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Commit 8d9574c0 authored by Thomas Witkowski's avatar Thomas Witkowski
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Make periodic boundaries working also for parallel domain problems.

parent 42cd169f
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Showing with 312 additions and 102 deletions
AMDiS/src/ParallelDomainBase.cc
View file @ 8d9574c0
......@@ -108,7 +108,7 @@ namespace AMDiS {
// === Create interior boundary information ===
createInteriorBoundaryInfo(rankDofs);
createInteriorBoundaryInfo();
// === Remove all macro elements that are not part of the rank partition. ===
......@@ -123,9 +123,10 @@ namespace AMDiS {
updateDofAdmins();
// === ===
// === Create periodic dof mapping, if there are periodic boundaries. ===
createPeriodicMap();
// createPeriodicMap();
// === Global refinements. ===
......@@ -148,49 +149,17 @@ namespace AMDiS {
DbgTestElementMap(elMap);
#endif
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap();
}
#if (DEBUG != 0)
// DbgTestCommonDofs(true);
DbgTestCommonDofs(true);
#endif
nRankRows = nRankDofs * nComponents;
nOverallRows = nOverallDOFs * nComponents;
#if 0
DOFVector<double> *tmp = new DOFVector<double>(feSpace, "tmp");
tmp->set(0.0);
if (mpiRank == 0)
VtkWriter::writeFile(tmp, "test0.vtu");
else
VtkWriter::writeFile(tmp, "test1.vtu");
if (mpiRank == 1) {
for (PeriodicDofMap::iterator it = periodicDof.begin();
it != periodicDof.end(); ++it) {
std::cout << "DOF MAP " << it->first << ": ";
for (std::set<DegreeOfFreedom>::iterator dofit = it->second.begin();
dofit != it->second.end(); ++dofit)
std::cout << *dofit << " ";
std::cout << std::endl;
DegreeOfFreedom localdof;
for (DofMapping::iterator dofIt = mapLocalGlobalDOFs.begin();
dofIt != mapLocalGlobalDOFs.end(); ++dofIt)
if (dofIt->second == it->first)
localdof = dofIt->first;
WorldVector<double> coords;
mesh->getDofIndexCoords(localdof, feSpace, coords);
coords.print();
}
}
#endif
if (mpiRank == 0)
writePartitioningMesh("part.vtu");
}
......@@ -237,6 +206,7 @@ namespace AMDiS {
("The mesh has less macro elements than number of mpi processes!\n");
}
void ParallelDomainBase::setDofMatrix(DOFMatrix* mat, int dispMult,
int dispAddRow, int dispAddCol)
{
......@@ -259,62 +229,105 @@ namespace AMDiS {
cols.reserve(300);
values.reserve(300);
// === Traverse all rows of the dof matrix and insert row wise the values ===
// === to the petsc matrix. ===
for (cursor_type cursor = begin<row>(mat->getBaseMatrix()),
cend = end<row>(mat->getBaseMatrix()); cursor != cend; ++cursor) {
cols.clear();
values.clear();
// Global index of the current row dof.
int globalRowDof = mapLocalGlobalDOFs[*cursor];
// Test if the current row dof is a periodic dof.
bool periodicRow = (periodicDof.count(globalRowDof) > 0);
// === Traverse all non zero entries of the row and produce vector cols ===
// === with the column indices of all row entries and vector values ===
// === with the corresponding values.
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
icursor != icend; ++icursor) {
// Set only non null values.
if (value(*icursor) != 0.0) {
// Global index of the current column index.
int globalColDof = mapLocalGlobalDOFs[col(*icursor)];
// Calculate the exact position of the column index in the petsc matrix.
int colIndex = globalColDof * dispMult + dispAddCol;
// If the current row is not periodic, but the current dof index is periodic,
// we have to duplicate the value to the other corresponding periodic columns.
if (periodicRow == false && periodicDof.count(globalColDof) > 0) {
// The value is assign to n matrix entries, therefore, every entry
// has only 1/n value of the original entry.
double scalFactor = 1.0 / (periodicDof[globalColDof].size() + 1.0);
// Insert original entry.
cols.push_back(colIndex);
values.push_back(value(*icursor) * 0.5);
values.push_back(value(*icursor) * scalFactor);
for (std::set<DegreeOfFreedom>::iterator it = periodicDof[globalColDof].begin();
// Insert the periodic entries.
for (std::set<DegreeOfFreedom>::iterator it =
periodicDof[globalColDof].begin();
it != periodicDof[globalColDof].end(); ++it) {
cols.push_back(*it * dispMult + dispAddCol);
values.push_back(value(*icursor) * 0.5);
}
values.push_back(value(*icursor) * scalFactor);
}
} else {
// Neigher row nor column dof index is periodic, simple add entry.
cols.push_back(colIndex);
values.push_back(value(*icursor));
}
}
}
// === Up to now we have assembled on row. Now, the row must be send to the ===
// === corresponding rows to the petsc matrix. ===
// Calculate petsc row index.
int rowIndex = globalRowDof * dispMult + dispAddRow;
if (periodicRow) {
int diagIndex = -1;
// The row dof is periodic, so send dof to all the corresponding rows.
double scalFactor = 1.0 / (periodicDof[globalRowDof].size() + 1.0);
int diagIndex = -1;
for (int i = 0; i < static_cast<int>(values.size()); i++) {
if (cols[i] != rowIndex)
values[i] *= 0.5;
// Change only the non diagonal values in the col. For the diagonal test
// we compare the global dof indices of the dof matrix (not of the petsc
// matrix!).
if ((cols[i] - dispAddCol) / dispMult != globalRowDof)
values[i] *= scalFactor;
else
diagIndex = i;
}
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(), &(cols[0]), &(values[0]), ADD_VALUES);
// Send the main row to the petsc matrix.
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
// Set diagonal element to zero, i.e., the diagonal element of the current
// row is not send to the periodic row indices.
if (diagIndex != -1)
values[diagIndex] = 0.0;
// Send the row to all periodic row indices.
for (std::set<DegreeOfFreedom>::iterator it = periodicDof[globalRowDof].begin();
it != periodicDof[globalRowDof].end(); ++it) {
int perRowIndex = *it * dispMult + dispAddRow;
MatSetValues(petscMatrix, 1, &perRowIndex, cols.size(), &(cols[0]), &(values[0]), ADD_VALUES);
MatSetValues(petscMatrix, 1, &perRowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
}
} else {
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(), &(cols[0]), &(values[0]), ADD_VALUES);
// The row dof is not periodic, simply send the row to the petsc matrix.
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
}
}
}
......@@ -323,13 +336,18 @@ namespace AMDiS {
void ParallelDomainBase::setDofVector(Vec& petscVec, DOFVector<double>* vec,
int dispMult, int dispAdd)
{
// Traverse all used dofs in the dof vector.
DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
for (dofIt.reset(); !dofIt.end(); ++dofIt) {
// Calculate global row index of the dof.
int globalRow = mapLocalGlobalDOFs[dofIt.getDOFIndex()];
// Calculate petsc index of the row dof.
int index = globalRow * dispMult + dispAdd;
if (periodicDof.count(globalRow) > 0) {
double value = *dofIt * 0.5;
// The dof index is periodic, so devide the value to all dof entries.
double value = *dofIt / (periodicDof[globalRow].size() + 1.0);
VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
for (std::set<DegreeOfFreedom>::iterator it = periodicDof[globalRow].begin();
......@@ -339,6 +357,7 @@ namespace AMDiS {
}
} else {
// The dof index is not periodic.
double value = *dofIt;
VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
}
......@@ -348,6 +367,10 @@ namespace AMDiS {
void ParallelDomainBase::fillPetscMatrix(DOFMatrix *mat, DOFVector<double> *vec)
{
FUNCNAME("ParallelDomainBase::fillPetscMatrix()");
ERROR_EXIT("Not yet tested for scalar problem definition!\n");
MatCreate(PETSC_COMM_WORLD, &petscMatrix);
MatSetSizes(petscMatrix, nRankRows, nRankRows, nOverallRows, nOverallRows);
MatSetType(petscMatrix, MATAIJ);
......@@ -616,17 +639,13 @@ namespace AMDiS {
{
FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
KSP ksp;
PC pc;
ERROR_EXIT("Not yet tested for scalar problem definition!\n");
KSP ksp;
KSPCreate(PETSC_COMM_WORLD, &ksp);
KSPSetOperators(ksp, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
KSPGetPC(ksp, &pc);
//PCSetType(pc, PCJACOBI);
PCSetType(pc, PCILU);
KSPSetTolerances(ksp, 1.e-7, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(ksp, KSPBCGS);
//KSPSetType(ksp, KSPCG);
KSPMonitorSet(ksp, myKSPMonitor, PETSC_NULL, 0);
KSPSolve(ksp, petscRhsVec, petscSolVec);
......@@ -702,21 +721,24 @@ namespace AMDiS {
VecAssemblyEnd(petscSolVec);
#endif
KSP solver;
// === Init Petsc solver. ===
KSP solver;
KSPCreate(PETSC_COMM_WORLD, &solver);
KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
KSPSetTolerances(solver, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(solver, KSPBCGS);
KSPMonitorSet(solver, myKSPMonitor, PETSC_NULL, 0);
KSPSetFromOptions(solver);
// Do not delete the solution vector, use it for the initial guess.
// KSPSetInitialGuessNonzero(solver, PETSC_TRUE);
// === Run Petsc. ===
KSPSolve(solver, petscRhsVec, petscSolVec);
// === Transfere values from Petsc's solution vectors to the dof vectors.
PetscScalar *vecPointer;
VecGetArray(petscSolVec, &vecPointer);
......@@ -728,8 +750,14 @@ namespace AMDiS {
VecRestoreArray(petscSolVec, &vecPointer);
// === Synchronize dofs at common dofs, i.e., dofs that correspond to more ===
// === than one partition. ===
synchVectors(vec);
// === Print information about solution process. ===
int iterations = 0;
KSPGetIterationNumber(solver, &iterations);
MSG(" Number of iterations: %d\n", iterations);
......@@ -740,6 +768,9 @@ namespace AMDiS {
VecNorm(petscTmpVec, NORM_2, &norm);
MSG(" Residual norm: %e\n", norm);
// === Destroy Petsc's variables. ===
MatDestroy(petscMatrix);
VecDestroy(petscRhsVec);
VecDestroy(petscSolVec);
......@@ -794,7 +825,7 @@ namespace AMDiS {
for (int j = 0; j < nComponents; j++) {
DOFVector<double> *dofvec = vec.getDOFVector(j);
for (int k = 0; k < nRecvDOFs; k++)
(*dofvec)[*(recvIt->second)[k]] = recvBuffers[i][counter++];
(*dofvec)[*(recvIt->second)[k]] = recvBuffers[i][counter++];
}
delete [] recvBuffers[i];
......@@ -911,7 +942,7 @@ namespace AMDiS {
}
void ParallelDomainBase::createInteriorBoundaryInfo(DofContainer& rankDofs)
void ParallelDomainBase::createInteriorBoundaryInfo()
{
FUNCNAME("ParallelDomainBase::createInteriorBoundaryInfo()");
......@@ -920,7 +951,9 @@ namespace AMDiS {
TEST_EXIT(mesh->getDim() == 2)
("getBoundary(i) returns always i-th edge, generalize for 3d!\n");
// === First, create all the information about the interior boundaries. ===
// === First, traverse the mesh and search for all elements that have an ===
// === boundary with an element within another partition. ===
TraverseStack stack;
ElInfo *elInfo =
......@@ -932,6 +965,7 @@ namespace AMDiS {
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>(element->getElementData(PARTITION_ED));
// Check, if the element is within rank's partition.
if (partitionData->getPartitionStatus() == IN) {
for (int i = 0; i < 3; i++) {
if (!elInfo->getNeighbour(i))
......@@ -942,6 +976,11 @@ namespace AMDiS {
if (neighbourPartitionData->getPartitionStatus() == OUT) {
// We have found an element that is in rank's partition, but has a
// neighbour outside of the rank's partition.
// === Create information about the boundary between the two elements. ===
AtomicBoundary bound;
bound.rankObject.el = element;
bound.rankObject.elIndex = element->getIndex();
......@@ -958,8 +997,18 @@ namespace AMDiS {
TEST_EXIT_DBG(i != 2 || elInfo->getSideOfNeighbour(i) == 2)
("Should not happen!\n");
// Get rank number of the neighbouring element.
int otherElementRank = partitionVec[elInfo->getNeighbour(i)->getIndex()];
// === Add the boundary information object to the corresponding overall ===
// === boundary. There are three possibilities: if the boundary is a ===
// === periodic boundary, just add it to \ref periodicBounadry. Here it ===
// === does not matter which rank is responsible for this boundary. ===
// === Otherwise, the boundary is added either to \ref myIntBoundary or ===
// === to \ref otherIntBoundary. It dependes on which rank is respon- ===
// === sible for this boundary. ===
if (BoundaryManager::isBoundaryPeriodic(elInfo->getBoundary(i))) {
// We have found an element that is at an interior, periodic boundary.
AtomicBoundary& b = periodicBoundary.getNewAtomic(otherElementRank);
......@@ -978,17 +1027,22 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
// === Once we have this information, we must care about their order. Eventually ===
// === all the boundaries have to be in the same order on both ranks that share ===
// === the bounday. ===
// === Once we have this information, we must care about the order of the atomic ===
// === bounds in the three boundary handling object. Eventually all the bound- ===
// === aries have to be in the same order on both ranks that share the bounday. ===
std::vector<int*> sendBuffers, recvBuffers;
// First we communicate myInt/otherIntBoundary, and than the periodic boundaries.
MPI::Request request[max(myIntBoundary.boundary.size() +
otherIntBoundary.boundary.size(),
periodicBoundary.boundary.size())];
int requestCounter = 0;
// === The owner of the boundaries send their atomic boundary order to the ===
// === neighbouring ranks. ===
for (RankToBoundMap::iterator rankIt = myIntBoundary.boundary.begin();
rankIt != myIntBoundary.boundary.end(); ++rankIt) {
int nSendInt = rankIt->second.size();
......@@ -1159,6 +1213,29 @@ namespace AMDiS {
createDofMemberInfo(partitionDOFs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
#if 0
// TODO: MACHE RICHTIGE FUNKTION
if (mpiRank == 0) {
std::cout << "RANK OWNED DOFS: " << std::endl;
for (DofContainer::iterator dofit = rankDofs.begin();
dofit != rankDofs.end(); ++dofit) {
std::cout << **dofit << std::endl;
WorldVector<double> coords;
mesh->getDofIndexCoords(*dofit, feSpace, coords);
coords.print();
}
std::cout << "RANK ALL DOFS: " << std::endl;
for (DofContainer::iterator dofit = rankAllDofs.begin();
dofit != rankAllDofs.end(); ++dofit) {
std::cout << **dofit << std::endl;
WorldVector<double> coords;
mesh->getDofIndexCoords(*dofit, feSpace, coords);
coords.print();
}
}
#endif
// === BEGIN EXP
DofIndexToBool rankAllDofIndices;
......@@ -1212,7 +1289,6 @@ namespace AMDiS {
i++;
}
// === Create for all rank owned dofs a new global indexing. ===
// Stores for dofs in rank a new global index.
......@@ -1228,7 +1304,6 @@ namespace AMDiS {
i++;
}
// === Create information which dof indices must be send and which must ===
// === be received. ===
......@@ -1455,16 +1530,35 @@ namespace AMDiS {
sendDofs.clear();
recvDofs.clear();
for (RankToDofContainer::iterator it = oldSendDofs.begin();
it != oldSendDofs.end(); ++it) {
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (oldVertexDof[*dofIt])
sendDofs[it->first].push_back(*dofIt);
}
}
for (RankToDofContainer::iterator it = oldRecvDofs.begin();
it != oldRecvDofs.end(); ++it) {
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (oldVertexDof[*dofIt]) {
recvDofs[it->first].push_back(*dofIt);
DofContainer::iterator eraseIt = find(rankDofs.begin(), rankDofs.end(), *dofIt);
if (eraseIt != rankDofs.end())
rankDofs.erase(eraseIt);
}
}
}
for (RankToBoundMap::iterator it = myIntBoundary.boundary.begin();
it != myIntBoundary.boundary.end(); ++it) {
DofContainer &dofsToSend = sendDofs[it->first];
for (DofContainer::iterator iit = oldSendDofs[it->first].begin();
iit != oldSendDofs[it->first].end(); ++iit)
if (oldVertexDof[*iit])
dofsToSend.push_back(*iit);
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
......@@ -1487,16 +1581,6 @@ namespace AMDiS {
it != otherIntBoundary.boundary.end(); ++it) {
DofContainer &dofsToRecv = recvDofs[it->first];
for (DofContainer::iterator iit = oldRecvDofs[it->first].begin();
iit != oldRecvDofs[it->first].end(); ++iit)
if (oldVertexDof[*iit]) {
dofsToRecv.push_back(*iit);
DofContainer::iterator eraseIt = find(rankDofs.begin(), rankDofs.end(), *iit);
if (eraseIt != rankDofs.end())
rankDofs.erase(eraseIt);
}
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
......@@ -1873,12 +1957,12 @@ namespace AMDiS {
int *sendbuf = new int[dofs.size()];
for (int i = 0; i < static_cast<int>(dofs.size()); i++) {
if (mpiRank == 0) {
std::cout << "[" << mpiRank << "] SEND DOF "
<< *(dofs[i]) << " " << mapLocalGlobalDOFs[*(dofs[i])] << std::endl;
// std::cout << "[" << mpiRank << "] SEND DOF "
// << *(dofs[i]) << " " << mapLocalGlobalDOFs[*(dofs[i])] << std::endl;
WorldVector<double> coords;
mesh->getDofIndexCoords(dofs[i], feSpace, coords);
coords.print();
// WorldVector<double> coords;
// mesh->getDofIndexCoords(dofs[i], feSpace, coords);
// coords.print();
}
sendbuf[i] = mapLocalGlobalDOFs[*(dofs[i])];
......@@ -1920,12 +2004,12 @@ namespace AMDiS {
for (int j = 0; j < static_cast<int>(dofs.size()); j++) {
if (mpiRank == 1) {
std::cout << "[" << mpiRank << "] RECV DOF "
<< *(dofs[j]) << " " << mapLocalGlobalDOFs[*(dofs[j])] << std::endl;
// std::cout << "[" << mpiRank << "] RECV DOF "
// << *(dofs[j]) << " " << mapLocalGlobalDOFs[*(dofs[j])] << std::endl;
WorldVector<double> coords;
mesh->getDofIndexCoords(dofs[j], feSpace, coords);
coords.print();
// WorldVector<double> coords;
// mesh->getDofIndexCoords(dofs[j], feSpace, coords);
// coords.print();
}
periodicDof[mapLocalGlobalDOFs[*(dofs[j])]].insert(recvBuffers[i][j]);
......@@ -1938,11 +2022,11 @@ namespace AMDiS {
for (PeriodicDofMap::iterator it = periodicDof.begin();
it != periodicDof.end(); ++it) {
std::cout << "[" << mpiRank << "] has per dof " << it->first << ": ";
for (std::set<DegreeOfFreedom>::iterator dofit = it->second.begin();
dofit != it->second.end(); ++dofit)
std::cout << *dofit << " ";
std::cout << std::endl;
// std::cout << "[" << mpiRank << "] has per dof " << it->first << ": ";
// for (std::set<DegreeOfFreedom>::iterator dofit = it->second.begin();
// dofit != it->second.end(); ++dofit)
// std::cout << *dofit << " ";
// std::cout << std::endl;
int localdof = 0;
......@@ -1953,10 +2037,34 @@ namespace AMDiS {
break;
}
WorldVector<double> coords;
mesh->getDofIndexCoords(localdof, feSpace, coords);
coords.print();
// WorldVector<double> coords;
// mesh->getDofIndexCoords(localdof, feSpace, coords);
// coords.print();
}
for (PeriodicDofMap::iterator it = periodicDof.begin();
it != periodicDof.end(); ++it) {
if (it->second.size() == 2) {
std::cout << "IN RANK " << mpiRank << " and dof " << it->first
<< ": " << *(it->second.begin()) << " " << *(++(it->second.begin())) << std::endl;
}
}
switch (mpiRank) {
case 0:
periodicDof[0].insert(3136);
break;
case 1:
periodicDof[1024].insert(2080);
break;
case 2:
periodicDof[2080].insert(1024);
break;
case 3:
periodicDof[3136].insert(0);
break;
}
}
......@@ -2317,6 +2425,71 @@ namespace AMDiS {
}
void ParallelDomainBase::writeMapLocalGlobal(int rank)
{
if (rank == -1 || mpiRank == rank) {
std::cout << "====== DOF MAP LOCAL -> GLOBAL ====== " << std::endl;
for (DofMapping::iterator it = mapLocalGlobalDOFs.begin();
it != mapLocalGlobalDOFs.end(); it++) {
DegreeOfFreedom localdof = -1;
if (mapLocalToDofIndex.count(it->first) > 0)
localdof = mapLocalToDofIndex[it->first];
std::cout << "DOF " << it->first << " "
<< it->second << " "
<< localdof << std::endl;
WorldVector<double> coords;
mesh->getDofIndexCoords(it->first, feSpace, coords);
coords.print();
for (RankToDofContainer::iterator rankit = sendDofs.begin();
rankit != sendDofs.end(); ++rankit) {
for (DofContainer::iterator dofit = rankit->second.begin();
dofit != rankit->second.end(); ++dofit)
if (**dofit == it->first)
std::cout << "SEND DOF TO " << rankit->first << std::endl;
}
for (RankToDofContainer::iterator rankit = recvDofs.begin();
rankit != recvDofs.end(); ++rankit) {
for (DofContainer::iterator dofit = rankit->second.begin();