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Commit ab3182cb authored by Thomas Witkowski's avatar Thomas Witkowski
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Solved several small problems with periodic boundaries in parallel computations, new file names.

parent 932281a3
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Showing with 329 additions and 310 deletions
AMDiS/CMakeLists.txt
View file @ ab3182cb
......@@ -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")
......
AMDiS/bin/Makefile.am
View file @ ab3182cb
......@@ -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
......
AMDiS/bin/Makefile.in
View file @ ab3182cb
......@@ -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; \
......
AMDiS/libtool
View file @ ab3182cb
......@@ -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=""
......
AMDiS/src/DOFMatrix.cc
View file @ ab3182cb
......@@ -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];
}
}
......
AMDiS/src/Element.h
View file @ ab3182cb
......@@ -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,
......
AMDiS/src/ProblemVec.cc
View file @ ab3182cb
......@@ -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;
......
AMDiS/src/VtkWriter.cc
View file @ ab3182cb
......@@ -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);
}
}
AMDiS/src/VtkWriter.h
View file @ ab3182cb
......@@ -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);
......
AMDiS/src/VtkWriter.hh
View file @ ab3182cb
......@@ -81,6 +81,7 @@ namespace AMDiS {
file << " </UnstructuredGrid>\n";