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Commit fb74c0af authored by Thomas Witkowski's avatar Thomas Witkowski
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* On the way to parallel amdis

parent a9897bbf
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Showing with 83 additions and 74 deletions
AMDiS/libtool
View file @ fb74c0af
......@@ -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 p2s154:
# 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.
......@@ -82,25 +82,25 @@ 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
gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# 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"
......@@ -174,7 +174,7 @@ 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"
......@@ -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 " /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"`
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"`
# 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="/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 "
# 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;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
# Libtool was configured on host NWRW15:
# Libtool was configured on host p2s154:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -6785,12 +6785,12 @@ fast_install=yes
# The host system.
host_alias=
host=i686-pc-linux-gnu
host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
build=i686-pc-linux-gnu
build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
......@@ -6801,25 +6801,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
CC="g++"
CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# 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"
......@@ -6893,7 +6893,7 @@ 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"
......@@ -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/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"`
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"`
# Dependencies to place after the objects being linked to create a
# shared library.
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"`
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"`
# 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="-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=`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"`
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"`
# 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 " /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"`
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"`
# 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="/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 "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
......@@ -7071,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
# Libtool was configured on host NWRW15:
# Libtool was configured on host p2s154:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -7093,12 +7093,12 @@ fast_install=yes
# The host system.
host_alias=
host=i686-pc-linux-gnu
host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
build=i686-pc-linux-gnu
build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
......@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
......@@ -7118,16 +7118,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
with_gcc=yes
with_gcc=
gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# 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"
......@@ -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 " /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"`
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"`
# 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="/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 "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
......
AMDiS/src/DOFAdmin.h
View file @ fb74c0af
......@@ -28,10 +28,6 @@
#ifndef AMDIS_DOFADMIN_H
#define AMDIS_DOFADMIN_H
// ============================================================================
// ===== includes =============================================================
// ============================================================================
#include "Global.h"
#include "FixVec.h"
#include "MemoryManager.h"
......@@ -43,10 +39,6 @@
namespace AMDiS {
// ============================================================================
// ===== forward declarations =================================================
// ============================================================================
class Mesh;
class FiniteElemSpace;
class ElInfo;
......@@ -57,10 +49,6 @@ namespace AMDiS {
template<typename T> class DOFVector;
// ============================================================================
// ===== class DOFAdmin =======================================================
// ============================================================================
/** \ingroup DOFAdministration
* \brief
* Holds all data about one set of DOFs. It includes information about used and
......@@ -161,8 +149,6 @@ namespace AMDiS {
return dofIndexedList.end();
}
// ===== getting methods ======================================================
/** \name getting methods
* \{
*/
......@@ -254,8 +240,6 @@ namespace AMDiS {
/** \} */
// ===== setting methods ======================================================
/** \name setting methods
* \{
*/
......@@ -305,10 +289,10 @@ namespace AMDiS {
*/
void freeDOFIndex(int dof);
// ===== Serializable implementation =====
///
void serialize(std::ostream &out);
///
void deserialize(std::istream &in);
protected:
......
AMDiS/src/Mesh.cc
View file @ fb74c0af
......@@ -354,6 +354,27 @@ namespace AMDiS {
nVertices = nRemainDofs;
}
void Mesh::createContinuousDofOrdering(FiniteElemSpace *feSpace, unsigned int addC)
{
FUNCNAME("Mesh::createContinuousDofOrdering()");
const BasisFunction* basisFcts = feSpace->getBasisFcts();
TEST_EXIT(dim == 2)("Not yet implemented!\n");
TEST_EXIT(basisFcts->getNumber() == 3)("Not yet implemented!\n");
std::set<DegreeOfFreedom*> dofs;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
for (int i = 0; i < 3; i++) {
dofs.insert(const_cast<DegreeOfFreedom*>(elInfo->getElement()->getDOF(i)));
}
elInfo = stack.traverseNext(elInfo);
}
}
int Mesh::traverse(int level, Flag flag, int (*el_fct)(ElInfo*))
{
FUNCNAME("Mesh::traverse()");
......
AMDiS/src/Mesh.h
View file @ fb74c0af
......@@ -33,10 +33,6 @@
#ifndef AMDIS_MESH_H
#define AMDIS_MESH_H
// ============================================================================
// ===== includes =============================================================
// ============================================================================
#include "DOFAdmin.h"
#include "Line.h"
#include "Triangle.h"
......@@ -53,10 +49,6 @@
namespace AMDiS {
// ============================================================================
// ===== forward declarations =================================================
// ============================================================================
template <typename T> class DimVec;
template <typename T> class VectorOfFixVecs;
class Boundary;
......@@ -73,10 +65,6 @@ namespace AMDiS {
class DOFVectorDOF;
class VertexVector;
// ============================================================================
// ===== class Mesh ===========================================================
// ============================================================================
/** \ingroup Triangulation
* \brief
* A Mesh holds all information about a triangulation.
......@@ -109,8 +97,6 @@ namespace AMDiS {
static int newDOFFct2(ElInfo* e);
/** \} */
// ==========================================================================
/** \name getting methods
* \{
*/
......@@ -267,7 +253,6 @@ namespace AMDiS {
/** \} */
// ==========================================================================
/** \name setting methods
* \{
*/
......@@ -421,6 +406,13 @@ namespace AMDiS {
*/
void removeMacroElements(std::vector<MacroElement*>& macros);
/* \brief
* Creates new numbers for all dofs such that the set of dof numbers is a
* continuous interval of natural numbers starting with 0. The constatnt addC
* may be added to the numbers.
*/
void createContinuousDofOrdering(FiniteElemSpace *feSpace, unsigned int addC = 0);
/// Frees the array of DOF pointers (see \ref createDOFPtrs)
void freeDOFPtrs(DegreeOfFreedom **ptrs);
......
AMDiS/src/ParallelDomainProblem.cc
View file @ fb74c0af
......@@ -14,10 +14,11 @@ namespace AMDiS {
ParallelDomainProblemBase::ParallelDomainProblemBase(const std::string& name,
ProblemIterationInterface *iIF,
ProblemTimeInterface *tIF,
Mesh *m)
FiniteElemSpace *fe)
: iterationIF(iIF),
timeIF(tIF),
mesh(m),
feSpace(fe),
mesh(fe->getMesh()),
initialPartitionMesh(true),
nRankDOFs(0)
{
......@@ -96,6 +97,8 @@ namespace AMDiS {
}
}
// === Remove all macro elements that are not part of the rank partition. ===
std::vector<MacroElement*> macrosToRemove;
for (std::deque<MacroElement*>::iterator it = mesh->firstMacroElement();
it != mesh->endOfMacroElements();
......@@ -110,6 +113,8 @@ namespace AMDiS {
mesh->removeMacroElements(macrosToRemove);
// === Create local and global dofs ordering. ===
int *gOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));
int *lOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));
......@@ -120,11 +125,14 @@ namespace AMDiS {
int rstart = 0;
MPI_Scan(&nRankDOFs, &rstart, 1, MPI_INT, MPI_SUM, PETSC_COMM_WORLD);
rstart -= nRankDOFs;
for (int i = 0; i < nRankDOFs; i++) {
lOrder[i] = rstart - nRankDOFs + i;
lOrder[i] = rstart + i;
}
mesh->createContinuousDofOrdering(feSpace, rstart);
AOCreateBasic(PETSC_COMM_WORLD, nRankDOFs, gOrder, lOrder, &applicationOrdering);
free(gOrder);
......@@ -187,7 +195,7 @@ namespace AMDiS {
ParallelDomainProblemScal::ParallelDomainProblemScal(const std::string& name,
ProblemScal *problem,
ProblemInstatScal *problemInstat)
: ParallelDomainProblemBase(name, problem, problemInstat, problem->getMesh())
: ParallelDomainProblemBase(name, problem, problemInstat, problem->getFESpace())
{
}
......
AMDiS/src/ParallelDomainProblem.h
View file @ fb74c0af
......@@ -27,6 +27,7 @@
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
#include "FiniteElemSpace.h"
#include "AdaptInfo.h"
#include "petscao.h"
#include "mpi.h"
......@@ -45,7 +46,7 @@ namespace AMDiS {
ParallelDomainProblemBase(const std::string& name,
ProblemIterationInterface *iterationIF,
ProblemTimeInterface *timeIF,
Mesh *mesh);
FiniteElemSpace *feSpace);
virtual ~ParallelDomainProblemBase() {}
......@@ -123,6 +124,9 @@ namespace AMDiS {
/// Name of the problem (as used in the init files)
std::string name;
/// Finite element space of the problem.
FiniteElemSpace *feSpace;
/// Mesh of the problem.
Mesh *mesh;
......
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