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Commit e6efd667 authored by Thomas Witkowski's avatar Thomas Witkowski
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UI, IT WORKS.....

parent 1f9daa76
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AMDiS/src/DOFMatrix.cc
View file @ e6efd667
......@@ -43,6 +43,7 @@ namespace AMDiS {
inserter(NULL)
{}
DOFMatrix::DOFMatrix(const FiniteElemSpace* rowSpace,
const FiniteElemSpace* colSpace,
std::string n)
......@@ -74,6 +75,7 @@ namespace AMDiS {
applyDBCs.clear();
}
DOFMatrix::DOFMatrix(const DOFMatrix& rhs)
: name(rhs.name + "copy")
{
......@@ -87,6 +89,7 @@ namespace AMDiS {
inserter = 0;
}
DOFMatrix::~DOFMatrix()
{
FUNCNAME("DOFMatrix::~DOFMatrix()");
......@@ -99,6 +102,7 @@ namespace AMDiS {
delete inserter;
}
void DOFMatrix::print() const
{
FUNCNAME("DOFMatrix::print()");
......@@ -107,6 +111,7 @@ namespace AMDiS {
inserter->print();
}
bool DOFMatrix::symmetric()
{
FUNCNAME("DOFMatrix::symmetric()");
......@@ -132,6 +137,7 @@ namespace AMDiS {
return true;
}
void DOFMatrix::test()
{
FUNCNAME("DOFMatrix::test()");
......@@ -144,6 +150,7 @@ namespace AMDiS {
MSG("Matrix `%s' is symmetric.\n", name.data());
}
DOFMatrix& DOFMatrix::operator=(const DOFMatrix& rhs)
{
rowFeSpace = rhs.rowFeSpace;
......@@ -168,6 +175,7 @@ namespace AMDiS {
return *this;
}
void DOFMatrix::addElementMatrix(const ElementMatrix& elMat,
const BoundaryType *bound,
ElInfo* rowElInfo,
......@@ -232,6 +240,8 @@ namespace AMDiS {
for (int j = 0; j < nCol; j++) {
DegreeOfFreedom col = colIndices[j];
ins[row][col] += elMat[i][j];
// MSG("El %d DOFs %d %d value %f\n", rowElInfo->getElement()->getIndex(), row, col, elMat[i][j]);
}
}
}
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ e6efd667
......@@ -611,8 +611,7 @@ namespace AMDiS {
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap();
createPeriodicMap();
INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n",
MPI::Wtime() - first);
......@@ -1429,10 +1428,10 @@ namespace AMDiS {
mesh->getDofIndexCoords(it->first.first, feSpace, c0);
mesh->getDofIndexCoords(it->first.second, feSpace, c1);
// MSG("CREATE BOUNDARY FOR DOF MAP: %d (%.3f %.3f %.3f)<-> %d (%.3f %.3f %.3f)\n", it->first.first,
// c0[0], c0[1], c0[2], it->first.second, c1[0], c1[1], c1[2]);
// MSG("CREATE BOUNDARY FOR DOF MAP: %d (%.3f %.3f %.3f)<-> %d (%.3f %.3f %.3f)\n", it->first.first,
// c0[0], c0[1], c0[2], it->first.second, c1[0], c1[1], c1[2]);
ElementObjectData& perDofEl0 = elObjects.getElementsInRank(it->first.first)[mpiRank];
// MSG("DATA: %d %d %d\n", perDofEl0.elIndex, VERTEX, perDofEl0.ithObject);
// MSG("DATA: %d %d %d\n", perDofEl0.elIndex, VERTEX, perDofEl0.ithObject);
for (map<int, ElementObjectData>::iterator elIt = elObjects.getElementsInRank(it->first.second).begin();
elIt != elObjects.getElementsInRank(it->first.second).end(); ++elIt) {
......@@ -1629,9 +1628,9 @@ namespace AMDiS {
periodicBoundary.boundary[rankIt->first][j].neighObj.ithObj);
}
}
*/
for (RankToBoundMap::iterator rankIt = periodicBoundary.boundary.begin();
rankIt != periodicBoundary.boundary.end(); ++rankIt) {
......@@ -1834,28 +1833,10 @@ namespace AMDiS {
ParallelDebug::testGlobalIndexByCoords(*this);
ParallelDebug::writeDebugFile(*this, debugOutputDir + "mpi-dbg", "dat");
#if 1
MSG("------------- Debug information -------------\n");
MSG("nRankDofs = %d\n", nRankDofs);
MSG("nOverallDofs = %d\n", nOverallDofs);
MSG("rstart %d\n", rstart);
/*
for (RankToDofContainer::iterator it = sendDofs.begin();
it != sendDofs.end(); ++it) {
MSG("send %d DOFs to rank %d\n", it->second.size(), it->first);
for (unsigned int i = 0; i < it->second.size(); i++)
MSG("%d send DOF: %d\n", i, *(it->second[i]));
}
for (RankToDofContainer::iterator it = recvDofs.begin();
it != recvDofs.end(); ++it) {
MSG("recv %d DOFs from rank %d\n", it->second.size(), it->first);
for (unsigned int i = 0; i < it->second.size(); i++)
MSG("%d recv DOF: %d\n", i, *(it->second[i]));
}
*/
#endif
#endif
}
......@@ -1882,7 +1863,7 @@ namespace AMDiS {
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
// MSG("------------- WITH RANK %d ------------------\n", it->first);
// MSG("------------- WITH RANK %d ------------------\n", it->first);
if (it->first == mpiRank) {
TEST_EXIT_DBG(it->second.size() % 2 == 0)("Should not happen!\n");
......@@ -1895,9 +1876,9 @@ namespace AMDiS {
bound.neighObj.el->getVertexDofs(feSpace, bound.neighObj, dofs1);
bound.neighObj.el->getNonVertexDofs(feSpace, bound.neighObj, dofs1);
// MSG("BOUND-I %d-%d-%d WITH %d-%d-%d\n",
// bound.rankObj.elIndex, bound.rankObj.subObj, bound.rankObj.ithObj,
// bound.neighObj.elIndex, bound.neighObj.subObj, bound.neighObj.ithObj);
// MSG("BOUND-I %d-%d-%d WITH %d-%d-%d\n",
// bound.rankObj.elIndex, bound.rankObj.subObj, bound.rankObj.ithObj,
// bound.neighObj.elIndex, bound.neighObj.subObj, bound.neighObj.ithObj);
TEST_EXIT_DBG(dofs0.size() == dofs1.size())("Should not happen!\n");
......@@ -1911,7 +1892,7 @@ namespace AMDiS {
periodicDof[type][globalDof0] = globalDof1;
periodicDofAssociations[globalDof0].insert(type);
// MSG("SET(A TYPE %d) DOF %d -> %d\n", type, globalDof0, globalDof1);
// MSG("SET(A TYPE %d) DOF %d -> %d\n", type, globalDof0, globalDof1);
}
}
}
......@@ -1924,19 +1905,19 @@ namespace AMDiS {
int nDofs = dofs.size();
// MSG("BOUND-R (T = %d) %d-%d-%d WITH %d-%d-%d\n",
// boundIt->type,
// boundIt->rankObj.elIndex, boundIt->rankObj.subObj, boundIt->rankObj.ithObj,
// boundIt->neighObj.elIndex, boundIt->neighObj.subObj, boundIt->neighObj.ithObj);
// MSG("BOUND-R (T = %d) %d-%d-%d WITH %d-%d-%d\n",
// boundIt->type,
// boundIt->rankObj.elIndex, boundIt->rankObj.subObj, boundIt->rankObj.ithObj,
// boundIt->neighObj.elIndex, boundIt->neighObj.subObj, boundIt->neighObj.ithObj);
boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < (dofs.size() - nDofs); i++) {
// WorldVector<double> c;
// mesh->getDofIndexCoords(*(dofs[nDofs + i]), feSpace, c);
// MSG(" SEND i = %d DOF = %d (%f %f %f)\n", nDofs + i, mapLocalGlobalDofs[*(dofs[nDofs + i])], c[0], c[1], c[2]);
// WorldVector<double> c;
// mesh->getDofIndexCoords(*(dofs[nDofs + i]), feSpace, c);
// MSG(" SEND i = %d DOF = %d (%f %f %f)\n", nDofs + i, mapLocalGlobalDofs[*(dofs[nDofs + i])], c[0], c[1], c[2]);
rankToDofType[it->first].push_back(boundIt->type);
}
}
......@@ -1964,7 +1945,7 @@ namespace AMDiS {
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
// MSG("------------- WITH RANK %d ------------------\n", it->first);
// MSG("------------- WITH RANK %d ------------------\n", it->first);
DofContainer& dofs = rankPeriodicDofs[it->first];
vector<int>& types = rankToDofType[it->first];
......@@ -1977,17 +1958,16 @@ namespace AMDiS {
int mapGlobalDofIndex = stdMpi.getRecvData(it->first)[i];
BoundaryType type = types[i];
// WorldVector<double> c;
// mesh->getDofIndexCoords(*(dofs[i]), feSpace, c);
// MSG(" RECV i = %d DOF = %d (%f %f %f)\n", i, *(dofs[i]), c[0], c[1], c[2]);
// WorldVector<double> c;
// mesh->getDofIndexCoords(*(dofs[i]), feSpace, c);
// MSG(" RECV i = %d DOF = %d (%f %f %f)\n", i, *(dofs[i]), c[0], c[1], c[2]);
// Check if this global dof with the corresponding boundary type was
// not added before by another periodic boundary from other rank.
if (periodicDofAssociations[globalDofIndex].count(type) == 0) {
// MSG("SET(B-%d TYPE %d) DOF %d -> %d\n", i, type, globalDofIndex, mapGlobalDofIndex);
// MSG("SET(B-%d TYPE %d) DOF %d -> %d\n", i, type, globalDofIndex, mapGlobalDofIndex);
periodicDof[type][globalDofIndex] = mapGlobalDofIndex;
periodicDofAssociations[globalDofIndex].insert(type);
......
AMDiS/src/parallel/MeshDistributor.h
View file @ e6efd667
......@@ -113,6 +113,11 @@ namespace AMDiS {
return name;
}
inline Mesh* getMesh()
{
return mesh;
}
/// Returns \ref feSpace.
inline const FiniteElemSpace* getFeSpace()
{
......@@ -131,6 +136,11 @@ namespace AMDiS {
return nOverallDofs;
}
inline DofMapping& getMapLocalGlobalDofs()
{
return mapLocalGlobalDofs;
}
/// Maps a local dof to its global index.
inline DegreeOfFreedom mapLocalToGlobal(DegreeOfFreedom dof)
{
......@@ -143,11 +153,20 @@ namespace AMDiS {
return mapLocalDofIndex[dof];
}
/// Returns the periodic mapping for all boundary DOFs in rank.
inline PeriodicDofMap& getPeriodicMapping()
{
return periodicDof;
}
/// Returns for a global dof index its periodic mapping for a given boundary type.
inline int getPeriodicMapping(BoundaryType type, int globalDofIndex)
{
FUNCNAME("MeshDistributor::getPeriodicMapping()");
TEST_EXIT_DBG(periodicDof[type].count(globalDofIndex) == 1)
("Should not happen!\n");
("There is no periodic association for global DOF %d for boundary type %d!\n",
globalDofIndex, type);
return periodicDof[type][globalDofIndex];
}
......@@ -194,6 +213,11 @@ namespace AMDiS {
return mpiRank;
}
inline int getMpiSize()
{
return mpiSize;
}
inline MPI::Intracomm& getMpiComm()
{
return mpiComm;
......
AMDiS/src/parallel/PetscSolver.cc
View file @ e6efd667
......@@ -10,6 +10,9 @@
// See also license.opensource.txt in the distribution.
#include <vector>
#include <set>
#include "parallel/PetscSolver.h"
#include "parallel/StdMpi.h"
#include "parallel/ParallelDebug.h"
......@@ -53,6 +56,52 @@ namespace AMDiS {
TEST_EXIT(mat)("No DOFMatrix!\n");
typedef map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;
typedef map<BoundaryType, DofMapping> PeriodicDofMap;
StdMpi<PeriodicDofMap> stdMpi(meshDistributor->getMpiComm());
if (meshDistributor->getMpiRank() == 0) {
for (int i = 1; i < meshDistributor->getMpiSize(); i++)
stdMpi.recv(i);
} else {
stdMpi.send(0, meshDistributor->getPeriodicMapping());
}
stdMpi.startCommunication<int>(MPI_INT);
StdMpi<PeriodicDofMap> stdMpi2(meshDistributor->getMpiComm());
PeriodicDofMap overallDofMap;
if (meshDistributor->getMpiRank() == 0) {
overallDofMap = meshDistributor->getPeriodicMapping();
for (int i = 1; i < meshDistributor->getMpiSize(); i++) {
PeriodicDofMap &rankDofMap = stdMpi.getRecvData(i);
for (PeriodicDofMap::iterator it = rankDofMap.begin(); it != rankDofMap.end(); ++it) {
for (DofMapping::iterator dofIt = it->second.begin(); dofIt != it->second.end(); ++dofIt) {
if (overallDofMap[it->first].count(dofIt->first) == 1) {
TEST_EXIT_DBG(overallDofMap[it->first][dofIt->first] == dofIt->second)
("Should not happen!\n");
} else {
overallDofMap[it->first][dofIt->first] = dofIt->second;
}
}
}
}
for (int i = 1; i < meshDistributor->getMpiSize(); i++)
stdMpi2.send(i, overallDofMap);
} else {
stdMpi2.recv(0);
}
stdMpi2.startCommunication<int>(MPI_INT);
if (meshDistributor->getMpiRank() > 0)
overallDofMap = stdMpi2.getRecvData(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;
......@@ -76,107 +125,123 @@ namespace AMDiS {
for (cursor_type cursor = begin<row>(mat->getBaseMatrix()),
cend = end<row>(mat->getBaseMatrix()); cursor != cend; ++cursor) {
cols.clear();
values.clear();
// Global index of the current row dof.
int globalRowDof = meshDistributor->mapLocalToGlobal(*cursor);
// Test if the current row dof is a periodic dof.
bool periodicRow = meshDistributor->isPeriodicDof(globalRowDof);
// Calculate petsc row index.
int rowIndex = globalRowDof * dispMult + dispAddRow;
if (!periodicRow) {
// Calculate petsc row index.
int rowIndex = globalRowDof * dispMult + dispAddRow;
// === Traverse all non zero entries of the row and produce vector cols ===
// === with the column indices of all row entries and vector values ===
// === with the corresponding values. ===
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
icursor != icend; ++icursor) {
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
icursor != icend; ++icursor) {
// Global index of the current column index.
int globalColDof = meshDistributor->mapLocalToGlobal(col(*icursor));
// Calculate the exact position of the column index in the petsc matrix.
int colIndex = globalColDof * dispMult + dispAddCol;
// Set only non zero values.
if (value(*icursor) != 0.0 || rowIndex == colIndex) {
// If the current row is not periodic, but the current dof index is periodic,
// we have to duplicate the value to the other corresponding periodic columns.
if (!periodicRow && meshDistributor->isPeriodicDof(globalColDof)) {
// The value is assign to n matrix entries, therefore, every entry
// has only 1/n value of the original entry.
std::set<int>& perAsc = meshDistributor->getPerDofAssociations(globalColDof);
double scalFactor = 1.0 / (perAsc.size() + 1.0);
// Insert original entry.
cols.push_back(colIndex);
values.push_back(value(*icursor) * scalFactor);
// Insert the periodic entries.
for (std::set<int>::iterator perIt = perAsc.begin(); perIt != perAsc.end(); ++perIt) {
int mappedDof = meshDistributor->getPeriodicMapping(*perIt, globalColDof);
cols.push_back(mappedDof * dispMult + dispAddCol);
values.push_back(value(*icursor) * scalFactor);
}
} else {
// The col dof index is not periodic, simple add entry.
cols.push_back(colIndex);
values.push_back(value(*icursor));
globalCols.push_back(globalColDof);
}
}
}
// Global index of the current column index.
int globalColDof = meshDistributor->mapLocalToGlobal(col(*icursor));
// Test if the current col dof is a periodic dof.
bool periodicCol = meshDistributor->isPeriodicDof(globalColDof);
if (!periodicCol) {
// Calculate the exact position of the column index in the petsc matrix.
int colIndex = globalColDof * dispMult + dispAddCol;
MatSetValue(petscMatrix, rowIndex, colIndex, value(*icursor), ADD_VALUES);
if (rowIndex == 0 && colIndex == 0) {
MSG("ADDED-C ON ZERO: %f (with no scal)\n", value(*icursor));
}
// === Up to now we have assembled one row. Now, the row must be send to the ===
// === corresponding rows in the petsc matrix. ===
if (periodicRow) {
// The row dof is periodic, so send dof to all the corresponding rows.
std::set<int>& perAsc = meshDistributor->getPerDofAssociations(globalRowDof);
} else {
std::set<int>& perColAsc = meshDistributor->getPerDofAssociations(globalColDof);
std::set<int> perAsc;
for (std::set<int>::iterator it = perColAsc.begin(); it != perColAsc.end(); ++it)
if (*it >= -3)
perAsc.insert(*it);
double scaledValue = value(*icursor) * std::pow(0.5, static_cast<double>(perAsc.size()));
std::vector<int> newCols;
newCols.push_back(globalColDof);
for (std::set<int>::iterator it = perAsc.begin(); it != perAsc.end(); ++it) {
int nCols = static_cast<int>(newCols.size());
for (int i = 0; i < nCols; i++) {
TEST_EXIT(overallDofMap[*it].count(newCols[i]) > 0)("Should not happen: %d %d\n", *it, newCols[i]);
double scalFactor = 1.0 / (perAsc.size() + 1.0);
for (unsigned int i = 0; i < values.size(); i++)
values[i] *= scalFactor;
newCols.push_back(overallDofMap[*it][newCols[i]]);
}
}
// Send the main row to the petsc matrix.
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
for (std::set<int>::iterator perIt = perAsc.begin();
perIt != perAsc.end(); ++perIt) {
std::vector<int> perCols;
perCols.reserve(300);
std::vector<double> perValues;
perValues.reserve(300);
for (unsigned int i = 0; i < cols.size(); i++) {
int tmp = (cols[i] - dispAddCol) / dispMult;
if (meshDistributor->isPeriodicDof(tmp, *perIt)) {
perCols.push_back((meshDistributor->getPeriodicMapping(*perIt, tmp) * dispMult) + dispAddCol);
} else {
perCols.push_back(cols[i]);
for (int i = 0; i < newCols.size(); i++) {
int colIndex = newCols[i] * dispMult + dispAddCol;
MatSetValue(petscMatrix, rowIndex, colIndex, scaledValue, ADD_VALUES);
if (rowIndex == 0 && colIndex == 0) {
MSG("ADDED-B ON ZERO: %f (with scal %f)\n", scaledValue, std::pow(0.5, static_cast<double>(perAsc.size())));
}
}
perValues.push_back(values[i]);
}
int perRowIndex = (meshDistributor->getPeriodicMapping(*perIt, globalRowDof) * dispMult) + dispAddRow;
MatSetValues(petscMatrix, 1, &perRowIndex, perCols.size(),
&(perCols[0]), &(perValues[0]), ADD_VALUES);
}
} else {
// The row dof is not periodic, simply send the row to the petsc matrix.
MatSetValues(petscMatrix, 1, &rowIndex, cols.size(),
&(cols[0]), &(values[0]), ADD_VALUES);
}
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
icursor != icend; ++icursor) {
// Global index of the current column index.
int globalColDof = meshDistributor->mapLocalToGlobal(col(*icursor));
std::set<int>& perColAsc = meshDistributor->getPerDofAssociations(globalColDof);
std::set<int> perAsc;
for (std::set<int>::iterator it = perColAsc.begin(); it != perColAsc.end(); ++it)
if (*it >= -3)
perAsc.insert(*it);
std::set<int>& perRowAsc = meshDistributor->getPerDofAssociations(globalRowDof);
for (std::set<int>::iterator it = perRowAsc.begin(); it != perRowAsc.end(); ++it)
if (*it >= -3)
perAsc.insert(*it);
double scaledValue = value(*icursor) * std::pow(0.5, static_cast<double>(perAsc.size()));
std::vector<std::pair<int, int> > entry;
entry.push_back(std::make_pair(globalRowDof, globalColDof));
for (std::set<int>::iterator it = perAsc.begin(); it != perAsc.end(); ++it) {
int nEntry = static_cast<int>(entry.size());
for (int i = 0; i < nEntry; i++) {
// TEST_EXIT(overallDofMap[*it].count(entry[i].first) > 0)
// ("Should not happen A: %d %d\n", *it, entry[i].first);
// TEST_EXIT(overallDofMap[*it].count(entry[i].second) > 0)
// ("Should not happen B: %d %d\n", *it, entry[i].second);
int rd;
if (overallDofMap[*it].count(entry[i].first) > 0)
rd = overallDofMap[*it][entry[i].first];
else
rd = entry[i].first;
int cd;
if (overallDofMap[*it].count(entry[i].second) > 0)
cd = overallDofMap[*it][entry[i].second];
else
cd = entry[i].second;
entry.push_back(std::make_pair(rd, cd));
}
}
int ccc = 0;
for (std::vector<std::pair<int, int> >::iterator eIt = entry.begin(); eIt != entry.end(); ++eIt) {
// Calculate petsc row index.
int rowIndex = eIt->first * dispMult + dispAddRow;
int colIndex = eIt->second * dispMult + dispAddCol;
MatSetValue(petscMatrix, rowIndex, colIndex, scaledValue, ADD_VALUES);
if (rowIndex == 0 && colIndex == 0) {
MSG("ADDED-A ON ZERO: %f (with scal %f not scaled %f) org DOF/COL: %d %d TEST %d\n",
scaledValue, std::pow(0.5, static_cast<double>(perAsc.size())), value(*icursor),
globalRowDof, globalColDof, ccc);
}
ccc++;
}
}
}
}
}
......
AMDiS/src/parallel/StdMpi.cc
View file @ e6efd667
......@@ -92,8 +92,6 @@ namespace AMDiS {
size += 2 + it->second.size() * 2;
}
MSG("RET SIZE = %d\n", size);
return size;
}
......
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