diff --git a/AMDiS/libtool b/AMDiS/libtool
index 4f4afd67949bd025c4883ad68bf263c224fa9462..db01bc59718f48797b60d36d16c9ae7d8fd0eab2 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="/usr/bin/sed"
+SED="/bin/sed"
# Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/usr/bin/sed -e 1s/^X//"
+Xsed="/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 p2s103:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-redhat-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-redhat-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -82,25 +82,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+CC="gcc"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -174,7 +174,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -328,10 +328,10 @@ 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=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /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/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7266,7 +7266,7 @@ disable_libs=static
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host p2s103:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7288,12 +7288,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-redhat-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-redhat-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7304,25 +7304,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
+CC="g++"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7396,7 +7396,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -7451,11 +7451,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=`echo "/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" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+predep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=`echo "/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" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+postdep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -7463,11 +7463,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=`echo "-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/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/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+compiler_lib_search_path=`echo "-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/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7547,10 +7547,10 @@ 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=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /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/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7574,7 +7574,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host p2s103:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7596,12 +7596,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-redhat-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-redhat-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7612,7 +7612,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7621,16 +7621,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7858,10 +7858,10 @@ 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=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /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/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/AdaptBase.h b/AMDiS/src/AdaptBase.h
index 77bdc46dccce1428dfa29ec26888d5744db39ee5..83660464d99cda495369e6ebaa0a9b0ab2ecd3c1 100644
--- a/AMDiS/src/AdaptBase.h
+++ b/AMDiS/src/AdaptBase.h
@@ -43,14 +43,14 @@ namespace AMDiS {
/** \brief
* Constructor
*/
- AdaptBase(const ::std::string& name,
+ AdaptBase(const ::std::string& name,
ProblemIterationInterface *problemIteration,
- AdaptInfo *adaptInfo_,
- ProblemTimeInterface *problemTime = NULL,
- AdaptInfo *initialAdaptInfo = NULL)
+ AdaptInfo *adaptInfo,
+ ProblemTimeInterface *problemTime = NULL,
+ AdaptInfo *initialAdaptInfo = NULL)
: name_(name),
problemIteration_(problemIteration),
- adaptInfo(adaptInfo_),
+ adaptInfo_(adaptInfo),
problemTime_(problemTime),
initialAdaptInfo_(initialAdaptInfo)
{};
@@ -85,10 +85,10 @@ namespace AMDiS {
};
/** \brief
- * Returns \ref adaptInfo
+ * Returns \ref adaptInfo_
*/
inline AdaptInfo *getAdaptInfo() {
- return adaptInfo;
+ return adaptInfo_;
};
/** \brief
@@ -123,7 +123,7 @@ namespace AMDiS {
/** \brief
* Main adapt info
*/
- AdaptInfo *adaptInfo;
+ AdaptInfo *adaptInfo_;
/** \brief
* problem time interface
diff --git a/AMDiS/src/AdaptInstationary.cc b/AMDiS/src/AdaptInstationary.cc
index c23cb21b1c1565b82cb17f50d34d3bf45a5ae423..e6f67c8161a888cbca7f7dad13710dffb223a08c 100644
--- a/AMDiS/src/AdaptInstationary.cc
+++ b/AMDiS/src/AdaptInstationary.cc
@@ -77,24 +77,24 @@ namespace AMDiS {
FUNCNAME("AdaptInstationary::explicitTimeStrategy()");
// estimate before first adaption
- if (adaptInfo->getTime() <= adaptInfo->getStartTime()) {
- problemIteration_->oneIteration(adaptInfo, ESTIMATE);
+ if (adaptInfo_->getTime() <= adaptInfo_->getStartTime()) {
+ problemIteration_->oneIteration(adaptInfo_, ESTIMATE);
}
// increment time
- adaptInfo->setTime(adaptInfo->getTime() + adaptInfo->getTimestep());
+ adaptInfo_->setTime(adaptInfo_->getTime() + adaptInfo_->getTimestep());
- problemTime_->setTime(adaptInfo);
+ problemTime_->setTime(adaptInfo_);
INFO(info_,6)("time = %e, timestep = %e\n",
- adaptInfo->getTime(), adaptInfo->getTimestep());
+ adaptInfo_->getTime(), adaptInfo_->getTimestep());
- adaptInfo->setSpaceIteration(0);
+ adaptInfo_->setSpaceIteration(0);
// do the iteration
- problemIteration_->beginIteration(adaptInfo);
- problemIteration_->oneIteration(adaptInfo, FULL_ITERATION);
- problemIteration_->endIteration(adaptInfo);
+ problemIteration_->beginIteration(adaptInfo_);
+ problemIteration_->oneIteration(adaptInfo_, FULL_ITERATION);
+ problemIteration_->endIteration(adaptInfo_);
}
void AdaptInstationary::implicitTimeStrategy()
@@ -102,54 +102,54 @@ namespace AMDiS {
FUNCNAME("AdaptInstationary::implicitTimeStrategy()");
do {
- adaptInfo->setTime(adaptInfo->getTime() + adaptInfo->getTimestep());
- problemTime_->setTime(adaptInfo);
+ adaptInfo_->setTime(adaptInfo_->getTime() + adaptInfo_->getTimestep());
+ problemTime_->setTime(adaptInfo_);
INFO(info_,6)("time = %e, try timestep = %e\n",
- adaptInfo->getTime(), adaptInfo->getTimestep());
+ adaptInfo_->getTime(), adaptInfo_->getTimestep());
- problemIteration_->oneIteration(adaptInfo, NO_ADAPTION);
+ problemIteration_->oneIteration(adaptInfo_, NO_ADAPTION);
- adaptInfo->incTimestepIteration();
+ adaptInfo_->incTimestepIteration();
if (!fixedTimestep_ &&
- !adaptInfo->timeToleranceReached() &&
- !adaptInfo->getTimestep() <= adaptInfo->getMinTimestep())
+ !adaptInfo_->timeToleranceReached() &&
+ !adaptInfo_->getTimestep() <= adaptInfo_->getMinTimestep())
{
- adaptInfo->setTime(adaptInfo->getTime() - adaptInfo->getTimestep());
- adaptInfo->setTimestep(adaptInfo->getTimestep() * time_delta_1);
+ adaptInfo_->setTime(adaptInfo_->getTime() - adaptInfo_->getTimestep());
+ adaptInfo_->setTimestep(adaptInfo_->getTimestep() * time_delta_1);
continue;
}
- adaptInfo->setSpaceIteration(0);
+ adaptInfo_->setSpaceIteration(0);
do {
- problemIteration_->beginIteration(adaptInfo);
+ problemIteration_->beginIteration(adaptInfo_);
- if (problemIteration_->oneIteration(adaptInfo, FULL_ITERATION)) {
+ if (problemIteration_->oneIteration(adaptInfo_, FULL_ITERATION)) {
if (!fixedTimestep_ &&
- !adaptInfo->timeToleranceReached() &&
- !adaptInfo->getTimestep() <= adaptInfo->getMinTimestep())
+ !adaptInfo_->timeToleranceReached() &&
+ !adaptInfo_->getTimestep() <= adaptInfo_->getMinTimestep())
{
- adaptInfo->setTime(adaptInfo->getTime() - adaptInfo->getTimestep());
- adaptInfo->setTimestep(adaptInfo->getTimestep() * time_delta_1);
- problemIteration_->endIteration(adaptInfo);
- adaptInfo->incSpaceIteration();
+ adaptInfo_->setTime(adaptInfo_->getTime() - adaptInfo_->getTimestep());
+ adaptInfo_->setTimestep(adaptInfo_->getTimestep() * time_delta_1);
+ problemIteration_->endIteration(adaptInfo_);
+ adaptInfo_->incSpaceIteration();
break;
}
}
- adaptInfo->incSpaceIteration();
- problemIteration_->endIteration(adaptInfo);
+ adaptInfo_->incSpaceIteration();
+ problemIteration_->endIteration(adaptInfo_);
- } while(!adaptInfo->spaceToleranceReached() &&
- adaptInfo->getSpaceIteration() <= adaptInfo->getMaxSpaceIteration());
- } while(!adaptInfo->timeToleranceReached() &&
- !adaptInfo->getTimestep() <= adaptInfo->getMinTimestep() &&
- adaptInfo->getTimestepIteration() <= adaptInfo->getMaxTimestepIteration());
+ } while(!adaptInfo_->spaceToleranceReached() &&
+ adaptInfo_->getSpaceIteration() <= adaptInfo_->getMaxSpaceIteration());
+ } while(!adaptInfo_->timeToleranceReached() &&
+ !adaptInfo_->getTimestep() <= adaptInfo_->getMinTimestep() &&
+ adaptInfo_->getTimestepIteration() <= adaptInfo_->getMaxTimestepIteration());
- if (!fixedTimestep_ && adaptInfo->timeErrorLow()) {
- adaptInfo->setTimestep(adaptInfo->getTimestep() *time_delta_2);
+ if (!fixedTimestep_ && adaptInfo_->timeErrorLow()) {
+ adaptInfo_->setTimestep(adaptInfo_->getTimestep() *time_delta_2);
}
}
@@ -157,7 +157,7 @@ namespace AMDiS {
{
FUNCNAME("AdaptInstationary::oneTimestep");
- adaptInfo->setTimestepIteration(0);
+ adaptInfo_->setTimestepIteration(0);
switch(strategy)
{
@@ -172,7 +172,7 @@ namespace AMDiS {
explicitTimeStrategy();
}
- adaptInfo->incTimestepNumber();
+ adaptInfo_->incTimestepNumber();
}
int AdaptInstationary::adapt()
@@ -181,30 +181,29 @@ namespace AMDiS {
int errorCode = 0;
- TEST_EXIT(adaptInfo->getTimestep() >= adaptInfo->getMinTimestep())
+ TEST_EXIT(adaptInfo_->getTimestep() >= adaptInfo_->getMinTimestep())
("timestep < min timestep\n");
- TEST_EXIT(adaptInfo->getTimestep() <= adaptInfo->getMaxTimestep())
+ TEST_EXIT(adaptInfo_->getTimestep() <= adaptInfo_->getMaxTimestep())
("timestep > max timestep\n");
- TEST_EXIT(adaptInfo->getTimestep() > 0)("timestep <= 0!\n");
+ TEST_EXIT(adaptInfo_->getTimestep() > 0)("timestep <= 0!\n");
- if (adaptInfo->getTimestepNumber() == 0) {
- adaptInfo->setTime(adaptInfo->getStartTime());
- initialAdaptInfo_->setStartTime(adaptInfo->getStartTime());
- initialAdaptInfo_->setTime(adaptInfo->getStartTime());
+ if (adaptInfo_->getTimestepNumber() == 0) {
+ adaptInfo_->setTime(adaptInfo_->getStartTime());
+ initialAdaptInfo_->setStartTime(adaptInfo_->getStartTime());
+ initialAdaptInfo_->setTime(adaptInfo_->getStartTime());
- problemTime_->setTime(adaptInfo);
+ problemTime_->setTime(adaptInfo_);
// initial adaption
problemTime_->solveInitialProblem(initialAdaptInfo_);
- problemTime_->transferInitialSolution(adaptInfo);
+ problemTime_->transferInitialSolution(adaptInfo_);
}
- // while (adaptInfo->getTime() < adaptInfo->getEndTime() - DBL_TOL) {
- while (adaptInfo->getEndTime() - adaptInfo->getTime() > DBL_TOL) {
+ while (adaptInfo_->getTime() < adaptInfo_->getEndTime() - DBL_TOL) {
iterationTimestamp_ = time(NULL);
- problemTime_->initTimestep(adaptInfo);
+ problemTime_->initTimestep(adaptInfo_);
#ifdef _OPENMP
if (problemTime_->existsDelayedCalculation()) {
@@ -224,9 +223,9 @@ namespace AMDiS {
oneTimestep();
#endif
- problemTime_->closeTimestep(adaptInfo);
+ problemTime_->closeTimestep(adaptInfo_);
- if (breakWhenStable && (adaptInfo->getSolverIterations() == 0)) {
+ if (breakWhenStable && (adaptInfo_->getSolverIterations() == 0)) {
break;
}
@@ -270,7 +269,7 @@ namespace AMDiS {
FUNCNAME("AdaptInstationary::serialize()");
problemIteration_->serialize(out);
- adaptInfo->serialize(out);
+ adaptInfo_->serialize(out);
if (problemTime_) {
problemTime_->serialize(out);
}
@@ -281,7 +280,7 @@ namespace AMDiS {
FUNCNAME("AdaptInstationary::deserialize()");
problemIteration_->deserialize(in);
- adaptInfo->deserialize(in);
+ adaptInfo_->deserialize(in);
if (problemTime_) {
problemTime_->deserialize(in);
}
@@ -299,20 +298,20 @@ namespace AMDiS {
time_t currentTimestamp = time(NULL);
// Update list with the last iteration runtimes.
- lastIterationsDuration.push(currentTimestamp - iterationTimestamp_);
+ lastIterationsDuration_.push(currentTimestamp - iterationTimestamp_);
// The list should not contain more than 5 elements. If so, delete the oldest one.
- if (lastIterationsDuration.size() > 5) {
- lastIterationsDuration.pop();
+ if (lastIterationsDuration_.size() > 5) {
+ lastIterationsDuration_.pop();
}
// Calculate the avarage of the last iterations.
- ::std::queue<int> tmpQueue = lastIterationsDuration;
+ ::std::queue<int> tmpQueue = lastIterationsDuration_;
int avrgLastIterations = 0;
while (!tmpQueue.empty()) {
avrgLastIterations += tmpQueue.front();
tmpQueue.pop();
}
- avrgLastIterations /= lastIterationsDuration.size();
+ avrgLastIterations /= lastIterationsDuration_.size();
// Check if there is enough time for a further iteration.
if (initialTimestamp_ + queueRuntime_ - currentTimestamp < avrgLastIterations * 2) {
diff --git a/AMDiS/src/AdaptInstationary.h b/AMDiS/src/AdaptInstationary.h
index c0ed8235673405a79e038a3ecaac4c17c77dab80..0ca426ac36358dd011f80f97e4608f93f8b3b120 100644
--- a/AMDiS/src/AdaptInstationary.h
+++ b/AMDiS/src/AdaptInstationary.h
@@ -186,7 +186,7 @@ namespace AMDiS {
/** \brief
* Stores the runtime (in seconds) of some last timestep iterations.
*/
- ::std::queue<int> lastIterationsDuration;
+ ::std::queue<int> lastIterationsDuration_;
};
}
diff --git a/AMDiS/src/AdaptStationary.cc b/AMDiS/src/AdaptStationary.cc
index b5265570007526a9bb60596e00a7f42c0b0fe63d..62a297d153258dd0d2e69217db19c6314a117669 100644
--- a/AMDiS/src/AdaptStationary.cc
+++ b/AMDiS/src/AdaptStationary.cc
@@ -20,26 +20,26 @@ namespace AMDiS {
FUNCNAME("AdaptStationary::adapt()");
// initial iteration
- if (adaptInfo->getSpaceIteration() == -1) {
- problemIteration_->beginIteration(adaptInfo);
- problemIteration_->oneIteration(adaptInfo, NO_ADAPTION);
- problemIteration_->endIteration(adaptInfo);
- adaptInfo->incSpaceIteration();
+ if (adaptInfo_->getSpaceIteration() == -1) {
+ problemIteration_->beginIteration(adaptInfo_);
+ problemIteration_->oneIteration(adaptInfo_, NO_ADAPTION);
+ problemIteration_->endIteration(adaptInfo_);
+ adaptInfo_->incSpaceIteration();
}
// adaption loop
- while (!adaptInfo->spaceToleranceReached() &&
- (adaptInfo->getSpaceIteration() < adaptInfo->getMaxSpaceIteration() ||
- adaptInfo->getMaxSpaceIteration() < 0) ) {
+ while (!adaptInfo_->spaceToleranceReached() &&
+ (adaptInfo_->getSpaceIteration() < adaptInfo_->getMaxSpaceIteration() ||
+ adaptInfo_->getMaxSpaceIteration() < 0) ) {
- problemIteration_->beginIteration(adaptInfo);
- Flag adapted = problemIteration_->oneIteration(adaptInfo, FULL_ITERATION);
- problemIteration_->endIteration(adaptInfo);
+ problemIteration_->beginIteration(adaptInfo_);
+ Flag adapted = problemIteration_->oneIteration(adaptInfo_, FULL_ITERATION);
+ problemIteration_->endIteration(adaptInfo_);
if (!adapted)
break;
- adaptInfo->incSpaceIteration();
+ adaptInfo_->incSpaceIteration();
}
return 0;
diff --git a/AMDiS/src/DOFVector.hh b/AMDiS/src/DOFVector.hh
index 501265872158252cd4f3be4ad5669da7b100d97e..fb1e841098bf61ee9de10640e0d86b4aaaecf30a 100644
--- a/AMDiS/src/DOFVector.hh
+++ b/AMDiS/src/DOFVector.hh
@@ -785,24 +785,23 @@ namespace AMDiS {
}
template<typename T>
- DOFVector<T>& DOFVector<T>::operator=(const DOFVector<T>& rhs)
+ DOFVector<T>& DOFVector<T>::operator=(const DOFVector<T>& rhs )
{
- feSpace = rhs.feSpace;
- vec = rhs.vec;
- this->elementVector = NULL;
- interFct = rhs.interFct;
- refineInter = rhs.refineInter;
- coarsenOperation = rhs.coarsenOperation;
- this->operators = rhs.operators;
- this->operatorFactor = rhs.operatorFactor;
+ feSpace=rhs.feSpace;
+ vec=rhs.vec;
+ this->elementVector=NULL;
+ interFct=rhs.interFct;
+ refineInter=rhs.refineInter;
+ coarsenOperation=rhs.coarsenOperation;
+ this->operators=rhs.operators;
+ this->operatorFactor=rhs.operatorFactor;
if (rhs.boundaryManager) {
- if (this->boundaryManager)
- delete this->boundaryManager;
+ if(this->boundaryManager) delete this->boundaryManager;
this->boundaryManager = new BoundaryManager(*rhs.boundaryManager);
// boundaryManager->setDOFVector(this);
- } else {
- this->boundaryManager = NULL;
}
+ else
+ this->boundaryManager=NULL;
return *this;
}
diff --git a/AMDiS/src/DataCollector.h b/AMDiS/src/DataCollector.h
index 0c91d07770c278bb855ec1f97694080704f1ba10..86d6cf5fca1f97db450c9aae20f0344c5e6f4887 100644
--- a/AMDiS/src/DataCollector.h
+++ b/AMDiS/src/DataCollector.h
@@ -137,6 +137,10 @@ namespace AMDiS {
*/
Mesh* getMesh();
+ void setMesh(Mesh *mesh) {
+ mesh_ = mesh;
+ };
+
protected:
/** \brief
* Start collecting element and vertex data of the problem.
diff --git a/AMDiS/src/ElementFileWriter.cc b/AMDiS/src/ElementFileWriter.cc
index 38e1533da89ea7d3c3370fcb3210ec2ea4f1a822..ba5717157f1daaebd95b2f69241a080f5d828070 100644
--- a/AMDiS/src/ElementFileWriter.cc
+++ b/AMDiS/src/ElementFileWriter.cc
@@ -36,10 +36,8 @@ namespace AMDiS {
GET_PARAMETER(0, name + "->output->append index", "%d", &appendIndex);
GET_PARAMETER(0, name + "->output->index length", "%d", &indexLength);
GET_PARAMETER(0, name + "->output->index decimals", "%d", &indexDecimals);
- GET_PARAMETER(0, name + "->output->write every i-th timestep", "%d", &tsModulo);
-
- TEST_EXIT(tsModulo > 0)
- ("Init file option \"write every i-th timestep\" is smaller than 1!\n");
+ GET_PARAMETER(0, name + "->output->write every i-th timestep", "%d",
+ &tsModulo);
}
void ElementFileWriter::writeFiles(AdaptInfo *adaptInfo, bool force,
diff --git a/AMDiS/src/FileWriter.cc b/AMDiS/src/FileWriter.cc
index 9e990aadcabcf1f7f0da256aeb917af04ae90f75..592292385f9430e75e0322dba14adcfbb0930459 100644
--- a/AMDiS/src/FileWriter.cc
+++ b/AMDiS/src/FileWriter.cc
@@ -155,9 +155,6 @@ namespace AMDiS {
TEST_EXIT(!delayWriting_ || amdisHaveOpenMP)
("Delayed writing only possible with OpenMP support!\n");
- TEST_EXIT(tsModulo > 0)
- ("Init file option \"write every i-th timestep\" is smaller than 1!\n");
-
}
void FileWriter::writeFiles(AdaptInfo *adaptInfo,
diff --git a/AMDiS/src/MeshStructure.cc b/AMDiS/src/MeshStructure.cc
index eb432902ea489f5ec061d99003a23e613ab2a970..cb79462554e55748ac28468c93b04e0c929a56a3 100644
--- a/AMDiS/src/MeshStructure.cc
+++ b/AMDiS/src/MeshStructure.cc
@@ -142,12 +142,12 @@ namespace AMDiS {
reset();
elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
- TEST_EXIT_DBG(cont)("unexpected structure code end!\n");
+ TEST_EXIT(cont)("unexpected structure code end!\n");
Element *element = elInfo->getElement();
if (isLeafElement()) {
- TEST_EXIT_DBG(element->isLeaf())("mesh finer than code\n");
+ TEST_EXIT(element->isLeaf())("mesh finer than code\n");
};
if (element->isLeaf() && !isLeafElement()) {
@@ -159,7 +159,7 @@ namespace AMDiS {
if (checkPartition) {
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- TEST_EXIT_DBG(partitionData)("no partition element data\n");
+ TEST_EXIT(partitionData)("no partition element data\n");
PartitionStatus status = partitionData->getPartitionStatus();
if ((debugMode == false) && (status == OUT || status == UNDEFINED)) {
decorate = false;
diff --git a/AMDiS/src/ParMetisPartitioner.cc b/AMDiS/src/ParMetisPartitioner.cc
index d5da44333ca1fc47379402a7086d42bb936299b8..5381ca913cb3e496f95a705b2a433f7154931a69 100644
--- a/AMDiS/src/ParMetisPartitioner.cc
+++ b/AMDiS/src/ParMetisPartitioner.cc
@@ -12,12 +12,13 @@
namespace AMDiS {
- ParMetisMesh::ParMetisMesh(Mesh *mesh)
- : numElements_(0)
+ ParMetisMesh::ParMetisMesh(Mesh *mesh, MPI::Comm *comm)
+ : numElements_(0),
+ mpiComm(comm)
{
FUNCNAME("ParMetisMesh::ParMetisMesh()");
- int i;
- int mpiSize = MPI::COMM_WORLD.Get_size();
+
+ int mpiSize = mpiComm->Get_size();
int nodeCounter = 0;
int elementCounter = 0;
@@ -28,17 +29,16 @@ namespace AMDiS {
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
// get partition data
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- if(partitionData &&
- partitionData->getPartitionStatus() == IN &&
- partitionData->getLevel() == 0)
- {
+ if (partitionData &&
+ partitionData->getPartitionStatus() == IN &&
+ partitionData->getLevel() == 0) {
elementCounter++;
}
@@ -56,7 +56,7 @@ namespace AMDiS {
elem_p2a_ = GET_MEMORY(int, numElements_);
- if(dim_ == dow) {
+ if (dim_ == dow) {
xyz_ = GET_MEMORY(float, numElements_ * dim_);
} else {
xyz_ = NULL;
@@ -69,10 +69,10 @@ namespace AMDiS {
float *ptr_xyz = xyz_;
// gather element numbers and create elmdist
- MPI::COMM_WORLD.Allgather(&numElements_, 1, MPI_INT,
- elmdist_ + 1, 1, MPI_INT);
+ mpiComm->Allgather(&numElements_, 1, MPI_INT, elmdist_ + 1, 1, MPI_INT);
+
elmdist_[0] = 0;
- for(i = 2; i < mpiSize + 1; i++) {
+ for (int i = 2; i < mpiSize + 1; i++) {
elmdist_[i] += elmdist_[i - 1];
}
@@ -85,7 +85,7 @@ namespace AMDiS {
elInfo = stack.traverseFirst(mesh, -1,
Mesh::CALL_EVERY_EL_PREORDER |
Mesh::FILL_COORDS);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
int index = element->getIndex();
@@ -94,10 +94,9 @@ namespace AMDiS {
(element->getElementData(PARTITION_ED));
// if element in partition
- if(partitionData &&
- partitionData->getPartitionStatus() == IN &&
- partitionData->getLevel() == 0)
- {
+ if (partitionData &&
+ partitionData->getPartitionStatus() == IN &&
+ partitionData->getLevel() == 0) {
// remember index
setParMetisIndex(index, elementCounter);
setAMDiSIndex(elementCounter, index);
@@ -108,15 +107,15 @@ namespace AMDiS {
ptr_eptr++;
// write eind entries (element nodes)
- for(i = 0; i < dim_ + 1; i++) {
+ for (int i = 0; i < dim_ + 1; i++) {
*ptr_eind = element->getDOF(i, 0);
ptr_eind++;
}
// write xyz element coordinates
- if(ptr_xyz) {
+ if (ptr_xyz) {
elInfo->coordToWorld(bary, &world);
- for(i = 0; i < dim_; i++) {
+ for (int i = 0; i < dim_; i++) {
*ptr_xyz = static_cast<float>(world[i]);
ptr_xyz++;
}
@@ -130,22 +129,33 @@ namespace AMDiS {
ParMetisMesh::~ParMetisMesh()
{
- if(eptr_) FREE_MEMORY(eptr_, int, numElements_ + 1);
- if(eind_) FREE_MEMORY(eind_, int, numElements_ * (dim_ + 1));
- if(elmdist_) FREE_MEMORY(elmdist_, int, MPI::COMM_WORLD.Get_size() + 1);
- if(xyz_) FREE_MEMORY(xyz_, float, numElements_ * dim_);
- if(elem_p2a_) FREE_MEMORY(elem_p2a_, int, numElements_);
+ if (eptr_)
+ FREE_MEMORY(eptr_, int, numElements_ + 1);
+
+ if (eind_)
+ FREE_MEMORY(eind_, int, numElements_ * (dim_ + 1));
+
+ if (elmdist_)
+ FREE_MEMORY(elmdist_, int, mpiComm->Get_size() + 1);
+
+ if (xyz_)
+ FREE_MEMORY(xyz_, float, numElements_ * dim_);
+
+ if (elem_p2a_)
+ FREE_MEMORY(elem_p2a_, int, numElements_);
}
ParMetisGraph::ParMetisGraph(ParMetisMesh *parMetisMesh,
+ MPI::Comm *comm,
int ncommonnodes)
: parMetisMesh_(parMetisMesh)
{
int numflag = 0;
- if(ncommonnodes == -1) ncommonnodes = parMetisMesh->getDim();
+ if (ncommonnodes == -1)
+ ncommonnodes = parMetisMesh->getDim();
- MPI_Comm comm = MPI_COMM_WORLD;
+ MPI_Comm tmpComm = MPI_Comm(*comm);
ParMETIS_V3_Mesh2Dual(parMetisMesh_->getElementDist(),
parMetisMesh_->getElementPtr(),
@@ -154,23 +164,22 @@ namespace AMDiS {
&ncommonnodes,
&xadj_,
&adjncy_,
- &comm);
+ &tmpComm);
}
ParMetisGraph::~ParMetisGraph()
{
free(xadj_);
free(adjncy_);
-// if(xadj_) delete [] xadj_;
-// if(adjncy_) delete [] adjncy_;
}
+
void ParMetisPartitioner::deletePartitionData()
{
TraverseStack stack;
ElInfo *elInfo;
elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
element->deleteElementData(PARTITION_ED);
elInfo = stack.traverseNext(elInfo);
@@ -178,8 +187,8 @@ namespace AMDiS {
}
void ParMetisPartitioner::createPartitionData() {
- int mpiRank = MPI::COMM_WORLD.Get_rank();
- int mpiSize = MPI::COMM_WORLD.Get_size();
+ int mpiRank = mpiComm->Get_rank();
+ int mpiSize = mpiComm->Get_size();
TraverseStack stack;
ElInfo *elInfo;
@@ -187,7 +196,7 @@ namespace AMDiS {
// === create initial partitioning on AMDiS mesh ===
int totalElementCounter = 0;
elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_LEAF_EL);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
//int index = element->getIndex();
@@ -198,7 +207,7 @@ namespace AMDiS {
NEW PartitionElementData(element->getElementData());
element->setElementData(elData);
- if(totalElementCounter % mpiSize == mpiRank) {
+ if (totalElementCounter % mpiSize == mpiRank) {
elData->setPartitionStatus(IN);
} else {
elData->setPartitionStatus(UNDEFINED);
@@ -207,61 +216,21 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
-
-// elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_LEAF_EL);
-// while(elInfo) {
-// Element *element = elInfo->getElement();
-// int index = element->getIndex();
-
-// TEST_EXIT(element->getElementData(PARTITION_ED) == NULL)
-// ("mesh already partitioned\n");
-
-// PartitionElementData *elData =
-// NEW PartitionElementData(element->getElementData());
-// element->setElementData(elData);
-// elData->setPartitionStatus(UNDEFINED);
-// elData->setLevel(0);
-// elInfo = stack.traverseNext(elInfo);
-// }
}
void ParMetisPartitioner::partition(std::map<int, double> *elemWeights,
PartitionMode mode,
float itr)
{
- int mpiSize = MPI::COMM_WORLD.Get_size();
+ int mpiSize = mpiComm->Get_size();
TraverseStack stack;
ElInfo *elInfo;
- // === create initial partitioning on AMDiS mesh ===
-
-// if(mode == INITIAL) {
-// int totalElementCounter = 0;
-// elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_EVERY_EL_PREORDER);
-// while(elInfo) {
-// Element *element = elInfo->getElement();
-// int index = element->getIndex();
-
-// // get partition data
-// PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
-// (element->getElementData(PARTITION_ED));
-
-// if(partitionData && partitionData->getLevel() == 0) {
-// if(totalElementCounter % mpiSize == mpiRank) {
-// partitionData->setPartitionStatus(IN);
-// } else {
-// partitionData->setPartitionStatus(UNDEFINED);
-// }
-// totalElementCounter++;
-// }
-// elInfo = stack.traverseNext(elInfo);
-// }
-// }
-
// === create parmetis mesh ===
- if(parMetisMesh_) DELETE parMetisMesh_;
- parMetisMesh_ = NEW ParMetisMesh(mesh_);
+ if (parMetisMesh_)
+ DELETE parMetisMesh_;
+ parMetisMesh_ = NEW ParMetisMesh(mesh_, mpiComm);
int numElements = parMetisMesh_->getNumElements();
@@ -271,20 +240,18 @@ namespace AMDiS {
float maxWgt = 0.0;
float *ptr_floatWgts = floatWgts;
- //int *ptr_wgts = wgts;
elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
// get partition data
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- if(partitionData &&
- partitionData->getPartitionStatus() == IN &&
- partitionData->getLevel() == 0)
- {
+ if (partitionData &&
+ partitionData->getPartitionStatus() == IN &&
+ partitionData->getLevel() == 0) {
int index = element->getIndex();
// get weight
@@ -299,23 +266,15 @@ namespace AMDiS {
}
float tmp;
- MPI::COMM_WORLD.Allreduce(&maxWgt,
- &tmp,
- 1,
- MPI_FLOAT,
- MPI_MAX);
+ mpiComm->Allreduce(&maxWgt, &tmp, 1, MPI_FLOAT, MPI_MAX);
maxWgt = tmp;
// === create dual graph ===
- ParMetisGraph parMetisGraph(parMetisMesh_);
+ ParMetisGraph parMetisGraph(parMetisMesh_, mpiComm);
// === partitioning of dual graph ===
- MPI_Comm comm = MPI_COMM_WORLD;
-
- int i;
int wgtflag = elemWeights ? 2 : 0; // weights at vertices only!
int numflag = 0; // c numbering style!
- //int ndims = mesh_->getDim();
int ncon = elemWeights ? 1 : 0; // one weight at each vertex!
int nparts = mpiSize; // number of partitions
float *tpwgts = elemWeights ? GET_MEMORY(float, mpiSize) : NULL;
@@ -324,39 +283,23 @@ namespace AMDiS {
int edgecut = -1;
int *part = GET_MEMORY(int, numElements);
- if(elemWeights) {
- for(i = 0; i < mpiSize; i++) {
+ if (elemWeights) {
+ for (int i = 0; i < mpiSize; i++) {
// set tpwgts
- tpwgts[i] = 1.0/nparts;
+ tpwgts[i] = 1.0 / nparts;
}
float scale = 10000 / maxWgt;
- for(i = 0; i < numElements; i++) {
+ for (int i = 0; i < numElements; i++) {
// scale wgts
wgts[i] = static_cast<int>(floatWgts[i] * scale);
}
}
+ MPI_Comm tmpComm = MPI_Comm(*mpiComm);
+
switch(mode) {
case INITIAL:
-// if(parMetisMesh_->getXYZ()) {
-// ParMETIS_V3_PartGeomKway(parMetisMesh_->getElementDist(),
-// parMetisGraph.getXAdj(),
-// parMetisGraph.getAdjncy(),
-// wgts,
-// NULL,
-// &wgtflag,
-// &numflag,
-// &ndims,
-// parMetisMesh_->getXYZ(),
-// &ncon,
-// &nparts,
-// tpwgts,
-// &ubvec,
-// options,
-// &edgecut,
-// part,
-// &comm);
ParMETIS_V3_PartKway(parMetisMesh_->getElementDist(),
parMetisGraph.getXAdj(),
parMetisGraph.getAdjncy(),
@@ -371,15 +314,12 @@ namespace AMDiS {
options,
&edgecut,
part,
- &comm);
-// } else {
-// ERROR_EXIT("not yet dim != dow (no xyz)\n");
-// }
+ &tmpComm);
break;
case ADAPTIVE_REPART:
{
int *vsize = GET_MEMORY(int, numElements);
- for(i = 0; i < numElements; i++) {
+ for (int i = 0; i < numElements; i++) {
vsize[i] = 1;
}
ParMETIS_V3_AdaptiveRepart(parMetisMesh_->getElementDist(),
@@ -398,7 +338,7 @@ namespace AMDiS {
options,
&edgecut,
part,
- &comm);
+ &tmpComm);
FREE_MEMORY(vsize, int, numElements);
}
break;
@@ -417,7 +357,7 @@ namespace AMDiS {
options,
&edgecut,
part,
- &comm);
+ &tmpComm);
break;
default:
ERROR_EXIT("unknown partitioning mode\n");
@@ -426,9 +366,12 @@ namespace AMDiS {
// === distribute new partition data ===
distributePartitioning(part);
- if(floatWgts) FREE_MEMORY(floatWgts, float, numElements);
- if(wgts) FREE_MEMORY(wgts, int, numElements);
- if(tpwgts) FREE_MEMORY(tpwgts, float, mpiSize);
+ if (floatWgts)
+ FREE_MEMORY(floatWgts, float, numElements);
+ if (wgts)
+ FREE_MEMORY(wgts, int, numElements);
+ if (tpwgts)
+ FREE_MEMORY(tpwgts, float, mpiSize);
FREE_MEMORY(part, int, numElements);
}
@@ -439,43 +382,38 @@ namespace AMDiS {
partitionVec->clear();
// update ParMETIS mesh to new partitioning
- if(!parMetisMesh_) parMetisMesh_ = NEW ParMetisMesh(mesh_);
+ if (!parMetisMesh_)
+ parMetisMesh_ = NEW ParMetisMesh(mesh_, mpiComm);
- int i, j;
- //int dim = mesh_->getDim();
- int mpiRank = MPI::COMM_WORLD.Get_rank();
- int mpiSize = MPI::COMM_WORLD.Get_size();
+ int mpiRank = mpiComm->Get_rank();
+ int mpiSize = mpiComm->Get_size();
int *numPartitionElements = GET_MEMORY(int, mpiSize);
int *elmdist = parMetisMesh_->getElementDist();
- for(i = 0; i < mpiSize; i++) {
+ for (int i = 0; i < mpiSize; i++) {
numPartitionElements[i] = elmdist[i+1] - elmdist[i];
}
// === count number of elements ===
int numElements = 0;
int localElements = parMetisMesh_->getNumElements();
- MPI::COMM_WORLD.Allreduce(&localElements,
- &numElements,
- 1,
- MPI_INT,
- MPI_SUM);
+ mpiComm->Allreduce(&localElements, &numElements, 1, MPI_INT, MPI_SUM);
int *partitionElements = GET_MEMORY(int, numElements);
// distribute partition elements
- MPI::COMM_WORLD.Allgatherv(parMetisMesh_->getAMDiSIndices(),
- numPartitionElements[mpiRank],
- MPI_INT,
- partitionElements,
- numPartitionElements,
- elmdist,
- MPI_INT);
+ mpiComm->Allgatherv(parMetisMesh_->getAMDiSIndices(),
+ numPartitionElements[mpiRank],
+ MPI_INT,
+ partitionElements,
+ numPartitionElements,
+ elmdist,
+ MPI_INT);
// fill partitionVec
- for(i = 0; i < mpiSize; i++) {
- for(j = 0; j < numPartitionElements[i]; j++) {
+ for (int i = 0; i < mpiSize; i++) {
+ for (int j = 0; j < numPartitionElements[i]; j++) {
(*partitionVec)[partitionElements[elmdist[i] + j]] = i;
}
}
@@ -486,50 +424,45 @@ namespace AMDiS {
void ParMetisPartitioner::distributePartitioning(int *part)
{
- int i;
- int mpiSize = MPI::COMM_WORLD.Get_size();
- int mpiRank = MPI::COMM_WORLD.Get_rank();
-
+ int mpiSize = mpiComm->Get_size();
+ int mpiRank = mpiComm->Get_rank();
int numElements = parMetisMesh_->getNumElements();
// count elements per partition in this rank
int *numPartitionElements = GET_MEMORY(int, mpiSize);
- for(i = 0; i < mpiSize; i++)
+ for (int i = 0; i < mpiSize; i++)
numPartitionElements[i] = 0;
- for(i = 0; i < numElements; i++) {
+ for (int i = 0; i < numElements; i++) {
numPartitionElements[part[i]]++;
}
// collect number of partition elements from all ranks for this rank
int *numRankElements = GET_MEMORY(int, mpiSize);
- MPI::COMM_WORLD.Alltoall(numPartitionElements, 1, MPI_INT,
- numRankElements, 1, MPI_INT);
+ mpiComm->Alltoall(numPartitionElements, 1, MPI_INT,
+ numRankElements, 1, MPI_INT);
// sum up partition elements over all ranks
int *sumPartitionElements = GET_MEMORY(int, mpiSize);
- MPI::COMM_WORLD.Allreduce(numPartitionElements,
- sumPartitionElements,
- mpiSize,
- MPI_INT,
- MPI_SUM);
+ mpiComm->Allreduce(numPartitionElements, sumPartitionElements, mpiSize,
+ MPI_INT, MPI_SUM);
// prepare distribution (fill partitionElements with AMDiS indices)
int *bufferOffset = GET_MEMORY(int, mpiSize);
bufferOffset[0] = 0;
- for(i = 1; i < mpiSize; i++) {
+ for (int i = 1; i < mpiSize; i++) {
bufferOffset[i] = bufferOffset[i - 1] + numPartitionElements[i - 1];
}
int *partitionElements = GET_MEMORY(int, numElements);
int **partitionPtr = GET_MEMORY(int*, mpiSize);
- for(i = 0; i < mpiSize; i++) {
+ for (int i = 0; i < mpiSize; i++) {
partitionPtr[i] = partitionElements + bufferOffset[i];
}
- for(i = 0; i < numElements; i++) {
+ for (int i = 0; i < numElements; i++) {
int partition = part[i];
int amdisIndex = parMetisMesh_->getAMDiSIndex(i);
*(partitionPtr[partition]) = amdisIndex;
@@ -540,45 +473,44 @@ namespace AMDiS {
int *rankElements = GET_MEMORY(int, sumPartitionElements[mpiRank]);
int *recvBufferOffset = GET_MEMORY(int, mpiSize);
recvBufferOffset[0] = 0;
- for(i = 1; i < mpiSize; i++) {
+ for (int i = 1; i < mpiSize; i++) {
recvBufferOffset[i] = recvBufferOffset[i - 1] + numRankElements[i - 1];
}
- MPI::COMM_WORLD.Alltoallv(partitionElements,
- numPartitionElements,
- bufferOffset,
- MPI_INT,
- rankElements,
- numRankElements,
- recvBufferOffset,
- MPI_INT);
+ mpiComm->Alltoallv(partitionElements,
+ numPartitionElements,
+ bufferOffset,
+ MPI_INT,
+ rankElements,
+ numRankElements,
+ recvBufferOffset,
+ MPI_INT);
// === partition AMDiS mesh ===
// write data in stl map
std::map<int, bool> elementInPartition;
- for(i = 0; i < mpiSize; i++) {
- int *rankPtr;
+ for (int i = 0; i < mpiSize; i++) {
int *rankStart = rankElements + recvBufferOffset[i];
int *rankEnd = rankStart + numRankElements[i];
- for(rankPtr = rankStart; rankPtr < rankEnd; ++rankPtr) {
+ for (int *rankPtr = rankStart; rankPtr < rankEnd; ++rankPtr) {
elementInPartition[*rankPtr] = true;
}
}
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
// get partition data
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- if(partitionData && partitionData->getLevel() == 0) {
+ if (partitionData && partitionData->getLevel() == 0) {
int amdisIndex = element->getIndex();
- if(elementInPartition[amdisIndex]) {
+ if (elementInPartition[amdisIndex]) {
partitionData->setPartitionStatus(IN);
} else {
partitionData->setPartitionStatus(OUT);
@@ -591,10 +523,6 @@ namespace AMDiS {
DELETE parMetisMesh_;
parMetisMesh_ = NULL;
- //parMetisMesh_ = NEW ParMetisMesh(mesh_);
-
-// MSG("rank %d partition elements: %d\n",
-// mpiRank, sumPartitionElements[mpiRank]);
FREE_MEMORY(rankElements, int, sumPartitionElements[mpiRank]);
FREE_MEMORY(numPartitionElements, int, mpiSize);
@@ -608,7 +536,7 @@ namespace AMDiS {
void ParMetisPartitioner::descendPartitionData(Element *element)
{
- if(!element->isLeaf()) {
+ if (!element->isLeaf()) {
Element *child0 = element->getChild(0);
Element *child1 = element->getChild(1);
@@ -637,12 +565,12 @@ namespace AMDiS {
int partition = -1;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- if(partitionData) {
- if(partitionData->getLevel() == 0) {
+ if (partitionData) {
+ if (partitionData->getLevel() == 0) {
partition = (*(coarseVec))[element->getIndex()];
}
if(element->isLeaf()) {
diff --git a/AMDiS/src/ParMetisPartitioner.h b/AMDiS/src/ParMetisPartitioner.h
index 194f0b6549ca08f21ba18356bc169e37d332dc35..b5633721e1b89816e3ddc2c44eb3ce8bd34f261a 100644
--- a/AMDiS/src/ParMetisPartitioner.h
+++ b/AMDiS/src/ParMetisPartitioner.h
@@ -46,7 +46,7 @@ namespace AMDiS {
public:
MEMORY_MANAGED(ParMetisMesh);
- ParMetisMesh(Mesh *mesh);
+ ParMetisMesh(Mesh *mesh, MPI::Comm *comm);
~ParMetisMesh();
@@ -98,23 +98,35 @@ namespace AMDiS {
protected:
int *eptr_;
+
int *eind_;
+
int *elmdist_;
+
int dim_;
+
float *xyz_;
int numElements_;
std::map<int, int> elem_a2p_;
+
int *elem_p2a_;
+
+ /** \brief
+ * The MPI communicator that should be used for mesh partition.
+ */
+ MPI::Comm *mpiComm;
};
+
class ParMetisGraph
{
public:
MEMORY_MANAGED(ParMetisGraph);
ParMetisGraph(ParMetisMesh *parMetisMesh,
+ MPI::Comm *comm,
int ncommonnodes = -1);
~ParMetisGraph();
@@ -134,11 +146,13 @@ namespace AMDiS {
int *adjncy_;
};
+
class ParMetisPartitioner
{
public:
- ParMetisPartitioner(Mesh *mesh)
+ ParMetisPartitioner(Mesh *mesh, MPI::Comm *comm)
: mesh_(mesh),
+ mpiComm(comm),
parMetisMesh_(NULL)
{};
@@ -162,6 +176,9 @@ namespace AMDiS {
protected:
Mesh *mesh_;
+
+ MPI::Comm *mpiComm;
+
ParMetisMesh *parMetisMesh_;
};
}
diff --git a/AMDiS/src/ParallelProblem.cc b/AMDiS/src/ParallelProblem.cc
index 39811f5aebc5f58b24cb3183c2b7dc97f1cc1518..9665ab5432be19474eda226ad0c94ca0d924f9b0 100644
--- a/AMDiS/src/ParallelProblem.cc
+++ b/AMDiS/src/ParallelProblem.cc
@@ -9,6 +9,7 @@
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
+#include "MacroElement.h"
#include "PartitionElementData.h"
#include "ParMetisPartitioner.h"
#include "Mesh.h"
@@ -23,8 +24,10 @@
#include "MacroWriter.h"
#include "ValueWriter.h"
#include "SystemVector.h"
+#include "VtkWriter.h"
#include "mpi.h"
#include <queue>
+#include <time.h>
namespace AMDiS {
@@ -39,17 +42,6 @@ namespace AMDiS {
}
}
- bool elementInPartitionDbg(ElInfo *elInfo)
- {
- // In debug mode, the first partition has to write the whole domain.
- if (MPI::COMM_WORLD.Get_rank() == 0) {
- return true;
- }
-
- return elementInPartition(elInfo);
- }
-
-
class MyDualTraverse : public DualTraverse
{
public:
@@ -61,8 +53,8 @@ namespace AMDiS {
{
PartitionElementData *elementData = dynamic_cast<PartitionElementData*>
(elInfo->getElement()->getElementData(PARTITION_ED));
- if(elementData) {
- if(elInfo->getElement()->isLeaf() &&
+ if (elementData) {
+ if (elInfo->getElement()->isLeaf() &&
elementData->getLevel() < coarseLevel_)
return false;
if(elementData->getLevel() == coarseLevel_)
@@ -78,15 +70,98 @@ namespace AMDiS {
// ===== class ParallelProblemBase =========================================
// =========================================================================
- ParallelProblemBase::ParallelProblemBase(ProblemIterationInterface *iterationIF,
+ ParallelProblemBase::ParallelProblemBase(const std::string& name,
+ ProblemIterationInterface *iterationIF,
ProblemTimeInterface *timeIF)
: iterationIF_(iterationIF),
- timeIF_(timeIF)
+ timeIF_(timeIF),
+ debugMode(0)
{
mpiRank = MPI::COMM_WORLD.Get_rank();
mpiSize = MPI::COMM_WORLD.Get_size();
+
+ GET_PARAMETER(0, name + "->debug mode", "%d", &debugMode);
+
+ if (debugMode) {
+ MPI::Group group = MPI::COMM_WORLD.Get_group();
+
+ int rankSize = mpiSize - 1;
+ int *ranks = GET_MEMORY(int, rankSize);
+ for (int i = 0; i < rankSize; i++) {
+ ranks[i] = i + 1;
+ }
+
+ amdisGroup = group.Incl(rankSize, ranks);
+
+ mpiComm = MPI::COMM_WORLD.Create(amdisGroup);
+
+ if (mpiComm != MPI::COMM_NULL) {
+ mpiRank = mpiComm.Get_rank();
+ mpiSize = mpiComm.Get_size();
+ debugServerProcess = false;
+ } else {
+ debugServerProcess = true;
+ }
+
+ FREE_MEMORY(ranks, int, rankSize);
+ } else {
+ mpiComm = MPI::COMM_WORLD;
+ }
}
+ void ParallelProblemBase::exitParallelization(AdaptInfo *adaptInfo)
+ {
+ if (!timeIF_)
+ closeTimestep(adaptInfo);
+
+ amdisGroup.Free();
+ };
+
+ Flag ParallelProblemBase::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
+ {
+ Flag flag;
+
+ if (mpiSize > 1 && toDo.isSet(MARK | ADAPT)) {
+ flag = iterationIF_->oneIteration(adaptInfo, MARK | ADAPT);
+
+ double localWeightSum = setElemWeights(adaptInfo);
+ if (doPartitioning(adaptInfo, localWeightSum)) {
+ clock_t partitioningStart = clock();
+
+ synchronizeMeshes(adaptInfo);
+ partitionMesh(adaptInfo);
+ refineOverlap(adaptInfo);
+ createOverlap(adaptInfo);
+ synchronizeMeshes(adaptInfo);
+ exchangeDOFVectors(adaptInfo);
+ coarsenOutOfPartition(adaptInfo);
+
+ clock_t partitioningEnd = clock();
+ partitioningTime = TIME_USED(partitioningStart,
+ partitioningEnd);
+ computationStart = partitioningEnd;
+ }
+
+ flag |= iterationIF_->oneIteration(adaptInfo, toDo & ~(MARK | ADAPT));
+ } else {
+ flag = iterationIF_->oneIteration(adaptInfo, toDo);
+ }
+
+ // synchronize adaption flag
+ unsigned long *flagBuffer = GET_MEMORY(unsigned long, mpiSize);
+
+ unsigned long localFlag = flag.getFlags();
+
+ mpiComm.Allgather(&localFlag, 1, MPI_UNSIGNED_LONG,
+ flagBuffer, 1, MPI_UNSIGNED_LONG);
+ for (int i = 0; i < mpiSize; i++) {
+ flag.setFlag(flagBuffer[i]);
+ }
+ FREE_MEMORY(flagBuffer, unsigned long, mpiSize);
+
+ return flag;
+ };
+
// =========================================================================
// ===== class ParallelProblem =============================================
// =========================================================================
@@ -98,7 +173,7 @@ namespace AMDiS {
Mesh *mesh,
RefinementManager *rm,
CoarseningManager *cm)
- : ParallelProblemBase(iterationIF, timeIF),
+ : ParallelProblemBase(name, iterationIF, timeIF),
name_(name),
mesh(mesh),
refinementManager(rm),
@@ -114,8 +189,7 @@ namespace AMDiS {
adaptiveThresholds_(0),
thresholdIncFactor_(2.0),
thresholdDecFactor_(0.5),
- repartTimeFactor_(10.0),
- debugMode(0)
+ repartTimeFactor_(10.0)
{
GET_PARAMETER(0, name_ + "->upper part threshold", "%f",
&upperPartThreshold_);
@@ -132,7 +206,7 @@ namespace AMDiS {
TEST_EXIT(localCoarseGridLevel_ >= globalCoarseGridLevel_)
("local coarse grid level < global coarse grid level\n");
- partitioner_ = NEW ParMetisPartitioner(mesh);
+ partitioner_ = NEW ParMetisPartitioner(mesh, &mpiComm);
GET_PARAMETER(0, name_ + "->adaptive thresholds", "%d",
&adaptiveThresholds_);
@@ -153,21 +227,11 @@ namespace AMDiS {
}
minUpperTH_ = upperPartThreshold_;
maxLowerTH_ = lowerPartThreshold_;
-
- GET_PARAMETER(0, name_ + "->debug mode", "%d", &debugMode);
-
- if (debugMode) {
- dbgMesh = NEW Mesh(mesh->getName(), mesh->getDim());
- }
}
ParallelProblem::~ParallelProblem()
{
DELETE partitioner_;
-
- if (debugMode) {
- DELETE dbgMesh;
- }
}
bool ParallelProblem::doPartitioning(AdaptInfo *adaptInfo, double localWeightSum)
@@ -178,8 +242,8 @@ namespace AMDiS {
int *partArray = GET_MEMORY(int, mpiSize);
int part = 0;
- MPI::COMM_WORLD.Gather(&localWeightSum, 1, MPI_DOUBLE,
- weightSum, 1, MPI_DOUBLE, 0);
+ mpiComm.Gather(&localWeightSum, 1, MPI_DOUBLE,
+ weightSum, 1, MPI_DOUBLE, 0);
if (mpiRank == 0) {
@@ -230,8 +294,8 @@ namespace AMDiS {
}
}
- MPI::COMM_WORLD.Scatter(partArray, 1, MPI_INT,
- &part, 1, MPI_INT, 0);
+ mpiComm.Scatter(partArray, 1, MPI_INT,
+ &part, 1, MPI_INT, 0);
FREE_MEMORY(weightSum, double, mpiSize);
FREE_MEMORY(partArray, int, mpiSize);
@@ -246,49 +310,53 @@ namespace AMDiS {
void ParallelProblem::partitionMesh(AdaptInfo *adaptInfo)
{
static bool initial = true;
- if(initial) {
+ if (initial) {
initial = false;
- partitioner_->fillCoarsePartitionVec(&oldPartitionVec_);
+ partitioner_->fillCoarsePartitionVec(&oldPartitionVec);
partitioner_->partition(&elemWeights_, INITIAL);
} else {
- oldPartitionVec_ = partitionVec_;
+ oldPartitionVec = partitionVec;
partitioner_->partition(&elemWeights_, ADAPTIVE_REPART, 100.0 /*0.000001*/);
}
- partitioner_->fillCoarsePartitionVec(&partitionVec_);
+ partitioner_->fillCoarsePartitionVec(&partitionVec);
}
void ParallelProblem::refineOverlap(AdaptInfo *adaptInfo)
{
- int i, dim = mesh->getDim();
+ int dim = mesh->getDim();
bool finished = (localCoarseGridLevel_ == 0);
//for(j = globalCoarseGridLevel_; j < localCoarseGridLevel_; j++) {
- while(!finished) {
+ while (!finished) {
std::map<DegreeOfFreedom, int> inOut; // 1: in, 2: out, 3: border dof
// mark in/out/border dofs
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(elInfo->getElement()->getElementData(PARTITION_ED));
const DegreeOfFreedom **dofs = element->getDOF();
- if(partitionData->getPartitionStatus() == IN) {
- for(i = 0; i < dim + 1; i++) {
+ if (partitionData->getPartitionStatus() == IN) {
+ for (int i = 0; i < dim + 1; i++) {
DegreeOfFreedom dof = dofs[i][0];
- if(inOut[dof] == 2) inOut[dof] = 3;
- if(inOut[dof] == 0) inOut[dof] = 1;
+ if (inOut[dof] == 2)
+ inOut[dof] = 3;
+ if (inOut[dof] == 0)
+ inOut[dof] = 1;
}
} else {
- for(i = 0; i < dim + 1; i++) {
+ for (int i = 0; i < dim + 1; i++) {
DegreeOfFreedom dof = dofs[i][0];
- if(inOut[dof] == 1) inOut[dof] = 3;
- if(inOut[dof] == 0) inOut[dof] = 2;
+ if (inOut[dof] == 1)
+ inOut[dof] = 3;
+ if (inOut[dof] == 0)
+ inOut[dof] = 2;
}
}
@@ -299,35 +367,38 @@ namespace AMDiS {
finished = true;
bool marked = false;
elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(elInfo->getElement()->getElementData(PARTITION_ED));
int level = partitionData->getLevel();
- if(level < localCoarseGridLevel_) {
- if(partitionData->getPartitionStatus() != IN) {
+ if (level < localCoarseGridLevel_) {
+ if (partitionData->getPartitionStatus() != IN) {
const DegreeOfFreedom **dofs = element->getDOF();
- for(i = 0; i < dim + 1; i++) {
+ for (int i = 0; i < dim + 1; i++) {
DegreeOfFreedom dof = dofs[i][0];
- if(inOut[dof] == 3) {
+ if (inOut[dof] == 3) {
element->setMark(1);
marked = true;
- if((level + 1) < localCoarseGridLevel_) finished = false;
+ if ((level + 1) < localCoarseGridLevel_)
+ finished = false;
break;
}
}
} else {
element->setMark(1);
marked = true;
- if((level + 1) < localCoarseGridLevel_) finished = false;
+ if ((level + 1) < localCoarseGridLevel_)
+ finished = false;
}
}
elInfo = stack.traverseNext(elInfo);
}
- if(marked) refinementManager->refineMesh(mesh);
+ if (marked)
+ refinementManager->refineMesh(mesh);
}
}
@@ -335,7 +406,7 @@ namespace AMDiS {
{
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while(elInfo) {
+ while (elInfo) {
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(elInfo->getElement()->getElementData(PARTITION_ED));
int refinements = globalCoarseGridLevel_ - partitionData->getLevel();
@@ -366,7 +437,7 @@ namespace AMDiS {
}
meshCoarsened = coarseningManager->coarsenMesh(mesh);
}
- MPI::COMM_WORLD.Barrier();
+ mpiComm.Barrier();
}
void ParallelProblem::exchangeMeshStructureCodes(MeshStructure *structures)
@@ -378,15 +449,20 @@ namespace AMDiS {
// broadcast code sizes
int *codeSize = GET_MEMORY(int, mpiSize);
int tmp = static_cast<int>(myCode.size());
+ mpiComm.Allgather(&tmp, 1, MPI_INT, codeSize, 1, MPI_INT);
+ if (debugMode) {
+ // send code sizes also to debug server
+ MPI::COMM_WORLD.Gather(&tmp, 1, MPI_INT, NULL, 1, MPI_INT, 0);
+ }
- MPI::COMM_WORLD.Allgather(&tmp, 1, MPI_INT,
- codeSize, 1, MPI_INT);
-
// broadcast number of elements
int *elements = GET_MEMORY(int, mpiSize);
tmp = structures[mpiRank].getNumElements();
- MPI::COMM_WORLD.Allgather(&tmp, 1, MPI_INT,
- elements, 1, MPI_INT);
+ mpiComm.Allgather(&tmp, 1, MPI_INT, elements, 1, MPI_INT);
+ if (debugMode) {
+ // send number of elements also to debug server
+ MPI::COMM_WORLD.Gather(&tmp, 1, MPI_INT, NULL, 1, MPI_INT, 0);
+ }
// broadcast codes
int *codeOffset = GET_MEMORY(int, mpiSize);
@@ -397,22 +473,25 @@ namespace AMDiS {
}
unsigned long int *code = GET_MEMORY(unsigned long int, codeSizeSum);
- unsigned long int *localCode = GET_MEMORY(unsigned long int, codeSize[mpiRank]);
-
+ unsigned long int *localCode = GET_MEMORY(unsigned long int, codeSize[mpiRank]);
unsigned long int *ptr;
std::vector<unsigned long int>::const_iterator it, end = myCode.end();
for (ptr = localCode, it = myCode.begin();
it != end;
- ++it, ++ptr)
- {
+ ++it, ++ptr) {
*ptr = *it;
}
-
- MPI::COMM_WORLD.Allgatherv(localCode, codeSize[mpiRank],
- MPI_UNSIGNED_LONG,
- code, codeSize, codeOffset,
- MPI_UNSIGNED_LONG);
+
+ mpiComm.Allgatherv(localCode, codeSize[mpiRank],
+ MPI_UNSIGNED_LONG,
+ code, codeSize, codeOffset,
+ MPI_UNSIGNED_LONG);
+ if (debugMode) {
+ // send codes also to debug server
+ MPI::COMM_WORLD.Send(localCode, codeSize[mpiRank],
+ MPI_UNSIGNED_LONG, 0, 100);
+ }
for (int rank = 0; rank < mpiSize; rank++) {
if (rank != mpiRank) {
@@ -457,16 +536,6 @@ namespace AMDiS {
refinementManager,
true);
- // In debug mode, process 0 builds the global solution mesh.
- if (debugMode) {
- dbgMesh = mesh;
- if (mpiRank == 0) {
- structures[mpiRank].fitMeshToStructure(dbgMesh,
- refinementManager,
- true, true);
- }
- }
-
DELETE [] structures;
}
@@ -490,20 +559,16 @@ namespace AMDiS {
{
FUNCNAME("ParallelProblem::exchangeRankSolutions()");
- int level = localCoarseGridLevel_, overlap = 1;
- bool openOverlap = true;
- ParallelProblem::fillVertexPartitions(level, overlap, openOverlap,
- overlapDistance_);
+ ParallelProblem::fillVertexPartitions(localCoarseGridLevel_, 1, true, overlapDistance_);
overlapDistance_.clear();
-
const FiniteElemSpace *feSpace = rankSolutions[0]->getFESpace();
int dim = workMesh->getDim();
const BasisFunction *basFcts = feSpace->getBasisFcts();
int numFcts = basFcts->getNumber();
DegreeOfFreedom *coarseDOFs = GET_MEMORY(DegreeOfFreedom, numFcts);
DegreeOfFreedom *fineDOFs = GET_MEMORY(DegreeOfFreedom, numFcts);
- DOFAdmin *admin = feSpace->getAdmin();
+ DOFAdmin *admin = feSpace->getAdmin();
std::vector<std::vector<DegreeOfFreedom> > sendOrder(mpiSize);
std::vector<std::vector<DegreeOfFreedom> > recvOrder(mpiSize);
@@ -522,7 +587,7 @@ namespace AMDiS {
if (partitionData) {
if (partitionData->getLevel() == 0) {
- elementPartition = partitionVec_[element->getIndex()];
+ elementPartition = partitionVec[element->getIndex()];
}
PartitionStatus status = partitionData->getPartitionStatus();
@@ -533,8 +598,8 @@ namespace AMDiS {
// collect other partitions element belongs to
for (int i = 0; i < dim + 1; i++) {
- std::set<int>::iterator setBegin = vertexPartitions_[coarseDOFs[i]].begin();
- std::set<int>::iterator setEnd = vertexPartitions_[coarseDOFs[i]].end();
+ std::set<int>::iterator setBegin = vertexPartitions[coarseDOFs[i]].begin();
+ std::set<int>::iterator setEnd = vertexPartitions[coarseDOFs[i]].end();
for (std::set<int>::iterator setIt = setBegin; setIt != setEnd; ++setIt) {
elementPartitions_[element].insert(*setIt);
}
@@ -586,34 +651,34 @@ namespace AMDiS {
sendBufferSize[partition] = sendSize;
recvBufferSize[partition] = recvSize;
- if(sendSize > 0) {
+ if (sendSize > 0) {
sendBuffer[partition] = GET_MEMORY(double, sendSize);
std::vector<DegreeOfFreedom>::iterator dofIt;
dofIt = sendOrder[partition].begin();
double *bufferIt, *bufferBegin, *bufferEnd;
bufferBegin = sendBuffer[partition];
bufferEnd = bufferBegin + sendSize;
- for(bufferIt = bufferBegin;
- bufferIt < bufferEnd;
- ++bufferIt, ++dofIt)
- {
+ for (bufferIt = bufferBegin;
+ bufferIt < bufferEnd;
+ ++bufferIt, ++dofIt) {
*bufferIt = (*solution)[*dofIt];
}
}
- if(recvSize > 0)
+ if (recvSize > 0) {
recvBuffer[partition] = GET_MEMORY(double, recvSize);
+ }
}
}
// non-blocking sends
for (int partition = 0; partition < mpiSize; partition++) {
if (partition != mpiRank) {
- if(sendBufferSize[partition] > 0) {
- MPI::COMM_WORLD.Isend(sendBuffer[partition],
- sendBufferSize[partition],
- MPI_DOUBLE,
- partition,
- 0);
+ if (sendBufferSize[partition] > 0) {
+ mpiComm.Isend(sendBuffer[partition],
+ sendBufferSize[partition],
+ MPI_DOUBLE,
+ partition,
+ 0);
}
}
}
@@ -622,17 +687,17 @@ namespace AMDiS {
for (int partition = 0; partition < mpiSize; partition++) {
if (partition != mpiRank) {
if (recvBufferSize[partition] > 0) {
- MPI::COMM_WORLD.Recv(recvBuffer[partition],
- recvBufferSize[partition],
- MPI_DOUBLE,
- partition,
- 0);
+ mpiComm.Recv(recvBuffer[partition],
+ recvBufferSize[partition],
+ MPI_DOUBLE,
+ partition,
+ 0);
}
}
}
// wait for end of communication
- MPI::COMM_WORLD.Barrier();
+ mpiComm.Barrier();
// copy values into rank solutions
for (int partition = 0; partition < mpiSize; partition++) {
@@ -648,14 +713,12 @@ namespace AMDiS {
// free send and recv buffers
for (int partition = 0; partition < mpiSize; partition++) {
if (partition != mpiRank) {
- if (sendBufferSize[partition] > 0)
- FREE_MEMORY(sendBuffer[partition],
- double,
- sendBufferSize[partition]);
- if(recvBufferSize[partition] > 0)
- FREE_MEMORY(recvBuffer[partition],
- double,
- recvBufferSize[partition]);
+ if (sendBufferSize[partition] > 0) {
+ FREE_MEMORY(sendBuffer[partition], double, sendBufferSize[partition]);
+ }
+ if (recvBufferSize[partition] > 0) {
+ FREE_MEMORY(recvBuffer[partition], double, recvBufferSize[partition]);
+ }
}
}
@@ -666,8 +729,8 @@ namespace AMDiS {
void ParallelProblem::exchangeDOFVector(AdaptInfo *adaptInfo,
DOFVector<double> *values)
{
- partitioner_->fillLeafPartitionVec(&oldPartitionVec_, &oldPartitionVec_);
- partitioner_->fillLeafPartitionVec(&partitionVec_, &partitionVec_);
+ partitioner_->fillLeafPartitionVec(&oldPartitionVec, &oldPartitionVec);
+ partitioner_->fillLeafPartitionVec(&partitionVec, &partitionVec);
// === get send and recieve orders ===
std::vector<std::vector<DegreeOfFreedom> > sendOrder;
@@ -690,8 +753,8 @@ namespace AMDiS {
while(elInfo) {
Element *element = elInfo->getElement();
int index = element->getIndex();
- int oldPartition = oldPartitionVec_[index];
- int newPartition = partitionVec_[index];
+ int oldPartition = oldPartitionVec[index];
+ int newPartition = partitionVec[index];
if(oldPartition != newPartition) {
// get dof indices
@@ -723,77 +786,65 @@ namespace AMDiS {
std::map<int, int> recvBufferSize;
int partition;
- for(partition = 0; partition < mpiSize; partition++) {
- if(partition != mpiRank) {
+ for (partition = 0; partition < mpiSize; partition++) {
+ if (partition != mpiRank) {
int sendSize = static_cast<int>(sendOrder[partition].size());
int recvSize = static_cast<int>(recvOrder[partition].size());
sendBufferSize[partition] = sendSize;
recvBufferSize[partition] = recvSize;
- if(sendSize > 0) {
+ if (sendSize > 0) {
sendBuffer[partition] = GET_MEMORY(double, sendSize);
std::vector<DegreeOfFreedom>::iterator dofIt;
dofIt = sendOrder[partition].begin();
double *bufferIt, *bufferBegin, *bufferEnd;
bufferBegin = sendBuffer[partition];
bufferEnd = bufferBegin + sendSize;
- for(bufferIt = bufferBegin;
- bufferIt < bufferEnd;
- ++bufferIt, ++dofIt)
- {
+ for (bufferIt = bufferBegin;
+ bufferIt < bufferEnd;
+ ++bufferIt, ++dofIt) {
*bufferIt = (*values)[*dofIt];
}
}
- if(recvSize > 0)
+ if (recvSize > 0)
recvBuffer[partition] = GET_MEMORY(double, recvSize);
}
}
-// MSG("rank %d: send %d %d %d %d recv %d %d %d %d\n",
-// mpiRank,
-// sendBufferSize[0],
-// sendBufferSize[1],
-// sendBufferSize[2],
-// sendBufferSize[3],
-// recvBufferSize[0],
-// recvBufferSize[1],
-// recvBufferSize[2],
-// recvBufferSize[3]);
-
// === non-blocking sends ===
- for(partition = 0; partition < mpiSize; partition++) {
- if(partition != mpiRank) {
- if(sendBufferSize[partition] > 0) {
- MPI::COMM_WORLD.Isend(sendBuffer[partition],
- sendBufferSize[partition],
- MPI_DOUBLE,
- partition,
- 0);
+ for (partition = 0; partition < mpiSize; partition++) {
+ if (partition != mpiRank) {
+ if (sendBufferSize[partition] > 0) {
+ mpiComm.Isend(sendBuffer[partition],
+ sendBufferSize[partition],
+ MPI_DOUBLE,
+ partition,
+ 0);
}
}
}
// === blocking receives ===
- for(partition = 0; partition < mpiSize; partition++) {
- if(partition != mpiRank) {
- if(recvBufferSize[partition] > 0) {
- MPI::COMM_WORLD.Recv(recvBuffer[partition],
- recvBufferSize[partition],
- MPI_DOUBLE,
- partition,
- 0);
+ for (partition = 0; partition < mpiSize; partition++) {
+ if (partition != mpiRank) {
+ if (recvBufferSize[partition] > 0) {
+ mpiComm.Recv(recvBuffer[partition],
+ recvBufferSize[partition],
+ MPI_DOUBLE,
+ partition,
+ 0);
}
}
}
// === wait for end of MPI communication ===
- MPI::COMM_WORLD.Barrier();
+ mpiComm.Barrier();
// === copy received values into DOFVector ===
- for(partition = 0; partition < mpiSize; partition++) {
- if(partition != mpiRank) {
+ for (partition = 0; partition < mpiSize; partition++) {
+ if (partition != mpiRank) {
std::vector<DegreeOfFreedom>::iterator dofIt = recvOrder[partition].begin();
- for(i = 0; i < recvBufferSize[partition]; i++) {
+ for (i = 0; i < recvBufferSize[partition]; i++) {
(*values)[*dofIt] = recvBuffer[partition][i];
++dofIt;
}
@@ -801,13 +852,13 @@ namespace AMDiS {
}
// === free send and receive buffers ===
- for(partition = 0; partition < mpiSize; partition++) {
- if(partition != mpiRank) {
- if(sendBufferSize[partition] > 0)
+ for (partition = 0; partition < mpiSize; partition++) {
+ if (partition != mpiRank) {
+ if (sendBufferSize[partition] > 0)
FREE_MEMORY(sendBuffer[partition],
double,
sendBufferSize[partition]);
- if(recvBufferSize[partition] > 0)
+ if (recvBufferSize[partition] > 0)
FREE_MEMORY(recvBuffer[partition],
double,
recvBufferSize[partition]);
@@ -891,8 +942,8 @@ namespace AMDiS {
// for all coarse vertex DOFs
for (int j = 0; j < dim + 1; j++) {
- partBegin = vertexPartitions_[coarseDOFs[j]].begin();
- partEnd = vertexPartitions_[coarseDOFs[j]].end();
+ partBegin = vertexPartitions[coarseDOFs[j]].begin();
+ partEnd = vertexPartitions[coarseDOFs[j]].end();
for (partIt = partBegin; partIt != partEnd; ++partIt) {
int partition = *partIt/* - 1*/;
double val = (*(linearFunctions->getPhi(j)))(baryCoord);
@@ -943,7 +994,8 @@ namespace AMDiS {
int elNum = -1;
double totalErr, error;
- if(!add) errVec.clear();
+ if (!add)
+ errVec.clear();
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh,
@@ -1036,7 +1088,7 @@ namespace AMDiS {
void ParallelProblem::createOverlap(int level, int overlap, bool openOverlap,
std::map<Element*, int> &overlapDistance)
{
- int i, dim = mesh->getDim();
+ int dim = mesh->getDim();
// === create dual graph (one common node) and prepare breadth-first search ===
std::map<DegreeOfFreedom, std::vector<Element*> > vertexElements;
@@ -1044,14 +1096,14 @@ namespace AMDiS {
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
Element *element = elInfo->getElement();
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(element->getElementData(PARTITION_ED));
- if(partitionData) {
- if(partitionData->getLevel() == level) {
- for(i = 0; i < dim + 1; i++) {
+ if (partitionData) {
+ if (partitionData->getLevel() == level) {
+ for (int i = 0; i < dim + 1; i++) {
vertexElements[element->getDOF(i, 0)].push_back(element);
}
@@ -1069,7 +1121,7 @@ namespace AMDiS {
// === breadth-first search on dual graph ===
std::vector<Element*>::iterator it, itBegin, itEnd;
- while(!overlapQueue.empty()) {
+ while (!overlapQueue.empty()) {
// get first element in queue
Element *element = overlapQueue.front();
overlapQueue.pop();
@@ -1078,14 +1130,15 @@ namespace AMDiS {
int distance = overlapDistance[element];
TEST_EXIT(distance >= 0)("invalid distance\n");
- if(distance >= overlap) continue;
+ if (distance >= overlap)
+ continue;
// get all adjacent elements
- for(i = 0; i < dim + 1; i++) {
+ for (int i = 0; i < dim + 1; i++) {
itBegin = vertexElements[element->getDOF(i, 0)].begin();
itEnd = vertexElements[element->getDOF(i, 0)].end();
- for(it = itBegin; it != itEnd; ++it) {
- if(overlapDistance[*it] == -1) {
+ for (it = itBegin; it != itEnd; ++it) {
+ if (overlapDistance[*it] == -1) {
// set distance for new member
overlapDistance[*it] = distance + 1;
// push neighbour to queue
@@ -1108,27 +1161,24 @@ namespace AMDiS {
{
int dim = mesh->getDim();
- TraverseStack stack;
- ElInfo *elInfo;
-
// clear partition dof vector
- vertexPartitions_.clear();
+ vertexPartitions.clear();
// first: partition elements ...
- int index, partition;
- elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
+ int partition;
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
Element *element = elInfo->getElement();
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(element->getElementData(PARTITION_ED));
if (partitionData) {
if (partitionData->getLevel() == 0) {
- index = element->getIndex();
- partition = partitionVec_[index];
+ partition = partitionVec[element->getIndex()];
}
if (partitionData->getLevel() == level) {
for (int i = 0; i < dim + 1; i++) {
- vertexPartitions_[element->getDOF(i, 0)].insert(partition);
+ vertexPartitions[element->getDOF(i, 0)].insert(partition);
}
}
}
@@ -1141,9 +1191,8 @@ namespace AMDiS {
exchangeMeshStructureCodes(structures);
// merge codes
- int rank;
- for(rank = 0; rank < mpiSize; rank++) {
- if(rank != mpiRank) {
+ for (int rank = 0; rank < mpiSize; rank++) {
+ if (rank != mpiRank) {
structures[mpiRank].merge(&structures[rank]);
}
}
@@ -1185,13 +1234,12 @@ namespace AMDiS {
// exchange number of overlap elements
int *numOverlapElements = GET_MEMORY(int, mpiSize);
int tmp = static_cast<int>(innerOverlapElements.size());
- MPI::COMM_WORLD.Allgather(&tmp, 1, MPI_INT,
- numOverlapElements, 1, MPI_INT);
+ mpiComm.Allgather(&tmp, 1, MPI_INT, numOverlapElements, 1, MPI_INT);
// exchange overlap elements
int *offset = GET_MEMORY(int, mpiSize);
int sum = 0;
- for(rank = 0; rank < mpiSize; rank++) {
+ for (int rank = 0; rank < mpiSize; rank++) {
offset[rank] = sum;
sum += numOverlapElements[rank];
}
@@ -1202,31 +1250,24 @@ namespace AMDiS {
int *ptr;
std::vector<int>::iterator elemIt, elemEnd = innerOverlapElements.end();
- for(ptr = sendBuffer, elemIt = innerOverlapElements.begin();
- elemIt != elemEnd;
- ++elemIt, ++ptr)
- {
+ for (ptr = sendBuffer, elemIt = innerOverlapElements.begin();
+ elemIt != elemEnd;
+ ++elemIt, ++ptr) {
*ptr = *elemIt;
}
- MPI::COMM_WORLD.Allgatherv(sendBuffer, numOverlapElements[mpiRank],
- MPI_INT,
- recvBuffer, numOverlapElements, offset,
- MPI_INT);
-
+ mpiComm.Allgatherv(sendBuffer, numOverlapElements[mpiRank], MPI_INT,
+ recvBuffer, numOverlapElements, offset, MPI_INT);
// fill vertexPartitions for 'inner' overlap elements
- int el;
- for (rank = 0; rank < mpiSize; rank++) {
+ for (int rank = 0; rank < mpiSize; rank++) {
int numElements = numOverlapElements[rank];
- // MSG("rank %d overlap elements with %d: %d\n",
- // mpiRank, rank, numOverlapElements[rank]);
int *elements = recvBuffer + offset[rank];
- for (el = 0; el < numElements; el++) {
+ for (int el = 0; el < numElements; el++) {
Element *element = indexElement[elements[el]];
for (int i = 0; i < dim + 1; i++) {
- vertexPartitions_[element->getDOF(i, 0)].insert(rank/* + 1*/);
+ vertexPartitions[element->getDOF(i, 0)].insert(rank/* + 1*/);
}
}
}
@@ -1273,20 +1314,7 @@ namespace AMDiS {
for (int i = 0; i < mpiSize; i++) {
rankSolution[i] = NEW DOFVector<double>(problem->getFESpace(), "rank solution");
}
-
- // Create vectors for debuging information
- if (debugMode) {
- dbgRankSolution.resize(mpiSize);
- for (int i = 0; i < mpiSize; i++) {
- dbgRankSolution[i] = NEW DOFVector<double>(problem->getFESpace(), "debug rank solution");
- }
-
- if (mpiRank == 0) {
- dbgSolution = NEW DOFVector<double>(problem->getFESpace(), "debug solution");
- }
- }
-
-
+
if (problemInstat_) {
dofVectors_.push_back(problemInstat_->getOldSolution());
}
@@ -1297,16 +1325,6 @@ namespace AMDiS {
for (int i = 0; i < mpiSize; i++) {
DELETE rankSolution[i];
}
-
- if (debugMode) {
- for (int i = 0; i < mpiSize; i++) {
- DELETE dbgRankSolution[i];
- }
-
- if (mpiRank == 0) {
- DELETE dbgSolution;
- }
- }
}
@@ -1419,13 +1437,6 @@ namespace AMDiS {
ParallelProblem::exchangeRankSolutions(adaptInfo,
mesh,
rankSolution);
-
- if (debugMode) {
- dbgRankSolution[mpiRank]->copy(*(problem->getSolution()));
- ParallelProblem::exchangeRankSolutions(adaptInfo,
- dbgMesh,
- dbgRankSolution);
- }
}
void ParallelProblemScal::buildGlobalSolution(AdaptInfo *adaptInfo)
@@ -1433,12 +1444,6 @@ namespace AMDiS {
ParallelProblem::buildGlobalSolution(adaptInfo,
rankSolution,
problem->getSolution());
-
- if (debugMode && mpiRank == 0) {
- ParallelProblem::buildGlobalSolution(adaptInfo,
- dbgRankSolution,
- dbgSolution);
- }
}
void ParallelProblemScal::coarsenOutOfPartition(AdaptInfo *adaptInfo)
@@ -1484,24 +1489,6 @@ namespace AMDiS {
}
}
- if (debugMode) {
- dbgRankSolution.resize(mpiSize);
- for (int i = 0; i < mpiSize; i++) {
- dbgRankSolution[i] = NEW SystemVector("debug rank solution", feSpaces, nComponents);
- for (int j = 0; j < nComponents; j++) {
- dbgRankSolution[i]->setDOFVector(j, NEW DOFVector<double>(feSpaces[j],
- "debug rank solution"));
- }
- }
-
- if (mpiRank == 0) {
- dbgSolution = NEW SystemVector("debug solution", feSpaces, nComponents);
- for (int i = 0; i < nComponents; i++) {
- dbgSolution->setDOFVector(i, NEW DOFVector<double>(feSpaces[i], "debug solution"));
- }
- }
- }
-
if (problemInstat_) {
for (int i = 0; i < nComponents; i++) {
dofVectors_.push_back(problemInstat_->getOldSolution()->getDOFVector(i));
@@ -1517,22 +1504,6 @@ namespace AMDiS {
}
DELETE rankSolution[i];
}
-
- if (debugMode) {
- for (int i = 0; i < mpiSize; i++) {
- for (int j = 0; j < nComponents; j++) {
- DELETE dbgRankSolution[i]->getDOFVector(j);
- }
- DELETE dbgRankSolution[i];
- }
-
- if (mpiRank == 0) {
- for (int i = 0; i < nComponents; i++) {
- DELETE dbgSolution->getDOFVector(i);
- }
- DELETE dbgSolution;
- }
- }
}
void ParallelProblemVec::initParallelization(AdaptInfo *adaptInfo)
@@ -1580,7 +1551,7 @@ namespace AMDiS {
// modify file writers
char number[10];
- sprintf(number, "%d", MPI::COMM_WORLD.Get_rank());
+ sprintf(number, "%d", mpiComm.Get_rank());
::std::vector<FileWriterInterface*> fileWriters = problem->getFileWriterList();
::std::vector<FileWriterInterface*>::iterator fwIt, fwBegin, fwEnd;
fwBegin = fileWriters.begin();
@@ -1633,10 +1604,6 @@ namespace AMDiS {
void ParallelProblemVec::exchangeRankSolutions(AdaptInfo *adaptInfo)
{
rankSolution[mpiRank]->copy(*(problem->getSolution()));
- if (debugMode) {
- dbgRankSolution[mpiRank]->copy(*(problem->getSolution()));
- }
-
std::vector<DOFVector<double>*> rankSol(mpiSize);
for (int i = 0; i < nComponents; i++) {
@@ -1646,15 +1613,24 @@ namespace AMDiS {
ParallelProblem::exchangeRankSolutions(adaptInfo,
mesh,
rankSol);
+ }
- if (debugMode) {
- for (int j = 0; j < mpiSize; j++) {
- rankSol[j] = dbgRankSolution[j]->getDOFVector(i);
- }
- ParallelProblem::exchangeRankSolutions(adaptInfo,
- dbgMesh,
- rankSol);
+ // In debug mode, mpiRank 0 sends the map partitionVec, which is
+ // equal on all ranks, to the debug server.
+ if (debugMode && mpiRank == 0) {
+ int sendSize = partitionVec.size() * 2;
+ MPI::COMM_WORLD.Send(&sendSize, 1, MPI_INT, 0, 100);
+
+ int *sendBuffer = GET_MEMORY(int, sendSize);
+ int bufferPos = 0;
+ for (std::map<int, int>::iterator it = partitionVec.begin();
+ it != partitionVec.end();
+ ++it) {
+ sendBuffer[bufferPos++] = it->first;
+ sendBuffer[bufferPos++] = it->second;
}
+ MPI::COMM_WORLD.Send(sendBuffer, sendSize, MPI_INT, 0, 100);
+ FREE_MEMORY(sendBuffer, int, sendSize);
}
}
@@ -1669,15 +1645,55 @@ namespace AMDiS {
ParallelProblem::buildGlobalSolution(adaptInfo,
rankSol,
problem->getSolution()->getDOFVector(i));
+ }
+
+ // In debug mode, every rank sends its solution to the debug server.
+ if (debugMode) {
+ const FiniteElemSpace *feSpace = problem->getFESpace(0);
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ DOFAdmin *admin = feSpace->getAdmin();
+ int numFcts = basFcts->getNumber();
+ DegreeOfFreedom *elDOFs = GET_MEMORY(DegreeOfFreedom, numFcts);
+
+ int elementPartition = -1;
+ std::vector<double> sendDOFs(0);
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
+ while (elInfo) {
+ Element *element = elInfo->getElement();
+
+ PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
+ (element->getElementData(PARTITION_ED));
+
+ if (partitionData && (partitionData->getLevel() == 0)) {
+ elementPartition = partitionVec[element->getIndex()];
+ }
+
+ // On leaf level, each rank assemble its own solution part.
+ if (element->isLeaf() && (elementPartition == mpiRank)) {
+ basFcts->getLocalIndices(element, admin, elDOFs);
- if (debugMode && mpiRank == 0) {
- for (int j = 0; j < mpiSize; j++) {
- rankSol[j] = dbgRankSolution[j]->getDOFVector(i);
+ for (int i = 0; i < numFcts; i++) {
+ sendDOFs.push_back((*problem->getSolution()->getDOFVector(0))[elDOFs[i]]);
+ }
}
- ParallelProblem::buildGlobalSolution(adaptInfo,
- rankSol,
- dbgSolution->getDOFVector(i));
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ // First, send number of values the will be send after that.
+ int sendSize = sendDOFs.size();
+ MPI::COMM_WORLD.Send(&sendSize, 1, MPI_INT, 0, 100);
+
+ // Create send buffer of values and send it to the debug server.
+ double *sendBuffer = GET_MEMORY(double, sendSize);
+ for (int i = 0; i < sendSize; i++) {
+ sendBuffer[i] = sendDOFs[i];
}
+ MPI::COMM_WORLD.Send(sendBuffer, sendSize, MPI_DOUBLE, 0, 100);
+
+ FREE_MEMORY(sendBuffer, double, sendSize);
+ FREE_MEMORY(elDOFs, DegreeOfFreedom, numFcts);
}
}
@@ -1711,4 +1727,126 @@ namespace AMDiS {
}
}
+ void ParallelProblemVec::startDebugServer()
+ {
+ FUNCNAME("ParallelProblemVec::startDebugServer()");
+
+ TEST_EXIT(debugMode)("Debug server applicable only in debug mode!\n");
+
+ const FiniteElemSpace *feSpace = problem->getFESpace(0);
+ DOFAdmin *admin = feSpace->getAdmin();
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ int numFcts = basFcts->getNumber();
+ int mpiWorldSize = MPI::COMM_WORLD.Get_size();
+ int *codeSize = GET_MEMORY(int, mpiWorldSize);
+ int *nElements = GET_MEMORY(int, mpiWorldSize);
+ DegreeOfFreedom *elDOFs = GET_MEMORY(DegreeOfFreedom, numFcts);
+ unsigned long int *code;
+ int mpiTag = 100;
+
+ while (true) {
+ MeshStructure *structures = NEW MeshStructure[mpiWorldSize];
+
+ /* ===== Communication with exchangeMeshStructureCode() ====== */
+
+ // Get mesh structure code size of all meshes
+ MPI::COMM_WORLD.Gather(&codeSize, 1, MPI_INT, codeSize, 1, MPI_INT, 0);
+
+ // Get number of elements of all meshes
+ MPI::COMM_WORLD.Gather(&nElements, 1, MPI_INT, nElements, 1, MPI_INT, 0);
+
+ // Get all mesh structure codes
+ for (int i = 1; i < mpiWorldSize; i++) {
+ code = GET_MEMORY(unsigned long int, codeSize[i]);
+
+ MPI::COMM_WORLD.Recv(code, codeSize[i], MPI_UNSIGNED_LONG,
+ i, mpiTag);
+
+ std::vector<unsigned long int> codeVec(codeSize[i]);
+ for (int j = 0; j < codeSize[i]; j++) {
+ codeVec[j] = code[j];
+ }
+ structures[i].init(codeVec, nElements[i]);
+
+ FREE_MEMORY(code, unsigned long int, codeSize[i]);
+ }
+
+
+ /* ======== Simulate synchronizeMeshes() ======= */
+
+ // Build finest mesh starting from rank 1 solution
+ for (int rank = 2; rank < mpiWorldSize; rank++) {
+ structures[1].merge(&structures[rank]);
+ }
+
+ structures[1].fitMeshToStructure(mesh, refinementManager, false);
+
+ DELETE [] structures;
+
+
+ /* ======= Communication with exchangeRankSolution() ======= */
+
+ // receive the vector partitionVec from COMM_WORLD.rank = 1 to know
+ // the mesh partitioning on localCoarseGridLevel
+ int recvSize = 0;
+ MPI::COMM_WORLD.Recv(&recvSize, 1, MPI_INT, 1, mpiTag);
+
+ int *recvBuffer = GET_MEMORY(int, recvSize);
+ MPI::COMM_WORLD.Recv(recvBuffer, recvSize, MPI_INT, 1, mpiTag);
+ partitionVec.clear();
+ for (int i = 0; i < recvSize; i += 2) {
+ partitionVec[recvBuffer[i]] = recvBuffer[i + 1];
+ }
+ FREE_MEMORY(recvBuffer, int, recvSize);
+
+
+ /* ======= Communication with buildGlobalSolution() ======= */
+
+ // Get final solutions from all ranks
+ for (int i = 1; i < mpiSize; i++) {
+ // First, get number of DOFs that will be send from rank i
+ MPI::COMM_WORLD.Recv(&recvSize, 1, MPI_INT, i, mpiTag);
+
+ // Now, receive the solution DOFS of rank i
+ double *recvBufferDouble = GET_MEMORY(double, recvSize);
+ MPI::COMM_WORLD.Recv(recvBufferDouble, recvSize, MPI_DOUBLE, i, mpiTag);
+
+ // Traverse through the overall mesh, get all elements that are refined from
+ // an element with localCoarseGridLevel i, and set there the solutions DOFs.
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
+ int elementOwner = -1;
+ int dofCount = 0;
+ while (elInfo) {
+ Element *element = elInfo->getElement();
+ if (partitionVec.count(element->getIndex()) > 0) {
+ elementOwner = partitionVec[element->getIndex()];
+ }
+
+ if (element->isLeaf()) {
+ basFcts->getLocalIndices(element, admin, elDOFs);
+ if (elementOwner == (i - 1)) {
+ for (int i = 0; i < numFcts; i++) {
+ (*problem->getSolution()->getDOFVector(0))[elDOFs[i]] =
+ recvBufferDouble[dofCount + i];
+ }
+ dofCount += numFcts;
+ }
+ }
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ FREE_MEMORY(recvBufferDouble, double, recvSize);
+ }
+
+
+ /* ====== Finally, call debug function ====== */
+ debugFunction();
+ }
+
+ FREE_MEMORY(elDOFs, DegreeOfFreedom, numFcts);
+ FREE_MEMORY(codeSize, int, mpiWorldSize);
+ FREE_MEMORY(nElements, int, mpiWorldSize);
+ }
}
diff --git a/AMDiS/src/ParallelProblem.h b/AMDiS/src/ParallelProblem.h
index 74518172e561b211d4f5d8f9b965c8dc7c82f791..1763f7fc992423f04fb3e2227bb2d663ea526279 100644
--- a/AMDiS/src/ParallelProblem.h
+++ b/AMDiS/src/ParallelProblem.h
@@ -59,7 +59,8 @@ namespace AMDiS {
public ProblemTimeInterface
{
public:
- ParallelProblemBase(ProblemIterationInterface *iterationIF,
+ ParallelProblemBase(const std::string& name,
+ ProblemIterationInterface *iterationIF,
ProblemTimeInterface *timeIF);
virtual ~ParallelProblemBase() {};
@@ -101,11 +102,7 @@ namespace AMDiS {
*/
virtual void buildGlobalSolution(AdaptInfo *adaptInfo) = 0;
- virtual void exitParallelization(AdaptInfo *adaptInfo)
- {
- if (!timeIF_)
- closeTimestep(adaptInfo);
- };
+ virtual void exitParallelization(AdaptInfo *adaptInfo);
virtual void setTime(AdaptInfo *adaptInfo)
{
@@ -149,50 +146,7 @@ namespace AMDiS {
iterationIF_->beginIteration(adaptInfo);
};
- virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION)
- {
- Flag flag;
-
- if (mpiSize > 1 && toDo.isSet(MARK | ADAPT)) {
- flag = iterationIF_->oneIteration(adaptInfo, MARK | ADAPT);
-
- double localWeightSum = setElemWeights(adaptInfo);
- if (doPartitioning(adaptInfo, localWeightSum)) {
- clock_t partitioningStart = clock();
-
- synchronizeMeshes(adaptInfo);
- partitionMesh(adaptInfo);
- refineOverlap(adaptInfo);
- createOverlap(adaptInfo);
- synchronizeMeshes(adaptInfo);
- exchangeDOFVectors(adaptInfo);
- coarsenOutOfPartition(adaptInfo);
-
- clock_t partitioningEnd = clock();
- partitioningTime = TIME_USED(partitioningStart,
- partitioningEnd);
- computationStart = partitioningEnd;
- }
-
- flag |= iterationIF_->oneIteration(adaptInfo, toDo & ~(MARK | ADAPT));
- } else {
- flag = iterationIF_->oneIteration(adaptInfo, toDo);
- }
-
- // synchronize adaption flag
- unsigned long *flagBuffer = GET_MEMORY(unsigned long, mpiSize);
-
- unsigned long localFlag = flag.getFlags();
-
- MPI::COMM_WORLD.Allgather(&localFlag, 1, MPI_UNSIGNED_LONG,
- flagBuffer, 1, MPI_UNSIGNED_LONG);
- for (int i = 0; i < mpiSize; i++) {
- flag.setFlag(flagBuffer[i]);
- }
- FREE_MEMORY(flagBuffer, unsigned long, mpiSize);
-
- return flag;
- };
+ virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);
virtual void endIteration(AdaptInfo *adaptInfo) {
iterationIF_->endIteration(adaptInfo);
@@ -204,12 +158,15 @@ namespace AMDiS {
return false;
};
+ MPI::Intracomm* getMpiComm() {
+ return &mpiComm;
+ };
- protected:
- int mpiRank;
-
- int mpiSize;
+ bool getDebugServerProcess() {
+ return debugServerProcess;
+ }
+ protected:
ProblemIterationInterface *iterationIF_;
ProblemTimeInterface *timeIF_;
@@ -217,6 +174,41 @@ namespace AMDiS {
clock_t computationStart;
double partitioningTime;
+
+ /** \brief
+ * The rank of the current process.
+ */
+ int mpiRank;
+
+ /** \brief
+ * Overall number of processes.
+ */
+ int mpiSize;
+
+ /** \brief
+ * MPI communicator collected all processes, which should
+ * be used for calculation. The Debug procces is not included
+ * in this communicator.
+ */
+ MPI::Intracomm mpiComm;
+
+ /** \brief
+ * The MPI group, which is used for the communicator
+ * \ref mpiComm.
+ */
+ MPI::Group amdisGroup;
+
+ /** \brief
+ * Defines the debug mode. If it is 1, a debug server will be started
+ * on rank 0.
+ */
+ int debugMode;
+
+ /** \brief
+ * If true, the current process is the debug server. Otherwise, the
+ * processes is a working processes calculating part of the solution.
+ */
+ bool debugServerProcess;
};
// =========================================================================
@@ -296,9 +288,7 @@ namespace AMDiS {
static bool writeElement(ElInfo *elInfo);
- Mesh* getDbgMesh() {
- return dbgMesh;
- }
+ virtual void startDebugServer() {};
virtual void serialize(std::ostream&) {};
@@ -338,15 +328,16 @@ namespace AMDiS {
ParMetisPartitioner *partitioner_;
/** \brief
- * Stores to every element index the number of the partition it corresponds to.
+ * Stores to every coarse element index the number of the partition it
+ * corresponds to.
*/
- std::map<int, int> partitionVec_;
+ std::map<int, int> partitionVec;
/** \brief
- * Stores an old partitioning of elements. To every element index the number of
- * the parition it corresponds to is stored.
+ * Stores an old partitioning of elements. To every element index the number
+ * of the parition it corresponds to is stored.
*/
- std::map<int, int> oldPartitionVec_;
+ std::map<int, int> oldPartitionVec;
/** \brief
*
@@ -354,14 +345,14 @@ namespace AMDiS {
std::map<int, double> elemWeights_;
/** \brief
- *
+ * Stores to every element the set of partitions it corresponds to.
*/
std::map<Element*, std::set<int> > elementPartitions_;
/** \brief
* Stores to every DOF the set of partitions it corresponds to.
*/
- std::map<DegreeOfFreedom, std::set<int> > vertexPartitions_;
+ std::map<DegreeOfFreedom, std::set<int> > vertexPartitions;
/** \brief
*
@@ -437,20 +428,6 @@ namespace AMDiS {
*
*/
double maxLowerTH_;
-
- /** \brief
- * Defines the debug mode. If it is 1, the processor with rank 0
- * fills \ref dbgMesh, which than contains the whole mesh domain after
- * each timestep. This makes it easy to check the whole result without
- * manually fitting the subresults together.
- */
- int debugMode;
-
- /** \brief
- * In debug mode on process 0, this mesh contains the composition of all
- * rank meshes.
- */
- Mesh *dbgMesh;
};
// =========================================================================
@@ -517,18 +494,6 @@ namespace AMDiS {
*/
std::vector<DOFVector<double>*> rankSolution;
- /** \brief
- * Is used in debug mode in the same context as \ref rankSolution.
- * But the solution is build using \ref dbgMesh.
- */
- std::vector<DOFVector<double>*> dbgRankSolution;
-
- /** \brief
- * In debug mode and on process 0 only, this vector will be initialized
- * to store the overall solution of all processes.
- */
- DOFVector<double>* dbgSolution;
-
/** \brief
*
*/
@@ -588,9 +553,9 @@ namespace AMDiS {
return name_;
};
- SystemVector* getDbgSolution() {
- return dbgSolution;
- };
+ virtual void startDebugServer();
+
+ virtual void debugFunction() {};
protected:
ProblemVec *problem;
@@ -615,18 +580,6 @@ namespace AMDiS {
*/
std::vector<SystemVector*> rankSolution;
- /** \brief
- * Is used in debug mode in the same context as \ref rankSolution.
- * But the solution is build using \ref dbgMesh.
- */
- std::vector<SystemVector*> dbgRankSolution;
-
- /** \brief
- * In debug mode and on process 0 only, this vector will be initialized
- * to store the overall solution of all processes.
- */
- SystemVector* dbgSolution;
-
/** \brief
*
*/
diff --git a/AMDiS/src/PartitionElementData.h b/AMDiS/src/PartitionElementData.h
index b7fcb748ce53fcd63a63f07e0d31e55d9581c960..03de5d114329054d71abc0b588d0004d1391c38e 100644
--- a/AMDiS/src/PartitionElementData.h
+++ b/AMDiS/src/PartitionElementData.h
@@ -58,8 +58,8 @@ namespace AMDiS {
PartitionElementData(ElementData *decorated = NULL)
: ElementData(decorated),
- status_(UNDEFINED),
- level_(0)
+ status(UNDEFINED),
+ level(0)
{};
bool refineElementData(Element* parent,
@@ -70,10 +70,10 @@ namespace AMDiS {
ElementData::refineElementData(parent, child1, child2, elType);
PartitionElementData *child1Data = NEW PartitionElementData(child1->getElementData());
PartitionElementData *child2Data = NEW PartitionElementData(child2->getElementData());
- child1Data->setPartitionStatus(status_);
- child2Data->setPartitionStatus(status_);
- child1Data->setLevel(level_ + 1);
- child2Data->setLevel(level_ + 1);
+ child1Data->setPartitionStatus(status);
+ child2Data->setPartitionStatus(status);
+ child1Data->setLevel(level + 1);
+ child2Data->setLevel(level + 1);
child1->setElementData(child1Data);
child2->setElementData(child2Data);
return false;
@@ -96,33 +96,31 @@ namespace AMDiS {
void serialize(std::ostream& out)
{
ElementData::serialize(out);
- out.write(reinterpret_cast<const char*>(&status_),
- sizeof(PartitionStatus));
- out.write(reinterpret_cast<const char*>(&level_), sizeof(int));
+ out.write(reinterpret_cast<const char*>(&status), sizeof(PartitionStatus));
+ out.write(reinterpret_cast<const char*>(&level), sizeof(int));
};
void deserialize(std::istream& in)
{
ElementData::deserialize(in);
- in.read(reinterpret_cast<char*>(&status_),
- sizeof(PartitionStatus));
- in.read(reinterpret_cast<char*>(&level_), sizeof(int));
+ in.read(reinterpret_cast<char*>(&status), sizeof(PartitionStatus));
+ in.read(reinterpret_cast<char*>(&level), sizeof(int));
};
- inline void setPartitionStatus(PartitionStatus status) {
- status_ = status;
+ inline void setPartitionStatus(PartitionStatus status_) {
+ status = status_;
};
inline PartitionStatus getPartitionStatus() {
- return status_;
+ return status;
};
- inline void setLevel(int level) {
- level_ = level;
+ inline void setLevel(int level_) {
+ level = level_;
};
inline int getLevel() {
- return level_;
+ return level;
};
void descend(Element *element)
@@ -148,8 +146,9 @@ namespace AMDiS {
};
protected:
- PartitionStatus status_;
- int level_;
+ PartitionStatus status;
+
+ int level;
};
}
diff --git a/AMDiS/src/ProblemIterationInterface.h b/AMDiS/src/ProblemIterationInterface.h
index 0c2bca5dcaf09002d0914f4099c317f7b3d4e3d7..d8d6c266230223724708acaf49cf2bc1606ca59c 100644
--- a/AMDiS/src/ProblemIterationInterface.h
+++ b/AMDiS/src/ProblemIterationInterface.h
@@ -84,9 +84,7 @@ namespace AMDiS {
/** \brief
* Returns the problem with the given name.
*/
- virtual ProblemStatBase *getProblem(const ::std::string& name) {
- return NULL;
- };
+ virtual ProblemStatBase *getProblem(const ::std::string& name) { return NULL; };
/** \brief
* Returns the name of the problem.
diff --git a/AMDiS/src/ProblemScal.h b/AMDiS/src/ProblemScal.h
index 6abf2784f81c61964996496883e25b0b747cbcee..3d42a2bd484f86915149142994a4d26571250dfb 100644
--- a/AMDiS/src/ProblemScal.h
+++ b/AMDiS/src/ProblemScal.h
@@ -177,24 +177,18 @@ namespace AMDiS {
/** \brief
* Returns number of managed problems
*/
- virtual int getNumProblems() {
- return 1;
- };
+ virtual int getNumProblems() { return 1; };
/** \brief
* Implementation of ProblemStatBase::getNumComponents()
*/
- virtual int getNumComponents() {
- return 1;
- };
+ virtual int getNumComponents() { return 1; };
/** \brief
* Returns the problem with the given number. If only one problem
* is managed by this master problem, the number hasn't to be given.
*/
- virtual ProblemStatBase *getProblem(int number = 0) {
- return this;
- };
+ virtual ProblemStatBase *getProblem(int number = 0) { return this; };
/** \brief
* Writes output files.
diff --git a/AMDiS/src/Serializer.h b/AMDiS/src/Serializer.h
index cf8b595160d2130d4d0f234b3854c6ac1fbc87f8..ba4f607925f1db29412df9e5555ac21f24f07c6d 100644
--- a/AMDiS/src/Serializer.h
+++ b/AMDiS/src/Serializer.h
@@ -39,18 +39,14 @@ namespace AMDiS {
Serializer(ProblemType *problem)
: name_(""),
problem_(problem),
- tsModulo(1),
+ tsModulo_(1),
timestepNumber_(-1)
{
GET_PARAMETER(0, problem_->getName() + "->output->serialization filename",
&name_);
GET_PARAMETER(0, problem_->getName() + "->output->write every i-th timestep",
- "%d", &tsModulo);
-
+ "%d", &tsModulo_);
TEST_EXIT(name_ != "")("no filename\n");
-
- TEST_EXIT(tsModulo > 0)
- ("Init file option \"write every i-th timestep\" is smaller than 1!\n");
};
virtual ~Serializer() {};
@@ -64,7 +60,7 @@ namespace AMDiS {
FUNCNAME("Serializer::writeFiles()");
timestepNumber_++;
- timestepNumber_ %= tsModulo;
+ timestepNumber_ %= tsModulo_;
if ((timestepNumber_ != 0) && !force) {
return;
}
@@ -99,7 +95,7 @@ namespace AMDiS {
/** \brief
* The problem is serialized every tsModulo-th timestep.
*/
- int tsModulo;
+ int tsModulo_;
/** \brief
* Current timestep number.