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Commit 5781e1c6 authored by Thomas Witkowski's avatar Thomas Witkowski
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Added --with-petsc parameter to automake system.

parent d288b938
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Showing with 102 additions and 252 deletions
AMDiS/Makefile.in
View file @ 5781e1c6
......@@ -138,6 +138,7 @@ PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PETSC_DIR = @PETSC_DIR@
RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
......
AMDiS/bin/Makefile.am
View file @ 5781e1c6
......@@ -33,8 +33,7 @@ if USE_PARALLEL_DOMAIN_AMDIS
$(PARALLEL_DIR)/ParallelDomainScal.h $(PARALLEL_DIR)/ParallelDomainScal.cc \
$(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
# AMDIS_INCLUDES += -I/work/home7/witkowsk/local/include
AMDIS_INCLUDES += -I/u/witkowski/local/petsc-3.0.0-p4/include -I/u/witkowski/local/petsc-3.0.0-p4/linux-gnu-c-debug/include
AMDIS_INCLUDES += -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
endif
if ENABLE_UMFPACK
......
AMDiS/bin/Makefile.in
View file @ 5781e1c6
......@@ -43,8 +43,7 @@ host_triplet = @host@
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
# AMDIS_INCLUDES += -I/work/home7/witkowsk/local/include
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I/u/witkowski/local/petsc-3.0.0-p4/include -I/u/witkowski/local/petsc-3.0.0-p4/linux-gnu-c-debug/include
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
@ENABLE_UMFPACK_TRUE@am__append_5 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
@ENABLE_UMFPACK_TRUE@am__append_6 = -I$(LIB_DIR)/UFconfig \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/AMD/Include \
......@@ -395,6 +394,7 @@ PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PETSC_DIR = @PETSC_DIR@
RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
......
AMDiS/configure
View file @ 5781e1c6
......@@ -462,7 +462,7 @@ ac_includes_default="\
# include <unistd.h>
#endif"
 
ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE USE_PARALLEL_DOMAIN_AMDIS_TRUE USE_PARALLEL_DOMAIN_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os SED EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR PETSC_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE USE_PARALLEL_DOMAIN_AMDIS_TRUE USE_PARALLEL_DOMAIN_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os SED EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
ac_subst_files=''
 
# Initialize some variables set by options.
......@@ -1046,6 +1046,7 @@ Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
--with-mpi=MPI_DIR
--with-petsc=PETSC_DIR
--with-dune=DUNE_DIR
--with-gnu-ld assume the C compiler uses GNU ld [default=no]
--with-pic try to use only PIC/non-PIC objects [default=use
......@@ -2078,6 +2079,17 @@ if test $mpidir != no ; then
 
fi
 
# Check whether --with-petsc or --without-petsc was given.
if test "${with_petsc+set}" = set; then
withval="$with_petsc"
petscdir=$withval
else
petscdir=no
fi;
PETSC_DIR=$petscdir
# Check whether --enable-parmetis or --disable-parmetis was given.
if test "${enable_parmetis+set}" = set; then
enableval="$enable_parmetis"
......@@ -4410,7 +4422,7 @@ ia64-*-hpux*)
;;
*-*-irix6*)
# Find out which ABI we are using.
echo '#line 4413 "configure"' > conftest.$ac_ext
echo '#line 4425 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
......@@ -5545,7 +5557,7 @@ fi
 
 
# Provide some information about the compiler.
echo "$as_me:5548:" \
echo "$as_me:5560:" \
"checking for Fortran 77 compiler version" >&5
ac_compiler=`set X $ac_compile; echo $2`
{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
......@@ -6608,11 +6620,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:6611: $lt_compile\"" >&5)
(eval echo "\"\$as_me:6623: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:6615: \$? = $ac_status" >&5
echo "$as_me:6627: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -6876,11 +6888,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:6879: $lt_compile\"" >&5)
(eval echo "\"\$as_me:6891: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:6883: \$? = $ac_status" >&5
echo "$as_me:6895: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -6980,11 +6992,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:6983: $lt_compile\"" >&5)
(eval echo "\"\$as_me:6995: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
echo "$as_me:6987: \$? = $ac_status" >&5
echo "$as_me:6999: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
......@@ -8449,7 +8461,7 @@ linux*)
libsuff=
case "$host_cpu" in
x86_64*|s390x*|powerpc64*)
echo '#line 8452 "configure"' > conftest.$ac_ext
echo '#line 8464 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
......@@ -9346,7 +9358,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
#line 9349 "configure"
#line 9361 "configure"
#include "confdefs.h"
 
#if HAVE_DLFCN_H
......@@ -9446,7 +9458,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
#line 9449 "configure"
#line 9461 "configure"
#include "confdefs.h"
 
#if HAVE_DLFCN_H
......@@ -11789,11 +11801,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:11792: $lt_compile\"" >&5)
(eval echo "\"\$as_me:11804: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:11796: \$? = $ac_status" >&5
echo "$as_me:11808: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -11893,11 +11905,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:11896: $lt_compile\"" >&5)
(eval echo "\"\$as_me:11908: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
echo "$as_me:11900: \$? = $ac_status" >&5
echo "$as_me:11912: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
......@@ -12429,7 +12441,7 @@ linux*)
libsuff=
case "$host_cpu" in
x86_64*|s390x*|powerpc64*)
echo '#line 12432 "configure"' > conftest.$ac_ext
echo '#line 12444 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
......@@ -13487,11 +13499,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:13490: $lt_compile\"" >&5)
(eval echo "\"\$as_me:13502: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:13494: \$? = $ac_status" >&5
echo "$as_me:13506: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -13591,11 +13603,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:13594: $lt_compile\"" >&5)
(eval echo "\"\$as_me:13606: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
echo "$as_me:13598: \$? = $ac_status" >&5
echo "$as_me:13610: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
......@@ -15040,7 +15052,7 @@ linux*)
libsuff=
case "$host_cpu" in
x86_64*|s390x*|powerpc64*)
echo '#line 15043 "configure"' > conftest.$ac_ext
echo '#line 15055 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
......@@ -15818,11 +15830,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:15821: $lt_compile\"" >&5)
(eval echo "\"\$as_me:15833: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:15825: \$? = $ac_status" >&5
echo "$as_me:15837: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -16086,11 +16098,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:16089: $lt_compile\"" >&5)
(eval echo "\"\$as_me:16101: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
echo "$as_me:16093: \$? = $ac_status" >&5
echo "$as_me:16105: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -16190,11 +16202,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:16193: $lt_compile\"" >&5)
(eval echo "\"\$as_me:16205: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
echo "$as_me:16197: \$? = $ac_status" >&5
echo "$as_me:16209: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
......@@ -17659,7 +17671,7 @@ linux*)
libsuff=
case "$host_cpu" in
x86_64*|s390x*|powerpc64*)
echo '#line 17662 "configure"' > conftest.$ac_ext
echo '#line 17674 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
......@@ -19661,6 +19673,7 @@ s,@AMDIS_OPENMP_TRUE@,$AMDIS_OPENMP_TRUE,;t t
s,@AMDIS_OPENMP_FALSE@,$AMDIS_OPENMP_FALSE,;t t
s,@OPENMP_FLAG@,$OPENMP_FLAG,;t t
s,@MPI_DIR@,$MPI_DIR,;t t
s,@PETSC_DIR@,$PETSC_DIR,;t t
s,@USE_PARALLEL_AMDIS_TRUE@,$USE_PARALLEL_AMDIS_TRUE,;t t
s,@USE_PARALLEL_AMDIS_FALSE@,$USE_PARALLEL_AMDIS_FALSE,;t t
s,@USE_PARALLEL_DOMAIN_AMDIS_TRUE@,$USE_PARALLEL_DOMAIN_AMDIS_TRUE,;t t
......
AMDiS/configure.ac
View file @ 5781e1c6
......@@ -54,6 +54,9 @@ if test $mpidir != no ; then
AC_SUBST(CC, $mpidir/bin/mpicc)
fi
AC_ARG_WITH(petsc, [ --with-petsc=PETSC_DIR], petscdir=$withval, petscdir=no)
AC_SUBST(PETSC_DIR, $petscdir)
AC_ARG_ENABLE(parmetis,
[ --enable-parmetis Compile with the ParMetis library],
[case "${enableval}" in
......
AMDiS/src/DOFMatrix.h
View file @ 5781e1c6
......@@ -256,12 +256,14 @@ namespace AMDiS {
}
/** \brief
* Finishes insertion. For compressed matrix types, this is where the
* compression happens.
* Finishes insertion. For compressed matrix types, this is where the
* compression happens.
*/
void finishInsertion()
{
TEST_EXIT(inserter)("Inserter wasn't used or is already finished.");
FUNCNAME("DOFMatrix::finishInsertion()");
TEST_EXIT(inserter)("Inserter wasn't used or is already finished.\n");
delete inserter;
inserter= 0;
......
AMDiS/src/ParallelDomainBase.cc
View file @ 5781e1c6
......@@ -67,23 +67,6 @@ namespace AMDiS {
if (mpiSize <= 1)
return;
#if 0
if (mpiRank == 0) {
std::map<int, double> vec;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
while (elInfo) {
vec[elInfo->getElement()->getIndex()] = static_cast<double>(elInfo->getElement()->getIndex());
elInfo = stack.traverseNext(elInfo);
}
ElementFileWriter::writeFile(vec, feSpace, "test.vtu");
}
#endif
// 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.
......@@ -130,23 +113,6 @@ namespace AMDiS {
updateDofAdmins();
#if 0
if (mpiRank == 0) {
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
if (elInfo->getElement()->getIndex() == 4) {
WorldVector<double> x;
mesh->getDofIndexCoords(elInfo->getElement()->getDOF(0), feSpace, x);
std::cout << "FOUND!" << std::endl;
x.print();
}
elInfo = stack.traverseNext(elInfo);
}
}
#endif
// === Global refinements. ===
......@@ -317,7 +283,7 @@ namespace AMDiS {
clock_t first = clock();
using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits= mtl::traits;
typedef DOFMatrix::base_matrix_type Matrix;
......@@ -334,32 +300,32 @@ namespace AMDiS {
if ((*mat)[i][j]) {
Matrix bmat = (*mat)[i][j]->getBaseMatrix();
traits::row<Matrix>::type row(bmat);
traits::col<Matrix>::type col(bmat);
traits::const_value<Matrix>::type value(bmat);
typedef traits::range_generator<major, Matrix>::type cursor_type;
typedef traits::range_generator<row, Matrix>::type cursor_type;
typedef traits::range_generator<nz, cursor_type>::type icursor_type;
for (cursor_type cursor = begin<major>(bmat),
cend = end<major>(bmat); cursor != cend; ++cursor) {
for (cursor_type cursor = begin<row>(bmat),
cend = end<row>(bmat); cursor != cend; ++cursor) {
int r = mapLocalGlobalDOFs[*cursor] * nComponents + i;
r -= rstart * nComponents;
if (r >= nRankRows)
continue;
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor)
if (value(*icursor) != 0.0) {
int r = mapLocalGlobalDOFs[row(*icursor)] * nComponents + i;
r -= rstart * nComponents;
int c = mapLocalGlobalDOFs[col(*icursor)] * nComponents + j;
if (r < nRankRows) {
if (c >= rstart * nComponents &&
c < rstart * nComponents + nRankRows)
d_nnz[r]++;
else
o_nnz[r]++;
}
}
if (c >= rstart * nComponents &&
c < rstart * nComponents + nRankRows)
d_nnz[r]++;
else
o_nnz[r]++;
}
}
}
......@@ -389,6 +355,9 @@ namespace AMDiS {
for (int i = 0; i < nComponents; i++)
setDofVector(vec->getDOFVector(i), nComponents, i);
VecAssemblyBegin(petscRhsVec);
VecAssemblyEnd(petscRhsVec);
INFO(info, 8)("Fill petsc matrix needed %.5f seconds\n", TIME_USED(first, clock()));
}
......@@ -401,7 +370,7 @@ namespace AMDiS {
PC pc;
KSPCreate(PETSC_COMM_WORLD, &ksp);
KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
KSPSetOperators(ksp, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
KSPGetPC(ksp, &pc);
//PCSetType(pc, PCJACOBI);
PCSetType(pc, PCILU);
......@@ -471,17 +440,21 @@ namespace AMDiS {
{
FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
KSP ksp;
KSP solver;
PC pc;
KSPCreate(PETSC_COMM_WORLD, &ksp);
KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
KSPGetPC(ksp, &pc);
KSPCreate(PETSC_COMM_WORLD, &solver);
KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
KSPSetTolerances(solver, 1.e-8, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(solver, KSPBCGS);
KSPMonitorSet(solver, myKSPMonitor, PETSC_NULL, 0);
KSPGetPC(solver, &pc);
PCSetType(pc, PCKSP);
KSPSetTolerances(ksp, 1.e-8, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(ksp, KSPBCGS);
KSPMonitorSet(ksp, myKSPMonitor, PETSC_NULL, 0);
KSPSolve(ksp, petscRhsVec, petscSolVec);
KSPSetUp(solver);
KSPSolve(solver, petscRhsVec, petscSolVec);
PetscScalar *vecPointer;
VecGetArray(petscSolVec, &vecPointer);
......@@ -550,6 +523,8 @@ namespace AMDiS {
delete [] sendBuffers[i];
MatDestroy(petscMatrix);
PCDestroy(pc);
KSPDestroy(solver);
}
......@@ -655,24 +630,6 @@ namespace AMDiS {
bool isRankDOF2 = (find(rankDOFs.begin(), rankDOFs.end(), boundDOF2) != rankDOFs.end());
bool ranksBoundary = isRankDOF1 || isRankDOF2;
#if 0
if (mpiRank == 3 && ranksBoundary &&
partitionVec[elInfo->getNeighbour(i)->getIndex()] == 2) {
std::cout << "ADD MY BOUND " << element->getIndex() << "/" << i
<< " with "
<< elInfo->getNeighbour(i)->getIndex() << "/"
<< elInfo->getSideOfNeighbour(i) << std::endl;
}
if (mpiRank == 2 && !ranksBoundary &&
partitionVec[elInfo->getNeighbour(i)->getIndex()] == 3) {
std::cout << "ADD OT BOUND " << element->getIndex() << "/" << i
<< " with "
<< elInfo->getNeighbour(i)->getIndex() << "/"
<< elInfo->getSideOfNeighbour(i) << std::endl;
}
#endif
// === And add the part of the interior boundary. ===
AtomicBoundary& bound =
......@@ -832,15 +789,6 @@ namespace AMDiS {
for (DofContainer::iterator dofIt = rankAllDofs.begin();
dofIt != rankAllDofs.end(); ++dofIt) {
#if 0
if (mpiRank == 0) {
std::cout << "COORDs of dof = " << i << std::endl;
WorldVector<double> x;
mesh->getDofIndexCoords(*dofIt, feSpace, x);
x.print();
}
#endif
rankDofsNewLocalIndex[*dofIt] = i;
// First, we set all dofs in ranks partition to be owend by the rank. Later,
// the dofs in ranks partition that are owned by other rank are set to false.
......@@ -930,11 +878,6 @@ namespace AMDiS {
sendBuffers[i][c++] = *(dofIt->first);
sendBuffers[i][c++] = dofIt->second;
#if 0
if (mpiRank == 3 && sendIt->first == 2)
std::cout << "SEND DOF: " << dofIt->first << std::endl;
#endif
sendDofs[sendIt->first].push_back(dofIt->first);
}
......@@ -997,11 +940,6 @@ namespace AMDiS {
if (*(dofIt->first) == oldDof && !dofChanged[dofIt->first]) {
dofChanged[dofIt->first] = true;
#if 0
if (mpiRank == 2 && recvIt->first == 3)
std::cout << "RECV DOF: " << dofIt->first << std::endl;
#endif
recvDofs[recvIt->first].push_back(dofIt->first);
rankDofsNewGlobalIndex[dofIt->first] = newGlobalDof;
isRankDof[rankDofsNewLocalIndex[dofIt->first]] = false;
......@@ -1065,16 +1003,6 @@ namespace AMDiS {
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
#if 0
if (mpiRank == 3 && it->first == 2)
std::cout << "GO ON MY BOUND: " << boundIt->rankObject.elIndex
<< "/" << boundIt->rankObject.ithObjAtBoundary << " with "
<< boundIt->neighbourObject.elIndex << "/"
<< boundIt->neighbourObject.ithObjAtBoundary
<< std::endl;
#endif
DofContainer dofs;
DofContainer &dofsToSend = sendDofs[it->first];
......@@ -1095,17 +1023,6 @@ namespace AMDiS {
ERROR_EXIT("Should never happen!\n");
}
#if 0
if (mpiRank == 3 && it->first == 2) {
WorldVector<double> x;
mesh->getDofIndexCoords(dofs[0], feSpace, x);
x.print();
mesh->getDofIndexCoords(dofs[1], feSpace, x);
x.print();
}
#endif
for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt)
if (find(dofsToSend.begin(), dofsToSend.end(), *dofIt) == dofsToSend.end())
dofsToSend.push_back(*dofIt);
......@@ -1128,16 +1045,6 @@ namespace AMDiS {
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
#if 0
if (mpiRank == 2 && it->first == 3)
std::cout << "GO ON OT BOUND: " << boundIt->rankObject.elIndex
<< "/" << boundIt->rankObject.ithObjAtBoundary << " with "
<< boundIt->neighbourObject.elIndex << "/"
<< boundIt->neighbourObject.ithObjAtBoundary
<< std::endl;
#endif
DofContainer dofs;
DofContainer &dofsToRecv = recvDofs[it->first];
......@@ -1168,16 +1075,6 @@ namespace AMDiS {
ERROR_EXIT("Should never happen!\n");
}
#if 0
if (mpiRank == 2 && it->first == 3) {
WorldVector<double> x;
mesh->getDofIndexCoords(dofs[0], feSpace, x);
x.print();
mesh->getDofIndexCoords(dofs[1], feSpace, x);
x.print();
}
#endif
for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt) {
DofContainer::iterator eraseIt = find(rankDOFs.begin(), rankDOFs.end(), *dofIt);
if (eraseIt != rankDOFs.end())
......@@ -1547,22 +1444,9 @@ namespace AMDiS {
int nSendInt = rankIt->second.size();
int* buffer = new int[nSendInt];
for (int i = 0; i < nSendInt; i++) {
#if 0
if (mpiRank == 3 && rankIt->first == 2) {
std::cout << "MY BOUND: " << (rankIt->second)[i].rankObject.elIndex
<< "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
<< " with neig "
<< (rankIt->second)[i].neighbourObject.elIndex
<< "/" << (rankIt->second)[i].neighbourObject.ithObjAtBoundary
<< std::endl;
}
#endif
for (int i = 0; i < nSendInt; i++)
buffer[i] = (rankIt->second)[i].rankObject.elIndex;
}
sendBuffers.push_back(buffer);
request[requestCounter++] =
......@@ -1593,20 +1477,6 @@ namespace AMDiS {
("Boundaries does not fit together!\n");
for (int i = 0; i < static_cast<int>(rankIt->second.size()); i++) {
#if 0
if (mpiRank == 2 && rankIt->first == 3) {
std::cout << "OT BOUND: " << (rankIt->second)[i].rankObject.elIndex
<< "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
<< " with neig "