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Commit a56007bd authored by Thomas Witkowski's avatar Thomas Witkowski
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Bugfix in domain parallelization.

parent eb258668
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Showing with 300 additions and 79 deletions
AMDiS/src/AdaptInstationary.cc
View file @ a56007bd
......@@ -108,7 +108,7 @@ namespace AMDiS {
INFO(info_,6)("time = %e, try timestep = %e\n",
adaptInfo->getTime(), adaptInfo->getTimestep());
problemIteration_->oneIteration(adaptInfo, NO_ADAPTION);
adaptInfo->incTimestepIteration();
......
AMDiS/src/ElementFileWriter.cc
View file @ a56007bd
......@@ -6,7 +6,7 @@
namespace AMDiS {
ElementFileWriter::ElementFileWriter(const std::string& name_,
ElementFileWriter::ElementFileWriter(std::string name_,
const FiniteElemSpace *feSpace_,
std::map<int, double> &mapvec)
: name(name_),
......@@ -95,14 +95,14 @@ namespace AMDiS {
void ElementFileWriter::writeFile(std::map<int, double> &vec,
const FiniteElemSpace *feSpace,
const std::string& filename)
std::string filename)
{
ElementFileWriter efw("", feSpace, vec);
efw.writeVtkValues(filename);
}
void ElementFileWriter::writeTecPlotValues(const std::string &filename)
void ElementFileWriter::writeTecPlotValues(std::string filename)
{
FUNCNAME("ElementFileWriter::writeTecPlotValues()");
std::ofstream fout(filename.c_str());
......@@ -154,10 +154,9 @@ namespace AMDiS {
// Write coordinates of all element vertices and element value.
for (int i = 0; i <= dim; ++i) {
for (int j = 0; j < dim; ++j) {
for (int j = 0; j < dim; ++j)
fout << elInfo->getCoord(i)[j] << " ";
}
fout << val << "\n";
}
......@@ -182,7 +181,7 @@ namespace AMDiS {
fout.close();
}
void ElementFileWriter::writeMeshDatValues(const std::string &filename, double time)
void ElementFileWriter::writeMeshDatValues(std::string filename, double time)
{
FUNCNAME("ElementFileWriter::writeMeshDatValues()");
std::ofstream fout(filename.c_str());
......@@ -281,7 +280,7 @@ namespace AMDiS {
fout.close();
}
void ElementFileWriter::writeVtkValues(const std::string &filename)
void ElementFileWriter::writeVtkValues(std::string filename)
{
FUNCNAME("ElementFileWriter::writeVtkValues()");
std::ofstream fout(filename.c_str());
......@@ -289,6 +288,7 @@ namespace AMDiS {
TEST_EXIT(fout)("Could not open file %s !\n", filename.c_str());
int dim = mesh->getDim();
int dimOfWorld = Global::getGeo(WORLD);
int vertices = mesh->getGeo(VERTEX);
int nElements = mesh->getNumberOfLeaves();
double val;
......@@ -312,12 +312,12 @@ namespace AMDiS {
while (elInfo) {
// Write coordinates of all element vertices.
for (int i = 0; i <= dim; i++) {
for (int j = 0; j < dim; j++) {
for (int j = 0; j < dimOfWorld; j++)
fout << elInfo->getCoord(i)[j] << " ";
}
for (int j = dim; j < 3; j++) {
for (int j = dimOfWorld; j < 3; j++)
fout << "0.0";
}
fout << "\n";
}
......@@ -329,9 +329,8 @@ namespace AMDiS {
fout << " <Cells>" << std::endl;
fout << " <DataArray type=\"Int32\" Name=\"offsets\">" << std::endl;
for (int i = 0; i < nElements; i++) {
fout << " " << (i + 1) * vertices << std::endl;
}
for (int i = 0; i < nElements; i++)
fout << " " << (i + 1) * vertices << std::endl;
fout << " </DataArray>" << std::endl;
......
AMDiS/src/ElementFileWriter.h
View file @ a56007bd
......@@ -21,7 +21,7 @@ namespace AMDiS {
{
public:
/// Constructor.
ElementFileWriter(const std::string& name,
ElementFileWriter(std::string name,
const FiniteElemSpace *feSpace,
std::map<int, double> &vec);
......@@ -34,17 +34,17 @@ namespace AMDiS {
/// Simple writing procedure for one element map.
static void writeFile(std::map<int, double> &vec,
const FiniteElemSpace *feSpace,
const std::string& filename);
std::string filename);
protected:
/// Writes element data in tecplot format.
void writeTecPlotValues(const std::string &filename);
void writeTecPlotValues(std::string filename);
/// Writes element data in AMDiS format (1 file !).
void writeMeshDatValues(const std::string &filename, double time);
void writeMeshDatValues(std::string filename, double time);
/// Writes element data in VTK format.
void writeVtkValues(const std::string &filename);
void writeVtkValues(std::string filename);
protected:
/// Name.
......
AMDiS/src/InteriorBoundary.h
View file @ a56007bd
......@@ -35,6 +35,9 @@ namespace AMDiS {
/// The macro element to which the boundary element corresponds to.
Element* el;
/// Index of the macro element.
int elIndex;
/** \brief
* Defines the geometrical object at the boundary. It must be "a part" of the
* macro element \ref el, i.e., either 1 (a vertex), 2 (an edge) or 3 (a face).
......
AMDiS/src/Lagrange.cc
View file @ a56007bd
......@@ -48,12 +48,11 @@ namespace AMDiS {
Lagrange::~Lagrange()
{
for (int i = 0; i < static_cast<int>(bary->size()); i++) {
for (int i = 0; i < static_cast<int>(bary->size()); i++)
if ((*bary)[i]) {
delete (*bary)[i];
(*bary)[i] = NULL;
}
}
}
Lagrange* Lagrange::getLagrange(int dim, int degree)
......@@ -70,13 +69,12 @@ namespace AMDiS {
void Lagrange::clear()
{
std::list<Lagrange*>::iterator it;
for (it = allBasFcts.begin(); it != allBasFcts.end(); it++) {
for (std::list<Lagrange*>::iterator it = allBasFcts.begin();
it != allBasFcts.end(); it++)
if (*it) {
delete *it;
*it = NULL;
}
}
}
void Lagrange::setFunctionPointer()
......
AMDiS/src/ParallelDomainBase.cc
View file @ a56007bd
......@@ -15,6 +15,7 @@
#include "ElementDofIterator.h"
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
#include "ElementFileWriter.h"
#include "petscksp.h"
......@@ -22,7 +23,7 @@ namespace AMDiS {
PetscErrorCode myKSPMonitor(KSP ksp, PetscInt iter, PetscReal rnorm, void *)
{
if (iter % 100 == 0 && MPI::COMM_WORLD.Get_rank() == 0)
// if (iter % 100 == 0 && MPI::COMM_WORLD.Get_rank() == 0)
std::cout << " Iteration " << iter << ": " << rnorm << std::endl;
return 0;
......@@ -66,6 +67,23 @@ namespace AMDiS {
if (mpiSize <= 1)
return;
#if 0
if (mpiRank == 0) {
std::map<int, double> vec;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
while (elInfo) {
vec[elInfo->getElement()->getIndex()] = static_cast<double>(elInfo->getElement()->getIndex());
elInfo = stack.traverseNext(elInfo);
}
ElementFileWriter::writeFile(vec, feSpace, "test.vtu");
}
#endif
// Test, if the mesh is the macro mesh only! Paritioning of the mesh is supported
// only for macro meshes, so it will not work yet if the mesh is already refined
// in some way.
......@@ -112,6 +130,41 @@ namespace AMDiS {
updateDofAdmins();
#if 0
if (mpiRank == 0) {
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
if (elInfo->getElement()->getIndex() == 4) {
WorldVector<double> x;
mesh->getDofIndexCoords(elInfo->getElement()->getDOF(0), feSpace, x);
std::cout << "FOUND!" << std::endl;
x.print();
}
elInfo = stack.traverseNext(elInfo);
}
}
if (mpiRank == 1) {
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
if (elInfo->getElement()->getIndex() == 3) {
WorldVector<double> x;
mesh->getDofIndexCoords(elInfo->getElement()->getDOF(2), feSpace, x);
std::cout << "FOUND!" << std::endl;
x.print();
}
elInfo = stack.traverseNext(elInfo);
}
}
exit(0);
#endif
// === Global refinements. ===
......@@ -137,7 +190,7 @@ namespace AMDiS {
#if (DEBUG != 0)
DbgTestCommonDofs();
DbgTestCommonDofs(true);
#endif
......@@ -293,7 +346,7 @@ namespace AMDiS {
KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
KSPGetPC(ksp, &pc);
// PCSetType(pc, PCNONE);
PCSetType(pc, PCJACOBI);
PCSetType(pc, PCILU);
KSPSetTolerances(ksp, 1.e-7, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
KSPSetType(ksp, KSPBCGS);
//KSPSetType(ksp, KSPCG);
......@@ -555,6 +608,24 @@ namespace AMDiS {
bool isRankDOF2 = (find(rankDOFs.begin(), rankDOFs.end(), boundDOF2) != rankDOFs.end());
bool ranksBoundary = isRankDOF1 || isRankDOF2;
#if 0
if (mpiRank == 3 && ranksBoundary &&
partitionVec[elInfo->getNeighbour(i)->getIndex()] == 2) {
std::cout << "ADD MY BOUND " << element->getIndex() << "/" << i
<< " with "
<< elInfo->getNeighbour(i)->getIndex() << "/"
<< elInfo->getSideOfNeighbour(i) << std::endl;
}
if (mpiRank == 2 && !ranksBoundary &&
partitionVec[elInfo->getNeighbour(i)->getIndex()] == 3) {
std::cout << "ADD OT BOUND " << element->getIndex() << "/" << i
<< " with "
<< elInfo->getNeighbour(i)->getIndex() << "/"
<< elInfo->getSideOfNeighbour(i) << std::endl;
}
#endif
// === And add the part of the interior boundary. ===
AtomicBoundary& bound =
......@@ -563,11 +634,19 @@ namespace AMDiS {
otherIntBoundary.getNewAtomicBoundary(partitionVec[elInfo->getNeighbour(i)->getIndex()]));
bound.rankObject.el = element;
bound.rankObject.elIndex = element->getIndex();
bound.rankObject.subObjAtBoundary = EDGE;
bound.rankObject.ithObjAtBoundary = i;
bound.neighbourObject.el = elInfo->getNeighbour(i);
// Do not set a pointer to the element, because if will be deleted from
// mesh after partitioning and the pointer would become invalid.
bound.neighbourObject.el = NULL;
bound.neighbourObject.elIndex = elInfo->getNeighbour(i)->getIndex();
bound.neighbourObject.subObjAtBoundary = EDGE;
bound.neighbourObject.ithObjAtBoundary = -1;
bound.neighbourObject.ithObjAtBoundary = elInfo->getSideOfNeighbour(i);
// i == 2 => getSideOfNeighbour(i) == 2
TEST_EXIT_DBG(i != 2 || elInfo->getSideOfNeighbour(i) == 2)
("Should not happen!\n");
}
}
}
......@@ -589,23 +668,25 @@ namespace AMDiS {
for (RankToBoundMap::iterator rankIt = myIntBoundary.boundary.begin();
rankIt != myIntBoundary.boundary.end(); ++rankIt) {
int nSendInt = rankIt->second.size();
int* buffer = new int[nSendInt];
for (int i = 0; i < nSendInt; i++)
buffer[i] = (rankIt->second)[i].rankObject.el->getIndex();
int* buffer = new int[nSendInt * 2];
for (int i = 0; i < nSendInt; i++) {
buffer[i * 2] = (rankIt->second)[i].rankObject.elIndex;
buffer[i * 2 + 1] = (rankIt->second)[i].rankObject.ithObjAtBoundary;
}
sendBuffers.push_back(buffer);
request[requestCounter++] =
mpiComm.Isend(buffer, nSendInt, MPI_INT, rankIt->first, 0);
mpiComm.Isend(buffer, nSendInt * 2, MPI_INT, rankIt->first, 0);
}
for (RankToBoundMap::iterator rankIt = otherIntBoundary.boundary.begin();
rankIt != otherIntBoundary.boundary.end(); ++rankIt) {
int nRecvInt = rankIt->second.size();
int *buffer = new int[nRecvInt];
int *buffer = new int[nRecvInt * 2];
recvBuffers.push_back(buffer);
request[requestCounter++] =
mpiComm.Irecv(buffer, nRecvInt, MPI_INT, rankIt->first, 0);
mpiComm.Irecv(buffer, nRecvInt * 2, MPI_INT, rankIt->first, 0);
}
......@@ -622,10 +703,12 @@ namespace AMDiS {
for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {
// If the expected object is not at place, search for it.
if ((rankIt->second)[j].neighbourObject.el->getIndex() != recvBuffers[i][j]) {
if ((rankIt->second)[j].neighbourObject.elIndex != recvBuffers[i][j * 2] ||
(rankIt->second)[j].neighbourObject.ithObjAtBoundary != recvBuffers[i][j * 2 + 1]) {
int k = j + 1;
for (; k < static_cast<int>(rankIt->second.size()); k++)
if ((rankIt->second)[k].neighbourObject.el->getIndex() == recvBuffers[i][j])
if ((rankIt->second)[k].neighbourObject.elIndex == recvBuffers[i][j * 2] &&
(rankIt->second)[k].neighbourObject.ithObjAtBoundary == recvBuffers[i][j * 2 + 1])
break;
// The element must always be found, because the list is just in another order.
......@@ -790,6 +873,11 @@ namespace AMDiS {
sendBuffers[i][c++] = *(dofIt->first);
sendBuffers[i][c++] = dofIt->second;
#if 0
if (mpiRank == 3 && sendIt->first == 2)
std::cout << "SEND DOF: " << dofIt->first << std::endl;
#endif
sendDofs[sendIt->first].push_back(dofIt->first);
}
......@@ -852,6 +940,11 @@ namespace AMDiS {
if (*(dofIt->first) == oldDof && !dofChanged[dofIt->first]) {
dofChanged[dofIt->first] = true;
#if 0
if (mpiRank == 2 && recvIt->first == 3)
std::cout << "RECV DOF: " << dofIt->first << std::endl;
#endif
recvDofs[recvIt->first].push_back(dofIt->first);
rankDofsNewGlobalIndex[dofIt->first] = newGlobalDof;
isRankDof[rankDofsNewLocalIndex[dofIt->first]] = false;
......@@ -897,8 +990,15 @@ namespace AMDiS {
}
DofContainer rankAllDofs;
for (DofSet::iterator dofIt = rankDOFSet.begin(); dofIt != rankDOFSet.end(); ++dofIt)
for (DofSet::iterator dofIt = rankDOFSet.begin(); dofIt != rankDOFSet.end(); ++dofIt) {
/* if (mpiRank == 1) {
std::cout << "COORDs of dof = " << **dofIt << std::endl;
WorldVector<double> x;
mesh->getDofIndexCoords(*dofIt, feSpace, x);
x.print();
}*/
rankAllDofs.push_back(*dofIt);
}
sort(rankAllDofs.begin(), rankAllDofs.end(), cmpDofsByValue);
DofContainer rankDOFs = rankAllDofs;
......@@ -915,6 +1015,16 @@ namespace AMDiS {
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
#if 0
if (mpiRank == 3 && it->first == 2)
std::cout << "GO ON MY BOUND: " << boundIt->rankObject.elIndex
<< "/" << boundIt->rankObject.ithObjAtBoundary << " with "
<< boundIt->neighbourObject.elIndex << "/"
<< boundIt->neighbourObject.ithObjAtBoundary
<< std::endl;
#endif
DofContainer dofs;
DofContainer &dofsToSend = sendDofs[it->first];
......@@ -935,22 +1045,32 @@ namespace AMDiS {
ERROR_EXIT("Should never happen!\n");
}
for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt) {
if (find(dofsToSend.begin(), dofsToSend.end(), *dofIt) == dofsToSend.end())
dofsToSend.push_back(*dofIt);
#if 0
if (mpiRank == 3 && it->first == 2) {
WorldVector<double> x;
mesh->getDofIndexCoords(dofs[0], feSpace, x);
x.print();
mesh->getDofIndexCoords(dofs[1], feSpace, x);
x.print();
}
#endif
for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt)
if (find(dofsToSend.begin(), dofsToSend.end(), *dofIt) == dofsToSend.end())
dofsToSend.push_back(*dofIt);
dofs.clear();
addAllVertexDOFs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
dofs);
addAllEdgeDOFs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
dofs);
for (int i = 0; i < static_cast<int>(dofs.size()); i++) {
for (int i = 0; i < static_cast<int>(dofs.size()); i++)
dofsToSend.push_back(dofs[i]);
}
}
}
}
for (RankToBoundMap::iterator it = otherIntBoundary.boundary.begin();
it != otherIntBoundary.boundary.end(); ++it) {
......@@ -958,17 +1078,37 @@ namespace AMDiS {
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
#if 0
if (mpiRank == 2 && it->first == 3)
std::cout << "GO ON OT BOUND: " << boundIt->rankObject.elIndex
<< "/" << boundIt->rankObject.ithObjAtBoundary << " with "
<< boundIt->neighbourObject.elIndex << "/"
<< boundIt->neighbourObject.ithObjAtBoundary
<< std::endl;
#endif
DofContainer dofs;
DofContainer &dofsToRecv = recvDofs[it->first];
switch (boundIt->rankObject.ithObjAtBoundary) {
case 0:
dofs.push_back(boundIt->rankObject.el->getDOF(1));
dofs.push_back(boundIt->rankObject.el->getDOF(2));
if (boundIt->neighbourObject.ithObjAtBoundary == 0) {
dofs.push_back(boundIt->rankObject.el->getDOF(2));
dofs.push_back(boundIt->rankObject.el->getDOF(1));
} else {
dofs.push_back(boundIt->rankObject.el->getDOF(1));
dofs.push_back(boundIt->rankObject.el->getDOF(2));
}
break;
case 1:
dofs.push_back(boundIt->rankObject.el->getDOF(0));
dofs.push_back(boundIt->rankObject.el->getDOF(2));
if (boundIt->neighbourObject.ithObjAtBoundary == 0) {
dofs.push_back(boundIt->rankObject.el->getDOF(0));
dofs.push_back(boundIt->rankObject.el->getDOF(2));
} else {
dofs.push_back(boundIt->rankObject.el->getDOF(2));
dofs.push_back(boundIt->rankObject.el->getDOF(0));
}
break;
case 2:
dofs.push_back(boundIt->rankObject.el->getDOF(1));
......@@ -978,6 +1118,16 @@ namespace AMDiS {
ERROR_EXIT("Should never happen!\n");
}
#if 0
if (mpiRank == 2 && it->first == 3) {
WorldVector<double> x;
mesh->getDofIndexCoords(dofs[0], feSpace, x);
x.print();
mesh->getDofIndexCoords(dofs[1], feSpace, x);
x.print();
}
#endif
for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt) {
DofContainer::iterator eraseIt = find(rankDOFs.begin(), rankDOFs.end(), *dofIt);
if (eraseIt != rankDOFs.end())
......@@ -1002,6 +1152,7 @@ namespace AMDiS {
dofsToRecv.push_back(dofs[i]);
}
}
}
......@@ -1344,10 +1495,25 @@ namespace AMDiS {
for (RankToBoundMap::iterator rankIt = myIntBoundary.boundary.begin();
rankIt != myIntBoundary.boundary.end(); ++rankIt) {
int nSendInt = rankIt->second.size();
int* buffer = new int[nSendInt];
for (int i = 0; i < nSendInt; i++)
buffer[i] = (rankIt->second)[i].rankObject.el->getIndex();
for (int i = 0; i < nSendInt; i++) {
#if 0
if (mpiRank == 3 && rankIt->first == 2) {
std::cout << "MY BOUND: " << (rankIt->second)[i].rankObject.elIndex
<< "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
<< " with neig "
<< (rankIt->second)[i].neighbourObject.elIndex
<< "/" << (rankIt->second)[i].neighbourObject.ithObjAtBoundary
<< std::endl;
}
#endif
buffer[i] = (rankIt->second)[i].rankObject.elIndex;
}
sendBuffers.push_back(buffer);
request[requestCounter++] =
......@@ -1378,8 +1544,22 @@ namespace AMDiS {
("Boundaries does not fit together!\n");
for (int i = 0; i < static_cast<int>(rankIt->second.size()); i++) {
#if 0
if (mpiRank == 2 && rankIt->first == 3) {
std::cout << "OT BOUND: " << (rankIt->second)[i].rankObject.elIndex
<< "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
<< " with neig "
<< (rankIt->second)[i].neighbourObject.elIndex
<< "/" << (rankIt->second)[i].neighbourObject.ithObjAtBoundary
<< std::endl;
}
#endif
int elIndex1 = recvBuffers[bufCounter][i];
int elIndex2 = otherIntBoundary.boundary[rankIt->first][i].neighbourObject.el->getIndex();
int elIndex2 = otherIntBoundary.boundary[rankIt->first][i].neighbourObject.elIndex;
TEST_EXIT(elIndex1 == elIndex2)("Wrong element index at interior boundary!\n");
}
......@@ -1393,6 +1573,27 @@ namespace AMDiS {
{
FUNCNAME("ParallelDomainBase::DbgTestCommonDofs()");
#if 0
{
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
Element *el = elInfo->getElement();
for (int i = 0; i < 3; i++) {
if (mpiRank == 2 && el->getDOF(i, 0) == 3)
std::cout << "RANK 2 EL = " << el->getIndex() << " i = " << i << std::endl;
if (mpiRank == 3 && el->getDOF(i, 0) == 4)
std::cout << "RANK 3 EL = " << el->getIndex() << " i = " << i << std::endl;
}
elInfo = stack.traverseNext(elInfo);
}
}
#endif
// Maps to each neighbour rank an array of WorldVectors. This array contain the
// coordinates of all dofs this rank shares on the interior boundary with the
// neighbour rank. A rank sends the coordinates to another rank, if it owns the
......@@ -1411,6 +1612,14 @@ namespace AMDiS {
dofIt != it->second.end(); ++dofIt) {
bool b = mesh->getDofIndexCoords(*dofIt, feSpace, coords);
TEST_EXIT(b)("Cannot find DOF in mesh!\n");
#if 0
if (mpiRank == 3 && it->first == 2) {
std::cout << "SEND COORDS: " << *dofIt << " = " << **dofIt << std::endl;
coords.print();
}
#endif
sendCoords[it->first].push_back(coords);
}
}
......@@ -1422,6 +1631,14 @@ namespace AMDiS {
bool b = mesh->getDofIndexCoords(*dofIt, feSpace, coords);