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Merge pull request #4215 from trilinos/master_merge_20190118_020615
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Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20190118_020615 branch to master
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@william76
william76 authored Jan 19, 2019
2 parents 59b802f + 28ff0df commit 4f15e6f
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Showing 26 changed files with 802 additions and 673 deletions.
511 changes: 136 additions & 375 deletions packages/amesos2/test/solvers/Solver_Test.cpp
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12 changes: 7 additions & 5 deletions packages/muelu/src/Graph/StructuredAggregation/MueLu_AggregationStructuredAlgorithm_decl.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ namespace MueLu {

/*! @brief Local aggregation. */

void BuildGraph(const GraphBase& graph, RCP<IndexManager>& geoData,
void BuildGraph(const GraphBase& graph, RCP<IndexManager>& geoData, const LO dofsPerNode,
RCP<CrsGraph>& myGraph, RCP<const Map>& coarseCoordinatesFineMap,
RCP<const Map>& coarseCoordinatesMap) const;
//@}
Expand All @@ -116,12 +116,14 @@ namespace MueLu {
private:

void ComputeGraphDataConstant(const GraphBase& graph, RCP<IndexManager>& geoData,
const int numInterpolationPoints, ArrayRCP<size_t>& nnzOnRow,
Array<size_t>& rowPtr, Array<LO>& colIndex) const;
const LO dofsPerNode, const int numInterpolationPoints,
ArrayRCP<size_t>& nnzOnRow, Array<size_t>& rowPtr,
Array<LO>& colIndex) const;

void ComputeGraphDataLinear(const GraphBase& graph, RCP<IndexManager>& geoData,
const int numInterpolationPoints, ArrayRCP<size_t>& nnzOnRow,
Array<size_t>& rowPtr, Array<LO>& colIndex) const;
const LO dofsPerNode, const int numInterpolationPoints,
ArrayRCP<size_t>& nnzOnRow, Array<size_t>& rowPtr,
Array<LO>& colIndex) const;

};

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111 changes: 64 additions & 47 deletions packages/muelu/src/Graph/StructuredAggregation/MueLu_AggregationStructuredAlgorithm_def.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -129,8 +129,9 @@ namespace MueLu {

template <class LocalOrdinal, class GlobalOrdinal, class Node>
void AggregationStructuredAlgorithm<LocalOrdinal, GlobalOrdinal, Node>::
BuildGraph(const GraphBase& graph, RCP<IndexManager>& geoData, RCP<CrsGraph>& myGraph,
RCP<const Map>& coarseCoordinatesFineMap, RCP<const Map>& coarseCoordinatesMap) const {
BuildGraph(const GraphBase& graph, RCP<IndexManager>& geoData, const LO dofsPerNode,
RCP<CrsGraph>& myGraph, RCP<const Map>& coarseCoordinatesFineMap,
RCP<const Map>& coarseCoordinatesMap) const {
Monitor m(*this, "BuildGraphP");

RCP<Teuchos::FancyOStream> out;
Expand All @@ -153,20 +154,23 @@ namespace MueLu {
}
*out << "numInterpolationPoints=" << numInterpolationPoints << std::endl;

Array<LO> colIndex( geoData->getNumLocalCoarseNodes() + numInterpolationPoints*
(geoData->getNumLocalFineNodes() - geoData->getNumLocalCoarseNodes()) );
Array<size_t> rowPtr(geoData->getNumLocalFineNodes()+1);
Array<LO> colIndex((geoData->getNumLocalCoarseNodes() + numInterpolationPoints*
(geoData->getNumLocalFineNodes() - geoData->getNumLocalCoarseNodes()))*dofsPerNode);
Array<size_t> rowPtr(geoData->getNumLocalFineNodes()*dofsPerNode + 1);
rowPtr[0] = 0;
ArrayRCP<size_t> nnzOnRow(geoData->getNumLocalFineNodes());
ArrayRCP<size_t> nnzOnRow(geoData->getNumLocalFineNodes()*dofsPerNode);

*out << "Compute prolongatorGraph data" << std::endl;
if(geoData->getInterpolationOrder() == 0) {
ComputeGraphDataConstant(graph, geoData, numInterpolationPoints, nnzOnRow, rowPtr, colIndex);
ComputeGraphDataConstant(graph, geoData, dofsPerNode, numInterpolationPoints,
nnzOnRow, rowPtr, colIndex);
} else if(geoData->getInterpolationOrder() == 1) {
ComputeGraphDataLinear(graph, geoData, numInterpolationPoints, nnzOnRow, rowPtr, colIndex);
ComputeGraphDataLinear(graph, geoData, dofsPerNode, numInterpolationPoints,
nnzOnRow, rowPtr, colIndex);
}

// Compute graph's colMap and domainMap
// Compute graph's rowMap, colMap and domainMap
RCP<Map> rowMap = MapFactory::Build(graph.GetDomainMap(), dofsPerNode);
RCP<Map> colMap, domainMap;
*out << "Compute domain and column maps of the CrsGraph" << std::endl;
if(coupled){
Expand Down Expand Up @@ -215,11 +219,10 @@ namespace MueLu {
graph.GetDomainMap()->getNode());
} else {
// In this case the map will compute the global number of nodes on the coarse mesh
// since geoData->getNumGlobalCoarseNodes() == Teuchos::OrdinalTraits<GO>::invalid()
// and it will assign GIDs to the local coarse nodes.
colMap = MapFactory::Build(graph.GetDomainMap()->lib(),
geoData->getNumGlobalCoarseNodes(),
geoData->getNumLocalCoarseNodes(),
Teuchos::OrdinalTraits<GO>::invalid(),
geoData->getNumLocalCoarseNodes()*dofsPerNode,
graph.GetDomainMap()->getIndexBase(),
graph.GetDomainMap()->getComm(),
graph.GetDomainMap()->getNode());
Expand All @@ -229,32 +232,36 @@ namespace MueLu {
Array<GO> coarseNodeFineGIDs(geoData->getNumLocalCoarseNodes());
geoData->getCoarseNodesData(graph.GetDomainMap(), coarseNodeCoarseGIDs, coarseNodeFineGIDs);
coarseCoordinatesMap = MapFactory::Build(graph.GetDomainMap()->lib(),
geoData->getNumGlobalCoarseNodes(),
Teuchos::OrdinalTraits<GO>::invalid(),
geoData->getNumLocalCoarseNodes(),
graph.GetDomainMap()->getIndexBase(),
graph.GetDomainMap()->getComm(),
graph.GetDomainMap()->getNode());
coarseCoordinatesFineMap = MapFactory::Build(graph.GetDomainMap()->lib(),
geoData->getNumGlobalCoarseNodes(),
Teuchos::OrdinalTraits<GO>::invalid(),
coarseNodeFineGIDs(),
graph.GetDomainMap()->getIndexBase(),
graph.GetDomainMap()->getComm(),
graph.GetDomainMap()->getNode());
}

*out << "Call constructor of CrsGraph" << std::endl;
myGraph = CrsGraphFactory::Build(graph.GetDomainMap(),
myGraph = CrsGraphFactory::Build(rowMap,
colMap,
nnzOnRow,
Xpetra::DynamicProfile);

*out << "Fill CrsGraph" << std::endl;
LO rowIdx = 0;
for(LO nodeIdx = 0; nodeIdx < geoData->getNumLocalFineNodes(); ++nodeIdx) {
myGraph->insertLocalIndices(nodeIdx, colIndex(rowPtr[nodeIdx], nnzOnRow[nodeIdx]) );
for(LO dof = 0; dof < dofsPerNode; ++dof) {
rowIdx = nodeIdx*dofsPerNode + dof;
myGraph->insertLocalIndices(rowIdx, colIndex(rowPtr[rowIdx], nnzOnRow[rowIdx]) );
}
}

*out << "Call fillComplete on CrsGraph" << std::endl;
myGraph->fillComplete(domainMap, graph.GetDomainMap());
myGraph->fillComplete(domainMap, rowMap);
*out << "Prolongator CrsGraph computed" << std::endl;

} // BuildAggregates()
Expand All @@ -263,8 +270,9 @@ namespace MueLu {
template <class LocalOrdinal, class GlobalOrdinal, class Node>
void AggregationStructuredAlgorithm<LocalOrdinal, GlobalOrdinal, Node>::
ComputeGraphDataConstant(const GraphBase& graph, RCP<IndexManager>& geoData,
const int numInterpolationPoints, ArrayRCP<size_t>& nnzOnRow,
Array<size_t>& rowPtr, Array<LO>& colIndex) const {
const LO dofsPerNode, const int numInterpolationPoints,
ArrayRCP<size_t>& nnzOnRow, Array<size_t>& rowPtr,
Array<LO>& colIndex) const {

RCP<Teuchos::FancyOStream> out;
if(const char* dbg = std::getenv("MUELU_STRUCTUREDALGORITHM_DEBUG")) {
Expand All @@ -283,9 +291,6 @@ namespace MueLu {
LO ghostedCoarseNodeCoarseLID, rem, rate;
Array<LO> ghostedIdx(3), coarseIdx(3);
for(LO nodeIdx = 0; nodeIdx < geoData->getNumLocalFineNodes(); ++nodeIdx) {
// For piece-wise constant interpolation we only get one nnz per row
nnzOnRow[nodeIdx] = Teuchos::as<size_t>(1);
rowPtr[nodeIdx + 1] = rowPtr[nodeIdx] + 1; // These needs to change for kokkos: rowPtr[nodeIdx + 1] = nodeIdx + 1;

// Compute coarse ID associated with fine LID
geoData->getFineNodeGhostedTuple(nodeIdx, ghostedIdx[0], ghostedIdx[1], ghostedIdx[2]);
Expand All @@ -306,7 +311,13 @@ namespace MueLu {

geoData->getCoarseNodeGhostedLID(coarseIdx[0], coarseIdx[1], coarseIdx[2],
ghostedCoarseNodeCoarseLID);
colIndex[rowPtr[nodeIdx]] = ghostedCoarseNodeCoarseLIDs[ghostedCoarseNodeCoarseLID]; // Here too, substitute nodeIdx for rowPtr[nodeIdx]

for(LO dof = 0; dof < dofsPerNode; ++dof) {
nnzOnRow[nodeIdx*dofsPerNode + dof] = 1;
rowPtr[nodeIdx*dofsPerNode + dof + 1] = rowPtr[nodeIdx*dofsPerNode + dof] + 1;
colIndex[rowPtr[nodeIdx*dofsPerNode + dof]] =
ghostedCoarseNodeCoarseLIDs[ghostedCoarseNodeCoarseLID]*dofsPerNode + dof;
}
} // Loop over fine points

} // ComputeGraphDataConstant()
Expand All @@ -315,8 +326,9 @@ namespace MueLu {
template <class LocalOrdinal, class GlobalOrdinal, class Node>
void AggregationStructuredAlgorithm<LocalOrdinal, GlobalOrdinal, Node>::
ComputeGraphDataLinear(const GraphBase& graph, RCP<IndexManager>& geoData,
const int numInterpolationPoints, ArrayRCP<size_t>& nnzOnRow,
Array<size_t>& rowPtr, Array<LO>& colIndex) const {
const LO dofsPerNode, const int numInterpolationPoints,
ArrayRCP<size_t>& nnzOnRow, Array<size_t>& rowPtr,
Array<LO>& colIndex) const {

RCP<Teuchos::FancyOStream> out;
if(const char* dbg = std::getenv("MUELU_STRUCTUREDALGORITHM_DEBUG")) {
Expand All @@ -332,6 +344,8 @@ namespace MueLu {
Array<LO> coarseIdx(3,0);
Array<LO> ijkRem(3,0);
int rate = 0;
const LO coarsePointOffset[8][3] = {{0, 0, 0}, {1, 0, 0}, {0, 1, 0}, {1, 1, 0},
{0, 0, 1}, {1, 0, 1}, {0, 1, 1}, {1, 1, 1}};

for(LO nodeIdx = 0; nodeIdx < geoData->getNumLocalFineNodes(); ++nodeIdx) {

Expand Down Expand Up @@ -373,35 +387,38 @@ namespace MueLu {
allCoarse = false;
}

LO rowIdx = 0, colIdx = 0;
if(allCoarse) {
// Fine node lies on Coarse node, easy case, we only need the LID of the coarse node.
geoData->getCoarseNodeGhostedLID(coarseIdx[0], coarseIdx[1], coarseIdx[2],
colIndex[rowPtr[nodeIdx]]);
nnzOnRow[nodeIdx] = Teuchos::as<size_t>(1);
rowPtr[nodeIdx + 1] = rowPtr[nodeIdx] + 1;
for(LO dof = 0; dof < dofsPerNode; ++dof) {
rowIdx = nodeIdx*dofsPerNode + dof;
nnzOnRow[rowIdx] = 1;
rowPtr[rowIdx + 1] = rowPtr[rowIdx] + 1;

// Fine node lies on Coarse node, easy case, we only need the LID of the coarse node.
geoData->getCoarseNodeGhostedLID(coarseIdx[0], coarseIdx[1], coarseIdx[2], colIdx);
colIndex[rowPtr[rowIdx]] = colIdx*dofsPerNode + dof;
}
} else {
// Harder case, we need the LIDs of all the coarse nodes contributing to the interpolation
// at the current node.
nnzOnRow[nodeIdx] = Teuchos::as<size_t>( numInterpolationPoints );
rowPtr[nodeIdx + 1] = rowPtr[nodeIdx] + Teuchos::as<LO>( numInterpolationPoints );

for(int dim = 0; dim < numDimensions; ++dim) {
if(coarseIdx[dim] == geoData->getGhostedNodesInDir(dim) - 1)
--coarseIdx[dim];
}
// Compute Coarse Node LID
geoData->getCoarseNodeGhostedLID( coarseIdx[0], coarseIdx[1], coarseIdx[2], colIndex[ rowPtr[nodeIdx]+0]);
geoData->getCoarseNodeGhostedLID( coarseIdx[0]+1, coarseIdx[1], coarseIdx[2], colIndex[ rowPtr[nodeIdx]+1]);
if(numDimensions > 1) {
geoData->getCoarseNodeGhostedLID( coarseIdx[0], coarseIdx[1]+1, coarseIdx[2], colIndex[ rowPtr[nodeIdx]+2]);
geoData->getCoarseNodeGhostedLID( coarseIdx[0]+1, coarseIdx[1]+1, coarseIdx[2], colIndex[ rowPtr[nodeIdx]+3]);
if(numDimensions > 2) {
geoData->getCoarseNodeGhostedLID(coarseIdx[0], coarseIdx[1], coarseIdx[2]+1, colIndex[ rowPtr[nodeIdx]+4]);
geoData->getCoarseNodeGhostedLID(coarseIdx[0]+1, coarseIdx[1], coarseIdx[2]+1, colIndex[ rowPtr[nodeIdx]+5]);
geoData->getCoarseNodeGhostedLID(coarseIdx[0], coarseIdx[1]+1, coarseIdx[2]+1, colIndex[ rowPtr[nodeIdx]+6]);
geoData->getCoarseNodeGhostedLID(coarseIdx[0]+1, coarseIdx[1]+1, coarseIdx[2]+1, colIndex[ rowPtr[nodeIdx]+7]);
}
}

for(LO dof = 0; dof < dofsPerNode; ++dof) {
// at the current node.
rowIdx = nodeIdx*dofsPerNode + dof;
nnzOnRow[rowIdx] = Teuchos::as<size_t>( numInterpolationPoints );
rowPtr[rowIdx + 1] = rowPtr[rowIdx] + Teuchos::as<LO>(numInterpolationPoints);
// Compute Coarse Node LID
for(LO interpIdx = 0; interpIdx < numInterpolationPoints; ++interpIdx) {
geoData->getCoarseNodeGhostedLID(coarseIdx[0] + coarsePointOffset[interpIdx][0],
coarseIdx[1] + coarsePointOffset[interpIdx][1],
coarseIdx[2] + coarsePointOffset[interpIdx][2],
colIdx);
colIndex[rowPtr[rowIdx] + interpIdx] = colIdx*dofsPerNode + dof;
} // Loop over numInterpolationPoints
} // Loop over dofsPerNode
}
} // Loop over fine points
} // ComputeGraphDataLinear()
Expand Down
17 changes: 10 additions & 7 deletions packages/muelu/src/Graph/StructuredAggregation/MueLu_StructuredAggregationFactory_def.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,6 @@ namespace MueLu {

validParamList->set<RCP<const FactoryBase> >("aggregation: mesh data", Teuchos::null,
"Mesh ordering associated data");

validParamList->set<RCP<const FactoryBase> >("Graph", Teuchos::null,
"Graph of the matrix after amalgamation but without dropping.");
validParamList->set<RCP<const FactoryBase> >("numDimensions", Teuchos::null,
Expand All @@ -106,6 +105,8 @@ namespace MueLu {
"Global number of nodes per spatial dimension provided by CoordinatesTransferFactory.");
validParamList->set<RCP<const FactoryBase> >("lNodesPerDim", Teuchos::null,
"Local number of nodes per spatial dimension provided by CoordinatesTransferFactory.");
validParamList->set<RCP<const FactoryBase> >("DofsPerNode", Teuchos::null,
"Generating factory for variable \'DofsPerNode\', usually the same as the \'Graph\' factory");

return validParamList;
} // GetValidParameterList
Expand All @@ -114,6 +115,7 @@ namespace MueLu {
void StructuredAggregationFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
DeclareInput(Level& currentLevel) const {
Input(currentLevel, "Graph");
Input(currentLevel, "DofsPerNode");

ParameterList pL = GetParameterList();
std::string coupling = pL.get<std::string>("aggregation: coupling");
Expand Down Expand Up @@ -175,10 +177,11 @@ namespace MueLu {

// General problem informations are gathered from data stored in the problem matix.
RCP<const GraphBase> graph = Get< RCP<GraphBase> >(currentLevel, "Graph");
RCP<const Map> fineMap = graph->GetDomainMap();
const int myRank = fineMap->getComm()->getRank();
const int numRanks = fineMap->getComm()->getSize();
const GO minGlobalIndex = fineMap->getMinGlobalIndex();
RCP<const Map> fineMap = graph->GetDomainMap();
const int myRank = fineMap->getComm()->getRank();
const int numRanks = fineMap->getComm()->getSize();
const GO minGlobalIndex = fineMap->getMinGlobalIndex();
const LO dofsPerNode = Get<LO>(currentLevel, "DofsPerNode");

// Since we want to operate on nodes and not dof, we need to modify the rowMap in order to
// obtain a nodeMap.
Expand Down Expand Up @@ -332,8 +335,8 @@ namespace MueLu {
} else {
// Create Coarse Data
RCP<CrsGraph> myGraph;
myStructuredAlgorithm->BuildGraph(*graph, geoData, myGraph, coarseCoordinatesFineMap,
coarseCoordinatesMap);
myStructuredAlgorithm->BuildGraph(*graph, geoData, dofsPerNode, myGraph,
coarseCoordinatesFineMap, coarseCoordinatesMap);
Set(currentLevel, "prolongatorGraph", myGraph);
}

Expand Down
4 changes: 2 additions & 2 deletions packages/muelu/src/Transfers/GeneralGeometric/MueLu_GeometricInterpolationPFactory_decl.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -98,8 +98,8 @@ namespace MueLu{
//@}

private:
void BuildConstantP(RCP<Matrix>& P, RCP<CrsGraph>& prolongatorGraph, RCP<Matrix>& A) const;
void BuildLinearP(RCP<Matrix>& A, RCP<CrsGraph>& prolongatorGraph,
void BuildConstantP(RCP<Matrix>& P, RCP<const CrsGraph>& prolongatorGraph, RCP<Matrix>& A) const;
void BuildLinearP(RCP<Matrix>& A, RCP<const CrsGraph>& prolongatorGraph,
RCP<realvaluedmultivector_type>& fineCoordinates,
RCP<realvaluedmultivector_type>& ghostCoordinates,
const int numDimensions, RCP<Matrix>& P) const;
Expand Down
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