From c4f4223d15bcab3c2ee1d48cfb06c1db4c53b8da Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Mon, 24 Jan 2011 10:10:15 +0000
Subject: [PATCH] Abstract interface for mesh partitioner.
---
AMDiS/CMakeLists.txt | 1 +
AMDiS/bin/Makefile.am | 1 +
AMDiS/bin/Makefile.in | 12 +++
AMDiS/libtool | 64 ++++++------
AMDiS/src/Serializer.h | 3 +
AMDiS/src/parallel/MeshDistributor.cc | 104 +++----------------
AMDiS/src/parallel/MeshDistributor.h | 11 +-
AMDiS/src/parallel/MeshPartitioner.cc | 62 ++++++++++++
AMDiS/src/parallel/MeshPartitioner.h | 109 ++++++++++++++++++++
AMDiS/src/parallel/ParMetisPartitioner.cc | 116 ++--------------------
AMDiS/src/parallel/ParMetisPartitioner.h | 83 ++++------------
AMDiS/src/parallel/ParallelDebug.cc | 2 +-
12 files changed, 262 insertions(+), 306 deletions(-)
create mode 100644 AMDiS/src/parallel/MeshPartitioner.cc
create mode 100644 AMDiS/src/parallel/MeshPartitioner.h
diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index f56f4fee..f7ac49d2 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -177,6 +177,7 @@ if(ENABLE_PARALLEL_DOMAIN)
SET(PARALLEL_DOMAIN_AMDIS_SRC
${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
${SOURCE_DIR}/parallel/MeshDistributor.cc
+ ${SOURCE_DIR}/parallel/MeshPartitioner.cc
${SOURCE_DIR}/parallel/MeshManipulation.cc
${SOURCE_DIR}/parallel/StdMpi.cc
${SOURCE_DIR}/parallel/ParallelDebug.cc
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index e9f356fd..bc35ae7a 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -18,6 +18,7 @@ if USE_PARALLEL_DOMAIN_AMDIS
$(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
$(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
+ $(SOURCE_DIR)/parallel/MeshPartitioner.h $(SOURCE_DIR)/parallel/MeshPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshManipulation.h $(SOURCE_DIR)/parallel/MeshManipulation.cc \
$(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
$(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index 9aa0041a..82e32247 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -40,6 +40,7 @@ host_triplet = @host@
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MeshPartitioner.h $(SOURCE_DIR)/parallel/MeshPartitioner.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MeshManipulation.h $(SOURCE_DIR)/parallel/MeshManipulation.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
@@ -85,6 +86,8 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshDistributor.h \
$(SOURCE_DIR)/parallel/MeshDistributor.cc \
+ $(SOURCE_DIR)/parallel/MeshPartitioner.h \
+ $(SOURCE_DIR)/parallel/MeshPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshManipulation.h \
$(SOURCE_DIR)/parallel/MeshManipulation.cc \
$(SOURCE_DIR)/parallel/ParallelDebug.h \
@@ -252,6 +255,7 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-StdMpi.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParMetisPartitioner.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshDistributor.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshPartitioner.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshManipulation.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDebug.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelProblemStatBase.lo \
@@ -799,6 +803,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Mesh.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MeshDistributor.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MeshManipulation.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MeshPartitioner.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MeshStructure.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MpiHelper.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-NonLinUpdater.Plo@am__quote@
@@ -906,6 +911,13 @@ libamdis_la-MeshDistributor.lo: $(SOURCE_DIR)/parallel/MeshDistributor.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-MeshDistributor.lo `test -f '$(SOURCE_DIR)/parallel/MeshDistributor.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshDistributor.cc
+libamdis_la-MeshPartitioner.lo: $(SOURCE_DIR)/parallel/MeshPartitioner.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshPartitioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-MeshPartitioner.Tpo" -c -o libamdis_la-MeshPartitioner.lo `test -f '$(SOURCE_DIR)/parallel/MeshPartitioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshPartitioner.cc; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-MeshPartitioner.Tpo" "$(DEPDIR)/libamdis_la-MeshPartitioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-MeshPartitioner.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/MeshPartitioner.cc' object='libamdis_la-MeshPartitioner.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-MeshPartitioner.lo `test -f '$(SOURCE_DIR)/parallel/MeshPartitioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshPartitioner.cc
+
libamdis_la-MeshManipulation.lo: $(SOURCE_DIR)/parallel/MeshManipulation.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshManipulation.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-MeshManipulation.Tpo" -c -o libamdis_la-MeshManipulation.lo `test -f '$(SOURCE_DIR)/parallel/MeshManipulation.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshManipulation.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-MeshManipulation.Tpo" "$(DEPDIR)/libamdis_la-MeshManipulation.Plo"; else rm -f "$(DEPDIR)/libamdis_la-MeshManipulation.Tpo"; exit 1; fi
diff --git a/AMDiS/libtool b/AMDiS/libtool
index 6a7f3c76..ace48e58 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -30,10 +30,10 @@
# the same distribution terms that you use for the rest of that program.
# A sed program that does not truncate output.
-SED="/bin/sed"
+SED="/usr/bin/sed"
# Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/bin/sed -e 1s/^X//"
+Xsed="/usr/bin/sed -e 1s/^X//"
# The HP-UX ksh and POSIX shell print the target directory to stdout
# if CDPATH is set.
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1q024:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="gcc"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -97,7 +97,7 @@ with_gcc=yes
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -171,7 +171,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -325,10 +325,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/i386-redhat-linux/4.1.2/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /fastfs/wir/local/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/mysql /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1q024:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6782,12 +6782,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -6798,13 +6798,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g++"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicxx"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6813,7 +6813,7 @@ with_gcc=yes
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -6887,7 +6887,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
+predep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbeginS.o"
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
+postdep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o"
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -6954,11 +6954,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path="-L/u/witkowski/local/lib -L/u/witkowski/local/intel/mkl/10.0.1.014/lib/32 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7038,10 +7038,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/i386-redhat-linux/4.1.2/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /fastfs/wir/local/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/mysql /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1q024:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7087,12 +7087,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7103,7 +7103,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7112,13 +7112,13 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=yes
+with_gcc=
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7346,10 +7346,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/3.4.6/ /u/witkowski/local/lib/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/i386-redhat-linux/3.4.6/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/"
+sys_lib_search_path_spec=" /fastfs/wir/local/lib/x86_64-suse-linux/3.3.5/ /fastfs/wir/local/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/ /usr/lib/gcc/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../ /lib/x86_64-suse-linux/3.3.5/ /lib/ /usr/lib/x86_64-suse-linux/3.3.5/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/mysql /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/Serializer.h b/AMDiS/src/Serializer.h
index 4ef1a772..dbc0f30a 100644
--- a/AMDiS/src/Serializer.h
+++ b/AMDiS/src/Serializer.h
@@ -81,6 +81,9 @@ namespace AMDiS {
{
FUNCNAME("Serializer::writeFiles()");
+ TEST_EXIT(tsModulo > 0)
+ ("Parameter 'write every ith timestep' must be larger than zero!\n");
+
timestepNumber++;
timestepNumber %= tsModulo;
if ((timestepNumber != 0) && !force)
diff --git a/AMDiS/src/parallel/MeshDistributor.cc b/AMDiS/src/parallel/MeshDistributor.cc
index 9c64ffde..3afa0c58 100644
--- a/AMDiS/src/parallel/MeshDistributor.cc
+++ b/AMDiS/src/parallel/MeshDistributor.cc
@@ -22,6 +22,7 @@
#include "parallel/MeshManipulation.h"
#include "parallel/ParallelDebug.h"
#include "parallel/StdMpi.h"
+#include "parallel/MeshPartitioner.h"
#include "parallel/ParMetisPartitioner.h"
#include "parallel/MpiHelper.h"
#include "io/ElementFileWriter.h"
@@ -148,12 +149,12 @@ namespace AMDiS {
setInitialElementWeights();
// and now partition the mesh
- partitioner->fillCoarsePartitionVec(&oldPartitionVec);
+ partitioner->getPartitionMap(oldPartitionMap);
bool partitioningSucceed = partitioner->partition(elemWeights, INITIAL);
TEST_EXIT(partitioningSucceed)("Initial partitioning does not work!\n");
- partitioner->fillCoarsePartitionVec(&partitionVec);
+ partitioner->getPartitionMap(partitionMap);
#if (DEBUG != 0)
@@ -928,13 +929,12 @@ namespace AMDiS {
// === Run ParMETiS to calculate a new mesh partitioning. ===
partitioner->useLocalGlobalDofMap(&mapLocalGlobalDofs);
- bool partitioningSucceed =
- partitioner->partition(elemWeights, ADAPTIVE_REPART, 1000.0);
+ bool partitioningSucceed = partitioner->partition(elemWeights, ADAPTIVE_REPART);
if (!partitioningSucceed) {
MSG("ParMETIS created empty partition!\n");
return;
}
- oldPartitionVec = partitionVec;
+ oldPartitionMap = partitionMap;
// === Create map that maps macro element indices to pointers to the ===
@@ -1112,93 +1112,13 @@ namespace AMDiS {
MeshManipulation meshManipulation(feSpace);
meshManipulation.deleteDoubleDofs(newMacroEl, elObjects);
-#if 0
- {
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
- while (elInfo) {
- MSG("HAVE MACRO EL %d\n", elInfo->getMacroElement()->getIndex());
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-
- {
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- MSG("A-CHECK DOFs ON %d: %d %d %d %d\n",
- elInfo->getElement()->getIndex(),
- elInfo->getElement()->getDof(0, 0),
- elInfo->getElement()->getDof(1, 0),
- elInfo->getElement()->getDof(2, 0),
- elInfo->getElement()->getDof(3, 0));
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-#endif
-
mesh->dofCompress();
- partitioner->fillCoarsePartitionVec(&partitionVec);
-
-#if 0
- {
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- MSG("B-CHECK DOFs ON %d: %d %d %d %d\n",
- elInfo->getElement()->getIndex(),
- elInfo->getElement()->getDof(0, 0),
- elInfo->getElement()->getDof(1, 0),
- elInfo->getElement()->getDof(2, 0),
- elInfo->getElement()->getDof(3, 0));
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-#endif
+ partitioner->getPartitionMap(partitionMap);
updateInteriorBoundaryInfo();
-#if 0
- {
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- MSG("C-CHECK DOFs ON %d: %d %d %d %d\n",
- elInfo->getElement()->getIndex(),
- elInfo->getElement()->getDof(0, 0),
- elInfo->getElement()->getDof(1, 0),
- elInfo->getElement()->getDof(2, 0),
- elInfo->getElement()->getDof(3, 0));
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-#endif
-
updateLocalGlobalNumbering();
-#if 0
- {
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- MSG("D-CHECK DOFs ON %d: %d %d %d %d\n",
- elInfo->getElement()->getIndex(),
- elInfo->getElement()->getDof(0, 0),
- elInfo->getElement()->getDof(1, 0),
- elInfo->getElement()->getDof(2, 0),
- elInfo->getElement()->getDof(3, 0));
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-#endif
-
-
-
#if (DEBUG != 0)
MSG("AMDiS runs in debug mode, so make some test ...\n");
@@ -1229,7 +1149,7 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::updateInteriorBoundaryInfo()");
- elObjects.createRankData(partitionVec);
+ elObjects.createRankData(partitionMap);
createBoundaryData();
#if (DEBUG != 0)
@@ -1270,7 +1190,7 @@ namespace AMDiS {
// === Create mesh element data for this rank. ===
- elObjects.createRankData(partitionVec);
+ elObjects.createRankData(partitionMap);
}
@@ -1996,8 +1916,8 @@ namespace AMDiS {
partitioner->serialize(out);
SerUtil::serialize(out, elemWeights);
- SerUtil::serialize(out, partitionVec);
- SerUtil::serialize(out, oldPartitionVec);
+ SerUtil::serialize(out, partitionMap);
+ SerUtil::serialize(out, oldPartitionMap);
SerUtil::serialize(out, nRankDofs);
SerUtil::serialize(out, nOverallDofs);
@@ -2037,8 +1957,8 @@ namespace AMDiS {
partitioner->deserialize(in);
SerUtil::deserialize(in, elemWeights);
- SerUtil::deserialize(in, partitionVec);
- SerUtil::deserialize(in, oldPartitionVec);
+ SerUtil::deserialize(in, partitionMap);
+ SerUtil::deserialize(in, oldPartitionMap);
SerUtil::deserialize(in, nRankDofs);
SerUtil::deserialize(in, nOverallDofs);
diff --git a/AMDiS/src/parallel/MeshDistributor.h b/AMDiS/src/parallel/MeshDistributor.h
index 6bf1eba4..1e760b56 100644
--- a/AMDiS/src/parallel/MeshDistributor.h
+++ b/AMDiS/src/parallel/MeshDistributor.h
@@ -29,6 +29,7 @@
#include <vector>
#include <mpi.h>
+#include "parallel/MeshPartitioner.h"
#include "parallel/InteriorBoundary.h"
#include "Global.h"
#include "ProblemTimeInterface.h"
@@ -43,8 +44,6 @@ namespace AMDiS {
using namespace std;
- class ParMetisPartitioner;
-
class MeshDistributor
{
protected:
@@ -437,8 +436,8 @@ namespace AMDiS {
/// Info level.
int info;
- /// Pointer to the paritioner which is used to devide a mesh into partitions.
- ParMetisPartitioner *partitioner;
+ /// Pointer to a mesh partitioner that is used to partition the mesh to the ranks.
+ MeshPartitioner *partitioner;
/// Weights for the elements, i.e., the number of leaf elements within this element.
map<int, double> elemWeights;
@@ -447,13 +446,13 @@ namespace AMDiS {
* Stores to every macro element index the number of the rank that owns this
* macro element.
*/
- map<int, int> partitionVec;
+ map<int, int> partitionMap;
/** \brief
* Stores an old partitioning of elements. To every macro element index the
* number of the rank it corresponds to is stored.
*/
- map<int, int> oldPartitionVec;
+ map<int, int> oldPartitionMap;
/// Number of DOFs in the rank mesh.
int nRankDofs;
diff --git a/AMDiS/src/parallel/MeshPartitioner.cc b/AMDiS/src/parallel/MeshPartitioner.cc
new file mode 100644
index 00000000..77115afa
--- /dev/null
+++ b/AMDiS/src/parallel/MeshPartitioner.cc
@@ -0,0 +1,62 @@
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "parallel/MeshPartitioner.h"
+#include "Mesh.h"
+#include "Traverse.h"
+#include "Serializer.h"
+
+namespace AMDiS {
+
+ void MeshPartitioner::createInitialPartitioning()
+ {
+ FUNCNAME("MeshPartitioner::createInitialPartitioning()");
+
+ int mpiRank = mpiComm->Get_rank();
+ int mpiSize = mpiComm->Get_size();
+ int nLeaves = mesh->getNumberOfLeaves();
+ int elPerRank = nLeaves / mpiSize;
+
+ // === Create initial partitioning of the AMDiS mesh. ===
+
+ elementInRank.clear();
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
+ while (elInfo) {
+ Element *element = elInfo->getElement();
+
+ if ((element->getIndex() >= mpiRank * elPerRank &&
+ element->getIndex() < (mpiRank + 1) * elPerRank) ||
+ (element->getIndex() >= mpiSize * elPerRank &&
+ mpiRank == mpiSize - 1))
+ elementInRank[element->getIndex()] = true;
+ else
+ elementInRank[element->getIndex()] = false;
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+
+ void MeshPartitioner::serialize(std::ostream &out)
+ {
+ SerUtil::serialize(out, elementInRank);
+ }
+
+
+ void MeshPartitioner::deserialize(std::istream &in)
+ {
+ SerUtil::deserialize(in, elementInRank);
+ }
+
+}
diff --git a/AMDiS/src/parallel/MeshPartitioner.h b/AMDiS/src/parallel/MeshPartitioner.h
new file mode 100644
index 00000000..a288062c
--- /dev/null
+++ b/AMDiS/src/parallel/MeshPartitioner.h
@@ -0,0 +1,109 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// == http://www.amdis-fem.org ==
+// == ==
+// ============================================================================
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+
+/** \file MeshPartitioner.h */
+
+#ifndef AMDIS_MESH_PARTITIONER_H
+#define AMDIS_MESH_PARTITIONER_H
+
+#include <map>
+#include "AMDiS_fwd.h"
+#include "Mesh.h"
+
+namespace AMDiS {
+
+
+ using namespace std;
+
+
+ enum PartitionMode {
+ INITIAL = 0, // initial partitioning of a unpartitioned mesh
+ ADAPTIVE_REPART = 1, // repartitioning of a adaptively refined mesh
+ REFINE_PART = 2 // quality improvement of the current partitioning
+ };
+
+
+
+ class MeshPartitioner
+ {
+ public:
+ MeshPartitioner(MPI::Intracomm *comm)
+ : mpiComm(comm),
+ mesh(NULL),
+ mapLocalGlobal(NULL)
+ {}
+
+ virtual ~MeshPartitioner() {}
+
+ /// Creates an initial paritioning of the AMDiS mesh.
+ void createInitialPartitioning();
+
+ virtual bool partition(map<int, double> &elemWeights,
+ PartitionMode mode = INITIAL) = 0;
+
+ /// Creates a map which stores for each element the rank that owns this element.
+ virtual void getPartitionMap(map<int, int> &partitionMap) = 0;
+
+ /// Write partitioner state to disk.
+ void serialize(ostream &out);
+
+ /// Read partitioner state from disk.
+ void deserialize(istream &in);
+
+ void setMesh(Mesh *m)
+ {
+ mesh = m;
+ }
+
+ void useLocalGlobalDofMap(map<DegreeOfFreedom, DegreeOfFreedom> *m)
+ {
+ mapLocalGlobal = m;
+ }
+
+ map<int, bool>& getElementInRank()
+ {
+ return elementInRank;
+ }
+
+ map<int, vector<int> >& getRecvElements()
+ {
+ return recvElements;
+ }
+
+ map<int, vector<int> >& getSendElements()
+ {
+ return sendElements;
+ }
+
+ protected:
+ MPI::Intracomm *mpiComm;
+
+ Mesh *mesh;
+
+ map<DegreeOfFreedom, DegreeOfFreedom> *mapLocalGlobal;
+
+ /// Maps to each macro element index if it is in rank's partition or not.
+ map<int, bool> elementInRank;
+
+ map<int, vector<int> > recvElements, sendElements;
+ };
+}
+
+#endif
diff --git a/AMDiS/src/parallel/ParMetisPartitioner.cc b/AMDiS/src/parallel/ParMetisPartitioner.cc
index f8d4dfd3..c59a85fe 100644
--- a/AMDiS/src/parallel/ParMetisPartitioner.cc
+++ b/AMDiS/src/parallel/ParMetisPartitioner.cc
@@ -222,40 +222,8 @@ namespace AMDiS {
}
- void ParMetisPartitioner::createInitialPartitioning()
- {
- FUNCNAME("ParMetrisPartitioner::createInitialPartitioning()");
-
- int mpiRank = mpiComm->Get_rank();
- int mpiSize = mpiComm->Get_size();
- int nLeaves = mesh->getNumberOfLeaves();
- int elPerRank = nLeaves / mpiSize;
-
- // === Create initial partitioning of the AMDiS mesh. ===
-
- elementInRank.clear();
-
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
- while (elInfo) {
- Element *element = elInfo->getElement();
-
- if ((element->getIndex() >= mpiRank * elPerRank &&
- element->getIndex() < (mpiRank + 1) * elPerRank) ||
- (element->getIndex() >= mpiSize * elPerRank &&
- mpiRank == mpiSize - 1))
- elementInRank[element->getIndex()] = true;
- else
- elementInRank[element->getIndex()] = false;
-
- elInfo = stack.traverseNext(elInfo);
- }
- }
-
-
bool ParMetisPartitioner::partition(std::map<int, double> &elemWeights,
- PartitionMode mode,
- float itr)
+ PartitionMode mode)
{
FUNCNAME("ParMetisPartitioner::partition()");
@@ -403,8 +371,6 @@ namespace AMDiS {
break;
case ADAPTIVE_REPART:
{
- // parMetisGraph.print();
-
std::vector<int> vsize(nElements);
for (int i = 0; i < nElements; i++)
vsize[i] = static_cast<int>(floatWgts[i]);
@@ -453,72 +419,15 @@ namespace AMDiS {
// === Distribute new partition data. ===
- bool b = distributePartitioning(&(part[0]));
-
- if (!b) {
- MSG("RETRY ParMETIS!\n");
-
- std::vector<float> testub(14);
-
- testub[0] = 1.001;
- testub[1] = 1.01;
- testub[2] = 1.02;
- testub[3] = 1.03;
- testub[4] = 1.04;
- testub[5] = 1.06;
- testub[6] = 1.07;
- testub[7] = 1.08;
- testub[8] = 1.09;
- testub[9] = 1.1;
- testub[10] = 1.25;
- testub[11] = 1.5;
- testub[12] = 2.0;
- testub[13] = 2.5;
-
- for (int jj = 0; jj < testub.size(); jj++) {
- ubvec = testub[jj];
-
- std::vector<int> vsize(nElements);
- for (int i = 0; i < nElements; i++)
- vsize[i] = static_cast<int>(floatWgts[i]);
-
-
- ParMETIS_V3_AdaptiveRepart(parMetisMesh->getElementDist(),
- parMetisGraph.getXAdj(),
- parMetisGraph.getAdjncy(),
- &(wgts[0]),
- NULL,
- &(vsize[0]),
- &wgtflag,
- &numflag,
- &ncon,
- &nparts,
- &(tpwgts[0]),
- &ubvec,
- &itr,
- options,
- &edgecut,
- &(part[0]),
- &tmpComm);
-
-
- b = distributePartitioning(&(part[0]));
-
- MSG("ParMETIS RETRY with %f: %d\n", ubvec, b);
- }
- }
-
- return b;
+ return distributePartitioning(&(part[0]));
}
- void ParMetisPartitioner::fillCoarsePartitionVec(std::map<int, int> *partitionVec)
+ void ParMetisPartitioner::getPartitionMap(std::map<int, int> &partitionMap)
{
- FUNCNAME("ParMetisPartitioner::fillCoarsePartitionVec()");
-
- TEST_EXIT_DBG(partitionVec)("No partition vector!\n");
+ FUNCNAME("ParMetisPartitioner::getPartitionMap()");
- partitionVec->clear();
+ partitionMap.clear();
// update ParMETIS mesh to new partitioning
if (!parMetisMesh)
@@ -551,7 +460,7 @@ namespace AMDiS {
// fill partitionVec
for (int i = 0; i < mpiSize; i++)
for (int j = 0; j < nPartitionElements[i]; j++)
- (*partitionVec)[partitionElements[elmdist[i] + j]] = i;
+ partitionMap[partitionElements[elmdist[i] + j]] = i;
}
@@ -660,16 +569,5 @@ namespace AMDiS {
return true;
}
-
-
- void ParMetisPartitioner::serialize(std::ostream &out)
- {
- SerUtil::serialize(out, elementInRank);
- }
-
-
- void ParMetisPartitioner::deserialize(std::istream &in)
- {
- SerUtil::deserialize(in, elementInRank);
- }
+
}
diff --git a/AMDiS/src/parallel/ParMetisPartitioner.h b/AMDiS/src/parallel/ParMetisPartitioner.h
index a96974fd..3b11c09a 100644
--- a/AMDiS/src/parallel/ParMetisPartitioner.h
+++ b/AMDiS/src/parallel/ParMetisPartitioner.h
@@ -25,30 +25,24 @@
#include <map>
#include <set>
-#include "parmetis.h"
+#include "AMDiS_fwd.h"
#include "Global.h"
+#include "parallel/MeshPartitioner.h"
+#include "parmetis.h"
#include "mpi.h"
namespace AMDiS {
- class FiniteElemSpace;
-
- enum PartitionMode {
- INITIAL = 0, // initial partitioning of a unpartitioned mesh
- ADAPTIVE_REPART = 1, // repartitioning of a adaptively refined mesh
- REFINE_PART = 2 // quality improvement of the current partitioning
- };
+ using namespace std;
class ParMetisGraph;
- class Mesh;
- template<typename T > class DOFVector;
class ParMetisMesh
{
public:
ParMetisMesh(Mesh *mesh, MPI::Intracomm *comm,
- std::map<int, bool>& elementInRank,
- std::map<DegreeOfFreedom, DegreeOfFreedom> *mapLocalGlobal);
+ map<int, bool>& elementInRank,
+ map<DegreeOfFreedom, DegreeOfFreedom> *mapLocalGlobal);
~ParMetisMesh();
@@ -130,7 +124,7 @@ namespace AMDiS {
int nElements;
- std::map<int, int> elem_a2p;
+ map<int, int> elem_a2p;
int *elem_p2a;
@@ -169,80 +163,37 @@ namespace AMDiS {
};
- class ParMetisPartitioner
+ class ParMetisPartitioner : public MeshPartitioner
{
public:
ParMetisPartitioner(MPI::Intracomm *comm)
- : mpiComm(comm),
- mesh(NULL),
+ : MeshPartitioner(comm),
parMetisMesh(NULL),
- mapLocalGlobal(NULL)
+ itr(1000.0)
{}
~ParMetisPartitioner();
- void setMesh(Mesh *m)
- {
- mesh = m;
- }
+ bool partition(map<int, double> &elemWeights,
+ PartitionMode mode = INITIAL);
- bool partition(std::map<int, double> &elemWeights,
- PartitionMode mode = INITIAL,
- float itr = 1000000.0);
+ /// Creates a map which stores for each element the rank that owns this element.
+ void getPartitionMap(map<int, int> &partitionMap);
- /* \brief
- * Creates a map which stores for each element on partitioning level the
- * rank the element corresponds to.
- */
- void fillCoarsePartitionVec(std::map<int, int> *partitionVec);
-
- /// Creates an initial paritioning of the AMDiS mesh.
- void createInitialPartitioning();
-
- void useLocalGlobalDofMap(std::map<DegreeOfFreedom, DegreeOfFreedom> *m)
- {
- mapLocalGlobal = m;
- }
-
- std::map<int, bool>& getElementInRank()
+ void setItr(float value)
{
- return elementInRank;
+ itr = value;
}
- std::map<int, std::vector<int> >& getRecvElements()
- {
- return recvElements;
- }
-
- std::map<int, std::vector<int> >& getSendElements()
- {
- return sendElements;
- }
-
- /// Write partitioner state to disk.
- void serialize(std::ostream &out);
-
- /// Read partitioner state from disk.
- void deserialize(std::istream &in);
-
protected:
// Returns true, if the mesh partitioning could be distributed. If this is not the
// case, i.e., because there are empty partitions, the function returns false.
bool distributePartitioning(int *part);
protected:
- MPI::Intracomm *mpiComm;
-
- Mesh *mesh;
-
ParMetisMesh *parMetisMesh;
- std::map<DegreeOfFreedom, DegreeOfFreedom> *mapLocalGlobal;
-
- /// Maps to each macro element index if it is in rank's partition or not.
- std::map<int, bool> elementInRank;
-
- std::map<int, std::vector<int> > recvElements, sendElements;
+ float itr;
};
}
diff --git a/AMDiS/src/parallel/ParallelDebug.cc b/AMDiS/src/parallel/ParallelDebug.cc
index 6e130c7f..c93e0074 100644
--- a/AMDiS/src/parallel/ParallelDebug.cc
+++ b/AMDiS/src/parallel/ParallelDebug.cc
@@ -819,7 +819,7 @@ namespace AMDiS {
while (elInfo) {
int index = elInfo->getElement()->getIndex();
- vec[index] = pdb.partitionVec[index];
+ vec[index] = pdb.partitionMap[index];
elInfo = stack.traverseNext(elInfo);
}
--
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