Skip to content

GitLab

Commit b359d1a9 authored by Thomas Witkowski's avatar Thomas Witkowski
Browse files

Fixed several small problems in 3D refinement in parallel code.

parent 6058784f
Hide whitespace changes
Inline Side-by-side
AMDiS/libtool
View file @ b359d1a9
......@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
# Libtool was configured on host deimos101:
# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -7263,7 +7263,7 @@ disable_libs=static
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
# Libtool was configured on host deimos101:
# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -7568,7 +7568,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
# Libtool was configured on host deimos101:
# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......
AMDiS/other/include/Makefile_AMDiS.mk
View file @ b359d1a9
......@@ -39,7 +39,7 @@ MPCCI_LIB = -L$(MPCCI_DIR)/lib/linux-x86-glibc22 -lmpcci
PARMETIS_LIB = -L$(PARMETIS_DIR) -lparmetis -lmetis
LIBS = $(AMDIS_LIB) $(PNG_LIB)
LIBS += -lboost_iostreams -lboost_filesystem -lboost_system
LIBS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_date_time
ifeq ($(strip $(USE_UMFPACK)), 1)
LIBS += $(UMFPACK_LIB)
......
AMDiS/src/ElInfo3d.cc
View file @ b359d1a9
#include <typeinfo>
#include "ElInfo3d.h"
#include "BasisFunction.h"
#include "Element.h"
......@@ -478,6 +480,8 @@ namespace AMDiS {
{
FUNCNAME("ElInfo3d::fillElInfo()");
TEST_EXIT_DBG(elInfoOld)("Missing old elInfo!\n");
int ochild = 0; /* index of other child = 1-ichild */
int *cv = NULL; /* cv = child_vertex[el_type][ichild] */
const int (*cvg)[4] = NULL; /* cvg = child_vertex[el_type] */
......@@ -497,7 +501,13 @@ namespace AMDiS {
parent = el_old;
level = elInfoOld->level + 1;
iChild = ichild;
int el_type_local = (dynamic_cast<const ElInfo3d*>(elInfoOld))->getType();
int el_type_local = 0;
try {
el_type_local = (dynamic_cast<const ElInfo3d*>(elInfoOld))->getType();
} catch (const std::bad_cast& e) {
ERROR_EXIT("ElInfo is not of type ElInfo3D but %s!\n", typeid(*elInfoOld).name());
}
elType = (el_type_local + 1) % 3;
TEST_EXIT_DBG(element)("missing child %d?\n", ichild);
......
AMDiS/src/Element.cc
View file @ b359d1a9
......@@ -11,6 +11,7 @@ namespace AMDiS {
std::map<DegreeOfFreedom*, bool> Element::deletedDOFs;
int Element::getRegion() const
{
if (!elementData)
......@@ -25,6 +26,7 @@ namespace AMDiS {
return -1;
}
void Element::setDOFPtrs()
{
FUNCNAME("Element::setDOFPtrs()");
......@@ -34,6 +36,7 @@ namespace AMDiS {
dof = mesh->createDOFPtrs();
}
Element::Element(Mesh *aMesh)
{
mesh = aMesh;
......@@ -51,6 +54,7 @@ namespace AMDiS {
}
}
// call destructor through Mesh::freeElement !!!
Element::~Element()
{
......@@ -69,6 +73,7 @@ namespace AMDiS {
}
}
bool Element::deleteElementData(int typeID)
{
FUNCNAME("Element::deleteElementData()");
......@@ -87,6 +92,7 @@ namespace AMDiS {
return false;
}
void Element::deleteElementDOFs()
{
int dim = mesh->getDim();
......@@ -310,6 +316,7 @@ namespace AMDiS {
#undef CHANGE_DOFS_1
#undef CHANGE_DOFS_2
/****************************************************************************/
/* opp_vertex checks whether the face with vertices dof[0],..,dof[DIM-1] is */
/* part of mel's boundary. returns the opposite vertex if true, -1 else */
......@@ -362,13 +369,16 @@ namespace AMDiS {
}
}
void Element::eraseNewCoord() {
void Element::eraseNewCoord()
{
if (newCoord != NULL) {
delete newCoord;
newCoord = NULL;
}
}
void Element::serialize(std::ostream &out)
{
// write children
......@@ -445,6 +455,7 @@ namespace AMDiS {
}
}
void Element::deserialize(std::istream &in)
{
FUNCNAME("Element::deserialize()");
......@@ -555,6 +566,7 @@ namespace AMDiS {
}
}
int Element::calcMemoryUsage()
{
int result = 0;
......@@ -568,4 +580,55 @@ namespace AMDiS {
return result;
}
void writeDotFile(Element *el, std::string filename, int maxLevels)
{
std::vector<int> graphNodes;
std::vector<std::pair<int, int> > graphEdges;
std::vector<Element*> traverseElements, nextTraverseElements;
traverseElements.push_back(el);
int nLevels = 0;
while (!traverseElements.empty() && (maxLevels == -1 || nLevels < maxLevels)) {
nextTraverseElements.clear();
for (unsigned int i = 0; i < traverseElements.size(); i++) {
graphNodes.push_back(traverseElements[i]->getIndex());
if (!traverseElements[i]->isLeaf() &&
(maxLevels == -1 || nLevels + 1 < maxLevels)) {
graphEdges.push_back(std::make_pair(traverseElements[i]->getIndex(),
traverseElements[i]->getChild(0)->getIndex()));
graphEdges.push_back(std::make_pair(traverseElements[i]->getIndex(),
traverseElements[i]->getChild(1)->getIndex()));
nextTraverseElements.push_back(traverseElements[i]->getChild(0));
nextTraverseElements.push_back(traverseElements[i]->getChild(1));
}
}
traverseElements = nextTraverseElements;
nLevels++;
}
std::ofstream file;
file.open(filename.c_str());
file << "digraph G\n";
file << "{\n";
for (unsigned int i = 0; i < graphNodes.size(); i++)
file << " node" << graphNodes[i]
<< " [ label = \"" << graphNodes[i] << "\"];\n";
for (unsigned int i = 0; i < graphEdges.size(); i++)
file << " \"node" << graphEdges[i].first << "\" -> \"node"
<< graphEdges[i].second << "\";\n";
file << "}\n";
file.close();
}
}
AMDiS/src/Element.h
View file @ b359d1a9
......@@ -583,6 +583,11 @@ namespace AMDiS {
friend class Mesh;
};
/// Writes the element hierarchie to a Graphviz dot-file. Using the dot-tool from
/// Graphvis, this dot-file can be converted to a ps-file. Useful for debugging!
void writeDotFile(Element *el, std::string filename, int maxLevels = -1);
}
#endif // AMDIS_ELEMENT_H
......
AMDiS/src/FixVec.h
View file @ b359d1a9
......@@ -504,7 +504,7 @@ namespace AMDiS {
/// returns the euclidian distance of a and b
template<typename T, GeoIndex d>
double absteukl(const FixVec<T,d>& a,const FixVec<T,d>& b);
double absteukl(const FixVec<T,d>& a, const FixVec<T,d>& b);
/// FixVec operator for stream output
template<typename T, GeoIndex d>
......@@ -587,6 +587,15 @@ namespace AMDiS {
template<typename T>
const WorldMatrix<T>& operator+=(WorldMatrix<T>& m1, const WorldMatrix<T>& m2);
inline double norm(const WorldVector<double>& v)
{
double val = 0.0;
for (int i = 0; i < Global::getGeo(WORLD); i++)
val += v[i] * v[i];
return sqrt(val);
}
}
#include "FixVec.hh"
......
AMDiS/src/MeshStructure.cc
View file @ b359d1a9
......@@ -330,8 +330,16 @@ namespace AMDiS {
cont = nextElement();
}
}
MSG("Mesh structure code: %s\n", oss.str().c_str());
if (oss.str().length() < 255) {
MSG("Mesh structure code: %s\n", oss.str().c_str());
} else {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
std::cout << "[" << MPI::COMM_WORLD.Get_rank() << "] Mesh structure code: " << oss.str() << "\n";
#else
std::cout << " Mesh structure code: " << oss.str() << "\n";
#endif
}
}
......
AMDiS/src/parallel/InteriorBoundary.cc
View file @ b359d1a9
......@@ -18,6 +18,9 @@ namespace AMDiS {
break;
case 3:
TEST_EXIT_DBG(otherBound.elType == 0)
("Only 3D macro elements with level 0 are supported!\n");
if (subObj == EDGE) {
int el0_v0 = el->getVertexOfEdge(ithObj, 0);
int el0_v1 = el->getVertexOfEdge(ithObj, 1);
......@@ -52,7 +55,7 @@ namespace AMDiS {
otherMode = (localDofs0[0] != localDofs1[0]);
if (ithObj == 0)
otherMode = localDofs0[1] != localDofs1[1];
otherMode = (localDofs0[1] != localDofs1[1]);
}
break;
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ b359d1a9
......@@ -105,10 +105,12 @@ namespace AMDiS {
int writePartMesh = 1;
GET_PARAMETER(0, "dbg->write part mesh", "%d", &writePartMesh);
if (writePartMesh > 0)
if (writePartMesh > 0) {
debug::writeElementIndexMesh(mesh, "elementIndex.vtu");
writePartitioningMesh("part.vtu");
else
} else {
MSG("Skip write part mesh!\n");
}
}
ParallelDebug::testAllElements(*this);
......@@ -157,7 +159,6 @@ namespace AMDiS {
createPeriodicMap();
// === Global refinements. ===
int globalRefinement = 0;
......@@ -172,7 +173,8 @@ namespace AMDiS {
mesh->dofCompress();
updateLocalGlobalNumbering();
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap();
......@@ -492,7 +494,7 @@ namespace AMDiS {
RankToBoundMap allBound;
for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it)
if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
allBound[it.getRank()].push_back(*it);
for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
......@@ -500,7 +502,7 @@ namespace AMDiS {
allBound[it.getRank()].push_back(*it);
for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it)
if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
allBound[it.getRank()].push_back(*it);
......@@ -579,7 +581,7 @@ namespace AMDiS {
MeshStructure elCode;
elCode.init(boundIt->rankObj);
if (elCode.getCode() != recvCodes[i].getCode()) {
TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
......@@ -1083,7 +1085,7 @@ namespace AMDiS {
bound.neighObj.el = elIndexMap[it2->second.elIndex];
bound.neighObj.elIndex = it2->second.elIndex;
bound.neighObj.elType = -1;
bound.neighObj.elType = elIndexTypeMap[it2->second.elIndex];
bound.neighObj.subObj = geoIndex;
bound.neighObj.ithObj = it2->second.ithObject;
......@@ -1435,7 +1437,7 @@ namespace AMDiS {
it->rankObj.el->getNonVertexDofs(feSpace, it->rankObj, dofs);
for (unsigned int i = 0; i < dofs.size(); i++)
sendDofs[it.getRank()].push_back(dofs[i]);
sendDofs[it.getRank()].push_back(dofs[i]);
}
......@@ -1448,7 +1450,7 @@ namespace AMDiS {
DofContainer::iterator eraseIt =
find(rankDofs.begin(), rankDofs.end(), dofs[i]);
if (eraseIt != rankDofs.end())
rankDofs.erase(eraseIt);
rankDofs.erase(eraseIt);
recvDofs[it.getRank()].push_back(dofs[i]);
}
......@@ -1796,7 +1798,7 @@ namespace AMDiS {
int *sendbuf = new int[2];
sendbuf[0] = periodicDof[type0][it->first];
sendbuf[1] = periodicDof[type1][it->first];
request[requestCounter++] =
mpiComm.Isend(sendbuf, 2, MPI_INT, *(it->second.begin()), 0);
request[requestCounter++] =
......
AMDiS/src/parallel/ParallelDebug.cc
View file @ b359d1a9
......@@ -139,13 +139,13 @@ namespace AMDiS {
typedef std::map<int, DofContainer> RankToDofContainer;
// Maps to each neighbour rank an array of WorldVectors. This array contains the
// coordinates of all dofs this rank shares on the interior boundary with 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
// boundarys dof.
// boundarys DOFs.
RankToCoords sendCoords;
// A rank receives all boundary dofs that are at its interior boundaries but are
// not owned by the rank. This map stores for each rank the coordinates of dofs
// A rank receives all boundary DOFs that are at its interior boundaries but are
// not owned by the rank. This map stores for each rank the coordinates of DOFs
// this rank expectes to receive from.
RankToCoords recvCoords;
......@@ -180,14 +180,16 @@ namespace AMDiS {
if (i == pdb.mpiRank)
continue;
request[requestCounter++] = pdb.mpiComm.Isend(&(sendSize[i]), 1, MPI_INT, i, 0);
request[requestCounter++] =
pdb.mpiComm.Isend(&(sendSize[i]), 1, MPI_INT, i, 0);
}
for (int i = 0; i < pdb.mpiSize; i++) {
if (i == pdb.mpiRank)
continue;
request[requestCounter++] = pdb.mpiComm.Irecv(&(recvSizeBuffer[i]), 1, MPI_INT, i, 0);
request[requestCounter++] =
pdb.mpiComm.Irecv(&(recvSizeBuffer[i]), 1, MPI_INT, i, 0);
}
MPI::Request::Waitall(requestCounter, request);
......@@ -217,26 +219,24 @@ namespace AMDiS {
stdMpi.recv(recvCoords);
stdMpi.startCommunication<double>(MPI_DOUBLE);
double eps = 1e-13;
int dimOfWorld = Global::getGeo(WORLD);
// === Compare the received with the expected coordinates. ===
for (RankToCoords::iterator it = stdMpi.getRecvData().begin();
it != stdMpi.getRecvData().end(); ++it) {
for (int i = 0; i < static_cast<int>(it->second.size()); i++) {
for (int j = 0; j < dimOfWorld; j++) {
bool c = fabs((it->second)[i][j] - recvCoords[it->first][i][j]) < eps;
// === Print error message if the coordinates are not the same. ===
if (printCoords && !c) {
MSG("[DBG] i = %d\n", i);
for (unsigned int i = 0; i < it->second.size(); i++) {
WorldVector<double> tmp = (it->second)[i];
tmp -= recvCoords[it->first][i];
if (norm(tmp) > 1e-13) {
// === Print error message if the coordinates are not the same. ===
if (printCoords) {
MSG("[DBG] i = %d\n", i);
std::stringstream oss;
oss.precision(5);
oss << "[DBG] Rank " << pdb.mpiRank << " from rank " << it->first
<< " expect coords (";
<< " expect coords (";
for (int k = 0; k < dimOfWorld; k++) {
oss << recvCoords[it->first][i][k];
if (k + 1 < dimOfWorld)
......@@ -250,16 +250,13 @@ namespace AMDiS {
}
oss << ")";
MSG("%s\n", oss.str().c_str());
debug::printInfoByDof(pdb.feSpace, *(pdb.recvDofs[it->first][i]));
}
if (!c) {
ERROR("Wrong DOFs in rank %d!\n", pdb.mpiRank);
foundError = 1;
}
}
}
ERROR("Wrong DOFs in rank %d!\n", pdb.mpiRank);
foundError = 1;
}
}
}
mpi::globalAdd(foundError);
TEST_EXIT(foundError == 0)("Error found on at least on rank!\n");
......@@ -459,6 +456,14 @@ namespace AMDiS {
MSG(" neigh obj-ind: %d sub-obj: %d ith-obj: %d\n",
it->neighObj.elIndex, it->neighObj.subObj, it->neighObj.ithObj);
}
for (InteriorBoundary::iterator it(pdb.periodicBoundary); !it.end(); ++it) {
MSG("Periodic boundary with rank %d: \n", it.getRank());
MSG(" ranks obj-ind: %d sub-obj: %d ith-obj: %d\n",
it->rankObj.elIndex, it->rankObj.subObj, it->rankObj.ithObj);
MSG(" neigh obj-ind: %d sub-obj: %d ith-obj: %d\n",
it->neighObj.elIndex, it->neighObj.subObj, it->neighObj.ithObj);
}
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment