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Commit 41774d49 authored by Thomas Witkowski's avatar Thomas Witkowski
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* Update due to small bug in Residualestimator

parent 44e4efd1
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Showing with 96 additions and 116 deletions
AMDiS/src/ParMetisPartitioner.cc
View file @ 41774d49
......@@ -13,7 +13,7 @@
namespace AMDiS {
ParMetisMesh::ParMetisMesh(Mesh *mesh, MPI::Comm *comm)
: numElements_(0),
: nElements(0),
mpiComm(comm)
{
FUNCNAME("ParMetisMesh::ParMetisMesh()");
......@@ -45,19 +45,19 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
numElements_ = elementCounter;
nElements = elementCounter;
TEST_EXIT(numElements_ > 0)("no elements in ParMETIS mesh\n");
TEST_EXIT(nElements > 0)("no elements in ParMETIS mesh\n");
// allocate memory
eptr_ = GET_MEMORY(int, numElements_ + 1);
eind_ = GET_MEMORY(int, numElements_ * (dim_ + 1));
elmdist_ = GET_MEMORY(int, mpiSize + 1);
eptr_ = GET_MEMORY(int, nElements + 1);
eind_ = GET_MEMORY(int, nElements * (dim_ + 1));
elmdist = GET_MEMORY(int, mpiSize + 1);
elem_p2a_ = GET_MEMORY(int, numElements_);
elem_p2a_ = GET_MEMORY(int, nElements);
if (dim_ == dow) {
xyz_ = GET_MEMORY(float, numElements_ * dim_);
xyz_ = GET_MEMORY(float, nElements * dim_);
} else {
xyz_ = NULL;
}
......@@ -69,11 +69,11 @@ namespace AMDiS {
float *ptr_xyz = xyz_;
// gather element numbers and create elmdist
mpiComm->Allgather(&numElements_, 1, MPI_INT, elmdist_ + 1, 1, MPI_INT);
mpiComm->Allgather(&nElements, 1, MPI_INT, elmdist + 1, 1, MPI_INT);
elmdist_[0] = 0;
elmdist[0] = 0;
for (int i = 2; i < mpiSize + 1; i++) {
elmdist_[i] += elmdist_[i - 1];
elmdist[i] += elmdist[i - 1];
}
// traverse mesh and fill distributed ParMETIS data
......@@ -130,19 +130,19 @@ namespace AMDiS {
ParMetisMesh::~ParMetisMesh()
{
if (eptr_)
FREE_MEMORY(eptr_, int, numElements_ + 1);
FREE_MEMORY(eptr_, int, nElements + 1);
if (eind_)
FREE_MEMORY(eind_, int, numElements_ * (dim_ + 1));
FREE_MEMORY(eind_, int, nElements * (dim_ + 1));
if (elmdist_)
FREE_MEMORY(elmdist_, int, mpiComm->Get_size() + 1);
if (elmdist)
FREE_MEMORY(elmdist, int, mpiComm->Get_size() + 1);
if (xyz_)
FREE_MEMORY(xyz_, float, numElements_ * dim_);
FREE_MEMORY(xyz_, float, nElements * dim_);
if (elem_p2a_)
FREE_MEMORY(elem_p2a_, int, numElements_);
FREE_MEMORY(elem_p2a_, int, nElements);
}
ParMetisGraph::ParMetisGraph(ParMetisMesh *parMetisMesh,
......@@ -198,7 +198,6 @@ namespace AMDiS {
elInfo = stack.traverseFirst(mesh_, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
Element *element = elInfo->getElement();
//int index = element->getIndex();
TEST_EXIT(element->getElementData(PARTITION_ED) == NULL)
("mesh already partitioned\n");
......
AMDiS/src/ParMetisPartitioner.h
View file @ 41774d49
......@@ -81,7 +81,7 @@ namespace AMDiS {
}
inline int *getElementDist() {
return elmdist_;
return elmdist;
}
inline int getDim() {
......@@ -93,7 +93,7 @@ namespace AMDiS {
}
inline int getNumElements() {
return numElements_;
return nElements;
}
protected:
......@@ -101,13 +101,21 @@ namespace AMDiS {
int *eind_;
int *elmdist_;
/* \brief
* Array that specifies the distribution of the mesh elements.
*
* elmdist[0] = 0;
* elmdist[1] = number of elements of proc 0;
* elmdist[2] = elmdist[1] + number of elements of proc 1;
* ...
*/
int *elmdist;
int dim_;
float *xyz_;
int numElements_;
int nElements;
std::map<int, int> elem_a2p_;
......@@ -131,11 +139,11 @@ namespace AMDiS {
inline int *getXAdj() {
return xadj_;
};
}
inline int *getAdjncy() {
return adjncy_;
};
}
protected:
ParMetisMesh *parMetisMesh_;
......@@ -152,7 +160,7 @@ namespace AMDiS {
: mesh_(mesh),
mpiComm(comm),
parMetisMesh_(NULL)
{};
{}
void partition(std::map<int, double> *elemWeights,
PartitionMode mode = INITIAL,
......@@ -163,6 +171,10 @@ namespace AMDiS {
void fillLeafPartitionVec(std::map<int, int> *coarseVec,
std::map<int, int> *fineVec);
/* \brief
* Creates an initial paritioning of the AMDiS mesh by seting the partition status
* of all elements to either IN or UNDEFINED.
*/
void createPartitionData();
void deletePartitionData();
......
AMDiS/src/ParallelProblem.cc
View file @ 41774d49
......@@ -226,7 +226,7 @@ namespace AMDiS {
TEST_EXIT(localCoarseGridLevel_ >= globalCoarseGridLevel_)
("local coarse grid level < global coarse grid level\n");
partitioner_ = NEW ParMetisPartitioner(mesh, &mpiComm);
partitioner = NEW ParMetisPartitioner(mesh, &mpiComm);
GET_PARAMETER(0, name_ + "->adaptive thresholds", "%d",
&adaptiveThresholds_);
......@@ -251,7 +251,7 @@ namespace AMDiS {
ParallelProblem::~ParallelProblem()
{
DELETE partitioner_;
DELETE partitioner;
}
bool ParallelProblem::doPartitioning(AdaptInfo *adaptInfo, double localWeightSum)
......@@ -262,8 +262,7 @@ namespace AMDiS {
int *partArray = GET_MEMORY(int, mpiSize);
int part = 0;
mpiComm.Gather(&localWeightSum, 1, MPI_DOUBLE,
weightSum, 1, MPI_DOUBLE, 0);
mpiComm.Gather(&localWeightSum, 1, MPI_DOUBLE, weightSum, 1, MPI_DOUBLE, 0);
if (mpiRank == 0) {
......@@ -332,14 +331,14 @@ namespace AMDiS {
static bool initial = true;
if (initial) {
initial = false;
partitioner_->fillCoarsePartitionVec(&oldPartitionVec);
partitioner_->partition(&elemWeights_, INITIAL);
partitioner->fillCoarsePartitionVec(&oldPartitionVec);
partitioner->partition(&elemWeights_, INITIAL);
} else {
oldPartitionVec = partitionVec;
partitioner_->partition(&elemWeights_, ADAPTIVE_REPART, 100.0 /*0.000001*/);
partitioner->partition(&elemWeights_, ADAPTIVE_REPART, 100.0 /*0.000001*/);
}
partitioner_->fillCoarsePartitionVec(&partitionVec);
partitioner->fillCoarsePartitionVec(&partitionVec);
}
void ParallelProblem::refineOverlap(AdaptInfo *adaptInfo)
......@@ -749,8 +748,8 @@ namespace AMDiS {
void ParallelProblem::exchangeDOFVector(AdaptInfo *adaptInfo,
DOFVector<double> *values)
{
partitioner_->fillLeafPartitionVec(&oldPartitionVec, &oldPartitionVec);
partitioner_->fillLeafPartitionVec(&partitionVec, &partitionVec);
partitioner->fillLeafPartitionVec(&oldPartitionVec, &oldPartitionVec);
partitioner->fillLeafPartitionVec(&partitionVec, &partitionVec);
// === get send and recieve orders ===
std::vector<std::vector<DegreeOfFreedom> > sendOrder;
......@@ -1353,7 +1352,7 @@ namespace AMDiS {
if (mpiSize > 1) {
clock_t partitioningStart = clock();
partitioner_->createPartitionData();
partitioner->createPartitionData();
setElemWeights(adaptInfo);
partitionMesh(adaptInfo);
......@@ -1388,8 +1387,7 @@ namespace AMDiS {
if (mpiRank == 0) {
clock_t partitioningEnd = clock();
partitioningTime = TIME_USED(partitioningStart,
partitioningEnd);
partitioningTime = TIME_USED(partitioningStart, partitioningEnd);
computationStart = partitioningEnd;
}
......@@ -1416,7 +1414,7 @@ namespace AMDiS {
if (!timeIF_)
problem->writeFiles(adaptInfo, true);
partitioner_->deletePartitionData();
partitioner->deletePartitionData();
if (!usersEstimator)
DELETE problem->getEstimator();
......@@ -1531,7 +1529,7 @@ namespace AMDiS {
FUNCNAME("ParallelProblem::initParallelization()");
if (mpiSize > 1) {
partitioner_->createPartitionData();
partitioner->createPartitionData();
setElemWeights(adaptInfo);
partitionMesh(adaptInfo);
......@@ -1594,7 +1592,7 @@ namespace AMDiS {
if (!timeIF_)
problem->writeFiles(adaptInfo, true);
partitioner_->deletePartitionData();
partitioner->deletePartitionData();
for (int i = 0; i < nComponents; i++) {
if (static_cast<int>(usersEstimator.size()) == nComponents)
......
AMDiS/src/ParallelProblem.h
View file @ 41774d49
......@@ -63,7 +63,7 @@ namespace AMDiS {
ProblemIterationInterface *iterationIF,
ProblemTimeInterface *timeIF);
virtual ~ParallelProblemBase() {};
virtual ~ParallelProblemBase() {}
/** \brief
* Must return true, if a new partitioning of the domain (due to unbalanced
......@@ -104,53 +104,47 @@ namespace AMDiS {
virtual void exitParallelization(AdaptInfo *adaptInfo);
virtual void setTime(AdaptInfo *adaptInfo)
{
virtual void setTime(AdaptInfo *adaptInfo) {
if (timeIF_)
timeIF_->setTime(adaptInfo);
};
}
virtual void initTimestep(AdaptInfo *adaptInfo)
{
virtual void initTimestep(AdaptInfo *adaptInfo) {
if (timeIF_)
timeIF_->initTimestep(adaptInfo);
};
}
virtual void closeTimestep(AdaptInfo *adaptInfo);
virtual void solveInitialProblem(AdaptInfo *adaptInfo)
{
virtual void solveInitialProblem(AdaptInfo *adaptInfo) {
if (timeIF_)
timeIF_->solveInitialProblem(adaptInfo);
};
}
virtual void transferInitialSolution(AdaptInfo *adaptInfo)
{
virtual void transferInitialSolution(AdaptInfo *adaptInfo) {
if (timeIF_)
timeIF_->transferInitialSolution(adaptInfo);
};
}
virtual void beginIteration(AdaptInfo *adaptInfo)
{
virtual void beginIteration(AdaptInfo *adaptInfo) {
iterationIF_->beginIteration(adaptInfo);
};
}
virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);
virtual void endIteration(AdaptInfo *adaptInfo) {
iterationIF_->endIteration(adaptInfo);
};
}
virtual void startDelayedTimestepCalculation() {};
virtual void startDelayedTimestepCalculation() {}
virtual bool existsDelayedCalculation() {
return false;
};
}
MPI::Intracomm* getMpiComm() {
return &mpiComm;
};
}
bool getDebugServerProcess() {
return debugServerProcess;
......@@ -260,15 +254,15 @@ namespace AMDiS {
void setRepartitionSteps(int steps) {
repartitionSteps_ = steps;
};
}
void puEveryTimestep(bool pu) {
puEveryTimestep_ = pu;
};
}
void addDOFVector(DOFVector<double> *vec) {
dofVectors_.push_back(vec);
};
}
/** \brief
* Every process creates the mesh structure code of its mesh, and all
......@@ -278,44 +272,33 @@ namespace AMDiS {
static bool writeElement(ElInfo *elInfo);
virtual void startDebugServer() {};
virtual void startDebugServer() {}
virtual void serialize(std::ostream&) {};
virtual void serialize(std::ostream&) {}
virtual void deserialize(std::istream&) {};
virtual void deserialize(std::istream&) {}
protected:
/** \brief
*
*/
///
double errors2map(std::map<int, double> &errMap, int comp, bool add);
///
std::vector<int> iList;
/** \brief
*
*/
///
std::string name_;
/** \brief
* Mesh of the problem.
*/
/// Mesh of the problem.
Mesh *mesh;
/** \brief
*
*/
///
RefinementManager *refinementManager;
/** \brief
*
*/
///
CoarseningManager *coarseningManager;
/** \brief
* Pointer to the paritioner which is used to devide a mesh into partitions.
*/
ParMetisPartitioner *partitioner_;
/// Pointer to the paritioner which is used to devide a mesh into partitions.
ParMetisPartitioner *partitioner;
/** \brief
* Stores to every coarse element index the number of the partition it
......@@ -329,24 +312,16 @@ namespace AMDiS {
*/
std::map<int, int> oldPartitionVec;
/** \brief
*
*/
///
std::map<int, double> elemWeights_;
/** \brief
* Stores to every element the set of partitions it corresponds to.
*/
/// Stores to every element the set of partitions it corresponds to.
std::map<Element*, std::set<int> > elementPartitions_;
/** \brief
* Stores to every DOF the set of partitions it corresponds to.
*/
/// Stores to every DOF the set of partitions it corresponds to.
std::map<DegreeOfFreedom, std::set<int> > vertexPartitions;
/** \brief
*
*/
///
int repartitionSteps_;
/** \brief
......@@ -418,7 +393,7 @@ namespace AMDiS {
*
*/
double maxLowerTH_;
};
}
// =========================================================================
// ===== class ParallelProblemScal =========================================
......@@ -460,15 +435,15 @@ namespace AMDiS {
void setEstimator(Estimator *est) {
usersEstimator = est;
};
}
void setMarker(Marker *marker) {
usersMarker = marker;
};
}
inline virtual const std::string& getName() {
return name_;
};
}
protected:
ProblemScal *problem;
......@@ -533,19 +508,19 @@ namespace AMDiS {
void setEstimator(std::vector<Estimator*> est) {
usersEstimator = est;
};
}
void setMarker(std::vector<Marker*> marker) {
usersMarker = marker;
};
}
inline virtual const std::string& getName() {
return name_;
};
}
virtual void startDebugServer(AdaptInfo *adaptInfo);
virtual void debugFunction(AdaptInfo *adaptInfo) {};
virtual void debugFunction(AdaptInfo *adaptInfo) {}
protected:
ProblemVec *problem;
......
AMDiS/src/ProblemScal.h
View file @ 41774d49
......@@ -206,16 +206,12 @@ namespace AMDiS {
void
interpolInitialSolution(AbstractFunction<double, WorldVector<double> > *fct);
/** \brief
* Adds an Operator to \ref systemMatrix.
*/
/// Adds an Operator to \ref systemMatrix.
void addMatrixOperator(Operator *op,
double *factor = NULL,
double *estFactor = NULL);
/** \brief
* Adds an Operator to \ref rhs.
*/
/// Adds an Operator to \ref rhs.
void addVectorOperator(Operator *op,
double *factor = NULL,
double *estFactor = NULL);
......
AMDiS/src/ResidualEstimator.cc
View file @ 41774d49
......@@ -206,7 +206,7 @@ namespace AMDiS {
itfac = const_cast<DOFMatrix*>(matrix[system])->getOperatorEstFactorBegin();
it != const_cast<DOFMatrix*>(matrix[system])->getOperatorsEnd();
++it, ++itfac) {
if (**itfac != 0.0) {
if (*itfac == NULL || **itfac != 0.0) {
(*it)->getAssembler(omp_get_thread_num())->initElement(elInfo, NULL, quad);
}
}
......@@ -246,7 +246,7 @@ namespace AMDiS {
itfac = const_cast<DOFMatrix*>(matrix[system])->getOperatorEstFactorBegin();
it != const_cast<DOFMatrix*>(matrix[system])->getOperatorsEnd();
++it, ++itfac) {
if (**itfac != 0.0) {
if (*itfac == NULL || **itfac != 0.0) {
if ((uhQP == NULL) && (*it)->zeroOrderTerms()) {
uhQP = GET_MEMORY(double, nPoints);
uh[system]->getVecAtQPs(elInfo, NULL, quadFast[system], uhQP);
......@@ -404,7 +404,7 @@ namespace AMDiS {
it != const_cast<DOFMatrix*>(matrix[system])->getOperatorsEnd();
++it, ++fac) {
if (**fac != 0.0) {
if (*fac == NULL || **fac != 0.0) {
for (int iq = 0; iq < nPointsSurface_; iq++) {
localJump_[iq].set(0.0);
}
......
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