[j];
- break;
- }
- }
- if (k == myrinfo->nnbrs) {
- mynbrs[k].pid = other;
- mynbrs[k].ed = adjwgt[j];
- myrinfo->nnbrs++;
- }
- }
- }
-
- ASSERT(myrinfo->nnbrs <= xadj[i+1]-xadj[i]);
-
- /* Only ed-id>=0 nodes are considered to be in the boundary */
- if (myrinfo->ed-myrinfo->id >= 0)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- else {
- myrinfo->inbr = -1;
- }
- }
-
- graph->mincut = mincut/2;
- graph->nbnd = nbnd;
-
- }
- ASSERT(CheckBnd2(graph));
- break;
-
- case METIS_OBJTYPE_VOL:
- {
- vkrinfo_t *myrinfo;
- vnbr_t *mynbrs;
-
- memset(graph->vkrinfo, 0, sizeof(vkrinfo_t)*nvtxs);
- vnbrpoolReset(ctrl);
-
- /* Compute now the id/ed degrees */
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- myrinfo = graph->vkrinfo+i;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (me == where[adjncy[j]])
- myrinfo->nid++;
- else
- myrinfo->ned++;
- }
-
- /* Time to compute the particular external degrees */
- if (myrinfo->ned > 0) {
- mincut += myrinfo->ned;
-
- myrinfo->inbr = vnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- other = where[adjncy[j]];
- if (me != other) {
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == other) {
- mynbrs[k].ned++;
- break;
- }
- }
- if (k == myrinfo->nnbrs) {
- mynbrs[k].gv = 0;
- mynbrs[k].pid = other;
- mynbrs[k].ned = 1;
- myrinfo->nnbrs++;
- }
- }
- }
- ASSERT(myrinfo->nnbrs <= xadj[i+1]-xadj[i]);
- }
- else {
- myrinfo->inbr = -1;
- }
- }
- graph->mincut = mincut/2;
-
- ComputeKWayVolGains(ctrl, graph);
- }
- ASSERT(graph->minvol == ComputeVolume(graph, graph->where));
- break;
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
-}
-
-
-/*************************************************************************/
-/*! This function projects a partition, and at the same time computes the
- parameters for refinement. */
-/*************************************************************************/
-void ProjectKWayPartition(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, k, nvtxs, nbnd, nparts, me, other, istart, iend, tid, ted;
- idx_t *xadj, *adjncy, *adjwgt;
- idx_t *cmap, *where, *bndptr, *bndind, *cwhere, *htable;
- graph_t *cgraph;
-
- WCOREPUSH;
-
- nparts = ctrl->nparts;
-
- cgraph = graph->coarser;
- cwhere = cgraph->where;
-
- nvtxs = graph->nvtxs;
- cmap = graph->cmap;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- AllocateKWayPartitionMemory(ctrl, graph);
-
- where = graph->where;
- bndind = graph->bndind;
- bndptr = iset(nvtxs, -1, graph->bndptr);
-
- htable = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
-
- /* Compute the required info for refinement */
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- ASSERT(CheckBnd2(cgraph));
- {
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- /* go through and project partition and compute id/ed for the nodes */
- for (i=0; i<nvtxs; i++) {
- k = cmap[i];
- where[i] = cwhere[k];
- cmap[i] = cgraph->ckrinfo[k].ed; /* For optimization */
- }
-
- memset(graph->ckrinfo, 0, sizeof(ckrinfo_t)*nvtxs);
- cnbrpoolReset(ctrl);
-
- for (nbnd=0, i=0; i<nvtxs; i++) {
- istart = xadj[i];
- iend = xadj[i+1];
-
- myrinfo = graph->ckrinfo+i;
-
- if (cmap[i] == 0) { /* Interior node. Note that cmap[i] = crinfo[cmap[i]].ed */
- for (tid=0, j=istart; j<iend; j++)
- tid += adjwgt[j];
-
- myrinfo->id = tid;
- myrinfo->inbr = -1;
- }
- else { /* Potentially an interface node */
- myrinfo->inbr = cnbrpoolGetNext(ctrl, iend-istart+1);
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- me = where[i];
- for (tid=0, ted=0, j=istart; j<iend; j++) {
- other = where[adjncy[j]];
- if (me == other) {
- tid += adjwgt[j];
- }
- else {
- ted += adjwgt[j];
- if ((k = htable[other]) == -1) {
- htable[other] = myrinfo->nnbrs;
- mynbrs[myrinfo->nnbrs].pid = other;
- mynbrs[myrinfo->nnbrs++].ed = adjwgt[j];
- }
- else {
- mynbrs[k].ed += adjwgt[j];
- }
- }
- }
- myrinfo->id = tid;
- myrinfo->ed = ted;
-
- /* Remove space for edegrees if it was interior */
- if (ted == 0) {
- ctrl->nbrpoolcpos -= iend-istart+1;
- myrinfo->inbr = -1;
- }
- else {
- if (ted-tid >= 0)
- BNDInsert(nbnd, bndind, bndptr, i);
-
- for (j=0; j<myrinfo->nnbrs; j++)
- htable[mynbrs[j].pid] = -1;
- }
- }
- }
-
- graph->nbnd = nbnd;
-
- }
- ASSERT(CheckBnd2(graph));
- break;
-
- case METIS_OBJTYPE_VOL:
- {
- vkrinfo_t *myrinfo;
- vnbr_t *mynbrs;
-
- ASSERT(cgraph->minvol == ComputeVolume(cgraph, cgraph->where));
-
- /* go through and project partition and compute id/ed for the nodes */
- for (i=0; i<nvtxs; i++) {
- k = cmap[i];
- where[i] = cwhere[k];
- cmap[i] = cgraph->vkrinfo[k].ned; /* For optimization */
- }
-
- memset(graph->vkrinfo, 0, sizeof(vkrinfo_t)*nvtxs);
- vnbrpoolReset(ctrl);
-
- for (i=0; i<nvtxs; i++) {
- istart = xadj[i];
- iend = xadj[i+1];
- myrinfo = graph->vkrinfo+i;
-
- if (cmap[i] == 0) { /* Note that cmap[i] = crinfo[cmap[i]].ed */
- myrinfo->nid = iend-istart;
- myrinfo->inbr = -1;
- }
- else { /* Potentially an interface node */
- myrinfo->inbr = vnbrpoolGetNext(ctrl, iend-istart+1);
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- me = where[i];
- for (tid=0, ted=0, j=istart; j<iend; j++) {
- other = where[adjncy[j]];
- if (me == other) {
- tid++;
- }
- else {
- ted++;
- if ((k = htable[other]) == -1) {
- htable[other] = myrinfo->nnbrs;
- mynbrs[myrinfo->nnbrs].gv = 0;
- mynbrs[myrinfo->nnbrs].pid = other;
- mynbrs[myrinfo->nnbrs++].ned = 1;
- }
- else {
- mynbrs[k].ned++;
- }
- }
- }
- myrinfo->nid = tid;
- myrinfo->ned = ted;
-
- /* Remove space for edegrees if it was interior */
- if (ted == 0) {
- ctrl->nbrpoolcpos -= iend-istart+1;
- myrinfo->inbr = -1;
- }
- else {
- for (j=0; j<myrinfo->nnbrs; j++)
- htable[mynbrs[j].pid] = -1;
- }
- }
- }
-
- ComputeKWayVolGains(ctrl, graph);
-
- ASSERT(graph->minvol == ComputeVolume(graph, graph->where));
- }
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
- graph->mincut = cgraph->mincut;
- icopy(nparts*graph->ncon, cgraph->pwgts, graph->pwgts);
-
- FreeGraph(&graph->coarser);
- graph->coarser = NULL;
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function computes the boundary definition for balancing. */
-/*************************************************************************/
-void ComputeKWayBoundary(ctrl_t *ctrl, graph_t *graph, idx_t bndtype)
-{
- idx_t i, nvtxs, nbnd;
- idx_t *bndind, *bndptr;
-
- nvtxs = graph->nvtxs;
- bndind = graph->bndind;
- bndptr = iset(nvtxs, -1, graph->bndptr);
-
- nbnd = 0;
-
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- /* Compute the boundary */
- if (bndtype == BNDTYPE_REFINE) {
- for (i=0; i<nvtxs; i++) {
- if (graph->ckrinfo[i].ed-graph->ckrinfo[i].id >= 0)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- }
- else { /* BNDTYPE_BALANCE */
- for (i=0; i<nvtxs; i++) {
- if (graph->ckrinfo[i].ed > 0)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- }
- break;
-
- case METIS_OBJTYPE_VOL:
- /* Compute the boundary */
- if (bndtype == BNDTYPE_REFINE) {
- for (i=0; i<nvtxs; i++) {
- if (graph->vkrinfo[i].gv >= 0)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- }
- else { /* BNDTYPE_BALANCE */
- for (i=0; i<nvtxs; i++) {
- if (graph->vkrinfo[i].ned > 0)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- }
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
- graph->nbnd = nbnd;
-}
-
-
-/*************************************************************************/
-/*! This function computes the initial gains in the communication volume */
-/*************************************************************************/
-void ComputeKWayVolGains(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, k, l, nvtxs, nparts, me, other, pid;
- idx_t *xadj, *vsize, *adjncy, *adjwgt, *where,
- *bndind, *bndptr, *ophtable;
- vkrinfo_t *myrinfo, *orinfo;
- vnbr_t *mynbrs, *onbrs;
-
- WCOREPUSH;
-
- nparts = ctrl->nparts;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- bndind = graph->bndind;
- bndptr = iset(nvtxs, -1, graph->bndptr);
-
- ophtable = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
-
- /* Compute the volume gains */
- graph->minvol = graph->nbnd = 0;
- for (i=0; i<nvtxs; i++) {
- myrinfo = graph->vkrinfo+i;
- myrinfo->gv = IDX_MIN;
-
- if (myrinfo->nnbrs > 0) {
- me = where[i];
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- graph->minvol += myrinfo->nnbrs*vsize[i];
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
-
- for (k=0; k<orinfo->nnbrs; k++)
- ophtable[onbrs[k].pid] = k;
- ophtable[other] = 1; /* this is to simplify coding */
-
- if (me == other) {
- /* Find which domains 'i' is connected to but 'ii' is not
- and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (ophtable[mynbrs[k].pid] == -1)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- else {
- ASSERT(ophtable[me] != -1);
-
- if (onbrs[ophtable[me]].ned == 1) {
- /* I'm the only connection of 'ii' in 'me' */
- /* Increase the gains for all the common domains between 'i' and 'ii' */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (ophtable[mynbrs[k].pid] != -1)
- mynbrs[k].gv += vsize[ii];
- }
- }
- else {
- /* Find which domains 'i' is connected to and 'ii' is not
- and update their gain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (ophtable[mynbrs[k].pid] == -1)
- mynbrs[k].gv -= vsize[ii];
- }
- }
- }
-
- /* Reset the marker vector */
- for (k=0; k<orinfo->nnbrs; k++)
- ophtable[onbrs[k].pid] = -1;
- ophtable[other] = -1;
- }
-
- /* Compute the max vgain */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].gv > myrinfo->gv)
- myrinfo->gv = mynbrs[k].gv;
- }
-
- /* Add the extra gain due to id == 0 */
- if (myrinfo->ned > 0 && myrinfo->nid == 0)
- myrinfo->gv += vsize[i];
- }
-
- if (myrinfo->gv >= 0)
- BNDInsert(graph->nbnd, bndind, bndptr, i);
- }
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function checks if the partition weights are within the balance
-contraints */
-/*************************************************************************/
-int IsBalanced(ctrl_t *ctrl, graph_t *graph, real_t ffactor)
-{
- return
- (ComputeLoadImbalanceDiff(graph, ctrl->nparts, ctrl->pijbm, ctrl->ubfactors)
- <= ffactor);
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/macros.h b/3rdParty/metis/metis-5.1.0/libmetis/macros.h
deleted file mode 100644
index 3f6f7d9ed..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/macros.h
+++ /dev/null
@@ -1,258 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * macros.h
- *
- * This file contains macros used in multilevel
- *
- * Started 9/25/94
- * George
- *
- * $Id: macros.h 10060 2011-06-02 18:56:30Z karypis $
- *
- */
-
-#ifndef _LIBMETIS_MACROS_H_
-#define _LIBMETIS_MACROS_H_
-
-/*************************************************************************
-* The following macro returns a random number in the specified range
-**************************************************************************/
-#define AND(a, b) ((a) < 0 ? ((-(a))&(b)) : ((a)&(b)))
-#define OR(a, b) ((a) < 0 ? -((-(a))|(b)) : ((a)|(b)))
-#define XOR(a, b) ((a) < 0 ? -((-(a))^(b)) : ((a)^(b)))
-
-//#define icopy(n, a, b) (idx_t *)memcpy((void *)(b), (void *)(a), sizeof(idx_t)*(n))
-
-#define HASHFCT(key, size) ((key)%(size))
-#define SWAP gk_SWAP
-
-/* gets the appropriate option value */
-#define GETOPTION(options, idx, defval) \
- ((options) == NULL || (options)[idx] == -1 ? defval : (options)[idx])
-
-/* converts a user provided ufactor into a real ubfactor */
-#define I2RUBFACTOR(ufactor) (1.0+0.001*(ufactor))
-
-/* set/reset the current workspace core */
-#define WCOREPUSH wspacepush(ctrl)
-#define WCOREPOP wspacepop(ctrl)
-
-
-
-/*************************************************************************
-* These macros insert and remove nodes from a Direct Access list
-**************************************************************************/
-#define ListInsert(n, lind, lptr, i) \
- do { \
- ASSERT(lptr[i] == -1); \
- lind[n] = i; \
- lptr[i] = (n)++;\
- } while(0)
-
-#define ListDelete(n, lind, lptr, i) \
- do { \
- ASSERT(lptr[i] != -1); \
- lind[lptr[i]] = lind[--(n)]; \
- lptr[lind[n]] = lptr[i]; \
- lptr[i] = -1; \
- } while(0)
-
-
-/*************************************************************************
-* These macros insert and remove nodes from the boundary list
-**************************************************************************/
-#define BNDInsert(nbnd, bndind, bndptr, vtx) \
- ListInsert(nbnd, bndind, bndptr, vtx)
-
-#define BNDDelete(nbnd, bndind, bndptr, vtx) \
- ListDelete(nbnd, bndind, bndptr, vtx)
-
-
-/*************************************************************************
-* These macros deal with id/ed updating during k-way refinement
-**************************************************************************/
-#define UpdateMovedVertexInfoAndBND(i, from, k, to, myrinfo, mynbrs, where, \
- nbnd, bndptr, bndind, bndtype) \
- do { \
- where[i] = to; \
- myrinfo->ed += myrinfo->id-mynbrs[k].ed; \
- SWAP(myrinfo->id, mynbrs[k].ed, j); \
- if (mynbrs[k].ed == 0) \
- mynbrs[k] = mynbrs[--myrinfo->nnbrs]; \
- else \
- mynbrs[k].pid = from; \
- \
- /* Update the boundary information. Both deletion and addition is \
- allowed as this routine can be used for moving arbitrary nodes. */ \
- if (bndtype == BNDTYPE_REFINE) { \
- if (bndptr[i] != -1 && myrinfo->ed - myrinfo->id < 0) \
- BNDDelete(nbnd, bndind, bndptr, i); \
- if (bndptr[i] == -1 && myrinfo->ed - myrinfo->id >= 0) \
- BNDInsert(nbnd, bndind, bndptr, i); \
- } \
- else { \
- if (bndptr[i] != -1 && myrinfo->ed <= 0) \
- BNDDelete(nbnd, bndind, bndptr, i); \
- if (bndptr[i] == -1 && myrinfo->ed > 0) \
- BNDInsert(nbnd, bndind, bndptr, i); \
- } \
- } while(0)
-
-
-#define UpdateAdjacentVertexInfoAndBND(ctrl, vid, adjlen, me, from, to, \
- myrinfo, ewgt, nbnd, bndptr, bndind, bndtype) \
- do { \
- idx_t k; \
- cnbr_t *mynbrs; \
- \
- if (myrinfo->inbr == -1) { \
- myrinfo->inbr = cnbrpoolGetNext(ctrl, adjlen+1); \
- myrinfo->nnbrs = 0; \
- } \
- ASSERT(CheckRInfo(ctrl, myrinfo)); \
- \
- mynbrs = ctrl->cnbrpool + myrinfo->inbr; \
- \
- /* Update global ID/ED and boundary */ \
- if (me == from) { \
- INC_DEC(myrinfo->ed, myrinfo->id, (ewgt)); \
- if (bndtype == BNDTYPE_REFINE) { \
- if (myrinfo->ed-myrinfo->id >= 0 && bndptr[(vid)] == -1) \
- BNDInsert(nbnd, bndind, bndptr, (vid)); \
- } \
- else { \
- if (myrinfo->ed > 0 && bndptr[(vid)] == -1) \
- BNDInsert(nbnd, bndind, bndptr, (vid)); \
- } \
- } \
- else if (me == to) { \
- INC_DEC(myrinfo->id, myrinfo->ed, (ewgt)); \
- if (bndtype == BNDTYPE_REFINE) { \
- if (myrinfo->ed-myrinfo->id < 0 && bndptr[(vid)] != -1) \
- BNDDelete(nbnd, bndind, bndptr, (vid)); \
- } \
- else { \
- if (myrinfo->ed <= 0 && bndptr[(vid)] != -1) \
- BNDDelete(nbnd, bndind, bndptr, (vid)); \
- } \
- } \
- \
- /* Remove contribution from the .ed of 'from' */ \
- if (me != from) { \
- for (k=0; k<myrinfo->nnbrs; k++) { \
- if (mynbrs[k].pid == from) { \
- if (mynbrs[k].ed == (ewgt)) \
- mynbrs[k] = mynbrs[--myrinfo->nnbrs]; \
- else \
- mynbrs[k].ed -= (ewgt); \
- break; \
- } \
- } \
- } \
- \
- /* Add contribution to the .ed of 'to' */ \
- if (me != to) { \
- for (k=0; k<myrinfo->nnbrs; k++) { \
- if (mynbrs[k].pid == to) { \
- mynbrs[k].ed += (ewgt); \
- break; \
- } \
- } \
- if (k == myrinfo->nnbrs) { \
- mynbrs[k].pid = to; \
- mynbrs[k].ed = (ewgt); \
- myrinfo->nnbrs++; \
- } \
- } \
- \
- ASSERT(CheckRInfo(ctrl, myrinfo));\
- } while(0)
-
-
-#define UpdateQueueInfo(queue, vstatus, vid, me, from, to, myrinfo, oldnnbrs, \
- nupd, updptr, updind, bndtype) \
- do { \
- real_t rgain; \
- \
- if (me == to || me == from || oldnnbrs != myrinfo->nnbrs) { \
- rgain = (myrinfo->nnbrs > 0 ? \
- 1.0*myrinfo->ed/sqrt(myrinfo->nnbrs) : 0.0) - myrinfo->id; \
- \
- if (bndtype == BNDTYPE_REFINE) { \
- if (vstatus[(vid)] == VPQSTATUS_PRESENT) { \
- if (myrinfo->ed-myrinfo->id >= 0) \
- rpqUpdate(queue, (vid), rgain); \
- else { \
- rpqDelete(queue, (vid)); \
- vstatus[(vid)] = VPQSTATUS_NOTPRESENT; \
- ListDelete(nupd, updind, updptr, (vid)); \
- } \
- } \
- else if (vstatus[(vid)] == VPQSTATUS_NOTPRESENT && myrinfo->ed-myrinfo->id >= 0) { \
- rpqInsert(queue, (vid), rgain); \
- vstatus[(vid)] = VPQSTATUS_PRESENT; \
- ListInsert(nupd, updind, updptr, (vid)); \
- } \
- } \
- else { \
- if (vstatus[(vid)] == VPQSTATUS_PRESENT) { \
- if (myrinfo->ed > 0) \
- rpqUpdate(queue, (vid), rgain); \
- else { \
- rpqDelete(queue, (vid)); \
- vstatus[(vid)] = VPQSTATUS_NOTPRESENT; \
- ListDelete(nupd, updind, updptr, (vid)); \
- } \
- } \
- else if (vstatus[(vid)] == VPQSTATUS_NOTPRESENT && myrinfo->ed > 0) { \
- rpqInsert(queue, (vid), rgain); \
- vstatus[(vid)] = VPQSTATUS_PRESENT; \
- ListInsert(nupd, updind, updptr, (vid)); \
- } \
- } \
- } \
- } while(0)
-
-
-
-/*************************************************************************/
-/*! This macro determines the set of subdomains that a vertex can move to
- without increasins the maxndoms. */
-/*************************************************************************/
-#define SelectSafeTargetSubdomains(myrinfo, mynbrs, nads, adids, maxndoms, safetos, vtmp) \
- do { \
- idx_t j, k, l, nadd, to; \
- for (j=0; j<myrinfo->nnbrs; j++) { \
- safetos[to = mynbrs[j].pid] = 0; \
- \
- /* uncompress the connectivity info for the 'to' subdomain */ \
- for (k=0; k<nads[to]; k++) \
- vtmp[adids[to][k]] = 1; \
- \
- for (nadd=0, k=0; k<myrinfo->nnbrs; k++) { \
- if (k == j) \
- continue; \
- \
- l = mynbrs[k].pid; \
- if (vtmp[l] == 0) { \
- if (nads[l] > maxndoms-1) { \
- nadd = maxndoms; \
- break; \
- } \
- nadd++; \
- } \
- } \
- if (nads[to]+nadd <= maxndoms) \
- safetos[to] = 1; \
- if (nadd == 0) \
- safetos[to] = 2; \
- \
- /* cleanup the connectivity info due to the 'to' subdomain */ \
- for (k=0; k<nads[to]; k++) \
- vtmp[adids[to][k]] = 0; \
- } \
- } while (0)
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/mcutil.c b/3rdParty/metis/metis-5.1.0/libmetis/mcutil.c
deleted file mode 100644
index 6e20f556a..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/mcutil.c
+++ /dev/null
@@ -1,330 +0,0 @@
-/*
- * mutil.c
- *
- * This file contains various utility functions for the MOC portion of the
- * code
- *
- * Started 2/15/98
- * George
- *
- * $Id: mcutil.c 13901 2013-03-24 16:17:03Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function compares two vectors x & y and returns true
- if \forall i, x[i] <= y[i].
-*/
-/**************************************************************************/
-int rvecle(idx_t n, real_t *x, real_t *y)
-{
- for (n--; n>=0; n--) {
- if (x[n] > y[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function compares two vectors x & y and returns true
- if \forall i, x[i] >= y[i].
-*/
-/**************************************************************************/
-int rvecge(idx_t n, real_t *x, real_t *y)
-{
- for (n--; n>=0; n--) {
- if (x[n] < y[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function compares vectors x1+x2 against y and returns true
- if \forall i, x1[i]+x2[i] <= y[i].
-*/
-/**************************************************************************/
-int rvecsumle(idx_t n, real_t *x1, real_t *x2, real_t *y)
-{
- for (n--; n>=0; n--) {
- if (x1[n]+x2[n] > y[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function returns max_i(x[i]-y[i]) */
-/**************************************************************************/
-real_t rvecmaxdiff(idx_t n, real_t *x, real_t *y)
-{
- real_t max;
-
- max = x[0]-y[0];
-
- for (n--; n>0; n--) {
- if (max < x[n]-y[n])
- max = x[n]-y[n];
- }
-
- return max;
-}
-
-
-/*************************************************************************/
-/*! This function returns true if \forall i, x[i] <= z[i]. */
-/**************************************************************************/
-int ivecle(idx_t n, idx_t *x, idx_t *z)
-{
- for (n--; n>=0; n--) {
- if (x[n] > z[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function returns true if \forall i, x[i] >= z[i]. */
-/**************************************************************************/
-int ivecge(idx_t n, idx_t *x, idx_t *z)
-{
- for (n--; n>=0; n--) {
- if (x[n] < z[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function returns true if \forall i, a*x[i]+y[i] <= z[i]. */
-/**************************************************************************/
-int ivecaxpylez(idx_t n, idx_t a, idx_t *x, idx_t *y, idx_t *z)
-{
- for (n--; n>=0; n--) {
- if (a*x[n]+y[n] > z[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function returns true if \forall i, a*x[i]+y[i] >= z[i]. */
-/**************************************************************************/
-int ivecaxpygez(idx_t n, idx_t a, idx_t *x, idx_t *y, idx_t *z)
-{
- for (n--; n>=0; n--) {
- if (a*x[n]+y[n] < z[n])
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function checks if v+u2 provides a better balance in the weight
- vector that v+u1 */
-/*************************************************************************/
-int BetterVBalance(idx_t ncon, real_t *invtvwgt, idx_t *v_vwgt, idx_t *u1_vwgt,
- idx_t *u2_vwgt)
-{
- idx_t i;
- real_t sum1=0.0, sum2=0.0, diff1=0.0, diff2=0.0;
-
- for (i=0; i<ncon; i++) {
- sum1 += (v_vwgt[i]+u1_vwgt[i])*invtvwgt[i];
- sum2 += (v_vwgt[i]+u2_vwgt[i])*invtvwgt[i];
- }
- sum1 = sum1/ncon;
- sum2 = sum2/ncon;
-
- for (i=0; i<ncon; i++) {
- diff1 += rabs(sum1 - (v_vwgt[i]+u1_vwgt[i])*invtvwgt[i]);
- diff2 += rabs(sum2 - (v_vwgt[i]+u2_vwgt[i])*invtvwgt[i]);
- }
-
- return (diff1 - diff2 >= 0);
-}
-
-
-/*************************************************************************/
-/*! This function takes two ubfactor-centered load imbalance vectors x & y,
- and returns true if y is better balanced than x. */
-/*************************************************************************/
-int BetterBalance2Way(idx_t n, real_t *x, real_t *y)
-{
- real_t nrm1=0.0, nrm2=0.0;
-
- for (--n; n>=0; n--) {
- if (x[n] > 0) nrm1 += x[n]*x[n];
- if (y[n] > 0) nrm2 += y[n]*y[n];
- }
- return nrm2 < nrm1;
-}
-
-
-/*************************************************************************/
-/*! Given a vertex and two weights, this function returns 1, if the second
- partition will be more balanced than the first after the weighted
- additional of that vertex.
- The balance determination takes into account the ideal target weights
- of the two partitions.
-*/
-/*************************************************************************/
-int BetterBalanceKWay(idx_t ncon, idx_t *vwgt, real_t *ubvec,
- idx_t a1, idx_t *pt1, real_t *bm1,
- idx_t a2, idx_t *pt2, real_t *bm2)
-{
- idx_t i;
- real_t tmp, nrm1=0.0, nrm2=0.0, max1=0.0, max2=0.0;
-
- for (i=0; i<ncon; i++) {
- tmp = bm1[i]*(pt1[i]+a1*vwgt[i]) - ubvec[i];
- //printf("BB: %d %+.4f ", (int)i, (float)tmp);
- nrm1 += tmp*tmp;
- max1 = (tmp > max1 ? tmp : max1);
-
- tmp = bm2[i]*(pt2[i]+a2*vwgt[i]) - ubvec[i];
- //printf("%+.4f ", (float)tmp);
- nrm2 += tmp*tmp;
- max2 = (tmp > max2 ? tmp : max2);
-
- //printf("%4d %4d %4d %4d %4d %4d %4d %.2f\n",
- // (int)vwgt[i],
- // (int)a1, (int)pt1[i], (int)tpt1[i],
- // (int)a2, (int)pt2[i], (int)tpt2[i], ubvec[i]);
- }
- //printf(" %.3f %.3f %.3f %.3f\n", (float)max1, (float)nrm1, (float)max2, (float)nrm2);
-
- if (max2 < max1)
- return 1;
-
- if (max2 == max1 && nrm2 < nrm1)
- return 1;
-
- return 0;
-}
-
-
-/*************************************************************************/
-/*! Computes the maximum load imbalance of a partitioning solution over
- all the constraints. */
-/**************************************************************************/
-real_t ComputeLoadImbalance(graph_t *graph, idx_t nparts, real_t *pijbm)
-{
- idx_t i, j, ncon, *pwgts;
- real_t max, cur;
-
- ncon = graph->ncon;
- pwgts = graph->pwgts;
-
- max = 1.0;
- for (i=0; i<ncon; i++) {
- for (j=0; j<nparts; j++) {
- cur = pwgts[j*ncon+i]*pijbm[j*ncon+i];
- if (cur > max)
- max = cur;
- }
- }
-
- return max;
-}
-
-
-/*************************************************************************/
-/*! Computes the maximum load imbalance difference of a partitioning
- solution over all the constraints.
- The difference is defined with respect to the allowed maximum
- unbalance for the respective constraint.
- */
-/**************************************************************************/
-real_t ComputeLoadImbalanceDiff(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *ubvec)
-{
- idx_t i, j, ncon, *pwgts;
- real_t max, cur;
-
- ncon = graph->ncon;
- pwgts = graph->pwgts;
-
- max = -1.0;
- for (i=0; i<ncon; i++) {
- for (j=0; j<nparts; j++) {
- cur = pwgts[j*ncon+i]*pijbm[j*ncon+i] - ubvec[i];
- if (cur > max)
- max = cur;
- }
- }
-
- return max;
-}
-
-
-/*************************************************************************/
-/*! Computes the difference between load imbalance of each constraint across
- the partitions minus the desired upper bound on the load imabalnce.
- It also returns the maximum load imbalance across the partitions &
- constraints. */
-/**************************************************************************/
-real_t ComputeLoadImbalanceDiffVec(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *ubfactors, real_t *diffvec)
-{
- idx_t i, j, ncon, *pwgts;
- real_t cur, max;
-
- ncon = graph->ncon;
- pwgts = graph->pwgts;
-
- for (max=-1.0, i=0; i<ncon; i++) {
- diffvec[i] = pwgts[i]*pijbm[i] - ubfactors[i];
- for (j=1; j<nparts; j++) {
- cur = pwgts[j*ncon+i]*pijbm[j*ncon+i] - ubfactors[i];
- if (cur > diffvec[i])
- diffvec[i] = cur;
- }
- if (max < diffvec[i])
- max = diffvec[i];
- }
-
- return max;
-}
-
-
-/*************************************************************************/
-/*! Computes the load imbalance of each constraint across the partitions. */
-/**************************************************************************/
-void ComputeLoadImbalanceVec(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *lbvec)
-{
- idx_t i, j, ncon, *pwgts;
- real_t cur;
-
- ncon = graph->ncon;
- pwgts = graph->pwgts;
-
- for (i=0; i<ncon; i++) {
- lbvec[i] = pwgts[i]*pijbm[i];
- for (j=1; j<nparts; j++) {
- cur = pwgts[j*ncon+i]*pijbm[j*ncon+i];
- if (cur > lbvec[i])
- lbvec[i] = cur;
- }
- }
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/mesh.c b/3rdParty/metis/metis-5.1.0/libmetis/mesh.c
deleted file mode 100644
index 3c5261211..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/mesh.c
+++ /dev/null
@@ -1,412 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * mesh.c
- *
- * This file contains routines for converting 3D and 4D finite element
- * meshes into dual or nodal graphs
- *
- * Started 8/18/97
- * George
- *
- * $Id: mesh.c 13804 2013-03-04 23:49:08Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*****************************************************************************/
-/*! This function creates a graph corresponding to the dual of a finite element
- mesh.
-
- \param ne is the number of elements in the mesh.
- \param nn is the number of nodes in the mesh.
- \param eptr is an array of size ne+1 used to mark the start and end
- locations in the nind array.
- \param eind is an array that stores for each element the set of node IDs
- (indices) that it is made off. The length of this array is equal
- to the total number of nodes over all the mesh elements.
- \param ncommon is the minimum number of nodes that two elements must share
- in order to be connected via an edge in the dual graph.
- \param numflag is either 0 or 1 indicating if the numbering of the nodes
- starts from 0 or 1, respectively. The same numbering is used for the
- returned graph as well.
- \param r_xadj indicates where the adjacency list of each vertex is stored
- in r_adjncy. The memory for this array is allocated by this routine.
- It can be freed by calling METIS_free().
- \param r_adjncy stores the adjacency list of each vertex in the generated
- dual graph. The memory for this array is allocated by this routine.
- It can be freed by calling METIS_free().
-
-*/
-/*****************************************************************************/
-int METIS_MeshToDual(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *ncommon, idx_t *numflag, idx_t **r_xadj, idx_t **r_adjncy)
-{
- int sigrval=0, renumber=0;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
-
- /* renumber the mesh */
- if (*numflag == 1) {
- ChangeMesh2CNumbering(*ne, eptr, eind);
- renumber = 1;
- }
-
- /* create dual graph */
- *r_xadj = *r_adjncy = NULL;
- CreateGraphDual(*ne, *nn, eptr, eind, *ncommon, r_xadj, r_adjncy);
-
-
-SIGTHROW:
- if (renumber)
- ChangeMesh2FNumbering(*ne, eptr, eind, *ne, *r_xadj, *r_adjncy);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- if (sigrval != 0) {
- if (*r_xadj != NULL)
- free(*r_xadj);
- if (*r_adjncy != NULL)
- free(*r_adjncy);
- *r_xadj = *r_adjncy = NULL;
- }
-
- return metis_rcode(sigrval);
-}
-
-
-/*****************************************************************************/
-/*! This function creates a graph corresponding to (almost) the nodal of a
- finite element mesh. In the nodal graph, each node is connected to the
- nodes corresponding to the union of nodes present in all the elements
- in which that node belongs.
-
- \param ne is the number of elements in the mesh.
- \param nn is the number of nodes in the mesh.
- \param eptr is an array of size ne+1 used to mark the start and end
- locations in the nind array.
- \param eind is an array that stores for each element the set of node IDs
- (indices) that it is made off. The length of this array is equal
- to the total number of nodes over all the mesh elements.
- \param numflag is either 0 or 1 indicating if the numbering of the nodes
- starts from 0 or 1, respectively. The same numbering is used for the
- returned graph as well.
- \param r_xadj indicates where the adjacency list of each vertex is stored
- in r_adjncy. The memory for this array is allocated by this routine.
- It can be freed by calling METIS_free().
- \param r_adjncy stores the adjacency list of each vertex in the generated
- dual graph. The memory for this array is allocated by this routine.
- It can be freed by calling METIS_free().
-
-*/
-/*****************************************************************************/
-int METIS_MeshToNodal(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *numflag, idx_t **r_xadj, idx_t **r_adjncy)
-{
- int sigrval=0, renumber=0;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
-
- /* renumber the mesh */
- if (*numflag == 1) {
- ChangeMesh2CNumbering(*ne, eptr, eind);
- renumber = 1;
- }
-
- /* create nodal graph */
- *r_xadj = *r_adjncy = NULL;
- CreateGraphNodal(*ne, *nn, eptr, eind, r_xadj, r_adjncy);
-
-
-SIGTHROW:
- if (renumber)
- ChangeMesh2FNumbering(*ne, eptr, eind, *nn, *r_xadj, *r_adjncy);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- if (sigrval != 0) {
- if (*r_xadj != NULL)
- free(*r_xadj);
- if (*r_adjncy != NULL)
- free(*r_adjncy);
- *r_xadj = *r_adjncy = NULL;
- }
-
- return metis_rcode(sigrval);
-}
-
-
-/*****************************************************************************/
-/*! This function creates the dual of a finite element mesh */
-/*****************************************************************************/
-void CreateGraphDual(idx_t ne, idx_t nn, idx_t *eptr, idx_t *eind, idx_t ncommon,
- idx_t **r_xadj, idx_t **r_adjncy)
-{
- idx_t i, j, nnbrs;
- idx_t *nptr, *nind;
- idx_t *xadj, *adjncy;
- idx_t *marker, *nbrs;
-
- if (ncommon < 1) {
- printf(" Increased ncommon to 1, as it was initially %"PRIDX"\n", ncommon);
- ncommon = 1;
- }
-
- /* construct the node-element list first */
- nptr = ismalloc(nn+1, 0, "CreateGraphDual: nptr");
- nind = imalloc(eptr[ne], "CreateGraphDual: nind");
-
- for (i=0; i<ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nptr[eind[j]]++;
- }
- MAKECSR(i, nn, nptr);
-
- for (i=0; i<ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nind[nptr[eind[j]]++] = i;
- }
- SHIFTCSR(i, nn, nptr);
-
-
- /* Allocate memory for xadj, since you know its size.
- These are done using standard malloc as they are returned
- to the calling function */
- if ((xadj = (idx_t *)malloc((ne+1)*sizeof(idx_t))) == NULL)
- gk_errexit(SIGMEM, "***Failed to allocate memory for xadj.\n");
- *r_xadj = xadj;
- iset(ne+1, 0, xadj);
-
- /* allocate memory for working arrays used by FindCommonElements */
- marker = ismalloc(ne, 0, "CreateGraphDual: marker");
- nbrs = imalloc(ne, "CreateGraphDual: nbrs");
-
- for (i=0; i<ne; i++) {
- xadj[i] = FindCommonElements(i, eptr[i+1]-eptr[i], eind+eptr[i], nptr,
- nind, eptr, ncommon, marker, nbrs);
- }
- MAKECSR(i, ne, xadj);
-
- /* Allocate memory for adjncy, since you now know its size.
- These are done using standard malloc as they are returned
- to the calling function */
- if ((adjncy = (idx_t *)malloc(xadj[ne]*sizeof(idx_t))) == NULL) {
- free(xadj);
- *r_xadj = NULL;
- gk_errexit(SIGMEM, "***Failed to allocate memory for adjncy.\n");
- }
- *r_adjncy = adjncy;
-
- for (i=0; i<ne; i++) {
- nnbrs = FindCommonElements(i, eptr[i+1]-eptr[i], eind+eptr[i], nptr,
- nind, eptr, ncommon, marker, nbrs);
- for (j=0; j<nnbrs; j++)
- adjncy[xadj[i]++] = nbrs[j];
- }
- SHIFTCSR(i, ne, xadj);
-
- gk_free((void **)&nptr, &nind, &marker, &nbrs, LTERM);
-}
-
-
-/*****************************************************************************/
-/*! This function finds all elements that share at least ncommon nodes with
- the ``query'' element.
-*/
-/*****************************************************************************/
-idx_t FindCommonElements(idx_t qid, idx_t elen, idx_t *eind, idx_t *nptr,
- idx_t *nind, idx_t *eptr, idx_t ncommon, idx_t *marker, idx_t *nbrs)
-{
- idx_t i, ii, j, jj, k, l, overlap;
-
- /* find all elements that share at least one node with qid */
- for (k=0, i=0; i<elen; i++) {
- j = eind[i];
- for (ii=nptr[j]; ii<nptr[j+1]; ii++) {
- jj = nind[ii];
-
- if (marker[jj] == 0)
- nbrs[k++] = jj;
- marker[jj]++;
- }
- }
-
- /* put qid into the neighbor list (in case it is not there) so that it
- will be removed in the next step */
- if (marker[qid] == 0)
- nbrs[k++] = qid;
- marker[qid] = 0;
-
- /* compact the list to contain only those with at least ncommon nodes */
- for (j=0, i=0; i<k; i++) {
- overlap = marker[l = nbrs[i]];
- if (overlap >= ncommon ||
- overlap >= elen-1 ||
- overlap >= eptr[l+1]-eptr[l]-1)
- nbrs[j++] = l;
- marker[l] = 0;
- }
-
- return j;
-}
-
-
-/*****************************************************************************/
-/*! This function creates the (almost) nodal of a finite element mesh */
-/*****************************************************************************/
-void CreateGraphNodal(idx_t ne, idx_t nn, idx_t *eptr, idx_t *eind,
- idx_t **r_xadj, idx_t **r_adjncy)
-{
- idx_t i, j, nnbrs;
- idx_t *nptr, *nind;
- idx_t *xadj, *adjncy;
- idx_t *marker, *nbrs;
-
-
- /* construct the node-element list first */
- nptr = ismalloc(nn+1, 0, "CreateGraphNodal: nptr");
- nind = imalloc(eptr[ne], "CreateGraphNodal: nind");
-
- for (i=0; i<ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nptr[eind[j]]++;
- }
- MAKECSR(i, nn, nptr);
-
- for (i=0; i<ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nind[nptr[eind[j]]++] = i;
- }
- SHIFTCSR(i, nn, nptr);
-
-
- /* Allocate memory for xadj, since you know its size.
- These are done using standard malloc as they are returned
- to the calling function */
- if ((xadj = (idx_t *)malloc((nn+1)*sizeof(idx_t))) == NULL)
- gk_errexit(SIGMEM, "***Failed to allocate memory for xadj.\n");
- *r_xadj = xadj;
- iset(nn+1, 0, xadj);
-
- /* allocate memory for working arrays used by FindCommonElements */
- marker = ismalloc(nn, 0, "CreateGraphNodal: marker");
- nbrs = imalloc(nn, "CreateGraphNodal: nbrs");
-
- for (i=0; i<nn; i++) {
- xadj[i] = FindCommonNodes(i, nptr[i+1]-nptr[i], nind+nptr[i], eptr,
- eind, marker, nbrs);
- }
- MAKECSR(i, nn, xadj);
-
- /* Allocate memory for adjncy, since you now know its size.
- These are done using standard malloc as they are returned
- to the calling function */
- if ((adjncy = (idx_t *)malloc(xadj[nn]*sizeof(idx_t))) == NULL) {
- free(xadj);
- *r_xadj = NULL;
- gk_errexit(SIGMEM, "***Failed to allocate memory for adjncy.\n");
- }
- *r_adjncy = adjncy;
-
- for (i=0; i<nn; i++) {
- nnbrs = FindCommonNodes(i, nptr[i+1]-nptr[i], nind+nptr[i], eptr,
- eind, marker, nbrs);
- for (j=0; j<nnbrs; j++)
- adjncy[xadj[i]++] = nbrs[j];
- }
- SHIFTCSR(i, nn, xadj);
-
- gk_free((void **)&nptr, &nind, &marker, &nbrs, LTERM);
-}
-
-
-/*****************************************************************************/
-/*! This function finds the union of nodes that are in the same elements with
- the ``query'' node.
-*/
-/*****************************************************************************/
-idx_t FindCommonNodes(idx_t qid, idx_t nelmnts, idx_t *elmntids, idx_t *eptr,
- idx_t *eind, idx_t *marker, idx_t *nbrs)
-{
- idx_t i, ii, j, jj, k;
-
- /* find all nodes that share at least one element with qid */
- marker[qid] = 1; /* this is to prevent self-loops */
- for (k=0, i=0; i<nelmnts; i++) {
- j = elmntids[i];
- for (ii=eptr[j]; ii<eptr[j+1]; ii++) {
- jj = eind[ii];
- if (marker[jj] == 0) {
- nbrs[k++] = jj;
- marker[jj] = 1;
- }
- }
- }
-
- /* reset the marker */
- marker[qid] = 0;
- for (i=0; i<k; i++) {
- marker[nbrs[i]] = 0;
- }
-
- return k;
-}
-
-
-
-/*************************************************************************/
-/*! This function creates and initializes a mesh_t structure */
-/*************************************************************************/
-mesh_t *CreateMesh(void)
-{
- mesh_t *mesh;
-
- mesh = (mesh_t *)gk_malloc(sizeof(mesh_t), "CreateMesh: mesh");
-
- InitMesh(mesh);
-
- return mesh;
-}
-
-
-/*************************************************************************/
-/*! This function initializes a mesh_t data structure */
-/*************************************************************************/
-void InitMesh(mesh_t *mesh)
-{
- memset((void *)mesh, 0, sizeof(mesh_t));
-}
-
-
-/*************************************************************************/
-/*! This function deallocates any memory stored in a mesh */
-/*************************************************************************/
-void FreeMesh(mesh_t **r_mesh)
-{
- mesh_t *mesh = *r_mesh;
-
- gk_free((void **)&mesh->eptr, &mesh->eind, &mesh->ewgt, &mesh, LTERM);
-
- *r_mesh = NULL;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/meshpart.c b/3rdParty/metis/metis-5.1.0/libmetis/meshpart.c
deleted file mode 100644
index a66d10610..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/meshpart.c
+++ /dev/null
@@ -1,262 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * meshpart.c
- *
- * This file contains routines for partitioning finite element meshes.
- *
- * Started 9/29/97
- * George
- *
- * $Id: meshpart.c 13931 2013-03-29 16:48:48Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************
-* This function partitions a finite element mesh by partitioning its nodal
-* graph using KMETIS and then assigning elements in a load balanced fashion.
-**************************************************************************/
-int METIS_PartMeshNodal(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *vwgt, idx_t *vsize, idx_t *nparts, real_t *tpwgts,
- idx_t *options, idx_t *objval, idx_t *epart, idx_t *npart)
-{
- int sigrval=0, renumber=0, ptype;
- idx_t *xadj=NULL, *adjncy=NULL;
- idx_t ncon=1, pnumflag=0;
- int rstatus=METIS_OK;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
- renumber = GETOPTION(options, METIS_OPTION_NUMBERING, 0);
- ptype = GETOPTION(options, METIS_OPTION_PTYPE, METIS_PTYPE_KWAY);
-
- /* renumber the mesh */
- if (renumber) {
- ChangeMesh2CNumbering(*ne, eptr, eind);
- options[METIS_OPTION_NUMBERING] = 0;
- }
-
- /* get the nodal graph */
- rstatus = METIS_MeshToNodal(ne, nn, eptr, eind, &pnumflag, &xadj, &adjncy);
- if (rstatus != METIS_OK)
- raise(SIGERR);
-
- /* partition the graph */
- if (ptype == METIS_PTYPE_KWAY)
- rstatus = METIS_PartGraphKway(nn, &ncon, xadj, adjncy, vwgt, vsize, NULL,
- nparts, tpwgts, NULL, options, objval, npart);
- else
- rstatus = METIS_PartGraphRecursive(nn, &ncon, xadj, adjncy, vwgt, vsize, NULL,
- nparts, tpwgts, NULL, options, objval, npart);
-
- if (rstatus != METIS_OK)
- raise(SIGERR);
-
- /* partition the other side of the mesh */
- InduceRowPartFromColumnPart(*ne, eptr, eind, epart, npart, *nparts, tpwgts);
-
-
-SIGTHROW:
- if (renumber) {
- ChangeMesh2FNumbering2(*ne, *nn, eptr, eind, epart, npart);
- options[METIS_OPTION_NUMBERING] = 1;
- }
-
- METIS_Free(xadj);
- METIS_Free(adjncy);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- return metis_rcode(sigrval);
-}
-
-
-
-/*************************************************************************
-* This function partitions a finite element mesh by partitioning its dual
-* graph using KMETIS and then assigning nodes in a load balanced fashion.
-**************************************************************************/
-int METIS_PartMeshDual(idx_t *ne, idx_t *nn, idx_t *eptr, idx_t *eind,
- idx_t *vwgt, idx_t *vsize, idx_t *ncommon, idx_t *nparts,
- real_t *tpwgts, idx_t *options, idx_t *objval, idx_t *epart,
- idx_t *npart)
-{
- int sigrval=0, renumber=0, ptype;
- idx_t i, j;
- idx_t *xadj=NULL, *adjncy=NULL, *nptr=NULL, *nind=NULL;
- idx_t ncon=1, pnumflag=0;
- int rstatus = METIS_OK;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
- renumber = GETOPTION(options, METIS_OPTION_NUMBERING, 0);
- ptype = GETOPTION(options, METIS_OPTION_PTYPE, METIS_PTYPE_KWAY);
-
- /* renumber the mesh */
- if (renumber) {
- ChangeMesh2CNumbering(*ne, eptr, eind);
- options[METIS_OPTION_NUMBERING] = 0;
- }
-
- /* get the dual graph */
- rstatus = METIS_MeshToDual(ne, nn, eptr, eind, ncommon, &pnumflag, &xadj, &adjncy);
- if (rstatus != METIS_OK)
- raise(SIGERR);
-
- /* partition the graph */
- if (ptype == METIS_PTYPE_KWAY)
- rstatus = METIS_PartGraphKway(ne, &ncon, xadj, adjncy, vwgt, vsize, NULL,
- nparts, tpwgts, NULL, options, objval, epart);
- else
- rstatus = METIS_PartGraphRecursive(ne, &ncon, xadj, adjncy, vwgt, vsize, NULL,
- nparts, tpwgts, NULL, options, objval, epart);
-
- if (rstatus != METIS_OK)
- raise(SIGERR);
-
-
- /* construct the node-element list */
- nptr = ismalloc(*nn+1, 0, "METIS_PartMeshDual: nptr");
- nind = imalloc(eptr[*ne], "METIS_PartMeshDual: nind");
-
- for (i=0; i<*ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nptr[eind[j]]++;
- }
- MAKECSR(i, *nn, nptr);
-
- for (i=0; i<*ne; i++) {
- for (j=eptr[i]; j<eptr[i+1]; j++)
- nind[nptr[eind[j]]++] = i;
- }
- SHIFTCSR(i, *nn, nptr);
-
- /* partition the other side of the mesh */
- InduceRowPartFromColumnPart(*nn, nptr, nind, npart, epart, *nparts, tpwgts);
-
- gk_free((void **)&nptr, &nind, LTERM);
-
-
-SIGTHROW:
- if (renumber) {
- ChangeMesh2FNumbering2(*ne, *nn, eptr, eind, epart, npart);
- options[METIS_OPTION_NUMBERING] = 1;
- }
-
- METIS_Free(xadj);
- METIS_Free(adjncy);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- return metis_rcode(sigrval);
-}
-
-
-
-/*************************************************************************/
-/*! Induces a partitioning of the rows based on a a partitioning of the
- columns. It is used by both the Nodal and Dual routines. */
-/*************************************************************************/
-void InduceRowPartFromColumnPart(idx_t nrows, idx_t *rowptr, idx_t *rowind,
- idx_t *rpart, idx_t *cpart, idx_t nparts, real_t *tpwgts)
-{
- idx_t i, j, k, me;
- idx_t nnbrs, *pwgts, *nbrdom, *nbrwgt, *nbrmrk;
- idx_t *itpwgts;
-
- pwgts = ismalloc(nparts, 0, "InduceRowPartFromColumnPart: pwgts");
- nbrdom = ismalloc(nparts, 0, "InduceRowPartFromColumnPart: nbrdom");
- nbrwgt = ismalloc(nparts, 0, "InduceRowPartFromColumnPart: nbrwgt");
- nbrmrk = ismalloc(nparts, -1, "InduceRowPartFromColumnPart: nbrmrk");
-
- iset(nrows, -1, rpart);
-
- /* setup the integer target partition weights */
- itpwgts = imalloc(nparts, "InduceRowPartFromColumnPart: itpwgts");
- if (tpwgts == NULL) {
- iset(nparts, 1+nrows/nparts, itpwgts);
- }
- else {
- for (i=0; i<nparts; i++)
- itpwgts[i] = 1+nrows*tpwgts[i];
- }
-
- /* first assign the rows consisting only of columns that belong to
- a single partition. Assign rows that are empty to -2 (un-assigned) */
- for (i=0; i<nrows; i++) {
- if (rowptr[i+1]-rowptr[i] == 0) {
- rpart[i] = -2;
- continue;
- }
-
- me = cpart[rowind[rowptr[i]]];
- for (j=rowptr[i]+1; j<rowptr[i+1]; j++) {
- if (cpart[rowind[j]] != me)
- break;
- }
- if (j == rowptr[i+1]) {
- rpart[i] = me;
- pwgts[me]++;
- }
- }
-
- /* next assign the rows consisting of columns belonging to multiple
- partitions in a balanced way */
- for (i=0; i<nrows; i++) {
- if (rpart[i] == -1) {
- for (nnbrs=0, j=rowptr[i]; j<rowptr[i+1]; j++) {
- me = cpart[rowind[j]];
- if (nbrmrk[me] == -1) {
- nbrdom[nnbrs] = me;
- nbrwgt[nnbrs] = 1;
- nbrmrk[me] = nnbrs++;
- }
- else {
- nbrwgt[nbrmrk[me]]++;
- }
- }
- ASSERT(nnbrs > 0);
-
- /* assign it first to the domain with most things in common */
- rpart[i] = nbrdom[iargmax(nnbrs, nbrwgt)];
-
- /* if overweight, assign it to the light domain */
- if (pwgts[rpart[i]] > itpwgts[rpart[i]]) {
- for (j=0; j<nnbrs; j++) {
- if (pwgts[nbrdom[j]] < itpwgts[nbrdom[j]] ||
- pwgts[nbrdom[j]]-itpwgts[nbrdom[j]] < pwgts[rpart[i]]-itpwgts[rpart[i]]) {
- rpart[i] = nbrdom[j];
- break;
- }
- }
- }
- pwgts[rpart[i]]++;
-
- /* reset nbrmrk array */
- for (j=0; j<nnbrs; j++)
- nbrmrk[nbrdom[j]] = -1;
- }
- }
-
- gk_free((void **)&pwgts, &nbrdom, &nbrwgt, &nbrmrk, &itpwgts, LTERM);
-
-}
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/metislib.h b/3rdParty/metis/metis-5.1.0/libmetis/metislib.h
deleted file mode 100644
index 93d48f011..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/metislib.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * metis.h
- *
- * This file includes all necessary header files
- *
- * Started 8/27/94
- * George
- *
- * $Id: metislib.h 10655 2011-08-02 17:38:11Z benjamin $
- */
-
-#ifndef _LIBMETIS_METISLIB_H_
-#define _LIBMETIS_METISLIB_H_
-
-#include <GKlib.h>
-
-#if defined(ENABLE_OPENMP)
- #include <omp.h>
-#endif
-
-
-#include <metis.h>
-#include <rename.h>
-#include <gklib_defs.h>
-
-#include <defs.h>
-#include <struct.h>
-#include <macros.h>
-#include <proto.h>
-
-
-#if defined(COMPILER_MSC)
-#if defined(rint)
- #undef rint
-#endif
-#define rint(x) ((idx_t)((x)+0.5)) /* MSC does not have rint() function */
-#endif
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/minconn.c b/3rdParty/metis/metis-5.1.0/libmetis/minconn.c
deleted file mode 100644
index 86dc90fbe..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/minconn.c
+++ /dev/null
@@ -1,729 +0,0 @@
-/*!
-\file
-\brief Functions that deal with prunning the number of adjacent subdomains in kmetis
-
-\date Started 7/15/98
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version $Id: minconn.c 10513 2011-07-07 22:06:03Z karypis $
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function computes the subdomain graph storing the result in the
- pre-allocated worspace arrays */
-/*************************************************************************/
-void ComputeSubDomainGraph(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, pid, other, nparts, nvtxs, nnbrs;
- idx_t *xadj, *adjncy, *adjwgt, *where;
- idx_t *pptr, *pind;
- idx_t nads=0, *vadids, *vadwgts;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- where = graph->where;
-
- nparts = ctrl->nparts;
-
- vadids = ctrl->pvec1;
- vadwgts = iset(nparts, 0, ctrl->pvec2);
-
- pptr = iwspacemalloc(ctrl, nparts+1);
- pind = iwspacemalloc(ctrl, nvtxs);
- iarray2csr(nvtxs, nparts, where, pptr, pind);
-
- for (pid=0; pid<nparts; pid++) {
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- {
- ckrinfo_t *rinfo;
- cnbr_t *nbrs;
-
- rinfo = graph->ckrinfo;
- for (nads=0, ii=pptr[pid]; ii<pptr[pid+1]; ii++) {
- i = pind[ii];
- ASSERT(pid == where[i]);
-
- if (rinfo[i].ed > 0) {
- nnbrs = rinfo[i].nnbrs;
- nbrs = ctrl->cnbrpool + rinfo[i].inbr;
-
- for (j=0; j<nnbrs; j++) {
- other = nbrs[j].pid;
- if (vadwgts[other] == 0)
- vadids[nads++] = other;
- vadwgts[other] += nbrs[j].ed;
- }
- }
- }
- }
- break;
-
- case METIS_OBJTYPE_VOL:
- {
- vkrinfo_t *rinfo;
- vnbr_t *nbrs;
-
- rinfo = graph->vkrinfo;
- for (nads=0, ii=pptr[pid]; ii<pptr[pid+1]; ii++) {
- i = pind[ii];
- ASSERT(pid == where[i]);
-
- if (rinfo[i].ned > 0) {
- nnbrs = rinfo[i].nnbrs;
- nbrs = ctrl->vnbrpool + rinfo[i].inbr;
-
- for (j=0; j<nnbrs; j++) {
- other = nbrs[j].pid;
- if (vadwgts[other] == 0)
- vadids[nads++] = other;
- vadwgts[other] += nbrs[j].ned;
- }
- }
- }
- }
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype: %d\n", ctrl->objtype);
- }
-
- /* See if you have enough memory to store the adjacent info for that subdomain */
- if (ctrl->maxnads[pid] < nads) {
- ctrl->maxnads[pid] = 2*nads;
- ctrl->adids[pid] = irealloc(ctrl->adids[pid], ctrl->maxnads[pid],
- "ComputeSubDomainGraph: adids[pid]");
- ctrl->adwgts[pid] = irealloc(ctrl->adwgts[pid], ctrl->maxnads[pid],
- "ComputeSubDomainGraph: adids[pid]");
- }
-
- ctrl->nads[pid] = nads;
- for (j=0; j<nads; j++) {
- ctrl->adids[pid][j] = vadids[j];
- ctrl->adwgts[pid][j] = vadwgts[vadids[j]];
-
- vadwgts[vadids[j]] = 0;
- }
- }
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function updates the weight of an edge in the subdomain graph by
- adding to it the value of ewgt. The update can either increase or
- decrease the weight of the subdomain edge based on the value of ewgt.
-
- \param u is the ID of one of the incident subdomains to the edge
- \param v is the ID of the other incident subdomains to the edge
- \param ewgt is the weight to be added to the subdomain edge
- \param nparts is the number of subdomains
- \param r_maxndoms is the maximum number of adjacent subdomains and is
- updated as necessary. The update is skipped if a NULL value is
- supplied.
-*/
-/*************************************************************************/
-void UpdateEdgeSubDomainGraph(ctrl_t *ctrl, idx_t u, idx_t v, idx_t ewgt,
- idx_t *r_maxndoms)
-{
- idx_t i, j, nads;
-
- if (ewgt == 0)
- return;
-
- for (i=0; i<2; i++) {
- nads = ctrl->nads[u];
- /* Find the edge */
- for (j=0; j<nads; j++) {
- if (ctrl->adids[u][j] == v) {
- ctrl->adwgts[u][j] += ewgt;
- break;
- }
- }
-
- if (j == nads) {
- /* Deal with the case in which the edge was not found */
- ASSERT(ewgt > 0);
- if (ctrl->maxnads[u] == nads) {
- ctrl->maxnads[u] = 2*(nads+1);
- ctrl->adids[u] = irealloc(ctrl->adids[u], ctrl->maxnads[u],
- "IncreaseEdgeSubDomainGraph: adids[pid]");
- ctrl->adwgts[u] = irealloc(ctrl->adwgts[u], ctrl->maxnads[u],
- "IncreaseEdgeSubDomainGraph: adids[pid]");
- }
- ctrl->adids[u][nads] = v;
- ctrl->adwgts[u][nads] = ewgt;
- nads++;
- if (r_maxndoms != NULL && nads > *r_maxndoms) {
- printf("You just increased the maxndoms: %"PRIDX" %"PRIDX"\n",
- nads, *r_maxndoms);
- *r_maxndoms = nads;
- }
- }
- else {
- /* See if the updated edge becomes 0 */
- ASSERT(ctrl->adwgts[u][j] >= 0);
- if (ctrl->adwgts[u][j] == 0) {
- ctrl->adids[u][j] = ctrl->adids[u][nads-1];
- ctrl->adwgts[u][j] = ctrl->adwgts[u][nads-1];
- nads--;
- if (r_maxndoms != NULL && nads+1 == *r_maxndoms)
- *r_maxndoms = ctrl->nads[iargmax(ctrl->nparts, ctrl->nads)];
- }
- }
- ctrl->nads[u] = nads;
-
- SWAP(u, v, j);
- }
-}
-
-
-/*************************************************************************/
-/*! This function computes the subdomain graph */
-/*************************************************************************/
-void EliminateSubDomainEdges(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, k, ncon, nparts, scheme, pid_from, pid_to, me, other, nvtxs,
- total, max, avg, totalout, nind=0, ncand=0, ncand2, target, target2,
- nadd, bestnadd=0;
- idx_t min, move, *cpwgt;
- idx_t *xadj, *adjncy, *vwgt, *adjwgt, *pwgts, *where, *maxpwgt,
- *mypmat, *otherpmat, *kpmat, *ind;
- idx_t *nads, **adids, **adwgts;
- ikv_t *cand, *cand2;
- ipq_t queue;
- real_t *tpwgts, badfactor=1.4;
- idx_t *pptr, *pind;
- idx_t *vmarker=NULL, *pmarker=NULL, *modind=NULL; /* volume specific work arrays */
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
- adjwgt = (ctrl->objtype == METIS_OBJTYPE_VOL ? NULL : graph->adjwgt);
-
- where = graph->where;
- pwgts = graph->pwgts; /* We assume that this is properly initialized */
-
- nparts = ctrl->nparts;
- tpwgts = ctrl->tpwgts;
-
- cpwgt = iwspacemalloc(ctrl, ncon);
- maxpwgt = iwspacemalloc(ctrl, nparts*ncon);
- ind = iwspacemalloc(ctrl, nvtxs);
- otherpmat = iset(nparts, 0, iwspacemalloc(ctrl, nparts));
-
- cand = ikvwspacemalloc(ctrl, nparts);
- cand2 = ikvwspacemalloc(ctrl, nparts);
-
- pptr = iwspacemalloc(ctrl, nparts+1);
- pind = iwspacemalloc(ctrl, nvtxs);
- iarray2csr(nvtxs, nparts, where, pptr, pind);
-
- if (ctrl->objtype == METIS_OBJTYPE_VOL) {
- /* Vol-refinement specific working arrays */
- modind = iwspacemalloc(ctrl, nvtxs);
- vmarker = iset(nvtxs, 0, iwspacemalloc(ctrl, nvtxs));
- pmarker = iset(nparts, -1, iwspacemalloc(ctrl, nparts));
- }
-
-
- /* Compute the pmat matrix and ndoms */
- ComputeSubDomainGraph(ctrl, graph);
-
- nads = ctrl->nads;
- adids = ctrl->adids;
- adwgts = ctrl->adwgts;
-
- mypmat = iset(nparts, 0, ctrl->pvec1);
- kpmat = iset(nparts, 0, ctrl->pvec2);
-
- /* Compute the maximum allowed weight for each domain */
- for (i=0; i<nparts; i++) {
- for (j=0; j<ncon; j++)
- maxpwgt[i*ncon+j] =
- (ncon == 1 ? 1.25 : 1.025)*tpwgts[i]*graph->tvwgt[j]*ctrl->ubfactors[j];
- }
-
- ipqInit(&queue, nparts);
-
- /* Get into the loop eliminating subdomain connections */
- while (1) {
- total = isum(nparts, nads, 1);
- avg = total/nparts;
- max = nads[iargmax(nparts, nads)];
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONNINFO,
- printf("Adjacent Subdomain Stats: Total: %3"PRIDX", "
- "Max: %3"PRIDX"[%zu], Avg: %3"PRIDX"\n",
- total, max, iargmax(nparts, nads), avg));
-
- if (max < badfactor*avg)
- break;
-
- /* Add the subdomains that you will try to reduce their connectivity */
- ipqReset(&queue);
- for (i=0; i<nparts; i++) {
- if (nads[i] >= avg + (max-avg)/2)
- ipqInsert(&queue, i, nads[i]);
- }
-
- move = 0;
- while ((me = ipqGetTop(&queue)) != -1) {
- totalout = isum(nads[me], adwgts[me], 1);
-
- for (ncand2=0, i=0; i<nads[me]; i++) {
- mypmat[adids[me][i]] = adwgts[me][i];
-
- /* keep track of the weakly connected adjacent subdomains */
- if (2*nads[me]*adwgts[me][i] < totalout) {
- cand2[ncand2].val = adids[me][i];
- cand2[ncand2++].key = adwgts[me][i];
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONNINFO,
- printf("Me: %"PRIDX", Degree: %4"PRIDX", TotalOut: %"PRIDX",\n",
- me, nads[me], totalout));
-
- /* Sort the connections according to their cut */
- ikvsorti(ncand2, cand2);
-
- /* Two schemes are used for eliminating subdomain edges.
- The first, tries to eliminate subdomain edges by moving remote groups
- of vertices to subdomains that 'me' is already connected to.
- The second, tries to eliminate subdomain edges by moving entire sets of
- my vertices that connect to the 'other' subdomain to a subdomain that
- I'm already connected to.
- These two schemes are applied in sequence. */
- target = target2 = -1;
- for (scheme=0; scheme<2; scheme++) {
- for (min=0; min<ncand2; min++) {
- other = cand2[min].val;
-
- /* pid_from is the subdomain from where the vertices will be removed.
- pid_to is the adjacent subdomain to pid_from that defines the
- (me, other) subdomain edge that needs to be removed */
- if (scheme == 0) {
- pid_from = other;
- pid_to = me;
- }
- else {
- pid_from = me;
- pid_to = other;
- }
-
- /* Go and find the vertices in 'other' that are connected in 'me' */
- for (nind=0, ii=pptr[pid_from]; ii<pptr[pid_from+1]; ii++) {
- i = pind[ii];
- ASSERT(where[i] == pid_from);
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (where[adjncy[j]] == pid_to) {
- ind[nind++] = i;
- break;
- }
- }
- }
-
- /* Go and construct the otherpmat to see where these nind vertices are
- connected to */
- iset(ncon, 0, cpwgt);
- for (ncand=0, ii=0; ii<nind; ii++) {
- i = ind[ii];
- iaxpy(ncon, 1, vwgt+i*ncon, 1, cpwgt, 1);
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if ((k = where[adjncy[j]]) == pid_from)
- continue;
- if (otherpmat[k] == 0)
- cand[ncand++].val = k;
- otherpmat[k] += (adjwgt ? adjwgt[j] : 1);
- }
- }
-
- for (i=0; i<ncand; i++) {
- cand[i].key = otherpmat[cand[i].val];
- ASSERT(cand[i].key > 0);
- }
-
- ikvsortd(ncand, cand);
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONNINFO,
- printf("\tMinOut: %4"PRIDX", to: %3"PRIDX", TtlWgt: %5"PRIDX"[#:%"PRIDX"]\n",
- mypmat[other], other, isum(ncon, cpwgt, 1), nind));
-
- /* Go through and select the first domain that is common with 'me', and does
- not increase the nads[target] higher than nads[me], subject to the maxpwgt
- constraint. Traversal is done from the mostly connected to the least. */
- for (i=0; i<ncand; i++) {
- k = cand[i].val;
-
- if (mypmat[k] > 0) {
- /* Check if balance will go off */
- if (!ivecaxpylez(ncon, 1, cpwgt, pwgts+k*ncon, maxpwgt+k*ncon))
- continue;
-
- /* get a dense vector out of k's connectivity */
- for (j=0; j<nads[k]; j++)
- kpmat[adids[k][j]] = adwgts[k][j];
-
- /* Check if the move to domain k will increase the nads of another
- subdomain j that the set of vertices being moved are connected
- to but domain k is not connected to. */
- for (j=0; j<nparts; j++) {
- if (otherpmat[j] > 0 && kpmat[j] == 0 && nads[j]+1 >= nads[me])
- break;
- }
-
- /* There were no bad second level effects. See if you can find a
- subdomain to move to. */
- if (j == nparts) {
- for (nadd=0, j=0; j<nparts; j++) {
- if (otherpmat[j] > 0 && kpmat[j] == 0)
- nadd++;
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_CONNINFO,
- printf("\t\tto=%"PRIDX", nadd=%"PRIDX", %"PRIDX"\n", k, nadd, nads[k]));
-
- if (nads[k]+nadd < nads[me]) {
- if (target2 == -1 || nads[target2]+bestnadd > nads[k]+nadd ||
- (nads[target2]+bestnadd == nads[k]+nadd && bestnadd > nadd)) {
- target2 = k;
- bestnadd = nadd;
- }
- }
-
- if (nadd == 0)
- target = k;
- }
-
- /* reset kpmat for the next iteration */
- for (j=0; j<nads[k]; j++)
- kpmat[adids[k][j]] = 0;
- }
-
- if (target != -1)
- break;
- }
-
- /* reset the otherpmat for the next iteration */
- for (i=0; i<ncand; i++)
- otherpmat[cand[i].val] = 0;
-
- if (target == -1 && target2 != -1)
- target = target2;
-
- if (target != -1) {
- IFSET(ctrl->dbglvl, METIS_DBG_CONNINFO,
- printf("\t\tScheme: %"PRIDX". Moving to %"PRIDX"\n", scheme, target));
- move = 1;
- break;
- }
- }
-
- if (target != -1)
- break; /* A move was found. No need to try the other scheme */
- }
-
- /* reset the mypmat for next iteration */
- for (i=0; i<nads[me]; i++)
- mypmat[adids[me][i]] = 0;
-
- /* Note that once a target is found the above loops exit right away. So the
- following variables are valid */
- if (target != -1) {
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- MoveGroupMinConnForCut(ctrl, graph, target, nind, ind);
- break;
- case METIS_OBJTYPE_VOL:
- MoveGroupMinConnForVol(ctrl, graph, target, nind, ind, vmarker,
- pmarker, modind);
- break;
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
- /* Update the csr representation of the partitioning vector */
- iarray2csr(nvtxs, nparts, where, pptr, pind);
- }
- }
-
- if (move == 0)
- break;
- }
-
- ipqFree(&queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function moves a collection of vertices and updates their rinfo */
-/*************************************************************************/
-void MoveGroupMinConnForCut(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t nind,
- idx_t *ind)
-{
- idx_t i, ii, j, jj, k, l, nvtxs, nbnd, from, me;
- idx_t *xadj, *adjncy, *adjwgt, *where, *bndptr, *bndind;
- ckrinfo_t *myrinfo;
- cnbr_t *mynbrs;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
-
- nbnd = graph->nbnd;
-
- while (--nind>=0) {
- i = ind[nind];
- from = where[i];
-
- myrinfo = graph->ckrinfo+i;
- if (myrinfo->inbr == -1) {
- myrinfo->inbr = cnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- myrinfo->nnbrs = 0;
- }
- mynbrs = ctrl->cnbrpool + myrinfo->inbr;
-
- /* find the location of 'to' in myrinfo or create it if it is not there */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == to)
- break;
- }
- if (k == myrinfo->nnbrs) {
- ASSERT(k < xadj[i+1]-xadj[i]);
- mynbrs[k].pid = to;
- mynbrs[k].ed = 0;
- myrinfo->nnbrs++;
- }
-
- /* Update pwgts */
- iaxpy(graph->ncon, 1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+to*graph->ncon, 1);
- iaxpy(graph->ncon, -1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+from*graph->ncon, 1);
-
- /* Update mincut */
- graph->mincut -= mynbrs[k].ed-myrinfo->id;
-
- /* Update subdomain connectivity graph to reflect the move of 'i' */
- UpdateEdgeSubDomainGraph(ctrl, from, to, myrinfo->id-mynbrs[k].ed, NULL);
-
- /* Update ID/ED and BND related information for the moved vertex */
- UpdateMovedVertexInfoAndBND(i, from, k, to, myrinfo, mynbrs, where, nbnd,
- bndptr, bndind, BNDTYPE_REFINE);
-
- /* Update the degrees of adjacent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- me = where[ii];
- myrinfo = graph->ckrinfo+ii;
-
- UpdateAdjacentVertexInfoAndBND(ctrl, ii, xadj[ii+1]-xadj[ii], me,
- from, to, myrinfo, adjwgt[j], nbnd, bndptr, bndind, BNDTYPE_REFINE);
-
- /* Update subdomain graph to reflect the move of 'i' for domains other
- than 'from' and 'to' */
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -adjwgt[j], NULL);
- UpdateEdgeSubDomainGraph(ctrl, to, me, adjwgt[j], NULL);
- }
- }
- }
-
- ASSERT(ComputeCut(graph, where) == graph->mincut);
-
- graph->nbnd = nbnd;
-
-}
-
-
-/*************************************************************************/
-/*! This function moves a collection of vertices and updates their rinfo */
-/*************************************************************************/
-void MoveGroupMinConnForVol(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t nind,
- idx_t *ind, idx_t *vmarker, idx_t *pmarker, idx_t *modind)
-{
- idx_t i, ii, j, jj, k, l, nvtxs, from, me, other, xgain, ewgt;
- idx_t *xadj, *vsize, *adjncy, *where;
- vkrinfo_t *myrinfo, *orinfo;
- vnbr_t *mynbrs, *onbrs;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vsize = graph->vsize;
- adjncy = graph->adjncy;
- where = graph->where;
-
- while (--nind>=0) {
- i = ind[nind];
- from = where[i];
-
- myrinfo = graph->vkrinfo+i;
- if (myrinfo->inbr == -1) {
- myrinfo->inbr = vnbrpoolGetNext(ctrl, xadj[i+1]-xadj[i]+1);
- myrinfo->nnbrs = 0;
- }
- mynbrs = ctrl->vnbrpool + myrinfo->inbr;
-
- xgain = (myrinfo->nid == 0 && myrinfo->ned > 0 ? vsize[i] : 0);
-
- //printf("Moving %"PRIDX" from %"PRIDX" to %"PRIDX" [vsize: %"PRIDX"] [xgain: %"PRIDX"]\n",
- // i, from, to, vsize[i], xgain);
-
- /* find the location of 'to' in myrinfo or create it if it is not there */
- for (k=0; k<myrinfo->nnbrs; k++) {
- if (mynbrs[k].pid == to)
- break;
- }
-
- if (k == myrinfo->nnbrs) {
- //printf("Missing neighbor\n");
-
- if (myrinfo->nid > 0)
- xgain -= vsize[i];
-
- /* determine the volume gain resulting from that move */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- ii = adjncy[j];
- other = where[ii];
- orinfo = graph->vkrinfo+ii;
- onbrs = ctrl->vnbrpool + orinfo->inbr;
- ASSERT(other != to)
-
- //printf(" %8d %8d %3d\n", (int)ii, (int)vsize[ii], (int)other);
-
- if (from == other) {
- /* Same subdomain vertex: Decrease the gain if 'to' is a new neighbor. */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == to)
- break;
- }
- if (l == orinfo->nnbrs)
- xgain -= vsize[ii];
- }
- else {
- /* Remote vertex: increase if 'to' is a new subdomain */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == to)
- break;
- }
- if (l == orinfo->nnbrs)
- xgain -= vsize[ii];
-
- /* Remote vertex: decrease if i is the only connection to 'from' */
- for (l=0; l<orinfo->nnbrs; l++) {
- if (onbrs[l].pid == from && onbrs[l].ned == 1) {
- xgain += vsize[ii];
- break;
- }
- }
- }
- }
- graph->minvol -= xgain;
- graph->mincut -= -myrinfo->nid;
- ewgt = myrinfo->nid;
- }
- else {
- graph->minvol -= (xgain + mynbrs[k].gv);
- graph->mincut -= mynbrs[k].ned-myrinfo->nid;
- ewgt = myrinfo->nid-mynbrs[k].ned;
- }
-
- /* Update where and pwgts */
- where[i] = to;
- iaxpy(graph->ncon, 1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+to*graph->ncon, 1);
- iaxpy(graph->ncon, -1, graph->vwgt+i*graph->ncon, 1, graph->pwgts+from*graph->ncon, 1);
-
- /* Update subdomain connectivity graph to reflect the move of 'i' */
- UpdateEdgeSubDomainGraph(ctrl, from, to, ewgt, NULL);
-
- /* Update the subdomain connectivity of the adjacent vertices */
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- me = where[adjncy[j]];
- if (me != from && me != to) {
- UpdateEdgeSubDomainGraph(ctrl, from, me, -1, NULL);
- UpdateEdgeSubDomainGraph(ctrl, to, me, 1, NULL);
- }
- }
-
- /* Update the id/ed/gains/bnd of potentially affected nodes */
- KWayVolUpdate(ctrl, graph, i, from, to, NULL, NULL, NULL, NULL,
- NULL, BNDTYPE_REFINE, vmarker, pmarker, modind);
-
- /*CheckKWayVolPartitionParams(ctrl, graph);*/
- }
- ASSERT(ComputeCut(graph, where) == graph->mincut);
- ASSERTP(ComputeVolume(graph, where) == graph->minvol,
- ("%"PRIDX" %"PRIDX"\n", ComputeVolume(graph, where), graph->minvol));
-
-}
-
-
-/*************************************************************************/
-/*! This function computes the subdomain graph. For deubuging purposes. */
-/*************************************************************************/
-void PrintSubDomainGraph(graph_t *graph, idx_t nparts, idx_t *where)
-{
- idx_t i, j, k, me, nvtxs, total, max;
- idx_t *xadj, *adjncy, *adjwgt, *pmat;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- pmat = ismalloc(nparts*nparts, 0, "ComputeSubDomainGraph: pmat");
-
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- k = adjncy[j];
- if (where[k] != me)
- pmat[me*nparts+where[k]] += adjwgt[j];
- }
- }
-
- /* printf("Subdomain Info\n"); */
- total = max = 0;
- for (i=0; i<nparts; i++) {
- for (k=0, j=0; j<nparts; j++) {
- if (pmat[i*nparts+j] > 0)
- k++;
- }
- total += k;
-
- if (k > max)
- max = k;
-/*
- printf("%2"PRIDX" -> %2"PRIDX" ", i, k);
- for (j=0; j<nparts; j++) {
- if (pmat[i*nparts+j] > 0)
- printf("[%2"PRIDX" %4"PRIDX"] ", j, pmat[i*nparts+j]);
- }
- printf("\n");
-*/
- }
- printf("Total adjacent subdomains: %"PRIDX", Max: %"PRIDX"\n", total, max);
-
- gk_free((void **)&pmat, LTERM);
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/mincover.c b/3rdParty/metis/metis-5.1.0/libmetis/mincover.c
deleted file mode 100644
index ed437fff1..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/mincover.c
+++ /dev/null
@@ -1,259 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * mincover.c
- *
- * This file implements the minimum cover algorithm
- *
- * Started 8/1/97
- * George
- *
- * $Id: mincover.c 9942 2011-05-17 22:09:52Z karypis $
- */
-
-#include "metislib.h"
-
-/*************************************************************************
-* Constants used by mincover algorithm
-**************************************************************************/
-#define INCOL 10
-#define INROW 20
-#define VC 1
-#define SC 2
-#define HC 3
-#define VR 4
-#define SR 5
-#define HR 6
-
-
-/*************************************************************************
-* This function returns the min-cover of a bipartite graph.
-* The algorithm used is due to Hopcroft and Karp as modified by Duff etal
-* adj: the adjacency list of the bipartite graph
-* asize: the number of vertices in the first part of the bipartite graph
-* bsize-asize: the number of vertices in the second part
-* 0..(asize-1) > A vertices
-* asize..bsize > B vertices
-*
-* Returns:
-* cover : the actual cover (array)
-* csize : the size of the cover
-**************************************************************************/
-void MinCover(idx_t *xadj, idx_t *adjncy, idx_t asize, idx_t bsize, idx_t *cover, idx_t *csize)
-{
- idx_t i, j;
- idx_t *mate, *queue, *flag, *level, *lst;
- idx_t fptr, rptr, lstptr;
- idx_t row, maxlevel, col;
-
- mate = ismalloc(bsize, -1, "MinCover: mate");
- flag = imalloc(bsize, "MinCover: flag");
- level = imalloc(bsize, "MinCover: level");
- queue = imalloc(bsize, "MinCover: queue");
- lst = imalloc(bsize, "MinCover: lst");
-
- /* Get a cheap matching */
- for (i=0; i<asize; i++) {
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (mate[adjncy[j]] == -1) {
- mate[i] = adjncy[j];
- mate[adjncy[j]] = i;
- break;
- }
- }
- }
-
- /* Get into the main loop */
- while (1) {
- /* Initialization */
- fptr = rptr = 0; /* Empty Queue */
- lstptr = 0; /* Empty List */
- for (i=0; i<bsize; i++) {
- level[i] = -1;
- flag[i] = 0;
- }
- maxlevel = bsize;
-
- /* Insert free nodes into the queue */
- for (i=0; i<asize; i++)
- if (mate[i] == -1) {
- queue[rptr++] = i;
- level[i] = 0;
- }
-
- /* Perform the BFS */
- while (fptr != rptr) {
- row = queue[fptr++];
- if (level[row] < maxlevel) {
- flag[row] = 1;
- for (j=xadj[row]; j<xadj[row+1]; j++) {
- col = adjncy[j];
- if (!flag[col]) { /* If this column has not been accessed yet */
- flag[col] = 1;
- if (mate[col] == -1) { /* Free column node was found */
- maxlevel = level[row];
- lst[lstptr++] = col;
- }
- else { /* This column node is matched */
- if (flag[mate[col]])
- printf("\nSomething wrong, flag[%"PRIDX"] is 1",mate[col]);
- queue[rptr++] = mate[col];
- level[mate[col]] = level[row] + 1;
- }
- }
- }
- }
- }
-
- if (lstptr == 0)
- break; /* No free columns can be reached */
-
- /* Perform restricted DFS from the free column nodes */
- for (i=0; i<lstptr; i++)
- MinCover_Augment(xadj, adjncy, lst[i], mate, flag, level, maxlevel);
- }
-
- MinCover_Decompose(xadj, adjncy, asize, bsize, mate, cover, csize);
-
- gk_free((void **)&mate, &flag, &level, &queue, &lst, LTERM);
-
-}
-
-
-/*************************************************************************
-* This function perfoms a restricted DFS and augments matchings
-**************************************************************************/
-idx_t MinCover_Augment(idx_t *xadj, idx_t *adjncy, idx_t col, idx_t *mate, idx_t *flag, idx_t *level, idx_t maxlevel)
-{
- idx_t i;
- idx_t row = -1;
- idx_t status;
-
- flag[col] = 2;
- for (i=xadj[col]; i<xadj[col+1]; i++) {
- row = adjncy[i];
-
- if (flag[row] == 1) { /* First time through this row node */
- if (level[row] == maxlevel) { /* (col, row) is an edge of the G^T */
- flag[row] = 2; /* Mark this node as being visited */
- if (maxlevel != 0)
- status = MinCover_Augment(xadj, adjncy, mate[row], mate, flag, level, maxlevel-1);
- else
- status = 1;
-
- if (status) {
- mate[col] = row;
- mate[row] = col;
- return 1;
- }
- }
- }
- }
-
- return 0;
-}
-
-
-
-/*************************************************************************
-* This function performs a coarse decomposition and determines the
-* min-cover.
-* REF: Pothen ACMTrans. on Amth Software
-**************************************************************************/
-void MinCover_Decompose(idx_t *xadj, idx_t *adjncy, idx_t asize, idx_t bsize, idx_t *mate, idx_t *cover, idx_t *csize)
-{
- idx_t i, k;
- idx_t *where;
- idx_t card[10];
-
- where = imalloc(bsize, "MinCover_Decompose: where");
- for (i=0; i<10; i++)
- card[i] = 0;
-
- for (i=0; i<asize; i++)
- where[i] = SC;
- for (; i<bsize; i++)
- where[i] = SR;
-
- for (i=0; i<asize; i++)
- if (mate[i] == -1)
- MinCover_ColDFS(xadj, adjncy, i, mate, where, INCOL);
- for (; i<bsize; i++)
- if (mate[i] == -1)
- MinCover_RowDFS(xadj, adjncy, i, mate, where, INROW);
-
- for (i=0; i<bsize; i++)
- card[where[i]]++;
-
- k = 0;
- if (iabs(card[VC]+card[SC]-card[HR]) < iabs(card[VC]-card[SR]-card[HR])) { /* S = VC+SC+HR */
- /* printf("%"PRIDX" %"PRIDX" ",vc+sc, hr); */
- for (i=0; i<bsize; i++)
- if (where[i] == VC || where[i] == SC || where[i] == HR)
- cover[k++] = i;
- }
- else { /* S = VC+SR+HR */
- /* printf("%"PRIDX" %"PRIDX" ",vc, hr+sr); */
- for (i=0; i<bsize; i++)
- if (where[i] == VC || where[i] == SR || where[i] == HR)
- cover[k++] = i;
- }
-
- *csize = k;
- gk_free((void **)&where, LTERM);
-
-}
-
-
-/*************************************************************************
-* This function perfoms a dfs starting from an unmatched col node
-* forming alternate paths
-**************************************************************************/
-void MinCover_ColDFS(idx_t *xadj, idx_t *adjncy, idx_t root, idx_t *mate, idx_t *where, idx_t flag)
-{
- idx_t i;
-
- if (flag == INCOL) {
- if (where[root] == HC)
- return;
- where[root] = HC;
- for (i=xadj[root]; i<xadj[root+1]; i++)
- MinCover_ColDFS(xadj, adjncy, adjncy[i], mate, where, INROW);
- }
- else {
- if (where[root] == HR)
- return;
- where[root] = HR;
- if (mate[root] != -1)
- MinCover_ColDFS(xadj, adjncy, mate[root], mate, where, INCOL);
- }
-
-}
-
-/*************************************************************************
-* This function perfoms a dfs starting from an unmatched col node
-* forming alternate paths
-**************************************************************************/
-void MinCover_RowDFS(idx_t *xadj, idx_t *adjncy, idx_t root, idx_t *mate, idx_t *where, idx_t flag)
-{
- idx_t i;
-
- if (flag == INROW) {
- if (where[root] == VR)
- return;
- where[root] = VR;
- for (i=xadj[root]; i<xadj[root+1]; i++)
- MinCover_RowDFS(xadj, adjncy, adjncy[i], mate, where, INCOL);
- }
- else {
- if (where[root] == VC)
- return;
- where[root] = VC;
- if (mate[root] != -1)
- MinCover_RowDFS(xadj, adjncy, mate[root], mate, where, INROW);
- }
-
-}
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/mmd.c b/3rdParty/metis/metis-5.1.0/libmetis/mmd.c
deleted file mode 100644
index 778cc1548..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/mmd.c
+++ /dev/null
@@ -1,593 +0,0 @@
-/*
- * mmd.c
- *
- * **************************************************************
- * The following C function was developed from a FORTRAN subroutine
- * in SPARSPAK written by Eleanor Chu, Alan George, Joseph Liu
- * and Esmond Ng.
- *
- * The FORTRAN-to-C transformation and modifications such as dynamic
- * memory allocation and deallocation were performed by Chunguang
- * Sun.
- * **************************************************************
- *
- * Taken from SMMS, George 12/13/94
- *
- * The meaning of invperm, and perm vectors is different from that
- * in genqmd_ of SparsPak
- *
- * $Id: mmd.c 5993 2009-01-07 02:09:57Z karypis $
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************
-* genmmd -- multiple minimum external degree
-* purpose -- this routine implements the minimum degree
-* algorithm. it makes use of the implicit representation
-* of elimination graphs by quotient graphs, and the notion
-* of indistinguishable nodes. It also implements the modifications
-* by multiple elimination and minimum external degree.
-* Caution -- the adjacency vector adjncy will be destroyed.
-* Input parameters --
-* neqns -- number of equations.
-* (xadj, adjncy) -- the adjacency structure.
-* delta -- tolerance value for multiple elimination.
-* maxint -- maximum machine representable (short) integer
-* (any smaller estimate will do) for marking nodes.
-* Output parameters --
-* perm -- the minimum degree ordering.
-* invp -- the inverse of perm.
-* *ncsub -- an upper bound on the number of nonzero subscripts
-* for the compressed storage scheme.
-* Working parameters --
-* head -- vector for head of degree lists.
-* invp -- used temporarily for degree forward link.
-* perm -- used temporarily for degree backward link.
-* qsize -- vector for size of supernodes.
-* list -- vector for temporary linked lists.
-* marker -- a temporary marker vector.
-* Subroutines used -- mmdelm, mmdint, mmdnum, mmdupd.
-**************************************************************************/
-void genmmd(idx_t neqns, idx_t *xadj, idx_t *adjncy, idx_t *invp, idx_t *perm,
- idx_t delta, idx_t *head, idx_t *qsize, idx_t *list, idx_t *marker,
- idx_t maxint, idx_t *ncsub)
-{
- idx_t ehead, i, mdeg, mdlmt, mdeg_node, nextmd, num, tag;
-
- if (neqns <= 0)
- return;
-
- /* Adjust from C to Fortran */
- xadj--; adjncy--; invp--; perm--; head--; qsize--; list--; marker--;
-
- /* initialization for the minimum degree algorithm. */
- *ncsub = 0;
- mmdint(neqns, xadj, adjncy, head, invp, perm, qsize, list, marker);
-
- /* 'num' counts the number of ordered nodes plus 1. */
- num = 1;
-
- /* eliminate all isolated nodes. */
- nextmd = head[1];
- while (nextmd > 0) {
- mdeg_node = nextmd;
- nextmd = invp[mdeg_node];
- marker[mdeg_node] = maxint;
- invp[mdeg_node] = -num;
- num = num + 1;
- }
-
- /* search for node of the minimum degree. 'mdeg' is the current */
- /* minimum degree; 'tag' is used to facilitate marking nodes. */
- if (num > neqns)
- goto n1000;
- tag = 1;
- head[1] = 0;
- mdeg = 2;
-
- /* infinite loop here ! */
- while (1) {
- while (head[mdeg] <= 0)
- mdeg++;
-
- /* use value of 'delta' to set up 'mdlmt', which governs */
- /* when a degree update is to be performed. */
- mdlmt = mdeg + delta;
- ehead = 0;
-
-n500:
- mdeg_node = head[mdeg];
- while (mdeg_node <= 0) {
- mdeg++;
-
- if (mdeg > mdlmt)
- goto n900;
- mdeg_node = head[mdeg];
- };
-
- /* remove 'mdeg_node' from the degree structure. */
- nextmd = invp[mdeg_node];
- head[mdeg] = nextmd;
- if (nextmd > 0)
- perm[nextmd] = -mdeg;
- invp[mdeg_node] = -num;
- *ncsub += mdeg + qsize[mdeg_node] - 2;
- if ((num+qsize[mdeg_node]) > neqns)
- goto n1000;
-
- /* eliminate 'mdeg_node' and perform quotient graph */
- /* transformation. reset 'tag' value if necessary. */
- tag++;
- if (tag >= maxint) {
- tag = 1;
- for (i = 1; i <= neqns; i++)
- if (marker[i] < maxint)
- marker[i] = 0;
- };
-
- mmdelm(mdeg_node, xadj, adjncy, head, invp, perm, qsize, list, marker, maxint, tag);
-
- num += qsize[mdeg_node];
- list[mdeg_node] = ehead;
- ehead = mdeg_node;
- if (delta >= 0)
- goto n500;
-
- n900:
- /* update degrees of the nodes involved in the */
- /* minimum degree nodes elimination. */
- if (num > neqns)
- goto n1000;
- mmdupd( ehead, neqns, xadj, adjncy, delta, &mdeg, head, invp, perm, qsize, list, marker, maxint, &tag);
- }; /* end of -- while ( 1 ) -- */
-
-n1000:
- mmdnum( neqns, perm, invp, qsize );
-
- /* Adjust from Fortran back to C*/
- xadj++; adjncy++; invp++; perm++; head++; qsize++; list++; marker++;
-}
-
-
-/**************************************************************************
-* mmdelm ...... multiple minimum degree elimination
-* Purpose -- This routine eliminates the node mdeg_node of minimum degree
-* from the adjacency structure, which is stored in the quotient
-* graph format. It also transforms the quotient graph representation
-* of the elimination graph.
-* Input parameters --
-* mdeg_node -- node of minimum degree.
-* maxint -- estimate of maximum representable (short) integer.
-* tag -- tag value.
-* Updated parameters --
-* (xadj, adjncy) -- updated adjacency structure.
-* (head, forward, backward) -- degree doubly linked structure.
-* qsize -- size of supernode.
-* marker -- marker vector.
-* list -- temporary linked list of eliminated nabors.
-***************************************************************************/
-void mmdelm(idx_t mdeg_node, idx_t *xadj, idx_t *adjncy, idx_t *head, idx_t *forward,
- idx_t *backward, idx_t *qsize, idx_t *list, idx_t *marker, idx_t maxint, idx_t tag)
-{
- idx_t element, i, istop, istart, j,
- jstop, jstart, link,
- nabor, node, npv, nqnbrs, nxnode,
- pvnode, rlmt, rloc, rnode, xqnbr;
-
- /* find the reachable set of 'mdeg_node' and */
- /* place it in the data structure. */
- marker[mdeg_node] = tag;
- istart = xadj[mdeg_node];
- istop = xadj[mdeg_node+1] - 1;
-
- /* 'element' points to the beginning of the list of */
- /* eliminated nabors of 'mdeg_node', and 'rloc' gives the */
- /* storage location for the next reachable node. */
- element = 0;
- rloc = istart;
- rlmt = istop;
- for ( i = istart; i <= istop; i++ ) {
- nabor = adjncy[i];
- if ( nabor == 0 ) break;
- if ( marker[nabor] < tag ) {
- marker[nabor] = tag;
- if ( forward[nabor] < 0 ) {
- list[nabor] = element;
- element = nabor;
- } else {
- adjncy[rloc] = nabor;
- rloc++;
- };
- }; /* end of -- if -- */
- }; /* end of -- for -- */
-
- /* merge with reachable nodes from generalized elements. */
- while ( element > 0 ) {
- adjncy[rlmt] = -element;
- link = element;
-
-n400:
- jstart = xadj[link];
- jstop = xadj[link+1] - 1;
- for ( j = jstart; j <= jstop; j++ ) {
- node = adjncy[j];
- link = -node;
- if ( node < 0 ) goto n400;
- if ( node == 0 ) break;
- if ((marker[node]<tag)&&(forward[node]>=0)) {
- marker[node] = tag;
- /*use storage from eliminated nodes if necessary.*/
- while ( rloc >= rlmt ) {
- link = -adjncy[rlmt];
- rloc = xadj[link];
- rlmt = xadj[link+1] - 1;
- };
- adjncy[rloc] = node;
- rloc++;
- };
- }; /* end of -- for ( j = jstart; -- */
- element = list[element];
- }; /* end of -- while ( element > 0 ) -- */
- if ( rloc <= rlmt ) adjncy[rloc] = 0;
- /* for each node in the reachable set, do the following. */
- link = mdeg_node;
-
-n1100:
- istart = xadj[link];
- istop = xadj[link+1] - 1;
- for ( i = istart; i <= istop; i++ ) {
- rnode = adjncy[i];
- link = -rnode;
- if ( rnode < 0 ) goto n1100;
- if ( rnode == 0 ) return;
-
- /* 'rnode' is in the degree list structure. */
- pvnode = backward[rnode];
- if (( pvnode != 0 ) && ( pvnode != (-maxint) )) {
- /* then remove 'rnode' from the structure. */
- nxnode = forward[rnode];
- if ( nxnode > 0 ) backward[nxnode] = pvnode;
- if ( pvnode > 0 ) forward[pvnode] = nxnode;
- npv = -pvnode;
- if ( pvnode < 0 ) head[npv] = nxnode;
- };
-
- /* purge inactive quotient nabors of 'rnode'. */
- jstart = xadj[rnode];
- jstop = xadj[rnode+1] - 1;
- xqnbr = jstart;
- for ( j = jstart; j <= jstop; j++ ) {
- nabor = adjncy[j];
- if ( nabor == 0 ) break;
- if ( marker[nabor] < tag ) {
- adjncy[xqnbr] = nabor;
- xqnbr++;
- };
- };
-
- /* no active nabor after the purging. */
- nqnbrs = xqnbr - jstart;
- if ( nqnbrs <= 0 ) {
- /* merge 'rnode' with 'mdeg_node'. */
- qsize[mdeg_node] += qsize[rnode];
- qsize[rnode] = 0;
- marker[rnode] = maxint;
- forward[rnode] = -mdeg_node;
- backward[rnode] = -maxint;
- } else {
- /* flag 'rnode' for degree update, and */
- /* add 'mdeg_node' as a nabor of 'rnode'. */
- forward[rnode] = nqnbrs + 1;
- backward[rnode] = 0;
- adjncy[xqnbr] = mdeg_node;
- xqnbr++;
- if ( xqnbr <= jstop ) adjncy[xqnbr] = 0;
- };
- }; /* end of -- for ( i = istart; -- */
- return;
- }
-
-/***************************************************************************
-* mmdint ---- mult minimum degree initialization
-* purpose -- this routine performs initialization for the
-* multiple elimination version of the minimum degree algorithm.
-* input parameters --
-* neqns -- number of equations.
-* (xadj, adjncy) -- adjacency structure.
-* output parameters --
-* (head, dfrow, backward) -- degree doubly linked structure.
-* qsize -- size of supernode ( initialized to one).
-* list -- linked list.
-* marker -- marker vector.
-****************************************************************************/
-idx_t mmdint(idx_t neqns, idx_t *xadj, idx_t *adjncy, idx_t *head, idx_t *forward,
- idx_t *backward, idx_t *qsize, idx_t *list, idx_t *marker)
-{
- idx_t fnode, ndeg, node;
-
- for ( node = 1; node <= neqns; node++ ) {
- head[node] = 0;
- qsize[node] = 1;
- marker[node] = 0;
- list[node] = 0;
- };
-
- /* initialize the degree doubly linked lists. */
- for ( node = 1; node <= neqns; node++ ) {
- ndeg = xadj[node+1] - xadj[node]/* + 1*/; /* george */
- if (ndeg == 0)
- ndeg = 1;
- fnode = head[ndeg];
- forward[node] = fnode;
- head[ndeg] = node;
- if ( fnode > 0 ) backward[fnode] = node;
- backward[node] = -ndeg;
- };
- return 0;
-}
-
-/****************************************************************************
-* mmdnum --- multi minimum degree numbering
-* purpose -- this routine performs the final step in producing
-* the permutation and inverse permutation vectors in the
-* multiple elimination version of the minimum degree
-* ordering algorithm.
-* input parameters --
-* neqns -- number of equations.
-* qsize -- size of supernodes at elimination.
-* updated parameters --
-* invp -- inverse permutation vector. on input,
-* if qsize[node] = 0, then node has been merged
-* into the node -invp[node]; otherwise,
-* -invp[node] is its inverse labelling.
-* output parameters --
-* perm -- the permutation vector.
-****************************************************************************/
-void mmdnum(idx_t neqns, idx_t *perm, idx_t *invp, idx_t *qsize)
-{
- idx_t father, nextf, node, nqsize, num, root;
-
- for ( node = 1; node <= neqns; node++ ) {
- nqsize = qsize[node];
- if ( nqsize <= 0 ) perm[node] = invp[node];
- if ( nqsize > 0 ) perm[node] = -invp[node];
- };
-
- /* for each node which has been merged, do the following. */
- for ( node = 1; node <= neqns; node++ ) {
- if ( perm[node] <= 0 ) {
-
- /* trace the merged tree until one which has not */
- /* been merged, call it root. */
- father = node;
- while ( perm[father] <= 0 )
- father = - perm[father];
-
- /* number node after root. */
- root = father;
- num = perm[root] + 1;
- invp[node] = -num;
- perm[root] = num;
-
- /* shorten the merged tree. */
- father = node;
- nextf = - perm[father];
- while ( nextf > 0 ) {
- perm[father] = -root;
- father = nextf;
- nextf = -perm[father];
- };
- }; /* end of -- if ( perm[node] <= 0 ) -- */
- }; /* end of -- for ( node = 1; -- */
-
- /* ready to compute perm. */
- for ( node = 1; node <= neqns; node++ ) {
- num = -invp[node];
- invp[node] = num;
- perm[num] = node;
- };
- return;
-}
-
-/****************************************************************************
-* mmdupd ---- multiple minimum degree update
-* purpose -- this routine updates the degrees of nodes after a
-* multiple elimination step.
-* input parameters --
-* ehead -- the beginning of the list of eliminated nodes
-* (i.e., newly formed elements).
-* neqns -- number of equations.
-* (xadj, adjncy) -- adjacency structure.
-* delta -- tolerance value for multiple elimination.
-* maxint -- maximum machine representable (short) integer.
-* updated parameters --
-* mdeg -- new minimum degree after degree update.
-* (head, forward, backward) -- degree doubly linked structure.
-* qsize -- size of supernode.
-* list -- marker vector for degree update.
-* *tag -- tag value.
-****************************************************************************/
-void mmdupd(idx_t ehead, idx_t neqns, idx_t *xadj, idx_t *adjncy, idx_t delta, idx_t *mdeg,
- idx_t *head, idx_t *forward, idx_t *backward, idx_t *qsize, idx_t *list,
- idx_t *marker, idx_t maxint, idx_t *tag)
-{
- idx_t deg, deg0, element, enode, fnode, i, iq2, istop,
- istart, j, jstop, jstart, link, mdeg0, mtag, nabor,
- node, q2head, qxhead;
-
- mdeg0 = *mdeg + delta;
- element = ehead;
-
-n100:
- if ( element <= 0 ) return;
-
- /* for each of the newly formed element, do the following. */
- /* reset tag value if necessary. */
- mtag = *tag + mdeg0;
- if ( mtag >= maxint ) {
- *tag = 1;
- for ( i = 1; i <= neqns; i++ )
- if ( marker[i] < maxint ) marker[i] = 0;
- mtag = *tag + mdeg0;
- };
-
- /* create two linked lists from nodes associated with 'element': */
- /* one with two nabors (q2head) in the adjacency structure, and the*/
- /* other with more than two nabors (qxhead). also compute 'deg0',*/
- /* number of nodes in this element. */
- q2head = 0;
- qxhead = 0;
- deg0 = 0;
- link =element;
-
-n400:
- istart = xadj[link];
- istop = xadj[link+1] - 1;
- for ( i = istart; i <= istop; i++ ) {
- enode = adjncy[i];
- link = -enode;
- if ( enode < 0 ) goto n400;
- if ( enode == 0 ) break;
- if ( qsize[enode] != 0 ) {
- deg0 += qsize[enode];
- marker[enode] = mtag;
-
- /*'enode' requires a degree update*/
- if ( backward[enode] == 0 ) {
- /* place either in qxhead or q2head list. */
- if ( forward[enode] != 2 ) {
- list[enode] = qxhead;
- qxhead = enode;
- } else {
- list[enode] = q2head;
- q2head = enode;
- };
- };
- }; /* enf of -- if ( qsize[enode] != 0 ) -- */
- }; /* end of -- for ( i = istart; -- */
-
- /* for each node in q2 list, do the following. */
- enode = q2head;
- iq2 = 1;
-
-n900:
- if ( enode <= 0 ) goto n1500;
- if ( backward[enode] != 0 ) goto n2200;
- (*tag)++;
- deg = deg0;
-
- /* identify the other adjacent element nabor. */
- istart = xadj[enode];
- nabor = adjncy[istart];
- if ( nabor == element ) nabor = adjncy[istart+1];
- link = nabor;
- if ( forward[nabor] >= 0 ) {
- /* nabor is uneliminated, increase degree count. */
- deg += qsize[nabor];
- goto n2100;
- };
-
- /* the nabor is eliminated. for each node in the 2nd element */
- /* do the following. */
-n1000:
- istart = xadj[link];
- istop = xadj[link+1] - 1;
- for ( i = istart; i <= istop; i++ ) {
- node = adjncy[i];
- link = -node;
- if ( node != enode ) {
- if ( node < 0 ) goto n1000;
- if ( node == 0 ) goto n2100;
- if ( qsize[node] != 0 ) {
- if ( marker[node] < *tag ) {
- /* 'node' is not yet considered. */
- marker[node] = *tag;
- deg += qsize[node];
- } else {
- if ( backward[node] == 0 ) {
- if ( forward[node] == 2 ) {
- /* 'node' is indistinguishable from 'enode'.*/
- /* merge them into a new supernode. */
- qsize[enode] += qsize[node];
- qsize[node] = 0;
- marker[node] = maxint;
- forward[node] = -enode;
- backward[node] = -maxint;
- } else {
- /* 'node' is outmacthed by 'enode' */
- if (backward[node]==0) backward[node] = -maxint;
- };
- }; /* end of -- if ( backward[node] == 0 ) -- */
- }; /* end of -- if ( marker[node] < *tag ) -- */
- }; /* end of -- if ( qsize[node] != 0 ) -- */
- }; /* end of -- if ( node != enode ) -- */
- }; /* end of -- for ( i = istart; -- */
- goto n2100;
-
-n1500:
- /* for each 'enode' in the 'qx' list, do the following. */
- enode = qxhead;
- iq2 = 0;
-
-n1600: if ( enode <= 0 ) goto n2300;
- if ( backward[enode] != 0 ) goto n2200;
- (*tag)++;
- deg = deg0;
-
- /*for each unmarked nabor of 'enode', do the following.*/
- istart = xadj[enode];
- istop = xadj[enode+1] - 1;
- for ( i = istart; i <= istop; i++ ) {
- nabor = adjncy[i];
- if ( nabor == 0 ) break;
- if ( marker[nabor] < *tag ) {
- marker[nabor] = *tag;
- link = nabor;
- if ( forward[nabor] >= 0 )
- /*if uneliminated, include it in deg count.*/
- deg += qsize[nabor];
- else {
-n1700:
- /* if eliminated, include unmarked nodes in this*/
- /* element into the degree count. */
- jstart = xadj[link];
- jstop = xadj[link+1] - 1;
- for ( j = jstart; j <= jstop; j++ ) {
- node = adjncy[j];
- link = -node;
- if ( node < 0 ) goto n1700;
- if ( node == 0 ) break;
- if ( marker[node] < *tag ) {
- marker[node] = *tag;
- deg += qsize[node];
- };
- }; /* end of -- for ( j = jstart; -- */
- }; /* end of -- if ( forward[nabor] >= 0 ) -- */
- }; /* end of -- if ( marker[nabor] < *tag ) -- */
- }; /* end of -- for ( i = istart; -- */
-
-n2100:
- /* update external degree of 'enode' in degree structure, */
- /* and '*mdeg' if necessary. */
- deg = deg - qsize[enode] + 1;
- fnode = head[deg];
- forward[enode] = fnode;
- backward[enode] = -deg;
- if ( fnode > 0 ) backward[fnode] = enode;
- head[deg] = enode;
- if ( deg < *mdeg ) *mdeg = deg;
-
-n2200:
- /* get next enode in current element. */
- enode = list[enode];
- if ( iq2 == 1 ) goto n900;
- goto n1600;
-
-n2300:
- /* get next element in the list. */
- *tag = mtag;
- element = list[element];
- goto n100;
- }
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/ometis.c b/3rdParty/metis/metis-5.1.0/libmetis/ometis.c
deleted file mode 100644
index 51e39754c..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/ometis.c
+++ /dev/null
@@ -1,701 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * ometis.c
- *
- * This file contains the top level routines for the multilevel recursive
- * bisection algorithm PMETIS.
- *
- * Started 7/24/97
- * George
- *
- * $Id: ometis.c 10513 2011-07-07 22:06:03Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point for the multilevel nested dissection
- ordering code. At each bisection, a node-separator is computed using
- a node-based refinement approach.
-
- \param nvtxs is the number of vertices in the graph.
- \param xadj is of length nvtxs+1 marking the start of the adjancy
- list of each vertex in adjncy.
- \param adjncy stores the adjacency lists of the vertices. The adjnacy
- list of a vertex should not contain the vertex itself.
- \param vwgt is an array of size nvtxs storing the weight of each
- vertex. If vwgt is NULL, then the vertices are considered
- to have unit weight.
- \param numflag is either 0 or 1 indicating that the numbering of
- the vertices starts from 0 or 1, respectively.
- \param options is an array of size METIS_NOPTIONS used to pass
- various options impacting the of the algorithm. A NULL
- value indicates use of default options.
- \param perm is an array of size nvtxs such that if A and A' are
- the original and permuted matrices, then A'[i] = A[perm[i]].
- \param iperm is an array of size nvtxs such that if A and A' are
- the original and permuted matrices, then A[i] = A'[iperm[i]].
-*/
-/*************************************************************************/
-int METIS_NodeND(idx_t *nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t *options, idx_t *perm, idx_t *iperm)
-{
- int sigrval=0, renumber=0;
- idx_t i, ii, j, l, nnvtxs=0;
- graph_t *graph=NULL;
- ctrl_t *ctrl;
- idx_t *cptr, *cind, *piperm;
- int numflag = 0;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
-
- /* set up the run time parameters */
- ctrl = SetupCtrl(METIS_OP_OMETIS, options, 1, 3, NULL, NULL);
- if (!ctrl) {
- gk_siguntrap();
- return METIS_ERROR_INPUT;
- }
-
- /* if required, change the numbering to 0 */
- if (ctrl->numflag == 1) {
- Change2CNumbering(*nvtxs, xadj, adjncy);
- renumber = 1;
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, InitTimers(ctrl));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->TotalTmr));
-
- /* prune the dense columns */
- if (ctrl->pfactor > 0.0) {
- piperm = imalloc(*nvtxs, "OMETIS: piperm");
-
- graph = PruneGraph(ctrl, *nvtxs, xadj, adjncy, vwgt, piperm, ctrl->pfactor);
- if (graph == NULL) {
- /* if there was no prunning, cleanup the pfactor */
- gk_free((void **)&piperm, LTERM);
- ctrl->pfactor = 0.0;
- }
- else {
- nnvtxs = graph->nvtxs;
- ctrl->compress = 0; /* disable compression if prunning took place */
- }
- }
-
- /* compress the graph; note that compression only happens if not prunning
- has taken place. */
- if (ctrl->compress) {
- cptr = imalloc(*nvtxs+1, "OMETIS: cptr");
- cind = imalloc(*nvtxs, "OMETIS: cind");
-
- graph = CompressGraph(ctrl, *nvtxs, xadj, adjncy, vwgt, cptr, cind);
- if (graph == NULL) {
- /* if there was no compression, cleanup the compress flag */
- gk_free((void **)&cptr, &cind, LTERM);
- ctrl->compress = 0;
- }
- else {
- nnvtxs = graph->nvtxs;
- ctrl->cfactor = 1.0*(*nvtxs)/nnvtxs;
- if (ctrl->cfactor > 1.5 && ctrl->nseps == 1)
- ctrl->nseps = 2;
- //ctrl->nseps = (idx_t)(ctrl->cfactor*ctrl->nseps);
- }
- }
-
- /* if no prunning and no compression, setup the graph in the normal way. */
- if (ctrl->pfactor == 0.0 && ctrl->compress == 0)
- graph = SetupGraph(ctrl, *nvtxs, 1, xadj, adjncy, vwgt, NULL, NULL);
-
- ASSERT(CheckGraph(graph, ctrl->numflag, 1));
-
- /* allocate workspace memory */
- AllocateWorkSpace(ctrl, graph);
-
- /* do the nested dissection ordering */
- if (ctrl->ccorder)
- MlevelNestedDissectionCC(ctrl, graph, iperm, graph->nvtxs);
- else
- MlevelNestedDissection(ctrl, graph, iperm, graph->nvtxs);
-
-
- if (ctrl->pfactor > 0.0) { /* Order any prunned vertices */
- icopy(nnvtxs, iperm, perm); /* Use perm as an auxiliary array */
- for (i=0; i<nnvtxs; i++)
- iperm[piperm[i]] = perm[i];
- for (i=nnvtxs; i<*nvtxs; i++)
- iperm[piperm[i]] = i;
-
- gk_free((void **)&piperm, LTERM);
- }
- else if (ctrl->compress) { /* Uncompress the ordering */
- /* construct perm from iperm */
- for (i=0; i<nnvtxs; i++)
- perm[iperm[i]] = i;
- for (l=ii=0; ii<nnvtxs; ii++) {
- i = perm[ii];
- for (j=cptr[i]; j<cptr[i+1]; j++)
- iperm[cind[j]] = l++;
- }
-
- gk_free((void **)&cptr, &cind, LTERM);
- }
-
- for (i=0; i<*nvtxs; i++)
- perm[iperm[i]] = i;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->TotalTmr));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, PrintTimers(ctrl));
-
- /* clean up */
- FreeCtrl(&ctrl);
-
-SIGTHROW:
- /* if required, change the numbering back to 1 */
- if (renumber)
- Change2FNumberingOrder(*nvtxs, xadj, adjncy, perm, iperm);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- return metis_rcode(sigrval);
-}
-
-
-/*************************************************************************/
-/*! This is the driver for the recursive tri-section of a graph into the
- left, separator, and right partitions. The graphs correspond to the
- left and right parts are further tri-sected in a recursive fashion.
- The nodes in the separator are ordered at the end of the left & right
- nodes.
- */
-/*************************************************************************/
-void MlevelNestedDissection(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx)
-{
- idx_t i, j, nvtxs, nbnd;
- idx_t *label, *bndind;
- graph_t *lgraph, *rgraph;
-
- nvtxs = graph->nvtxs;
-
- MlevelNodeBisectionMultiple(ctrl, graph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_SEPINFO,
- printf("Nvtxs: %6"PRIDX", [%6"PRIDX" %6"PRIDX" %6"PRIDX"]\n",
- graph->nvtxs, graph->pwgts[0], graph->pwgts[1], graph->pwgts[2]));
-
-
- /* Order the nodes in the separator */
- nbnd = graph->nbnd;
- bndind = graph->bndind;
- label = graph->label;
- for (i=0; i<nbnd; i++)
- order[label[bndind[i]]] = --lastvtx;
-
- SplitGraphOrder(ctrl, graph, &lgraph, &rgraph);
-
- /* Free the memory of the top level graph */
- FreeGraph(&graph);
-
- /* Recurse on lgraph first, as its lastvtx depends on rgraph->nvtxs, which
- will not be defined upon return from MlevelNestedDissection. */
- if (lgraph->nvtxs > MMDSWITCH && lgraph->nedges > 0)
- MlevelNestedDissection(ctrl, lgraph, order, lastvtx-rgraph->nvtxs);
- else {
- MMDOrder(ctrl, lgraph, order, lastvtx-rgraph->nvtxs);
- FreeGraph(&lgraph);
- }
- if (rgraph->nvtxs > MMDSWITCH && rgraph->nedges > 0)
- MlevelNestedDissection(ctrl, rgraph, order, lastvtx);
- else {
- MMDOrder(ctrl, rgraph, order, lastvtx);
- FreeGraph(&rgraph);
- }
-}
-
-
-/*************************************************************************/
-/*! This routine is similar to its non 'CC' counterpart. The difference is
- that after each tri-section, the connected components of the original
- graph that result after removing the separator vertises are ordered
- independently (i.e., this may lead to more than just the left and
- the right subgraphs).
-*/
-/*************************************************************************/
-void MlevelNestedDissectionCC(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx)
-{
- idx_t i, j, nvtxs, nbnd, ncmps, rnvtxs, snvtxs;
- idx_t *label, *bndind;
- idx_t *cptr, *cind;
- graph_t **sgraphs;
-
- nvtxs = graph->nvtxs;
-
- MlevelNodeBisectionMultiple(ctrl, graph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_SEPINFO,
- printf("Nvtxs: %6"PRIDX", [%6"PRIDX" %6"PRIDX" %6"PRIDX"]\n",
- graph->nvtxs, graph->pwgts[0], graph->pwgts[1], graph->pwgts[2]));
-
- /* Order the nodes in the separator */
- nbnd = graph->nbnd;
- bndind = graph->bndind;
- label = graph->label;
- for (i=0; i<nbnd; i++)
- order[label[bndind[i]]] = --lastvtx;
-
- WCOREPUSH;
- cptr = iwspacemalloc(ctrl, nvtxs+1);
- cind = iwspacemalloc(ctrl, nvtxs);
- ncmps = FindSepInducedComponents(ctrl, graph, cptr, cind);
-
- if (ctrl->dbglvl&METIS_DBG_INFO) {
- if (ncmps > 2)
- printf(" Bisection resulted in %"PRIDX" connected components\n", ncmps);
- }
-
- sgraphs = SplitGraphOrderCC(ctrl, graph, ncmps, cptr, cind);
-
- WCOREPOP;
-
- /* Free the memory of the top level graph */
- FreeGraph(&graph);
-
- /* Go and process the subgraphs */
- for (rnvtxs=i=0; i<ncmps; i++) {
- /* Save the number of vertices in sgraphs[i] because sgraphs[i] is freed
- inside MlevelNestedDissectionCC, and as such it will be undefined. */
- snvtxs = sgraphs[i]->nvtxs;
-
- if (sgraphs[i]->nvtxs > MMDSWITCH && sgraphs[i]->nedges > 0) {
- MlevelNestedDissectionCC(ctrl, sgraphs[i], order, lastvtx-rnvtxs);
- }
- else {
- MMDOrder(ctrl, sgraphs[i], order, lastvtx-rnvtxs);
- FreeGraph(&sgraphs[i]);
- }
- rnvtxs += snvtxs;
- }
-
- gk_free((void **)&sgraphs, LTERM);
-}
-
-
-/*************************************************************************/
-/*! This function performs multilevel node bisection (i.e., tri-section).
- It performs multiple bisections and selects the best. */
-/*************************************************************************/
-void MlevelNodeBisectionMultiple(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, mincut;
- idx_t *bestwhere;
-
- /* if the graph is small, just find a single vertex separator */
- if (ctrl->nseps == 1 || graph->nvtxs < (ctrl->compress ? 1000 : 2000)) {
- MlevelNodeBisectionL2(ctrl, graph, LARGENIPARTS);
- return;
- }
-
- WCOREPUSH;
-
- bestwhere = iwspacemalloc(ctrl, graph->nvtxs);
-
- mincut = graph->tvwgt[0];
- for (i=0; i<ctrl->nseps; i++) {
- MlevelNodeBisectionL2(ctrl, graph, LARGENIPARTS);
-
- if (i == 0 || graph->mincut < mincut) {
- mincut = graph->mincut;
- if (i < ctrl->nseps-1)
- icopy(graph->nvtxs, graph->where, bestwhere);
- }
-
- if (mincut == 0)
- break;
-
- if (i < ctrl->nseps-1)
- FreeRData(graph);
- }
-
- if (mincut != graph->mincut) {
- icopy(graph->nvtxs, bestwhere, graph->where);
- Compute2WayNodePartitionParams(ctrl, graph);
- }
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function performs multilevel node bisection (i.e., tri-section).
- It performs multiple bisections and selects the best. */
-/*************************************************************************/
-void MlevelNodeBisectionL2(ctrl_t *ctrl, graph_t *graph, idx_t niparts)
-{
- idx_t i, mincut, nruns=5;
- graph_t *cgraph;
- idx_t *bestwhere;
-
- /* if the graph is small, just find a single vertex separator */
- if (graph->nvtxs < 5000) {
- MlevelNodeBisectionL1(ctrl, graph, niparts);
- return;
- }
-
- WCOREPUSH;
-
- ctrl->CoarsenTo = gk_max(100, graph->nvtxs/30);
-
- cgraph = CoarsenGraphNlevels(ctrl, graph, 4);
-
- bestwhere = iwspacemalloc(ctrl, cgraph->nvtxs);
-
- mincut = graph->tvwgt[0];
- for (i=0; i<nruns; i++) {
- MlevelNodeBisectionL1(ctrl, cgraph, 0.7*niparts);
-
- if (i == 0 || cgraph->mincut < mincut) {
- mincut = cgraph->mincut;
- if (i < nruns-1)
- icopy(cgraph->nvtxs, cgraph->where, bestwhere);
- }
-
- if (mincut == 0)
- break;
-
- if (i < nruns-1)
- FreeRData(cgraph);
- }
-
- if (mincut != cgraph->mincut)
- icopy(cgraph->nvtxs, bestwhere, cgraph->where);
-
- WCOREPOP;
-
- Refine2WayNode(ctrl, graph, cgraph);
-
-}
-
-
-/*************************************************************************/
-/*! The top-level routine of the actual multilevel node bisection */
-/*************************************************************************/
-void MlevelNodeBisectionL1(ctrl_t *ctrl, graph_t *graph, idx_t niparts)
-{
- graph_t *cgraph;
-
- ctrl->CoarsenTo = graph->nvtxs/8;
- if (ctrl->CoarsenTo > 100)
- ctrl->CoarsenTo = 100;
- else if (ctrl->CoarsenTo < 40)
- ctrl->CoarsenTo = 40;
-
- cgraph = CoarsenGraph(ctrl, graph);
-
- niparts = gk_max(1, (cgraph->nvtxs <= ctrl->CoarsenTo ? niparts/2: niparts));
- /*niparts = (cgraph->nvtxs <= ctrl->CoarsenTo ? SMALLNIPARTS : LARGENIPARTS);*/
- InitSeparator(ctrl, cgraph, niparts);
-
- Refine2WayNode(ctrl, graph, cgraph);
-}
-
-
-/*************************************************************************/
-/*! This function takes a graph and a tri-section (left, right, separator)
- and splits it into two graphs.
-
- This function relies on the fact that adjwgt is all equal to 1.
-*/
-/*************************************************************************/
-void SplitGraphOrder(ctrl_t *ctrl, graph_t *graph, graph_t **r_lgraph,
- graph_t **r_rgraph)
-{
- idx_t i, ii, j, k, l, istart, iend, mypart, nvtxs, snvtxs[3], snedges[3];
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *label, *where, *bndptr, *bndind;
- idx_t *sxadj[2], *svwgt[2], *sadjncy[2], *sadjwgt[2], *slabel[2];
- idx_t *rename;
- idx_t *auxadjncy;
- graph_t *lgraph, *rgraph;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->SplitTmr));
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- label = graph->label;
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
- ASSERT(bndptr != NULL);
-
- rename = iwspacemalloc(ctrl, nvtxs);
-
- snvtxs[0] = snvtxs[1] = snvtxs[2] = snedges[0] = snedges[1] = snedges[2] = 0;
- for (i=0; i<nvtxs; i++) {
- k = where[i];
- rename[i] = snvtxs[k]++;
- snedges[k] += xadj[i+1]-xadj[i];
- }
-
- lgraph = SetupSplitGraph(graph, snvtxs[0], snedges[0]);
- sxadj[0] = lgraph->xadj;
- svwgt[0] = lgraph->vwgt;
- sadjncy[0] = lgraph->adjncy;
- sadjwgt[0] = lgraph->adjwgt;
- slabel[0] = lgraph->label;
-
- rgraph = SetupSplitGraph(graph, snvtxs[1], snedges[1]);
- sxadj[1] = rgraph->xadj;
- svwgt[1] = rgraph->vwgt;
- sadjncy[1] = rgraph->adjncy;
- sadjwgt[1] = rgraph->adjwgt;
- slabel[1] = rgraph->label;
-
- /* Go and use bndptr to also mark the boundary nodes in the two partitions */
- for (ii=0; ii<graph->nbnd; ii++) {
- i = bndind[ii];
- for (j=xadj[i]; j<xadj[i+1]; j++)
- bndptr[adjncy[j]] = 1;
- }
-
- snvtxs[0] = snvtxs[1] = snedges[0] = snedges[1] = 0;
- sxadj[0][0] = sxadj[1][0] = 0;
- for (i=0; i<nvtxs; i++) {
- if ((mypart = where[i]) == 2)
- continue;
-
- istart = xadj[i];
- iend = xadj[i+1];
- if (bndptr[i] == -1) { /* This is an interior vertex */
- auxadjncy = sadjncy[mypart] + snedges[mypart] - istart;
- for(j=istart; j<iend; j++)
- auxadjncy[j] = adjncy[j];
- snedges[mypart] += iend-istart;
- }
- else {
- auxadjncy = sadjncy[mypart];
- l = snedges[mypart];
- for (j=istart; j<iend; j++) {
- k = adjncy[j];
- if (where[k] == mypart)
- auxadjncy[l++] = k;
- }
- snedges[mypart] = l;
- }
-
- svwgt[mypart][snvtxs[mypart]] = vwgt[i];
- slabel[mypart][snvtxs[mypart]] = label[i];
- sxadj[mypart][++snvtxs[mypart]] = snedges[mypart];
- }
-
- for (mypart=0; mypart<2; mypart++) {
- iend = snedges[mypart];
- iset(iend, 1, sadjwgt[mypart]);
-
- auxadjncy = sadjncy[mypart];
- for (i=0; i<iend; i++)
- auxadjncy[i] = rename[auxadjncy[i]];
- }
-
- lgraph->nvtxs = snvtxs[0];
- lgraph->nedges = snedges[0];
- rgraph->nvtxs = snvtxs[1];
- rgraph->nedges = snedges[1];
-
- SetupGraph_tvwgt(lgraph);
- SetupGraph_tvwgt(rgraph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->SplitTmr));
-
- *r_lgraph = lgraph;
- *r_rgraph = rgraph;
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function takes a graph and generates a set of graphs, each of
- which is a connected component in the original graph.
-
- This function relies on the fact that adjwgt is all equal to 1.
-
- \param ctrl stores run state info.
- \param graph is the graph to be split.
- \param ncmps is the number of connected components.
- \param cptr is an array of size ncmps+1 that marks the start and end
- locations of the vertices in cind that make up the respective
- components (i.e., cptr, cind is in CSR format).
- \param cind is an array of size equal to the number of vertices in
- the original graph and stores the vertices that belong to each
- connected component.
-
- \returns an array of subgraphs corresponding to the extracted subgraphs.
-*/
-/*************************************************************************/
-graph_t **SplitGraphOrderCC(ctrl_t *ctrl, graph_t *graph, idx_t ncmps,
- idx_t *cptr, idx_t *cind)
-{
- idx_t i, ii, iii, j, k, l, istart, iend, mypart, nvtxs, snvtxs, snedges;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *label, *where, *bndptr, *bndind;
- idx_t *sxadj, *svwgt, *sadjncy, *sadjwgt, *slabel;
- idx_t *rename;
- idx_t *auxadjncy;
- graph_t **sgraphs;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->SplitTmr));
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- label = graph->label;
- where = graph->where;
- bndptr = graph->bndptr;
- bndind = graph->bndind;
- ASSERT(bndptr != NULL);
-
- /* Go and use bndptr to also mark the boundary nodes in the two partitions */
- for (ii=0; ii<graph->nbnd; ii++) {
- i = bndind[ii];
- for (j=xadj[i]; j<xadj[i+1]; j++)
- bndptr[adjncy[j]] = 1;
- }
-
- rename = iwspacemalloc(ctrl, nvtxs);
-
- sgraphs = (graph_t **)gk_malloc(sizeof(graph_t *)*ncmps, "SplitGraphOrderCC: sgraphs");
-
- /* Go and split the graph a component at a time */
- for (iii=0; iii<ncmps; iii++) {
- irandArrayPermute(cptr[iii+1]-cptr[iii], cind+cptr[iii], cptr[iii+1]-cptr[iii], 0);
- snvtxs = snedges = 0;
- for (j=cptr[iii]; j<cptr[iii+1]; j++) {
- i = cind[j];
- rename[i] = snvtxs++;
- snedges += xadj[i+1]-xadj[i];
- }
-
- sgraphs[iii] = SetupSplitGraph(graph, snvtxs, snedges);
-
- sxadj = sgraphs[iii]->xadj;
- svwgt = sgraphs[iii]->vwgt;
- sadjncy = sgraphs[iii]->adjncy;
- sadjwgt = sgraphs[iii]->adjwgt;
- slabel = sgraphs[iii]->label;
-
- snvtxs = snedges = sxadj[0] = 0;
- for (ii=cptr[iii]; ii<cptr[iii+1]; ii++) {
- i = cind[ii];
-
- istart = xadj[i];
- iend = xadj[i+1];
- if (bndptr[i] == -1) { /* This is an interior vertex */
- auxadjncy = sadjncy + snedges - istart;
- for(j=istart; j<iend; j++)
- auxadjncy[j] = adjncy[j];
- snedges += iend-istart;
- }
- else {
- l = snedges;
- for (j=istart; j<iend; j++) {
- k = adjncy[j];
- if (where[k] != 2)
- sadjncy[l++] = k;
- }
- snedges = l;
- }
-
- svwgt[snvtxs] = vwgt[i];
- slabel[snvtxs] = label[i];
- sxadj[++snvtxs] = snedges;
- }
-
- iset(snedges, 1, sadjwgt);
- for (i=0; i<snedges; i++)
- sadjncy[i] = rename[sadjncy[i]];
-
- sgraphs[iii]->nvtxs = snvtxs;
- sgraphs[iii]->nedges = snedges;
-
- SetupGraph_tvwgt(sgraphs[iii]);
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->SplitTmr));
-
- WCOREPOP;
-
- return sgraphs;
-}
-
-
-/*************************************************************************/
-/*! This function uses MMD to order the graph. The vertices are numbered
- from lastvtx downwards. */
-/*************************************************************************/
-void MMDOrder(ctrl_t *ctrl, graph_t *graph, idx_t *order, idx_t lastvtx)
-{
- idx_t i, j, k, nvtxs, nofsub, firstvtx;
- idx_t *xadj, *adjncy, *label;
- idx_t *perm, *iperm, *head, *qsize, *list, *marker;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- /* Relabel the vertices so that it starts from 1 */
- k = xadj[nvtxs];
- for (i=0; i<k; i++)
- adjncy[i]++;
- for (i=0; i<nvtxs+1; i++)
- xadj[i]++;
-
- perm = iwspacemalloc(ctrl, nvtxs+5);
- iperm = iwspacemalloc(ctrl, nvtxs+5);
- head = iwspacemalloc(ctrl, nvtxs+5);
- qsize = iwspacemalloc(ctrl, nvtxs+5);
- list = iwspacemalloc(ctrl, nvtxs+5);
- marker = iwspacemalloc(ctrl, nvtxs+5);
-
- genmmd(nvtxs, xadj, adjncy, iperm, perm, 1, head, qsize, list, marker, IDX_MAX, &nofsub);
-
- label = graph->label;
- firstvtx = lastvtx-nvtxs;
- for (i=0; i<nvtxs; i++)
- order[label[i]] = firstvtx+iperm[i]-1;
-
- /* Relabel the vertices so that it starts from 0 */
- for (i=0; i<nvtxs+1; i++)
- xadj[i]--;
- k = xadj[nvtxs];
- for (i=0; i<k; i++)
- adjncy[i]--;
-
- WCOREPOP;
-}
-
-
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/options.c b/3rdParty/metis/metis-5.1.0/libmetis/options.c
deleted file mode 100644
index 3bc1ac93c..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/options.c
+++ /dev/null
@@ -1,532 +0,0 @@
-/**
- \file
- \brief This file contains various routines for dealing with options and ctrl_t.
-
- \date Started 5/12/2011
- \author George
- \author Copyright 1997-2011, Regents of the University of Minnesota
- \version\verbatim $Id: options.c 13901 2013-03-24 16:17:03Z karypis $ \endverbatim
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function creates and sets the run parameters (ctrl_t) */
-/*************************************************************************/
-ctrl_t *SetupCtrl(moptype_et optype, idx_t *options, idx_t ncon, idx_t nparts,
- real_t *tpwgts, real_t *ubvec)
-{
- idx_t i, j;
- ctrl_t *ctrl;
-
- ctrl = (ctrl_t *)gk_malloc(sizeof(ctrl_t), "SetupCtrl: ctrl");
-
- memset((void *)ctrl, 0, sizeof(ctrl_t));
-
- switch (optype) {
- case METIS_OP_PMETIS:
- ctrl->objtype = GETOPTION(options, METIS_OPTION_OBJTYPE, METIS_OBJTYPE_CUT);
- ctrl->rtype = METIS_RTYPE_FM;
- ctrl->ncuts = GETOPTION(options, METIS_OPTION_NCUTS, 1);
- ctrl->niter = GETOPTION(options, METIS_OPTION_NITER, 10);
-
- if (ncon == 1) {
- ctrl->iptype = GETOPTION(options, METIS_OPTION_IPTYPE, METIS_IPTYPE_GROW);
- ctrl->ufactor = GETOPTION(options, METIS_OPTION_UFACTOR, PMETIS_DEFAULT_UFACTOR);
- ctrl->CoarsenTo = 20;
- }
- else {
- ctrl->iptype = GETOPTION(options, METIS_OPTION_IPTYPE, METIS_IPTYPE_RANDOM);
- ctrl->ufactor = GETOPTION(options, METIS_OPTION_UFACTOR, MCPMETIS_DEFAULT_UFACTOR);
- ctrl->CoarsenTo = 100;
- }
-
- break;
-
-
- case METIS_OP_KMETIS:
- ctrl->objtype = GETOPTION(options, METIS_OPTION_OBJTYPE, METIS_OBJTYPE_CUT);
- ctrl->iptype = METIS_IPTYPE_METISRB;
- ctrl->rtype = METIS_RTYPE_GREEDY;
- ctrl->ncuts = GETOPTION(options, METIS_OPTION_NCUTS, 1);
- ctrl->niter = GETOPTION(options, METIS_OPTION_NITER, 10);
- ctrl->ufactor = GETOPTION(options, METIS_OPTION_UFACTOR, KMETIS_DEFAULT_UFACTOR);
- ctrl->minconn = GETOPTION(options, METIS_OPTION_MINCONN, 0);
- ctrl->contig = GETOPTION(options, METIS_OPTION_CONTIG, 0);
- break;
-
-
- case METIS_OP_OMETIS:
- ctrl->objtype = GETOPTION(options, METIS_OPTION_OBJTYPE, METIS_OBJTYPE_NODE);
- ctrl->rtype = GETOPTION(options, METIS_OPTION_RTYPE, METIS_RTYPE_SEP1SIDED);
- ctrl->iptype = GETOPTION(options, METIS_OPTION_IPTYPE, METIS_IPTYPE_EDGE);
- ctrl->nseps = GETOPTION(options, METIS_OPTION_NSEPS, 1);
- ctrl->niter = GETOPTION(options, METIS_OPTION_NITER, 10);
- ctrl->ufactor = GETOPTION(options, METIS_OPTION_UFACTOR, OMETIS_DEFAULT_UFACTOR);
- ctrl->compress = GETOPTION(options, METIS_OPTION_COMPRESS, 1);
- ctrl->ccorder = GETOPTION(options, METIS_OPTION_CCORDER, 0);
- ctrl->pfactor = 0.1*GETOPTION(options, METIS_OPTION_PFACTOR, 0);
-
- ctrl->CoarsenTo = 100;
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown optype of %d\n", optype);
- }
-
- /* common options */
- ctrl->ctype = GETOPTION(options, METIS_OPTION_CTYPE, METIS_CTYPE_SHEM);
- ctrl->no2hop = GETOPTION(options, METIS_OPTION_NO2HOP, 0);
- ctrl->seed = GETOPTION(options, METIS_OPTION_SEED, -1);
- ctrl->dbglvl = GETOPTION(options, METIS_OPTION_DBGLVL, 0);
- ctrl->numflag = GETOPTION(options, METIS_OPTION_NUMBERING, 0);
-
- /* set non-option information */
- ctrl->optype = optype;
- ctrl->ncon = ncon;
- ctrl->nparts = nparts;
- ctrl->maxvwgt = ismalloc(ncon, 0, "SetupCtrl: maxvwgt");
-
- /* setup the target partition weights */
- if (ctrl->optype != METIS_OP_OMETIS) {
- ctrl->tpwgts = rmalloc(nparts*ncon, "SetupCtrl: ctrl->tpwgts");
- if (tpwgts) {
- rcopy(nparts*ncon, tpwgts, ctrl->tpwgts);
- }
- else {
- for (i=0; i<nparts; i++) {
- for (j=0; j<ncon; j++)
- ctrl->tpwgts[i*ncon+j] = 1.0/nparts;
- }
- }
- }
- else { /* METIS_OP_OMETIS */
- /* this is required to allow the pijbm to be defined properly for
- the edge-based refinement during initial partitioning */
- ctrl->tpwgts = rsmalloc(2, .5, "SetupCtrl: ctrl->tpwgts");
- }
-
-
- /* setup the ubfactors */
- ctrl->ubfactors = rsmalloc(ctrl->ncon, I2RUBFACTOR(ctrl->ufactor), "SetupCtrl: ubfactors");
- if (ubvec)
- rcopy(ctrl->ncon, ubvec, ctrl->ubfactors);
- for (i=0; i<ctrl->ncon; i++)
- ctrl->ubfactors[i] += 0.0000499;
-
- /* Allocate memory for balance multipliers.
- Note that for PMETIS/OMETIS routines the memory allocated is more
- than required as balance multipliers for 2 parts is sufficient. */
- ctrl->pijbm = rmalloc(nparts*ncon, "SetupCtrl: ctrl->pijbm");
-
- InitRandom(ctrl->seed);
-
- IFSET(ctrl->dbglvl, METIS_DBG_INFO, PrintCtrl(ctrl));
-
- if (!CheckParams(ctrl)) {
- FreeCtrl(&ctrl);
- return NULL;
- }
- else {
- return ctrl;
- }
-}
-
-
-/*************************************************************************/
-/*! Computes the per-partition/constraint balance multipliers */
-/*************************************************************************/
-void SetupKWayBalMultipliers(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j;
-
- for (i=0; i<ctrl->nparts; i++) {
- for (j=0; j<graph->ncon; j++)
- ctrl->pijbm[i*graph->ncon+j] = graph->invtvwgt[j]/ctrl->tpwgts[i*graph->ncon+j];
- }
-}
-
-
-/*************************************************************************/
-/*! Computes the per-partition/constraint balance multipliers */
-/*************************************************************************/
-void Setup2WayBalMultipliers(ctrl_t *ctrl, graph_t *graph, real_t *tpwgts)
-{
- idx_t i, j;
-
- for (i=0; i<2; i++) {
- for (j=0; j<graph->ncon; j++)
- ctrl->pijbm[i*graph->ncon+j] = graph->invtvwgt[j]/tpwgts[i*graph->ncon+j];
- }
-}
-
-
-/*************************************************************************/
-/*! This function prints the various control fields */
-/*************************************************************************/
-void PrintCtrl(ctrl_t *ctrl)
-{
- idx_t i, j, modnum;
-
- printf(" Runtime parameters:\n");
-
- printf(" Objective type: ");
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- printf("METIS_OBJTYPE_CUT\n");
- break;
- case METIS_OBJTYPE_VOL:
- printf("METIS_OBJTYPE_VOL\n");
- break;
- case METIS_OBJTYPE_NODE:
- printf("METIS_OBJTYPE_NODE\n");
- break;
- default:
- printf("Unknown!\n");
- }
-
- printf(" Coarsening type: ");
- switch (ctrl->ctype) {
- case METIS_CTYPE_RM:
- printf("METIS_CTYPE_RM\n");
- break;
- case METIS_CTYPE_SHEM:
- printf("METIS_CTYPE_SHEM\n");
- break;
- default:
- printf("Unknown!\n");
- }
-
- printf(" Initial partitioning type: ");
- switch (ctrl->iptype) {
- case METIS_IPTYPE_GROW:
- printf("METIS_IPTYPE_GROW\n");
- break;
- case METIS_IPTYPE_RANDOM:
- printf("METIS_IPTYPE_RANDOM\n");
- break;
- case METIS_IPTYPE_EDGE:
- printf("METIS_IPTYPE_EDGE\n");
- break;
- case METIS_IPTYPE_NODE:
- printf("METIS_IPTYPE_NODE\n");
- break;
- case METIS_IPTYPE_METISRB:
- printf("METIS_IPTYPE_METISRB\n");
- break;
- default:
- printf("Unknown!\n");
- }
-
- printf(" Refinement type: ");
- switch (ctrl->rtype) {
- case METIS_RTYPE_FM:
- printf("METIS_RTYPE_FM\n");
- break;
- case METIS_RTYPE_GREEDY:
- printf("METIS_RTYPE_GREEDY\n");
- break;
- case METIS_RTYPE_SEP2SIDED:
- printf("METIS_RTYPE_SEP2SIDED\n");
- break;
- case METIS_RTYPE_SEP1SIDED:
- printf("METIS_RTYPE_SEP1SIDED\n");
- break;
- default:
- printf("Unknown!\n");
- }
-
- printf(" Perform a 2-hop matching: %s\n", (ctrl->no2hop ? "Yes" : "No"));
-
- printf(" Number of balancing constraints: %"PRIDX"\n", ctrl->ncon);
- printf(" Number of refinement iterations: %"PRIDX"\n", ctrl->niter);
- printf(" Random number seed: %"PRIDX"\n", ctrl->seed);
-
- if (ctrl->optype == METIS_OP_OMETIS) {
- printf(" Number of separators: %"PRIDX"\n", ctrl->nseps);
- printf(" Compress graph prior to ordering: %s\n", (ctrl->compress ? "Yes" : "No"));
- printf(" Detect & order connected components separately: %s\n", (ctrl->ccorder ? "Yes" : "No"));
- printf(" Prunning factor for high degree vertices: %"PRREAL"\n", ctrl->pfactor);
- }
- else {
- printf(" Number of partitions: %"PRIDX"\n", ctrl->nparts);
- printf(" Number of cuts: %"PRIDX"\n", ctrl->ncuts);
- printf(" User-supplied ufactor: %"PRIDX"\n", ctrl->ufactor);
-
- if (ctrl->optype == METIS_OP_KMETIS) {
- printf(" Minimize connectivity: %s\n", (ctrl->minconn ? "Yes" : "No"));
- printf(" Create contigous partitions: %s\n", (ctrl->contig ? "Yes" : "No"));
- }
-
- modnum = (ctrl->ncon==1 ? 5 : (ctrl->ncon==2 ? 3 : (ctrl->ncon==3 ? 2 : 1)));
- printf(" Target partition weights: ");
- for (i=0; i<ctrl->nparts; i++) {
- if (i%modnum == 0)
- printf("\n ");
- printf("%4"PRIDX"=[", i);
- for (j=0; j<ctrl->ncon; j++)
- printf("%s%.2e", (j==0 ? "" : " "), (double)ctrl->tpwgts[i*ctrl->ncon+j]);
- printf("]");
- }
- printf("\n");
- }
-
- printf(" Allowed maximum load imbalance: ");
- for (i=0; i<ctrl->ncon; i++)
- printf("%.3"PRREAL" ", ctrl->ubfactors[i]);
- printf("\n");
-
- printf("\n");
-}
-
-
-/*************************************************************************/
-/*! This function checks the validity of user-supplied parameters */
-/*************************************************************************/
-int CheckParams(ctrl_t *ctrl)
-{
- idx_t i, j;
- real_t sum;
- mdbglvl_et dbglvl=METIS_DBG_INFO;
-
- switch (ctrl->optype) {
- case METIS_OP_PMETIS:
- if (ctrl->objtype != METIS_OBJTYPE_CUT) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect objective type.\n"));
- return 0;
- }
- if (ctrl->ctype != METIS_CTYPE_RM && ctrl->ctype != METIS_CTYPE_SHEM) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect coarsening scheme.\n"));
- return 0;
- }
- if (ctrl->iptype != METIS_IPTYPE_GROW && ctrl->iptype != METIS_IPTYPE_RANDOM) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect initial partitioning scheme.\n"));
- return 0;
- }
- if (ctrl->rtype != METIS_RTYPE_FM) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect refinement scheme.\n"));
- return 0;
- }
- if (ctrl->ncuts <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ncuts.\n"));
- return 0;
- }
- if (ctrl->niter <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect niter.\n"));
- return 0;
- }
- if (ctrl->ufactor <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ufactor.\n"));
- return 0;
- }
- if (ctrl->numflag != 0 && ctrl->numflag != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect numflag.\n"));
- return 0;
- }
- if (ctrl->nparts <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect nparts.\n"));
- return 0;
- }
- if (ctrl->ncon <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ncon.\n"));
- return 0;
- }
-
- for (i=0; i<ctrl->ncon; i++) {
- sum = rsum(ctrl->nparts, ctrl->tpwgts+i, ctrl->ncon);
- if (sum < 0.99 || sum > 1.01) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect sum of %"PRREAL" for tpwgts for constraint %"PRIDX".\n", sum, i));
- return 0;
- }
- }
- for (i=0; i<ctrl->ncon; i++) {
- for (j=0; j<ctrl->nparts; j++) {
- if (ctrl->tpwgts[j*ctrl->ncon+i] <= 0.0) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect tpwgts for partition %"PRIDX" and constraint %"PRIDX".\n", j, i));
- return 0;
- }
- }
- }
-
- for (i=0; i<ctrl->ncon; i++) {
- if (ctrl->ubfactors[i] <= 1.0) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect ubfactor for constraint %"PRIDX".\n", i));
- return 0;
- }
- }
-
- break;
-
- case METIS_OP_KMETIS:
- if (ctrl->objtype != METIS_OBJTYPE_CUT && ctrl->objtype != METIS_OBJTYPE_VOL) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect objective type.\n"));
- return 0;
- }
- if (ctrl->ctype != METIS_CTYPE_RM && ctrl->ctype != METIS_CTYPE_SHEM) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect coarsening scheme.\n"));
- return 0;
- }
- if (ctrl->iptype != METIS_IPTYPE_METISRB) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect initial partitioning scheme.\n"));
- return 0;
- }
- if (ctrl->rtype != METIS_RTYPE_GREEDY) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect refinement scheme.\n"));
- return 0;
- }
- if (ctrl->ncuts <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ncuts.\n"));
- return 0;
- }
- if (ctrl->niter <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect niter.\n"));
- return 0;
- }
- if (ctrl->ufactor <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ufactor.\n"));
- return 0;
- }
- if (ctrl->numflag != 0 && ctrl->numflag != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect numflag.\n"));
- return 0;
- }
- if (ctrl->nparts <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect nparts.\n"));
- return 0;
- }
- if (ctrl->ncon <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ncon.\n"));
- return 0;
- }
- if (ctrl->contig != 0 && ctrl->contig != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect contig.\n"));
- return 0;
- }
- if (ctrl->minconn != 0 && ctrl->minconn != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect minconn.\n"));
- return 0;
- }
-
- for (i=0; i<ctrl->ncon; i++) {
- sum = rsum(ctrl->nparts, ctrl->tpwgts+i, ctrl->ncon);
- if (sum < 0.99 || sum > 1.01) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect sum of %"PRREAL" for tpwgts for constraint %"PRIDX".\n", sum, i));
- return 0;
- }
- }
- for (i=0; i<ctrl->ncon; i++) {
- for (j=0; j<ctrl->nparts; j++) {
- if (ctrl->tpwgts[j*ctrl->ncon+i] <= 0.0) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect tpwgts for partition %"PRIDX" and constraint %"PRIDX".\n", j, i));
- return 0;
- }
- }
- }
-
- for (i=0; i<ctrl->ncon; i++) {
- if (ctrl->ubfactors[i] <= 1.0) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect ubfactor for constraint %"PRIDX".\n", i));
- return 0;
- }
- }
-
- break;
-
-
-
- case METIS_OP_OMETIS:
- if (ctrl->objtype != METIS_OBJTYPE_NODE) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect objective type.\n"));
- return 0;
- }
- if (ctrl->ctype != METIS_CTYPE_RM && ctrl->ctype != METIS_CTYPE_SHEM) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect coarsening scheme.\n"));
- return 0;
- }
- if (ctrl->iptype != METIS_IPTYPE_EDGE && ctrl->iptype != METIS_IPTYPE_NODE) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect initial partitioning scheme.\n"));
- return 0;
- }
- if (ctrl->rtype != METIS_RTYPE_SEP1SIDED && ctrl->rtype != METIS_RTYPE_SEP2SIDED) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect refinement scheme.\n"));
- return 0;
- }
- if (ctrl->nseps <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect nseps.\n"));
- return 0;
- }
- if (ctrl->niter <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect niter.\n"));
- return 0;
- }
- if (ctrl->ufactor <= 0) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ufactor.\n"));
- return 0;
- }
- if (ctrl->numflag != 0 && ctrl->numflag != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect numflag.\n"));
- return 0;
- }
- if (ctrl->nparts != 3) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect nparts.\n"));
- return 0;
- }
- if (ctrl->ncon != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ncon.\n"));
- return 0;
- }
- if (ctrl->compress != 0 && ctrl->compress != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect compress.\n"));
- return 0;
- }
- if (ctrl->ccorder != 0 && ctrl->ccorder != 1) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect ccorder.\n"));
- return 0;
- }
- if (ctrl->pfactor < 0.0 ) {
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect pfactor.\n"));
- return 0;
- }
-
- for (i=0; i<ctrl->ncon; i++) {
- if (ctrl->ubfactors[i] <= 1.0) {
- IFSET(dbglvl, METIS_DBG_INFO,
- printf("Input Error: Incorrect ubfactor for constraint %"PRIDX".\n", i));
- return 0;
- }
- }
-
- break;
-
- default:
- IFSET(dbglvl, METIS_DBG_INFO, printf("Input Error: Incorrect optype\n"));
- return 0;
- }
-
- return 1;
-}
-
-
-/*************************************************************************/
-/*! This function frees the memory associated with a ctrl_t */
-/*************************************************************************/
-void FreeCtrl(ctrl_t **r_ctrl)
-{
- ctrl_t *ctrl = *r_ctrl;
-
- FreeWorkSpace(ctrl);
-
- gk_free((void **)&ctrl->tpwgts, &ctrl->pijbm,
- &ctrl->ubfactors, &ctrl->maxvwgt, &ctrl, LTERM);
-
- *r_ctrl = NULL;
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/parmetis.c b/3rdParty/metis/metis-5.1.0/libmetis/parmetis.c
deleted file mode 100644
index 631d811bc..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/parmetis.c
+++ /dev/null
@@ -1,723 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * parmetis.c
- *
- * This file contains top level routines that are used by ParMETIS
- *
- * Started 10/14/97
- * George
- *
- * $Id: parmetis.c 10481 2011-07-05 18:01:23Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point for the node ND code for ParMETIS.
- The difference between this routine and the standard METIS_NodeND are
- the following
-
- - It performs at least log2(npes) levels of nested dissection.
- - It stores the size of the log2(npes) top-level separators in the
- sizes array.
-*/
-/*************************************************************************/
-int METIS_NodeNDP(idx_t nvtxs, idx_t *xadj, idx_t *adjncy, idx_t *vwgt,
- idx_t npes, idx_t *options, idx_t *perm, idx_t *iperm, idx_t *sizes)
-{
- idx_t i, ii, j, l, nnvtxs=0;
- graph_t *graph;
- ctrl_t *ctrl;
- idx_t *cptr, *cind;
-
- ctrl = SetupCtrl(METIS_OP_OMETIS, options, 1, 3, NULL, NULL);
- if (!ctrl) return METIS_ERROR_INPUT;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, InitTimers(ctrl));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->TotalTmr));
-
- /* compress the graph; not that compression only happens if not prunning
- has taken place. */
- if (ctrl->compress) {
- cptr = imalloc(nvtxs+1, "OMETIS: cptr");
- cind = imalloc(nvtxs, "OMETIS: cind");
-
- graph = CompressGraph(ctrl, nvtxs, xadj, adjncy, vwgt, cptr, cind);
- if (graph == NULL) {
- /* if there was no compression, cleanup the compress flag */
- gk_free((void **)&cptr, &cind, LTERM);
- ctrl->compress = 0;
- }
- else {
- nnvtxs = graph->nvtxs;
- }
- }
-
- /* if no compression, setup the graph in the normal way. */
- if (ctrl->compress == 0)
- graph = SetupGraph(ctrl, nvtxs, 1, xadj, adjncy, vwgt, NULL, NULL);
-
-
- /* allocate workspace memory */
- AllocateWorkSpace(ctrl, graph);
-
-
- /* do the nested dissection ordering */
- iset(2*npes-1, 0, sizes);
- MlevelNestedDissectionP(ctrl, graph, iperm, graph->nvtxs, npes, 0, sizes);
-
-
- /* Uncompress the ordering */
- if (ctrl->compress) {
- /* construct perm from iperm */
- for (i=0; i<nnvtxs; i++)
- perm[iperm[i]] = i;
- for (l=ii=0; ii<nnvtxs; ii++) {
- i = perm[ii];
- for (j=cptr[i]; j<cptr[i+1]; j++)
- iperm[cind[j]] = l++;
- }
-
- gk_free((void **)&cptr, &cind, LTERM);
- }
-
-
- for (i=0; i<nvtxs; i++)
- perm[iperm[i]] = i;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->TotalTmr));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, PrintTimers(ctrl));
-
- /* clean up */
- FreeCtrl(&ctrl);
-
- return METIS_OK;
-}
-
-
-/*************************************************************************/
-/*! This function is similar to MlevelNestedDissection with the difference
- that it also records separator sizes for the top log2(npes) levels */
-/**************************************************************************/
-void MlevelNestedDissectionP(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx, idx_t npes, idx_t cpos, idx_t *sizes)
-{
- idx_t i, j, nvtxs, nbnd;
- idx_t *label, *bndind;
- graph_t *lgraph, *rgraph;
-
- nvtxs = graph->nvtxs;
-
- if (nvtxs == 0) {
- FreeGraph(&graph);
- return;
- }
-
- MlevelNodeBisectionMultiple(ctrl, graph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_SEPINFO,
- printf("Nvtxs: %6"PRIDX", [%6"PRIDX" %6"PRIDX" %6"PRIDX"]\n",
- graph->nvtxs, graph->pwgts[0], graph->pwgts[1], graph->pwgts[2]));
-
- if (cpos < npes-1) {
- sizes[2*npes-2-cpos] = graph->pwgts[2];
- sizes[2*npes-2-(2*cpos+1)] = graph->pwgts[1];
- sizes[2*npes-2-(2*cpos+2)] = graph->pwgts[0];
- }
-
- /* Order the nodes in the separator */
- nbnd = graph->nbnd;
- bndind = graph->bndind;
- label = graph->label;
- for (i=0; i<nbnd; i++)
- order[label[bndind[i]]] = --lastvtx;
-
- SplitGraphOrder(ctrl, graph, &lgraph, &rgraph);
-
- /* Free the memory of the top level graph */
- FreeGraph(&graph);
-
- if ((lgraph->nvtxs > MMDSWITCH || 2*cpos+2 < npes-1) && lgraph->nedges > 0)
- MlevelNestedDissectionP(ctrl, lgraph, order, lastvtx-rgraph->nvtxs, npes, 2*cpos+2, sizes);
- else {
- MMDOrder(ctrl, lgraph, order, lastvtx-rgraph->nvtxs);
- FreeGraph(&lgraph);
- }
- if ((rgraph->nvtxs > MMDSWITCH || 2*cpos+1 < npes-1) && rgraph->nedges > 0)
- MlevelNestedDissectionP(ctrl, rgraph, order, lastvtx, npes, 2*cpos+1, sizes);
- else {
- MMDOrder(ctrl, rgraph, order, lastvtx);
- FreeGraph(&rgraph);
- }
-}
-
-
-/*************************************************************************/
-/*! This function bisects a graph by computing a vertex separator */
-/**************************************************************************/
-int METIS_ComputeVertexSeparator(idx_t *nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *options, idx_t *r_sepsize, idx_t *part)
-{
- idx_t i, j;
- graph_t *graph;
- ctrl_t *ctrl;
-
- if ((ctrl = SetupCtrl(METIS_OP_OMETIS, options, 1, 3, NULL, NULL)) == NULL)
- return METIS_ERROR_INPUT;
-
- InitRandom(ctrl->seed);
-
- graph = SetupGraph(ctrl, *nvtxs, 1, xadj, adjncy, vwgt, NULL, NULL);
-
- AllocateWorkSpace(ctrl, graph);
-
- /*============================================================
- * Perform the bisection
- *============================================================*/
- ctrl->CoarsenTo = 100;
-
- MlevelNodeBisectionMultiple(ctrl, graph);
-
- *r_sepsize = graph->pwgts[2];
- icopy(*nvtxs, graph->where, part);
-
- FreeGraph(&graph);
-
- FreeCtrl(&ctrl);
-
- return METIS_OK;
-}
-
-
-/*************************************************************************/
-/*! This function is the entry point of a node-based separator refinement
- of the nodes with an hmarker[] of 0. */
-/*************************************************************************/
-int METIS_NodeRefine(idx_t nvtxs, idx_t *xadj, idx_t *vwgt, idx_t *adjncy,
- idx_t *where, idx_t *hmarker, real_t ubfactor)
-{
- graph_t *graph;
- ctrl_t *ctrl;
-
- /* set up the run time parameters */
- ctrl = SetupCtrl(METIS_OP_OMETIS, NULL, 1, 3, NULL, NULL);
- if (!ctrl) return METIS_ERROR_INPUT;
-
- /* set up the graph */
- graph = SetupGraph(ctrl, nvtxs, 1, xadj, adjncy, vwgt, NULL, NULL);
-
- /* allocate workspace memory */
- AllocateWorkSpace(ctrl, graph);
-
- /* set up the memory and the input partition */
- Allocate2WayNodePartitionMemory(ctrl, graph);
- icopy(nvtxs, where, graph->where);
-
- Compute2WayNodePartitionParams(ctrl, graph);
-
- FM_2WayNodeRefine1SidedP(ctrl, graph, hmarker, ubfactor, 10);
- /* FM_2WayNodeRefine2SidedP(ctrl, graph, hmarker, ubfactor, 10); */
-
- icopy(nvtxs, graph->where, where);
-
- FreeGraph(&graph);
- FreeCtrl(&ctrl);
-
- return METIS_OK;
-}
-
-
-/*************************************************************************/
-/*! This function performs a node-based 1-sided FM refinement that moves
- only nodes whose hmarker[] == -1. It is used by Parmetis. */
-/*************************************************************************/
-void FM_2WayNodeRefine1SidedP(ctrl_t *ctrl, graph_t *graph,
- idx_t *hmarker, real_t ubfactor, idx_t npasses)
-{
- idx_t i, ii, j, k, jj, kk, nvtxs, nbnd, nswaps, nmind, nbad, qsize;
- idx_t *xadj, *vwgt, *adjncy, *where, *pwgts, *edegrees, *bndind, *bndptr;
- idx_t *mptr, *mind, *swaps, *inqueue;
- rpq_t *queue;
- nrinfo_t *rinfo;
- idx_t higain, oldgain, mincut, initcut, mincutorder;
- idx_t pass, from, to, limit;
- idx_t badmaxpwgt, mindiff, newdiff;
-
- WCOREPUSH;
-
- ASSERT(graph->mincut == graph->pwgts[2]);
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
- pwgts = graph->pwgts;
- rinfo = graph->nrinfo;
-
- queue = rpqCreate(nvtxs);
-
- inqueue = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
- swaps = iwspacemalloc(ctrl, nvtxs);
- mptr = iwspacemalloc(ctrl, nvtxs+1);
- mind = iwspacemalloc(ctrl, 2*nvtxs);
-
- badmaxpwgt = (idx_t)(ubfactor*gk_max(pwgts[0], pwgts[1]));
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions-N1: [%6"PRIDX" %6"PRIDX"] Nv-Nb[%6"PRIDX" %6"PRIDX"] "
- "MaxPwgt[%6"PRIDX"]. ISep: %6"PRIDX"\n",
- pwgts[0], pwgts[1], graph->nvtxs, graph->nbnd, badmaxpwgt,
- graph->mincut));
-
- to = (pwgts[0] < pwgts[1] ? 1 : 0);
- for (pass=0; pass<npasses; pass++) {
- from = to;
- to = (from+1)%2;
-
- rpqReset(queue);
-
- mincutorder = -1;
- initcut = mincut = graph->mincut;
- nbnd = graph->nbnd;
-
- /* use the swaps array in place of the traditional perm array to save memory */
- irandArrayPermute(nbnd, swaps, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[swaps[ii]];
- ASSERT(where[i] == 2);
- if (hmarker[i] == -1 || hmarker[i] == to) {
- rpqInsert(queue, i, vwgt[i]-rinfo[i].edegrees[from]);
- inqueue[i] = pass;
- }
- }
- qsize = rpqLength(queue);
-
- ASSERT(CheckNodeBnd(graph, nbnd));
- ASSERT(CheckNodePartitionParams(graph));
-
- limit = nbnd;
-
- /******************************************************
- * Get into the FM loop
- *******************************************************/
- mptr[0] = nmind = nbad = 0;
- mindiff = abs(pwgts[0]-pwgts[1]);
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if ((higain = rpqGetTop(queue)) == -1)
- break;
-
- ASSERT(bndptr[higain] != -1);
-
- /* The following check is to ensure we break out if there is a posibility
- of over-running the mind array. */
- if (nmind + xadj[higain+1]-xadj[higain] >= 2*nvtxs-1)
- break;
-
- inqueue[higain] = -1;
-
- if (pwgts[to]+vwgt[higain] > badmaxpwgt) { /* Skip this vertex */
- if (nbad++ > limit)
- break;
- else {
- nswaps--;
- continue;
- }
- }
-
- pwgts[2] -= (vwgt[higain]-rinfo[higain].edegrees[from]);
-
- newdiff = abs(pwgts[to]+vwgt[higain] - (pwgts[from]-rinfo[higain].edegrees[from]));
- if (pwgts[2] < mincut || (pwgts[2] == mincut && newdiff < mindiff)) {
- mincut = pwgts[2];
- mincutorder = nswaps;
- mindiff = newdiff;
- nbad = 0;
- }
- else {
- if (nbad++ > limit) {
- pwgts[2] += (vwgt[higain]-rinfo[higain].edegrees[from]);
- break; /* No further improvement, break out */
- }
- }
-
- BNDDelete(nbnd, bndind, bndptr, higain);
- pwgts[to] += vwgt[higain];
- where[higain] = to;
- swaps[nswaps] = higain;
-
-
- /**********************************************************
- * Update the degrees of the affected nodes
- ***********************************************************/
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2) { /* For the in-separator vertices modify their edegree[to] */
- rinfo[k].edegrees[to] += vwgt[higain];
- }
- else if (where[k] == from) { /* This vertex is pulled into the separator */
- ASSERTP(bndptr[k] == -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", k, bndptr[k], where[k]));
- BNDInsert(nbnd, bndind, bndptr, k);
-
- mind[nmind++] = k; /* Keep track for rollback */
- where[k] = 2;
- pwgts[from] -= vwgt[k];
-
- edegrees = rinfo[k].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] != 2)
- edegrees[where[kk]] += vwgt[kk];
- else {
- oldgain = vwgt[kk]-rinfo[kk].edegrees[from];
- rinfo[kk].edegrees[from] -= vwgt[k];
-
- /* Update the gain of this node if it was not skipped */
- if (inqueue[kk] == pass)
- rpqUpdate(queue, kk, oldgain+vwgt[k]);
- }
- }
-
- /* Insert the new vertex into the priority queue. Safe due to one-sided moves */
- if (hmarker[k] == -1 || hmarker[k] == to) {
- rpqInsert(queue, k, vwgt[k]-edegrees[from]);
- inqueue[k] = pass;
- }
- }
- }
- mptr[nswaps+1] = nmind;
-
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" to %3"PRIDX", Gain: %5"PRIDX" [%5"PRIDX"] \t[%5"PRIDX" %5"PRIDX" %5"PRIDX"] [%3"PRIDX" %2"PRIDX"]\n",
- higain, to, (vwgt[higain]-rinfo[higain].edegrees[from]),
- vwgt[higain], pwgts[0], pwgts[1], pwgts[2], nswaps, limit));
-
- }
-
-
- /****************************************************************
- * Roll back computation
- *****************************************************************/
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- ASSERT(CheckNodePartitionParams(graph));
- ASSERT(where[higain] == to);
-
- INC_DEC(pwgts[2], pwgts[to], vwgt[higain]);
- where[higain] = 2;
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- edegrees = rinfo[higain].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2)
- rinfo[k].edegrees[to] -= vwgt[higain];
- else
- edegrees[where[k]] += vwgt[k];
- }
-
- /* Push nodes out of the separator */
- for (j=mptr[nswaps]; j<mptr[nswaps+1]; j++) {
- k = mind[j];
- ASSERT(where[k] == 2);
- where[k] = from;
- INC_DEC(pwgts[from], pwgts[2], vwgt[k]);
- BNDDelete(nbnd, bndind, bndptr, k);
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] == 2)
- rinfo[kk].edegrees[from] += vwgt[k];
- }
- }
- }
-
- ASSERT(mincut == pwgts[2]);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum sep: %6"PRIDX" at %5"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX", QSIZE: %6"PRIDX"\n",
- mincut, mincutorder, pwgts[0], pwgts[1], nbnd, qsize));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- if (pass%2 == 1 && (mincutorder == -1 || mincut >= initcut))
- break;
- }
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function performs a node-based (two-sided) FM refinement that
- moves only nodes whose hmarker[] == -1. It is used by Parmetis. */
-/*************************************************************************/
-void FM_2WayNodeRefine2SidedP(ctrl_t *ctrl, graph_t *graph,
- idx_t *hmarker, real_t ubfactor, idx_t npasses)
-{
- idx_t i, ii, j, k, jj, kk, nvtxs, nbnd, nswaps, nmind;
- idx_t *xadj, *vwgt, *adjncy, *where, *pwgts, *edegrees, *bndind, *bndptr;
- idx_t *mptr, *mind, *moved, *swaps;
- rpq_t *queues[2];
- nrinfo_t *rinfo;
- idx_t higain, oldgain, mincut, initcut, mincutorder;
- idx_t pass, to, other, limit;
- idx_t badmaxpwgt, mindiff, newdiff;
- idx_t u[2], g[2];
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
- pwgts = graph->pwgts;
- rinfo = graph->nrinfo;
-
- queues[0] = rpqCreate(nvtxs);
- queues[1] = rpqCreate(nvtxs);
-
- moved = iwspacemalloc(ctrl, nvtxs);
- swaps = iwspacemalloc(ctrl, nvtxs);
- mptr = iwspacemalloc(ctrl, nvtxs+1);
- mind = iwspacemalloc(ctrl, 2*nvtxs);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions: [%6"PRIDX" %6"PRIDX"] Nv-Nb[%6"PRIDX" %6"PRIDX"]. ISep: %6"PRIDX"\n", pwgts[0], pwgts[1], graph->nvtxs, graph->nbnd, graph->mincut));
-
- badmaxpwgt = (idx_t)(ubfactor*gk_max(pwgts[0], pwgts[1]));
-
- for (pass=0; pass<npasses; pass++) {
- iset(nvtxs, -1, moved);
- rpqReset(queues[0]);
- rpqReset(queues[1]);
-
- mincutorder = -1;
- initcut = mincut = graph->mincut;
- nbnd = graph->nbnd;
-
- /* use the swaps array in place of the traditional perm array to save memory */
- irandArrayPermute(nbnd, swaps, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[swaps[ii]];
- ASSERT(where[i] == 2);
- if (hmarker[i] == -1) {
- rpqInsert(queues[0], i, vwgt[i]-rinfo[i].edegrees[1]);
- rpqInsert(queues[1], i, vwgt[i]-rinfo[i].edegrees[0]);
- moved[i] = -5;
- }
- else if (hmarker[i] != 2) {
- rpqInsert(queues[hmarker[i]], i, vwgt[i]-rinfo[i].edegrees[(hmarker[i]+1)%2]);
- moved[i] = -(10+hmarker[i]);
- }
- }
-
- ASSERT(CheckNodeBnd(graph, nbnd));
- ASSERT(CheckNodePartitionParams(graph));
-
- limit = nbnd;
-
- /******************************************************
- * Get into the FM loop
- *******************************************************/
- mptr[0] = nmind = 0;
- mindiff = abs(pwgts[0]-pwgts[1]);
- to = (pwgts[0] < pwgts[1] ? 0 : 1);
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- u[0] = rpqSeeTopVal(queues[0]);
- u[1] = rpqSeeTopVal(queues[1]);
- if (u[0] != -1 && u[1] != -1) {
- g[0] = vwgt[u[0]]-rinfo[u[0]].edegrees[1];
- g[1] = vwgt[u[1]]-rinfo[u[1]].edegrees[0];
-
- to = (g[0] > g[1] ? 0 : (g[0] < g[1] ? 1 : pass%2));
-
- if (pwgts[to]+vwgt[u[to]] > badmaxpwgt)
- to = (to+1)%2;
- }
- else if (u[0] == -1 && u[1] == -1) {
- break;
- }
- else if (u[0] != -1 && pwgts[0]+vwgt[u[0]] <= badmaxpwgt) {
- to = 0;
- }
- else if (u[1] != -1 && pwgts[1]+vwgt[u[1]] <= badmaxpwgt) {
- to = 1;
- }
- else
- break;
-
- other = (to+1)%2;
-
- higain = rpqGetTop(queues[to]);
-
- /* Delete its matching entry in the other queue */
- if (moved[higain] == -5)
- rpqDelete(queues[other], higain);
-
- ASSERT(bndptr[higain] != -1);
-
- /* The following check is to ensure we break out if there is a posibility
- of over-running the mind array. */
- if (nmind + xadj[higain+1]-xadj[higain] >= 2*nvtxs-1)
- break;
-
- pwgts[2] -= (vwgt[higain]-rinfo[higain].edegrees[other]);
-
- newdiff = abs(pwgts[to]+vwgt[higain] - (pwgts[other]-rinfo[higain].edegrees[other]));
- if (pwgts[2] < mincut || (pwgts[2] == mincut && newdiff < mindiff)) {
- mincut = pwgts[2];
- mincutorder = nswaps;
- mindiff = newdiff;
- }
- else {
- if (nswaps - mincutorder > limit) {
- pwgts[2] += (vwgt[higain]-rinfo[higain].edegrees[other]);
- break; /* No further improvement, break out */
- }
- }
-
- BNDDelete(nbnd, bndind, bndptr, higain);
- pwgts[to] += vwgt[higain];
- where[higain] = to;
- moved[higain] = nswaps;
- swaps[nswaps] = higain;
-
-
- /**********************************************************
- * Update the degrees of the affected nodes
- ***********************************************************/
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2) { /* For the in-separator vertices modify their edegree[to] */
- oldgain = vwgt[k]-rinfo[k].edegrees[to];
- rinfo[k].edegrees[to] += vwgt[higain];
- if (moved[k] == -5 || moved[k] == -(10+other))
- rpqUpdate(queues[other], k, oldgain-vwgt[higain]);
- }
- else if (where[k] == other) { /* This vertex is pulled into the separator */
- ASSERTP(bndptr[k] == -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", k, bndptr[k], where[k]));
- BNDInsert(nbnd, bndind, bndptr, k);
-
- mind[nmind++] = k; /* Keep track for rollback */
- where[k] = 2;
- pwgts[other] -= vwgt[k];
-
- edegrees = rinfo[k].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] != 2)
- edegrees[where[kk]] += vwgt[kk];
- else {
- oldgain = vwgt[kk]-rinfo[kk].edegrees[other];
- rinfo[kk].edegrees[other] -= vwgt[k];
- if (moved[kk] == -5 || moved[kk] == -(10+to))
- rpqUpdate(queues[to], kk, oldgain+vwgt[k]);
- }
- }
-
- /* Insert the new vertex into the priority queue (if it has not been moved). */
- if (moved[k] == -1 && (hmarker[k] == -1 || hmarker[k] == to)) {
- rpqInsert(queues[to], k, vwgt[k]-edegrees[other]);
- moved[k] = -(10+to);
- }
-#ifdef FULLMOVES /* this does not work as well as the above partial one */
- if (moved[k] == -1) {
- if (hmarker[k] == -1) {
- rpqInsert(queues[0], k, vwgt[k]-edegrees[1]);
- rpqInsert(queues[1], k, vwgt[k]-edegrees[0]);
- moved[k] = -5;
- }
- else if (hmarker[k] != 2) {
- rpqInsert(queues[hmarker[k]], k, vwgt[k]-edegrees[(hmarker[k]+1)%2]);
- moved[k] = -(10+hmarker[k]);
- }
- }
-#endif
- }
- }
- mptr[nswaps+1] = nmind;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" to %3"PRIDX", Gain: %5"PRIDX" [%5"PRIDX"] "
- "[%4"PRIDX" %4"PRIDX"] \t[%5"PRIDX" %5"PRIDX" %5"PRIDX"]\n",
- higain, to, g[to], g[other], vwgt[u[to]], vwgt[u[other]],
- pwgts[0], pwgts[1], pwgts[2]));
-
- }
-
-
- /****************************************************************
- * Roll back computation
- *****************************************************************/
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- ASSERT(CheckNodePartitionParams(graph));
-
- to = where[higain];
- other = (to+1)%2;
- INC_DEC(pwgts[2], pwgts[to], vwgt[higain]);
- where[higain] = 2;
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- edegrees = rinfo[higain].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2)
- rinfo[k].edegrees[to] -= vwgt[higain];
- else
- edegrees[where[k]] += vwgt[k];
- }
-
- /* Push nodes out of the separator */
- for (j=mptr[nswaps]; j<mptr[nswaps+1]; j++) {
- k = mind[j];
- ASSERT(where[k] == 2);
- where[k] = other;
- INC_DEC(pwgts[other], pwgts[2], vwgt[k]);
- BNDDelete(nbnd, bndind, bndptr, k);
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] == 2)
- rinfo[kk].edegrees[other] += vwgt[k];
- }
- }
- }
-
- ASSERT(mincut == pwgts[2]);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum sep: %6"PRIDX" at %5"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", mincut, mincutorder, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- if (mincutorder == -1 || mincut >= initcut)
- break;
- }
-
- rpqDestroy(queues[0]);
- rpqDestroy(queues[1]);
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/pmetis.c b/3rdParty/metis/metis-5.1.0/libmetis/pmetis.c
deleted file mode 100644
index d32e84921..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/pmetis.c
+++ /dev/null
@@ -1,387 +0,0 @@
-/**
-\file
-\brief This file contains the top level routines for the multilevel recursive bisection
- algorithm PMETIS.
-
-\date Started 7/24/1997
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version\verbatim $Id: pmetis.c 10513 2011-07-07 22:06:03Z karypis $ \endverbatim
-*/
-
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! \ingroup api
- \brief Recursive partitioning routine.
-
- This function computes a partitioning of a graph based on multilevel
- recursive bisection. It can be used to partition a graph into \e k
- parts. The objective of the partitioning is to minimize the edgecut
- subject to one or more balancing constraints.
-
- \param[in] nvtxs is the number of vertices in the graph.
-
- \param[in] ncon is the number of balancing constraints. For the standard
- partitioning problem in which each vertex is either unweighted
- or has a single weight, ncon should be 1.
-
- \param[in] xadj is an array of size nvtxs+1 used to specify the starting
- positions of the adjacency structure of the vertices in the
- adjncy array.
-
- \param[in] adjncy is an array of size to the sum of the degrees of the
- graph that stores for each vertex the set of vertices that
- is adjancent to.
-
- \param[in] vwgt is an array of size nvtxs*ncon that stores the weights
- of the vertices for each constraint. The ncon weights for the
- ith vertex are stored in the ncon consecutive locations starting
- at vwgt[i*ncon]. When ncon==1, a NULL value can be passed indicating
- that all the vertices in the graph have the same weight.
-
- \param[in] adjwgt is an array of size equal to adjncy, specifying the weight
- for each edge (i.e., adjwgt[j] corresponds to the weight of the
- edge stored in adjncy[j]).
- A NULL value can be passed indicating that all the edges in the
- graph have the same weight.
-
- \param[in] nparts is the number of desired partitions.
-
- \param[in] tpwgts is an array of size nparts*ncon that specifies the
- desired weight for each part and constraint. The \e{target partition
- weight} for the ith part and jth constraint is specified
- at tpwgts[i*ncon+j] (the numbering of i and j starts from 0).
- For each constraint, the sum of the tpwgts[] entries must be
- 1.0 (i.e., \f$ \sum_i tpwgts[i*ncon+j] = 1.0 \f$).
- A NULL value can be passed indicating that the graph should
- be equally divided among the parts.
-
- \param[in] ubvec is an array of size ncon that specifies the allowed
- load imbalance tolerance for each constraint.
- For the ith part and jth constraint the allowed weight is the
- ubvec[j]*tpwgts[i*ncon+j] fraction of the jth's constraint total
- weight. The load imbalances must be greater than 1.0.
- A NULL value can be passed indicating that the load imbalance
- tolerance for each constraint should be 1.001 (for ncon==1)
- or 1.01 (for ncon>1).
-
- \params[in] options is the array for passing additional parameters
- in order to customize the behaviour of the partitioning
- algorithm.
-
- \params[out] edgecut stores the cut of the partitioning.
-
- \params[out] part is an array of size nvtxs used to store the
- computed partitioning. The partition number for the ith
- vertex is stored in part[i]. Based on the numflag parameter,
- the numbering of the parts starts from either 0 or 1.
-
-
- \returns
- \retval METIS_OK indicates that the function returned normally.
- \retval METIS_ERROR_INPUT indicates an input error.
- \retval METIS_ERROR_MEMORY indicates that it could not allocate
- the required memory.
-
-*/
-/*************************************************************************/
-int METIS_PartGraphRecursive(idx_t *nvtxs, idx_t *ncon, idx_t *xadj,
- idx_t *adjncy, idx_t *vwgt, idx_t *vsize, idx_t *adjwgt,
- idx_t *nparts, real_t *tpwgts, real_t *ubvec, idx_t *options,
- idx_t *objval, idx_t *part)
-{
- int sigrval=0, renumber=0;
- graph_t *graph;
- ctrl_t *ctrl;
-
- /* set up malloc cleaning code and signal catchers */
- if (!gk_malloc_init())
- return METIS_ERROR_MEMORY;
-
- gk_sigtrap();
-
- if ((sigrval = gk_sigcatch()) != 0)
- goto SIGTHROW;
-
-
- /* set up the run parameters */
- ctrl = SetupCtrl(METIS_OP_PMETIS, options, *ncon, *nparts, tpwgts, ubvec);
- if (!ctrl) {
- gk_siguntrap();
- return METIS_ERROR_INPUT;
- }
-
- /* if required, change the numbering to 0 */
- if (ctrl->numflag == 1) {
- Change2CNumbering(*nvtxs, xadj, adjncy);
- renumber = 1;
- }
-
- /* set up the graph */
- graph = SetupGraph(ctrl, *nvtxs, *ncon, xadj, adjncy, vwgt, vsize, adjwgt);
-
- /* allocate workspace memory */
- AllocateWorkSpace(ctrl, graph);
-
- /* start the partitioning */
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, InitTimers(ctrl));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->TotalTmr));
-
- *objval = MlevelRecursiveBisection(ctrl, graph, *nparts, part, ctrl->tpwgts, 0);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->TotalTmr));
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, PrintTimers(ctrl));
-
- /* clean up */
- FreeCtrl(&ctrl);
-
-SIGTHROW:
- /* if required, change the numbering back to 1 */
- if (renumber)
- Change2FNumbering(*nvtxs, xadj, adjncy, part);
-
- gk_siguntrap();
- gk_malloc_cleanup(0);
-
- return metis_rcode(sigrval);
-}
-
-
-/*************************************************************************/
-/*! This function is the top-level driver of the recursive bisection
- routine. */
-/*************************************************************************/
-idx_t MlevelRecursiveBisection(ctrl_t *ctrl, graph_t *graph, idx_t nparts,
- idx_t *part, real_t *tpwgts, idx_t fpart)
-{
- idx_t i, j, nvtxs, ncon, objval;
- idx_t *label, *where;
- graph_t *lgraph, *rgraph;
- real_t wsum, *tpwgts2;
-
- if ((nvtxs = graph->nvtxs) == 0) {
- printf("\t***Cannot bisect a graph with 0 vertices!\n"
- "\t***You are trying to partition a graph into too many parts!\n");
- return 0;
- }
-
- ncon = graph->ncon;
-
- /* determine the weights of the two partitions as a function of the weight of the
- target partition weights */
- WCOREPUSH;
- tpwgts2 = rwspacemalloc(ctrl, 2*ncon);
- for (i=0; i<ncon; i++) {
- tpwgts2[i] = rsum((nparts>>1), tpwgts+i, ncon);
- tpwgts2[ncon+i] = 1.0 - tpwgts2[i];
- }
-
- /* perform the bisection */
- objval = MultilevelBisect(ctrl, graph, tpwgts2);
-
- WCOREPOP;
-
- label = graph->label;
- where = graph->where;
- for (i=0; i<nvtxs; i++)
- part[label[i]] = where[i] + fpart;
-
- if (nparts > 2)
- SplitGraphPart(ctrl, graph, &lgraph, &rgraph);
-
- /* Free the memory of the top level graph */
- FreeGraph(&graph);
-
- /* Scale the fractions in the tpwgts according to the true weight */
- for (i=0; i<ncon; i++) {
- wsum = rsum((nparts>>1), tpwgts+i, ncon);
- rscale((nparts>>1), 1.0/wsum, tpwgts+i, ncon);
- rscale(nparts-(nparts>>1), 1.0/(1.0-wsum), tpwgts+(nparts>>1)*ncon+i, ncon);
- }
-
- /* Do the recursive call */
- if (nparts > 3) {
- objval += MlevelRecursiveBisection(ctrl, lgraph, (nparts>>1), part,
- tpwgts, fpart);
- objval += MlevelRecursiveBisection(ctrl, rgraph, nparts-(nparts>>1), part,
- tpwgts+(nparts>>1)*ncon, fpart+(nparts>>1));
- }
- else if (nparts == 3) {
- FreeGraph(&lgraph);
- objval += MlevelRecursiveBisection(ctrl, rgraph, nparts-(nparts>>1), part,
- tpwgts+(nparts>>1)*ncon, fpart+(nparts>>1));
- }
-
-
- return objval;
-}
-
-
-/*************************************************************************/
-/*! This function performs a multilevel bisection */
-/*************************************************************************/
-idx_t MultilevelBisect(ctrl_t *ctrl, graph_t *graph, real_t *tpwgts)
-{
- idx_t i, niparts, bestobj=0, curobj=0, *bestwhere=NULL;
- graph_t *cgraph;
- real_t bestbal=0.0, curbal=0.0;
-
- Setup2WayBalMultipliers(ctrl, graph, tpwgts);
-
- WCOREPUSH;
-
- if (ctrl->ncuts > 1)
- bestwhere = iwspacemalloc(ctrl, graph->nvtxs);
-
- for (i=0; i<ctrl->ncuts; i++) {
- cgraph = CoarsenGraph(ctrl, graph);
-
- niparts = (cgraph->nvtxs <= ctrl->CoarsenTo ? SMALLNIPARTS : LARGENIPARTS);
- Init2WayPartition(ctrl, cgraph, tpwgts, niparts);
-
- Refine2Way(ctrl, graph, cgraph, tpwgts);
-
- curobj = graph->mincut;
- curbal = ComputeLoadImbalanceDiff(graph, 2, ctrl->pijbm, ctrl->ubfactors);
-
- if (i == 0
- || (curbal <= 0.0005 && bestobj > curobj)
- || (bestbal > 0.0005 && curbal < bestbal)) {
- bestobj = curobj;
- bestbal = curbal;
- if (i < ctrl->ncuts-1)
- icopy(graph->nvtxs, graph->where, bestwhere);
- }
-
- if (bestobj == 0)
- break;
-
- if (i < ctrl->ncuts-1)
- FreeRData(graph);
- }
-
- if (bestobj != curobj) {
- icopy(graph->nvtxs, bestwhere, graph->where);
- Compute2WayPartitionParams(ctrl, graph);
- }
-
- WCOREPOP;
-
- return bestobj;
-}
-
-
-/*************************************************************************/
-/*! This function splits a graph into two based on its bisection */
-/*************************************************************************/
-void SplitGraphPart(ctrl_t *ctrl, graph_t *graph, graph_t **r_lgraph,
- graph_t **r_rgraph)
-{
- idx_t i, j, k, l, istart, iend, mypart, nvtxs, ncon, snvtxs[2], snedges[2];
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *label, *where, *bndptr;
- idx_t *sxadj[2], *svwgt[2], *sadjncy[2], *sadjwgt[2], *slabel[2];
- idx_t *rename;
- idx_t *auxadjncy, *auxadjwgt;
- graph_t *lgraph, *rgraph;
-
- WCOREPUSH;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->SplitTmr));
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
- label = graph->label;
- where = graph->where;
- bndptr = graph->bndptr;
-
- ASSERT(bndptr != NULL);
-
- rename = iwspacemalloc(ctrl, nvtxs);
-
- snvtxs[0] = snvtxs[1] = snedges[0] = snedges[1] = 0;
- for (i=0; i<nvtxs; i++) {
- k = where[i];
- rename[i] = snvtxs[k]++;
- snedges[k] += xadj[i+1]-xadj[i];
- }
-
- lgraph = SetupSplitGraph(graph, snvtxs[0], snedges[0]);
- sxadj[0] = lgraph->xadj;
- svwgt[0] = lgraph->vwgt;
- sadjncy[0] = lgraph->adjncy;
- sadjwgt[0] = lgraph->adjwgt;
- slabel[0] = lgraph->label;
-
- rgraph = SetupSplitGraph(graph, snvtxs[1], snedges[1]);
- sxadj[1] = rgraph->xadj;
- svwgt[1] = rgraph->vwgt;
- sadjncy[1] = rgraph->adjncy;
- sadjwgt[1] = rgraph->adjwgt;
- slabel[1] = rgraph->label;
-
- snvtxs[0] = snvtxs[1] = snedges[0] = snedges[1] = 0;
- sxadj[0][0] = sxadj[1][0] = 0;
- for (i=0; i<nvtxs; i++) {
- mypart = where[i];
-
- istart = xadj[i];
- iend = xadj[i+1];
- if (bndptr[i] == -1) { /* This is an interior vertex */
- auxadjncy = sadjncy[mypart] + snedges[mypart] - istart;
- auxadjwgt = sadjwgt[mypart] + snedges[mypart] - istart;
- for(j=istart; j<iend; j++) {
- auxadjncy[j] = adjncy[j];
- auxadjwgt[j] = adjwgt[j];
- }
- snedges[mypart] += iend-istart;
- }
- else {
- auxadjncy = sadjncy[mypart];
- auxadjwgt = sadjwgt[mypart];
- l = snedges[mypart];
- for (j=istart; j<iend; j++) {
- k = adjncy[j];
- if (where[k] == mypart) {
- auxadjncy[l] = k;
- auxadjwgt[l++] = adjwgt[j];
- }
- }
- snedges[mypart] = l;
- }
-
- /* copy vertex weights */
- for (k=0; k<ncon; k++)
- svwgt[mypart][snvtxs[mypart]*ncon+k] = vwgt[i*ncon+k];
-
- slabel[mypart][snvtxs[mypart]] = label[i];
- sxadj[mypart][++snvtxs[mypart]] = snedges[mypart];
- }
-
- for (mypart=0; mypart<2; mypart++) {
- iend = sxadj[mypart][snvtxs[mypart]];
- auxadjncy = sadjncy[mypart];
- for (i=0; i<iend; i++)
- auxadjncy[i] = rename[auxadjncy[i]];
- }
-
- lgraph->nedges = snedges[0];
- rgraph->nedges = snedges[1];
-
- SetupGraph_tvwgt(lgraph);
- SetupGraph_tvwgt(rgraph);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->SplitTmr));
-
- *r_lgraph = lgraph;
- *r_rgraph = rgraph;
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/proto.h b/3rdParty/metis/metis-5.1.0/libmetis/proto.h
deleted file mode 100644
index f852ff59e..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/proto.h
+++ /dev/null
@@ -1,348 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * proto.h
- *
- * This file contains header files
- *
- * Started 10/19/95
- * George
- *
- * $Id: proto.h 13933 2013-03-29 22:20:46Z karypis $
- *
- */
-
-#ifndef _LIBMETIS_PROTO_H_
-#define _LIBMETIS_PROTO_H_
-
-/* auxapi.c */
-
-/* balance.c */
-void Balance2Way(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts);
-void Bnd2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts);
-void General2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts);
-void McGeneral2WayBalance(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts);
-
-
-/* bucketsort.c */
-void BucketSortKeysInc(ctrl_t *ctrl, idx_t n, idx_t max, idx_t *keys,
- idx_t *tperm, idx_t *perm);
-
-
-/* checkgraph.c */
-int CheckGraph(graph_t *graph, int numflag, int verbose);
-int CheckInputGraphWeights(idx_t nvtxs, idx_t ncon, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *vsize, idx_t *adjwgt);
-graph_t *FixGraph(graph_t *graph);
-
-
-/* coarsen.c */
-graph_t *CoarsenGraph(ctrl_t *ctrl, graph_t *graph);
-graph_t *CoarsenGraphNlevels(ctrl_t *ctrl, graph_t *graph, idx_t nlevels);
-idx_t Match_RM(ctrl_t *ctrl, graph_t *graph);
-idx_t Match_SHEM(ctrl_t *ctrl, graph_t *graph);
-idx_t Match_2Hop(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t nunmatched);
-idx_t Match_2HopAny(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t *r_nunmatched, size_t maxdegree);
-idx_t Match_2HopAll(ctrl_t *ctrl, graph_t *graph, idx_t *perm, idx_t *match,
- idx_t cnvtxs, size_t *r_nunmatched, size_t maxdegree);
-void PrintCGraphStats(ctrl_t *ctrl, graph_t *graph);
-void CreateCoarseGraph(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match);
-void CreateCoarseGraphNoMask(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match);
-void CreateCoarseGraphPerm(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
- idx_t *match, idx_t *perm);
-graph_t *SetupCoarseGraph(graph_t *graph, idx_t cnvtxs, idx_t dovsize);
-void ReAdjustMemory(ctrl_t *ctrl, graph_t *graph, graph_t *cgraph);
-
-
-
-/* compress.c */
-graph_t *CompressGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *cptr, idx_t *cind);
-graph_t *PruneGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t *xadj, idx_t *adjncy,
- idx_t *vwgt, idx_t *iperm, real_t factor);
-
-
-/* contig.c */
-idx_t FindPartitionInducedComponents(graph_t *graph, idx_t *where,
- idx_t *cptr, idx_t *cind);
-void ComputeBFSOrdering(ctrl_t *ctrl, graph_t *graph, idx_t *bfsperm);
-idx_t IsConnected(graph_t *graph, idx_t report);
-idx_t IsConnectedSubdomain(ctrl_t *, graph_t *, idx_t, idx_t);
-idx_t FindSepInducedComponents(ctrl_t *, graph_t *, idx_t *, idx_t *);
-void EliminateComponents(ctrl_t *ctrl, graph_t *graph);
-void MoveGroupContigForCut(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t gid,
- idx_t *ptr, idx_t *ind);
-void MoveGroupContigForVol(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t gid,
- idx_t *ptr, idx_t *ind, idx_t *vmarker, idx_t *pmarker,
- idx_t *modind);
-
-
-/* debug.c */
-idx_t ComputeCut(graph_t *graph, idx_t *where);
-idx_t ComputeVolume(graph_t *, idx_t *);
-idx_t ComputeMaxCut(graph_t *graph, idx_t nparts, idx_t *where);
-idx_t CheckBnd(graph_t *);
-idx_t CheckBnd2(graph_t *);
-idx_t CheckNodeBnd(graph_t *, idx_t);
-idx_t CheckRInfo(ctrl_t *ctrl, ckrinfo_t *rinfo);
-idx_t CheckNodePartitionParams(graph_t *);
-idx_t IsSeparable(graph_t *);
-void CheckKWayVolPartitionParams(ctrl_t *ctrl, graph_t *graph);
-
-
-/* fm.c */
-void FM_2WayRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter);
-void FM_2WayCutRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter);
-void FM_Mc2WayCutRefine(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niter);
-void SelectQueue(graph_t *graph, real_t *pijbm, real_t *ubfactors, rpq_t **queues,
- idx_t *from, idx_t *cnum);
-void Print2WayRefineStats(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts,
- real_t deltabal, idx_t mincutorder);
-
-
-/* fortran.c */
-void Change2CNumbering(idx_t, idx_t *, idx_t *);
-void Change2FNumbering(idx_t, idx_t *, idx_t *, idx_t *);
-void Change2FNumbering2(idx_t, idx_t *, idx_t *);
-void Change2FNumberingOrder(idx_t, idx_t *, idx_t *, idx_t *, idx_t *);
-void ChangeMesh2CNumbering(idx_t n, idx_t *ptr, idx_t *ind);
-void ChangeMesh2FNumbering(idx_t n, idx_t *ptr, idx_t *ind, idx_t nvtxs,
- idx_t *xadj, idx_t *adjncy);
-void ChangeMesh2FNumbering2(idx_t ne, idx_t nn, idx_t *ptr, idx_t *ind,
- idx_t *epart, idx_t *npart);
-
-
-/* graph.c */
-graph_t *SetupGraph(ctrl_t *ctrl, idx_t nvtxs, idx_t ncon, idx_t *xadj,
- idx_t *adjncy, idx_t *vwgt, idx_t *vsize, idx_t *adjwgt);
-void SetupGraph_tvwgt(graph_t *graph);
-void SetupGraph_label(graph_t *graph);
-graph_t *SetupSplitGraph(graph_t *graph, idx_t snvtxs, idx_t snedges);
-graph_t *CreateGraph(void);
-void InitGraph(graph_t *graph);
-void FreeRData(graph_t *graph);
-void FreeGraph(graph_t **graph);
-
-
-/* initpart.c */
-void Init2WayPartition(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void InitSeparator(ctrl_t *ctrl, graph_t *graph, idx_t niparts);
-void RandomBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void GrowBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void McRandomBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void McGrowBisection(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void GrowBisectionNode(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-void GrowBisectionNode2(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts, idx_t niparts);
-
-
-/* kmetis.c */
-idx_t MlevelKWayPartitioning(ctrl_t *ctrl, graph_t *graph, idx_t *part);
-void InitKWayPartitioning(ctrl_t *ctrl, graph_t *graph);
-
-
-/* kwayfm.c */
-void Greedy_KWayOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode);
-void Greedy_KWayCutOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode);
-void Greedy_KWayVolOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode);
-void Greedy_McKWayCutOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode);
-void Greedy_McKWayVolOptimize(ctrl_t *ctrl, graph_t *graph, idx_t niter,
- real_t ffactor, idx_t omode);
-idx_t IsArticulationNode(idx_t i, idx_t *xadj, idx_t *adjncy, idx_t *where,
- idx_t *bfslvl, idx_t *bfsind, idx_t *bfsmrk);
-void KWayVolUpdate(ctrl_t *ctrl, graph_t *graph, idx_t v, idx_t from,
- idx_t to, ipq_t *queue, idx_t *vstatus, idx_t *r_nupd, idx_t *updptr,
- idx_t *updind, idx_t bndtype, idx_t *vmarker, idx_t *pmarker,
- idx_t *modind);
-
-
-/* kwayrefine.c */
-void RefineKWay(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph);
-void AllocateKWayPartitionMemory(ctrl_t *ctrl, graph_t *graph);
-void ComputeKWayPartitionParams(ctrl_t *ctrl, graph_t *graph);
-void ProjectKWayPartition(ctrl_t *ctrl, graph_t *graph);
-void ComputeKWayBoundary(ctrl_t *ctrl, graph_t *graph, idx_t bndtype);
-void ComputeKWayVolGains(ctrl_t *ctrl, graph_t *graph);
-int IsBalanced(ctrl_t *ctrl, graph_t *graph, real_t ffactor);
-
-
-/* mcutil.c */
-int rvecle(idx_t n, real_t *x, real_t *y);
-int rvecge(idx_t n, real_t *x, real_t *y);
-int rvecsumle(idx_t n, real_t *x1, real_t *x2, real_t *y);
-real_t rvecmaxdiff(idx_t n, real_t *x, real_t *y);
-int ivecle(idx_t n, idx_t *x, idx_t *z);
-int ivecge(idx_t n, idx_t *x, idx_t *z);
-int ivecaxpylez(idx_t n, idx_t a, idx_t *x, idx_t *y, idx_t *z);
-int ivecaxpygez(idx_t n, idx_t a, idx_t *x, idx_t *y, idx_t *z);
-int BetterVBalance(idx_t ncon, real_t *itvwgt, idx_t *v_vwgt, idx_t *u1_vwgt,
- idx_t *u2_vwgt);
-int BetterBalance2Way(idx_t n, real_t *x, real_t *y);
-int BetterBalanceKWay(idx_t ncon, idx_t *vwgt, real_t *itvwgt, idx_t a1,
- idx_t *pt1, real_t *bm1, idx_t a2, idx_t *pt2, real_t *bm2);
-real_t ComputeLoadImbalance(graph_t *graph, idx_t nparts, real_t *pijbm);
-real_t ComputeLoadImbalanceDiff(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *ubvec);
-real_t ComputeLoadImbalanceDiffVec(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *ubfactors, real_t *diffvec);
-void ComputeLoadImbalanceVec(graph_t *graph, idx_t nparts, real_t *pijbm,
- real_t *lbvec);
-
-
-/* mesh.c */
-void CreateGraphDual(idx_t ne, idx_t nn, idx_t *eptr, idx_t *eind, idx_t ncommon,
- idx_t **r_xadj, idx_t **r_adjncy);
-idx_t FindCommonElements(idx_t qid, idx_t elen, idx_t *eind, idx_t *nptr,
- idx_t *nind, idx_t *eptr, idx_t ncommon, idx_t *marker, idx_t *nbrs);
-void CreateGraphNodal(idx_t ne, idx_t nn, idx_t *eptr, idx_t *eind, idx_t **r_xadj,
- idx_t **r_adjncy);
-idx_t FindCommonNodes(idx_t qid, idx_t nelmnts, idx_t *elmntids, idx_t *eptr,
- idx_t *eind, idx_t *marker, idx_t *nbrs);
-mesh_t *CreateMesh(void);
-void InitMesh(mesh_t *mesh);
-void FreeMesh(mesh_t **mesh);
-
-
-/* meshpart.c */
-void InduceRowPartFromColumnPart(idx_t nrows, idx_t *rowptr, idx_t *rowind,
- idx_t *rpart, idx_t *cpart, idx_t nparts, real_t *tpwgts);
-
-
-/* minconn.c */
-void ComputeSubDomainGraph(ctrl_t *ctrl, graph_t *graph);
-void UpdateEdgeSubDomainGraph(ctrl_t *ctrl, idx_t u, idx_t v, idx_t ewgt,
- idx_t *r_maxndoms);
-void PrintSubDomainGraph(graph_t *graph, idx_t nparts, idx_t *where);
-void EliminateSubDomainEdges(ctrl_t *ctrl, graph_t *graph);
-void MoveGroupMinConnForCut(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t nind,
- idx_t *ind);
-void MoveGroupMinConnForVol(ctrl_t *ctrl, graph_t *graph, idx_t to, idx_t nind,
- idx_t *ind, idx_t *vmarker, idx_t *pmarker, idx_t *modind);
-
-
-/* mincover.o */
-void MinCover(idx_t *, idx_t *, idx_t, idx_t, idx_t *, idx_t *);
-idx_t MinCover_Augment(idx_t *, idx_t *, idx_t, idx_t *, idx_t *, idx_t *, idx_t);
-void MinCover_Decompose(idx_t *, idx_t *, idx_t, idx_t, idx_t *, idx_t *, idx_t *);
-void MinCover_ColDFS(idx_t *, idx_t *, idx_t, idx_t *, idx_t *, idx_t);
-void MinCover_RowDFS(idx_t *, idx_t *, idx_t, idx_t *, idx_t *, idx_t);
-
-
-/* mmd.c */
-void genmmd(idx_t, idx_t *, idx_t *, idx_t *, idx_t *, idx_t , idx_t *, idx_t *, idx_t *, idx_t *, idx_t, idx_t *);
-void mmdelm(idx_t, idx_t *xadj, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t, idx_t);
-idx_t mmdint(idx_t, idx_t *xadj, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *);
-void mmdnum(idx_t, idx_t *, idx_t *, idx_t *);
-void mmdupd(idx_t, idx_t, idx_t *, idx_t *, idx_t, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t *, idx_t, idx_t *tag);
-
-
-/* ometis.c */
-void MlevelNestedDissection(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx);
-void MlevelNestedDissectionCC(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx);
-void MlevelNodeBisectionMultiple(ctrl_t *ctrl, graph_t *graph);
-void MlevelNodeBisectionL2(ctrl_t *ctrl, graph_t *graph, idx_t niparts);
-void MlevelNodeBisectionL1(ctrl_t *ctrl, graph_t *graph, idx_t niparts);
-void SplitGraphOrder(ctrl_t *ctrl, graph_t *graph, graph_t **r_lgraph,
- graph_t **r_rgraph);
-graph_t **SplitGraphOrderCC(ctrl_t *ctrl, graph_t *graph, idx_t ncmps,
- idx_t *cptr, idx_t *cind);
-void MMDOrder(ctrl_t *ctrl, graph_t *graph, idx_t *order, idx_t lastvtx);
-
-
-/* options.c */
-ctrl_t *SetupCtrl(moptype_et optype, idx_t *options, idx_t ncon, idx_t nparts,
- real_t *tpwgts, real_t *ubvec);
-void SetupKWayBalMultipliers(ctrl_t *ctrl, graph_t *graph);
-void Setup2WayBalMultipliers(ctrl_t *ctrl, graph_t *graph, real_t *tpwgts);
-void PrintCtrl(ctrl_t *ctrl);
-int CheckParams(ctrl_t *ctrl);
-void FreeCtrl(ctrl_t **r_ctrl);
-
-
-/* parmetis.c */
-void MlevelNestedDissectionP(ctrl_t *ctrl, graph_t *graph, idx_t *order,
- idx_t lastvtx, idx_t npes, idx_t cpos, idx_t *sizes);
-void FM_2WayNodeRefine1SidedP(ctrl_t *ctrl, graph_t *graph, idx_t *hmarker,
- real_t ubfactor, idx_t npasses);
-void FM_2WayNodeRefine2SidedP(ctrl_t *ctrl, graph_t *graph, idx_t *hmarker,
- real_t ubfactor, idx_t npasses);
-
-
-/* pmetis.c */
-idx_t MlevelRecursiveBisection(ctrl_t *ctrl, graph_t *graph, idx_t nparts,
- idx_t *part, real_t *tpwgts, idx_t fpart);
-idx_t MultilevelBisect(ctrl_t *ctrl, graph_t *graph, real_t *tpwgts);
-void SplitGraphPart(ctrl_t *ctrl, graph_t *graph, graph_t **r_lgraph, graph_t **r_rgraph);
-
-
-/* refine.c */
-void Refine2Way(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph, real_t *rtpwgts);
-void Allocate2WayPartitionMemory(ctrl_t *ctrl, graph_t *graph);
-void Compute2WayPartitionParams(ctrl_t *ctrl, graph_t *graph);
-void Project2WayPartition(ctrl_t *ctrl, graph_t *graph);
-
-
-/* separator.c */
-void ConstructSeparator(ctrl_t *ctrl, graph_t *graph);
-void ConstructMinCoverSeparator(ctrl_t *ctrl, graph_t *graph);
-
-
-/* sfm.c */
-void FM_2WayNodeRefine2Sided(ctrl_t *ctrl, graph_t *graph, idx_t niter);
-void FM_2WayNodeRefine1Sided(ctrl_t *ctrl, graph_t *graph, idx_t niter);
-void FM_2WayNodeBalance(ctrl_t *ctrl, graph_t *graph);
-
-
-/* srefine.c */
-void Refine2WayNode(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph);
-void Allocate2WayNodePartitionMemory(ctrl_t *ctrl, graph_t *graph);
-void Compute2WayNodePartitionParams(ctrl_t *ctrl, graph_t *graph);
-void Project2WayNodePartition(ctrl_t *ctrl, graph_t *graph);
-
-
-/* stat.c */
-void ComputePartitionInfoBipartite(graph_t *, idx_t, idx_t *);
-void ComputePartitionBalance(graph_t *, idx_t, idx_t *, real_t *);
-real_t ComputeElementBalance(idx_t, idx_t, idx_t *);
-
-
-/* timing.c */
-void InitTimers(ctrl_t *);
-void PrintTimers(ctrl_t *);
-
-/* util.c */
-idx_t iargmax_strd(size_t, idx_t *, idx_t);
-idx_t iargmax_nrm(size_t n, idx_t *x, real_t *y);
-idx_t iargmax2_nrm(size_t n, idx_t *x, real_t *y);
-idx_t rargmax2(size_t, real_t *);
-void InitRandom(idx_t);
-int metis_rcode(int sigrval);
-
-
-
-/* wspace.c */
-void AllocateWorkSpace(ctrl_t *ctrl, graph_t *graph);
-void AllocateRefinementWorkSpace(ctrl_t *ctrl, idx_t nbrpoolsize);
-void FreeWorkSpace(ctrl_t *ctrl);
-void *wspacemalloc(ctrl_t *ctrl, size_t nbytes);
-void wspacepush(ctrl_t *ctrl);
-void wspacepop(ctrl_t *ctrl);
-idx_t *iwspacemalloc(ctrl_t *, idx_t);
-real_t *rwspacemalloc(ctrl_t *, idx_t);
-ikv_t *ikvwspacemalloc(ctrl_t *, idx_t);
-void cnbrpoolReset(ctrl_t *ctrl);
-idx_t cnbrpoolGetNext(ctrl_t *ctrl, idx_t nnbrs);
-void vnbrpoolReset(ctrl_t *ctrl);
-idx_t vnbrpoolGetNext(ctrl_t *ctrl, idx_t nnbrs);
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/refine.c b/3rdParty/metis/metis-5.1.0/libmetis/refine.c
deleted file mode 100644
index c08dc2ddb..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/refine.c
+++ /dev/null
@@ -1,211 +0,0 @@
-/*
-\file
-\brief This file contains the driving routines for multilevel refinement
-
-\date Started 7/24/1997
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version\verbatim $Id: refine.c 10513 2011-07-07 22:06:03Z karypis $ \endverbatim
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point of refinement */
-/*************************************************************************/
-void Refine2Way(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph, real_t *tpwgts)
-{
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->UncoarsenTmr));
-
- /* Compute the parameters of the coarsest graph */
- Compute2WayPartitionParams(ctrl, graph);
-
- for (;;) {
- ASSERT(CheckBnd(graph));
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->RefTmr));
-
- Balance2Way(ctrl, graph, tpwgts);
-
- FM_2WayRefine(ctrl, graph, tpwgts, ctrl->niter);
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->RefTmr));
-
- if (graph == orggraph)
- break;
-
- graph = graph->finer;
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ProjectTmr));
- Project2WayPartition(ctrl, graph);
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ProjectTmr));
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->UncoarsenTmr));
-}
-
-
-/*************************************************************************/
-/*! This function allocates memory for 2-way edge refinement */
-/*************************************************************************/
-void Allocate2WayPartitionMemory(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t nvtxs, ncon;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
-
- graph->pwgts = imalloc(2*ncon, "Allocate2WayPartitionMemory: pwgts");
- graph->where = imalloc(nvtxs, "Allocate2WayPartitionMemory: where");
- graph->bndptr = imalloc(nvtxs, "Allocate2WayPartitionMemory: bndptr");
- graph->bndind = imalloc(nvtxs, "Allocate2WayPartitionMemory: bndind");
- graph->id = imalloc(nvtxs, "Allocate2WayPartitionMemory: id");
- graph->ed = imalloc(nvtxs, "Allocate2WayPartitionMemory: ed");
-}
-
-
-/*************************************************************************/
-/*! This function computes the initial id/ed */
-/*************************************************************************/
-void Compute2WayPartitionParams(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, nvtxs, ncon, nbnd, mincut, istart, iend, tid, ted, me;
- idx_t *xadj, *vwgt, *adjncy, *adjwgt, *pwgts;
- idx_t *where, *bndptr, *bndind, *id, *ed;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
-
- pwgts = iset(2*ncon, 0, graph->pwgts);
- bndptr = iset(nvtxs, -1, graph->bndptr);
- bndind = graph->bndind;
-
- /* Compute pwgts */
- if (ncon == 1) {
- for (i=0; i<nvtxs; i++) {
- ASSERT(where[i] >= 0 && where[i] <= 1);
- pwgts[where[i]] += vwgt[i];
- }
- ASSERT(pwgts[0]+pwgts[1] == graph->tvwgt[0]);
- }
- else {
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- for (j=0; j<ncon; j++)
- pwgts[me*ncon+j] += vwgt[i*ncon+j];
- }
- }
-
-
- /* Compute the required info for refinement */
- for (nbnd=0, mincut=0, i=0; i<nvtxs; i++) {
- istart = xadj[i];
- iend = xadj[i+1];
-
- me = where[i];
- tid = ted = 0;
-
- for (j=istart; j<iend; j++) {
- if (me == where[adjncy[j]])
- tid += adjwgt[j];
- else
- ted += adjwgt[j];
- }
- id[i] = tid;
- ed[i] = ted;
-
- if (ted > 0 || istart == iend) {
- BNDInsert(nbnd, bndind, bndptr, i);
- mincut += ted;
- }
- }
-
- graph->mincut = mincut/2;
- graph->nbnd = nbnd;
-
-}
-
-
-/*************************************************************************/
-/*! Projects a partition and computes the refinement params. */
-/*************************************************************************/
-void Project2WayPartition(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, istart, iend, nvtxs, nbnd, me, tid, ted;
- idx_t *xadj, *adjncy, *adjwgt;
- idx_t *cmap, *where, *bndptr, *bndind;
- idx_t *cwhere, *cbndptr;
- idx_t *id, *ed;
- graph_t *cgraph;
-
- Allocate2WayPartitionMemory(ctrl, graph);
-
- cgraph = graph->coarser;
- cwhere = cgraph->where;
- cbndptr = cgraph->bndptr;
-
- nvtxs = graph->nvtxs;
- cmap = graph->cmap;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- adjwgt = graph->adjwgt;
-
- where = graph->where;
- id = graph->id;
- ed = graph->ed;
-
- bndptr = iset(nvtxs, -1, graph->bndptr);
- bndind = graph->bndind;
-
- /* Project the partition and record which of these nodes came from the
- coarser boundary */
- for (i=0; i<nvtxs; i++) {
- j = cmap[i];
- where[i] = cwhere[j];
- cmap[i] = cbndptr[j];
- }
-
- /* Compute the refinement information of the nodes */
- for (nbnd=0, i=0; i<nvtxs; i++) {
- istart = xadj[i];
- iend = xadj[i+1];
-
- tid = ted = 0;
- if (cmap[i] == -1) { /* Interior node. Note that cmap[i] = cbndptr[cmap[i]] */
- for (j=istart; j<iend; j++)
- tid += adjwgt[j];
- }
- else { /* Potentially an interface node */
- me = where[i];
- for (j=istart; j<iend; j++) {
- if (me == where[adjncy[j]])
- tid += adjwgt[j];
- else
- ted += adjwgt[j];
- }
- }
- id[i] = tid;
- ed[i] = ted;
-
- if (ted > 0 || istart == iend)
- BNDInsert(nbnd, bndind, bndptr, i);
- }
- graph->mincut = cgraph->mincut;
- graph->nbnd = nbnd;
-
- /* copy pwgts */
- icopy(2*graph->ncon, cgraph->pwgts, graph->pwgts);
-
- FreeGraph(&graph->coarser);
- graph->coarser = NULL;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/rename.h b/3rdParty/metis/metis-5.1.0/libmetis/rename.h
deleted file mode 100644
index 62b03b491..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/rename.h
+++ /dev/null
@@ -1,266 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * rename.h
- *
- * This file contains header files
- *
- * Started 10/2/97
- * George
- *
- * $Id: rename.h 13933 2013-03-29 22:20:46Z karypis $
- *
- */
-
-
-#ifndef _LIBMETIS_RENAME_H_
-#define _LIBMETIS_RENAME_H_
-
-
-/* balance.c */
-#define Balance2Way libmetis__Balance2Way
-#define Bnd2WayBalance libmetis__Bnd2WayBalance
-#define General2WayBalance libmetis__General2WayBalance
-#define McGeneral2WayBalance libmetis__McGeneral2WayBalance
-
-/* bucketsort.c */
-#define BucketSortKeysInc libmetis__BucketSortKeysInc
-
-/* checkgraph.c */
-#define CheckGraph libmetis__CheckGraph
-#define CheckInputGraphWeights libmetis__CheckInputGraphWeights
-#define FixGraph libmetis__FixGraph
-
-/* coarsen.c */
-#define CoarsenGraph libmetis__CoarsenGraph
-#define Match_RM libmetis__Match_RM
-#define Match_SHEM libmetis__Match_SHEM
-#define Match_2Hop libmetis__Match_2Hop
-#define Match_2HopAny libmetis__Match_2HopAny
-#define Match_2HopAll libmetis__Match_2HopAll
-#define PrintCGraphStats libmetis__PrintCGraphStats
-#define CreateCoarseGraph libmetis__CreateCoarseGraph
-#define CreateCoarseGraphNoMask libmetis__CreateCoarseGraphNoMask
-#define CreateCoarseGraphPerm libmetis__CreateCoarseGraphPerm
-#define SetupCoarseGraph libmetis__SetupCoarseGraph
-#define ReAdjustMemory libmetis__ReAdjustMemory
-
-/* compress.c */
-#define CompressGraph libmetis__CompressGraph
-#define PruneGraph libmetis__PruneGraph
-
-/* contig.c */
-#define FindPartitionInducedComponents libmetis__FindPartitionInducedComponents
-#define IsConnected libmetis__IsConnected
-#define IsConnectedSubdomain libmetis__IsConnectedSubdomain
-#define FindSepInducedComponents libmetis__FindSepInducedComponents
-#define EliminateComponents libmetis__EliminateComponents
-#define MoveGroupContigForCut libmetis__MoveGroupContigForCut
-#define MoveGroupContigForVol libmetis__MoveGroupContigForVol
-
-/* debug.c */
-#define ComputeCut libmetis__ComputeCut
-#define ComputeVolume libmetis__ComputeVolume
-#define ComputeMaxCut libmetis__ComputeMaxCut
-#define CheckBnd libmetis__CheckBnd
-#define CheckBnd2 libmetis__CheckBnd2
-#define CheckNodeBnd libmetis__CheckNodeBnd
-#define CheckRInfo libmetis__CheckRInfo
-#define CheckNodePartitionParams libmetis__CheckNodePartitionParams
-#define IsSeparable libmetis__IsSeparable
-#define CheckKWayVolPartitionParams libmetis__CheckKWayVolPartitionParams
-
-/* fm.c */
-#define FM_2WayRefine libmetis__FM_2WayRefine
-#define FM_2WayCutRefine libmetis__FM_2WayCutRefine
-#define FM_Mc2WayCutRefine libmetis__FM_Mc2WayCutRefine
-#define SelectQueue libmetis__SelectQueue
-#define Print2WayRefineStats libmetis__Print2WayRefineStats
-
-/* fortran.c */
-#define Change2CNumbering libmetis__Change2CNumbering
-#define Change2FNumbering libmetis__Change2FNumbering
-#define Change2FNumbering2 libmetis__Change2FNumbering2
-#define Change2FNumberingOrder libmetis__Change2FNumberingOrder
-#define ChangeMesh2CNumbering libmetis__ChangeMesh2CNumbering
-#define ChangeMesh2FNumbering libmetis__ChangeMesh2FNumbering
-#define ChangeMesh2FNumbering2 libmetis__ChangeMesh2FNumbering2
-
-/* graph.c */
-#define SetupGraph libmetis__SetupGraph
-#define SetupGraph_adjrsum libmetis__SetupGraph_adjrsum
-#define SetupGraph_tvwgt libmetis__SetupGraph_tvwgt
-#define SetupGraph_label libmetis__SetupGraph_label
-#define SetupSplitGraph libmetis__SetupSplitGraph
-#define CreateGraph libmetis__CreateGraph
-#define InitGraph libmetis__InitGraph
-#define FreeRData libmetis__FreeRData
-#define FreeGraph libmetis__FreeGraph
-
-/* initpart.c */
-#define Init2WayPartition libmetis__Init2WayPartition
-#define InitSeparator libmetis__InitSeparator
-#define RandomBisection libmetis__RandomBisection
-#define GrowBisection libmetis__GrowBisection
-#define McRandomBisection libmetis__McRandomBisection
-#define McGrowBisection libmetis__McGrowBisection
-#define GrowBisectionNode libmetis__GrowBisectionNode
-
-/* kmetis.c */
-#define MlevelKWayPartitioning libmetis__MlevelKWayPartitioning
-#define InitKWayPartitioning libmetis__InitKWayPartitioning
-
-/* kwayfm.c */
-#define Greedy_KWayOptimize libmetis__Greedy_KWayOptimize
-#define Greedy_KWayCutOptimize libmetis__Greedy_KWayCutOptimize
-#define Greedy_KWayVolOptimize libmetis__Greedy_KWayVolOptimize
-#define Greedy_McKWayCutOptimize libmetis__Greedy_McKWayCutOptimize
-#define Greedy_McKWayVolOptimize libmetis__Greedy_McKWayVolOptimize
-#define IsArticulationNode libmetis__IsArticulationNode
-#define KWayVolUpdate libmetis__KWayVolUpdate
-
-/* kwayrefine.c */
-#define RefineKWay libmetis__RefineKWay
-#define AllocateKWayPartitionMemory libmetis__AllocateKWayPartitionMemory
-#define ComputeKWayPartitionParams libmetis__ComputeKWayPartitionParams
-#define ProjectKWayPartition libmetis__ProjectKWayPartition
-#define ComputeKWayBoundary libmetis__ComputeKWayBoundary
-#define ComputeKWayVolGains libmetis__ComputeKWayVolGains
-#define IsBalanced libmetis__IsBalanced
-
-/* mcutil */
-#define rvecle libmetis__rvecle
-#define rvecge libmetis__rvecge
-#define rvecsumle libmetis__rvecsumle
-#define rvecmaxdiff libmetis__rvecmaxdiff
-#define ivecle libmetis__ivecle
-#define ivecge libmetis__ivecge
-#define ivecaxpylez libmetis__ivecaxpylez
-#define ivecaxpygez libmetis__ivecaxpygez
-#define BetterVBalance libmetis__BetterVBalance
-#define BetterBalance2Way libmetis__BetterBalance2Way
-#define BetterBalanceKWay libmetis__BetterBalanceKWay
-#define ComputeLoadImbalance libmetis__ComputeLoadImbalance
-#define ComputeLoadImbalanceDiff libmetis__ComputeLoadImbalanceDiff
-#define ComputeLoadImbalanceDiffVec libmetis__ComputeLoadImbalanceDiffVec
-#define ComputeLoadImbalanceVec libmetis__ComputeLoadImbalanceVec
-
-/* mesh.c */
-#define CreateGraphDual libmetis__CreateGraphDual
-#define FindCommonElements libmetis__FindCommonElements
-#define CreateGraphNodal libmetis__CreateGraphNodal
-#define FindCommonNodes libmetis__FindCommonNodes
-#define CreateMesh libmetis__CreateMesh
-#define InitMesh libmetis__InitMesh
-#define FreeMesh libmetis__FreeMesh
-
-/* meshpart.c */
-#define InduceRowPartFromColumnPart libmetis__InduceRowPartFromColumnPart
-
-/* minconn.c */
-#define ComputeSubDomainGraph libmetis__ComputeSubDomainGraph
-#define UpdateEdgeSubDomainGraph libmetis__UpdateEdgeSubDomainGraph
-#define PrintSubDomainGraph libmetis__PrintSubDomainGraph
-#define EliminateSubDomainEdges libmetis__EliminateSubDomainEdges
-#define MoveGroupMinConnForCut libmetis__MoveGroupMinConnForCut
-#define MoveGroupMinConnForVol libmetis__MoveGroupMinConnForVol
-
-/* mincover.c */
-#define MinCover libmetis__MinCover
-#define MinCover_Augment libmetis__MinCover_Augment
-#define MinCover_Decompose libmetis__MinCover_Decompose
-#define MinCover_ColDFS libmetis__MinCover_ColDFS
-#define MinCover_RowDFS libmetis__MinCover_RowDFS
-
-/* mmd.c */
-#define genmmd libmetis__genmmd
-#define mmdelm libmetis__mmdelm
-#define mmdint libmetis__mmdint
-#define mmdnum libmetis__mmdnum
-#define mmdupd libmetis__mmdupd
-
-
-/* ometis.c */
-#define MlevelNestedDissection libmetis__MlevelNestedDissection
-#define MlevelNestedDissectionCC libmetis__MlevelNestedDissectionCC
-#define MlevelNodeBisectionMultiple libmetis__MlevelNodeBisectionMultiple
-#define MlevelNodeBisectionL2 libmetis__MlevelNodeBisectionL2
-#define MlevelNodeBisectionL1 libmetis__MlevelNodeBisectionL1
-#define SplitGraphOrder libmetis__SplitGraphOrder
-#define SplitGraphOrderCC libmetis__SplitGraphOrderCC
-#define MMDOrder libmetis__MMDOrder
-
-/* options.c */
-#define SetupCtrl libmetis__SetupCtrl
-#define SetupKWayBalMultipliers libmetis__SetupKWayBalMultipliers
-#define Setup2WayBalMultipliers libmetis__Setup2WayBalMultipliers
-#define PrintCtrl libmetis__PrintCtrl
-#define FreeCtrl libmetis__FreeCtrl
-#define CheckParams libmetis__CheckParams
-
-/* parmetis.c */
-#define MlevelNestedDissectionP libmetis__MlevelNestedDissectionP
-#define FM_2WayNodeRefine1SidedP libmetis__FM_2WayNodeRefine1SidedP
-#define FM_2WayNodeRefine2SidedP libmetis__FM_2WayNodeRefine2SidedP
-
-/* pmetis.c */
-#define MlevelRecursiveBisection libmetis__MlevelRecursiveBisection
-#define MultilevelBisect libmetis__MultilevelBisect
-#define SplitGraphPart libmetis__SplitGraphPart
-
-/* refine.c */
-#define Refine2Way libmetis__Refine2Way
-#define Allocate2WayPartitionMemory libmetis__Allocate2WayPartitionMemory
-#define Compute2WayPartitionParams libmetis__Compute2WayPartitionParams
-#define Project2WayPartition libmetis__Project2WayPartition
-
-/* separator.c */
-#define ConstructSeparator libmetis__ConstructSeparator
-#define ConstructMinCoverSeparator libmetis__ConstructMinCoverSeparator
-
-/* sfm.c */
-#define FM_2WayNodeRefine2Sided libmetis__FM_2WayNodeRefine2Sided
-#define FM_2WayNodeRefine1Sided libmetis__FM_2WayNodeRefine1Sided
-#define FM_2WayNodeBalance libmetis__FM_2WayNodeBalance
-
-/* srefine.c */
-#define Refine2WayNode libmetis__Refine2WayNode
-#define Allocate2WayNodePartitionMemory libmetis__Allocate2WayNodePartitionMemory
-#define Compute2WayNodePartitionParams libmetis__Compute2WayNodePartitionParams
-#define Project2WayNodePartition libmetis__Project2WayNodePartition
-
-/* stat.c */
-#define ComputePartitionInfoBipartite libmetis__ComputePartitionInfoBipartite
-#define ComputePartitionBalance libmetis__ComputePartitionBalance
-#define ComputeElementBalance libmetis__ComputeElementBalance
-
-/* timing.c */
-#define InitTimers libmetis__InitTimers
-#define PrintTimers libmetis__PrintTimers
-
-/* util.c */
-#define iargmax_strd libmetis__iargmax_strd
-#define iargmax_nrm libmetis__iargmax_nrm
-#define iargmax2_nrm libmetis__iargmax2_nrm
-#define rargmax2 libmetis__rargmax2
-#define InitRandom libmetis__InitRandom
-#define metis_rcode libmetis__metis_rcode
-
-/* wspace.c */
-#define AllocateWorkSpace libmetis__AllocateWorkSpace
-#define AllocateRefinementWorkSpace libmetis__AllocateRefinementWorkSpace
-#define FreeWorkSpace libmetis__FreeWorkSpace
-#define wspacemalloc libmetis__wspacemalloc
-#define wspacepush libmetis__wspacepush
-#define wspacepop libmetis__wspacepop
-#define iwspacemalloc libmetis__iwspacemalloc
-#define rwspacemalloc libmetis__rwspacemalloc
-#define ikvwspacemalloc libmetis__ikvwspacemalloc
-#define cnbrpoolReset libmetis__cnbrpoolReset
-#define cnbrpoolGetNext libmetis__cnbrpoolGetNext
-#define vnbrpoolReset libmetis__vnbrpoolReset
-#define vnbrpoolGetNext libmetis__vnbrpoolGetNext
-
-#endif
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/separator.c b/3rdParty/metis/metis-5.1.0/libmetis/separator.c
deleted file mode 100644
index 72dae9b64..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/separator.c
+++ /dev/null
@@ -1,176 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * separator.c
- *
- * This file contains code for separator extraction
- *
- * Started 8/1/97
- * George
- *
- * $Id: separator.c 10481 2011-07-05 18:01:23Z karypis $
- *
- */
-
-#include "metislib.h"
-
-/*************************************************************************
-* This function takes a bisection and constructs a minimum weight vertex
-* separator out of it. It uses the node-based separator refinement for it.
-**************************************************************************/
-void ConstructSeparator(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, k, nvtxs, nbnd;
- idx_t *xadj, *where, *bndind;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- nbnd = graph->nbnd;
- bndind = graph->bndind;
-
- where = icopy(nvtxs, graph->where, iwspacemalloc(ctrl, nvtxs));
-
- /* Put the nodes in the boundary into the separator */
- for (i=0; i<nbnd; i++) {
- j = bndind[i];
- if (xadj[j+1]-xadj[j] > 0) /* Ignore islands */
- where[j] = 2;
- }
-
- FreeRData(graph);
-
- Allocate2WayNodePartitionMemory(ctrl, graph);
- icopy(nvtxs, where, graph->where);
-
- WCOREPOP;
-
- ASSERT(IsSeparable(graph));
-
- Compute2WayNodePartitionParams(ctrl, graph);
-
- ASSERT(CheckNodePartitionParams(graph));
-
- FM_2WayNodeRefine2Sided(ctrl, graph, 1);
- FM_2WayNodeRefine1Sided(ctrl, graph, 4);
-
- ASSERT(IsSeparable(graph));
-
-}
-
-
-
-/*************************************************************************
-* This function takes a bisection and constructs a minimum weight vertex
-* separator out of it. It uses an unweighted minimum-cover algorithm
-* followed by node-based separator refinement.
-**************************************************************************/
-void ConstructMinCoverSeparator(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, jj, k, l, nvtxs, nbnd, bnvtxs[3], bnedges[2], csize;
- idx_t *xadj, *adjncy, *bxadj, *badjncy;
- idx_t *where, *bndind, *bndptr, *vmap, *ivmap, *cover;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
-
- nbnd = graph->nbnd;
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
-
- vmap = iwspacemalloc(ctrl, nvtxs);
- ivmap = iwspacemalloc(ctrl, nbnd);
- cover = iwspacemalloc(ctrl, nbnd);
-
- if (nbnd > 0) {
- /* Go through the boundary and determine the sizes of the bipartite graph */
- bnvtxs[0] = bnvtxs[1] = bnedges[0] = bnedges[1] = 0;
- for (i=0; i<nbnd; i++) {
- j = bndind[i];
- k = where[j];
- if (xadj[j+1]-xadj[j] > 0) {
- bnvtxs[k]++;
- bnedges[k] += xadj[j+1]-xadj[j];
- }
- }
-
- bnvtxs[2] = bnvtxs[0]+bnvtxs[1];
- bnvtxs[1] = bnvtxs[0];
- bnvtxs[0] = 0;
-
- bxadj = iwspacemalloc(ctrl, bnvtxs[2]+1);
- badjncy = iwspacemalloc(ctrl, bnedges[0]+bnedges[1]+1);
-
- /* Construct the ivmap and vmap */
- ASSERT(iset(nvtxs, -1, vmap) == vmap);
- for (i=0; i<nbnd; i++) {
- j = bndind[i];
- k = where[j];
- if (xadj[j+1]-xadj[j] > 0) {
- vmap[j] = bnvtxs[k];
- ivmap[bnvtxs[k]++] = j;
- }
- }
-
- /* OK, go through and put the vertices of each part starting from 0 */
- bnvtxs[1] = bnvtxs[0];
- bnvtxs[0] = 0;
- bxadj[0] = l = 0;
- for (k=0; k<2; k++) {
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[ii];
- if (where[i] == k && xadj[i] < xadj[i+1]) {
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- jj = adjncy[j];
- if (where[jj] != k) {
- ASSERT(bndptr[jj] != -1);
- ASSERTP(vmap[jj] != -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", jj, vmap[jj], graph->bndptr[jj]));
- badjncy[l++] = vmap[jj];
- }
- }
- bxadj[++bnvtxs[k]] = l;
- }
- }
- }
-
- ASSERT(l <= bnedges[0]+bnedges[1]);
-
- MinCover(bxadj, badjncy, bnvtxs[0], bnvtxs[1], cover, &csize);
-
- IFSET(ctrl->dbglvl, METIS_DBG_SEPINFO,
- printf("Nvtxs: %6"PRIDX", [%5"PRIDX" %5"PRIDX"], Cut: %6"PRIDX", SS: [%6"PRIDX" %6"PRIDX"], Cover: %6"PRIDX"\n", nvtxs, graph->pwgts[0], graph->pwgts[1], graph->mincut, bnvtxs[0], bnvtxs[1]-bnvtxs[0], csize));
-
- for (i=0; i<csize; i++) {
- j = ivmap[cover[i]];
- where[j] = 2;
- }
- }
- else {
- IFSET(ctrl->dbglvl, METIS_DBG_SEPINFO,
- printf("Nvtxs: %6"PRIDX", [%5"PRIDX" %5"PRIDX"], Cut: %6"PRIDX", SS: [%6"PRIDX" %6"PRIDX"], Cover: %6"PRIDX"\n", nvtxs, graph->pwgts[0], graph->pwgts[1], graph->mincut, (idx_t)0, (idx_t)0, (idx_t)0));
- }
-
- /* Prepare to refine the vertex separator */
- icopy(nvtxs, graph->where, vmap);
-
- FreeRData(graph);
-
- Allocate2WayNodePartitionMemory(ctrl, graph);
- icopy(nvtxs, vmap, graph->where);
-
- WCOREPOP;
-
- Compute2WayNodePartitionParams(ctrl, graph);
-
- ASSERT(CheckNodePartitionParams(graph));
-
- FM_2WayNodeRefine1Sided(ctrl, graph, ctrl->niter);
-
- ASSERT(IsSeparable(graph));
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/sfm.c b/3rdParty/metis/metis-5.1.0/libmetis/sfm.c
deleted file mode 100644
index d41817380..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/sfm.c
+++ /dev/null
@@ -1,612 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * sfm.c
- *
- * This file contains code that implementes an FM-based separator refinement
- *
- * Started 8/1/97
- * George
- *
- * $Id: sfm.c 10874 2011-10-17 23:13:00Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function performs a node-based FM refinement */
-/**************************************************************************/
-void FM_2WayNodeRefine2Sided(ctrl_t *ctrl, graph_t *graph, idx_t niter)
-{
- idx_t i, ii, j, k, jj, kk, nvtxs, nbnd, nswaps, nmind;
- idx_t *xadj, *vwgt, *adjncy, *where, *pwgts, *edegrees, *bndind, *bndptr;
- idx_t *mptr, *mind, *moved, *swaps;
- rpq_t *queues[2];
- nrinfo_t *rinfo;
- idx_t higain, oldgain, mincut, initcut, mincutorder;
- idx_t pass, to, other, limit;
- idx_t badmaxpwgt, mindiff, newdiff;
- idx_t u[2], g[2];
- real_t mult;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
- pwgts = graph->pwgts;
- rinfo = graph->nrinfo;
-
- queues[0] = rpqCreate(nvtxs);
- queues[1] = rpqCreate(nvtxs);
-
- moved = iwspacemalloc(ctrl, nvtxs);
- swaps = iwspacemalloc(ctrl, nvtxs);
- mptr = iwspacemalloc(ctrl, nvtxs+1);
- mind = iwspacemalloc(ctrl, 2*nvtxs);
-
- mult = 0.5*ctrl->ubfactors[0];
- badmaxpwgt = (idx_t)(mult*(pwgts[0]+pwgts[1]+pwgts[2]));
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions-N2: [%6"PRIDX" %6"PRIDX"] Nv-Nb[%6"PRIDX" %6"PRIDX"]. ISep: %6"PRIDX"\n", pwgts[0], pwgts[1], graph->nvtxs, graph->nbnd, graph->mincut));
-
- for (pass=0; pass<niter; pass++) {
- iset(nvtxs, -1, moved);
- rpqReset(queues[0]);
- rpqReset(queues[1]);
-
- mincutorder = -1;
- initcut = mincut = graph->mincut;
- nbnd = graph->nbnd;
-
- /* use the swaps array in place of the traditional perm array to save memory */
- irandArrayPermute(nbnd, swaps, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[swaps[ii]];
- ASSERT(where[i] == 2);
- rpqInsert(queues[0], i, vwgt[i]-rinfo[i].edegrees[1]);
- rpqInsert(queues[1], i, vwgt[i]-rinfo[i].edegrees[0]);
- }
-
- ASSERT(CheckNodeBnd(graph, nbnd));
- ASSERT(CheckNodePartitionParams(graph));
-
- limit = (ctrl->compress ? gk_min(5*nbnd, 400) : gk_min(2*nbnd, 300));
-
- /******************************************************
- * Get into the FM loop
- *******************************************************/
- mptr[0] = nmind = 0;
- mindiff = iabs(pwgts[0]-pwgts[1]);
- to = (pwgts[0] < pwgts[1] ? 0 : 1);
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- u[0] = rpqSeeTopVal(queues[0]);
- u[1] = rpqSeeTopVal(queues[1]);
- if (u[0] != -1 && u[1] != -1) {
- g[0] = vwgt[u[0]]-rinfo[u[0]].edegrees[1];
- g[1] = vwgt[u[1]]-rinfo[u[1]].edegrees[0];
-
- to = (g[0] > g[1] ? 0 : (g[0] < g[1] ? 1 : pass%2));
-
- if (pwgts[to]+vwgt[u[to]] > badmaxpwgt)
- to = (to+1)%2;
- }
- else if (u[0] == -1 && u[1] == -1) {
- break;
- }
- else if (u[0] != -1 && pwgts[0]+vwgt[u[0]] <= badmaxpwgt) {
- to = 0;
- }
- else if (u[1] != -1 && pwgts[1]+vwgt[u[1]] <= badmaxpwgt) {
- to = 1;
- }
- else
- break;
-
- other = (to+1)%2;
-
- higain = rpqGetTop(queues[to]);
- if (moved[higain] == -1) /* Delete if it was in the separator originally */
- rpqDelete(queues[other], higain);
-
- ASSERT(bndptr[higain] != -1);
-
- /* The following check is to ensure we break out if there is a posibility
- of over-running the mind array. */
- if (nmind + xadj[higain+1]-xadj[higain] >= 2*nvtxs-1)
- break;
-
- pwgts[2] -= (vwgt[higain]-rinfo[higain].edegrees[other]);
-
- newdiff = iabs(pwgts[to]+vwgt[higain] - (pwgts[other]-rinfo[higain].edegrees[other]));
- if (pwgts[2] < mincut || (pwgts[2] == mincut && newdiff < mindiff)) {
- mincut = pwgts[2];
- mincutorder = nswaps;
- mindiff = newdiff;
- }
- else {
- if (nswaps - mincutorder > 2*limit ||
- (nswaps - mincutorder > limit && pwgts[2] > 1.10*mincut)) {
- pwgts[2] += (vwgt[higain]-rinfo[higain].edegrees[other]);
- break; /* No further improvement, break out */
- }
- }
-
- BNDDelete(nbnd, bndind, bndptr, higain);
- pwgts[to] += vwgt[higain];
- where[higain] = to;
- moved[higain] = nswaps;
- swaps[nswaps] = higain;
-
-
- /**********************************************************
- * Update the degrees of the affected nodes
- ***********************************************************/
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2) { /* For the in-separator vertices modify their edegree[to] */
- oldgain = vwgt[k]-rinfo[k].edegrees[to];
- rinfo[k].edegrees[to] += vwgt[higain];
- if (moved[k] == -1 || moved[k] == -(2+other))
- rpqUpdate(queues[other], k, oldgain-vwgt[higain]);
- }
- else if (where[k] == other) { /* This vertex is pulled into the separator */
- ASSERTP(bndptr[k] == -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", k, bndptr[k], where[k]));
- BNDInsert(nbnd, bndind, bndptr, k);
-
- mind[nmind++] = k; /* Keep track for rollback */
- where[k] = 2;
- pwgts[other] -= vwgt[k];
-
- edegrees = rinfo[k].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] != 2)
- edegrees[where[kk]] += vwgt[kk];
- else {
- oldgain = vwgt[kk]-rinfo[kk].edegrees[other];
- rinfo[kk].edegrees[other] -= vwgt[k];
- if (moved[kk] == -1 || moved[kk] == -(2+to))
- rpqUpdate(queues[to], kk, oldgain+vwgt[k]);
- }
- }
-
- /* Insert the new vertex into the priority queue. Only one side! */
- if (moved[k] == -1) {
- rpqInsert(queues[to], k, vwgt[k]-edegrees[other]);
- moved[k] = -(2+to);
- }
- }
- }
- mptr[nswaps+1] = nmind;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" to %3"PRIDX", Gain: %5"PRIDX" [%5"PRIDX"] [%4"PRIDX" %4"PRIDX"] \t[%5"PRIDX" %5"PRIDX" %5"PRIDX"]\n", higain, to, g[to], g[other], vwgt[u[to]], vwgt[u[other]], pwgts[0], pwgts[1], pwgts[2]));
-
- }
-
-
- /****************************************************************
- * Roll back computation
- *****************************************************************/
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- ASSERT(CheckNodePartitionParams(graph));
-
- to = where[higain];
- other = (to+1)%2;
- INC_DEC(pwgts[2], pwgts[to], vwgt[higain]);
- where[higain] = 2;
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- edegrees = rinfo[higain].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2)
- rinfo[k].edegrees[to] -= vwgt[higain];
- else
- edegrees[where[k]] += vwgt[k];
- }
-
- /* Push nodes out of the separator */
- for (j=mptr[nswaps]; j<mptr[nswaps+1]; j++) {
- k = mind[j];
- ASSERT(where[k] == 2);
- where[k] = other;
- INC_DEC(pwgts[other], pwgts[2], vwgt[k]);
- BNDDelete(nbnd, bndind, bndptr, k);
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] == 2)
- rinfo[kk].edegrees[other] += vwgt[k];
- }
- }
- }
-
- ASSERT(mincut == pwgts[2]);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum sep: %6"PRIDX" at %5"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", mincut, mincutorder, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- if (mincutorder == -1 || mincut >= initcut)
- break;
- }
-
- rpqDestroy(queues[0]);
- rpqDestroy(queues[1]);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function performs a node-based FM refinement.
- Each refinement iteration is split into two sub-iterations.
- In each sub-iteration only moves to one of the left/right partitions
- is allowed; hence, it is one-sided.
-*/
-/**************************************************************************/
-void FM_2WayNodeRefine1Sided(ctrl_t *ctrl, graph_t *graph, idx_t niter)
-{
- idx_t i, ii, j, k, jj, kk, nvtxs, nbnd, nswaps, nmind, iend;
- idx_t *xadj, *vwgt, *adjncy, *where, *pwgts, *edegrees, *bndind, *bndptr;
- idx_t *mptr, *mind, *swaps;
- rpq_t *queue;
- nrinfo_t *rinfo;
- idx_t higain, mincut, initcut, mincutorder;
- idx_t pass, to, other, limit;
- idx_t badmaxpwgt, mindiff, newdiff;
- real_t mult;
-
- WCOREPUSH;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
- pwgts = graph->pwgts;
- rinfo = graph->nrinfo;
-
- queue = rpqCreate(nvtxs);
-
- swaps = iwspacemalloc(ctrl, nvtxs);
- mptr = iwspacemalloc(ctrl, nvtxs+1);
- mind = iwspacemalloc(ctrl, 2*nvtxs);
-
- mult = 0.5*ctrl->ubfactors[0];
- badmaxpwgt = (idx_t)(mult*(pwgts[0]+pwgts[1]+pwgts[2]));
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions-N1: [%6"PRIDX" %6"PRIDX"] Nv-Nb[%6"PRIDX" %6"PRIDX"]. ISep: %6"PRIDX"\n", pwgts[0], pwgts[1], graph->nvtxs, graph->nbnd, graph->mincut));
-
- to = (pwgts[0] < pwgts[1] ? 1 : 0);
- for (pass=0; pass<2*niter; pass++) { /* the 2*niter is for the two sides */
- other = to;
- to = (to+1)%2;
-
- rpqReset(queue);
-
- mincutorder = -1;
- initcut = mincut = graph->mincut;
- nbnd = graph->nbnd;
-
- /* use the swaps array in place of the traditional perm array to save memory */
- irandArrayPermute(nbnd, swaps, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[swaps[ii]];
- ASSERT(where[i] == 2);
- rpqInsert(queue, i, vwgt[i]-rinfo[i].edegrees[other]);
- }
-
- ASSERT(CheckNodeBnd(graph, nbnd));
- ASSERT(CheckNodePartitionParams(graph));
-
- limit = (ctrl->compress ? gk_min(5*nbnd, 500) : gk_min(3*nbnd, 300));
-
- /******************************************************
- * Get into the FM loop
- *******************************************************/
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->Aux3Tmr));
- mptr[0] = nmind = 0;
- mindiff = iabs(pwgts[0]-pwgts[1]);
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if ((higain = rpqGetTop(queue)) == -1)
- break;
-
- ASSERT(bndptr[higain] != -1);
-
- /* The following check is to ensure we break out if there is a posibility
- of over-running the mind array. */
- if (nmind + xadj[higain+1]-xadj[higain] >= 2*nvtxs-1)
- break;
-
- if (pwgts[to]+vwgt[higain] > badmaxpwgt)
- break; /* No point going any further. Balance will be bad */
-
- pwgts[2] -= (vwgt[higain]-rinfo[higain].edegrees[other]);
-
- newdiff = iabs(pwgts[to]+vwgt[higain] - (pwgts[other]-rinfo[higain].edegrees[other]));
- if (pwgts[2] < mincut || (pwgts[2] == mincut && newdiff < mindiff)) {
- mincut = pwgts[2];
- mincutorder = nswaps;
- mindiff = newdiff;
- }
- else {
- if (nswaps - mincutorder > 3*limit ||
- (nswaps - mincutorder > limit && pwgts[2] > 1.10*mincut)) {
- pwgts[2] += (vwgt[higain]-rinfo[higain].edegrees[other]);
- break; /* No further improvement, break out */
- }
- }
-
- BNDDelete(nbnd, bndind, bndptr, higain);
- pwgts[to] += vwgt[higain];
- where[higain] = to;
- swaps[nswaps] = higain;
-
-
- /**********************************************************
- * Update the degrees of the affected nodes
- ***********************************************************/
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->Aux1Tmr));
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
-
- if (where[k] == 2) { /* For the in-separator vertices modify their edegree[to] */
- rinfo[k].edegrees[to] += vwgt[higain];
- }
- else if (where[k] == other) { /* This vertex is pulled into the separator */
- ASSERTP(bndptr[k] == -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", k, bndptr[k], where[k]));
- BNDInsert(nbnd, bndind, bndptr, k);
-
- mind[nmind++] = k; /* Keep track for rollback */
- where[k] = 2;
- pwgts[other] -= vwgt[k];
-
- edegrees = rinfo[k].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (jj=xadj[k], iend=xadj[k+1]; jj<iend; jj++) {
- kk = adjncy[jj];
- if (where[kk] != 2)
- edegrees[where[kk]] += vwgt[kk];
- else {
- rinfo[kk].edegrees[other] -= vwgt[k];
-
- /* Since the moves are one-sided this vertex has not been moved yet */
- rpqUpdate(queue, kk, vwgt[kk]-rinfo[kk].edegrees[other]);
- }
- }
-
- /* Insert the new vertex into the priority queue. Safe due to one-sided moves */
- rpqInsert(queue, k, vwgt[k]-edegrees[other]);
- }
- }
- mptr[nswaps+1] = nmind;
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->Aux1Tmr));
-
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" to %3"PRIDX", Gain: %5"PRIDX" [%5"PRIDX"] \t[%5"PRIDX" %5"PRIDX" %5"PRIDX"] [%3"PRIDX" %2"PRIDX"]\n",
- higain, to, (vwgt[higain]-rinfo[higain].edegrees[other]), vwgt[higain],
- pwgts[0], pwgts[1], pwgts[2], nswaps, limit));
- }
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->Aux3Tmr));
-
-
- /****************************************************************
- * Roll back computation
- *****************************************************************/
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->Aux2Tmr));
- for (nswaps--; nswaps>mincutorder; nswaps--) {
- higain = swaps[nswaps];
-
- ASSERT(CheckNodePartitionParams(graph));
- ASSERT(where[higain] == to);
-
- INC_DEC(pwgts[2], pwgts[to], vwgt[higain]);
- where[higain] = 2;
- BNDInsert(nbnd, bndind, bndptr, higain);
-
- edegrees = rinfo[higain].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2)
- rinfo[k].edegrees[to] -= vwgt[higain];
- else
- edegrees[where[k]] += vwgt[k];
- }
-
- /* Push nodes out of the separator */
- for (j=mptr[nswaps]; j<mptr[nswaps+1]; j++) {
- k = mind[j];
- ASSERT(where[k] == 2);
- where[k] = other;
- INC_DEC(pwgts[other], pwgts[2], vwgt[k]);
- BNDDelete(nbnd, bndind, bndptr, k);
- for (jj=xadj[k], iend=xadj[k+1]; jj<iend; jj++) {
- kk = adjncy[jj];
- if (where[kk] == 2)
- rinfo[kk].edegrees[other] += vwgt[k];
- }
- }
- }
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->Aux2Tmr));
-
- ASSERT(mincut == pwgts[2]);
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tMinimum sep: %6"PRIDX" at %5"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", mincut, mincutorder, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = mincut;
- graph->nbnd = nbnd;
-
- if (pass%2 == 1 && (mincutorder == -1 || mincut >= initcut))
- break;
- }
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
-
-/*************************************************************************/
-/*! This function balances the left/right partitions of a separator
- tri-section */
-/*************************************************************************/
-void FM_2WayNodeBalance(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, ii, j, k, jj, kk, nvtxs, nbnd, nswaps, gain;
- idx_t badmaxpwgt, higain, oldgain, pass, to, other;
- idx_t *xadj, *vwgt, *adjncy, *where, *pwgts, *edegrees, *bndind, *bndptr;
- idx_t *perm, *moved;
- rpq_t *queue;
- nrinfo_t *rinfo;
- real_t mult;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
-
- bndind = graph->bndind;
- bndptr = graph->bndptr;
- where = graph->where;
- pwgts = graph->pwgts;
- rinfo = graph->nrinfo;
-
- mult = 0.5*ctrl->ubfactors[0];
-
- badmaxpwgt = (idx_t)(mult*(pwgts[0]+pwgts[1]));
- if (gk_max(pwgts[0], pwgts[1]) < badmaxpwgt)
- return;
- if (iabs(pwgts[0]-pwgts[1]) < 3*graph->tvwgt[0]/nvtxs)
- return;
-
- WCOREPUSH;
-
- to = (pwgts[0] < pwgts[1] ? 0 : 1);
- other = (to+1)%2;
-
- queue = rpqCreate(nvtxs);
-
- perm = iwspacemalloc(ctrl, nvtxs);
- moved = iset(nvtxs, -1, iwspacemalloc(ctrl, nvtxs));
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("Partitions: [%6"PRIDX" %6"PRIDX"] Nv-Nb[%6"PRIDX" %6"PRIDX"]. ISep: %6"PRIDX" [B]\n", pwgts[0], pwgts[1], graph->nvtxs, graph->nbnd, graph->mincut));
-
- nbnd = graph->nbnd;
- irandArrayPermute(nbnd, perm, nbnd, 1);
- for (ii=0; ii<nbnd; ii++) {
- i = bndind[perm[ii]];
- ASSERT(where[i] == 2);
- rpqInsert(queue, i, vwgt[i]-rinfo[i].edegrees[other]);
- }
-
- ASSERT(CheckNodeBnd(graph, nbnd));
- ASSERT(CheckNodePartitionParams(graph));
-
- /******************************************************
- * Get into the FM loop
- *******************************************************/
- for (nswaps=0; nswaps<nvtxs; nswaps++) {
- if ((higain = rpqGetTop(queue)) == -1)
- break;
-
- moved[higain] = 1;
-
- gain = vwgt[higain]-rinfo[higain].edegrees[other];
- badmaxpwgt = (idx_t)(mult*(pwgts[0]+pwgts[1]));
-
- /* break if other is now underwight */
- if (pwgts[to] > pwgts[other])
- break;
-
- /* break if balance is achieved and no +ve or zero gain */
- if (gain < 0 && pwgts[other] < badmaxpwgt)
- break;
-
- /* skip this vertex if it will violate balance on the other side */
- if (pwgts[to]+vwgt[higain] > badmaxpwgt)
- continue;
-
- ASSERT(bndptr[higain] != -1);
-
- pwgts[2] -= gain;
-
- BNDDelete(nbnd, bndind, bndptr, higain);
- pwgts[to] += vwgt[higain];
- where[higain] = to;
-
- IFSET(ctrl->dbglvl, METIS_DBG_MOVEINFO,
- printf("Moved %6"PRIDX" to %3"PRIDX", Gain: %3"PRIDX", \t[%5"PRIDX" %5"PRIDX" %5"PRIDX"]\n", higain, to, vwgt[higain]-rinfo[higain].edegrees[other], pwgts[0], pwgts[1], pwgts[2]));
-
-
- /**********************************************************
- * Update the degrees of the affected nodes
- ***********************************************************/
- for (j=xadj[higain]; j<xadj[higain+1]; j++) {
- k = adjncy[j];
- if (where[k] == 2) { /* For the in-separator vertices modify their edegree[to] */
- rinfo[k].edegrees[to] += vwgt[higain];
- }
- else if (where[k] == other) { /* This vertex is pulled into the separator */
- ASSERTP(bndptr[k] == -1, ("%"PRIDX" %"PRIDX" %"PRIDX"\n", k, bndptr[k], where[k]));
- BNDInsert(nbnd, bndind, bndptr, k);
-
- where[k] = 2;
- pwgts[other] -= vwgt[k];
-
- edegrees = rinfo[k].edegrees;
- edegrees[0] = edegrees[1] = 0;
- for (jj=xadj[k]; jj<xadj[k+1]; jj++) {
- kk = adjncy[jj];
- if (where[kk] != 2)
- edegrees[where[kk]] += vwgt[kk];
- else {
- ASSERT(bndptr[kk] != -1);
- oldgain = vwgt[kk]-rinfo[kk].edegrees[other];
- rinfo[kk].edegrees[other] -= vwgt[k];
-
- if (moved[kk] == -1)
- rpqUpdate(queue, kk, oldgain+vwgt[k]);
- }
- }
-
- /* Insert the new vertex into the priority queue */
- rpqInsert(queue, k, vwgt[k]-edegrees[other]);
- }
- }
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_REFINE,
- printf("\tBalanced sep: %6"PRIDX" at %4"PRIDX", PWGTS: [%6"PRIDX" %6"PRIDX"], NBND: %6"PRIDX"\n", pwgts[2], nswaps, pwgts[0], pwgts[1], nbnd));
-
- graph->mincut = pwgts[2];
- graph->nbnd = nbnd;
-
- rpqDestroy(queue);
-
- WCOREPOP;
-}
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/srefine.c b/3rdParty/metis/metis-5.1.0/libmetis/srefine.c
deleted file mode 100644
index 603f782ad..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/srefine.c
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * srefine.c
- *
- * This file contains code for the separator refinement algortihms
- *
- * Started 8/1/97
- * George
- *
- * $Id: srefine.c 10515 2011-07-08 15:46:18Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function is the entry point of the separator refinement.
- It does not perform any refinement on graph, but it starts by first
- projecting it to the next level finer graph and proceeds from there. */
-/*************************************************************************/
-void Refine2WayNode(ctrl_t *ctrl, graph_t *orggraph, graph_t *graph)
-{
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->UncoarsenTmr));
-
- if (graph == orggraph) {
- Compute2WayNodePartitionParams(ctrl, graph);
- }
- else {
- do {
- graph = graph->finer;
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ProjectTmr));
- Project2WayNodePartition(ctrl, graph);
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->ProjectTmr));
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->RefTmr));
- FM_2WayNodeBalance(ctrl, graph);
-
- ASSERT(CheckNodePartitionParams(graph));
-
- switch (ctrl->rtype) {
- case METIS_RTYPE_SEP2SIDED:
- FM_2WayNodeRefine2Sided(ctrl, graph, ctrl->niter);
- break;
- case METIS_RTYPE_SEP1SIDED:
- FM_2WayNodeRefine1Sided(ctrl, graph, ctrl->niter);
- break;
- default:
- gk_errexit(SIGERR, "Unknown rtype of %d\n", ctrl->rtype);
- }
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->RefTmr));
-
- } while (graph != orggraph);
- }
-
- IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_stopcputimer(ctrl->UncoarsenTmr));
-}
-
-
-/*************************************************************************/
-/*! This function allocates memory for 2-way node-based refinement */
-/**************************************************************************/
-void Allocate2WayNodePartitionMemory(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t nvtxs;
-
- nvtxs = graph->nvtxs;
-
- graph->pwgts = imalloc(3, "Allocate2WayNodePartitionMemory: pwgts");
- graph->where = imalloc(nvtxs, "Allocate2WayNodePartitionMemory: where");
- graph->bndptr = imalloc(nvtxs, "Allocate2WayNodePartitionMemory: bndptr");
- graph->bndind = imalloc(nvtxs, "Allocate2WayNodePartitionMemory: bndind");
- graph->nrinfo = (nrinfo_t *)gk_malloc(nvtxs*sizeof(nrinfo_t), "Allocate2WayNodePartitionMemory: nrinfo");
-}
-
-
-/*************************************************************************/
-/*! This function computes the edegrees[] to the left & right sides */
-/*************************************************************************/
-void Compute2WayNodePartitionParams(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, nvtxs, nbnd;
- idx_t *xadj, *adjncy, *vwgt;
- idx_t *where, *pwgts, *bndind, *bndptr, *edegrees;
- nrinfo_t *rinfo;
- idx_t me, other;
-
- nvtxs = graph->nvtxs;
- xadj = graph->xadj;
- vwgt = graph->vwgt;
- adjncy = graph->adjncy;
-
- where = graph->where;
- rinfo = graph->nrinfo;
- pwgts = iset(3, 0, graph->pwgts);
- bndind = graph->bndind;
- bndptr = iset(nvtxs, -1, graph->bndptr);
-
-
- /*------------------------------------------------------------
- / Compute now the separator external degrees
- /------------------------------------------------------------*/
- nbnd = 0;
- for (i=0; i<nvtxs; i++) {
- me = where[i];
- pwgts[me] += vwgt[i];
-
- ASSERT(me >=0 && me <= 2);
-
- if (me == 2) { /* If it is on the separator do some computations */
- BNDInsert(nbnd, bndind, bndptr, i);
-
- edegrees = rinfo[i].edegrees;
- edegrees[0] = edegrees[1] = 0;
-
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- other = where[adjncy[j]];
- if (other != 2)
- edegrees[other] += vwgt[adjncy[j]];
- }
- }
- }
-
- ASSERT(CheckNodeBnd(graph, nbnd));
-
- graph->mincut = pwgts[2];
- graph->nbnd = nbnd;
-}
-
-
-/*************************************************************************/
-/*! This function projects the node-based bisection */
-/*************************************************************************/
-void Project2WayNodePartition(ctrl_t *ctrl, graph_t *graph)
-{
- idx_t i, j, nvtxs;
- idx_t *cmap, *where, *cwhere;
- graph_t *cgraph;
-
- cgraph = graph->coarser;
- cwhere = cgraph->where;
-
- nvtxs = graph->nvtxs;
- cmap = graph->cmap;
-
- Allocate2WayNodePartitionMemory(ctrl, graph);
- where = graph->where;
-
- /* Project the partition */
- for (i=0; i<nvtxs; i++) {
- where[i] = cwhere[cmap[i]];
- ASSERTP(where[i] >= 0 && where[i] <= 2, ("%"PRIDX" %"PRIDX" %"PRIDX" %"PRIDX"\n",
- i, cmap[i], where[i], cwhere[cmap[i]]));
- }
-
- FreeGraph(&graph->coarser);
- graph->coarser = NULL;
-
- Compute2WayNodePartitionParams(ctrl, graph);
-}
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/stat.c b/3rdParty/metis/metis-5.1.0/libmetis/stat.c
deleted file mode 100644
index f19791b53..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/stat.c
+++ /dev/null
@@ -1,179 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * stat.c
- *
- * This file computes various statistics
- *
- * Started 7/25/97
- * George
- *
- * $Id: stat.c 9942 2011-05-17 22:09:52Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************
-* This function computes cuts and balance information
-**************************************************************************/
-void ComputePartitionInfoBipartite(graph_t *graph, idx_t nparts, idx_t *where)
-{
- idx_t i, j, k, nvtxs, ncon, mustfree=0;
- idx_t *xadj, *adjncy, *vwgt, *vsize, *adjwgt, *kpwgts, *tmpptr;
- idx_t *padjncy, *padjwgt, *padjcut;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- xadj = graph->xadj;
- adjncy = graph->adjncy;
- vwgt = graph->vwgt;
- vsize = graph->vsize;
- adjwgt = graph->adjwgt;
-
- if (vwgt == NULL) {
- vwgt = graph->vwgt = ismalloc(nvtxs, 1, "vwgt");
- mustfree = 1;
- }
- if (adjwgt == NULL) {
- adjwgt = graph->adjwgt = ismalloc(xadj[nvtxs], 1, "adjwgt");
- mustfree += 2;
- }
-
- printf("%"PRIDX"-way Cut: %5"PRIDX", Vol: %5"PRIDX", ", nparts, ComputeCut(graph, where), ComputeVolume(graph, where));
-
- /* Compute balance information */
- kpwgts = ismalloc(ncon*nparts, 0, "ComputePartitionInfo: kpwgts");
-
- for (i=0; i<nvtxs; i++) {
- for (j=0; j<ncon; j++)
- kpwgts[where[i]*ncon+j] += vwgt[i*ncon+j];
- }
-
- if (ncon == 1) {
- printf("\tBalance: %5.3"PRREAL" out of %5.3"PRREAL"\n",
- 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1)),
- 1.0*nparts*vwgt[iargmax(nvtxs, vwgt)]/(1.0*isum(nparts, kpwgts, 1)));
- }
- else {
- printf("\tBalance:");
- for (j=0; j<ncon; j++)
- printf(" (%5.3"PRREAL" out of %5.3"PRREAL")",
- 1.0*nparts*kpwgts[ncon*iargmax_strd(nparts, kpwgts+j, ncon)+j]/(1.0*isum(nparts, kpwgts+j, ncon)),
- 1.0*nparts*vwgt[ncon*iargmax_strd(nvtxs, vwgt+j, ncon)+j]/(1.0*isum(nparts, kpwgts+j, ncon)));
- printf("\n");
- }
-
-
- /* Compute p-adjncy information */
- padjncy = ismalloc(nparts*nparts, 0, "ComputePartitionInfo: padjncy");
- padjwgt = ismalloc(nparts*nparts, 0, "ComputePartitionInfo: padjwgt");
- padjcut = ismalloc(nparts*nparts, 0, "ComputePartitionInfo: padjwgt");
-
- iset(nparts, 0, kpwgts);
- for (i=0; i<nvtxs; i++) {
- for (j=xadj[i]; j<xadj[i+1]; j++) {
- if (where[i] != where[adjncy[j]]) {
- padjncy[where[i]*nparts+where[adjncy[j]]] = 1;
- padjcut[where[i]*nparts+where[adjncy[j]]] += adjwgt[j];
- if (kpwgts[where[adjncy[j]]] == 0) {
- padjwgt[where[i]*nparts+where[adjncy[j]]] += vsize[i];
- kpwgts[where[adjncy[j]]] = 1;
- }
- }
- }
- for (j=xadj[i]; j<xadj[i+1]; j++)
- kpwgts[where[adjncy[j]]] = 0;
- }
-
- for (i=0; i<nparts; i++)
- kpwgts[i] = isum(nparts, padjncy+i*nparts, 1);
- printf("Min/Max/Avg/Bal # of adjacent subdomains: %5"PRIDX" %5"PRIDX" %5"PRIDX" %7.3"PRREAL"\n",
- kpwgts[iargmin(nparts, kpwgts)], kpwgts[iargmax(nparts, kpwgts)], isum(nparts, kpwgts, 1)/nparts,
- 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1)));
-
- for (i=0; i<nparts; i++)
- kpwgts[i] = isum(nparts, padjcut+i*nparts, 1);
- printf("Min/Max/Avg/Bal # of adjacent subdomain cuts: %5"PRIDX" %5"PRIDX" %5"PRIDX" %7.3"PRREAL"\n",
- kpwgts[iargmin(nparts, kpwgts)], kpwgts[iargmax(nparts, kpwgts)], isum(nparts, kpwgts, 1)/nparts,
- 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1)));
-
- for (i=0; i<nparts; i++)
- kpwgts[i] = isum(nparts, padjwgt+i*nparts, 1);
- printf("Min/Max/Avg/Bal/Frac # of interface nodes: %5"PRIDX" %5"PRIDX" %5"PRIDX" %7.3"PRREAL" %7.3"PRREAL"\n",
- kpwgts[iargmin(nparts, kpwgts)], kpwgts[iargmax(nparts, kpwgts)], isum(nparts, kpwgts, 1)/nparts,
- 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1)), 1.0*isum(nparts, kpwgts, 1)/(1.0*nvtxs));
-
-
- if (mustfree == 1 || mustfree == 3) {
- gk_free((void **)&vwgt, LTERM);
- graph->vwgt = NULL;
- }
- if (mustfree == 2 || mustfree == 3) {
- gk_free((void **)&adjwgt, LTERM);
- graph->adjwgt = NULL;
- }
-
- gk_free((void **)&kpwgts, &padjncy, &padjwgt, &padjcut, LTERM);
-}
-
-
-/*************************************************************************
-* This function computes the balance of the partitioning
-**************************************************************************/
-void ComputePartitionBalance(graph_t *graph, idx_t nparts, idx_t *where, real_t *ubvec)
-{
- idx_t i, j, nvtxs, ncon;
- idx_t *kpwgts, *vwgt;
- real_t balance;
-
- nvtxs = graph->nvtxs;
- ncon = graph->ncon;
- vwgt = graph->vwgt;
-
- kpwgts = ismalloc(nparts, 0, "ComputePartitionInfo: kpwgts");
-
- if (vwgt == NULL) {
- for (i=0; i<nvtxs; i++)
- kpwgts[where[i]]++;
- ubvec[0] = 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*nvtxs);
- }
- else {
- for (j=0; j<ncon; j++) {
- iset(nparts, 0, kpwgts);
- for (i=0; i<graph->nvtxs; i++)
- kpwgts[where[i]] += vwgt[i*ncon+j];
-
- ubvec[j] = 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1));
- }
- }
-
- gk_free((void **)&kpwgts, LTERM);
-
-}
-
-
-/*************************************************************************
-* This function computes the balance of the element partitioning
-**************************************************************************/
-real_t ComputeElementBalance(idx_t ne, idx_t nparts, idx_t *where)
-{
- idx_t i;
- idx_t *kpwgts;
- real_t balance;
-
- kpwgts = ismalloc(nparts, 0, "ComputeElementBalance: kpwgts");
-
- for (i=0; i<ne; i++)
- kpwgts[where[i]]++;
-
- balance = 1.0*nparts*kpwgts[iargmax(nparts, kpwgts)]/(1.0*isum(nparts, kpwgts, 1));
-
- gk_free((void **)&kpwgts, LTERM);
-
- return balance;
-
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/stdheaders.h b/3rdParty/metis/metis-5.1.0/libmetis/stdheaders.h
deleted file mode 100644
index 148f88d48..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/stdheaders.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * stdheaders.h
- *
- * This file includes all necessary header files
- *
- * Started 8/27/94
- * George
- *
- * $Id: stdheaders.h 5993 2009-01-07 02:09:57Z karypis $
- */
-
-#ifndef _LIBMETIS_STDHEADERS_H_
-#define _LIBMETIS_STDHEADERS_H_
-
-#include <stdio.h>
-#ifdef __STDC__
-#include <stdlib.h>
-#else
-#include <malloc.h>
-#endif
-#include <string.h>
-#include <ctype.h>
-#include <math.h>
-#include <stdarg.h>
-#include <time.h>
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/struct.h b/3rdParty/metis/metis-5.1.0/libmetis/struct.h
deleted file mode 100644
index 5fc8588df..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/struct.h
+++ /dev/null
@@ -1,206 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * struct.h
- *
- * This file contains data structures for ILU routines.
- *
- * Started 9/26/95
- * George
- *
- * $Id: struct.h 13900 2013-03-24 15:27:07Z karypis $
- */
-
-#ifndef _LIBMETIS_STRUCT_H_
-#define _LIBMETIS_STRUCT_H_
-
-
-
-/*************************************************************************/
-/*! This data structure stores cut-based k-way refinement info about an
- adjacent subdomain for a given vertex. */
-/*************************************************************************/
-typedef struct cnbr_t {
- idx_t pid; /*!< The partition ID */
- idx_t ed; /*!< The sum of the weights of the adjacent edges
- that are incident on pid */
-} cnbr_t;
-
-
-/*************************************************************************/
-/*! The following data structure stores holds information on degrees for k-way
- partition */
-/*************************************************************************/
-typedef struct ckrinfo_t {
- idx_t id; /*!< The internal degree of a vertex (sum of weights) */
- idx_t ed; /*!< The total external degree of a vertex */
- idx_t nnbrs; /*!< The number of neighboring subdomains */
- idx_t inbr; /*!< The index in the cnbr_t array where the nnbrs list
- of neighbors is stored */
-} ckrinfo_t;
-
-
-/*************************************************************************/
-/*! This data structure stores volume-based k-way refinement info about an
- adjacent subdomain for a given vertex. */
-/*************************************************************************/
-typedef struct vnbr_t {
- idx_t pid; /*!< The partition ID */
- idx_t ned; /*!< The number of the adjacent edges
- that are incident on pid */
- idx_t gv; /*!< The gain in volume achieved by moving the
- vertex to pid */
-} vnbr_t;
-
-
-/*************************************************************************/
-/*! The following data structure holds information on degrees for k-way
- vol-based partition */
-/*************************************************************************/
-typedef struct vkrinfo_t {
- idx_t nid; /*!< The internal degree of a vertex (count of edges) */
- idx_t ned; /*!< The total external degree of a vertex (count of edges) */
- idx_t gv; /*!< The volume gain of moving that vertex */
- idx_t nnbrs; /*!< The number of neighboring subdomains */
- idx_t inbr; /*!< The index in the vnbr_t array where the nnbrs list
- of neighbors is stored */
-} vkrinfo_t;
-
-
-/*************************************************************************/
-/*! The following data structure holds information on degrees for k-way
- partition */
-/*************************************************************************/
-typedef struct nrinfo_t {
- idx_t edegrees[2];
-} nrinfo_t;
-
-
-/*************************************************************************/
-/*! This data structure holds a graph */
-/*************************************************************************/
-typedef struct graph_t {
- idx_t nvtxs, nedges; /* The # of vertices and edges in the graph */
- idx_t ncon; /* The # of constrains */
- idx_t *xadj; /* Pointers to the locally stored vertices */
- idx_t *vwgt; /* Vertex weights */
- idx_t *vsize; /* Vertex sizes for min-volume formulation */
- idx_t *adjncy; /* Array that stores the adjacency lists of nvtxs */
- idx_t *adjwgt; /* Array that stores the weights of the adjacency lists */
-
- idx_t *tvwgt; /* The sum of the vertex weights in the graph */
- real_t *invtvwgt; /* The inverse of the sum of the vertex weights in the graph */
-
-
- /* These are to keep track control if the corresponding fields correspond to
- application or library memory */
- int free_xadj, free_vwgt, free_vsize, free_adjncy, free_adjwgt;
-
- idx_t *label;
-
- idx_t *cmap;
-
- /* Partition parameters */
- idx_t mincut, minvol;
- idx_t *where, *pwgts;
- idx_t nbnd;
- idx_t *bndptr, *bndind;
-
- /* Bisection refinement parameters */
- idx_t *id, *ed;
-
- /* K-way refinement parameters */
- ckrinfo_t *ckrinfo; /*!< The per-vertex cut-based refinement info */
- vkrinfo_t *vkrinfo; /*!< The per-vertex volume-based refinement info */
-
- /* Node refinement information */
- nrinfo_t *nrinfo;
-
- struct graph_t *coarser, *finer;
-} graph_t;
-
-
-/*************************************************************************/
-/*! This data structure holds a mesh */
-/*************************************************************************/
-typedef struct mesh_t {
- idx_t ne, nn; /*!< The # of elements and nodes in the mesh */
- idx_t ncon; /*!< The number of element balancing constraints (element weights) */
-
- idx_t *eptr, *eind; /*!< The CSR-structure storing the nodes in the elements */
- idx_t *ewgt; /*!< The weights of the elements */
-} mesh_t;
-
-
-
-/*************************************************************************/
-/*! The following structure stores information used by Metis */
-/*************************************************************************/
-typedef struct ctrl_t {
- moptype_et optype; /* Type of operation */
- mobjtype_et objtype; /* Type of refinement objective */
- mdbglvl_et dbglvl; /* Controls the debuging output of the program */
- mctype_et ctype; /* The type of coarsening */
- miptype_et iptype; /* The type of initial partitioning */
- mrtype_et rtype; /* The type of refinement */
-
- idx_t CoarsenTo; /* The # of vertices in the coarsest graph */
- idx_t nIparts; /* The number of initial partitions to compute */
- idx_t no2hop; /* Indicates if 2-hop matching will be used */
- idx_t minconn; /* Indicates if the subdomain connectivity will be minimized */
- idx_t contig; /* Indicates if contigous partitions are required */
- idx_t nseps; /* The number of separators to be found during multiple bisections */
- idx_t ufactor; /* The user-supplied load imbalance factor */
- idx_t compress; /* If the graph will be compressed prior to ordering */
- idx_t ccorder; /* If connected components will be ordered separately */
- idx_t seed; /* The seed for the random number generator */
- idx_t ncuts; /* The number of different partitionings to compute */
- idx_t niter; /* The number of iterations during each refinement */
- idx_t numflag; /* The user-supplied numflag for the graph */
- idx_t *maxvwgt; /* The maximum allowed weight for a vertex */
-
- idx_t ncon; /*!< The number of balancing constraints */
- idx_t nparts; /*!< The number of partitions */
-
- real_t pfactor; /* .1*(user-supplied prunning factor) */
-
- real_t *ubfactors; /*!< The per-constraint ubfactors */
-
- real_t *tpwgts; /*!< The target partition weights */
- real_t *pijbm; /*!< The nparts*ncon multiplies for the ith partition
- and jth constraint for obtaining the balance */
-
- real_t cfactor; /*!< The achieved compression factor */
-
- /* Various Timers */
- double TotalTmr, InitPartTmr, MatchTmr, ContractTmr, CoarsenTmr, UncoarsenTmr,
- RefTmr, ProjectTmr, SplitTmr, Aux1Tmr, Aux2Tmr, Aux3Tmr;
-
- /* Workspace information */
- gk_mcore_t *mcore; /*!< The persistent memory core for within function
- mallocs/frees */
-
- /* These are for use by the k-way refinement routines */
- size_t nbrpoolsize; /*!< The number of {c,v}nbr_t entries that have been allocated */
- size_t nbrpoolcpos; /*!< The position of the first free entry in the array */
- size_t nbrpoolreallocs; /*!< The number of times the pool was resized */
-
- cnbr_t *cnbrpool; /*!< The pool of cnbr_t entries to be used during refinement.
- The size and current position of the pool is controlled
- by nnbrs & cnbrs */
- vnbr_t *vnbrpool; /*!< The pool of vnbr_t entries to be used during refinement.
- The size and current position of the pool is controlled
- by nnbrs & cnbrs */
-
- /* The subdomain graph, in sparse format */
- idx_t *maxnads; /* The maximum allocated number of adjacent domains */
- idx_t *nads; /* The number of adjacent domains */
- idx_t **adids; /* The IDs of the adjacent domains */
- idx_t **adwgts; /* The edge-weight to the adjacent domains */
- idx_t *pvec1, *pvec2; /* Auxiliar nparts-size vectors for efficiency */
-
-} ctrl_t;
-
-
-
-#endif
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/timing.c b/3rdParty/metis/metis-5.1.0/libmetis/timing.c
deleted file mode 100644
index 9d6e05cf1..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/timing.c
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * timing.c
- *
- * This file contains routines that deal with timing Metis
- *
- * Started 7/24/97
- * George
- *
- * $Id: timing.c 13936 2013-03-30 03:59:09Z karypis $
- *
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************
-* This function clears the timers
-**************************************************************************/
-void InitTimers(ctrl_t *ctrl)
-{
- gk_clearcputimer(ctrl->TotalTmr);
- gk_clearcputimer(ctrl->InitPartTmr);
- gk_clearcputimer(ctrl->MatchTmr);
- gk_clearcputimer(ctrl->ContractTmr);
- gk_clearcputimer(ctrl->CoarsenTmr);
- gk_clearcputimer(ctrl->UncoarsenTmr);
- gk_clearcputimer(ctrl->RefTmr);
- gk_clearcputimer(ctrl->ProjectTmr);
- gk_clearcputimer(ctrl->SplitTmr);
- gk_clearcputimer(ctrl->Aux1Tmr);
- gk_clearcputimer(ctrl->Aux2Tmr);
- gk_clearcputimer(ctrl->Aux3Tmr);
-}
-
-
-
-/*************************************************************************
-* This function prints the various timers
-**************************************************************************/
-void PrintTimers(ctrl_t *ctrl)
-{
- printf("\nTiming Information -------------------------------------------------");
- printf("\n Multilevel: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->TotalTmr));
- printf("\n Coarsening: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->CoarsenTmr));
- printf("\n Matching: \t\t\t %7.3"PRREAL"", gk_getcputimer(ctrl->MatchTmr));
- printf("\n Contract: \t\t\t %7.3"PRREAL"", gk_getcputimer(ctrl->ContractTmr));
- printf("\n Initial Partition: \t %7.3"PRREAL"", gk_getcputimer(ctrl->InitPartTmr));
- printf("\n Uncoarsening: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->UncoarsenTmr));
- printf("\n Refinement: \t\t\t %7.3"PRREAL"", gk_getcputimer(ctrl->RefTmr));
- printf("\n Projection: \t\t\t %7.3"PRREAL"", gk_getcputimer(ctrl->ProjectTmr));
- printf("\n Splitting: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->SplitTmr));
-/*
- printf("\n Aux1Tmr: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->Aux1Tmr));
- printf("\n Aux2Tmr: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->Aux2Tmr));
- printf("\n Aux3Tmr: \t\t %7.3"PRREAL"", gk_getcputimer(ctrl->Aux3Tmr));
-*/
- printf("\n********************************************************************\n");
-}
-
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/util.c b/3rdParty/metis/metis-5.1.0/libmetis/util.c
deleted file mode 100644
index 7fbc46726..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/util.c
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
- * Copyright 1997, Regents of the University of Minnesota
- *
- * util.c
- *
- * This function contains various utility routines
- *
- * Started 9/28/95
- * George
- *
- * $Id: util.c 10495 2011-07-06 16:04:45Z karypis $
- */
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function initializes the random number generator
- */
-/*************************************************************************/
-void InitRandom(idx_t seed)
-{
- isrand((seed == -1 ? 4321 : seed));
-}
-
-
-/*************************************************************************/
-/*! Returns the highest weight index of x[i]*y[i]
- */
-/*************************************************************************/
-idx_t iargmax_nrm(size_t n, idx_t *x, real_t *y)
-{
- idx_t i, max=0;
-
- for (i=1; i<n; i++)
- max = (x[i]*y[i] > x[max]*y[max] ? i : max);
-
- return max;
-}
-
-
-/*************************************************************************/
-/*! These functions return the index of the maximum element in a vector
- */
-/*************************************************************************/
-idx_t iargmax_strd(size_t n, idx_t *x, idx_t incx)
-{
- size_t i, max=0;
-
- n *= incx;
- for (i=incx; i<n; i+=incx)
- max = (x[i] > x[max] ? i : max);
-
- return max/incx;
-}
-
-
-/*************************************************************************/
-/*! These functions return the index of the almost maximum element in a
- vector
- */
-/*************************************************************************/
-idx_t rargmax2(size_t n, real_t *x)
-{
- size_t i, max1, max2;
-
- if (x[0] > x[1]) {
- max1 = 0;
- max2 = 1;
- }
- else {
- max1 = 1;
- max2 = 0;
- }
-
- for (i=2; i<n; i++) {
- if (x[i] > x[max1]) {
- max2 = max1;
- max1 = i;
- }
- else if (x[i] > x[max2])
- max2 = i;
- }
-
- return max2;
-}
-
-
-/*************************************************************************/
-/*! These functions return the index of the second largest elements in the
- vector formed by x.y where '.' is element-wise multiplication */
-/*************************************************************************/
-idx_t iargmax2_nrm(size_t n, idx_t *x, real_t *y)
-{
- size_t i, max1, max2;
-
- if (x[0]*y[0] > x[1]*y[1]) {
- max1 = 0;
- max2 = 1;
- }
- else {
- max1 = 1;
- max2 = 0;
- }
-
- for (i=2; i<n; i++) {
- if (x[i]*y[i] > x[max1]*y[max1]) {
- max2 = max1;
- max1 = i;
- }
- else if (x[i]*y[i] > x[max2]*y[max2])
- max2 = i;
- }
-
- return max2;
-}
-
-
-/*************************************************************************/
-/*! converts a signal code into a Metis return code
- */
-/*************************************************************************/
-int metis_rcode(int sigrval)
-{
- switch (sigrval) {
- case 0:
- return METIS_OK;
- break;
- case SIGMEM:
- return METIS_ERROR_MEMORY;
- break;
- default:
- return METIS_ERROR;
- break;
- }
-}
-
-
diff --git a/3rdParty/metis/metis-5.1.0/libmetis/wspace.c b/3rdParty/metis/metis-5.1.0/libmetis/wspace.c
deleted file mode 100644
index a474c3cb6..000000000
--- a/3rdParty/metis/metis-5.1.0/libmetis/wspace.c
+++ /dev/null
@@ -1,214 +0,0 @@
-/*!
-\file
-\brief Functions dealing with memory allocation and workspace management
-
-\date Started 2/24/96
-\author George
-\author Copyright 1997-2009, Regents of the University of Minnesota
-\version $Id: wspace.c 10492 2011-07-06 09:28:42Z karypis $
-*/
-
-#include "metislib.h"
-
-
-/*************************************************************************/
-/*! This function allocates memory for the workspace */
-/*************************************************************************/
-void AllocateWorkSpace(ctrl_t *ctrl, graph_t *graph)
-{
- size_t coresize;
-
- switch (ctrl->optype) {
- case METIS_OP_PMETIS:
- coresize = 3*(graph->nvtxs+1)*sizeof(idx_t) +
- 5*(ctrl->nparts+1)*graph->ncon*sizeof(idx_t) +
- 5*(ctrl->nparts+1)*graph->ncon*sizeof(real_t);
- break;
- default:
- coresize = 4*(graph->nvtxs+1)*sizeof(idx_t) +
- 5*(ctrl->nparts+1)*graph->ncon*sizeof(idx_t) +
- 5*(ctrl->nparts+1)*graph->ncon*sizeof(real_t);
- }
- /*coresize = 0;*/
- ctrl->mcore = gk_mcoreCreate(coresize);
-
- ctrl->nbrpoolsize = 0;
- ctrl->nbrpoolcpos = 0;
-}
-
-
-/*************************************************************************/
-/*! This function allocates refinement-specific memory for the workspace */
-/*************************************************************************/
-void AllocateRefinementWorkSpace(ctrl_t *ctrl, idx_t nbrpoolsize)
-{
- ctrl->nbrpoolsize = nbrpoolsize;
- ctrl->nbrpoolcpos = 0;
- ctrl->nbrpoolreallocs = 0;
-
- switch (ctrl->objtype) {
- case METIS_OBJTYPE_CUT:
- ctrl->cnbrpool = (cnbr_t *)gk_malloc(ctrl->nbrpoolsize*sizeof(cnbr_t),
- "AllocateRefinementWorkSpace: cnbrpool");
- break;
-
- case METIS_OBJTYPE_VOL:
- ctrl->vnbrpool = (vnbr_t *)gk_malloc(ctrl->nbrpoolsize*sizeof(vnbr_t),
- "AllocateRefinementWorkSpace: vnbrpool");
- break;
-
- default:
- gk_errexit(SIGERR, "Unknown objtype of %d\n", ctrl->objtype);
- }
-
-
- /* Allocate the memory for the sparse subdomain graph */
- if (ctrl->minconn) {
- ctrl->pvec1 = imalloc(ctrl->nparts+1, "AllocateRefinementWorkSpace: pvec1");
- ctrl->pvec2 = imalloc(ctrl->nparts+1, "AllocateRefinementWorkSpace: pvec2");
- ctrl->maxnads = ismalloc(ctrl->nparts, INIT_MAXNAD, "AllocateRefinementWorkSpace: maxnads");
- ctrl->nads = imalloc(ctrl->nparts, "AllocateRefinementWorkSpace: nads");
- ctrl->adids = iAllocMatrix(ctrl->nparts, INIT_MAXNAD, 0, "AllocateRefinementWorkSpace: adids");
- ctrl->adwgts = iAllocMatrix(ctrl->nparts, INIT_MAXNAD, 0, "AllocateRefinementWorkSpace: adwgts");
- }
-}
-
-
-/*************************************************************************/
-/*! This function frees the workspace */
-/*************************************************************************/
-void FreeWorkSpace(ctrl_t *ctrl)
-{
- gk_mcoreDestroy(&ctrl->mcore, ctrl->dbglvl&METIS_DBG_INFO);
-
- IFSET(ctrl->dbglvl, METIS_DBG_INFO,
- printf(" nbrpool statistics\n"
- " nbrpoolsize: %12zu nbrpoolcpos: %12zu\n"
- " nbrpoolreallocs: %12zu\n\n",
- ctrl->nbrpoolsize, ctrl->nbrpoolcpos,
- ctrl->nbrpoolreallocs));
-
- gk_free((void **)&ctrl->cnbrpool, &ctrl->vnbrpool, LTERM);
- ctrl->nbrpoolsize = 0;
- ctrl->nbrpoolcpos = 0;
-
- if (ctrl->minconn) {
- iFreeMatrix(&(ctrl->adids), ctrl->nparts, INIT_MAXNAD);
- iFreeMatrix(&(ctrl->adwgts), ctrl->nparts, INIT_MAXNAD);
-
- gk_free((void **)&ctrl->pvec1, &ctrl->pvec2,
- &ctrl->maxnads, &ctrl->nads, LTERM);
- }
-}
-
-
-/*************************************************************************/
-/*! This function allocate space from the workspace/heap */
-/*************************************************************************/
-void *wspacemalloc(ctrl_t *ctrl, size_t nbytes)
-{
- return gk_mcoreMalloc(ctrl->mcore, nbytes);
-}
-
-
-/*************************************************************************/
-/*! This function sets a marker in the stack of malloc ops to be used
- subsequently for freeing purposes */
-/*************************************************************************/
-void wspacepush(ctrl_t *ctrl)
-{
- gk_mcorePush(ctrl->mcore);
-}
-
-
-/*************************************************************************/
-/*! This function frees all mops since the last push */
-/*************************************************************************/
-void wspacepop(ctrl_t *ctrl)
-{
- gk_mcorePop(ctrl->mcore);
-}
-
-
-/*************************************************************************/
-/*! This function allocate space from the core */
-/*************************************************************************/
-idx_t *iwspacemalloc(ctrl_t *ctrl, idx_t n)
-{
- return (idx_t *)wspacemalloc(ctrl, n*sizeof(idx_t));
-}
-
-
-/*************************************************************************/
-/*! This function allocate space from the core */
-/*************************************************************************/
-real_t *rwspacemalloc(ctrl_t *ctrl, idx_t n)
-{
- return (real_t *)wspacemalloc(ctrl, n*sizeof(real_t));
-}
-
-
-/*************************************************************************/
-/*! This function allocate space from the core */
-/*************************************************************************/
-ikv_t *ikvwspacemalloc(ctrl_t *ctrl, idx_t n)
-{
- return (ikv_t *)wspacemalloc(ctrl, n*sizeof(ikv_t));
-}
-
-
-/*************************************************************************/
-/*! This function resets the cnbrpool */
-/*************************************************************************/
-void cnbrpoolReset(ctrl_t *ctrl)
-{
- ctrl->nbrpoolcpos = 0;
-}
-
-
-/*************************************************************************/
-/*! This function gets the next free index from cnbrpool */
-/*************************************************************************/
-idx_t cnbrpoolGetNext(ctrl_t *ctrl, idx_t nnbrs)
-{
- ctrl->nbrpoolcpos += nnbrs;
-
- if (ctrl->nbrpoolcpos > ctrl->nbrpoolsize) {
- ctrl->nbrpoolsize += gk_max(10*nnbrs, ctrl->nbrpoolsize/2);
-
- ctrl->cnbrpool = (cnbr_t *)gk_realloc(ctrl->cnbrpool,
- ctrl->nbrpoolsize*sizeof(cnbr_t), "cnbrpoolGet: cnbrpool");
- ctrl->nbrpoolreallocs++;
- }
-
- return ctrl->nbrpoolcpos - nnbrs;
-}
-
-
-/*************************************************************************/
-/*! This function resets the vnbrpool */
-/*************************************************************************/
-void vnbrpoolReset(ctrl_t *ctrl)
-{
- ctrl->nbrpoolcpos = 0;
-}
-
-
-/*************************************************************************/
-/*! This function gets the next free index from vnbrpool */
-/*************************************************************************/
-idx_t vnbrpoolGetNext(ctrl_t *ctrl, idx_t nnbrs)
-{
- ctrl->nbrpoolcpos += nnbrs;
-
- if (ctrl->nbrpoolcpos > ctrl->nbrpoolsize) {
- ctrl->nbrpoolsize += gk_max(10*nnbrs, ctrl->nbrpoolsize/2);
-
- ctrl->vnbrpool = (vnbr_t *)gk_realloc(ctrl->vnbrpool,
- ctrl->nbrpoolsize*sizeof(vnbr_t), "vnbrpoolGet: vnbrpool");
- ctrl->nbrpoolreallocs++;
- }
-
- return ctrl->nbrpoolcpos - nnbrs;
-}
-
--
GitLab