diff --git a/AMDiS/libtool b/AMDiS/libtool
index 2972e4e6d433c76d54ad955d7217ff0c788c9954..41ace2e6aa8dc61f34efef5d3ac31a4138c1ba01 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 p1s046:
+# 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-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-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="/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
@@ -97,7 +97,7 @@ with_gcc=yes
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"
@@ -171,7 +171,7 @@ 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"
@@ -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/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/"
+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/"
# Run-time system search path for libraries
-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 "
+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=""
@@ -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 p1s046:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6782,12 +6782,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-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="/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
@@ -6813,7 +6813,7 @@ with_gcc=yes
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"
@@ -6887,7 +6887,7 @@ 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"
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-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"
+predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
# Dependencies to place after the objects being linked to create a
# shared library.
-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"
+postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../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="-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="-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/../../.."
+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/../../.."
# 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/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/"
+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/"
# Run-time system search path for libraries
-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 "
+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=""
@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host p1s046:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7087,12 +7087,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-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="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7112,13 +7112,13 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
# 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"
@@ -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/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/"
+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/"
# Run-time system search path for libraries
-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 "
+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/ProblemScal.cc b/AMDiS/src/ProblemScal.cc
index 760ccf38b72a9f8ae41ce19f5c6083bdc8a91820..08603d8b6eeed9bd47ecde8aaf81baae8c1f1bac 100644
--- a/AMDiS/src/ProblemScal.cc
+++ b/AMDiS/src/ProblemScal.cc
@@ -412,13 +412,12 @@ namespace AMDiS {
std::string valueFilename("");
GET_PARAMETER(0, mesh->getName() + "->value file name", &valueFilename);
if (valueFilename.length()) {
- ValueReader::readValue(valueFilename.c_str(),
+ ValueReader::readValue(valueFilename,
mesh,
solution,
mesh->getMacroFileInfo());
mesh->clearMacroFileInfo();
}
-
// === do global refinements ===
if (initFlag.isSet(INIT_GLOBAL_REFINES)) {
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index d3df02329d248e94296352687d05a2ab039242c0..5e4e8ad76841f651e9ddb3d8b92edb0ebc24b213 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -26,6 +26,7 @@
#include "Flag.h"
#include "TraverseParallel.h"
#include "VtkWriter.h"
+#include "ValueReader.h"
namespace AMDiS {
@@ -191,14 +192,25 @@ namespace AMDiS {
&globalRefinements);
// Initialize the meshes if there is no serialization file.
- for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
- if (initFlag.isSet(INIT_MESH) &&
- meshes[i] &&
- !(meshes[i]->isInitialized())) {
+ for (int i = 0; i < static_cast<int>(meshes.size()); i++)
+ if (initFlag.isSet(INIT_MESH) && meshes[i] && !(meshes[i]->isInitialized()))
meshes[i]->initialize();
+
+ // === read value file and use it for the mesh values ===
+ std::string valueFilename("");
+ GET_PARAMETER(0, meshes[0]->getName() + "->value file name", &valueFilename);
+ if (valueFilename.length()) {
+ ValueReader::readValue(valueFilename,
+ meshes[0],
+ solution->getDOFVector(0),
+ meshes[0]->getMacroFileInfo());
+ meshes[0]->clearMacroFileInfo();
+ }
+
+ // === do global refinements ===
+ for (int i = 0; i < static_cast<int>(meshes.size()); i++)
+ if (initFlag.isSet(INIT_MESH) && meshes[i])
refinementManager->globalRefine(meshes[i], globalRefinements);
- }
- }
}
}
diff --git a/AMDiS/src/ValueReader.cc b/AMDiS/src/ValueReader.cc
index 9988d5a67800558ac8b4b5b9713c3a0ce6ad1ae6..819a01ab306c5824f85a59203ff683d31f43726d 100644
--- a/AMDiS/src/ValueReader.cc
+++ b/AMDiS/src/ValueReader.cc
@@ -12,16 +12,14 @@ namespace AMDiS {
* macroFileInfo. The function now reads the corresponding value file and
* copies the values to the correct positions in the DOF vector.
*/
- void ValueReader::readValue(const char *filename,
+ void ValueReader::readValue(const std::string filename,
Mesh *mesh,
DOFVector<double> *dofVector,
MacroInfo *macroFileInfo)
{
FUNCNAME("ValueReader::readValue()");
- TEST_EXIT(filename)("no file specified; filename NULL pointer\n");
- TEST_EXIT(strlen(filename) < static_cast<unsigned int>(127))
- ("can only handle filenames up to 127 characters\n");
+ TEST_EXIT(filename != "")("Filename not specified!\n");
TEST_EXIT(mesh)("no mesh specified\n");
TEST_EXIT(dofVector)("no DOF vector specified\n");
TEST_EXIT(macroFileInfo)("no MacroInfo specified\n");
@@ -29,7 +27,7 @@ namespace AMDiS {
std::string line;
// open the file and read the data to the vector values.
- std::ifstream file(filename, std::ifstream::in);
+ std::ifstream file(filename.c_str(), std::ifstream::in);
while (!file.eof()) {
getline(file, line);
diff --git a/AMDiS/src/ValueReader.h b/AMDiS/src/ValueReader.h
index 56218bbc67bed14d4f02f6b6b363bfd80e3712a3..c10a476bced14ed40909605d3cf5559515b77b96 100644
--- a/AMDiS/src/ValueReader.h
+++ b/AMDiS/src/ValueReader.h
@@ -28,10 +28,6 @@
namespace AMDiS {
- // ===========================================================================
- // ===== class ValueReader ===================================================
- // ===========================================================================
-
/** \ingroup Input
*
* \brief
@@ -41,10 +37,8 @@ namespace AMDiS {
class ValueReader
{
public:
- /** \brief
- * Copies the values of a value file to a DOF vector.
- */
- static void readValue(const char *filename,
+ /// Copies the values of a value file to a DOF vector.
+ static void readValue(const std::string filename,
Mesh *mesh,
DOFVector<double> *dofVector,
MacroInfo *macroFileInfo);