From 41774d4946ce4d56928484e059c295aefdead91b Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Mon, 23 Mar 2009 15:02:21 +0000
Subject: [PATCH] * Update due to small bug in Residualestimator
---
AMDiS/src/ParMetisPartitioner.cc | 35 +++++-----
AMDiS/src/ParMetisPartitioner.h | 26 ++++++--
AMDiS/src/ParallelProblem.cc | 30 ++++-----
AMDiS/src/ParallelProblem.h | 107 ++++++++++++-------------------
AMDiS/src/ProblemScal.h | 8 +--
AMDiS/src/ResidualEstimator.cc | 6 +-
6 files changed, 96 insertions(+), 116 deletions(-)
diff --git a/AMDiS/src/ParMetisPartitioner.cc b/AMDiS/src/ParMetisPartitioner.cc
index 327238dc..415e6ac6 100644
--- a/AMDiS/src/ParMetisPartitioner.cc
+++ b/AMDiS/src/ParMetisPartitioner.cc
@@ -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");
diff --git a/AMDiS/src/ParMetisPartitioner.h b/AMDiS/src/ParMetisPartitioner.h
index 62cc9067..ea03fdc2 100644
--- a/AMDiS/src/ParMetisPartitioner.h
+++ b/AMDiS/src/ParMetisPartitioner.h
@@ -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();
diff --git a/AMDiS/src/ParallelProblem.cc b/AMDiS/src/ParallelProblem.cc
index fe3075bd..b193297c 100644
--- a/AMDiS/src/ParallelProblem.cc
+++ b/AMDiS/src/ParallelProblem.cc
@@ -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)
diff --git a/AMDiS/src/ParallelProblem.h b/AMDiS/src/ParallelProblem.h
index aaaa065c..0bde33ef 100644
--- a/AMDiS/src/ParallelProblem.h
+++ b/AMDiS/src/ParallelProblem.h
@@ -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;
diff --git a/AMDiS/src/ProblemScal.h b/AMDiS/src/ProblemScal.h
index 3571119f..6cecdf75 100644
--- a/AMDiS/src/ProblemScal.h
+++ b/AMDiS/src/ProblemScal.h
@@ -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);
diff --git a/AMDiS/src/ResidualEstimator.cc b/AMDiS/src/ResidualEstimator.cc
index f820c4a9..b65fd057 100644
--- a/AMDiS/src/ResidualEstimator.cc
+++ b/AMDiS/src/ResidualEstimator.cc
@@ -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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