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Commit 58aa7090 authored by Thomas Witkowski's avatar Thomas Witkowski
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FETI-DP matrices are assembled now.

parent 28eb4386
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Showing with 779 additions and 147 deletions
AMDiS/src/DOFAdmin.h
View file @ 58aa7090
......@@ -262,7 +262,7 @@ namespace AMDiS {
*/
int getDOFIndex();
/// Frees index dof. Used by Mesh::getDof()
/// Frees index DOF. Used by Mesh::getDof()
void freeDofIndex(int dof);
///
......@@ -287,10 +287,10 @@ namespace AMDiS {
/// allocated size of managed vectors and matrices
int size;
/// number of used dof indices
/// number of used DOF indices
int usedCount;
/// number of FREED dof indices (NOT size-sizeUsed)
/// number of FREED DOF indices (NOT size - sizeUsed)
int holeCount;
/// > max. index of a used entry
......@@ -302,7 +302,7 @@ namespace AMDiS {
*/
DimVec<int> nDof;
/// Dofs from previous DOFAdmins
/// DOFs from previous DOFAdmins
DimVec<int> nPreDof;
/// List of all managed DOFIndexed objects.
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ 58aa7090
......@@ -1685,42 +1685,35 @@ namespace AMDiS {
recvDofs.clear();
if (createBoundaryDofFlag.isSet(BOUNDARY_SUBOBJ_SORTED)) {
DofContainer dofs;
for (int geo = FACE; geo >= VERTEX; geo--)
boundaryDofInfo.geoDofs[static_cast<GeoIndex>(geo)].clear();
for (int geo = FACE; geo >= VERTEX; geo--) {
std::set<const DegreeOfFreedom*> &dofSet =
boundaryDofInfo.geoDofs[static_cast<GeoIndex>(geo)];
dofSet.clear();
for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it) {
if (it->rankObj.subObj == geo) {
dofs.clear();
DofContainer dofs;
it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
DofContainer& tmp = sendDofs[it.getRank()];
tmp.insert(tmp.end(), dofs.begin(), dofs.end());
if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_SEND_DOFS))
dofSet.insert(dofs.begin(), dofs.end());
boundaryDofInfo.geoDofs[static_cast<GeoIndex>(geo)].insert(dofs.begin(), dofs.end());
}
}
}
for (int geo = FACE; geo >= VERTEX; geo--) {
std::set<const DegreeOfFreedom*> &dofSet =
boundaryDofInfo.geoDofs[static_cast<GeoIndex>(geo)];
dofSet.clear();
for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it) {
if (it->rankObj.subObj == geo) {
dofs.clear();
DofContainer dofs;
it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
DofContainer& tmp = recvDofs[it.getRank()];
tmp.insert(tmp.end(), dofs.begin(), dofs.end());
if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_RECV_DOFS))
dofSet.insert(dofs.begin(), dofs.end());
boundaryDofInfo.geoDofs[static_cast<GeoIndex>(geo)].insert(dofs.begin(), dofs.end());
}
}
}
......
AMDiS/src/parallel/ParallelTypes.h
View file @ 58aa7090
......@@ -33,11 +33,17 @@ namespace AMDiS {
using namespace std;
/// Defines set of DOF indices.
typedef std::set<DegreeOfFreedom> DofIndexSet;
/// Defines a mapping type from DOFs to rank numbers.
typedef map<const DegreeOfFreedom*, int> DofToRank;
/// Defines a mapping type from DOFs to a set of rank numbers.
typedef map<const DegreeOfFreedom*, std::set<int> > DofToPartitions;
/// Defines a mapping type from DOF indices to a set of rank numbers.
typedef map<DegreeOfFreedom, std::set<int> > DofIndexToPartitions;
/// Defines a mapping type from rank numbers to sets of DOFs.
typedef map<int, DofContainer> RankToDofContainer;
......
AMDiS/src/parallel/PetscSolver.h
View file @ 58aa7090
......@@ -46,7 +46,8 @@ namespace AMDiS {
{
public:
PetscSolver()
: meshDistributor(NULL)
: meshDistributor(NULL),
mpiRank(-1)
{}
virtual ~PetscSolver() {}
......@@ -54,6 +55,7 @@ namespace AMDiS {
void setMeshDistributor(MeshDistributor *m)
{
meshDistributor = m;
mpiRank = meshDistributor->getMpiRank();
}
/** \brief
......@@ -81,6 +83,8 @@ namespace AMDiS {
protected:
MeshDistributor *meshDistributor;
int mpiRank;
/// Petsc's matrix structure.
Mat petscMatrix;
......
AMDiS/src/parallel/PetscSolverFeti.cc
View file @ 58aa7090
......@@ -20,33 +20,49 @@ namespace AMDiS {
#ifdef HAVE_PETSC_DEV
void PetscSolverFeti::updateDofData(int nComponents)
void PetscSolverFeti::updateDofData()
{
FUNCNAME("PetscSolverFeti::updateDofData()");
TEST_EXIT(meshDistributor->getMesh()->getDim() == 2)
("Works for 2D problems only!");
TEST_EXIT(meshDistributor->getFeSpace()->getBasisFcts()->getDegree() == 1)
("Works for linear basis functions only!\n");
definePrimals();
createPrimals();
createDuals();
createLagrange();
createIndexB();
}
void PetscSolverFeti::definePrimals()
void PetscSolverFeti::createPrimals()
{
FUNCNAME("PetscSolverFeti::definePrimals()");
FUNCNAME("PetscSolverFeti::createPrimals()");
TEST_EXIT_DBG(meshDistributor->getMesh()->getDim() == 2)
("Works for 2D problems only!");
primals.clear();
DofContainerSet& vertices =
meshDistributor->getBoundaryDofInfo().geoDofs[VERTEX];
TEST_EXIT_DBG(vertices.size())("No primal vertices on this rank!\n");
for (DofContainerSet::iterator it = vertices.begin();
it != vertices.end(); ++it)
primals.insert(**it);
primals = meshDistributor->getBoundaryDofInfo().geoDofs[VERTEX];
globalPrimalIndex.clear();
int nRankPrimals = 0;
for (DofContainerSet::iterator it = primals.begin();
it != primals.end(); ++it)
if (meshDistributor->getIsRankDof(**it)) {
globalPrimalIndex[**it] = nRankPrimals;
nRankPrimals = 0;
for (DofIndexSet::iterator it = primals.begin(); it != primals.end(); ++it)
if (meshDistributor->getIsRankDof(*it)) {
globalPrimalIndex[*it] = nRankPrimals;
nRankPrimals++;
}
int nOverallPrimals = 0, rStartPrimals = 0;
nOverallPrimals = 0;
int rStartPrimals = 0;
mpi::getDofNumbering(meshDistributor->getMpiComm(),
nRankPrimals, rStartPrimals, nOverallPrimals);
......@@ -56,18 +72,480 @@ namespace AMDiS {
MSG_DBG("nRankPrimals = %d nOverallPrimals = %d\n",
nRankPrimals, nOverallPrimals);
StdMpi<vector<int> > stdMpi(meshDistributor->getMpiComm());
RankToDofContainer& sendDofs = meshDistributor->getSendDofs();
for (RankToDofContainer::iterator it = sendDofs.begin();
it != sendDofs.end(); ++it)
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (globalPrimalIndex.count(**dofIt))
stdMpi.getSendData(it->first).push_back(globalPrimalIndex[**dofIt]);
stdMpi.updateSendDataSize();
RankToDofContainer& recvDofs = meshDistributor->getRecvDofs();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
bool recvFromRank = false;
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (primals.count(**dofIt) &&
meshDistributor->getIsRankDof(**dofIt) == false) {
recvFromRank = true;
break;
}
if (recvFromRank)
stdMpi.recv(it->first);
}
stdMpi.startCommunication();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
int i = 0;
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (primals.count(**dofIt) &&
meshDistributor->getIsRankDof(**dofIt) == false)
globalPrimalIndex[**dofIt] = stdMpi.getRecvData(it->first)[i++];
}
}
TEST_EXIT_DBG(primals.size() == globalPrimalIndex.size())
("Number of primals %d, but number of global primals on this rank is %d!\n",
primals.size(), globalPrimalIndex.size());
TEST_EXIT_DBG(nOverallPrimals > 0)
("There are zero primal nodes in domain!\n");
}
void PetscSolverFeti::createDuals()
{
FUNCNAME("PetscSolverFeti::createDuals()");
// === Create for each dual node the set of ranks that contain this ===
// === node (denoted by W(x_j)). ===
boundaryDofRanks.clear();
RankToDofContainer& sendDofs = meshDistributor->getSendDofs();
for (RankToDofContainer::iterator it = sendDofs.begin();
it != sendDofs.end(); ++it) {
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
// If DOF is not primal, i.e., its a dual node
if (primals.count(**dofIt) == 0) {
boundaryDofRanks[**dofIt].insert(mpiRank);
boundaryDofRanks[**dofIt].insert(it->first);
}
}
}
StdMpi<vector<std::set<int> > > stdMpi(meshDistributor->getMpiComm());
for (RankToDofContainer::iterator it = sendDofs.begin();
it != sendDofs.end(); ++it)
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (primals.count(**dofIt) == 0)
stdMpi.getSendData(it->first).push_back(boundaryDofRanks[**dofIt]);
stdMpi.updateSendDataSize();
RankToDofContainer& recvDofs = meshDistributor->getRecvDofs();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
bool recvFromRank = false;
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (primals.count(**dofIt) == 0) {
recvFromRank = true;
break;
}
if (recvFromRank)
stdMpi.recv(it->first);
}
stdMpi.startCommunication();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
int i = 0;
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (primals.count(**dofIt) == 0)
boundaryDofRanks[**dofIt] = stdMpi.getRecvData(it->first)[i++];
}
// === Create global index of the dual nodes on each rank. ===
duals.clear();
globalDualIndex.clear();
int nRankAllDofs = meshDistributor->getFeSpace()->getAdmin()->getUsedDofs();
nRankB = nRankAllDofs - primals.size();
nOverallB = 0;
rStartB = 0;
mpi::getDofNumbering(meshDistributor->getMpiComm(),
nRankB, rStartB, nOverallB);
DofContainer allBoundaryDofs;
meshDistributor->getAllBoundaryDofs(allBoundaryDofs);
int nRankInteriorDofs = nRankAllDofs - allBoundaryDofs.size();
int nRankDuals = 0;
for (DofContainer::iterator it = allBoundaryDofs.begin();
it != allBoundaryDofs.end(); ++it) {
if (primals.count(**it) == 0) {
duals.insert(**it);
globalDualIndex[**it] = rStartB + nRankInteriorDofs + nRankDuals;
nRankDuals++;
}
}
int nOverallDuals = nRankDuals;
mpi::globalAdd(nOverallDuals);
MSG_DBG("nRankDuals = %d nOverallDuals = %d\n",
nRankDuals, nOverallDuals);
}
void PetscSolverFeti::createLagrange()
{
FUNCNAME("PetscSolverFeti::createLagrange()");
nRankLagrange = 0;
for (DofIndexSet::iterator it = duals.begin(); it != duals.end(); ++it) {
if (meshDistributor->getIsRankDof(*it)) {
dofFirstLagrange[*it] = nRankLagrange;
int degree = boundaryDofRanks[*it].size();
nRankLagrange += (degree * (degree - 1)) / 2;
}
}
nOverallLagrange = 0;
int rStartLagrange = 0;
mpi::getDofNumbering(meshDistributor->getMpiComm(),
nRankLagrange, rStartLagrange, nOverallLagrange);
for (DofIndexSet::iterator it = duals.begin(); it != duals.end(); ++it)
if (meshDistributor->getIsRankDof(*it))
dofFirstLagrange[*it] += rStartLagrange;
MSG_DBG("nRankLagrange = %d nOverallLagrange = %d\n",
nRankLagrange, nOverallLagrange);
// === ===
StdMpi<vector<int> > stdMpi(meshDistributor->getMpiComm());
RankToDofContainer& sendDofs = meshDistributor->getSendDofs();
for (RankToDofContainer::iterator it = sendDofs.begin();
it != sendDofs.end(); ++it)
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (primals.count(**dofIt) == 0) {
TEST_EXIT_DBG(dofFirstLagrange.count(**dofIt))("Should not happen!\n");
stdMpi.getSendData(it->first).push_back(dofFirstLagrange[**dofIt]);
}
}
stdMpi.updateSendDataSize();
RankToDofContainer& recvDofs = meshDistributor->getRecvDofs();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
bool recvData = false;
for (DofContainer::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt)
if (primals.count(**dofIt) == 0) {
recvData = true;
break;
}
if (recvData)
stdMpi.recv(it->first);
}
stdMpi.startCommunication();
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
int counter = 0;
for (unsigned int i = 0; i < it->second.size(); i++)
if (primals.count(*(it->second[i])) == 0)
dofFirstLagrange[*(it->second[i])] = stdMpi.getRecvData(it->first)[counter++];
}
}
void PetscSolverFeti::createIndexB()
{
FUNCNAME("PetscSolverFeti::createIndeB()");
globalIndexB.clear();
DOFAdmin* admin = meshDistributor->getFeSpace()->getAdmin();
for (int i = 0; i < admin->getUsedSize(); i++)
if (admin->isDofFree(i) == false && primals.count(i) == 0)
if (duals.count(i) == 0 && primals.count(i) == 0)
globalIndexB[i] = -1;
int nInterior = 0;
for (DofMapping::iterator it = globalIndexB.begin();
it != globalIndexB.end(); ++it) {
it->second = nInterior + rStartB;
nInterior++;
}
TEST_EXIT_DBG(nInterior + primals.size() + duals.size() ==
static_cast<unsigned int>(admin->getUsedDofs()))
("Should not happen!\n");
for (DofIndexSet::iterator it = duals.begin();
it != duals.end(); ++it)
globalIndexB[*it] = globalDualIndex[*it];
}
void PetscSolverFeti::fillPetscMatrix(Matrix<DOFMatrix*> *mat, SystemVector *vec)
void PetscSolverFeti::createMatLagrange(int nComponents)
{
FUNCNAME("PetscSolverFeti::createMatLagrange()");
MatCreateMPIAIJ(PETSC_COMM_WORLD,
nRankLagrange * nComponents, nRankB * nComponents,
nOverallLagrange * nComponents, nOverallB * nComponents,
2, PETSC_NULL, 2, PETSC_NULL,
&mat_lagrange);
for (DofIndexSet::iterator it = duals.begin(); it != duals.end(); ++it) {
TEST_EXIT_DBG(dofFirstLagrange.count(*it))("Should not happen!\n");
TEST_EXIT_DBG(boundaryDofRanks.count(*it))("Should not happen!\n");
int index = dofFirstLagrange[*it];
vector<int> W(boundaryDofRanks[*it].begin(), boundaryDofRanks[*it].end());
int degree = W.size();
TEST_EXIT_DBG(globalDualIndex.count(*it))("Should not happen!\n");
int dualCol = globalDualIndex[*it];
for (int i = 0; i < degree; i++) {
for (int j = i + 1; j < degree; j++) {
if (W[i] == mpiRank || W[j] == mpiRank) {
for (int k = 0; k < nComponents; k++) {
int rowIndex = index * nComponents + k;
int colIndex = dualCol * nComponents + k;
double value = (W[i] == mpiRank ? 1.0 : -1.0);
MatSetValue(mat_lagrange, rowIndex, colIndex, value,
INSERT_VALUES);
}
}
index++;
}
}
}
MatAssemblyBegin(mat_lagrange, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(mat_lagrange, MAT_FINAL_ASSEMBLY);
}
void PetscSolverFeti::fillPetscMatrix(Matrix<DOFMatrix*> *mat,
SystemVector *vec)
{
FUNCNAME("PetscSolverFeti::fillPetscMatrix()");
updateDofData();
int nComponents = vec->getSize();
MatCreateMPIAIJ(PETSC_COMM_WORLD,
nRankB * nComponents, nRankB * nComponents,
nOverallB * nComponents, nOverallB * nComponents,
100, PETSC_NULL, 100, PETSC_NULL,
&mat_b_b);
MatCreateMPIAIJ(PETSC_COMM_WORLD,
nRankPrimals * nComponents, nRankPrimals * nComponents,
nOverallPrimals * nComponents, nOverallPrimals * nComponents,
10, PETSC_NULL, 10, PETSC_NULL,
&mat_primal_primal);
MatCreateMPIAIJ(PETSC_COMM_WORLD,
nRankB * nComponents, nRankPrimals * nComponents,
nOverallB * nComponents, nOverallPrimals * nComponents,
100, PETSC_NULL, 100, PETSC_NULL,
&mat_b_primal);
MatCreateMPIAIJ(PETSC_COMM_WORLD,
nRankPrimals * nComponents, nRankB * nComponents,
nOverallPrimals * nComponents, nOverallB * nComponents,
100, PETSC_NULL, 100, PETSC_NULL,
&mat_primal_b);
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 traits::range_generator<row, Matrix>::type cursor_type;
typedef traits::range_generator<nz, cursor_type>::type icursor_type;
vector<int> cols, colsOther;
vector<double> values, valuesOther;
cols.reserve(300);
colsOther.reserve(300);
values.reserve(300);
valuesOther.reserve(300);
for (int i = 0; i < nComponents; i++)
for (int j = 0; j < nComponents; j++)
if ((*mat)[i][j]) {
traits::col<Matrix>::type col((*mat)[i][j]->getBaseMatrix());
traits::const_value<Matrix>::type value((*mat)[i][j]->getBaseMatrix());
for (cursor_type cursor = begin<row>((*mat)[i][j]->getBaseMatrix()),
cend = end<row>((*mat)[i][j]->getBaseMatrix()); cursor != cend; ++cursor) {
bool rowPrimal = primals.count(*cursor) != 0;
cols.clear();
values.clear();
colsOther.clear();
valuesOther.clear();
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
icursor != icend; ++icursor) {
if (primals.count(col(*icursor)) != 0) {
TEST_EXIT_DBG(globalPrimalIndex.count(col(*icursor)))
("No global primal index for DOF %d!\n", col(*icursor));
int colIndex = globalPrimalIndex[col(*icursor)] * nComponents + j;
if (rowPrimal) {
cols.push_back(colIndex);
values.push_back(value(*icursor));
} else {
colsOther.push_back(colIndex);
valuesOther.push_back(value(*icursor));
}
} else {
TEST_EXIT_DBG(globalIndexB.count(col(*icursor)))
("No global B index for DOF %d!\n", col(*icursor));
int colIndex = globalIndexB[col(*icursor)] * nComponents + j;
if (rowPrimal) {
colsOther.push_back(colIndex);
valuesOther.push_back(value(*icursor));
} else {
cols.push_back(colIndex);
values.push_back(value(*icursor));
}
}
}
if (rowPrimal) {
TEST_EXIT_DBG(globalPrimalIndex.count(*cursor))
("Should not happen!\n");
int rowIndex = globalPrimalIndex[*cursor] * nComponents + i;
MatSetValues(mat_primal_primal, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
if (colsOther.size())
MatSetValues(mat_primal_b, 1, &rowIndex, colsOther.size(),
&(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
} else {
TEST_EXIT_DBG(globalIndexB.count(*cursor))
("Should not happen!\n");
int rowIndex = globalIndexB[*cursor] * nComponents + i;
MatSetValues(mat_b_b, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
if (colsOther.size())
MatSetValues(mat_b_primal, 1, &rowIndex, colsOther.size(),