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Commit f1d2d34b authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on pdd.

parent 3d53fff8
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Showing with 322 additions and 116 deletions
AMDiS/src/DOFMatrix.cc
View file @ f1d2d34b
......@@ -15,6 +15,8 @@
#include "BoundaryManager.h"
#include "Assembler.h"
#include "mpi.h"
namespace AMDiS {
using namespace mtl;
......@@ -221,18 +223,7 @@ namespace AMDiS {
for (int j = 0; j < nCol; j++) { // for all columns
DegreeOfFreedom col = colIndices[j];
double entry = elMat[i][j];
/*
if (MPI::COMM_WORLD.Get_rank() == 0 && (row >= 156 || col >= 156))
std::cout << "PROB 0: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 1 && (row >= 151 || col >= 151))
std::cout << "PROB 1: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 2 && (row >= 146 || col >= 146))
std::cout << "PROB 2: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 3 && (row >= 153 || col >= 153))
std::cout << "PROB 3: " << row << " " << col << std::endl;
*/
if (add)
ins[row][col] += sign * entry;
else
......
AMDiS/src/ElementDofIterator.cc
View file @ f1d2d34b
......@@ -82,5 +82,6 @@ namespace AMDiS {
}
return true;
}
}
}
AMDiS/src/ElementDofIterator.h
View file @ f1d2d34b
......@@ -66,6 +66,19 @@ namespace AMDiS {
return &dofs[node0 + elementPos][n0 + dofPos];
}
/// Returns \ref pos, the current position (vertex, edge, face) of the traverse.
int getCurrentPos()
{
return pos;
}
/// Returns \ref elementPos, the number of vertex, edge or face that is traversed.
int getCurrentElementPos()
{
return elementPos;
}
protected:
/// The dof admin for which dofs should be traversed.
const DOFAdmin* admin;
......@@ -108,7 +121,7 @@ namespace AMDiS {
*/
int nElements;
/// Current element (vertex, edge, face) that is traversed.
/// Current element, i.e., ith vertex, edge or face, that is traversed.
int elementPos;
/// Currrent dof that is traversed on the current element;
......
AMDiS/src/Mesh.cc
View file @ f1d2d34b
......@@ -8,6 +8,7 @@
#include "AdaptInstationary.h"
#include "FiniteElemSpace.h"
#include "ElementData.h"
#include "ElementDofIterator.h"
#include "MacroElement.h"
#include "MacroReader.h"
#include "Mesh.h"
......@@ -867,19 +868,23 @@ namespace AMDiS {
{
DimVec<double>* baryCoords;
bool found = false;
ElementDofIterator elDofIter(feSpace->getAdmin());
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(this, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
while (elInfo) {
for (int i = 0; i < nDOFEl; i++) {
if (elInfo->getElement()->getDOF(i) == dof) {
elDofIter.reset(elInfo->getElement());
int i = 0;
do {
if (elDofIter.getDofPtr() == dof) {
baryCoords = feSpace->getBasisFcts()->getCoords(i);
elInfo->coordToWorld(*baryCoords, coords);
found = true;
break;
}
}
i++;
} while (elDofIter.next());
if (found)
break;
......
AMDiS/src/ParallelDomainProblem.cc
View file @ f1d2d34b
......@@ -38,6 +38,13 @@ namespace AMDiS {
initialPartitionMesh(true),
nRankDOFs(0)
{
FUNCNAME("ParallelDomainBase::ParalleDomainBase()");
TEST_EXIT(mesh->getNumberOfDOFAdmin() == 1)
("Only meshes with one DOFAdmin are supported!\n");
TEST_EXIT(mesh->getDOFAdmin(0).getNumberOfPreDOFs(0) == 0)
("Wrong pre dof number for DOFAdmin!\n");
mpiRank = MPI::COMM_WORLD.Get_rank();
mpiSize = MPI::COMM_WORLD.Get_size();
mpiComm = MPI::COMM_WORLD;
......@@ -100,8 +107,6 @@ namespace AMDiS {
admin.setFirstHole(mapLocalGlobalDOFs.size());
}
exit(0);
// === Global refinements. ===
int globalRefinement = 0;
......@@ -114,9 +119,9 @@ namespace AMDiS {
}
// #if (DEBUG != 0)
// testInteriorBoundary();
// #endif
#if (DEBUG != 0)
testInteriorBoundary();
#endif
// === Create petsc matrix. ===
......@@ -182,7 +187,7 @@ namespace AMDiS {
icend = end<nz>(cursor); icursor != icend; ++icursor)
if (value(*icursor) != 0.0) {
int r = mapLocalGlobalDOFs[row(*icursor)];
int c = mapLocalGlobalDOFs[col(*icursor)];
int c = mapLocalGlobalDOFs[col(*icursor)];
double v = value(*icursor);
MatSetValues(petscMatrix, 1, &r, 1, &c, &v, ADD_VALUES);
......@@ -234,9 +239,8 @@ namespace AMDiS {
int requestCounter = 0;
int i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
sendIt = sendDofs.begin();
sendIt != sendDofs.end();
for (RankToDofContainer::iterator sendIt = sendDofs.begin();
sendIt != sendDofs.end();
++sendIt, i++) {
int nSendDOFs = sendIt->second.size();
sendBuffers[i] = new double[nSendDOFs];
......@@ -249,9 +253,8 @@ namespace AMDiS {
}
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvDofs.begin();
recvIt != recvDofs.end();
for (RankToDofContainer::iterator recvIt = recvDofs.begin();
recvIt != recvDofs.end();
++recvIt, i++) {
int nRecvDOFs = recvIt->second.size();
recvBuffers[i] = new double[nRecvDOFs];
......@@ -265,12 +268,12 @@ namespace AMDiS {
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvDofs.begin();
for (RankToDofContainer::iterator recvIt = recvDofs.begin();
recvIt != recvDofs.end();
++recvIt, i++) {
for (int j = 0; j < static_cast<int>(recvIt->second.size()); j++)
(*vec)[(recvIt->second)[j][0]] = recvBuffers[i][j];
for (int j = 0; j < static_cast<int>(recvIt->second.size()); j++) {
(*vec)[*(recvIt->second)[j]] = recvBuffers[i][j];
}
delete [] recvBuffers[i];
}
......@@ -330,8 +333,8 @@ namespace AMDiS {
}
void ParallelDomainBase::createInteriorBoundaryInfo(std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs)
void ParallelDomainBase::createInteriorBoundaryInfo(DofContainer& rankDOFs,
DofToRank& boundaryDOFs)
{
FUNCNAME("ParallelDomainBase::createInteriorBoundaryInfo()");
......@@ -499,14 +502,14 @@ namespace AMDiS {
}
void ParallelDomainBase::createLocalGlobalNumbering(
std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs,
int& nRankDOFs,
int& nOverallDOFs)
void ParallelDomainBase::createLocalGlobalNumbering(DofContainer& rankDOFs,
DofToRank& boundaryDOFs,
int& nRankDOFs,
int& nOverallDOFs)
{
FUNCNAME("ParallelDomainBase::createLocalGlobalNumbering()");
// === Get rank information about DOFs. ===
// Stores to each DOF pointer the set of ranks the DOF is part of.
......@@ -537,7 +540,7 @@ namespace AMDiS {
// another rank.
std::map<int, int> recvNewDofs;
for (std::map<const DegreeOfFreedom*, int>::iterator it = boundaryDOFs.begin();
for (DofToRank::iterator it = boundaryDOFs.begin();
it != boundaryDOFs.end();
++it) {
......@@ -570,7 +573,6 @@ namespace AMDiS {
}
}
// === Send and receive the dof indices at boundary. ===
std::vector<int*> sendBuffers(sendNewDofs.size());
......@@ -646,6 +648,20 @@ namespace AMDiS {
// === Change dof indices at boundary from other ranks. ===
// Within this small data structure we track which dof index was already changed.
// This is used to avoid the following situation: Assume, there are two dof indices
// a and b in boundaryDOFs. Then we have to change index a to b and b to c. When
// the second rule applies, we have to avoid that not the first b, resulted from
// changing a to b, is set to c, but the second one. Therefore, after the first
// rule was applied, the dof pointer is set to false in this data structure and
// is not allowed to be changed anymore.
std::map<const DegreeOfFreedom*, bool> dofChanged;
for (DofToRank::iterator dofIt = boundaryDOFs.begin();
dofIt != boundaryDOFs.end();
++dofIt) {
dofChanged[dofIt->first] = false;
}
i = 0;
for (std::map<int, int>::iterator recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end();
......@@ -659,13 +675,18 @@ namespace AMDiS {
bool found = false;
for (std::map<const DegreeOfFreedom*, int>::iterator dofIt = boundaryDOFs.begin();
// Iterate over all boundary dofs to find the dof, which index we have to change.
for (DofToRank::iterator dofIt = boundaryDOFs.begin();
dofIt != boundaryDOFs.end();
++dofIt) {
if ((dofIt->first)[0] == oldDof) {
if (*(dofIt->first) == oldDof && !dofChanged[dofIt->first]) {
dofChanged[dofIt->first] = true;
recvDofs[recvIt->first].push_back(dofIt->first);
const_cast<DegreeOfFreedom*>(dofIt->first)[0] = newLocalDof;
*(const_cast<DegreeOfFreedom*>(dofIt->first)) = newLocalDof;
mapLocalGlobalDOFs[newLocalDof] = newGlobalDof;
mapGlobalLocalDOFs[newGlobalDof] = newLocalDof;
isRankDOF[newLocalDof] = false;
......@@ -688,27 +709,31 @@ namespace AMDiS {
FUNCNAME("ParallelDomainBase::updateLocalGlobalNumbering()");
std::set<const DegreeOfFreedom*> rankDOFs;
std::map<const DegreeOfFreedom*, int> newBoundaryDOFs;
DofToRank newBoundaryDOFs;
// === Get all DOFs in ranks partition. ===
ElementDofIterator elDofIt(feSpace->getAdmin());
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
Element *element = elInfo->getElement();
for (int i = 0; i < 3; i++)
rankDOFs.insert(element->getDOF(i));
elDofIt.reset(element);
do {
rankDOFs.insert(elDofIt.getDofPtr());
} while(elDofIt.next());
elInfo = stack.traverseNext(elInfo);
}
// === Traverse on interior boundaries and move all not ranked owned DOFs from ===
// === rankDOFs to boundaryDOFs. ===
std::map<int, std::vector<const DegreeOfFreedom*> > sendNewDofs = sendDofs;
std::map<int, std::vector<const DegreeOfFreedom*> > recvNewDofs = recvDofs;
RankToDofContainer sendNewDofs;
RankToDofContainer recvNewDofs;
for (std::map<int, std::vector<AtomicBoundary> >::iterator it =
myIntBoundary.boundary.begin();
......@@ -744,10 +769,22 @@ namespace AMDiS {
newBoundaryDOFs[dof1] = boundaryDOFs[dof1];
newBoundaryDOFs[dof2] = boundaryDOFs[dof2];
if (find(sendNewDofs[it->first].begin(), sendNewDofs[it->first].end(), dof1) ==
sendNewDofs[it->first].end())
sendNewDofs[it->first].push_back(dof1);
if (find(sendNewDofs[it->first].begin(), sendNewDofs[it->first].end(), dof2) ==
sendNewDofs[it->first].end())
sendNewDofs[it->first].push_back(dof2);
DofContainer boundDOFs;
addAllVertexDOFs(boundIt->rankObject.el,
boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
addAllEdgeDOFs(boundIt->rankObject.el,
boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
std::vector<const DegreeOfFreedom*> boundDOFs;
addAllDOFs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
for (int i = 0; i < static_cast<int>(boundDOFs.size()); i++) {
newBoundaryDOFs[boundDOFs[i]] = mpiRank;
sendNewDofs[it->first].push_back(boundDOFs[i]);
......@@ -755,7 +792,6 @@ namespace AMDiS {
}
}
for (std::map<int, std::vector<AtomicBoundary> >::iterator it =
otherIntBoundary.boundary.begin();
it != otherIntBoundary.boundary.end();
......@@ -793,9 +829,21 @@ namespace AMDiS {
newBoundaryDOFs[dof1] = boundaryDOFs[dof1];
newBoundaryDOFs[dof2] = boundaryDOFs[dof2];
std::vector<const DegreeOfFreedom*> boundDOFs;
addAllDOFs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
if (find(recvNewDofs[it->first].begin(), recvNewDofs[it->first].end(), dof2) ==
recvNewDofs[it->first].end())
recvNewDofs[it->first].push_back(dof2);
if (find(recvNewDofs[it->first].begin(), recvNewDofs[it->first].end(), dof1) ==
recvNewDofs[it->first].end())
recvNewDofs[it->first].push_back(dof1);
DofContainer boundDOFs;
addAllEdgeDOFs(boundIt->rankObject.el,
boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
addAllVertexDOFs(boundIt->rankObject.el,
boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
for (int i = static_cast<int>(boundDOFs.size()) - 1; i >= 0; i--) {
// for (int i = 0; i < static_cast<int>(boundDOFs.size()); i++) {
rankDOFs.erase(boundDOFs[i]);
......@@ -803,7 +851,6 @@ namespace AMDiS {
recvNewDofs[it->first].push_back(boundDOFs[i]);
}
}
}
nRankDOFs = rankDOFs.size();
......@@ -846,14 +893,13 @@ namespace AMDiS {
int requestCounter = 0;
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
sendIt = sendNewDofs.begin();
for (RankToDofContainer::iterator sendIt = sendNewDofs.begin();
sendIt != sendNewDofs.end();
++sendIt, i++) {
int nSendDofs = sendIt->second.size();
sendBuffers[i] = new int[nSendDofs];
int c = 0;
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = sendIt->second.begin();
for (DofContainer::iterator dofIt = sendIt->second.begin();
dofIt != sendIt->second.end();
++dofIt)
sendBuffers[i][c++] = (*dofIt)[0] + rstart;
......@@ -863,9 +909,9 @@ namespace AMDiS {
}
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end(); ++recvIt, i++) {
for (RankToDofContainer::iterator recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end();
++recvIt, i++) {
int nRecvDofs = recvIt->second.size();
recvBuffers[i] = new int[nRecvDofs];
......@@ -873,28 +919,25 @@ namespace AMDiS {
mpiComm.Irecv(recvBuffers[i], nRecvDofs, MPI_INT, recvIt->first, 0);
}
MPI::Request::Waitall(requestCounter, request);
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
sendIt = sendNewDofs.begin();
for (RankToDofContainer::iterator sendIt = sendNewDofs.begin();
sendIt != sendNewDofs.end();
++sendIt)
delete [] sendBuffers[i++];
i = 0;
int newDofIndex = nRankDOFs;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end(); ++recvIt) {
for (RankToDofContainer::iterator recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end();
++recvIt) {
int j = 0;
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = recvIt->second.begin();
for (DofContainer::iterator dofIt = recvIt->second.begin();
dofIt != recvIt->second.end();
++dofIt) {
const_cast<DegreeOfFreedom*>(*dofIt)[0] = newDofIndex;
(*const_cast<DegreeOfFreedom*>(*dofIt)) = newDofIndex;
mapLocalGlobalDOFs[newDofIndex] = recvBuffers[i][j];
mapGlobalLocalDOFs[recvBuffers[i][j]] = newDofIndex;
isRankDOF[newDofIndex] = false;
......@@ -912,31 +955,31 @@ namespace AMDiS {
}
void ParallelDomainBase::addAllDOFs(Element *el, int ithEdge,
std::vector<const DegreeOfFreedom*>& dofs)
void ParallelDomainBase::addAllVertexDOFs(Element *el, int ithEdge,
DofContainer& dofs)
{
FUNCNAME("ParallelDomainBase::addAllDOFs()");
FUNCNAME("ParallelDomainBase::addAllVertexDOFs()");
switch (ithEdge) {
case 0:
if (el->getSecondChild() && el->getSecondChild()->getFirstChild()) {
addAllDOFs(el->getSecondChild()->getFirstChild(), 0, dofs);
addAllVertexDOFs(el->getSecondChild()->getFirstChild(), 0, dofs);
dofs.push_back(el->getSecondChild()->getFirstChild()->getDOF(2));
addAllDOFs(el->getSecondChild()->getSecondChild(), 1, dofs);
addAllVertexDOFs(el->getSecondChild()->getSecondChild(), 1, dofs);
}
break;
case 1:
if (el->getFirstChild() && el->getFirstChild()->getFirstChild()) {
addAllDOFs(el->getFirstChild()->getFirstChild(), 0, dofs);
addAllVertexDOFs(el->getFirstChild()->getFirstChild(), 0, dofs);
dofs.push_back(el->getFirstChild()->getFirstChild()->getDOF(2));
addAllDOFs(el->getFirstChild()->getSecondChild(), 1, dofs);
addAllVertexDOFs(el->getFirstChild()->getSecondChild(), 1, dofs);
}
break;
case 2:
if (el->getFirstChild()) {
addAllDOFs(el->getFirstChild(), 0, dofs);
addAllVertexDOFs(el->getFirstChild(), 0, dofs);
dofs.push_back(el->getFirstChild()->getDOF(2));
addAllDOFs(el->getSecondChild(), 1, dofs);
addAllVertexDOFs(el->getSecondChild(), 1, dofs);
}
break;
default:
......@@ -945,10 +988,57 @@ namespace AMDiS {
}
void ParallelDomainBase::createDOFMemberInfo(
std::map<const DegreeOfFreedom*, std::set<int> >& partitionDOFs,
std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs)
void ParallelDomainBase::addAllEdgeDOFs(Element *el, int ithEdge,
DofContainer& dofs)
{
FUNCNAME("ParallelDomainBase::addAllEdgeDOFs()");
bool addThisEdge = false;
switch (ithEdge) {
case 0:
if (el->getSecondChild())
addAllEdgeDOFs(el->getSecondChild(), 2, dofs);
else
addThisEdge = true;
break;
case 1:
if (el->getFirstChild())
addAllEdgeDOFs(el->getFirstChild(), 2, dofs);
else
addThisEdge = true;
break;
case 2:
if (el->getFirstChild()) {
addAllEdgeDOFs(el->getFirstChild(), 1, dofs);
addAllEdgeDOFs(el->getFirstChild(), 0, dofs);
} else {
addThisEdge = true;
}
break;
default:
ERROR_EXIT("Should never happen!\n");
}
if (addThisEdge) {
ElementDofIterator elDofIter(feSpace->getAdmin());
elDofIter.reset(el);
do {
if (elDofIter.getCurrentPos() == 1 &&
elDofIter.getCurrentElementPos() == ithEdge) {
dofs.push_back(elDofIter.getDofPtr());
}
} while(elDofIter.next());
}
}
void ParallelDomainBase::createDOFMemberInfo(DofToPartitions& partitionDOFs,
DofContainer& rankDOFs,
DofToRank& boundaryDOFs)
{
// === Determine to each dof the set of partitions the dof belongs to. ===
......@@ -972,7 +1062,7 @@ namespace AMDiS {
// === Determine the set of ranks dofs and the dofs ownership at the boundary. ===
// iterate over all DOFs
for (std::map<const DegreeOfFreedom*, std::set<int> >::iterator it = partitionDOFs.begin();
for (DofToPartitions::iterator it = partitionDOFs.begin();
it != partitionDOFs.end();
++it) {
......@@ -1052,13 +1142,99 @@ namespace AMDiS {
}
}
std::vector<int> sendSize(mpiSize, 0);
std::vector<int> recvSize(mpiSize, 0);
std::vector<int> recvSizeBuffer(mpiSize, 0);
MPI::Request request[(mpiSize - 1) * 2];
int requestCounter = 0;
for (std::map<int, std::vector<WorldVector<double> > >::iterator it
= sendCoords.begin();
= sendCoords.begin();
it != sendCoords.end(); ++it) {
sendSize[it->first] = it->second.size();
}
for (std::map<int, std::vector<WorldVector<double> > >::iterator it = recvCoords.begin();
it != recvCoords.end(); ++it) {
recvSize[it->first] = it->second.size();
}
for (int i = 0; i < mpiSize; i++) {
if (i == mpiRank)
continue;
request[requestCounter++] = mpiComm.Isend(&(sendSize[i]), 1, MPI_INT, i, 0);
}
for (int i = 0; i < mpiSize; i++) {
if (i == mpiRank)
continue;
request[requestCounter++] = mpiComm.Irecv(&(recvSizeBuffer[i]), 1, MPI_INT, i, 0);
}
MPI::Request::Waitall(requestCounter, request);
for (int i = 0; i < mpiSize; i++) {
if (i == mpiRank)
continue;
if (recvSize[i] != recvSizeBuffer[i]) {
std::cout << "Error: MPI rank " << mpiRank << " expectes to receive "
<< recvSize[i] << " DOFs from rank " << i << ". But this rank sends "
<< recvSizeBuffer[i] << " DOFs!" << std::endl;
ERROR_EXIT("Should not happen!\n");
}
}
std::map<int, double*> sendCoordsBuffer;
std::map<int, double*> recvCoordsBuffer;
requestCounter = 0;