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Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20190118_020615 branch to master #4215

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merged 25 commits into from
Jan 19, 2019
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Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20190118_020615 branch to master #4215

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f584735
add deprecation argument to CMakeLists to support macro disabling ord…
GeoffDanielson Oct 26, 2018
f65365f
added tribits support for switching, added descriptive default messag…
GeoffDanielson Nov 2, 2018
4a5ac85
Merge branch 'develop' into tpetra_disable_deprecated_cmake
GeoffDanielson Nov 2, 2018
45c850a
revise verbiage on deprecation and correct a cmake error
GeoffDanielson Nov 2, 2018
b653e0e
MueLu: modifying structured aggregation to compute graph of prolongator
lucbv Jan 11, 2019
67ed9e6
Merge Pull Request #4179 from lucbv/Trilinos/MueLu_StructuredAggregat…
trilinos-autotester Jan 15, 2019
165cd40
Tpetra: Fix warnings in unpackCrsGraphAndCombine & Import
Jan 15, 2019
3292b69
Amesos2: Fix #4194 (macros in Solver_Test.cpp breaking build)
Jan 15, 2019
2db50d1
Panzer: miniem: explicitly stop stacked timer
jhux2 Jan 15, 2019
ca06dab
Thyra: add function to reset the ModelEvaluatorDefaultBase lazyInit flag
rppawlo Jan 15, 2019
d3a1bbd
Merge Pull Request #4195 from trilinos/Trilinos/Fix-4194
trilinos-autotester Jan 15, 2019
8b2c633
Tpetra::DistObject::doTransfer*: Improve verbose output
Jan 15, 2019
56bb5d6
Tpetra: Fix #4199
Jan 16, 2019
e154ca8
Merge Pull Request #3742 from trilinos/Trilinos/tpetra_disable_deprec…
trilinos-autotester Jan 16, 2019
ede1539
Merge Pull Request #4198 from rppawlo/Trilinos/thyra-fix
trilinos-autotester Jan 16, 2019
e160fd1
Merge Pull Request #4197 from trilinos/Trilinos/jhu-2db50d1
trilinos-autotester Jan 16, 2019
72efa87
Merge Pull Request #4200 from trilinos/Trilinos/Fix-4199
trilinos-autotester Jan 16, 2019
a38b0cf
zoltan2: added test option to set additional parameter on command line
kddevin Jan 16, 2019
92a0cd9
zoltan2: fixed type of minimum_migration_imbalance
kddevin Jan 16, 2019
428d5f3
zoltan2: Test for MJ with integer coordinates and weights.
kddevin Jan 17, 2019
19d431c
zoltan2: a better test -- fails in serial for easier debugging
kddevin Jan 17, 2019
b4354e6
Revert "zoltan2: a better test -- fails in serial for easier debugging"
kddevin Jan 17, 2019
90b1d4f
Revert "zoltan2: Test for MJ with integer coordinates and weights."
kddevin Jan 17, 2019
0c080ed
zoltan2: changed all imbalance_tolerance fields to double; they shou…
kddevin Jan 17, 2019
28ff0df
Merge Pull Request #4214 from trilinos/Trilinos/zoltan2_smallMJChanges
trilinos-autotester Jan 18, 2019
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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;

};

Expand Down
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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