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Commit d552afce authored by Thomas Witkowski's avatar Thomas Witkowski
Browse files

Work on adaptivity in parallelization code and some code refactoring in this part too.

parent 35ef6dc6
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Showing with 143 additions and 307 deletions
AMDiS/libtool
View file @ d552afce
......@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
CC="gcc"
CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
......@@ -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"
......@@ -6801,13 +6801,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
CC="g++"
CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
......@@ -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"
......@@ -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 -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/lib/openmpi/1.3.2-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/../../.." | $SED -e "s@${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"
......@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
LTCC="gcc"
LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
......
AMDiS/src/AMDiS_fwd.h
View file @ d552afce
......@@ -58,6 +58,7 @@ namespace AMDiS {
class MacroInfo;
class Marker;
class Mesh;
class MeshStructure;
class OEMSolver;
class Operator;
class OperatorTerm;
......
AMDiS/src/DOFMatrix.cc
View file @ d552afce
......@@ -195,7 +195,7 @@ namespace AMDiS {
if (condition && condition->isDirichlet()) {
if (condition->applyBoundaryCondition()) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
if (rankDofs[rowIndices[i]])
if ((*rankDofs)[rowIndices[i]])
applyDBCs.insert(static_cast<int>(row));
#else
applyDBCs.insert(static_cast<int>(row));
......
AMDiS/src/DOFMatrix.h
View file @ d552afce
......@@ -406,7 +406,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void setRankDofs(std::map<DegreeOfFreedom, bool>& dofmap)
{
rankDofs = dofmap;
rankDofs = &dofmap;
}
#endif
......@@ -488,7 +488,7 @@ namespace AMDiS {
int nnzPerRow;
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
std::map<DegreeOfFreedom, bool> rankDofs;
std::map<DegreeOfFreedom, bool> *rankDofs;
#endif
/// Inserter object: implemented as pointer, allocated and deallocated as needed
......
AMDiS/src/DOFVector.h
View file @ d552afce
......@@ -211,16 +211,15 @@ namespace AMDiS {
}
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
inline void setRankDofs(std::map<DegreeOfFreedom, bool> dofmap)
inline void setRankDofs(std::map<DegreeOfFreedom, bool> &dofmap)
{
rankDofs.clear();
// rankDofs = dofmap;
// rankDofs = &dofmap;
}
inline bool isRankDof(DegreeOfFreedom dof)
{
return rankDofs[dof];
TEST_EXIT_DBG(rankDofs)("No rank dofs set!\n");
return (*rankDofs)[dof];
}
#endif
......@@ -269,7 +268,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
public:
std::map<DegreeOfFreedom, bool> rankDofs;
std::map<DegreeOfFreedom, bool> *rankDofs;
#endif
};
......
AMDiS/src/DirichletBC.cc
View file @ d552afce
......@@ -54,7 +54,7 @@ namespace AMDiS {
for (int i = 0; i < nBasFcts; i++) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
if (vector->isRankDof(dofIndices[i]))
// if (vector->isRankDof(dofIndices[i]))
#endif
if (localBound[i] == boundaryType) {
if (f) {
......
AMDiS/src/ElInfo.h
View file @ d552afce
......@@ -344,10 +344,7 @@ namespace AMDiS {
*/
double calcDet(const FixVec<WorldVector<double>, VERTEX> &coords) const;
/** \brief
* Checks whether flag is set in ElInfo's \ref fillFlag. If not, the program
* exits.
*/
/// Checks whether flag is set in ElInfo's \ref fillFlag. If not, the program exits.
void testFlag(const Flag& flag) const;
/** \brief
......@@ -411,7 +408,7 @@ namespace AMDiS {
ERROR("virtual function not implemented in this sub-class ");
return(0.0);
return 0.0;
}
/// Get ElInfo's \ref elType.
......
AMDiS/src/Element.cc
View file @ d552afce
......@@ -5,6 +5,7 @@
#include "FixVec.h"
#include "ElementRegion_ED.h"
#include "Serializer.h"
#include "MeshStructure.h"
namespace AMDiS {
......@@ -565,4 +566,31 @@ namespace AMDiS {
return result;
}
void fitElementToMeshCode(RefinementManager *refineManager, MeshStructure &code,
Element *el, int ithSide, int elType)
{
if (code.isLeafElement())
return;
if (el->isLeaf()) {
el->setMark(1);
refineManager->refineMesh(el->getMesh());
}
int s1 = el->getSideOfChild(0, ithSide, elType);
int s2 = el->getSideOfChild(1, ithSide, elType);
code.nextElement();
if (s1 != -1)
fitElementToMeshCode(refineManager, code,
el->getFirstChild(), s1, el->getChildType(elType));
code.nextElement();
if (s2 != -1)
fitElementToMeshCode(refineManager, code,
el->getSecondChild(), s2, el->getChildType(elType));
}
}
AMDiS/src/Element.h
View file @ d552afce
......@@ -574,6 +574,11 @@ namespace AMDiS {
friend class Mesh;
};
void fitElementToMeshCode(RefinementManager *refineManager,
MeshStructure &code,
Element *el,
int ithSide,
int elType);
}
#endif // AMDIS_ELEMENT_H
......
AMDiS/src/FiniteElemSpace.h
View file @ d552afce
......@@ -46,7 +46,7 @@ namespace AMDiS {
static FiniteElemSpace *provideFESpace(DOFAdmin *admin,
const BasisFunction *basFcts,
Mesh *mesh,
std::string name_ = "");
std::string name = "");
/// Destructor.
~FiniteElemSpace();
......@@ -92,7 +92,7 @@ namespace AMDiS {
* Constructs a FiniteElemSpace with name name_ and the given DOFAdmin,
* BasisFunction and Mesh.
*/
FiniteElemSpace(DOFAdmin* admin_,
FiniteElemSpace(DOFAdmin* admin,
const BasisFunction* basisFcts,
Mesh* mesh,
std::string name = "");
......
AMDiS/src/Mesh.h
View file @ d552afce
......@@ -99,7 +99,7 @@ namespace AMDiS {
}
/// Returns \ref dim of the mesh
inline int getDim() const \
inline int getDim() const
{
return dim;
}
......
AMDiS/src/MeshStructure.h
View file @ d552afce
......@@ -53,6 +53,10 @@ namespace AMDiS {
reset();
}
/** \brief
* Sets all position counters, that are used to traverse the code, to the starting
* position. The code itself is not changed.
*/
void reset();
inline void commit()
......
AMDiS/src/ParallelDomainBase.cc
View file @ d552afce
......@@ -40,13 +40,13 @@ namespace AMDiS {
ParallelDomainBase::ParallelDomainBase(ProblemIterationInterface *iIF,
ProblemTimeInterface *tIF,
FiniteElemSpace *fe,
RefinementManager *refineManager)
RefinementManager *refinementManager)
: iterationIF(iIF),
timeIF(tIF),
name(iIF->getName()),
feSpace(fe),
mesh(fe->getMesh()),
refinementManager(refineManager),
refineManager(refinementManager),
initialPartitionMesh(true),
nRankDofs(0),
rstart(0),
......@@ -100,14 +100,7 @@ namespace AMDiS {
// === Create new global and local DOF numbering. ===
// Set of all DOFs of the rank.
std::vector<const DegreeOfFreedom*> rankDofs;
// Number of DOFs in ranks partition that are owned by the rank.
nRankDofs = 0;
// Number of all DOFs in the macro mesh.
int nOverallDOFs = 0;
createLocalGlobalNumbering(rankDofs, nRankDofs, nOverallDOFs);
createLocalGlobalNumbering();
// === Create interior boundary information ===
......@@ -120,6 +113,7 @@ namespace AMDiS {
#if (DEBUG != 0)
dbgTestElementMap(elMap);
dbgTestInteriorBoundary();
dbgTestCommonDofs(true);
#endif
// === Reset all DOFAdmins of the mesh. ===
......@@ -136,33 +130,14 @@ namespace AMDiS {
GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);
if (globalRefinement > 0) {
refinementManager->globalRefine(mesh, globalRefinement);
#if (DEBUG != 0)
elMap.clear();
dbgCreateElementMap(elMap);
#endif
updateLocalGlobalNumbering(nRankDofs, nOverallDOFs);
refineManager->globalRefine(mesh, globalRefinement);
updateDofAdmins();
#if (DEBUG != 0)
dbgTestElementMap(elMap);
#endif
updateLocalGlobalNumbering();
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap();
}
lastMeshChangeIndex = mesh->getChangeIndex();
#if (DEBUG != 0)
dbgTestCommonDofs(true);
#endif
nRankRows = nRankDofs * nComponents;
nOverallRows = nOverallDOFs * nComponents;
}
......@@ -759,6 +734,8 @@ namespace AMDiS {
void ParallelDomainBase::checkMeshChange()
{
FUNCNAME("ParallelDomainBase::checkMeshChange()");
// === If mesh has not been changed, return. ===
if (mesh->getChangeIndex() == lastMeshChangeIndex)
......@@ -811,8 +788,14 @@ namespace AMDiS {
elCode.init(boundIt->rankObj.el, boundIt->rankObj.ithObj,
boundIt->rankObj.elType);
if (elCode.getCode() != recvCodes[i].getCode())
if (elCode.getCode() != recvCodes[i].getCode()) {
TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
// recvCodes[i].reset();
// fitElementToMeshCode(refineManager, recvCodes[i], boundIt->rankObj.el,
// boundIt->rankObj.ithObj, boundIt->rankObj.elType);
meshFitTogether = false;
}
i++;
}
......@@ -823,7 +806,7 @@ namespace AMDiS {
exit(0);
}
lastMeshChangeIndex = mesh->getChangeIndex();
updateLocalGlobalNumbering();
}
......@@ -1207,23 +1190,21 @@ namespace AMDiS {
}
void ParallelDomainBase::createLocalGlobalNumbering(DofContainer& rankDofs,
int& nRankDofs,
int& nOverallDOFs)
void ParallelDomainBase::createLocalGlobalNumbering()
{
FUNCNAME("ParallelDomainBase::createLocalGlobalNumbering()");
// === Get rank information about DOFs. ===
// Stores to each DOF pointer the set of ranks the DOF is part of.
std::map<const DegreeOfFreedom*, std::set<int> > partitionDOFs;
DofContainer rankAllDofs;
DofToPartitions partitionDofs;
DofContainer rankDofs, rankAllDofs;
DofToRank boundaryDofs;
createDofMemberInfo(partitionDOFs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
createDofMemberInfo(partitionDofs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
nRankDofs = rankDofs.size();
nOverallDOFs = partitionDOFs.size();
int nOverallDofs = partitionDofs.size();
// === Get starting position for global rank dof ordering. ====
......@@ -1284,8 +1265,8 @@ namespace AMDiS {
// If the boundary dof is a rank dof, it must be send to other ranks.
// Search for all ranks that have this dof too.
for (std::set<int>::iterator itRanks = partitionDOFs[it->first].begin();
itRanks != partitionDOFs[it->first].end();
for (std::set<int>::iterator itRanks = partitionDofs[it->first].begin();
itRanks != partitionDofs[it->first].end();
++itRanks) {
if (*itRanks != mpiRank) {
TEST_EXIT_DBG(rankDofsNewGlobalIndex.count(it->first) == 1)
......@@ -1376,12 +1357,22 @@ namespace AMDiS {
createLocalMappings(rankDofsNewLocalIndex, rankOwnedDofsNewLocalIndex,
rankDofsNewGlobalIndex);
nRankRows = nRankDofs * nComponents;
nOverallRows = nOverallDofs * nComponents;
lastMeshChangeIndex = mesh->getChangeIndex();
}
void ParallelDomainBase::updateLocalGlobalNumbering(int& nRankDofs, int& nOverallDOFs)
void ParallelDomainBase::updateLocalGlobalNumbering()
{
FUNCNAME("ParallelDomainBase::updateLocalGlobalNumbering()");
#if (DEBUG != 0)
ElementIdxToDofs elMap;
dbgCreateElementMap(elMap);
#endif
typedef std::set<const DegreeOfFreedom*> DofSet;
// === Get all DOFs in ranks partition. ===
......@@ -1525,10 +1516,11 @@ namespace AMDiS {
// === Calculate number of overall DOFs of all partitions. ===
mpiComm.Allreduce(&nRankDofs, &nOverallDOFs, 1, MPI_INT, MPI_SUM);
int nOverallDofs = 0;
mpiComm.Allreduce(&nRankDofs, &nOverallDofs, 1, MPI_INT, MPI_SUM);
// Do not change the indices now, but create a new indexing a store it here.
// Do not change the indices now, but create a new indexing and store it here.
DofIndexMap rankDofsNewLocalIndex;
isRankDof.clear();
int i = 0;
......@@ -1611,6 +1603,20 @@ namespace AMDiS {
createLocalMappings(rankDofsNewLocalIndex, rankOwnedDofsNewLocalIndex,
rankDofsNewGlobalIndex);
nRankRows = nRankDofs * nComponents;
nOverallRows = nOverallDofs * nComponents;
// === Update dof admins due to new number of dofs. ===
updateDofAdmins();
lastMeshChangeIndex = mesh->getChangeIndex();
#if (DEBUG != 0)
dbgTestElementMap(elMap);
dbgTestCommonDofs(true);
#endif
}
void ParallelDomainBase::createLocalMappings(DofIndexMap &rankDofsNewLocalIndex,
......@@ -1722,7 +1728,6 @@ namespace AMDiS {
sort(rankOwnedDofs.begin(), rankOwnedDofs.end(), cmpDofsByValue);
}
void ParallelDomainBase::createPeriodicMap()
{
FUNCNAME("ParallelDomainBase::createPeriodicMap()");
......
AMDiS/src/ParallelDomainBase.h
View file @ d552afce
......@@ -201,20 +201,11 @@ namespace AMDiS {
/// Removes all macro elements from the mesh that are not part of ranks partition.
void removeMacroElements();
/// Creates from a macro mesh a correct local and global DOF index numbering.
void createLocalGlobalNumbering();
/** \brief
* Creates from a macro mesh a correct local and global DOF index numbering.
*
* \param[out] rankDOFs Returns all DOFs from the macro mesh, which are owned
* by the rank after partitioning the macro mesh.
* \param[out] nRankDOFs Number of DOFs owned by rank.
* \param[out] nOverallDOFs Number of all DOFs in macro mesh.
*/
void createLocalGlobalNumbering(DofContainer& rankDOFs,
int& nRankDOFs,
int& nOverallDOFs);
void updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs);
/// Updates the local and global DOF numbering after the mesh has been changed.
void updateLocalGlobalNumbering();
/** \brief
* Creates to all dofs in rank's partition that are on a periodic boundary the
......@@ -452,12 +443,16 @@ namespace AMDiS {
/// Mesh of the problem.
Mesh *mesh;
/** \brief
* A refinement manager that should be used on the mesh. It is used to refine
* elements at interior boundaries in order to fit together with elements on the
* other side of the interior boundary.
*/
RefinementManager *refineManager;
/// Info level.
int info;
/// Refinement manager for the mesh.
RefinementManager *refinementManager;
/// Pointer to the paritioner which is used to devide a mesh into partitions.
ParMetisPartitioner *partitioner;
......
AMDiS/src/ProblemVec.cc
View file @ d552afce
......@@ -621,7 +621,6 @@ namespace AMDiS {
FUNCNAME("ProblemVec::buildAfterCoarsen()");
// printOpenmpTraverseInfo(this, true);
// buildAfterCoarsen_sebastianMode(adaptInfo, flag);
clock_t first = clock();
#ifdef _OPENMP
......@@ -791,200 +790,6 @@ namespace AMDiS {
#endif
}
void ProblemVec::buildAfterCoarsen_sebastianMode(AdaptInfo *adaptInfo, Flag flag)
{
FUNCNAME("ProblemVec::buildAfterCoarsen()");
clock_t first = clock();
#ifdef _OPENMP
double wtime = omp_get_wtime();
#endif
for (int i = 0; i < static_cast<int>(meshes.size()); i++)
meshes[i]->dofCompress();
Flag assembleFlag =
flag |
(*systemMatrix)[0][0]->getAssembleFlag() |
rhs->getDOFVector(0)->getAssembleFlag() |
Mesh::CALL_LEAF_EL |
Mesh::FILL_COORDS |
Mesh::FILL_DET |
Mesh::FILL_GRD_LAMBDA |
Mesh::FILL_NEIGH;
if (useGetBound)
assembleFlag |= Mesh::FILL_BOUND;
traverseInfo.updateStatus();
// Used to calculate the overall number of non zero entries.
int nnz = 0;
/// === INITIALIZE ===
for (int i = 0; i < nComponents; i++) {
MSG("%d DOFs for %s\n",
componentSpaces[i]->getAdmin()->getUsedSize(),
componentSpaces[i]->getName().c_str());
rhs->getDOFVector(i)->set(0.0);
for (int j = 0; j < nComponents; j++) {
// Only if this variable is true, the current matrix will be assembled.
bool assembleMatrix = true;
// The DOFMatrix which should be assembled (or not, if assembleMatrix
// will be set to false).
DOFMatrix *matrix = (*systemMatrix)[i][j];
if (matrix)
matrix->calculateNnz();
// If the matrix was assembled before and it is marked to be assembled
// only once, it will not be assembled.
if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) {
assembleMatrix = false;
} else if (matrix) {
matrix->getBaseMatrix().
change_dim(componentSpaces[i]->getAdmin()->getUsedSize(),
componentSpaces[j]->getAdmin()->getUsedSize());
set_to_zero(matrix->getBaseMatrix());
}
// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
if (!matrix || !assembleMatrix)
assembleMatrix = false;
// If the matrix should not be assembled, the rhs vector has to be considered.
// This will be only done, if i == j. So, if both is not true, we can jump
// to the next matrix.
if (!assembleMatrix && i != j) {
if (matrix)
nnz += matrix->getBaseMatrix().nnz();
continue;
}
if (assembleMatrix && matrix->getBoundaryManager())
matrix->getBoundaryManager()->initMatrix(matrix);
if (matrix && assembleMatrix)
matrix->startInsertion(matrix->getNnz());
}
}
// === TRAVERSE ===
Mesh *mesh = componentMeshes[0];
const FiniteElemSpace *feSpace = componentSpaces[0];
const BasisFunction *basisFcts = feSpace->getBasisFcts();
ElementMatrix elMat(basisFcts->getNumber(), basisFcts->getNumber());
ElementMatrix tmpElMat(elMat);