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Commit c8b7c594 authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on parallelization for higher order elements.

parent 710471a0
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Showing with 309 additions and 136 deletions
AMDiS/libtool
View file @ c8b7c594
......@@ -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 p2q024:
# 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;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
# Libtool was configured on host NWRW15:
# Libtool was configured on host p2q024:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -6785,12 +6785,12 @@ fast_install=yes
# The host system.
host_alias=
host=i686-pc-linux-gnu
host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
build=i686-pc-linux-gnu
build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
......@@ -6801,25 +6801,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
CC="g++"
CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
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 $srcfile for the compiler.
fix_srcfile_path=""
......@@ -7071,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
# Libtool was configured on host NWRW15:
# Libtool was configured on host p2q024:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -7093,12 +7093,12 @@ fast_install=yes
# The host system.
host_alias=
host=i686-pc-linux-gnu
host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
build=i686-pc-linux-gnu
build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
......@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
......@@ -7118,16 +7118,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
with_gcc=yes
with_gcc=
gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
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/BasisFunction.h
View file @ c8b7c594
......@@ -133,7 +133,7 @@ namespace AMDiS {
* all routines using this function on the elements need the FILL_BOUND
* flag during mesh traversal;
*/
virtual void getBound(const ElInfo*, BoundaryType *) const {};
virtual void getBound(const ElInfo*, BoundaryType *) const {}
/// Returns \ref degree of BasisFunction
inline const int getDegree() const
......@@ -197,11 +197,11 @@ namespace AMDiS {
double *coeff) = 0;
/// WorldVector<double> valued interpol function.
virtual const WorldVector<double>*
interpol(const ElInfo *el_info, int no,
const int *b_no,
AbstractFunction<WorldVector<double>,WorldVector<double> > *f,
WorldVector<double> *vec) = 0;
virtual const WorldVector<double>* interpol(const ElInfo *el_info, int no,
const int *b_no,
AbstractFunction<WorldVector<double>,
WorldVector<double> > *f,
WorldVector<double> *vec) = 0;
/// Returns the i-th local basis function
inline BasFctType *getPhi(int i) const
......@@ -305,7 +305,8 @@ namespace AMDiS {
* will be overwritten after the next call.
*/
const WorldVector<double>& evalUh(const DimVec<double>& lambda,
const WorldVector<double>* uh, WorldVector<double>* val) const;
const WorldVector<double>* uh,
WorldVector<double>* val) const;
/** \brief
* Evaluates the gradient at barycentric coordinates lambda. Lambda is the
......
AMDiS/src/ElInfo.cc
View file @ c8b7c594
......@@ -47,6 +47,8 @@ namespace AMDiS {
WorldVector<double>& w) const
{
testFlag(Mesh::FILL_COORDS);
double c = l[0];
for (int j = 0; j < dimOfWorld; j++)
......
AMDiS/src/ElementDofIterator.cc
View file @ c8b7c594
......@@ -47,6 +47,10 @@ namespace AMDiS {
// We are finished with all element.
elementPos = 0;
// If we have iterated over all positions, we can finish the iteration.
if (pos >= dim)
return false;
// Increase position, i.e., go from vertices to edges to faces and search
// for the next position with dofs.
do {
......@@ -55,16 +59,18 @@ namespace AMDiS {
posIndex = INDEX_OF_DIM(pos, dim);
// Get number of dofs in this position.
nDofs = admin->getNumberOfDOFs(posIndex);
} while (nDofs == 0 && pos <= dim);
} while (nDofs == 0 && pos < dim);
if (pos <= dim) {
if (nDofs > 0 && pos <= dim) {
// We have found on more position with dofs.
// Get number of elements in this position, i.e, the number of vertices,.
// edges and faces in the given dimension.
nElements = Global::getGeo(posIndex, dim);
// Calculate displacement. Is used if there is more than one dof admin on the mesh.
n0 = admin->getNumberOfPreDOFs(posIndex);
// Get first dof index position for the geo index position.
node0 = mesh->getNode(posIndex);
} else {
......
AMDiS/src/MacroReader.cc
View file @ c8b7c594
......@@ -292,10 +292,9 @@ namespace AMDiS {
macroInfo->fillBoundaryInfo(mesh);
if (mesh->getNumberOfDOFs(CENTER)) {
for (int i = 0; i < mesh->getNumberOfMacros(); i++) {
for (int i = 0; i < mesh->getNumberOfMacros(); i++)
const_cast<Element*>(mel[i]->getElement())->
setDOF(mesh->getNode(CENTER), mesh->getDOF(CENTER));
}
}
/****************************************************************************/
......@@ -1137,11 +1136,11 @@ namespace AMDiS {
mesh->incrementNumberOfFaces(1);
if (mesh->getNumberOfDOFs(FACE)) {
TEST_EXIT(!(*(mel+i))->getElement()->getDOF(lnode+k))
TEST_EXIT(!(*(mel+i))->getElement()->getDOF(lnode + k))
("dof %d on element %d already set\n",
lnode+k, (*(mel+i))->getIndex());
const_cast<Element*>((*(mel+i))->getElement())->setDOF(lnode+k,
const_cast<Element*>((*(mel+i))->getElement())->setDOF(lnode + k,
mesh->getDOF(FACE));
if (neigh) {
......
AMDiS/src/Mesh.cc
View file @ c8b7c594
......@@ -824,9 +824,8 @@ namespace AMDiS {
c_lambda2[3]);
if ((c_outside2 < 0) || (c_lambda2[c_outside2] > c_lambda[c_outside])) {
for (int i = 0; i <= dim; i++) {
c_lambda[i] = c_lambda2[i];
}
for (int i = 0; i <= dim; i++)
c_lambda[i] = c_lambda2[i];
c_outside = c_outside2;
*c_el_info = *c_el_info2;
ichild = 1 - ichild;
......@@ -862,6 +861,33 @@ namespace AMDiS {
return inside;
}
bool Mesh::getDofIndexCoords(const DegreeOfFreedom* dof,
const FiniteElemSpace* feSpace,
WorldVector<double>& coords)
{
DimVec<double>* baryCoords;
bool found = false;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(this, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
while (elInfo) {
for (int i = 0; i < nDOFEl; i++) {
if (elInfo->getElement()->getDOF(i) == dof) {
baryCoords = feSpace->getBasisFcts()->getCoords(i);
elInfo->coordToWorld(*baryCoords, coords);
found = true;
break;
}
}
if (found)
break;
elInfo = stack.traverseNext(elInfo);
}
return found;
}
void Mesh::setDiameter(const WorldVector<double>& w)
{
......
AMDiS/src/Mesh.h
View file @ c8b7c594
......@@ -484,6 +484,23 @@ namespace AMDiS {
const WorldVector<double> *xy0,
double *sp);
/** \brief
* Returns for a given dof its world coordinates in this mesh. Because we do
* not have any direct connection between dofs and coordinates, this function
* has to search for the element in this mesh, that contains the dof. Than the
* coordinates can be computed. Therefore, this function is very costly and
* should be used for debugging purpose only.
*
* @param[in] dof A pointer to the dof we have to search for.
* @param[in] feSpace The fe space to be used for the search.
* @param[out] coords World vector that stores the coordinates of the dof.
*
* The function returns true, if the dof was found, otherwise false.
*/
bool getDofIndexCoords(const DegreeOfFreedom* dof,
const FiniteElemSpace* feSpace,
WorldVector<double>& coords);
/// Returns FILL_ANY_?D
inline static const Flag& getFillAnyFlag(int dim)
......
AMDiS/src/ParallelDomainProblem.cc
View file @ c8b7c594
......@@ -11,16 +11,25 @@
#include "DOFMatrix.h"
#include "DOFVector.h"
#include "VtkWriter.h"
#include "ElementDofIterator.h"
#include "petscksp.h"
namespace AMDiS {
ParallelDomainProblemBase::ParallelDomainProblemBase(const std::string& name,
ProblemIterationInterface *iIF,
ProblemTimeInterface *tIF,
FiniteElemSpace *fe,
RefinementManager *refineManager)
PetscErrorCode myKSPMonitor(KSP ksp, PetscInt iter, PetscReal rnorm, void *)
{
if (iter % 100 == 0 && MPI::COMM_WORLD.Get_rank() == 0)
std::cout << " Iteration " << iter << ": " << rnorm << "\n";
return 0;
}
ParallelDomainBase::ParallelDomainBase(const std::string& name,
ProblemIterationInterface *iIF,
ProblemTimeInterface *tIF,
FiniteElemSpace *fe,
RefinementManager *refineManager)
: iterationIF(iIF),
timeIF(tIF),
feSpace(fe),
......@@ -35,11 +44,16 @@ namespace AMDiS {
partitioner = new ParMetisPartitioner(mesh, &mpiComm);
}
void ParallelDomainProblemBase::initParallelization(AdaptInfo *adaptInfo)
void ParallelDomainBase::initParallelization(AdaptInfo *adaptInfo)
{
if (mpiSize <= 1)
return;
// Test, if the mesh is the macro mesh only! Paritioning of the mesh is supported
// only for macro meshes, so it will not work yet if the mesh is already refined
// in some way.
testForMacroMesh();
// create an initial partitioning of the mesh
partitioner->createPartitionData();
// set the element weights, which are 1 at the very first begin
......@@ -86,6 +100,8 @@ namespace AMDiS {
admin.setFirstHole(mapLocalGlobalDOFs.size());
}
exit(0);
// === Global refinements. ===
int globalRefinement = 0;
......@@ -98,9 +114,9 @@ namespace AMDiS {
}
#if (DEBUG != 0)
testInteriorBoundary();
#endif
// #if (DEBUG != 0)
// testInteriorBoundary();
// #endif
// === Create petsc matrix. ===
......@@ -118,12 +134,36 @@ namespace AMDiS {
ierr = VecSetType(petscSolVec, VECMPI);
}
void ParallelDomainProblemBase::exitParallelization(AdaptInfo *adaptInfo)
{}
void ParallelDomainBase::exitParallelization(AdaptInfo *adaptInfo)
{
}
void ParallelDomainProblemBase::fillPetscMatrix(DOFMatrix *mat,
DOFVector<double> *vec)
void ParallelDomainBase::testForMacroMesh()
{
FUNCNAME("ParallelDomainBase::testForMacroMesh()");
int nMacroElements = 0;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
TEST_EXIT(elInfo->getLevel() == 0)
("Mesh is already refined! This does nor work with parallelization!\n");
nMacroElements++;
elInfo = stack.traverseNext(elInfo);
}
TEST_EXIT(nMacroElements >= mpiSize)
("The mesh has less macro elements than number of mpi processes!\n");
}
void ParallelDomainBase::fillPetscMatrix(DOFMatrix *mat,
DOFVector<double> *vec)
{
using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits= mtl::traits;
......@@ -136,8 +176,10 @@ namespace AMDiS {
typedef traits::range_generator<major, Matrix>::type cursor_type;
typedef traits::range_generator<nz, cursor_type>::type icursor_type;
for (cursor_type cursor = begin<major>(mat->getBaseMatrix()), cend = end<major>(mat->getBaseMatrix()); cursor != cend; ++cursor)
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
for (cursor_type cursor = begin<major>(mat->getBaseMatrix()),
cend = end<major>(mat->getBaseMatrix()); cursor != cend; ++cursor)
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor)
if (value(*icursor) != 0.0) {
int r = mapLocalGlobalDOFs[row(*icursor)];
int c = mapLocalGlobalDOFs[col(*icursor)];
......@@ -161,10 +203,8 @@ namespace AMDiS {
}
void ParallelDomainProblemBase::solvePetscMatrix(DOFVector<double> *vec)
void ParallelDomainBase::solvePetscMatrix(DOFVector<double> *vec)
{
clock_t t = clock();
KSP ksp;
PC pc;
......@@ -174,7 +214,7 @@ namespace AMDiS {
PCSetType(pc, PCJACOBI);
KSPSetTolerances(ksp, 1.e-7, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(ksp, KSPBCGS);
KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, 0);
KSPMonitorSet(ksp, myKSPMonitor, PETSC_NULL, 0);
KSPSolve(ksp, petscRhsVec, petscSolVec);
PetscScalar *vecPointer;
......@@ -237,12 +277,10 @@ namespace AMDiS {
for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
delete [] sendBuffers[i];
std::cout << "SOLUTION = " << TIME_USED(t,clock()) << std::endl;
}
double ParallelDomainProblemBase::setElemWeights(AdaptInfo *adaptInfo)
double ParallelDomainBase::setElemWeights(AdaptInfo *adaptInfo)
{
double localWeightSum = 0.0;
int elNum = -1;
......@@ -277,7 +315,7 @@ namespace AMDiS {
}
void ParallelDomainProblemBase::partitionMesh(AdaptInfo *adaptInfo)
void ParallelDomainBase::partitionMesh(AdaptInfo *adaptInfo)
{
if (initialPartitionMesh) {
initialPartitionMesh = false;
......@@ -292,15 +330,16 @@ namespace AMDiS {
}
void ParallelDomainProblemBase::createInteriorBoundaryInfo(std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs)
void ParallelDomainBase::createInteriorBoundaryInfo(std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs)
{
FUNCNAME("ParallelDomainProblemBase::createInteriorBoundaryInfo()");
FUNCNAME("ParallelDomainBase::createInteriorBoundaryInfo()");
// === First, create all the information about the interior boundaries. ===
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
while (elInfo) {
Element *element = elInfo->getElement();
......@@ -313,11 +352,12 @@ namespace AMDiS {
PartitionElementData *neighbourPartitionData =
dynamic_cast<PartitionElementData*>(elInfo->getNeighbour(i)->getElementData(PARTITION_ED));
if (neighbourPartitionData->getPartitionStatus() == OUT) {
// We have found an element that is at an interior boundary.
// === Find out, if the boundary part of the element corresponds to the
// rank or to the rank "on the other side" of the interoir boundary. ===
// === Find out, if the boundary part of the element corresponds to the ===
// === rank or to the rank "on the other side" of the interoir boundary. ===
const DegreeOfFreedom* boundDOF1 = NULL;
const DegreeOfFreedom