diff --git a/AMDiS/libtool b/AMDiS/libtool
index 45ef3ca14b51a55d7b5555ba1c6220bbc4a44fd8..3b6673371f6b9a9c8f45abefeac61e4c5b70b66e 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 p2s154:
+# 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.
@@ -82,25 +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=""
@@ -6763,7 +6763,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host p2s154:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6785,12 +6785,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -6801,25 +6801,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
+CC="g++"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+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"
@@ -6893,7 +6893,7 @@ 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"
@@ -6948,11 +6948,11 @@ 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.
@@ -6960,11 +6960,11 @@ 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"
@@ -7044,10 +7044,10 @@ 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 $srcfile for the compiler.
fix_srcfile_path=""
@@ -7071,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host p2s154:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7093,12 +7093,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7118,16 +7118,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+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"
@@ -7355,10 +7355,10 @@ 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 963642a0f02b0435994f6e1b08e3e57a64efd54b..c7c862ca43d4905cba022ef746fbb6723e0c62b6 100644
--- a/AMDiS/src/AdaptBase.h
+++ b/AMDiS/src/AdaptBase.h
@@ -39,7 +39,7 @@ namespace AMDiS {
{
public:
/// Constructor
- AdaptBase(const std::string& sname,
+ AdaptBase(std::string sname,
ProblemIterationInterface *problemIteration,
AdaptInfo *adapt,
ProblemTimeInterface *problemTime = NULL,
diff --git a/AMDiS/src/AdaptInstationary.cc b/AMDiS/src/AdaptInstationary.cc
index fe0baac5d9c5c4dd6ea8a9fffa09930426dab258..0d061a80fcbe19f43e449802a1e83682471d0fad 100644
--- a/AMDiS/src/AdaptInstationary.cc
+++ b/AMDiS/src/AdaptInstationary.cc
@@ -8,7 +8,7 @@
namespace AMDiS {
- AdaptInstationary::AdaptInstationary(const std::string &name,
+ AdaptInstationary::AdaptInstationary(std::string name,
ProblemIterationInterface *problemStat,
AdaptInfo *info,
ProblemTimeInterface *problemInstat,
diff --git a/AMDiS/src/AdaptInstationary.h b/AMDiS/src/AdaptInstationary.h
index ee2795a9384aedcf7bc5a933be660e688ec8fd17..7f5803d9d5d79d2bdafb797de3ef2812cc26c96d 100644
--- a/AMDiS/src/AdaptInstationary.h
+++ b/AMDiS/src/AdaptInstationary.h
@@ -54,45 +54,33 @@ namespace AMDiS {
* Creates a AdaptInstationary object with the given name for the time
* dependent problem problemInstat.
*/
- AdaptInstationary(const std::string &name,
+ AdaptInstationary(std::string name,
ProblemIterationInterface *problemStat,
AdaptInfo *info,
ProblemTimeInterface *problemInstat,
AdaptInfo *initialInfo,
time_t initialTimestamp = 0);
- /** \brief
- * Destructor
- */
+ /// Destructor
virtual ~AdaptInstationary();
- /** \brief
- * Sets \ref strategy to aStrategy
- */
+ /// Sets \ref strategy to aStrategy
inline void setStrategy(int aStrategy) {
strategy = aStrategy;
}
- /** \brief
- * Returns \ref strategy
- */
+ /// Returns \ref strategy
const int getStrategy() const {
return strategy;
}
- /** \brief
- * Implementation of AdaptBase::adapt()
- */
+ /// Implementation of AdaptBase::adapt()
virtual int adapt();
- /** \brief
- * serialization
- */
+ /// Serialization
virtual void serialize(std::ostream &out);
- /** \brief
- * deserialization
- */
+ /// deserialization
virtual void deserialize(std::istream &in);
@@ -108,19 +96,13 @@ namespace AMDiS {
*/
virtual void oneTimestep();
- /** \brief
- * Initialisation of this AdaptInstationary object
- */
+ /// Initialisation of this AdaptInstationary object
void initialize(const std::string& aName);
- /** \brief
- * Implements the explit time strategy. Used by \ref oneTimestep().
- */
+ /// Implements the explit time strategy. Used by \ref oneTimestep().
virtual void explicitTimeStrategy();
- /** \brief
- * Implements the implicit time strategy. Used by \ref oneTimestep().
- */
+ /// Implements the implicit time strategy. Used by \ref oneTimestep().
virtual void implicitTimeStrategy();
/** \brief
@@ -134,19 +116,13 @@ namespace AMDiS {
bool checkQueueRuntime();
protected:
- /** \brief
- * Strategy for choosing one timestep
- */
+ /// Strategy for choosing one timestep
int strategy;
- /** \brief
- * Parameter \f$ \delta_1 \f$ used in time step reduction
- */
+ /// Parameter \f$ \delta_1 \f$ used in time step reduction
double time_delta_1;
- /** \brief
- * Parameter \f$ \delta_2 \f$ used in time step enlargement
- */
+ /// Parameter \f$ \delta_2 \f$ used in time step enlargement
double time_delta_2;
/** \brief
@@ -155,9 +131,7 @@ namespace AMDiS {
*/
int breakWhenStable;
- /** \brief
- *
- */
+ ///
bool fixedTimestep_;
/** \brief
@@ -166,31 +140,27 @@ namespace AMDiS {
*/
int queueRuntime_;
- /** \brief
- * Name of the file used to automatically serialize the problem.
- */
+ /// Name of the file used to automatically serialize the problem.
std::string queueSerializationFilename_;
/** \brief
- * Timestamp at the beginning of all calculations. It is used to calculate the overall
- * runtime of the problem.
+ * Timestamp at the beginning of all calculations. It is used to calculate the
+ * overall runtime of the problem.
*/
time_t initialTimestamp_;
/** \brief
- * Timestamp at the beginning of the last timestep iteration. Is is used to calculate
- * the runtime of the last timestep.
+ * Timestamp at the beginning of the last timestep iteration. Is is used to
+ * calculate the runtime of the last timestep.
*/
time_t iterationTimestamp_;
- /** \brief
- * Stores the runtime (in seconds) of some last timestep iterations.
- */
+ /// Stores the runtime (in seconds) of some last timestep iterations.
std::queue<int> lastIterationsDuration_;
/** \brief
- * In debug mode, the adapt loop will print information about timestep
- * decreasing and increasing.
+ * In debug mode, the adapt loop will print information about timestep decreasing
+ * and increasing.
*/
bool dbgMode;
};
diff --git a/AMDiS/src/PngWriter.cc b/AMDiS/src/PngWriter.cc
index d8c24360f03aeeb1ed88d849ad434f5bf04f22c2..7e88e55fb7b26c648fe7ecc80a151df70030f8e3 100644
--- a/AMDiS/src/PngWriter.cc
+++ b/AMDiS/src/PngWriter.cc
@@ -48,7 +48,7 @@ namespace AMDiS {
rowPointers[i] = (png_byte*)png_malloc(png_ptr,
(imageType == 0 ? imageX : imageX * 3));
}
-
+
const BasisFunction* basisFcts = dataCollector->getFeSpace()->getBasisFcts();
Vector<DegreeOfFreedom> localDofs(3);
DOFVector<double>* dofvalues = dataCollector->getValues();
@@ -79,10 +79,10 @@ namespace AMDiS {
rowPointers[indexY][indexX + 2] = b;
}
- }
+ }
elInfo = stack.traverseNext(elInfo);
- }
+ }
FILE *fp = fopen(filename.c_str(), "wb");
TEST_EXIT(fp)("Cannot open file for writing matrix picture file!\n");