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amdis
Commit 2bbf10f7 authored by Thomas Witkowski's avatar Thomas Witkowski
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Fixed some problems with nnz computation with coarse grid, still not finished.

parent 53c5f965
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Showing with 184 additions and 139 deletions
AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
View file @ 2bbf10f7
......@@ -51,7 +51,9 @@ namespace AMDiS {
MatCreateAIJ(mpiCommGlobal, nRankRows, nRankRows,
nOverallRows, nOverallRows,
0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz, &matIntInt);
0, nnzInterior.dnnz,
0, nnzInterior.onnz,
&matIntInt);
MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
......@@ -132,28 +134,40 @@ namespace AMDiS {
bool localMatrix = (subdomainLevel == 0);
if (checkMeshChange(mat, localMatrix)) {
createPetscNnzStructureWithCoarseSpace(mat,
*interiorMap,
matInteriorDiagNnz,
matInteriorOffdiagNnz,
localMatrix);
if (coarseSpaceMap)
createPetscNnzStructureWithCoarseSpace(mat,
*interiorMap,
*interiorMap,
nnzInterior,
localMatrix);
if (coarseSpaceMap) {
createPetscNnzStructureWithCoarseSpace(mat,
*coarseSpaceMap,
*coarseSpaceMap,
nnzCoarse);
createPetscNnzStructureWithCoarseSpace(mat,
*coarseSpaceMap,
matCoarseDiagNnz,
matCoarseOffdiagNnz);
*coarseSpaceMap,
*interiorMap,
nnzCoarseInt);
createPetscNnzStructureWithCoarseSpace(mat,
*interiorMap,
*coarseSpaceMap,
nnzIntCoarse);
}
}
if (localMatrix) {
MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
0, matInteriorDiagNnz, &matIntInt);
0, nnzInterior.dnnz,
&matIntInt);
// MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
} else {
MatCreateAIJ(mpiCommLocal,
nRowsRankInterior, nRowsRankInterior,
nRowsOverallInterior, nRowsOverallInterior,
0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz,
0, nnzInterior.dnnz, 0, nnzInterior.onnz,
&matIntInt);
// MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
}
if (coarseSpaceMap) {
......@@ -163,13 +177,16 @@ namespace AMDiS {
MatCreateAIJ(mpiCommGlobal,
nRowsRankCoarse, nRowsRankCoarse,
nRowsOverallCoarse, nRowsOverallCoarse,
0, matCoarseDiagNnz, 0, matCoarseOffdiagNnz,
0, nnzCoarse.dnnz, 0, nnzCoarse.onnz,
// 100, PETSC_NULL, 100, PETSC_NULL,
&matCoarseCoarse);
// MatSetOption(matCoarseCoarse, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
MatCreateAIJ(mpiCommGlobal,
nRowsRankCoarse, nRowsRankInterior,
nRowsOverallCoarse, nGlobalOverallInterior,
100, PETSC_NULL, 100, PETSC_NULL,
// 0, nnzCoarseInt.dnnz, 0, nnzCoarseInt.onnz,
&matCoarseInt);
MatSetOption(matCoarseInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
......@@ -177,7 +194,7 @@ namespace AMDiS {
nRowsRankInterior, nRowsRankCoarse,
nGlobalOverallInterior, nRowsOverallCoarse,
100, PETSC_NULL, 100, PETSC_NULL,
// 0, matInteriorDiagNnz, 0, matCoarseOffdiagNnz,
// 0, nnzIntCoarse.dnnz, 0, nnzIntCoarse.onnz,
&matIntCoarse);
MatSetOption(matIntCoarse, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
}
......@@ -259,14 +276,19 @@ namespace AMDiS {
if (colsOther.size()) {
if (subdomainLevel == 0) {
for (unsigned int k = 0; k < colsOther.size(); k++)
for (unsigned int k = 0; k < colsOther.size(); k++) {
int local = interiorMap->getMatIndex(j, colsOther[k]) - interiorMap->getStartDofs();
if (rowIndex == 0 && local == 9297)
MSG("FOUND: %d %d %d\n", colsOther[k], j, interiorMap->getMatIndex(j, colsOther[k]));
colsOther[k] = interiorMap->getMatIndex(j, colsOther[k]);
}
} else {
for (unsigned int k = 0; k < colsOther.size(); k++)
colsOther[k] =
interiorMap->getMatIndex(j, colsOther[k]) + rStartInterior;
}
MatSetValues(matCoarseInt, 1, &rowIndex, colsOther.size(),
&(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
}
......@@ -318,6 +340,8 @@ namespace AMDiS {
MatAssemblyEnd(matCoarseInt, MAT_FINAL_ASSEMBLY);
}
AMDiS::finalize();
exit(0);
// === Remove Dirichlet BC DOFs. ===
......@@ -577,30 +601,18 @@ namespace AMDiS {
static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
if (!matInteriorDiagNnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
if (!nnzInterior.dnnz || 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;
}
nnzInterior.clear();
if (matCoarseDiagNnz) {
delete [] matCoarseDiagNnz;
matCoarseDiagNnz = NULL;
}
if (matCoarseOffdiagNnz) {
delete [] matCoarseOffdiagNnz;
matCoarseOffdiagNnz = NULL;
if (coarseSpaceMap) {
nnzCoarse.clear();
nnzCoarseInt.clear();
nnzIntCoarse.clear();
}
updateSubdomainData();
......@@ -1034,18 +1046,11 @@ namespace AMDiS {
{
FUNCNAME("PetscSolverGlobalMatrix::createPetscNnzStructure()");
TEST_EXIT_DBG(!matInteriorDiagNnz)("There is something wrong!\n");
vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
int nRankRows = interiorMap->getRankDofs();
int rankStartIndex = interiorMap->getStartDofs();
matInteriorDiagNnz = new int[nRankRows];
matInteriorOffdiagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++) {
matInteriorDiagNnz[i] = 0;
matInteriorOffdiagNnz[i] = 0;
}
nnzInterior.create(nRankRows, nRankRows);
using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits = mtl::traits;
......@@ -1143,9 +1148,9 @@ namespace AMDiS {
// otherwise the matInteriorDiagNnz value.
if (petscColIdx >= rankStartIndex &&
petscColIdx < rankStartIndex + nRankRows)
matInteriorDiagNnz[localPetscRowIdx]++;
nnzInterior.dnnz[localPetscRowIdx]++;
else
matInteriorOffdiagNnz[localPetscRowIdx]++;
nnzInterior.onnz[localPetscRowIdx]++;
}
}
} else {
......@@ -1202,9 +1207,9 @@ namespace AMDiS {
r, localRowIdx, nRankRows, it->first);
if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
matInteriorOffdiagNnz[localRowIdx]++;
nnzInterior.onnz[localRowIdx]++;
else
matInteriorDiagNnz[localRowIdx]++;
nnzInterior.dnnz[localRowIdx]++;
}
}
}
......@@ -1217,33 +1222,26 @@ namespace AMDiS {
if (nRankRows < 100)
for (int i = 0; i < nRankRows; i++)
matInteriorDiagNnz[i] = std::min(matInteriorDiagNnz[i], nRankRows);
nnzInterior.dnnz[i] = std::min(nnzInterior.dnnz[i], nRankRows);
}
void PetscSolverGlobalMatrix::createPetscNnzStructureWithCoarseSpace(Matrix<DOFMatrix*> *mat,
ParallelDofMapping &dofMap,
int*& diagNnz,
int*& offdiagNnz,
ParallelDofMapping &rowDofMap,
ParallelDofMapping &colDofMap,
NnzStructure &nnz,
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();
int nRankRows = rowDofMap.getRankDofs();
int rankStartRowIndex = rowDofMap.getStartDofs();
diagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++)
diagNnz[i] = 0;
int nRankCols = colDofMap.getRankDofs();
int rankStartColIndex = colDofMap.getStartDofs();
if (localMatrix == false) {
offdiagNnz = new int[nRankRows];
for (int i = 0; i < nRankRows; i++)
offdiagNnz[i] = 0;
}
nnz.create(nRankRows, (!localMatrix ? nRankRows : -1));
using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits = mtl::traits;
......@@ -1308,21 +1306,21 @@ namespace AMDiS {
for (cursor_type cursor = begin<row>(bmat),
cend = end<row>(bmat); cursor != cend; ++cursor) {
if (dofMap[feSpaces[i]].find(*cursor, rowDofIndex) == false)
if (rowDofMap[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);
petscRowIdx = rowDofMap.getLocalMatIndex(i, *cursor);
} else {
if (dofMap.isMatIndexFromGlobal())
petscRowIdx = dofMap.getMatIndex(i, rowDofIndex.global);
if (rowDofMap.isMatIndexFromGlobal())
petscRowIdx = rowDofMap.getMatIndex(i, rowDofIndex.global);
else
petscRowIdx = dofMap.getMatIndex(i, *cursor);
petscRowIdx = rowDofMap.getMatIndex(i, *cursor);
}
if (localMatrix || dofMap[feSpaces[i]].isRankDof(*cursor)) {
if (localMatrix || rowDofMap[feSpaces[i]].isRankDof(*cursor)) {
// === The current row DOF is a rank DOF, so create the ===
// === corresponding nnz values directly on rank's nnz data. ===
......@@ -1330,50 +1328,47 @@ namespace AMDiS {
// This is the local row index of the local PETSc matrix.
int localPetscRowIdx = petscRowIdx;
if (localMatrix == false) {
localPetscRowIdx -= rankStartIndex;
if (localMatrix == false)
localPetscRowIdx -= rankStartRowIndex;
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);
}
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,
rowDofMap[feSpaces[i]][*cursor].global,
petscRowIdx,
localPetscRowIdx,
rankStartRowIndex,
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]++;
if (colDofMap[feSpaces[j]].isSet(col(*icursor)))
nnz.dnnz[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)
if (colDofMap[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]++;
}
int petscColIdx = (colDofMap.isMatIndexFromGlobal() ?
colDofMap.getMatIndex(j, colDofIndex.global) :
colDofMap.getMatIndex(j, col(*icursor)));
// 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 >= rankStartColIndex &&
petscColIdx < rankStartColIndex + nRankCols)
nnz.dnnz[localPetscRowIdx]++;
else
nnz.onnz[localPetscRowIdx]++;
}
}
} else {
......@@ -1389,17 +1384,15 @@ namespace AMDiS {
for (icursor_type icursor = begin<nz>(cursor),
icend = end<nz>(cursor); icursor != icend; ++icursor) {
if (dofMap[feSpaces[j]].find(col(*icursor), colDofIndex) == false)
if (colDofMap[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));
}
int petscColIdx = (colDofMap.isMatIndexFromGlobal() ?
colDofMap.getMatIndex(j, colDofIndex.global) :
colDofMap.getMatIndex(j, col(*icursor)));
sendMatrixEntry[sendToRank].
push_back(make_pair(petscRowIdx, petscColIdx));
}
} // if (isRankDof[*cursor]) ... else ...
......@@ -1407,6 +1400,7 @@ namespace AMDiS {
}
}
if (localMatrix == false) {
// === Send and recv the nnz row structure to/from other ranks. ===
......@@ -1428,43 +1422,54 @@ namespace AMDiS {
int r = it->second[i].first;
int c = it->second[i].second;
int localRowIdx = r - rankStartIndex;
int localRowIdx = r - rankStartRowIndex;
TEST_EXIT_DBG(localRowIdx >= 0 && localRowIdx < nRankRows)
("Got row index %d/%d (nRankRows = %d) from rank %d. Should not happen!\n",
r, localRowIdx, nRankRows, it->first);
if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
offdiagNnz[localRowIdx]++;
if (c < rankStartColIndex || c >= rankStartColIndex + nRankCols)
nnz.onnz[localRowIdx]++;
else
diagNnz[localRowIdx]++;
nnz.dnnz[localRowIdx]++;
}
}
}
// The above algorithm for calculating the number of nnz per row over-
// approximates the value, i.e., the number is always equal or larger to
// the real number of nnz values in the global parallel matrix. For small
// matrices, the problem may arise, that the result is larger than the
// number of elements in a row. This is fixed in the following.
if (nRankRows < 100)
for (int i = 0; i < nRankRows; i++)
diagNnz[i] = std::min(diagNnz[i], nRankRows);
}
// The above algorithm for calculating the number of nnz per row over-
// approximates the value, i.e., the number is always equal or larger to
// the real number of nnz values in the global parallel matrix. For small
// matrices, the problem may arise, that the result is larger than the
// number of elements in a row. This is fixed in the following.
// if (nRankRows < 100)
// for (int i = 0; i < nRankRows; i++)
// nnzInterior.dnnz[i] = std::min(nnzInterior.dnnz[i], nRankCols);
#if (DEBUG != 0)
#if (DEBUG != 0)
int nMax = 0;
int nSum = 0;
for (int i = 0; i < nRankRows; i++) {
nMax = std::max(nMax, diagNnz[i]);
nSum += diagNnz[i];
nMax = std::max(nMax, nnz.dnnz[i]);
nSum += nnz.dnnz[i];
}
MSG("NNZ in matrix: max = %d, avrg = %.0f\n",
nMax, static_cast<double>(nSum) / nRankRows);
#endif
MSG("NNZ in diag block: max = %d, avrg = %.0f\n",
nMax, (nSum > 0 ? (static_cast<double>(nSum) / nRankRows) : 0));
if (!localMatrix) {
nMax = 0;
nSum = 0;
for (int i = 0; i < nRankRows; i++) {
nMax = std::max(nMax, nnz.onnz[i]);
nSum += nnz.onnz[i];
}
MSG("NNZ in offdiag block: max = %d, avrg = %.0f\n",
nMax, (nSum > 0 ? (static_cast<double>(nSum) / nRankRows) : 0));
}
}
#endif
}
AMDiS/src/parallel/PetscSolverGlobalMatrix.h
View file @ 2bbf10f7
......@@ -31,16 +31,56 @@ namespace AMDiS {
using namespace std;
struct NnzStructure {
NnzStructure()
: dnnz(NULL),
onnz(NULL)
{}
void clear()
{
if (dnnz) {
delete [] dnnz;
dnnz = NULL;
}
if (onnz) {
delete [] onnz;
onnz = NULL;
}
}
void create(int nRows0, int nRows1 = -1)
{
if (nRows0 == 0)
return;
TEST_EXIT_DBG(nRows0 > 0)("Should not happen!\n");
dnnz = new int[nRows0];
for (int i = 0; i < nRows0; i++)
dnnz[i] = 0;
if (nRows1 > 0) {
onnz = new int[nRows1];
for (int i = 0; i < nRows1; i++)
onnz[i] = 0;
}
}
int *dnnz;
int *onnz;
};
class PetscSolverGlobalMatrix : public PetscSolver
{
public:
PetscSolverGlobalMatrix()
: PetscSolver(),
petscSolVec(PETSC_NULL),
matInteriorDiagNnz(NULL),
matInteriorOffdiagNnz(NULL),
matCoarseDiagNnz(NULL),
matCoarseOffdiagNnz(NULL),
lastMeshNnz(0),
zeroStartVector(false),
alwaysCreateNnzStructure(false)
......@@ -81,9 +121,9 @@ namespace AMDiS {
void createPetscNnzStructure(Matrix<DOFMatrix*> *mat);
void createPetscNnzStructureWithCoarseSpace(Matrix<DOFMatrix*> *mat,
ParallelDofMapping &dofMap,
int*& diagNnz,
int*& offdiagNnz,
ParallelDofMapping &rowDofMap,
ParallelDofMapping &colDofMap,
NnzStructure &nnz,
bool localMatrix = false);
/// Takes a DOF matrix and sends the values to the global PETSc matrix.
......@@ -108,11 +148,11 @@ namespace AMDiS {
protected:
/// Arrays definig the non zero pattern of Petsc's interior matrix.
int *matInteriorDiagNnz, *matInteriorOffdiagNnz;
NnzStructure nnzInterior;
NnzStructure nnzCoarse;
/// Arrays definig the non zero pattern of Petsc's coarse space matrix.
int *matCoarseDiagNnz, *matCoarseOffdiagNnz;
NnzStructure nnzIntCoarse, nnzCoarseInt;
Vec petscSolVec;
......
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