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Commit 53c5f965 authored by Thomas Witkowski's avatar Thomas Witkowski
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Some work on using the nnz structure of the matrix in FETI-DP method.

parent 81d8d089
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AMDiS/src/parallel/MeshDistributor.cc
View file @ 53c5f965
......@@ -85,6 +85,7 @@ namespace AMDiS {
repartitionIthChange(20),
nMeshChangesAfterLastRepartitioning(0),
repartitioningCounter(0),
repartitioningFailed(0),
debugOutputDir(""),
lastMeshChangeIndex(0),
createBoundaryDofFlag(0),
......@@ -1006,9 +1007,13 @@ namespace AMDiS {
INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n",
MPI::Wtime() - first);
if (tryRepartition &&
repartitioningAllowed &&
nMeshChangesAfterLastRepartitioning >= repartitionIthChange) {
if (repartitioningFailed > 0) {
MSG_DBG("Repartitioning not tried because it has failed in the past!\n");
repartitioningFailed--;
} else if (tryRepartition &&
repartitioningAllowed &&
nMeshChangesAfterLastRepartitioning >= repartitionIthChange) {
repartitionMesh();
nMeshChangesAfterLastRepartitioning = 0;
} else {
......@@ -1314,6 +1319,7 @@ namespace AMDiS {
bool partitioningSucceed =
partitioner->partition(elemWeights, ADAPTIVE_REPART);
if (!partitioningSucceed) {
repartitioningFailed = 20;
MSG("Mesh partitioner created empty partition!\n");
return;
}
......@@ -1321,8 +1327,9 @@ namespace AMDiS {
// In the case the partitioner does not create a new mesh partition, return
// without and changes.
if (!partitioner->meshChanged()) {
repartitioningFailed = 20;
MSG("Mesh partition does not create a new partition!\n");
return;
return;
}
TEST_EXIT_DBG(!(partitioner->getSendElements().size() == mesh->getMacroElements().size() &&
......
AMDiS/src/parallel/MeshDistributor.h
View file @ 53c5f965
......@@ -527,6 +527,11 @@ namespace AMDiS {
/// variable is used only for debug outputs.
int repartitioningCounter;
/// If repartitioning of the mesh fail, this variable has a positive value
/// that gives the number of mesh changes the mesh distributer will wait
/// before trying new mesh repartitioning.
int repartitioningFailed;
/// Directory name where all debug output files should be written to.
string debugOutputDir;
......
AMDiS/src/parallel/ParMetisPartitioner.h
View file @ 53c5f965
......@@ -171,7 +171,7 @@ namespace AMDiS {
ParMetisPartitioner(MPI::Intracomm *comm)
: MeshPartitioner(comm),
parMetisMesh(NULL),
itr(1000.0)
itr(1000000.0)
{}
~ParMetisPartitioner();
......
AMDiS/src/parallel/ParallelDofMapping.h
View file @ 53c5f965
......@@ -131,6 +131,25 @@ namespace AMDiS {
return dofMap[d];
}
/** \brief
* Searchs the map for a given DOF. It does not fail, if the DOF is not
* mapped by this mapping. In this case, it returns false. If the DOF is
* mapped, the result is stored and the function returns true.
*
* \param[in] dof DOF index for which a mapping is searched.
* \param[out] index In the case that the DOF is mapped, the result
* is stored here.
*/
inline bool find(DegreeOfFreedom dof, MultiIndex& index)
{
DofMap::iterator it = dofMap.find(dof);
if (it == dofMap.end())
return false;
index = it->second;
return true;
}
/// Inserts a new DOF to rank's mapping. The DOF is assumed to be owend by
/// the rank.
......
AMDiS/src/parallel/PetscSolverFeti.cc
View file @ 53c5f965
......@@ -269,11 +269,11 @@ namespace AMDiS {
if (meshLevel == 0) {
subdomain->setMeshDistributor(meshDistributor,
mpiCommGlobal, mpiCommLocal);
mpiCommGlobal, mpiCommLocal);
} else {
subdomain->setMeshDistributor(meshDistributor,
levelData.getMpiComm(meshLevel - 1),
levelData.getMpiComm(meshLevel));
levelData.getMpiComm(meshLevel - 1),
levelData.getMpiComm(meshLevel));
subdomain->setLevel(meshLevel);
}
}
......@@ -417,12 +417,11 @@ namespace AMDiS {
("Should not happen!\n");
}
// If multi level test, inform sub domain solver about coarse space.
subdomain->setDofMapping(&localDofMap, &primalDofMap);
if (printTimings) {
timeCounter = MPI::Wtime() - timeCounter;
MSG("FETI-DP timing 01: %.5f seconds (creation of basic data structures)",
MSG("FETI-DP timing 01: %.5f seconds (creation of basic data structures)\n",
timeCounter);
}
}
......@@ -693,6 +692,7 @@ namespace AMDiS {
lagrangeMap.getOverallDofs(), nGlobalOverallInterior,
2, PETSC_NULL, 2, PETSC_NULL,
&mat_lagrange);
MatSetOption(mat_lagrange, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
// === Create for all duals the corresponding Lagrange constraints. On ===
// === each rank we traverse all pairs (n, m) of ranks, with n < m, ===
......@@ -792,7 +792,9 @@ namespace AMDiS {
MatCreateAIJ(mpiCommGlobal,
nRowsRankB, nRowsRankPrimal,
nGlobalOverallInterior, nRowsOverallPrimal,
30, PETSC_NULL, 30, PETSC_NULL, &matBPi);
150, PETSC_NULL, 150, PETSC_NULL, &matBPi);
MatSetOption(matBPi, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
Mat matPrimal;
PetscInt nCols;
......@@ -1209,7 +1211,7 @@ namespace AMDiS {
// === Create matrices for the FETI-DP method. ===
double wtime = MPI::Wtime();
subdomain->fillPetscMatrix(mat);
if (printTimings)
......@@ -1225,23 +1227,30 @@ namespace AMDiS {
int nRowsDual = dualDofMap.getRankDofs();
MatCreateSeqAIJ(PETSC_COMM_SELF,
nRowsDual, nRowsDual, 60, PETSC_NULL,
nRowsDual, nRowsDual, 100, PETSC_NULL,
&mat_duals_duals);
MatSetOption(mat_duals_duals, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
if (fetiPreconditioner == FETI_DIRICHLET) {
int nRowsInterior = interiorDofMap.getRankDofs();
MatCreateSeqAIJ(PETSC_COMM_SELF,
nRowsInterior, nRowsInterior, 60, PETSC_NULL,
nRowsInterior, nRowsInterior, 100, PETSC_NULL,
&mat_interior_interior);
MatSetOption(mat_interior_interior,
MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
MatCreateSeqAIJ(PETSC_COMM_SELF,
nRowsInterior, nRowsDual, 60, PETSC_NULL,
nRowsInterior, nRowsDual, 100, PETSC_NULL,
&mat_interior_duals);
MatSetOption(mat_interior_duals,
MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
MatCreateSeqAIJ(PETSC_COMM_SELF,
nRowsDual, nRowsInterior, 60, PETSC_NULL,
nRowsDual, nRowsInterior, 100, PETSC_NULL,
&mat_duals_interior);
MatSetOption(mat_duals_interior,
MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
}
// === Prepare traverse of sequentially created matrices. ===
......
AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
View file @ 53c5f965
......@@ -33,31 +33,10 @@ namespace AMDiS {
double wtime = MPI::Wtime();
// === Check if mesh was changed and, in this case, recompute matrix ===
// === nnz structure and matrix indices. ===
int recvAllValues = 0;
int sendValue =
static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
// === If required, recompute non zero structure of the matrix. ===
if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
interiorMap->setComputeMatIndex(true, true);
interiorMap->update(feSpaces);
if (d_nnz) {
delete [] d_nnz;
d_nnz = NULL;
delete [] o_nnz;
o_nnz = NULL;
}
updateSubdomainData();
if (checkMeshChange(mat))
createPetscNnzStructure(mat);
lastMeshNnz = meshDistributor->getLastMeshChangeIndex();
}
// === Create PETSc vector (solution and a temporary vector). ===
......@@ -72,7 +51,7 @@ namespace AMDiS {
MatCreateAIJ(mpiCommGlobal, nRankRows, nRankRows,
nOverallRows, nOverallRows,
0, d_nnz, 0, o_nnz, &matIntInt);
0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz, &matIntInt);
MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
......@@ -149,16 +128,34 @@ namespace AMDiS {
int nRowsRankInterior = interiorMap->getRankDofs();
int nRowsOverallInterior = interiorMap->getOverallDofs();
if (subdomainLevel == 0) {
// === If required, recompute non zero structure of the matrix. ===
bool localMatrix = (subdomainLevel == 0);
if (checkMeshChange(mat, localMatrix)) {
createPetscNnzStructureWithCoarseSpace(mat,
*interiorMap,
matInteriorDiagNnz,
matInteriorOffdiagNnz,
localMatrix);
if (coarseSpaceMap)
createPetscNnzStructureWithCoarseSpace(mat,
*coarseSpaceMap,
matCoarseDiagNnz,
matCoarseOffdiagNnz);
}
if (localMatrix) {
MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
60, PETSC_NULL, &matIntInt);
0, matInteriorDiagNnz, &matIntInt);
} else {
MatCreateAIJ(mpiCommLocal,
nRowsRankInterior, nRowsRankInterior,
nRowsOverallInterior, nRowsOverallInterior,
60, PETSC_NULL, 60, PETSC_NULL, &matIntInt);
0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz,
&matIntInt);
}
if (coarseSpaceMap) {
int nRowsRankCoarse = coarseSpaceMap->getRankDofs();
int nRowsOverallCoarse = coarseSpaceMap->getOverallDofs();
......@@ -166,17 +163,23 @@ namespace AMDiS {
MatCreateAIJ(mpiCommGlobal,
nRowsRankCoarse, nRowsRankCoarse,
nRowsOverallCoarse, nRowsOverallCoarse,
60, PETSC_NULL, 60, PETSC_NULL, &matCoarseCoarse);
0, matCoarseDiagNnz, 0, matCoarseOffdiagNnz,
&matCoarseCoarse);
MatCreateAIJ(mpiCommGlobal,
nRowsRankCoarse, nRowsRankInterior,
nRowsOverallCoarse, nGlobalOverallInterior,
60, PETSC_NULL, 60, PETSC_NULL, &matCoarseInt);
100, PETSC_NULL, 100, PETSC_NULL,
&matCoarseInt);
MatSetOption(matCoarseInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
MatCreateAIJ(mpiCommGlobal,
nRowsRankInterior, nRowsRankCoarse,
nGlobalOverallInterior, nRowsOverallCoarse,
60, PETSC_NULL, 60, PETSC_NULL, &matIntCoarse);
100, PETSC_NULL, 100, PETSC_NULL,
// 0, matInteriorDiagNnz, 0, matCoarseOffdiagNnz,
&matIntCoarse);
MatSetOption(matIntCoarse, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
}
// === Prepare traverse of sequentially created matrices. ===
......@@ -564,6 +567,52 @@ namespace AMDiS {
}
bool PetscSolverGlobalMatrix::checkMeshChange(Matrix<DOFMatrix*> *mat,
bool localMatrix)
{
FUNCNAME("PetscSolverGlobalMatrix::checkMeshChange()");
int recvAllValues = 0;
int sendValue =
static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
if (!matInteriorDiagNnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
interiorMap->setComputeMatIndex(true, !localMatrix);
interiorMap->update(feSpaces);
if (matInteriorDiagNnz) {
delete [] matInteriorDiagNnz;
matInteriorDiagNnz = NULL;
}
if (matInteriorOffdiagNnz) {
delete [] matInteriorOffdiagNnz;
matInteriorOffdiagNnz = NULL;
}
if (matCoarseDiagNnz) {
delete [] matCoarseDiagNnz;
matCoarseDiagNnz = NULL;
}
if (matCoarseOffdiagNnz) {
delete [] matCoarseOffdiagNnz;
matCoarseOffdiagNnz = NULL;
}
updateSubdomainData();
lastMeshNnz = meshDistributor->getLastMeshChangeIndex();
return true;
}
return false;
}
void PetscSolverGlobalMatrix::createFieldSplit(PC pc)
{
FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");
......@@ -985,18 +1034,17 @@ namespace AMDiS {
{
FUNCNAME("PetscSolverGlobalMatrix::createPetscNnzStructure()");
TEST_EXIT_DBG(!d_nnz)("There is something wrong!\n");
TEST_EXIT_DBG(!o_nnz)("There is something wrong!\n");
TEST_EXIT_DBG(!matInteriorDiagNnz)("There is something wrong!\n");
vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
int nRankRows = interiorMap->getRankDofs();
int rankStartIndex = interiorMap->getStartDofs();
d_nnz = new int[nRankRows];
o_nnz = new int[nRankRows];
matInteriorDiagNnz = new int[nRankRows];
matInteriorOffdiagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++) {
d_nnz[i] = 0;
o_nnz[i] = 0;
matInteriorDiagNnz[i] = 0;
matInteriorOffdiagNnz[i] = 0;
}
using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
......@@ -1091,13 +1139,13 @@ namespace AMDiS {
if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
// The row DOF is a rank DOF, if also the column is a rank DOF,
// increment the d_nnz values for this row, otherwise the
// o_nnz value.
// increment the matInteriorDiagNnz values for this row,
// otherwise the matInteriorDiagNnz value.
if (petscColIdx >= rankStartIndex &&
petscColIdx < rankStartIndex + nRankRows)
d_nnz[localPetscRowIdx]++;
matInteriorDiagNnz[localPetscRowIdx]++;
else
o_nnz[localPetscRowIdx]++;
matInteriorOffdiagNnz[localPetscRowIdx]++;
}
}
} else {
......@@ -1154,9 +1202,9 @@ namespace AMDiS {
r, localRowIdx, nRankRows, it->first);
if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
o_nnz[localRowIdx]++;
matInteriorOffdiagNnz[localRowIdx]++;
else
d_nnz[localRowIdx]++;
matInteriorDiagNnz[localRowIdx]++;
}
}
}
......@@ -1169,7 +1217,254 @@ namespace AMDiS {
if (nRankRows < 100)
for (int i = 0; i < nRankRows; i++)
d_nnz[i] = std::min(d_nnz[i], nRankRows);
matInteriorDiagNnz[i] = std::min(matInteriorDiagNnz[i], nRankRows);
}
void PetscSolverGlobalMatrix::createPetscNnzStructureWithCoarseSpace(Matrix<DOFMatrix*> *mat,
ParallelDofMapping &dofMap,
int*& diagNnz,
int*& offdiagNnz,
bool localMatrix)
{
FUNCNAME("PetscSolverGlobalMatrix::createPetscNnzStructure()");
TEST_EXIT_DBG(!diagNnz)("There is something wrong!\n");
vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
int nRankRows = dofMap.getRankDofs();
int rankStartIndex = dofMap.getStartDofs();
diagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++)
diagNnz[i] = 0;
if (localMatrix == false) {
offdiagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++)
offdiagNnz[i] = 0;
}
using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits = mtl::traits;
typedef DOFMatrix::base_matrix_type Matrix;
typedef vector<pair<int, int> > MatrixNnzEntry;
typedef map<int, DofContainer> RankToDofContainer;
// Stores to each rank a list of nnz entries (i.e. pairs of row and column
// index) that this rank will send to. These nnz entries will be assembled
// on this rank, but because the row DOFs are not DOFs of this rank they
// will be send to the owner of the row DOFs.
map<int, MatrixNnzEntry> sendMatrixEntry;
// Maps to each DOF that must be send to another rank the rank number of the
// receiving rank.
map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
// First, create for all ranks, to which we send data to, MatrixNnzEntry
// object with 0 entries.
for (unsigned int i = 0; i < feSpaces.size(); i++) {
for (DofComm::Iterator it(meshDistributor->getDofComm().getRecvDofs(), feSpaces[i]);
!it.end(); it.nextRank()) {
sendMatrixEntry[it.getRank()].resize(0);
for (; !it.endDofIter(); it.nextDof())
sendDofToRank[make_pair(it.getDofIndex(), i)] = it.getRank();
}
}
// Create list of ranks from which we receive data from.
std::set<int> recvFromRank;
for (unsigned int i = 0; i < feSpaces.size(); i++)
for (DofComm::Iterator it(meshDistributor->getDofComm().getSendDofs(), feSpaces[i]);
!it.end(); it.nextRank())
recvFromRank.insert(it.getRank());
// === Traverse matrices to create nnz data. ===
int nComponents = mat->getNumRows();
for (int i = 0; i < nComponents; i++) {
for (int j = 0; j < nComponents; j++) {
if (!(*mat)[i][j])
continue;
TEST_EXIT_DBG((*mat)[i][j]->getRowFeSpace() == feSpaces[i])
("Should not happen!\n");
TEST_EXIT_DBG((*mat)[i][j]->getColFeSpace() == feSpaces[j])
("Should not happen!\n");
Matrix bmat = (*mat)[i][j]->getBaseMatrix();
traits::col<Matrix>::type col(bmat);
traits::const_value<Matrix>::type value(bmat);
typedef traits::range_generator<row, Matrix>::type cursor_type;
typedef traits::range_generator<nz, cursor_type>::type icursor_type;
MultiIndex rowDofIndex;
for (cursor_type cursor = begin<row>(bmat),
cend = end<row>(bmat); cursor != cend; ++cursor) {
if (dofMap[feSpaces[i]].find(*cursor, rowDofIndex) == false)
continue;
// The corresponding global matrix row index of the current row DOF.
int petscRowIdx = 0;
if (localMatrix) {
petscRowIdx = dofMap.getLocalMatIndex(i, *cursor);
} else {
if (dofMap.isMatIndexFromGlobal())
petscRowIdx = dofMap.getMatIndex(i, rowDofIndex.global);
else
petscRowIdx = dofMap.getMatIndex(i, *cursor);
}
if (localMatrix || dofMap[feSpaces[i]].isRankDof(*cursor)) {
// === The current row DOF is a rank DOF, so create the ===
// === corresponding nnz values directly on rank's nnz data. ===
// This is the local row index of the local PETSc matrix.
int localPetscRowIdx = petscRowIdx;
if (localMatrix == false) {
localPetscRowIdx -= rankStartIndex;
TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
("Should not happen! \n Debug info: DOF = %d globalRowIndx = %d petscRowIdx = %d localPetscRowIdx = %d rStart = %d compontens = %d from %d nRankRows = %d\n",
*cursor,
dofMap[feSpaces[i]][*cursor].global,
petscRowIdx,
localPetscRowIdx,
rankStartIndex,
i,
nComponents,
nRankRows);
}
if (localMatrix) {
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor)
if (dofMap[feSpaces[j]].isSet(col(*icursor)))
diagNnz[localPetscRowIdx]++;
} else {
MultiIndex colDofIndex;
// Traverse all non zero entries in this row.
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor) {
if (dofMap[feSpaces[j]].find(col(*icursor), colDofIndex) == false)
continue;
int petscColIdx = (dofMap.isMatIndexFromGlobal() ?
dofMap.getMatIndex(j, colDofIndex.global) :
dofMap.getMatIndex(j, col(*icursor)));
if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
// The row DOF is a rank DOF, if also the column is a rank DOF,
// increment the diagNnz values for this row,
// otherwise the offdiagNnz value.
if (petscColIdx >= rankStartIndex &&
petscColIdx < rankStartIndex + nRankRows)
diagNnz[localPetscRowIdx]++;
else
offdiagNnz[localPetscRowIdx]++;
}
}
}
} else {
// === The current row DOF is not a rank DOF, i.e., its values ===
// === are also created on this rank, but afterthere they will ===
// === be send to another rank. So we need to send also the ===
// === corresponding nnz structure of this row to the corres- ===
// === ponding rank. ===
// Send all non zero entries to the member of the row DOF.
int sendToRank = sendDofToRank[make_pair(*cursor, i)];
MultiIndex colDofIndex;
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor) {
if (dofMap[feSpaces[j]].find(col(*icursor), colDofIndex) == false)
continue;
if (value(*icursor) != 0.0) {
int petscColIdx = (dofMap.isMatIndexFromGlobal() ?
dofMap.getMatIndex(j, colDofIndex.global) :
dofMap.getMatIndex(j, col(*icursor)));
sendMatrixEntry[sendToRank].
push_back(make_pair(petscRowIdx, petscColIdx));
}
}
} // if (isRankDof[*cursor]) ... else ...
} // for each row in mat[i][j]
}
}
if (localMatrix == false) {
// === Send and recv the nnz row structure to/from other ranks. ===
StdMpi<MatrixNnzEntry> stdMpi(mpiCommGlobal, true);
stdMpi.send(sendMatrixEntry);
for (std::set<int>::iterator it = recvFromRank.begin();
it != recvFromRank.end(); ++it)