diff --git a/AMDiS/libtool b/AMDiS/libtool
index 41ace2e6aa8dc61f34efef5d3ac31a4138c1ba01..d6ae6aec3bdfe931f7738cb747117b7a8a279992 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -30,10 +30,10 @@
# the same distribution terms that you use for the rest of that program.
# A sed program that does not truncate output.
-SED="/bin/sed"
+SED="/usr/bin/sed"
# Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/bin/sed -e 1s/^X//"
+Xsed="/usr/bin/sed -e 1s/^X//"
# The HP-UX ksh and POSIX shell print the target directory to stdout
# if CDPATH is set.
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host deimos102:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="gcc"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -97,7 +97,7 @@ with_gcc=yes
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -171,7 +171,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -325,10 +325,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=" /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host deimos102:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6782,12 +6782,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -6798,13 +6798,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g++"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6813,7 +6813,7 @@ with_gcc=yes
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -6887,7 +6887,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
+predep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbeginS.o"
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
+postdep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o"
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -6954,11 +6954,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path="-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7038,10 +7038,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=" /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host deimos102:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7087,12 +7087,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7103,7 +7103,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7112,13 +7112,13 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=yes
+with_gcc=
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7346,10 +7346,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/"
+sys_lib_search_path_spec=" /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/ /usr/lib/gcc/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../ /lib/x86_64-suse-linux/3.3.5/ /lib/ /usr/lib/x86_64-suse-linux/3.3.5/ /usr/lib/"
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/ConditionalEstimator.cc b/AMDiS/src/ConditionalEstimator.cc
index bc7997f69161dd5d4c11b33fd036c1dd37d535a1..2a17b00edce984e7270893464323be49b44ca1a4 100644
--- a/AMDiS/src/ConditionalEstimator.cc
+++ b/AMDiS/src/ConditionalEstimator.cc
@@ -30,9 +30,7 @@ namespace AMDiS {
TEST_EXIT_DBG(elData)("no partition data on leaf element %d (rank %d)\n",
elInfo->getElement()->getIndex(),
MPI::COMM_WORLD.Get_rank());
-
- PartitionStatus status = elData->getPartitionStatus();
-
+
//if(status == IN || status == OVERLAP) {
decoratedEstimator_->estimateElement(elInfo);
//} else {
@@ -45,7 +43,6 @@ namespace AMDiS {
while(elInfo) {
PartitionElementData *elData = dynamic_cast<PartitionElementData*>
(elInfo->getElement()->getElementData(PARTITION_ED));
- PartitionStatus status = elData->getPartitionStatus();
//if(status == IN) {
elementCount_++;
partition_sum += elInfo->getElement()->getEstimation(row_);
diff --git a/AMDiS/src/ElementDofIterator.h b/AMDiS/src/ElementDofIterator.h
index a09e1f305089d4d9c9d78735e69feadd204a0f4f..a64cee19461fac956af00d7fb9e95d3dd082fedc 100644
--- a/AMDiS/src/ElementDofIterator.h
+++ b/AMDiS/src/ElementDofIterator.h
@@ -34,7 +34,7 @@ namespace AMDiS {
*
* Should be used in the following way:
*
- * ElementDofIterator elDofIter(admin);
+ * ElementDofIterator elDofIter(feSpace);
* elDofIter.reset(el);
* do {
* elDofIter.getDOF();
diff --git a/AMDiS/src/Global.cc b/AMDiS/src/Global.cc
index 11923f5582b0d3f7aeaab7f15b5371ad473e5c49..cd4bdec5c68192a88e626428da23a7664d6b7cef 100644
--- a/AMDiS/src/Global.cc
+++ b/AMDiS/src/Global.cc
@@ -1,3 +1,7 @@
+#include <stdarg.h>
+#include <stdio.h>
+#include <sstream>
+
#include "Global.h"
#include "Parameters.h"
#include "Element.h"
@@ -5,10 +9,6 @@
#include "Triangle.h"
#include "Tetrahedron.h"
-
-#include <stdarg.h>
-#include <stdio.h>
-
namespace AMDiS {
const char *funcName = NULL;
@@ -36,7 +36,6 @@ namespace AMDiS {
MSG("wait for <enter> ...");
fgets(line, 9, stdin);
}
- return;
}
void Msg::change_out(std::ostream *fp)
@@ -53,33 +52,7 @@ namespace AMDiS {
} else {
ERROR("file pointer is pointer to nil;\n");
ERROR("use previous stream for errors furthermore\n");
- }
-
- return;
- }
-
- void Msg::open_file(const char *filename, OPENMODE type)
- {
- FUNCNAME("Msg::open_file()");
- std::ofstream *fp;
-
-
- if (filename && (fp = new std::ofstream(filename, type))) {
- if (out && *out != std::cout && *out != std::cerr) {
- dynamic_cast< std::ofstream*>(out)->close();
- delete out;
- }
-
- out = fp;
- } else {
- if (filename)
- ERROR("can not open %s;\n", filename);
- else
- ERROR("no filename specified;\n");
-
- ERROR("use previous stream for messages furthermore\n");
- }
- return;
+ }
}
void Msg::change_error_out(std::ofstream *fp)
@@ -97,8 +70,6 @@ namespace AMDiS {
ERROR("file pointer is pointer to nil;\n");
ERROR("use previous stream for errors furthermore\n");
}
-
- return;
}
void Msg::open_error_file(const char *filename, OPENMODE type)
@@ -120,34 +91,6 @@ namespace AMDiS {
ERROR("no filename specified;\n");
ERROR("use previous stream for errors furthermore\n");
}
-
- return;
- }
-
- const char *generate_filename(const char * path, const char * fn, int ntime)
- {
- static char name[256];
- char *cp;
-
- if (path == NULL || path[0] == '\0') {
- sprintf(name, "./%s", fn);
- } else {
- const char* ccp = path;
- while (*ccp)
- ccp++;
- ccp--;
- if (*ccp == '/')
- sprintf(name, "%s%s", path, fn);
- else
- sprintf(name, "%s/%s", path, fn);
- }
- cp = name;
- while (*cp)
- cp++;
- sprintf(cp, "%d", 100000 + ntime);
- if (ntime < 100000) *cp = '0';
-
- return(const_cast<const char *>(name));
}
void Msg::print_funcname(const char *funcName)
@@ -156,36 +99,37 @@ namespace AMDiS {
out = &std::cout;
if (funcName && oldFuncName != funcName) {
- (*out)<< funcName << ":" << std::endl;
+ PRINT_LINE((*out), funcName << ":" << std::endl);
} else if (!funcName) {
- (*out)<<"*unknown function*" << std::endl;
+ PRINT_LINE((*out), "*unknown function*" << std::endl);
}
- (*out) << " ";
+ PRINT_LINE((*out), " ");
+
oldFuncName = funcName;
}
- void Msg::print_error_funcname(const char *funcName,
- const char *file,
- int line)
+ void Msg::print_error_funcname(const char *funcName, const char *file, int line)
{
static int old_line = -1;
if (!error)
error = &std::cerr;
- if (funcName && oldFuncName != funcName) {
- (*error)<<funcName<< ": ";
- }
+ std::stringstream oss;
+
+ if (funcName && oldFuncName != funcName)
+ oss << funcName << ": ";
else if (!funcName) {
if (line-old_line > 5)
- (*error) << "*unknown function*";
+ oss << "*unknown function*";
}
if (oldFuncName != funcName) {
- (*error) << "ERROR in " << file << ", line " << line << "\n";
+ oss << "ERROR in " << file << ", line " << line << std::endl;;
oldFuncName = funcName;
} else if (line - old_line > 5)
- (*error) << "ERROR in " << file << ", line " << line << "\n";
+ oss << "ERROR in " << file << ", line " << line << "\n" << std::endl;
+ PRINT_LINE((*error), oss.str());
old_line = line;
}
@@ -199,7 +143,7 @@ namespace AMDiS {
va_start(arg, format);
vsprintf(buff, format, arg);
- (*error)<<buff;
+ PRINT_LINE((*error), buff);
va_end(arg);
exit(1);
@@ -216,10 +160,8 @@ namespace AMDiS {
va_start(arg, format);
vsprintf(buff, format, arg);
- (*error)<<buff;
+ PRINT_LINE((*error), buff);
va_end(arg);
-
- return;
}
void Msg::print_warn_funcname(const char *funcName,
@@ -231,17 +173,22 @@ namespace AMDiS {
if (!out)
out = &std::cout;
+ std::stringstream oss;
+
if (funcName && oldFuncName != funcName) {
- (*out) << funcName << ": ";
- }
- else if (!funcName){
- (*out) << "*unknown function*";
+ oss << funcName << ": ";
+ } else if (!funcName) {
+ oss << "*unknown function*";
}
+
if (oldFuncName != funcName) {
- (*out) << "WARNING in " << file << ", line " << line << "\n";
+ oss << "WARNING in " << file << ", line " << line << std::endl;
oldFuncName = funcName;
- } else if (line - old_line > 5)
- (*out) << "WARNING in " << file << ", line " << line << "\n";
+ } else if (line - old_line > 5) {
+ oss << "WARNING in " << file << ", line " << line << std::endl;
+ }
+
+ PRINT_LINE((*out), oss.str());
old_line = line;
}
@@ -256,10 +203,8 @@ namespace AMDiS {
va_start(arg, format);
vsprintf(buff, format, arg);
- (*out)<<buff;
+ PRINT_LINE((*out), buff);
va_end(arg);
-
- return;
}
@@ -273,7 +218,7 @@ namespace AMDiS {
va_start(arg, format);
vsprintf(buff, format, arg);
- (*out) << buff;
+ PRINT_LINE((*out), buff);
va_end(arg);
}
@@ -295,9 +240,8 @@ namespace AMDiS {
geoIndexTable.resize(4);
for (int i = 0; i < 4; i++) {
geoIndexTable[i].resize(geoTableSize);
- for (int j = 0; j < geoTableSize; j++) {
- geoIndexTable[i][j] = 0;
- }
+ for (int j = 0; j < geoTableSize; j++)
+ geoIndexTable[i][j] = 0;
}
geoIndexTable[0][PARTS - MINPART] = 1;
diff --git a/AMDiS/src/Global.h b/AMDiS/src/Global.h
index 6256f13a595cb04371daa8efe0e02b365961c68a..f30401efc9c784ac9a7d0a4b3b0498de6a84a020 100644
--- a/AMDiS/src/Global.h
+++ b/AMDiS/src/Global.h
@@ -47,6 +47,10 @@
#include <functional>
#include <float.h>
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+#include "mpi.h"
+#endif
+
#include "AMDiS_fwd.h"
namespace AMDiS {
@@ -76,6 +80,12 @@ namespace AMDiS {
/// returns the dimension of GeoIndex ind for dimension dim
#define DIM_OF_INDEX(ind, dim) ((static_cast<int>(ind) == 0) ? dim : static_cast<int>(ind) - 1)
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+#define PRINT_LINE(stream, line) stream << "[" << MPI::COMM_WORLD.Get_rank() << "]" << line
+#else
+#define PRINT_LINE(stream, line) stream << line
+#endif
+
/// Calculates factorial of i
int fac(int i);
@@ -172,20 +182,12 @@ namespace AMDiS {
/// Changes the message stream
static void change_out(std::ostream*);
- /// Creates a filestream and sets the message stream to this filestream
- static void open_file(const char *filename, OPENMODE);
-
/// Changes the error stream
static void change_error_out(std::ofstream *fp);
/// Creates a filestream and sets the error stream to this filestream
static void open_error_file(const char *filename, OPENMODE);
- /// Generates a filename from path, file and ntime
- static const char *generate_filename(const char *path,
- const char *file,
- int ntime);
-
/// Sets \ref msgInfo
static void setMsgInfo(int info)
{
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index 8229af0ec2fc7d7d61b3b30060b273f7b5c973d7..c77f2bb7a2097346bcb8d8fb5f1dc99400ab1ae5 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -244,6 +244,13 @@ namespace AMDiS {
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor)
if (value(*icursor) != 0.0) {
+ if (mpiRank == 0 && r == 0)
+ std::cout << "C = " << col(*icursor)
+ << " = " << mapLocalGlobalDOFs[col(*icursor)]
+ << " = " << mapLocalGlobalDOFs[col(*icursor)] * dispMult + dispAddCol
+ << " -> " << value(*icursor)
+ << std::endl;
+
cols.push_back(mapLocalGlobalDOFs[col(*icursor)] * dispMult + dispAddCol);
values.push_back(value(*icursor));
}
@@ -251,6 +258,7 @@ namespace AMDiS {
MatSetValues(petscMatrix, 1, &r, cols.size(), &(cols[0]), &(values[0]), ADD_VALUES);
}
+ std::cout << "==========" << std::endl;
}
@@ -338,7 +346,7 @@ namespace AMDiS {
icend = end<nz>(cursor); icursor != icend; ++icursor) {
if (value(*icursor) != 0.0) {
int c = mapLocalGlobalDOFs[col(*icursor)] * nComponents + j;
-
+
if (c >= rstart * nComponents &&
c < rstart * nComponents + nRankRows)
d_nnz[r]++;
@@ -475,13 +483,9 @@ namespace AMDiS {
i++;
}
- INFO(info, 8)("Fill petsc matrix 1 needed %.5f seconds\n", TIME_USED(first, clock()));
-
MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, nOverallRows, nOverallRows,
0, d_nnz, 0, o_nnz, &petscMatrix);
- INFO(info, 8)("Fill petsc matrix 2 needed %.5f seconds\n", TIME_USED(first, clock()));
-
#if (DEBUG != 0)
int a, b;
MatGetOwnershipRange(petscMatrix, &a, &b);
@@ -498,13 +502,9 @@ namespace AMDiS {
if ((*mat)[i][j])
setDofMatrix((*mat)[i][j], nComponents, i, j);
- INFO(info, 8)("Fill petsc matrix 3 needed %.5f seconds\n", TIME_USED(first, clock()));
-
MatAssemblyBegin(petscMatrix, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(petscMatrix, MAT_FINAL_ASSEMBLY);
- INFO(info, 8)("Fill petsc matrix 4 needed %.5f seconds\n", TIME_USED(first, clock()));
-
for (int i = 0; i < nComponents; i++)
setDofVector(vec->getDOFVector(i), nComponents, i);
@@ -589,7 +589,7 @@ namespace AMDiS {
}
- void ParallelDomainBase::solvePetscMatrix(SystemVector *vec)
+ void ParallelDomainBase::solvePetscMatrix(SystemVector &vec)
{
FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
@@ -610,14 +610,38 @@ namespace AMDiS {
VecGetArray(petscSolVec, &vecPointer);
for (int i = 0; i < nComponents; i++) {
- DOFVector<double> *dofvec = vec->getDOFVector(i);
- for (int j = 0; j < nRankDOFs; j++)
+ DOFVector<double> *dofvec = vec.getDOFVector(i);
+ for (int j = 0; j < nRankDOFs; j++) {
+ if (i == 0 && mapLocalToDofIndex[j] == 0)
+ std::cout << "ZUGRIFF AUF: " << j * nComponents + i << std::endl;
+
(*dofvec)[mapLocalToDofIndex[j]] = vecPointer[j * nComponents + i];
+ }
}
+ if (mpiRank == 0)
+ std::cout << "RESULT = " << (*(vec.getDOFVector(0)))[0] << std::endl;
+
VecRestoreArray(petscSolVec, &vecPointer);
+ synchVectors(vec);
+ int iterations = 0;
+ KSPGetIterationNumber(solver, &iterations);
+ MSG(" Number of iterations: %d\n", iterations);
+
+ double norm = 0.0;
+ MatMult(petscMatrix, petscSolVec, petscTmpVec);
+ VecAXPY(petscTmpVec, -1.0, petscRhsVec);
+ VecNorm(petscTmpVec, NORM_2, &norm);
+ MSG(" Residual norm: %e\n", norm);
+
+ MatDestroy(petscMatrix);
+ KSPDestroy(solver);
+ }
+
+ void ParallelDomainBase::synchVectors(SystemVector &vec)
+ {
std::vector<double*> sendBuffers(sendDofs.size());
std::vector<double*> recvBuffers(recvDofs.size());
@@ -632,7 +656,7 @@ namespace AMDiS {
int counter = 0;
for (int j = 0; j < nComponents; j++) {
- DOFVector<double> *dofvec = vec->getDOFVector(j);
+ DOFVector<double> *dofvec = vec.getDOFVector(j);
for (int k = 0; k < nSendDOFs; k++)
sendBuffers[i][counter++] = (*dofvec)[*((sendIt->second)[k])];
}
@@ -661,7 +685,7 @@ namespace AMDiS {
int counter = 0;
for (int j = 0; j < nComponents; j++) {
- DOFVector<double> *dofvec = vec->getDOFVector(j);
+ DOFVector<double> *dofvec = vec.getDOFVector(j);
for (int k = 0; k < nRecvDOFs; k++)
(*dofvec)[*(recvIt->second)[k]] = recvBuffers[i][counter++];
}
@@ -671,19 +695,6 @@ namespace AMDiS {
for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
delete [] sendBuffers[i];
-
- int iterations = 0;
- KSPGetIterationNumber(solver, &iterations);
- MSG(" Number of iterations: %d\n", iterations);
-
- double norm = 0.0;
- MatMult(petscMatrix, petscSolVec, petscTmpVec);
- VecAXPY(petscTmpVec, -1.0, petscRhsVec);
- VecNorm(petscTmpVec, NORM_2, &norm);
- MSG(" Residual norm: %e\n", norm);
-
- MatDestroy(petscMatrix);
- KSPDestroy(solver);
}
@@ -992,6 +1003,22 @@ namespace AMDiS {
sendDofs.clear();
recvDofs.clear();
+
+#if 0
+ StlMpi stlMpi(mpiComm);
+ stlMpi.prepareCommunication(false);
+ std::map<
+
+ for (std::map<int, DofIndexMap >::iterator sendIt = sendNewDofs.begin();
+ sendIt != sendNewDofs.end(); ++sendIt, i++)
+ stlMpi.send(it->second, it->first);
+
+ for (std::map<int, int>::iterator recvIt = recvNewDofs.begin();
+ recvIt != recvNewDofs.end(); ++recvIt, i++)
+ stlMpi.recv(it->first, it->second * 2);
+
+ stlMpi.startCommunication();
+#endif
MPI::Request request[sendNewDofs.size() + recvNewDofs.size()];
int requestCounter = 0;
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/ParallelDomainBase.h
index a4a0b4b838abe31eb1420971422ddf2895692504..3ab82d43579347e3f54aa6d5b11e14670e37fb5f 100644
--- a/AMDiS/src/ParallelDomainBase.h
+++ b/AMDiS/src/ParallelDomainBase.h
@@ -127,7 +127,7 @@ namespace AMDiS {
}
virtual void solveInitialProblem(AdaptInfo *adaptInfo)
- {
+ {
if (timeIF)
timeIF->solveInitialProblem(adaptInfo);
}
@@ -174,7 +174,7 @@ namespace AMDiS {
void solvePetscMatrix(DOFVector<double> *vec);
- void solvePetscMatrix(SystemVector *vec);
+ void solvePetscMatrix(SystemVector &vec);
virtual ProblemStatBase *getProblem(int number = 0)
{
@@ -279,6 +279,18 @@ namespace AMDiS {
*/
void writePartitioningMesh(std::string filename);
+ /** \brief
+ * This function must be used if the values of a SystemVector must be synchronised
+ * over all ranks. That means, that each rank sends the values of the DOFs, which
+ * are owned by the rank and lie on an interior bounday, to all other ranks also
+ * having this DOF.
+ *
+ * This function must be used, for example, after the lineary system is solved, or
+ * after the SystemVector is set by some user defined functions, e.g., initial
+ * solution functions.
+ */
+ void synchVectors(SystemVector &vec);
+
inline void orderDOFs(const DegreeOfFreedom* dof1,
const DegreeOfFreedom* dof2,
const DegreeOfFreedom* dof3,
diff --git a/AMDiS/src/ParallelDomainVec.cc b/AMDiS/src/ParallelDomainVec.cc
index 5416c468df63f2c78bae75529b3a6e1696f71ffd..cd5d47ca7bb490a9089d87c8274781d643d1dd0f 100644
--- a/AMDiS/src/ParallelDomainVec.cc
+++ b/AMDiS/src/ParallelDomainVec.cc
@@ -57,7 +57,7 @@ namespace AMDiS {
clock_t first = clock();
fillPetscMatrix(probVec->getSystemMatrix(), probVec->getRHS());
- solvePetscMatrix(probVec->getSolution());
+ solvePetscMatrix(*(probVec->getSolution()));
#ifdef _OPENMP
INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
diff --git a/AMDiS/src/ParallelDomainVec.h b/AMDiS/src/ParallelDomainVec.h
index 9c6638ce4a44e7eb3aa5f19981dd26b940a58b17..d4e44614f9649c951385fb53d7b966d2c6f56537 100644
--- a/AMDiS/src/ParallelDomainVec.h
+++ b/AMDiS/src/ParallelDomainVec.h
@@ -23,6 +23,7 @@
#define AMDIS_PARALLELDOMAINVEC_H
#include "ParallelDomainBase.h"
+#include "ProblemVec.h"
namespace AMDiS {
@@ -35,6 +36,13 @@ namespace AMDiS {
void initParallelization(AdaptInfo *adaptInfo);
+ virtual void solveInitialProblem(AdaptInfo *adaptInfo)
+ {
+ ParallelDomainBase::solveInitialProblem(adaptInfo);
+
+ synchVectors(*(probVec->getSolution()));
+ }
+
protected:
/// Starts the solution of the linear system using Petsc.
void solve();
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 4ebe67e867741fde0396eab6509747553e169f2e..a64f7ef2b4cf9c552ab5e49e2b9d9357c1020351 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -776,6 +776,11 @@ namespace AMDiS {
createPrecon();
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+ writeDbgMatrix("test0.mat");
+
+ exit(0);
+
INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
#ifdef _OPENMP
@@ -1322,6 +1327,7 @@ namespace AMDiS {
solution->deserialize(in);
}
+
void ProblemVec::computeError(AdaptInfo *adaptInfo)
{
FUNCNAME("ProblemVec::computeError()");
@@ -1377,5 +1383,173 @@ namespace AMDiS {
delete sol;
}
}
+
+
+ void ProblemVec::createDofToCoordMap(DofToCoord &dofMap)
+ {
+ const BasisFunction *basisFcts = componentSpaces[0]->getBasisFcts();
+ WorldVector<double> coords;
+ ElementDofIterator elDofIter(componentSpaces[0]);
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(componentMeshes[0], -1,
+ Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ while (elInfo) {
+ elDofIter.reset(elInfo->getElement());
+ int i = 0;
+ do {
+ DimVec<double> *baryCoord = basisFcts->getCoords(i);
+ elInfo->coordToWorld(*baryCoord, coords);
+ i++;
+ dofMap[elDofIter.getDof()] = coords;
+ } while (elDofIter.next());
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+
+ void ProblemVec::createCoordToDofMap(CoordToDof &dofMap)
+ {
+ const BasisFunction *basisFcts = componentSpaces[0]->getBasisFcts();
+ WorldVector<double> coords;
+ ElementDofIterator elDofIter(componentSpaces[0]);
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(componentMeshes[0], -1,
+ Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ while (elInfo) {
+ elDofIter.reset(elInfo->getElement());
+ int i = 0;
+ do {
+ DimVec<double> *baryCoord = basisFcts->getCoords(i);
+ elInfo->coordToWorld(*baryCoord, coords);
+ i++;
+ dofMap[coords] = elDofIter.getDof();
+ } while (elDofIter.next());
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+
+
+ void ProblemVec::writeDbgMatrix(std::string filename)
+ {
+ FUNCNAME("ProblemVec::writeDbMatrix()");
+
+ using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits = mtl::traits;
+ typedef DOFMatrix::base_matrix_type Matrix;
+ typedef traits::range_generator<major, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ DofToCoord dofToCoords;
+ createDofToCoordMap(dofToCoords);
+
+ std::ofstream out(filename.c_str());
+ out << dofToCoords.size() << std::endl;
+
+ int dimOfWorld = Global::getGeo(WORLD);
+ for (DofToCoord::iterator it = dofToCoords.begin(); it != dofToCoords.end(); ++it) {
+ out << it->first << std::endl;
+ for (int j = 0; j < dimOfWorld; j++)
+ out << (it->second)[j] << std::endl;
+ }
+
+ for (int i = 0; i < nComponents; i++) {
+ for (int j = 0; j < nComponents; j++) {
+ DOFMatrix *dofmatrix = (*systemMatrix)[i][j];
+
+ if (!dofmatrix)
+ continue;
+
+ Matrix& matrix = dofmatrix->getBaseMatrix();
+ int nnz = matrix.nnz();
+ int testNnz = 0;
+
+ out << nnz << std::endl;
+
+ traits::row<Matrix>::type row(matrix);
+ traits::col<Matrix>::type col(matrix);
+ traits::const_value<Matrix>::type value(matrix);
+
+ for (cursor_type cursor = begin<major>(matrix), cend = end<major>(matrix); cursor != cend; ++cursor) {
+ for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor) {
+ out << row(*icursor) << " "
+ << col(*icursor) << " "
+ << value(*icursor) << std::endl;
+ testNnz++;
+ }
+ }
+
+ TEST_EXIT(testNnz == nnz)("NNZ does not fit together!\n");
+ }
+ }
+
+ out.close();
+ }
+
+
+ void ProblemVec::readAndCompareDbgMatrix(std::string filename)
+ {
+ using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits = mtl::traits;
+ typedef DOFMatrix::base_matrix_type Matrix;
+ typedef traits::range_generator<major, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ CoordToDof coordToDof;
+ createCoordToDofMap(coordToDof);
+
+ DofToCoord dofToCoord;
+ WorldVector<double> coords;
+ DegreeOfFreedom dof;
+ int dimOfWorld = Global::getGeo(WORLD);
+
+ std::ifstream in(filename.c_str());
+ int nReadDofs;
+ in >> nReadDofs;
+ for (int i = 0; i < nReadDofs; i++) {
+ in >> dof;
+ for (int j = 0; j < dimOfWorld; j++)
+ in >> coords[j];
+ dofToCoord[dof] = coords;
+ }
+
+ for (int i = 0; i < nComponents; i++) {
+ for (int j = 0; j < nComponents; j++) {
+ DOFMatrix *dofmatrix = (*systemMatrix)[i][j];
+
+ if (!dofmatrix)
+ continue;
+
+ int readNnz;
+ in >> readNnz;
+
+ for (int k = 0; k < readNnz; k++) {
+ DegreeOfFreedom row, col;
+ double value;
+
+ in >> row;
+ in >> col;
+ in >> value;
+
+ WorldVector<double> rowCoords = dofToCoord[row];
+ WorldVector<double> colCoords = dofToCoord[col];
+
+ if (coordToDof.find(rowCoords) == coordToDof.end())
+ std::cout << "CANNOT FIND" << std::endl;
+
+ if (coordToDof.find(colCoords) == coordToDof.end())
+ std::cout << "CANNOT FIND" << std::endl;
+
+ }
+ }
+ }
+
+
+ in.close();
+ }
}
diff --git a/AMDiS/src/ProblemVec.h b/AMDiS/src/ProblemVec.h
index 3ff24293f4c99c5b89c3edc37380a7d45a7b352a..f4081696cb560013c91cd743d2d0c9cda57dd0e3 100644
--- a/AMDiS/src/ProblemVec.h
+++ b/AMDiS/src/ProblemVec.h
@@ -40,6 +40,13 @@ namespace AMDiS {
class ProblemVec : public ProblemStatBase,
public StandardProblemIteration
{
+ private:
+ // Defines a mapping type from dof indices to world coordinates.
+ typedef std::map<DegreeOfFreedom, WorldVector<double> > DofToCoord;
+
+ // Defines a mapping type from dof indices to world coordinates.
+ typedef std::map<WorldVector<double>, DegreeOfFreedom> CoordToDof;
+
public:
/// Constructor
ProblemVec(std::string nameStr,
@@ -473,6 +480,35 @@ namespace AMDiS {
*/
void computeError(AdaptInfo *adaptInfo);
+ /** \brief
+ * Create from the current problem a map from dof indices to world coordinates.
+ * This function is used by the debugging function \ref writeDbgMatrix and \ref
+ * readAndCompareDbgMatrix.
+ */
+ void createDofToCoordMap(DofToCoord &dofMap);
+
+ /** \brief
+ * Create from the current problem a map from world coordinates of all dofs to
+ * the corresponding dof indices. This function is used by the debugging function
+ * \ref writeDbgMatrix and \ref readAndCompareDbgMatrix.
+ */
+ void createCoordToDofMap(CoordToDof &dofMap);
+
+ /** \brief
+ * This function writes the system matrix and the system vector to a file
+ * for debugging. The entries of both, the matrix and the vector, are not
+ * indicated by the dof indices, but by the world coordinates of the dofs.
+ * This makes it possible to compare dof matrices, where the dof indices
+ * are different, e.g., when using domain decomposition parallelization.
+ */
+ void writeDbgMatrix(std::string filename);
+
+ /** \brief
+ * Reads a file, that was created using the function \ref writeDbgMatrix, and
+ * compares the date with the system matrix of this problem.
+ */
+ void readAndCompareDbgMatrix(std::string filename);
+
protected:
/// Name of this problem.