diff --git a/AMDiS/libtool b/AMDiS/libtool
index 008d56e2e6760e09a655addf980524aebb6a42ec..e3aa9300b4361aec8bf174c4b54114d19e1afe7c 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -51,32 +51,32 @@ build_old_libs=yes
pic_mode=default
# Whether or not to optimize for fast installation.
-fast_install=yes
+fast_install=needless
# The host system.
host_alias=
-host=i686-redhat-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-redhat-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# 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="$SED -e 1s/^X//"
# A grep program that handles long lines.
-GREP="/bin/grep"
+GREP="/usr/bin/grep"
# An ERE matcher.
-EGREP="/bin/grep -E"
+EGREP="/usr/bin/grep -E"
# A literal string matcher.
-FGREP="/bin/grep -F"
+FGREP="/usr/bin/grep -F"
# A BSD- or MS-compatible name lister.
NM="/usr/bin/nm -B"
@@ -85,7 +85,7 @@ NM="/usr/bin/nm -B"
LN_S="ln -s"
# What is the maximum length of a command?
-max_cmd_len=98304
+max_cmd_len=1572864
# Object file suffix (normally "o").
objext=o
@@ -204,7 +204,7 @@ runpath_var=LD_RUN_PATH
shlibpath_var=LD_LIBRARY_PATH
# Is shlibpath searched before the hard-coded library search path?
-shlibpath_overrides_runpath=no
+shlibpath_overrides_runpath=yes
# Format of library name prefix.
libname_spec="lib\$name"
@@ -233,10 +233,10 @@ finish_eval=""
hardcode_into_libs=yes
# Compile-time system search path for libraries.
-sys_lib_search_path_spec="/usr/lib/openmpi/1.4-gcc/lib /usr/lib /usr/lib/gcc/i386-redhat-linux/4.1.2 /lib"
+sys_lib_search_path_spec="/usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64 /lib64 /usr/x86_64-suse-linux/lib"
# Run-time system search path for libraries.
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/mysql /usr/lib/octave-3.0.1 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/lib64/Xaw3d /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/lib/Xaw3d /usr/x86_64-suse-linux/lib /usr/local/lib /opt/kde3/lib /lib64 /lib /usr/lib64 /usr/lib /usr/local/lib64 /opt/kde3/lib64 /usr/lib64/graphviz /usr/lib64/graphviz/sharp /usr/lib64/graphviz/java /usr/lib64/graphviz/perl /usr/lib64/graphviz/php /usr/lib64/graphviz/ocaml /usr/lib64/graphviz/python /usr/lib64/graphviz/lua /usr/lib64/graphviz/tcl /usr/lib64/graphviz/guile /usr/lib64/graphviz/ruby /usr/lib64/octave-3.2.4 "
# Whether dlopen is supported.
dlopen_support=unknown
@@ -253,7 +253,7 @@ striplib="strip --strip-unneeded"
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Commands used to build an old-style archive.
old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
@@ -8908,7 +8908,7 @@ build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
# ### BEGIN LIBTOOL TAG CONFIG: CXX
# The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Commands used to build an old-style archive.
old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
@@ -9039,17 +9039,17 @@ file_list_spec=""
hardcode_action=immediate
# The directories searched by this compiler when creating a shared library.
-compiler_lib_search_dirs=". /usr/lib/openmpi/1.4-gcc/lib /usr/lib/openmpi/1.4-gcc/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/../../.."
+compiler_lib_search_dirs="/usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib /usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
# Dependencies to place before and after the objects being linked to
# create a shared library.
-predep_objects="/usr/lib/crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/crtn.o"
+predep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.5/crtbeginS.o"
+postdep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crtn.o"
predeps=""
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. -L/usr/lib/openmpi/1.4-gcc/lib -L/usr/lib/openmpi/1.4-gcc/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/../../.."
+compiler_lib_search_path="-L/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
# ### END LIBTOOL TAG CONFIG: CXX
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index bff5e1f2aca3026e72bcf0a140a24860aa920539..ba79755b210f29ba981465c8fc1441801197e651 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -12,31 +12,6 @@ namespace AMDiS {
std::map<DegreeOfFreedom*, bool> Element::deletedDOFs;
- int Element::getRegion() const
- {
- if (!elementData)
- return -1;
-
- ElementRegion_ED* red =
- dynamic_cast<ElementRegion_ED*>(elementData->getElementData(ELEMENT_REGION));
-
- if (red)
- return red->getRegion();
-
- return -1;
- }
-
-
- void Element::setDOFPtrs()
- {
- FUNCNAME("Element::setDOFPtrs()");
-
- TEST_EXIT_DBG(mesh)("no mesh!\n");
-
- dof = mesh->createDOFPtrs();
- }
-
-
Element::Element(Mesh *aMesh)
{
mesh = aMesh;
@@ -48,7 +23,7 @@ namespace AMDiS {
mark = 0;
if (mesh) {
- setDOFPtrs();
+ setDofPtrs();
} else {
mesh = NULL;
}
@@ -74,6 +49,31 @@ namespace AMDiS {
}
+ int Element::getRegion() const
+ {
+ if (!elementData)
+ return -1;
+
+ ElementRegion_ED* red =
+ dynamic_cast<ElementRegion_ED*>(elementData->getElementData(ELEMENT_REGION));
+
+ if (red)
+ return red->getRegion();
+
+ return -1;
+ }
+
+
+ void Element::setDofPtrs()
+ {
+ FUNCNAME("Element::setDofPtrs()");
+
+ TEST_EXIT_DBG(mesh)("no mesh!\n");
+
+ dof = mesh->createDofPtrs();
+ }
+
+
bool Element::deleteElementData(int typeID)
{
FUNCNAME("Element::deleteElementData()");
diff --git a/AMDiS/src/Element.h b/AMDiS/src/Element.h
index 9a733d1651b708e48c820da1d766f0cfa2da2557..e5d226afeb2cf32165d00994dfbd0779b015b925 100644
--- a/AMDiS/src/Element.h
+++ b/AMDiS/src/Element.h
@@ -513,7 +513,7 @@ namespace AMDiS {
protected:
/// Sets Element's \ref dof pointer. Used by friend class Mesh.
- void setDOFPtrs();
+ void setDofPtrs();
/// Sets Element's \ref index. Used by friend class Mesh.
inline void setIndex(int i)
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index cedead16e986d62417f2c97dd9a27f0dc4a30a31..dd691e3d5b9281ff955d9ec7c1f2c2ce59a57a99 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -500,9 +500,9 @@ namespace AMDiS {
}
- DegreeOfFreedom **Mesh::createDOFPtrs()
+ DegreeOfFreedom **Mesh::createDofPtrs()
{
- FUNCNAME("Mesh::createDOFPtrs()");
+ FUNCNAME("Mesh::createDofPtrs()");
if (nNodeEl <= 0)
return NULL;
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 1afe8995b8f58022b1e3aa5b813bfdb30b439cb2..eb265b9c2cf7d63542f7199ed36c0dca1f69867d 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -220,7 +220,7 @@ namespace AMDiS {
const DOFAdmin* getVertexAdmin() const;
/// Allocates a array of DOF pointers. The array holds one pointer for each node.
- DegreeOfFreedom **createDOFPtrs();
+ DegreeOfFreedom **createDofPtrs();
/// Returns \ref preserveCoarseDOFs of the mesh
inline bool queryCoarseDOFs() const
@@ -406,7 +406,7 @@ namespace AMDiS {
void removeMacroElements(std::set<MacroElement*>& macros,
const FiniteElemSpace* feSpace);
- /// Frees the array of DOF pointers (see \ref createDOFPtrs)
+ /// Frees the array of DOF pointers (see \ref createDofPtrs)
void freeDOFPtrs(DegreeOfFreedom **ptrs);
/// Used by \ref findElementAtPoint.
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index ac15d66350ee65285356597a330804d582fb3721..d8b2219cf826b73cb43876750b467e79ad883d6f 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -138,6 +138,7 @@ namespace AMDiS {
// === create marker ===
if (initFlag.isSet(INIT_MARKER))
createMarker();
+
if (adoptProblem && adoptFlag.isSet(INIT_MARKER))
marker = adoptProblem->getMarkers();
@@ -197,8 +198,8 @@ namespace AMDiS {
&globalRefinements);
#endif
- bool initMesh = initFlag.isSet(INIT_MESH) ||
- (adoptProblem && adoptFlag.isSet(INIT_MESH));
+ bool initMesh = initFlag.isSet(INIT_MESH);
+ // || (adoptProblem && adoptFlag.isSet(INIT_MESH));
// Initialize the meshes if there is no serialization file.
diff --git a/AMDiS/src/VtkWriter.cc b/AMDiS/src/VtkWriter.cc
index 45a033ed35b5668d40ff48bf51a122d89f651067..d4eab046d0b0ab58198fd13c556898708f953126 100644
--- a/AMDiS/src/VtkWriter.cc
+++ b/AMDiS/src/VtkWriter.cc
@@ -68,8 +68,6 @@ namespace AMDiS {
swapfile.close();
}
file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc));
-// std::ofstream file;
-// file.open(name.c_str());
file << "<?xml version=\"1.0\"?>\n";
file << "<VTKFile type=\"PUnstructuredGrid\">\n";
@@ -102,8 +100,6 @@ namespace AMDiS {
file << " </PUnstructuredGrid>\n";
file << "</VTKFile>\n";
-
-// file.close();
}
@@ -121,8 +117,6 @@ namespace AMDiS {
swapfile.close();
}
file.push(boost::iostreams::file_descriptor_sink(animationFilename, std::ios::trunc));
-// std::ofstream file;
-// file.open(animationFilename.c_str());
file << "<?xml version=\"1.0\"?>\n";
file << "<VTKFile type=\"Collection\" version=\"0.1\" >" << "\n";
@@ -140,8 +134,6 @@ namespace AMDiS {
file << "</Collection>\n";
file << "</VTKFile>\n";
-// file.close();
-
return 0;
}