diff --git a/AMDiS/libtool b/AMDiS/libtool
index 1a37a1c4572b62407064c5fbf948ba43cd0594c4..dae4215704b4d0dc09fb1c65f4b44d11e5b80b38 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 deimos102:
+# 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=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /fastfs/wir/local/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
+sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
# 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 /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
# 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 deimos102:
+# 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/mpicxx"
+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/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/u/witkowski/local/lib -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
# 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=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /fastfs/wir/local/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
+sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
# 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 /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
# 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 deimos102:
+# 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=" /fastfs/wir/local/lib/x86_64-suse-linux/3.3.5/ /fastfs/wir/local/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/ /usr/lib/gcc/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../ /lib/x86_64-suse-linux/3.3.5/ /lib/ /usr/lib/x86_64-suse-linux/3.3.5/ /usr/lib/"
+sys_lib_search_path_spec=" /u/witkowski/local/lib/i386-redhat-linux/3.4.6/ /u/witkowski/local/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/"
# 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 /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index b7787d017e8caf36f90ba463cfed002c04075cbd..d8cb296c14826a7229b451f89d3600aac7fe6cf3 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -219,9 +219,13 @@ namespace AMDiS {
// === do global refinements ===
- for (unsigned int i = 0; i < meshes.size(); i++)
- if (initFlag.isSet(INIT_MESH) && meshes[i])
+ for (unsigned int i = 0; i < meshes.size(); i++) {
+ bool initMesh = initFlag.isSet(INIT_MESH) ||
+ (adoptProblem && adoptFlag.isSet(INIT_MESH));
+
+ if (initMesh && meshes[i])
refinementManager->globalRefine(meshes[i], globalRefinements);
+ }
}
}
diff --git a/AMDiS/src/SecondOrderAssembler.cc b/AMDiS/src/SecondOrderAssembler.cc
index 06bbd4bc68ab6f7f0257693b0d7386fb5382fa85..c5cb2b7f3dc6aea0552a6f8f36399254e3c5f83d 100644
--- a/AMDiS/src/SecondOrderAssembler.cc
+++ b/AMDiS/src/SecondOrderAssembler.cc
@@ -45,7 +45,7 @@ namespace AMDiS {
sort(opTerms.begin(), opTerms.end());
// check if a new assembler is needed
- for (int i = 0; i < static_cast<int>(subAssemblers->size()); i++) {
+ for (unsigned int i = 0; i < subAssemblers->size(); i++) {
std::vector<OperatorTerm*> assTerms = *((*subAssemblers)[i]->getTerms());
sort(assTerms.begin(), assTerms.end());
@@ -56,7 +56,7 @@ namespace AMDiS {
// check if all terms are pw_const
bool pwConst = true;
- for (int i = 0; i < static_cast<int>(op->secondOrder[myRank].size()); i++) {
+ for (unsigned int i = 0; i < op->secondOrder[myRank].size(); i++) {
if (!op->secondOrder[myRank][i]->isPWConst()) {
pwConst = false;
break;
@@ -97,7 +97,7 @@ namespace AMDiS {
Pre2::~Pre2()
{
- for (int i = 0; i < static_cast<int>(tmpLALt.size()); i++) {
+ for (unsigned int i = 0; i < tmpLALt.size(); i++) {
delete *(tmpLALt[i]);
delete tmpLALt[i];
}
@@ -115,9 +115,8 @@ namespace AMDiS {
DimMat<double> &tmpMat = *LALt[0];
tmpMat.set(0.0);
- for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++) {
- (static_cast<SecondOrderTerm*>(terms[myRank][i]))->getLALt(elInfo, 1, LALt);
- }
+ for (unsigned int i = 0; i < terms[myRank].size(); i++)
+ (static_cast<SecondOrderTerm*>(terms[myRank][i]))->getLALt(elInfo, 1, LALt);
tmpMat *= elInfo->getDet();
nEntries = q11->getNumberEntries();
@@ -178,7 +177,7 @@ namespace AMDiS {
{
if (!firstCall) {
int nPoints = quadrature->getNumPoints();
- for (int i = 0; i < static_cast<int>(tmpLALt.size()); i++) {
+ for (unsigned int i = 0; i < tmpLALt.size(); i++) {
for (int j = 0; j < nPoints; j++)
delete tmpLALt[i][j];
@@ -217,7 +216,7 @@ namespace AMDiS {
for (int i = 0; i < nPoints; i++)
LALt[i]->set(0.0);
- for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++)
+ for (unsigned int i = 0; i < terms[myRank].size(); i++)
(static_cast<SecondOrderTerm*>(terms[myRank][i]))->getLALt(elInfo, nPoints, LALt);
VectorOfFixVecs< DimVec<double> > *grdPsi, *grdPhi;
@@ -283,8 +282,8 @@ namespace AMDiS {
int myRank = omp_get_thread_num();
- for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++)
- (static_cast<SecondOrderTerm*>(terms[myRank][i]))->getLALt(elInfo, nPoints, LALt);
+ for (unsigned int i = 0; i < terms[myRank].size(); i++)
+ (static_cast<SecondOrderTerm*>(terms[myRank][i]))->getLALt(elInfo, nPoints, LALt);
if (symmetric) {
TEST_EXIT_DBG(nCol == nRow)("nCol != nRow, but symmetric assembling!\n");
@@ -328,7 +327,7 @@ namespace AMDiS {
for (int iq = 0; iq < nPoints; iq++)
delete LALt[iq];
-
+
delete [] LALt;
}