From ab3182cb4e0b193c6598fa91e90c42a607b405f3 Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Fri, 2 Jul 2010 11:37:40 +0000
Subject: [PATCH] Solved several small problems with periodic boundaries in
parallel computations, new file names.
---
AMDiS/CMakeLists.txt | 4 +-
AMDiS/bin/Makefile.am | 4 +-
AMDiS/bin/Makefile.in | 40 ++---
AMDiS/libtool | 64 ++++----
AMDiS/src/DOFMatrix.cc | 5 +
AMDiS/src/Element.h | 12 +-
AMDiS/src/ProblemVec.cc | 10 +-
AMDiS/src/VtkWriter.cc | 148 +++++++++---------
AMDiS/src/VtkWriter.h | 7 +-
AMDiS/src/VtkWriter.hh | 8 +-
AMDiS/src/parallel/GlobalMatrixSolver.cc | 57 ++++---
AMDiS/src/parallel/GlobalMatrixSolver.h | 2 +-
...rallelDomainBase.cc => MeshDistributor.cc} | 145 ++++++-----------
...ParallelDomainBase.h => MeshDistributor.h} | 15 +-
...{ParallelDomainDbg.cc => ParallelDebug.cc} | 105 +++++++++----
.../{ParallelDomainDbg.h => ParallelDebug.h} | 13 +-
16 files changed, 329 insertions(+), 310 deletions(-)
rename AMDiS/src/parallel/{ParallelDomainBase.cc => MeshDistributor.cc} (94%)
rename AMDiS/src/parallel/{ParallelDomainBase.h => MeshDistributor.h} (98%)
rename AMDiS/src/parallel/{ParallelDomainDbg.cc => ParallelDebug.cc} (80%)
rename AMDiS/src/parallel/{ParallelDomainDbg.h => ParallelDebug.h} (95%)
diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index af080f62..b8cfd3eb 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -155,9 +155,9 @@ endif(ENABLE_PARMETIS)
if(ENABLE_PARALLEL_DOMAIN)
include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
SET(PARALLEL_DOMAIN_AMDIS_SRC
- ${SOURCE_DIR}/parallel/ParallelDomainBase.cc
+ ${SOURCE_DIR}/parallel/MeshDistributor.cc
${SOURCE_DIR}/parallel/StdMpi.cc
- ${SOURCE_DIR}/parallel/ParallelDomainDbg.cc
+ ${SOURCE_DIR}/parallel/ParallelDebug.cc
${SOURCE_DIR}/parallel/GlobalMatrixSolver.cc
${SOURCE_DIR}/parallel/MpiHelper.cc)
SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_PARALLEL_DOMAIN_AMDIS=1")
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index 6aec26c1..470d86ac 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -29,8 +29,8 @@ endif
if USE_PARALLEL_DOMAIN_AMDIS
PARALLEL_AMDIS_SOURCES += \
$(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
- $(SOURCE_DIR)/parallel/ParallelDomainBase.h $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
- $(SOURCE_DIR)/parallel/ParallelDomainDbg.h $(SOURCE_DIR)/parallel/ParallelDomainDbg.cc \
+ $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
+ $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
$(SOURCE_DIR)/parallel/GlobalMatrixSolver.h $(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc \
$(SOURCE_DIR)/parallel/MpiHelper.h $(SOURCE_DIR)/parallel/MpiHelper.cc
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index e22b3803..0fc9dc80 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -39,8 +39,8 @@ host_triplet = @host@
@USE_PARALLEL_AMDIS_TRUE@am__append_1 = -DHAVE_PARALLEL_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_2 = \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDomainBase.h $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDomainDbg.h $(SOURCE_DIR)/parallel/ParallelDomainDbg.cc \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/GlobalMatrixSolver.h $(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MpiHelper.h $(SOURCE_DIR)/parallel/MpiHelper.cc
@@ -77,10 +77,10 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
libamdis_la_LIBADD =
am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/parallel/StdMpi.cc \
- $(SOURCE_DIR)/parallel/ParallelDomainBase.h \
- $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
- $(SOURCE_DIR)/parallel/ParallelDomainDbg.h \
- $(SOURCE_DIR)/parallel/ParallelDomainDbg.cc \
+ $(SOURCE_DIR)/parallel/MeshDistributor.h \
+ $(SOURCE_DIR)/parallel/MeshDistributor.cc \
+ $(SOURCE_DIR)/parallel/ParallelDebug.h \
+ $(SOURCE_DIR)/parallel/ParallelDebug.cc \
$(SOURCE_DIR)/parallel/GlobalMatrixSolver.h \
$(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc \
$(SOURCE_DIR)/parallel/MpiHelper.h \
@@ -247,8 +247,8 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/time/RosenbrockMethod.h \
$(SOURCE_DIR)/time/RosenbrockMethod.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-StdMpi.lo \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDomainBase.lo \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDomainDbg.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshDistributor.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDebug.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-GlobalMatrixSolver.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MpiHelper.lo
@USE_PARALLEL_AMDIS_FALSE@am__objects_2 = $(am__objects_1)
@@ -807,14 +807,14 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MacroWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Marker.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(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-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@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Operator.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-OperatorTerm.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParMetisPartitioner.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDomainBase.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDomainDbg.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDebug.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelProblem.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parameters.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parametric.Plo@am__quote@
@@ -901,19 +901,19 @@ libamdis_la-StdMpi.lo: $(SOURCE_DIR)/parallel/StdMpi.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-StdMpi.lo `test -f '$(SOURCE_DIR)/parallel/StdMpi.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/StdMpi.cc
-libamdis_la-ParallelDomainBase.lo: $(SOURCE_DIR)/parallel/ParallelDomainBase.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainBase.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo" -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainBase.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainBase.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' object='libamdis_la-ParallelDomainBase.lo' libtool=yes @AMDEPBACKSLASH@
+libamdis_la-MeshDistributor.lo: $(SOURCE_DIR)/parallel/MeshDistributor.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshDistributor.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-MeshDistributor.Tpo" -c -o libamdis_la-MeshDistributor.lo `test -f '$(SOURCE_DIR)/parallel/MeshDistributor.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshDistributor.cc; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-MeshDistributor.Tpo" "$(DEPDIR)/libamdis_la-MeshDistributor.Plo"; else rm -f "$(DEPDIR)/libamdis_la-MeshDistributor.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/MeshDistributor.cc' object='libamdis_la-MeshDistributor.lo' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainBase.cc
+@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-ParallelDomainDbg.lo: $(SOURCE_DIR)/parallel/ParallelDomainDbg.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainDbg.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainDbg.Tpo" -c -o libamdis_la-ParallelDomainDbg.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainDbg.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainDbg.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainDbg.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainDbg.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainDbg.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParallelDomainDbg.cc' object='libamdis_la-ParallelDomainDbg.lo' libtool=yes @AMDEPBACKSLASH@
+libamdis_la-ParallelDebug.lo: $(SOURCE_DIR)/parallel/ParallelDebug.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDebug.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDebug.Tpo" -c -o libamdis_la-ParallelDebug.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDebug.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDebug.cc; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDebug.Tpo" "$(DEPDIR)/libamdis_la-ParallelDebug.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDebug.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParallelDebug.cc' object='libamdis_la-ParallelDebug.lo' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainDbg.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainDbg.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainDbg.cc
+@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDebug.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDebug.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDebug.cc
libamdis_la-GlobalMatrixSolver.lo: $(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-GlobalMatrixSolver.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-GlobalMatrixSolver.Tpo" -c -o libamdis_la-GlobalMatrixSolver.lo `test -f '$(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/GlobalMatrixSolver.cc; \
diff --git a/AMDiS/libtool b/AMDiS/libtool
index dae42157..1a37a1c4 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 deimos102:
# 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/ /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/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 deimos102:
# 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/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/ /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/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 deimos102:
# 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/ /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/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/DOFMatrix.cc b/AMDiS/src/DOFMatrix.cc
index 64b339ff..4533d159 100644
--- a/AMDiS/src/DOFMatrix.cc
+++ b/AMDiS/src/DOFMatrix.cc
@@ -219,6 +219,11 @@ namespace AMDiS {
} else {
for (int j = 0; j < nCol; j++) {
DegreeOfFreedom col = colIndices[j];
+
+// if (MPI::COMM_WORLD.Get_rank() == 0 && row <= 10 && col <= 10) {
+// MSG("%d/%d entry: %e\n", row, col, elMat[i][j]);
+// }
+
ins[row][col] += elMat[i][j];
}
}
diff --git a/AMDiS/src/Element.h b/AMDiS/src/Element.h
index e1f06894..f1500f02 100644
--- a/AMDiS/src/Element.h
+++ b/AMDiS/src/Element.h
@@ -393,10 +393,8 @@ namespace AMDiS {
* are assembled and put together to a list.
*
* \param[in] feSpace FE space which is used to get the dofs.
- * \param[in] ith Defines the edge/face on which all the vertex dofs
- * are assembled.
- * \param[in] geoPos Must be either EDGE or FACE. Defines whether an
- * edge or a face (only in 3d) should be traversed.
+ * \param[in] bound Defines the edge/face of the element on which
+ * all vertex dofs are assembled.
* \param[out] dofs List of dofs, where the result is stored.
*/
virtual void getVertexDofs(FiniteElemSpace* feSpace,
@@ -409,10 +407,8 @@ namespace AMDiS {
* are assembled and put together to a list.
*
* \param[in] feSpace FE space which is used to get the dofs.
- * \param[in] ith Defines the edge/face on which all the non vertex
- * dofs are assembled.
- * \param[in] geoPos Must be either EDGE or FACE. Defines whether an
- * edge or a face (only in 3d) should be traversed.
+ * \param[in] bound Defines the edge/face of the element on which
+ * all non vertex dofs are assembled.
* \param[out] dofs All dofs are put to this dof list.
*/
virtual void getNonVertexDofs(FiniteElemSpace* feSpace,
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 1f9b8f49..b7787d01 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -451,8 +451,8 @@ namespace AMDiS {
}
fileWriters.push_back(new FileWriter(numberedName,
- componentMeshes[0],
- solutionList));
+ componentMeshes[0],
+ solutionList));
}
// Create own filewriters for each components of the problem
@@ -464,7 +464,7 @@ namespace AMDiS {
if (filename != "")
fileWriters.push_back(new FileWriter(numberedName,
componentMeshes[i],
- solution->getDOFVector(i)));
+ solution->getDOFVector(i)));
}
// Check for serializer
@@ -674,8 +674,8 @@ namespace AMDiS {
for (int j = 0; j < nComponents; j++) {
- if (writeAsmInfo)
- MSG("--------- %d %d -------------\n", i, j);
+ // if (writeAsmInfo)
+ // MSG("--------- %d %d -------------\n", i, j);
// Only if this variable is true, the current matrix will be assembled.
bool assembleMatrix = true;
diff --git a/AMDiS/src/VtkWriter.cc b/AMDiS/src/VtkWriter.cc
index 8b3f9917..2153ae00 100644
--- a/AMDiS/src/VtkWriter.cc
+++ b/AMDiS/src/VtkWriter.cc
@@ -128,94 +128,94 @@ namespace AMDiS {
return 0;
}
+
void VtkWriter::writeFile(DOFVector<double> *values,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- FUNCNAME("VtkWriter::writeFile()");
-
- DataCollector dc(values->getFeSpace(), values);
- std::vector<DataCollector*> dcList(0);
- dcList.push_back(&dc);
- writeFile(dcList,filename,writeParallel);
- };
+ FUNCNAME("VtkWriter::writeFile()");
+
+ DataCollector dc(values->getFeSpace(), values);
+ std::vector<DataCollector*> dcList(0);
+ dcList.push_back(&dc);
+ writeFile(dcList,filename,writeParallel);
+ }
+
void VtkWriter::writeFile(std::vector<DOFVector<double>* > &values,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- std::vector<DataCollector*> dcList(0);
- for(unsigned i=0; i<values.size(); ++i) {
- dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
- }
- writeFile(dcList,filename,writeParallel);
- for(unsigned i=0; i<values.size(); ++i) {
- delete dcList[i];
- }
- };
+ std::vector<DataCollector*> dcList(0);
+ for (unsigned int i = 0; i < values.size(); i++)
+ dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
+ writeFile(dcList, filename, writeParallel);
+ for (unsigned int i = 0; i < values.size(); i++)
+ delete dcList[i];
+ }
+
void VtkWriter::writeFile(WorldVector<DOFVector<double>* > &values,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- std::vector<DataCollector*> dcList(0);
- for(unsigned i=0; i<static_cast<unsigned>(values.getSize()); ++i) {
- dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
- }
- writeFile(dcList,filename,writeParallel);
- for(unsigned i=0; i<static_cast<unsigned>(values.getSize()); ++i) {
- delete dcList[i];
- }
- };
+ std::vector<DataCollector*> dcList(0);
+ for (int i = 0; i < values.getSize(); i++)
+ dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
+ writeFile(dcList, filename, writeParallel);
+ for (int i = 0; i < values.getSize(); i++)
+ delete dcList[i];
+ }
+
void VtkWriter::writeFile(DOFVector<WorldVector<double> > *values,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- WorldVector<DOFVector<double>*> valuesWV;
- for(unsigned i=0; i<static_cast<unsigned>(valuesWV.getSize()); ++i)
- valuesWV[i] = new DOFVector<double>(values->getFeSpace(), "valuesWV_i");
- transform(values, &valuesWV);
- writeFile(valuesWV,filename,writeParallel);
- for(unsigned i=0; i<static_cast<unsigned>(valuesWV.getSize()); ++i) {
- delete valuesWV[i];
- }
- };
+ WorldVector<DOFVector<double>*> valuesWV;
+ for (int i =0 ; i < valuesWV.getSize(); i++)
+ valuesWV[i] = new DOFVector<double>(values->getFeSpace(), "valuesWV_i");
+ transform(values, &valuesWV);
+ writeFile(valuesWV, filename, writeParallel);
+ for (int i = 0; i < valuesWV.getSize(); i++)
+ delete valuesWV[i];
+ }
+
void VtkWriter::writeFile(SystemVector *values,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- std::vector<DataCollector*> dcList(0);
- for(unsigned i=0; i<static_cast<unsigned>(values->getSize()); ++i) {
- dcList.push_back(new DataCollector(values->getDOFVector(i)->getFeSpace(), values->getDOFVector(i)));
- }
- writeFile(dcList,filename,writeParallel);
- for(unsigned i=0; i<static_cast<unsigned>(dcList.size()); ++i) {
- delete dcList[i];
- }
- };
-
+ std::vector<DataCollector*> dcList(0);
+ for (int i = 0; i < values->getSize(); i++)
+ dcList.push_back(new DataCollector(values->getDOFVector(i)->getFeSpace(),
+ values->getDOFVector(i)));
+ writeFile(dcList, filename, writeParallel);
+ for (unsigned i = 0; i < dcList.size(); i++)
+ delete dcList[i];
+ }
+
+
void VtkWriter::writeFile(std::vector<DataCollector*> &dcList,
- std::string filename,
- bool writeParallel)
+ std::string filename,
+ bool writeParallel)
{
- VtkWriter writer(&dcList);
-
- #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- if (writeParallel) {
- using boost::lexical_cast;
-
- int sPos = filename.find(".vtu");
- TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
- std::string name = filename.substr(0, sPos);
-
- if (MPI::COMM_WORLD.Get_rank() == 0)
- writer.writeParallelFile(name + ".pvtu", MPI::COMM_WORLD.Get_size(), name, ".vtu");
-
- filename = name + "-p" + lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
- }
- #endif
- writer.writeFile(filename);
- };
+ VtkWriter writer(&dcList);
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ if (writeParallel) {
+ using boost::lexical_cast;
+
+ int sPos = filename.find(".vtu");
+ TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
+ std::string name = filename.substr(0, sPos);
+
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+ writer.writeParallelFile(name + ".pvtu", MPI::COMM_WORLD.Get_size(), name, ".vtu");
+
+ filename = name + "-p" + lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
+ }
+#endif
+ writer.writeFile(filename);
+ }
}
diff --git a/AMDiS/src/VtkWriter.h b/AMDiS/src/VtkWriter.h
index f89271c3..c7be36da 100644
--- a/AMDiS/src/VtkWriter.h
+++ b/AMDiS/src/VtkWriter.h
@@ -72,17 +72,22 @@ namespace AMDiS {
static void writeFile(std::vector<DOFVector<double>*> &values,
std::string filename,
bool writeParallel = true);
+
static void writeFile(WorldVector<DOFVector<double>*> &values,
std::string filename,
bool writeParallel = true);
+
static void writeFile(DOFVector<WorldVector<double> > *values,
std::string filename,
bool writeParallel = true);
+
static void writeFile(DOFVector<WorldVector<double> > &values,
std::string filename,
- bool writeParallel = true) {
+ bool writeParallel = true)
+ {
writeFile(&values, filename, writeParallel);
}
+
static void writeFile(SystemVector *values,
std::string filename,
bool writeParallel = true);
diff --git a/AMDiS/src/VtkWriter.hh b/AMDiS/src/VtkWriter.hh
index 721252ea..010a1c8d 100644
--- a/AMDiS/src/VtkWriter.hh
+++ b/AMDiS/src/VtkWriter.hh
@@ -81,6 +81,7 @@ namespace AMDiS {
file << " </UnstructuredGrid>\n";
file << "</VTKFile>\n";
}
+
template<typename T>
void VtkWriter::writeVertexCoords(T &file)
@@ -115,6 +116,7 @@ namespace AMDiS {
}
}
+
template<typename T>
void VtkWriter::writeVertexValues(T &file, int componentNo)
{
@@ -149,12 +151,13 @@ namespace AMDiS {
++intPointIt, ++valueIt, ++interpCoordIt) {
if (*intPointIt >= 0) {
- for (int i = 0; i < static_cast<int>(interpCoordIt->size()); i++)
+ for (unsigned int i = 0; i < interpCoordIt->size(); i++)
file << " " << (fabs(*valueIt) < 1e-40 ? 0.0 : *valueIt) << "\n";
}
}
}
}
+
template<typename T>
void VtkWriter::writeConnectivity(T &file)
@@ -182,6 +185,7 @@ namespace AMDiS {
}
}
+
template<typename T>
void VtkWriter::writeConnectivity_dim2_degree2(T &file)
{
@@ -215,6 +219,7 @@ namespace AMDiS {
}
}
+
template<typename T>
void VtkWriter::writeConnectivity_dim2_degree3(T &file)
{
@@ -270,6 +275,7 @@ namespace AMDiS {
}
}
+
template<typename T>
void VtkWriter::writeConnectivity_dim2_degree4(T &file)
{
diff --git a/AMDiS/src/parallel/GlobalMatrixSolver.cc b/AMDiS/src/parallel/GlobalMatrixSolver.cc
index 4ae8d8f9..0359b421 100644
--- a/AMDiS/src/parallel/GlobalMatrixSolver.cc
+++ b/AMDiS/src/parallel/GlobalMatrixSolver.cc
@@ -1,9 +1,9 @@
-#include "GlobalMatrixSolver.h"
+#include "parallel/GlobalMatrixSolver.h"
+#include "parallel/StdMpi.h"
+#include "parallel/ParallelDebug.h"
#include "DOFVector.h"
#include "Debug.h"
#include "SystemVector.h"
-#include "parallel/StdMpi.h"
-#include "parallel/ParallelDomainDbg.h"
#include "petscksp.h"
@@ -117,7 +117,7 @@ namespace AMDiS {
// The value is assign to n matrix entries, therefore, every entry
// has only 1/n value of the original entry.
double scalFactor =
- 1.0 / (meshDistributor->getPeriodicDof(globalColDof).size() + 1.0);
+ 1.0 / pow(2.0, meshDistributor->getPeriodicDof(globalColDof).size());
// Insert original entry.
cols.push_back(colIndex);
@@ -131,7 +131,7 @@ namespace AMDiS {
values.push_back(value(*icursor) * scalFactor);
}
} else {
- // Neigher row nor column dof index is periodic, simple add entry.
+ // The col dof index is not periodic, simple add entry.
cols.push_back(colIndex);
values.push_back(value(*icursor));
}
@@ -149,34 +149,39 @@ namespace AMDiS {
// The row dof is periodic, so send dof to all the corresponding rows.
double scalFactor =
- 1.0 / (meshDistributor->getPeriodicDof(globalRowDof).size() + 1.0);
-
- int diagIndex = -1;
- for (int i = 0; i < static_cast<int>(values.size()); i++) {
- // Change only the non diagonal values in the col. For the diagonal test
- // we compare the global dof indices of the dof matrix (not of the petsc
- // matrix!).
- if ((cols[i] - dispAddCol) / dispMult != globalRowDof)
- values[i] *= scalFactor;
- else
- diagIndex = i;
- }
-
+ 1.0 / pow(2.0, meshDistributor->getPeriodicDof(globalRowDof).size());
+ for (unsigned int i = 0; i < values.size(); i++)
+ values[i] *= scalFactor;
+
// Send the main row to the petsc matrix.
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
- // Set diagonal element to zero, i.e., the diagonal element of the current
- // row is not send to the periodic row indices.
- if (diagIndex != -1)
- values[diagIndex] = 0.0;
+ std::vector<int> perCols;
+ perCols.reserve(300);
+ std::vector<double> perValues;
+ perValues.reserve(300);
+ for (unsigned int i = 0; i < cols.size(); i++) {
+ int tmp = (cols[i] - dispAddCol) / dispMult;
+ if (meshDistributor->getPeriodicDofMap().count(tmp) == 0) {
+ perCols.push_back(cols[i]);
+ perValues.push_back(values[i]);
+ } else {
+ for (std::set<DegreeOfFreedom>::iterator it = meshDistributor->getPeriodicDof(tmp).begin();
+ it != meshDistributor->getPeriodicDof(tmp).end(); ++it) {
+ perValues.push_back(values[i]);
+ perCols.push_back((*it * dispMult) + dispAddCol);
+ }
+ }
+ }
// Send the row to all periodic row indices.
for (std::set<DegreeOfFreedom>::iterator it = meshDistributor->getPeriodicDof(globalRowDof).begin();
it != meshDistributor->getPeriodicDof(globalRowDof).end(); ++it) {
int perRowIndex = *it * dispMult + dispAddRow;
- MatSetValues(petscMatrix, 1, &perRowIndex, cols.size(),
- &(cols[0]), &(values[0]), ADD_VALUES);
+
+ MatSetValues(petscMatrix, 1, &perRowIndex, perCols.size(),
+ &(perCols[0]), &(perValues[0]), ADD_VALUES);
}
} else {
@@ -372,7 +377,7 @@ namespace AMDiS {
d_nnz[localRowIdx]++;
}
}
- }
+ }
}
@@ -436,7 +441,7 @@ namespace AMDiS {
for (int i = 0; i < nComponents; i++)
for (int j = 0; j < nComponents; j++)
if ((*mat)[i][j])
- setDofMatrix((*mat)[i][j], nComponents, i, j);
+ setDofMatrix((*mat)[i][j], nComponents, i, j);
INFO(info, 8)("Fill petsc matrix 2 needed %.5f seconds\n", TIME_USED(first, clock()));
diff --git a/AMDiS/src/parallel/GlobalMatrixSolver.h b/AMDiS/src/parallel/GlobalMatrixSolver.h
index 25228935..d6ca31e4 100644
--- a/AMDiS/src/parallel/GlobalMatrixSolver.h
+++ b/AMDiS/src/parallel/GlobalMatrixSolver.h
@@ -24,7 +24,7 @@
#include "AMDiS_fwd.h"
#include "Global.h"
-#include "ParallelDomainBase.h"
+#include "MeshDistributor.h"
#include "ProblemVec.h"
#include "ProblemInstat.h"
diff --git a/AMDiS/src/parallel/ParallelDomainBase.cc b/AMDiS/src/parallel/MeshDistributor.cc
similarity index 94%
rename from AMDiS/src/parallel/ParallelDomainBase.cc
rename to AMDiS/src/parallel/MeshDistributor.cc
index d909fc44..68c9f012 100644
--- a/AMDiS/src/parallel/ParallelDomainBase.cc
+++ b/AMDiS/src/parallel/MeshDistributor.cc
@@ -4,8 +4,8 @@
#include <boost/lexical_cast.hpp>
#include <boost/filesystem.hpp>
-#include "parallel/ParallelDomainBase.h"
-#include "parallel/ParallelDomainDbg.h"
+#include "parallel/MeshDistributor.h"
+#include "parallel/ParallelDebug.h"
#include "parallel/StdMpi.h"
#include "ParMetisPartitioner.h"
#include "Mesh.h"
@@ -108,7 +108,7 @@ namespace AMDiS {
MSG("Skip write part mesh!\n");
}
- ParallelDomainDbg::testAllElements(*this);
+ ParallelDebug::testAllElements(*this);
#endif
@@ -117,7 +117,7 @@ namespace AMDiS {
createInteriorBoundaryInfo();
#if (DEBUG != 0)
- ParallelDomainDbg::printBoundaryInfo(*this);
+ ParallelDebug::printBoundaryInfo(*this);
#endif
@@ -142,8 +142,8 @@ namespace AMDiS {
#if (DEBUG != 0)
MSG("AMDiS runs in debug mode, so make some test ...\n");
debug::testSortedDofs(mesh, elMap);
- ParallelDomainDbg::testInteriorBoundary(*this);
- ParallelDomainDbg::testCommonDofs(*this, true);
+ ParallelDebug::testInteriorBoundary(*this);
+ ParallelDebug::testCommonDofs(*this, true);
MSG("Debug mode tests finished!\n");
debug::writeMesh(feSpace, -1, "macro_mesh");
@@ -898,21 +898,20 @@ namespace AMDiS {
// === indices. Now, we have to sort the corresponding list in this rank to ===
// === get the same order. ===
- for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {
+ for (unsigned int j = 0; j < rankIt->second.size(); j++) {
// If the expected object is not at place, search for it.
BoundaryObject &recvedBound = stdMpi.getRecvData()[rankIt->first][j].rankObj;
if ((rankIt->second)[j].neighObj != recvedBound) {
- int k = j + 1;
- for (; k < static_cast<int>(rankIt->second.size()); k++)
+ unsigned int k = j + 1;
+ for (; k < rankIt->second.size(); k++)
if ((rankIt->second)[k].neighObj == recvedBound)
break;
// The element must always be found, because the list is just in another order.
- TEST_EXIT_DBG(k < static_cast<int>(rankIt->second.size()))
- ("Should never happen!\n");
+ TEST_EXIT_DBG(k < rankIt->second.size())("Should never happen!\n");
// Swap the current with the found element.
AtomicBoundary tmpBound = (rankIt->second)[k];
@@ -949,20 +948,19 @@ namespace AMDiS {
if (rankIt->first <= mpiRank)
continue;
- for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {
+ for (unsigned int j = 0; j < rankIt->second.size(); j++) {
BoundaryObject &recvedBound = stdMpi.getRecvData()[rankIt->first][j].rankObj;
if (periodicBoundary.boundary[rankIt->first][j].neighObj != recvedBound) {
- int k = j + 1;
- for (; k < static_cast<int>(rankIt->second.size()); k++)
+ unsigned int k = j + 1;
+ for (; k < rankIt->second.size(); k++)
if (periodicBoundary.boundary[rankIt->first][k].neighObj == recvedBound)
break;
// The element must always be found, because the list is just in
// another order.
- TEST_EXIT_DBG(k < static_cast<int>(rankIt->second.size()))
- ("Should never happen!\n");
+ TEST_EXIT_DBG(k < rankIt->second.size())("Should never happen!\n");
// Swap the current with the found element.
AtomicBoundary tmpBound = (rankIt->second)[k];
@@ -1366,11 +1364,6 @@ namespace AMDiS {
b.rankObj = rankDofs[it->second[i]];
b.neighObj = stdMpiObjs.getRecvData(it->first)[i];
- if (mpiRank == 3 && it->first == 0) {
- MSG("ADDED VERTEX BOUNDARY WITH RANK 0!: %d %d %d\n",
- it->second[i], b.rankObj.el->getIndex(), b.rankObj.ithObj);
- }
-
sendObjects[it->first].push_back(b.rankObj);
}
}
@@ -1682,7 +1675,7 @@ namespace AMDiS {
it->rankObj.el->getVertexDofs(feSpace, it->rankObj, dofs);
it->rankObj.el->getNonVertexDofs(feSpace, it->rankObj, dofs);
- for (int i = 0; i < static_cast<int>(dofs.size()); i++)
+ for (unsigned int i = 0; i < dofs.size(); i++)
sendDofs[it.getRank()].push_back(dofs[i]);
}
@@ -1692,7 +1685,7 @@ namespace AMDiS {
it->rankObj.el->getVertexDofs(feSpace, it->rankObj, dofs);
it->rankObj.el->getNonVertexDofs(feSpace, it->rankObj, dofs);
- for (int i = 0; i < static_cast<int>(dofs.size()); i++) {
+ for (unsigned int i = 0; i < dofs.size(); i++) {
DofContainer::iterator eraseIt =
find(rankDofs.begin(), rankDofs.end(), dofs[i]);
if (eraseIt != rankDofs.end())
@@ -1730,7 +1723,7 @@ namespace AMDiS {
// === Send new DOF indices. ===
#if (DEBUG != 0)
- ParallelDomainDbg::testDofContainerCommunication(*this, sendDofs, recvDofs);
+ ParallelDebug::testDofContainerCommunication(*this, sendDofs, recvDofs);
#endif
int i = 0;
@@ -1780,7 +1773,7 @@ namespace AMDiS {
#if (DEBUG != 0)
debug::testSortedDofs(mesh, elMap);
- ParallelDomainDbg::testCommonDofs(*this, true);
+ ParallelDebug::testCommonDofs(*this, true);
#if 0
MSG("------------- Debug information -------------\n");
@@ -1967,112 +1960,70 @@ namespace AMDiS {
// === Each rank traverse its periodic boundaries and sends the dof indices ===
// === to the rank "on the other side" of the periodic boundary. ===
+ RankToDofContainer rankPeriodicDofs;
+
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
TEST_EXIT_DBG(it->first != mpiRank)
("Periodic interior boundary within the rank itself is not possible!\n");
// Create dof indices on the boundary.
- DofContainer dofs;
+ DofContainer& dofs = rankPeriodicDofs[it->first];
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
- boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
- boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
+ Element *el = boundIt->rankObj.el;
+
+ if (boundIt->rankObj.reverseMode) {
+ for (int i = mesh->getDim() - 1; i >= 0; i--) {
+ int localDofIndex =
+ el->getVertexOfPosition(boundIt->rankObj.subObj, boundIt->rankObj.ithObj, i);
+ dofs.push_back(el->getDOF(localDofIndex));
+ }
+ } else {
+ for (int i = 0; i < mesh->getDim(); i++) {
+ int localDofIndex =
+ el->getVertexOfPosition(boundIt->rankObj.subObj, boundIt->rankObj.ithObj, i);
+ dofs.push_back(el->getDOF(localDofIndex));
+ }
+ }
+ el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
+ el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
}
// Send the global indices to the rank on the other side.
stdMpi.getSendData(it->first).reserve(dofs.size());
for (unsigned int i = 0; i < dofs.size(); i++)
- stdMpi.getSendData(it->first).push_back(mapLocalGlobalDofs[*(dofs[i])]);
+ stdMpi.getSendData(it->first).push_back(mapLocalGlobalDofs[*(dofs[i])]);
// Receive from this rank the same number of dofs.
- stdMpi.recv(it->first, dofs.size());
+ stdMpi.recv(it->first, dofs.size());
+ // rankPeriodicDofs[it->first] = dofs;
}
stdMpi.updateSendDataSize();
stdMpi.startCommunication<int>(MPI_INT);
+
// === The rank has received the dofs from the rank on the other side of ===
// === the boundary. Now it can use them to create the mapping between ===
// === the periodic dofs in this rank and the corresponding periodic ===
// === dofs from the other ranks. ===
- std::map<DegreeOfFreedom, std::set<int> > dofFromRank;
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
- DofContainer dofs;
-
- // Create the dofs on the boundary in inverse order.
- for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
- boundIt != it->second.end(); ++boundIt) {
- DofContainer tmpdofs;
- boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, tmpdofs);
- boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, tmpdofs);
-
- for (unsigned int i = 0; i < tmpdofs.size(); i++)
- dofs.push_back(tmpdofs[i]);
- }
+ DofContainer& dofs = rankPeriodicDofs[it->first];
// Added the received dofs to the mapping.
- for (int i = 0; i < static_cast<int>(dofs.size()); i++) {
+ for (unsigned int i = 0; i < dofs.size(); i++) {
int globalDofIndex = mapLocalGlobalDofs[*(dofs[i])];
periodicDof[globalDofIndex].insert(stdMpi.getRecvData(it->first)[i]);
- dofFromRank[globalDofIndex].insert(it->first);
- }
- }
-
- if (dofFromRank.size() > 0)
- TEST_EXIT_DBG(mesh->getDim() == 2)
- ("Periodic boundary corner problem must be generalized to 3d!\n");
-
- MPI::Request request[min(static_cast<int>(periodicBoundary.boundary.size() * 2), 4)];
- int requestCounter = 0;
- std::vector<int*> sendBuffers, recvBuffers;
-
- for (std::map<DegreeOfFreedom, std::set<int> >::iterator it = dofFromRank.begin();
- it != dofFromRank.end(); ++it) {
- if (it->second.size() == 2) {
- TEST_EXIT_DBG(periodicDof[it->first].size() == 2)("Missing periodic dof!\n");
-
- int *sendbuf = new int[2];
- sendbuf[0] = *(periodicDof[it->first].begin());
- sendbuf[1] = *(++(periodicDof[it->first].begin()));
-
- request[requestCounter++] =
- mpiComm.Isend(sendbuf, 2, MPI_INT, *(it->second.begin()), 0);
- request[requestCounter++] =
- mpiComm.Isend(sendbuf, 2, MPI_INT, *(++(it->second.begin())), 0);
-
- sendBuffers.push_back(sendbuf);
-
- int *recvbuf1 = new int[2];
- int *recvbuf2 = new int[2];
-
- request[requestCounter++] =
- mpiComm.Irecv(recvbuf1, 2, MPI_INT, *(it->second.begin()), 0);
- request[requestCounter++] =
- mpiComm.Irecv(recvbuf2, 2, MPI_INT, *(++(it->second.begin())), 0);
-
- recvBuffers.push_back(recvbuf1);
- recvBuffers.push_back(recvbuf2);
- }
- }
-
- MPI::Request::Waitall(requestCounter, request);
-
- int i = 0;
- for (std::map<DegreeOfFreedom, std::set<int> >::iterator it = dofFromRank.begin();
- it != dofFromRank.end(); ++it) {
- if (it->second.size() == 2) {
- for (int k = 0; k < 2; k++)
- for (int j = 0; j < 2; j++)
- if (recvBuffers[i + k][j] != it->first)
- periodicDof[it->first].insert(recvBuffers[i + k][j]);
-
- i++;
}
}
+
+ for (PeriodicDofMap::iterator it = periodicDof.begin(); it != periodicDof.end(); ++it)
+ if (it->second.size() == 2)
+ periodicDof.erase(it++);
}
diff --git a/AMDiS/src/parallel/ParallelDomainBase.h b/AMDiS/src/parallel/MeshDistributor.h
similarity index 98%
rename from AMDiS/src/parallel/ParallelDomainBase.h
rename to AMDiS/src/parallel/MeshDistributor.h
index bd986ca6..fc42d49a 100644
--- a/AMDiS/src/parallel/ParallelDomainBase.h
+++ b/AMDiS/src/parallel/MeshDistributor.h
@@ -17,10 +17,10 @@
// == ==
// ============================================================================
-/** \file ParallelDomainBase.h */
+/** \file MeshDistributor.h */
-#ifndef AMDIS_PARALLELDOMAINBASE_H
-#define AMDIS_PARALLELDOMAINBASE_H
+#ifndef AMDIS_MESHDISTRIBUTOR_H
+#define AMDIS_MESHDISTRIBUTOR_H
#include <map>
@@ -437,7 +437,7 @@ namespace AMDiS {
/// Number of DOFs in the rank mesh.
int nRankDofs;
- ///
+ /// Number of DOFs in the whole domain.
int nOverallDofs;
/** \brief
@@ -457,7 +457,8 @@ namespace AMDiS {
InteriorBoundary otherIntBoundary;
/** \brief
- *
+ * Defines the periodic boundaries with other ranks. Periodic boundaries have
+ * no owner, as it is the case of interior boundaries.
*/
InteriorBoundary periodicBoundary;
@@ -525,8 +526,8 @@ namespace AMDiS {
/// may not be the case.
bool macroElementStructureConsisten;
- friend class ParallelDomainDbg;
+ friend class ParallelDebug;
};
}
-#endif // AMDIS_PARALLELDOMAINBASE_H
+#endif // AMDIS_MESHDISTRIBUTOR_H
diff --git a/AMDiS/src/parallel/ParallelDomainDbg.cc b/AMDiS/src/parallel/ParallelDebug.cc
similarity index 80%
rename from AMDiS/src/parallel/ParallelDomainDbg.cc
rename to AMDiS/src/parallel/ParallelDebug.cc
index 4391379c..98e0619e 100644
--- a/AMDiS/src/parallel/ParallelDomainDbg.cc
+++ b/AMDiS/src/parallel/ParallelDebug.cc
@@ -1,5 +1,5 @@
-#include "ParallelDomainDbg.h"
-#include "ParallelDomainBase.h"
+#include "ParallelDebug.h"
+#include "MeshDistributor.h"
#include "PartitionElementData.h"
#include "ProblemVec.h"
#include "DOFVector.h"
@@ -10,18 +10,22 @@
namespace AMDiS {
- void ParallelDomainDbg::testInteriorBoundary(MeshDistributor &pdb)
+ void ParallelDebug::testInteriorBoundary(MeshDistributor &pdb)
{
- FUNCNAME("ParallelDomainDbg::testInteriorBoundary()");
+ FUNCNAME("ParallelDebug::testInteriorBoundary()");
typedef MeshDistributor::RankToBoundMap RankToBoundMap;
std::vector<int*> sendBuffers, recvBuffers;
MPI::Request request[pdb.myIntBoundary.boundary.size() +
- pdb.otherIntBoundary.boundary.size()];
+ pdb.otherIntBoundary.boundary.size() +
+ pdb.periodicBoundary.boundary.size() * 2];
int requestCounter = 0;
+
+ // === Send rank's boundary information. ===
+
for (RankToBoundMap::iterator rankIt = pdb.myIntBoundary.boundary.begin();
rankIt != pdb.myIntBoundary.boundary.end(); ++rankIt) {
@@ -36,6 +40,9 @@ namespace AMDiS {
pdb.mpiComm.Isend(buffer, nSendInt, MPI_INT, rankIt->first, 0);
}
+
+ // === Receive information from other ranks about the interior boundaries. ====
+
for (RankToBoundMap::iterator rankIt = pdb.otherIntBoundary.boundary.begin();
rankIt != pdb.otherIntBoundary.boundary.end(); ++rankIt) {
int nRecvInt = rankIt->second.size();
@@ -46,19 +53,48 @@ namespace AMDiS {
pdb.mpiComm.Irecv(buffer, nRecvInt, MPI_INT, rankIt->first, 0);
}
- MPI::Request::Waitall(requestCounter, request);
+ // === To the last, do the same of periodic boundaries. ===
+
+ for (RankToBoundMap::iterator rankIt = pdb.periodicBoundary.boundary.begin();
+ rankIt != pdb.periodicBoundary.boundary.end(); ++rankIt) {
+ int nValues = rankIt->second.size();
+ int* sBuffer = new int[nValues];
+ for (int i = 0; i < nValues; i++)
+ sBuffer[i] = (rankIt->second)[i].rankObj.elIndex;
+
+ sendBuffers.push_back(sBuffer);
+
+ request[requestCounter++] =
+ pdb.mpiComm.Isend(sBuffer, nValues, MPI_INT, rankIt->first, 0);
+
+ int *rBuffer = new int[nValues];
+ recvBuffers.push_back(rBuffer);
+
+ request[requestCounter++] =
+ pdb.mpiComm.Irecv(rBuffer, nValues, MPI_INT, rankIt->first, 0);
+ }
+
+ // === Finish communication and delete all send buffers. ===
+
+ MPI::Request::Waitall(requestCounter, request);
for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
delete [] sendBuffers[i];
+
+ // === Finally, check the results, i.e., the indices of element at the ===
+ // === boundaries, if they fit together. First check the interior bounds, ===
+ // === and after this the periodic ones. ===
+
int bufCounter = 0;
for (RankToBoundMap::iterator rankIt = pdb.otherIntBoundary.boundary.begin();
rankIt != pdb.otherIntBoundary.boundary.end(); ++rankIt) {
- TEST_EXIT(rankIt->second.size() == pdb.otherIntBoundary.boundary[rankIt->first].size())
+ TEST_EXIT(rankIt->second.size() ==
+ pdb.otherIntBoundary.boundary[rankIt->first].size())
("Boundaries does not fit together!\n");
- for (int i = 0; i < static_cast<int>(rankIt->second.size()); i++) {
+ for (unsigned int i = 0; i < rankIt->second.size(); i++) {
int elIndex1 = recvBuffers[bufCounter][i];
int elIndex2 = pdb.otherIntBoundary.boundary[rankIt->first][i].neighObj.elIndex;
@@ -67,12 +103,25 @@ namespace AMDiS {
delete [] recvBuffers[bufCounter++];
}
+
+
+ for (RankToBoundMap::iterator rankIt = pdb.periodicBoundary.boundary.begin();
+ rankIt != pdb.periodicBoundary.boundary.end(); ++rankIt) {
+ for (unsigned int i = 0; i < rankIt->second.size(); i++) {
+ int elIndex1 = recvBuffers[bufCounter][i];
+ int elIndex2 = pdb.periodicBoundary.boundary[rankIt->first][i].neighObj.elIndex;
+
+ TEST_EXIT(elIndex1 == elIndex2)("Wrong element index at periodic boundary!\n");
+ }
+
+ delete [] recvBuffers[bufCounter++];
+ }
}
- void ParallelDomainDbg::testCommonDofs(MeshDistributor &pdb, bool printCoords)
+ void ParallelDebug::testCommonDofs(MeshDistributor &pdb, bool printCoords)
{
- FUNCNAME("ParallelDomainDbg::testCommonDofs()");
+ FUNCNAME("ParallelDebug::testCommonDofs()");
clock_t first = clock();
@@ -216,9 +265,9 @@ namespace AMDiS {
}
- void ParallelDomainDbg::testAllElements(MeshDistributor &pdb)
+ void ParallelDebug::testAllElements(MeshDistributor &pdb)
{
- FUNCNAME("ParallelDomainDbg::testAllElements()");
+ FUNCNAME("ParallelDebug::testAllElements()");
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(pdb.mesh, -1, Mesh::CALL_LEAF_EL);
@@ -247,11 +296,11 @@ namespace AMDiS {
}
- void ParallelDomainDbg::testDofContainerCommunication(MeshDistributor &pdb,
- RankToDofContainer &sendDofs,
- RankToDofContainer &recvDofs)
+ void ParallelDebug::testDofContainerCommunication(MeshDistributor &pdb,
+ RankToDofContainer &sendDofs,
+ RankToDofContainer &recvDofs)
{
- FUNCNAME("ParallelDomainDbg::testDofContainerCommunication()");
+ FUNCNAME("ParallelDebug::testDofContainerCommunication()");
std::map<int, int> sendNumber;
for (RankToDofContainer::iterator it = sendDofs.begin(); it != sendDofs.end(); ++it)
@@ -278,7 +327,7 @@ namespace AMDiS {
}
- void ParallelDomainDbg::printMapLocalGlobal(MeshDistributor &pdb, int rank)
+ void ParallelDebug::printMapLocalGlobal(MeshDistributor &pdb, int rank)
{
if (rank == -1 || pdb.mpiRank == rank) {
std::cout << "====== DOF MAP LOCAL -> GLOBAL ====== " << std::endl;
@@ -321,9 +370,9 @@ namespace AMDiS {
}
- void ParallelDomainDbg::printMapPeriodic(MeshDistributor &pdb, int rank)
+ void ParallelDebug::printMapPeriodic(MeshDistributor &pdb, int rank)
{
- FUNCNAME("ParallelDomainDbg::printMapPeriodic()");
+ FUNCNAME("ParallelDebug::printMapPeriodic()");
typedef std::map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;
typedef std::map<DegreeOfFreedom, std::set<DegreeOfFreedom> > PeriodicDofMap;
@@ -355,10 +404,10 @@ namespace AMDiS {
}
- void ParallelDomainDbg::printRankDofs(MeshDistributor &pdb,
- int rank,
- DofContainer& rankDofs,
- DofContainer& rankAllDofs)
+ void ParallelDebug::printRankDofs(MeshDistributor &pdb,
+ int rank,
+ DofContainer& rankDofs,
+ DofContainer& rankAllDofs)
{
if (rank == -1 || pdb.mpiRank == rank) {
std::cout << "====== RANK DOF INFORMATION ====== " << std::endl;
@@ -384,9 +433,9 @@ namespace AMDiS {
}
- void ParallelDomainDbg::printBoundaryInfo(MeshDistributor &pdb)
+ void ParallelDebug::printBoundaryInfo(MeshDistributor &pdb)
{
- FUNCNAME("ParallelDomainDbg::printBoundaryInfo()");
+ FUNCNAME("ParallelDebug::printBoundaryInfo()");
for (InteriorBoundary::iterator it(pdb.myIntBoundary); !it.end(); ++it) {
MSG("Rank owned boundary with rank %d: \n", it.getRank());
@@ -406,10 +455,10 @@ namespace AMDiS {
}
- void ParallelDomainDbg::writeCoordsFile(MeshDistributor &pdb,
- std::string prefix, std::string postfix)
+ void ParallelDebug::writeCoordsFile(MeshDistributor &pdb,
+ std::string prefix, std::string postfix)
{
- FUNCNAME("ParallelDomainDbg::writeCoordsFile()");
+ FUNCNAME("ParallelDebug::writeCoordsFile()");
std::stringstream filename;
filename << prefix << "-" << pdb.mpiRank << "." << postfix;
diff --git a/AMDiS/src/parallel/ParallelDomainDbg.h b/AMDiS/src/parallel/ParallelDebug.h
similarity index 95%
rename from AMDiS/src/parallel/ParallelDomainDbg.h
rename to AMDiS/src/parallel/ParallelDebug.h
index d5523b91..1318f442 100644
--- a/AMDiS/src/parallel/ParallelDomainDbg.h
+++ b/AMDiS/src/parallel/ParallelDebug.h
@@ -17,23 +17,24 @@
// == ==
// ============================================================================
-/** \file ParallelDomainDbg.h */
+/** \file ParallelDebug.h */
-#ifndef AMDIS_PARALLELDOMAINDBG_H
-#define AMDIS_PARALLELDOMAINDBG_H
+#ifndef AMDIS_PARALLELDEBUG_H
+#define AMDIS_PARALLELDEBUG_H
-#include "parallel/ParallelDomainBase.h"
+#include "parallel/MeshDistributor.h"
namespace AMDiS {
- class ParallelDomainDbg
+ class ParallelDebug
{
protected:
typedef MeshDistributor::RankToDofContainer RankToDofContainer;
public:
/** \brief
- * Tests the interior boundaries on all ranks if their order fits together.
+ * Tests the interior and the periodic boundaries on all ranks if their order
+ * fits together.
*
* \param[in] pdb Parallel problem definition used for debugging.
*/
--
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