MueLu_TentativePFactory_def.hpp

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#ifndef MUELU_TENTATIVEPFACTORY_DEF_HPP
#define MUELU_TENTATIVEPFACTORY_DEF_HPP
 
#include <Xpetra_MapFactory.hpp>
#include <Xpetra_Map.hpp>
#include <Xpetra_CrsMatrix.hpp>
#include <Xpetra_Matrix.hpp>
#include <Xpetra_MultiVector.hpp>
#include <Xpetra_MultiVectorFactory.hpp>
#include <Xpetra_VectorFactory.hpp>
#include <Xpetra_Import.hpp>
#include <Xpetra_ImportFactory.hpp>
#include <Xpetra_CrsMatrixWrap.hpp>
#include <Xpetra_StridedMap.hpp>
#include <Xpetra_StridedMapFactory.hpp>
 
#include "MueLu_TentativePFactory_decl.hpp"
 
#include "MueLu_Aggregates.hpp"
#include "MueLu_AmalgamationFactory.hpp"
#include "MueLu_AmalgamationInfo.hpp"
#include "MueLu_CoarseMapFactory.hpp"
#include "MueLu_MasterList.hpp"
#include "MueLu_Monitor.hpp"
#include "MueLu_NullspaceFactory.hpp"
#include "MueLu_PerfUtils.hpp"
#include "MueLu_Utilities.hpp"
 
namespace MueLu {
 
  template <class Scalar, class LocalOrdinal, class GlobalOrdinal, class Node>
  RCP<const ParameterList> TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::GetValidParameterList() const {
    RCP<ParameterList> validParamList = rcp(new ParameterList());
 
#define SET_VALID_ENTRY(name) validParamList->setEntry(name, MasterList::getEntry(name))
    SET_VALID_ENTRY("tentative: calculate qr");
    SET_VALID_ENTRY("tentative: build coarse coordinates");
#undef  SET_VALID_ENTRY
    validParamList->set< std::string >("Nullspace name", "Nullspace", "Name for the input nullspace");
 
    validParamList->set< RCP<const FactoryBase> >("A",                  Teuchos::null, "Generating factory of the matrix A");
    validParamList->set< RCP<const FactoryBase> >("Aggregates",         Teuchos::null, "Generating factory of the aggregates");
    validParamList->set< RCP<const FactoryBase> >("Nullspace",          Teuchos::null, "Generating factory of the nullspace");
    validParamList->set< RCP<const FactoryBase> >("Scaled Nullspace",   Teuchos::null, "Generating factory of the scaled nullspace");
    validParamList->set< RCP<const FactoryBase> >("UnAmalgamationInfo", Teuchos::null, "Generating factory of UnAmalgamationInfo");
    validParamList->set< RCP<const FactoryBase> >("CoarseMap",          Teuchos::null, "Generating factory of the coarse map");
    validParamList->set< RCP<const FactoryBase> >("Coordinates",        Teuchos::null, "Generating factory of the coordinates");
    validParamList->set< RCP<const FactoryBase> >("Node Comm",          Teuchos::null, "Generating factory of the node level communicator");
 
    // Make sure we don't recursively validate options for the matrixmatrix kernels
    ParameterList norecurse;
    norecurse.disableRecursiveValidation();
    validParamList->set<ParameterList> ("matrixmatrix: kernel params", norecurse, "MatrixMatrix kernel parameters");
 
    return validParamList;
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  void TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::DeclareInput(Level& fineLevel, Level& /* coarseLevel */) const {
 
    const ParameterList& pL = GetParameterList();
    // NOTE: This guy can only either be 'Nullspace' or 'Scaled Nullspace' or else the validator above will cause issues
    std::string nspName = "Nullspace";
    if(pL.isParameter("Nullspace name")) nspName = pL.get<std::string>("Nullspace name");
 
    Input(fineLevel, "A");
    Input(fineLevel, "Aggregates");
    Input(fineLevel, nspName);
    Input(fineLevel, "UnAmalgamationInfo");
    Input(fineLevel, "CoarseMap");
    if( fineLevel.GetLevelID() == 0 &&
        fineLevel.IsAvailable("Coordinates", NoFactory::get()) &&     // we have coordinates (provided by user app)
        pL.get<bool>("tentative: build coarse coordinates") ) {       // and we want coordinates on other levels
      bTransferCoordinates_ = true;                                   // then set the transfer coordinates flag to true
      Input(fineLevel, "Coordinates");
    } else if (bTransferCoordinates_) {
      Input(fineLevel, "Coordinates");
    }
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  void TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Build(Level& fineLevel, Level& coarseLevel) const {
    return BuildP(fineLevel, coarseLevel);
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  void TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::BuildP(Level& fineLevel, Level& coarseLevel) const {
    FactoryMonitor m(*this, "Build", coarseLevel);
    typedef typename Teuchos::ScalarTraits<Scalar>::coordinateType coordinate_type;
    typedef Xpetra::MultiVector<coordinate_type,LO,GO,NO> RealValuedMultiVector;
    typedef Xpetra::MultiVectorFactory<coordinate_type,LO,GO,NO> RealValuedMultiVectorFactory;
 
    const ParameterList& pL = GetParameterList();
    std::string nspName = "Nullspace";
    if(pL.isParameter("Nullspace name")) nspName = pL.get<std::string>("Nullspace name");
 
 
    RCP<Matrix>                A             = Get< RCP<Matrix> >               (fineLevel, "A");
    RCP<Aggregates>            aggregates    = Get< RCP<Aggregates> >           (fineLevel, "Aggregates");
    RCP<AmalgamationInfo>      amalgInfo     = Get< RCP<AmalgamationInfo> >     (fineLevel, "UnAmalgamationInfo");
    RCP<MultiVector>           fineNullspace = Get< RCP<MultiVector> >          (fineLevel, nspName);
    RCP<const Map>             coarseMap     = Get< RCP<const Map> >            (fineLevel, "CoarseMap");
    RCP<RealValuedMultiVector> fineCoords;
    if(bTransferCoordinates_) {
      fineCoords = Get< RCP<RealValuedMultiVector> >(fineLevel, "Coordinates");
    }
 
    // FIXME: We should remove the NodeComm on levels past the threshold
    if(fineLevel.IsAvailable("Node Comm")) {
      RCP<const Teuchos::Comm<int> > nodeComm = Get<RCP<const Teuchos::Comm<int> > >(fineLevel,"Node Comm");
      Set<RCP<const Teuchos::Comm<int> > >(coarseLevel, "Node Comm", nodeComm);
    }
 
    TEUCHOS_TEST_FOR_EXCEPTION(A->getRowMap()->getNodeNumElements() != fineNullspace->getMap()->getNodeNumElements(),
             Exceptions::RuntimeError,"MueLu::TentativePFactory::MakeTentative: Size mismatch between A and Nullspace");
 
    RCP<Matrix>                Ptentative;
    RCP<MultiVector>           coarseNullspace;
    RCP<RealValuedMultiVector> coarseCoords;
 
    if(bTransferCoordinates_) {
      //*** Create the coarse coordinates ***
      // First create the coarse map and coarse multivector
      ArrayView<const GO> elementAList   = coarseMap->getNodeElementList();
      LO                  blkSize        = 1;
      if (rcp_dynamic_cast<const StridedMap>(coarseMap) != Teuchos::null) {
        blkSize = rcp_dynamic_cast<const StridedMap>(coarseMap)->getFixedBlockSize();
      }
      GO                  indexBase      = coarseMap->getIndexBase();
      LO                  numCoarseNodes = Teuchos::as<LO>(elementAList.size() / blkSize);
      Array<GO>           nodeList(numCoarseNodes);
      const int           numDimensions  = fineCoords->getNumVectors();
 
      for (LO i = 0; i < numCoarseNodes; i++) {
        nodeList[i] = (elementAList[i*blkSize]-indexBase)/blkSize + indexBase;
      }
      RCP<const Map> coarseCoordsMap = MapFactory::Build(fineCoords->getMap()->lib(),
                                                         Teuchos::OrdinalTraits<Xpetra::global_size_t>::invalid(),
                                                         nodeList,
                                                         indexBase,
                                                         fineCoords->getMap()->getComm());
      coarseCoords = RealValuedMultiVectorFactory::Build(coarseCoordsMap, numDimensions);
 
      // Create overlapped fine coordinates to reduce global communication
      RCP<RealValuedMultiVector> ghostedCoords;
      if (aggregates->AggregatesCrossProcessors()) {
        RCP<const Map>    aggMap = aggregates->GetMap();
        RCP<const Import> importer     = ImportFactory::Build(fineCoords->getMap(), aggMap);
 
        ghostedCoords = RealValuedMultiVectorFactory::Build(aggMap, numDimensions);
        ghostedCoords->doImport(*fineCoords, *importer, Xpetra::INSERT);
      } else {
        ghostedCoords = fineCoords;
      }
 
      // Get some info about aggregates
      int                         myPID        = coarseCoordsMap->getComm()->getRank();
      LO                          numAggs      = aggregates->GetNumAggregates();
      ArrayRCP<LO>                aggSizes     = aggregates->ComputeAggregateSizes();
      const ArrayRCP<const LO>    vertex2AggID = aggregates->GetVertex2AggId()->getData(0);
      const ArrayRCP<const LO>    procWinner   = aggregates->GetProcWinner()->getData(0);
 
      // Fill in coarse coordinates
      for (int dim = 0; dim < numDimensions; ++dim) {
        ArrayRCP<const coordinate_type> fineCoordsData = ghostedCoords->getData(dim);
        ArrayRCP<coordinate_type>     coarseCoordsData = coarseCoords->getDataNonConst(dim);
 
        for (LO lnode = 0; lnode < Teuchos::as<LO>(vertex2AggID.size()); lnode++) {
          if (procWinner[lnode] == myPID &&
              lnode < fineCoordsData.size() &&
              vertex2AggID[lnode] < coarseCoordsData.size() &&
              Teuchos::ScalarTraits<coordinate_type>::isnaninf(fineCoordsData[lnode]) == false) {
            coarseCoordsData[vertex2AggID[lnode]] += fineCoordsData[lnode];
          }
        }
        for (LO agg = 0; agg < numAggs; agg++) {
          coarseCoordsData[agg] /= aggSizes[agg];
        }
      }
    }
 
    if (!aggregates->AggregatesCrossProcessors())
      BuildPuncoupled(A, aggregates, amalgInfo, fineNullspace, coarseMap, Ptentative, coarseNullspace,coarseLevel.GetLevelID());
    else
      BuildPcoupled  (A, aggregates, amalgInfo, fineNullspace, coarseMap, Ptentative, coarseNullspace);
 
    // If available, use striding information of fine level matrix A for range
    // map and coarseMap as domain map; otherwise use plain range map of
    // Ptent = plain range map of A for range map and coarseMap as domain map.
    // NOTE:
    // The latter is not really safe, since there is no striding information
    // for the range map. This is not really a problem, since striding
    // information is always available on the intermedium levels and the
    // coarsest levels.
    if (A->IsView("stridedMaps") == true)
      Ptentative->CreateView("stridedMaps", A->getRowMap("stridedMaps"), coarseMap);
    else
      Ptentative->CreateView("stridedMaps", Ptentative->getRangeMap(),   coarseMap);
 
    if(bTransferCoordinates_) {
      Set(coarseLevel, "Coordinates", coarseCoords);
    }
    Set(coarseLevel, "Nullspace",   coarseNullspace);
    Set(coarseLevel, "P",           Ptentative);
 
    if (IsPrint(Statistics2)) {
      RCP<ParameterList> params = rcp(new ParameterList());
      params->set("printLoadBalancingInfo", true);
      GetOStream(Statistics2) << PerfUtils::PrintMatrixInfo(*Ptentative, "Ptent", params);
    }
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  void TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
  BuildPuncoupled(RCP<Matrix> A, RCP<Aggregates> aggregates, RCP<AmalgamationInfo> amalgInfo, RCP<MultiVector> fineNullspace,
                RCP<const Map> coarseMap, RCP<Matrix>& Ptentative, RCP<MultiVector>& coarseNullspace, const int levelID) const {
    RCP<const Map> rowMap = A->getRowMap();
    RCP<const Map> colMap = A->getColMap();
 
    const size_t numRows   = rowMap->getNodeNumElements();
 
    typedef Teuchos::ScalarTraits<SC> STS;
    typedef typename STS::magnitudeType Magnitude;
    const SC     zero      = STS::zero();
    const SC     one       = STS::one();
    const LO     INVALID   = Teuchos::OrdinalTraits<LO>::invalid();
 
    const GO     numAggs   = aggregates->GetNumAggregates();
    const size_t NSDim     = fineNullspace->getNumVectors();
 
    // Aggregates map is based on the amalgamated column map
    // We can skip global-to-local conversion if LIDs in row map are
    // same as LIDs in column map
    bool goodMap = isGoodMap(*rowMap, *colMap);
 
    // Create a lookup table to determine the rows (fine DOFs) that belong to a given aggregate.
    // aggStart is a pointer into aggToRowMapLO
    // aggStart[i]..aggStart[i+1] are indices into aggToRowMapLO
    // aggToRowMapLO[aggStart[i]]..aggToRowMapLO[aggStart[i+1]-1] are the DOFs in aggregate i
    ArrayRCP<LO> aggStart;
    ArrayRCP<LO> aggToRowMapLO;
    ArrayRCP<GO> aggToRowMapGO;
    if (goodMap) {
      amalgInfo->UnamalgamateAggregatesLO(*aggregates, aggStart, aggToRowMapLO);
      GetOStream(Runtime1) << "Column map is consistent with the row map, good." << std::endl;
 
    } else {
      amalgInfo->UnamalgamateAggregates(*aggregates, aggStart, aggToRowMapGO);
      GetOStream(Warnings0) << "Column map is not consistent with the row map\n"
                            << "using GO->LO conversion with performance penalty" << std::endl;
    }
 
    coarseNullspace = MultiVectorFactory::Build(coarseMap, NSDim);
 
    const ParameterList& pL = GetParameterList();
    const bool &doQRStep = pL.get<bool>("tentative: calculate qr");
 
    // Pull out the nullspace vectors so that we can have random access.
    ArrayRCP<ArrayRCP<const SC> > fineNS  (NSDim);
    ArrayRCP<ArrayRCP<SC> >       coarseNS(NSDim);
    for (size_t i = 0; i < NSDim; i++) {
      fineNS[i] = fineNullspace->getData(i);
      if (coarseMap->getNodeNumElements() > 0)
        coarseNS[i] = coarseNullspace->getDataNonConst(i);
    }
 
    size_t nnzEstimate = numRows * NSDim;
 
    // Time to construct the matrix and fill in the values
    Ptentative = rcp(new CrsMatrixWrap(rowMap, coarseMap, 0, Xpetra::StaticProfile));
    RCP<CrsMatrix> PtentCrs   = rcp_dynamic_cast<CrsMatrixWrap>(Ptentative)->getCrsMatrix();
 
    ArrayRCP<size_t>  iaPtent;
    ArrayRCP<LO>      jaPtent;
    ArrayRCP<SC>     valPtent;
 
    PtentCrs->allocateAllValues(nnzEstimate, iaPtent, jaPtent, valPtent);
 
    ArrayView<size_t> ia  = iaPtent();
    ArrayView<LO>     ja  = jaPtent();
    ArrayView<SC>     val = valPtent();
 
    ia[0] = 0;
    for (size_t i = 1; i <= numRows; i++)
      ia[i] = ia[i-1] + NSDim;
 
    for (size_t j = 0; j < nnzEstimate; j++) {
      ja [j] = INVALID;
      val[j] = zero;
    }
 
 
    if (doQRStep) {
      // Standard aggregate-wise QR //
      for (GO agg = 0; agg < numAggs; agg++) {
        LO aggSize = aggStart[agg+1] - aggStart[agg];
 
        Xpetra::global_size_t offset = agg*NSDim;
 
        // Extract the piece of the nullspace corresponding to the aggregate, and
        // put it in the flat array, "localQR" (in column major format) for the
        // QR routine.
        Teuchos::SerialDenseMatrix<LO,SC> localQR(aggSize, NSDim);
        if (goodMap) {
          for (size_t j = 0; j < NSDim; j++)
            for (LO k = 0; k < aggSize; k++)
              localQR(k,j) = fineNS[j][aggToRowMapLO[aggStart[agg]+k]];
        } else {
          for (size_t j = 0; j < NSDim; j++)
            for (LO k = 0; k < aggSize; k++)
              localQR(k,j) = fineNS[j][rowMap->getLocalElement(aggToRowMapGO[aggStart[agg]+k])];
        }
 
        // Test for zero columns
        for (size_t j = 0; j < NSDim; j++) {
          bool bIsZeroNSColumn = true;
 
          for (LO k = 0; k < aggSize; k++)
            if (localQR(k,j) != zero)
              bIsZeroNSColumn = false;
 
          TEUCHOS_TEST_FOR_EXCEPTION(bIsZeroNSColumn == true, Exceptions::RuntimeError,
                                     "MueLu::TentativePFactory::MakeTentative: fine level NS part has a zero column");
        }
 
        // Calculate QR decomposition (standard)
        // NOTE: Q is stored in localQR and R is stored in coarseNS
        if (aggSize >= Teuchos::as<LO>(NSDim)) {
 
          if (NSDim == 1) {
            // Only one nullspace vector, calculate Q and R by hand
            Magnitude norm = STS::magnitude(zero);
            for (size_t k = 0; k < Teuchos::as<size_t>(aggSize); k++)
              norm += STS::magnitude(localQR(k,0)*localQR(k,0));
            norm = Teuchos::ScalarTraits<Magnitude>::squareroot(norm);
 
            // R = norm
            coarseNS[0][offset] = norm;
 
            // Q = localQR(:,0)/norm
            for (LO i = 0; i < aggSize; i++)
              localQR(i,0) /= norm;
 
          } else {
            Teuchos::SerialQRDenseSolver<LO,SC> qrSolver;
            qrSolver.setMatrix(Teuchos::rcp(&localQR, false));
            qrSolver.factor();
 
            // R = upper triangular part of localQR
            for (size_t j = 0; j < NSDim; j++)
              for (size_t k = 0; k <= j; k++)
                coarseNS[j][offset+k] = localQR(k,j); //TODO is offset+k the correct local ID?!
 
            // Calculate Q, the tentative prolongator.
            // The Lapack GEQRF call only works for myAggsize >= NSDim
            qrSolver.formQ();
            Teuchos::RCP<Teuchos::SerialDenseMatrix<LO,SC> > qFactor = qrSolver.getQ();
            for (size_t j = 0; j < NSDim; j++)
              for (size_t i = 0; i < Teuchos::as<size_t>(aggSize); i++)
                localQR(i,j) = (*qFactor)(i,j);
          }
 
        } else {
          // Special handling for aggSize < NSDim (i.e. single node aggregates in structural mechanics)
 
          // The local QR decomposition is not possible in the "overconstrained"
          // case (i.e. number of columns in localQR > number of rows), which
          // corresponds to #DOFs in Aggregate < NSDim. For usual problems this
          // is only possible for single node aggregates in structural mechanics.
          // (Similar problems may arise in discontinuous Galerkin problems...)
          // We bypass the QR decomposition and use an identity block in the
          // tentative prolongator for the single node aggregate and transfer the
          // corresponding fine level null space information 1-to-1 to the coarse
          // level null space part.
 
          // NOTE: The resulting tentative prolongation operator has
          // (aggSize*DofsPerNode-NSDim) zero columns leading to a singular
          // coarse level operator A.  To deal with that one has the following
          // options:
          // - Use the "RepairMainDiagonal" flag in the RAPFactory (default:
          //   false) to add some identity block to the diagonal of the zero rows
          //   in the coarse level operator A, such that standard level smoothers
          //   can be used again.
          // - Use special (projection-based) level smoothers, which can deal
          //   with singular matrices (very application specific)
          // - Adapt the code below to avoid zero columns. However, we do not
          //   support a variable number of DOFs per node in MueLu/Xpetra which
          //   makes the implementation really hard.
 
          // R = extended (by adding identity rows) localQR
          for (size_t j = 0; j < NSDim; j++)
            for (size_t k = 0; k < NSDim; k++)
              if (k < as<size_t>(aggSize))
                coarseNS[j][offset+k] = localQR(k,j);
              else
                coarseNS[j][offset+k] = (k == j ? one : zero);
 
          // Q = I (rectangular)
          for (size_t i = 0; i < as<size_t>(aggSize); i++)
            for (size_t j = 0; j < NSDim; j++)
              localQR(i,j) = (j == i ? one : zero);
        }
 
 
        // Process each row in the local Q factor
        // FIXME: What happens if maps are blocked?
        for (LO j = 0; j < aggSize; j++) {
          LO localRow = (goodMap ? aggToRowMapLO[aggStart[agg]+j] : rowMap->getLocalElement(aggToRowMapGO[aggStart[agg]+j]));
 
          size_t rowStart = ia[localRow];
          for (size_t k = 0, lnnz = 0; k < NSDim; k++) {
            // Skip zeros (there may be plenty of them, i.e., NSDim > 1 or boundary conditions)
            if (localQR(j,k) != zero) {
              ja [rowStart+lnnz] = offset + k;
              val[rowStart+lnnz] = localQR(j,k);
              lnnz++;
            }
          }
        }
      }
 
    } else {
      GetOStream(Runtime1) << "TentativePFactory : bypassing local QR phase" << std::endl;
      if (NSDim>1)
        GetOStream(Warnings0) << "TentativePFactor : for nontrivial nullspace, this may degrade performance" << std::endl;
      //      "no-QR" option     //
      // Local Q factor is just the fine nullspace support over the current aggregate.
      // Local R factor is the identity.
      // TODO I have not implemented any special handling for aggregates that are too
      // TODO small to locally support the nullspace, as is done in the standard QR
      // TODO case above.
      if (goodMap) {
        for (GO agg = 0; agg < numAggs; agg++) {
          const LO aggSize = aggStart[agg+1] - aggStart[agg];
          Xpetra::global_size_t offset = agg*NSDim;
 
          // Process each row in the local Q factor
          // FIXME: What happens if maps are blocked?
          for (LO j = 0; j < aggSize; j++) {
 
            //TODO Here I do not check for a zero nullspace column on the aggregate.
            //     as is done in the standard QR case.
 
            const LO localRow = aggToRowMapLO[aggStart[agg]+j];
 
            const size_t rowStart = ia[localRow];
 
            for (size_t k = 0, lnnz = 0; k < NSDim; k++) {
              // Skip zeros (there may be plenty of them, i.e., NSDim > 1 or boundary conditions)
              const SC qr_jk = fineNS[k][aggToRowMapLO[aggStart[agg]+j]];
              if (qr_jk != zero) {
                ja [rowStart+lnnz] = offset + k;
                val[rowStart+lnnz] = qr_jk;
                lnnz++;
              }
            }
          }
          for (size_t j = 0; j < NSDim; j++)
            coarseNS[j][offset+j] = one;
        } //for (GO agg = 0; agg < numAggs; agg++)
 
      } else {
        for (GO agg = 0; agg < numAggs; agg++) {
          const LO aggSize = aggStart[agg+1] - aggStart[agg];
          Xpetra::global_size_t offset = agg*NSDim;
          for (LO j = 0; j < aggSize; j++) {
 
            const LO localRow = rowMap->getLocalElement(aggToRowMapGO[aggStart[agg]+j]);
 
            const size_t rowStart = ia[localRow];
 
            for (size_t k = 0, lnnz = 0; k < NSDim; k++) {
              // Skip zeros (there may be plenty of them, i.e., NSDim > 1 or boundary conditions)
              const SC qr_jk = fineNS[k][rowMap->getLocalElement(aggToRowMapGO[aggStart[agg]+j])];
              if (qr_jk != zero) {
                ja [rowStart+lnnz] = offset + k;
                val[rowStart+lnnz] = qr_jk;
                lnnz++;
              }
            }
          }
          for (size_t j = 0; j < NSDim; j++)
            coarseNS[j][offset+j] = one;
        } //for (GO agg = 0; agg < numAggs; agg++)
 
      } //if (goodmap) else ...
 
    } //if doQRStep ... else
 
    // Compress storage (remove all INVALID, which happen when we skip zeros)
    // We do that in-place
    size_t ia_tmp = 0, nnz = 0;
    for (size_t i = 0; i < numRows; i++) {
      for (size_t j = ia_tmp; j < ia[i+1]; j++)
        if (ja[j] != INVALID) {
          ja [nnz] = ja [j];
          val[nnz] = val[j];
          nnz++;
        }
      ia_tmp  = ia[i+1];
      ia[i+1] = nnz;
    }
    if (rowMap->lib() == Xpetra::UseTpetra) {
      // - Cannot resize for Epetra, as it checks for same pointers
      // - Need to resize for Tpetra, as it check ().size() == ia[numRows]
      // NOTE: these invalidate ja and val views
      jaPtent .resize(nnz);
      valPtent.resize(nnz);
    }
 
    GetOStream(Runtime1) << "TentativePFactory : aggregates do not cross process boundaries" << std::endl;
 
    PtentCrs->setAllValues(iaPtent, jaPtent, valPtent);
 
 
    // Managing labels & constants for ESFC
    RCP<ParameterList> FCparams;
    if(pL.isSublist("matrixmatrix: kernel params"))
      FCparams=rcp(new ParameterList(pL.sublist("matrixmatrix: kernel params")));
    else
      FCparams= rcp(new ParameterList);
    // By default, we don't need global constants for TentativeP
    FCparams->set("compute global constants",FCparams->get("compute global constants",false));
    std::string levelIDs = toString(levelID);
    FCparams->set("Timer Label",std::string("MueLu::TentativeP-")+levelIDs);
    RCP<const Export> dummy_e;
    RCP<const Import> dummy_i;
 
    PtentCrs->expertStaticFillComplete(coarseMap, A->getDomainMap(),dummy_i,dummy_e,FCparams);
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  void TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
  BuildPcoupled(RCP<Matrix> A, RCP<Aggregates> aggregates, RCP<AmalgamationInfo> amalgInfo, RCP<MultiVector> fineNullspace,
                RCP<const Map> coarseMap, RCP<Matrix>& Ptentative, RCP<MultiVector>& coarseNullspace) const {
    typedef Teuchos::ScalarTraits<SC> STS;
    typedef typename STS::magnitudeType Magnitude;
    const SC     zero      = STS::zero();
    const SC     one       = STS::one();
 
    // number of aggregates
    GO numAggs = aggregates->GetNumAggregates();
 
    // Create a lookup table to determine the rows (fine DOFs) that belong to a given aggregate.
    // aggStart is a pointer into aggToRowMap
    // aggStart[i]..aggStart[i+1] are indices into aggToRowMap
    // aggToRowMap[aggStart[i]]..aggToRowMap[aggStart[i+1]-1] are the DOFs in aggregate i
    ArrayRCP<LO> aggStart;
    ArrayRCP< GO > aggToRowMap;
    amalgInfo->UnamalgamateAggregates(*aggregates, aggStart, aggToRowMap);
 
    // find size of the largest aggregate
    LO maxAggSize=0;
    for (GO i=0; i<numAggs; ++i) {
      LO sizeOfThisAgg = aggStart[i+1] - aggStart[i];
      if (sizeOfThisAgg > maxAggSize) maxAggSize = sizeOfThisAgg;
    }
 
    // dimension of fine level nullspace
    const size_t NSDim = fineNullspace->getNumVectors();
 
    // index base for coarse Dof map (usually 0)
    GO indexBase=A->getRowMap()->getIndexBase();
 
    const RCP<const Map> nonUniqueMap = amalgInfo->ComputeUnamalgamatedImportDofMap(*aggregates);
    const RCP<const Map> uniqueMap    = A->getDomainMap();
    RCP<const Import> importer = ImportFactory::Build(uniqueMap, nonUniqueMap);
    RCP<MultiVector> fineNullspaceWithOverlap = MultiVectorFactory::Build(nonUniqueMap,NSDim);
    fineNullspaceWithOverlap->doImport(*fineNullspace,*importer,Xpetra::INSERT);
 
    // Pull out the nullspace vectors so that we can have random access.
    ArrayRCP< ArrayRCP<const SC> > fineNS(NSDim);
    for (size_t i=0; i<NSDim; ++i)
      fineNS[i] = fineNullspaceWithOverlap->getData(i);
 
    //Allocate storage for the coarse nullspace.
    coarseNullspace = MultiVectorFactory::Build(coarseMap, NSDim);
 
    ArrayRCP< ArrayRCP<SC> > coarseNS(NSDim);
    for (size_t i=0; i<NSDim; ++i)
      if (coarseMap->getNodeNumElements() > 0) coarseNS[i] = coarseNullspace->getDataNonConst(i);
 
    //This makes the rowmap of Ptent the same as that of A->
    //This requires moving some parts of some local Q's to other processors
    //because aggregates can span processors.
    RCP<const Map > rowMapForPtent = A->getRowMap();
    const Map& rowMapForPtentRef = *rowMapForPtent;
 
    // Set up storage for the rows of the local Qs that belong to other processors.
    // FIXME This is inefficient and could be done within the main loop below with std::vector's.
    RCP<const Map> colMap = A->getColMap();
 
    RCP<const Map > ghostQMap;
    RCP<MultiVector> ghostQvalues;
    Array<RCP<Xpetra::Vector<GO,LO,GO,Node> > > ghostQcolumns;
    RCP<Xpetra::Vector<GO,LO,GO,Node> > ghostQrowNums;
    ArrayRCP< ArrayRCP<SC> > ghostQvals;
    ArrayRCP< ArrayRCP<GO> > ghostQcols;
    ArrayRCP< GO > ghostQrows;
 
    Array<GO> ghostGIDs;
    for (LO j=0; j<numAggs; ++j) {
      for (LO k=aggStart[j]; k<aggStart[j+1]; ++k) {
        if (rowMapForPtentRef.isNodeGlobalElement(aggToRowMap[k]) == false) {
          ghostGIDs.push_back(aggToRowMap[k]);
        }
      }
    }
    ghostQMap = MapFactory::Build(A->getRowMap()->lib(),
                                  Teuchos::OrdinalTraits<Xpetra::global_size_t>::invalid(),
                                  ghostGIDs,
                                  indexBase, A->getRowMap()->getComm()); //JG:Xpetra::global_size_t>?
    //Vector to hold bits of Q that go to other processors.
    ghostQvalues = MultiVectorFactory::Build(ghostQMap,NSDim);
    //Note that Epetra does not support MultiVectors templated on Scalar != double.
    //So to work around this, we allocate an array of Vectors.  This shouldn't be too
    //expensive, as the number of Vectors is NSDim.
    ghostQcolumns.resize(NSDim);
    for (size_t i=0; i<NSDim; ++i)
      ghostQcolumns[i] = Xpetra::VectorFactory<GO,LO,GO,Node>::Build(ghostQMap);
    ghostQrowNums = Xpetra::VectorFactory<GO,LO,GO,Node>::Build(ghostQMap);
    if (ghostQvalues->getLocalLength() > 0) {
      ghostQvals.resize(NSDim);
      ghostQcols.resize(NSDim);
      for (size_t i=0; i<NSDim; ++i) {
        ghostQvals[i] = ghostQvalues->getDataNonConst(i);
        ghostQcols[i] = ghostQcolumns[i]->getDataNonConst(0);
      }
      ghostQrows = ghostQrowNums->getDataNonConst(0);
    }
 
    //importer to handle moving Q
    importer = ImportFactory::Build(ghostQMap, A->getRowMap());
 
    // Dense QR solver
    Teuchos::SerialQRDenseSolver<LO,SC> qrSolver;
 
    //Allocate temporary storage for the tentative prolongator.
    Array<GO> globalColPtr(maxAggSize*NSDim,0);
    Array<LO> localColPtr(maxAggSize*NSDim,0);
    Array<SC> valPtr(maxAggSize*NSDim,0.);
 
    //Create column map for Ptent, estimate local #nonzeros in Ptent,  and create Ptent itself.
    const Map& coarseMapRef = *coarseMap;
 
    // For the 3-arrays constructor
    ArrayRCP<size_t>  ptent_rowptr;
    ArrayRCP<LO>      ptent_colind;
    ArrayRCP<Scalar>  ptent_values;
 
    // Because ArrayRCPs are slow...
    ArrayView<size_t> rowptr_v;
    ArrayView<LO>     colind_v;
    ArrayView<Scalar> values_v;
 
    // For temporary usage
    Array<size_t>    rowptr_temp;
    Array<LO>        colind_temp;
    Array<Scalar>    values_temp;
 
    RCP<CrsMatrix> PtentCrs;
 
    RCP<CrsMatrixWrap> PtentCrsWrap = rcp(new CrsMatrixWrap(rowMapForPtent, NSDim, Xpetra::StaticProfile));
    PtentCrs   = PtentCrsWrap->getCrsMatrix();
    Ptentative = PtentCrsWrap;
 
    //*****************************************************************
    //Loop over all aggregates and calculate local QR decompositions.
    //*****************************************************************
    GO qctr=0; //for indexing into Ptent data vectors
    const Map& nonUniqueMapRef = *nonUniqueMap;
 
    size_t total_nnz_count=0;
 
    for (GO agg=0; agg<numAggs; ++agg)
    {
      LO myAggSize = aggStart[agg+1]-aggStart[agg];
      // For each aggregate, extract the corresponding piece of the nullspace and put it in the flat array,
      // "localQR" (in column major format) for the QR routine.
      Teuchos::SerialDenseMatrix<LO,SC> localQR(myAggSize, NSDim);
      for (size_t j=0; j<NSDim; ++j) {
        bool bIsZeroNSColumn = true;
        for (LO k=0; k<myAggSize; ++k)
        {
          // aggToRowMap[aggPtr[i]+k] is the kth DOF in the ith aggregate
          // fineNS[j][n] is the nth entry in the jth NS vector
          try{
            SC nsVal = fineNS[j][ nonUniqueMapRef.getLocalElement(aggToRowMap[aggStart[agg]+k]) ]; // extract information from fine level NS
            localQR(k,j) = nsVal;
            if (nsVal != zero) bIsZeroNSColumn = false;
          }
          catch(...) {
            GetOStream(Runtime1,-1) << "length of fine level nsp: " << fineNullspace->getGlobalLength() << std::endl;
            GetOStream(Runtime1,-1) << "length of fine level nsp w overlap: " << fineNullspaceWithOverlap->getGlobalLength() << std::endl;
            GetOStream(Runtime1,-1) << "(local?) aggId=" << agg << std::endl;
            GetOStream(Runtime1,-1) << "aggSize=" << myAggSize << std::endl;
            GetOStream(Runtime1,-1) << "agg DOF=" << k << std::endl;
            GetOStream(Runtime1,-1) << "NS vector j=" << j << std::endl;
            GetOStream(Runtime1,-1) << "j*myAggSize + k = " << j*myAggSize + k << std::endl;
            GetOStream(Runtime1,-1) << "aggToRowMap["<<agg<<"][" << k << "] = " << aggToRowMap[aggStart[agg]+k] << std::endl;
            GetOStream(Runtime1,-1) << "id aggToRowMap[agg][k]=" << aggToRowMap[aggStart[agg]+k] << " is global element in nonUniqueMap = " <<
                nonUniqueMapRef.isNodeGlobalElement(aggToRowMap[aggStart[agg]+k]) << std::endl;
            GetOStream(Runtime1,-1) << "colMap local id aggToRowMap[agg][k]=" << nonUniqueMapRef.getLocalElement(aggToRowMap[aggStart[agg]+k]) << std::endl;
            GetOStream(Runtime1,-1) << "fineNS...=" << fineNS[j][ nonUniqueMapRef.getLocalElement(aggToRowMap[aggStart[agg]+k]) ] << std::endl;
            GetOStream(Errors,-1) << "caught an error!" << std::endl;
          }
        } //for (LO k=0 ...
        TEUCHOS_TEST_FOR_EXCEPTION(bIsZeroNSColumn == true, Exceptions::RuntimeError, "MueLu::TentativePFactory::MakeTentative: fine level NS part has a zero column. Error.");
      } //for (LO j=0 ...
 
      Xpetra::global_size_t offset=agg*NSDim;
 
      if(myAggSize >= Teuchos::as<LocalOrdinal>(NSDim)) {
        // calculate QR decomposition (standard)
        // R is stored in localQR (size: myAggSize x NSDim)
 
        // Householder multiplier
        SC tau = localQR(0,0);
 
        if (NSDim == 1) {
          // Only one nullspace vector, so normalize by hand
          Magnitude dtemp=0;
          for (size_t k = 0; k < Teuchos::as<size_t>(myAggSize); ++k) {
              Magnitude tmag = STS::magnitude(localQR(k,0));
            dtemp += tmag*tmag;
          }
          dtemp = Teuchos::ScalarTraits<Magnitude>::squareroot(dtemp);
          tau = localQR(0,0);
          localQR(0,0) = dtemp;
        } else {
          qrSolver.setMatrix( Teuchos::rcp(&localQR, false) );
          qrSolver.factor();
        }
 
         // Extract R, the coarse nullspace.  This is stored in upper triangular part of localQR.
         // Note:  coarseNS[i][.] is the ith coarse nullspace vector, which may be counter to your intuition.
         // This stores the (offset+k)th entry only if it is local according to the coarseMap.
         for (size_t j=0; j<NSDim; ++j) {
           for (size_t k=0; k<=j; ++k) {
             try {
               if (coarseMapRef.isNodeLocalElement(offset+k)) {
                 coarseNS[j][offset+k] = localQR(k, j); //TODO is offset+k the correct local ID?!
               }
             }
             catch(...) {
               GetOStream(Errors,-1) << "caught error in coarseNS insert, j="<<j<<", offset+k = "<<offset+k<<std::endl;
             }
           }
         }
 
         // Calculate Q, the tentative prolongator.
         // The Lapack GEQRF call only works for myAggsize >= NSDim
 
         if (NSDim == 1) {
           // Only one nullspace vector, so calculate Q by hand
           Magnitude dtemp = Teuchos::ScalarTraits<SC>::magnitude(localQR(0,0));
           localQR(0,0) = tau;
           dtemp = 1 / dtemp;
           for (LocalOrdinal i=0; i<myAggSize; ++i) {
             localQR(i,0) *= dtemp ;
           }
         } else {
           qrSolver.formQ();
           Teuchos::RCP<Teuchos::SerialDenseMatrix<LO,SC> > qFactor = qrSolver.getQ();
           for (size_t j=0; j<NSDim; j++) {
             for (size_t i = 0; i < Teuchos::as<size_t>(myAggSize); i++) {
               localQR(i,j) = (*qFactor)(i,j);
             }
           }
         }
 
         // end default case (myAggSize >= NSDim)
      } else {  // special handling for myAggSize < NSDim (i.e. 1pt nodes)
        // See comments for the uncoupled case
 
        // R = extended (by adding identity rows) localQR
        for (size_t j = 0; j < NSDim; j++)
          for (size_t k = 0; k < NSDim; k++) {
            TEUCHOS_TEST_FOR_EXCEPTION(!coarseMapRef.isNodeLocalElement(offset+k), Exceptions::RuntimeError,
                                       "Caught error in coarseNS insert, j=" << j << ", offset+k = " << offset+k);
 
            if (k < as<size_t>(myAggSize))
              coarseNS[j][offset+k] = localQR(k,j);
            else
              coarseNS[j][offset+k] = (k == j ? one : zero);
          }
 
        // Q = I (rectangular)
        for (size_t i = 0; i < as<size_t>(myAggSize); i++)
          for (size_t j = 0; j < NSDim; j++)
            localQR(i,j) = (j == i ? one : zero);
      } // end else (special handling for 1pt aggregates)
 
      //Process each row in the local Q factor.  If the row is local to the current processor
      //according to the rowmap, insert it into Ptentative.  Otherwise, save it in ghostQ
      //to be communicated later to the owning processor.
      //FIXME -- what happens if maps are blocked?
      for (GO j=0; j<myAggSize; ++j) {
        //This loop checks whether row associated with current DOF is local, according to rowMapForPtent.
        //If it is, the row is inserted.  If not, the row number, columns, and values are saved in
        //MultiVectors that will be sent to other processors.
        GO globalRow = aggToRowMap[aggStart[agg]+j];
 
        //TODO is the use of Xpetra::global_size_t below correct?
        if (rowMapForPtentRef.isNodeGlobalElement(globalRow) == false ) {
          ghostQrows[qctr] = globalRow;
          for (size_t k=0; k<NSDim; ++k) {
            ghostQcols[k][qctr] = coarseMapRef.getGlobalElement(agg*NSDim+k);
            ghostQvals[k][qctr] = localQR(j,k);
          }
          ++qctr;
        } else {
          size_t nnz=0;
          for (size_t k=0; k<NSDim; ++k) {
            try{
              if (localQR(j,k) != Teuchos::ScalarTraits<SC>::zero()) {
                localColPtr[nnz]  = agg * NSDim + k;
                globalColPtr[nnz] = coarseMapRef.getGlobalElement(localColPtr[nnz]);
                valPtr[nnz] = localQR(j,k);
                ++total_nnz_count;
                ++nnz;
              }
            }
            catch(...) {
              GetOStream(Errors,-1) << "caught error in colPtr/valPtr insert, current index="<<nnz<<std::endl;
            }
          } //for (size_t k=0; k<NSDim; ++k)
 
          try{
              Ptentative->insertGlobalValues(globalRow,globalColPtr.view(0,nnz),valPtr.view(0,nnz));
          }
          catch(...) {
            GetOStream(Errors,-1) << "pid " << A->getRowMap()->getComm()->getRank()
                << "caught error during Ptent row insertion, global row "
                << globalRow << std::endl;
          }
        }
      } //for (GO j=0; j<myAggSize; ++j)
 
    } // for (LO agg=0; agg<numAggs; ++agg)
 
 
    // ***********************************************************
    // ************* end of aggregate-wise QR ********************
    // ***********************************************************
    GetOStream(Runtime1) << "TentativePFactory : aggregates may cross process boundaries" << std::endl;
    // Import ghost parts of Q factors and insert into Ptentative.
    // First import just the global row numbers.
    RCP<Xpetra::Vector<GO,LO,GO,Node> > targetQrowNums = Xpetra::VectorFactory<GO,LO,GO,Node>::Build(rowMapForPtent);
    targetQrowNums->putScalar(-1);
    targetQrowNums->doImport(*ghostQrowNums,*importer,Xpetra::INSERT);
    ArrayRCP< GO > targetQrows = targetQrowNums->getDataNonConst(0);
 
    // Now create map based on just the row numbers imported.
    Array<GO> gidsToImport;
    gidsToImport.reserve(targetQrows.size());
    for (typename ArrayRCP<GO>::iterator r=targetQrows.begin(); r!=targetQrows.end(); ++r) {
      if (*r > -1) {
        gidsToImport.push_back(*r);
      }
    }
    RCP<const Map > reducedMap = MapFactory::Build( A->getRowMap()->lib(),
                                                    Teuchos::OrdinalTraits<Xpetra::global_size_t>::invalid(),
                                                    gidsToImport, indexBase, A->getRowMap()->getComm()    );
 
    // Import using the row numbers that this processor will receive.
    importer = ImportFactory::Build(ghostQMap, reducedMap);
 
    Array<RCP<Xpetra::Vector<GO,LO,GO,Node> > > targetQcolumns(NSDim);
    for (size_t i=0; i<NSDim; ++i) {
      targetQcolumns[i] = Xpetra::VectorFactory<GO,LO,GO,Node>::Build(reducedMap);
      targetQcolumns[i]->doImport(*(ghostQcolumns[i]),*importer,Xpetra::INSERT);
    }
    RCP<MultiVector> targetQvalues = MultiVectorFactory::Build(reducedMap,NSDim);
    targetQvalues->doImport(*ghostQvalues,*importer,Xpetra::INSERT);
 
    ArrayRCP< ArrayRCP<SC> > targetQvals;
    ArrayRCP<ArrayRCP<GO> > targetQcols;
    if (targetQvalues->getLocalLength() > 0) {
      targetQvals.resize(NSDim);
      targetQcols.resize(NSDim);
      for (size_t i=0; i<NSDim; ++i) {
        targetQvals[i] = targetQvalues->getDataNonConst(i);
        targetQcols[i] = targetQcolumns[i]->getDataNonConst(0);
      }
    }
 
    valPtr = Array<SC>(NSDim,0.);
    globalColPtr = Array<GO>(NSDim,0);
    for (typename Array<GO>::iterator r=gidsToImport.begin(); r!=gidsToImport.end(); ++r) {
      if (targetQvalues->getLocalLength() > 0) {
        for (size_t j=0; j<NSDim; ++j) {
          valPtr[j] = targetQvals[j][reducedMap->getLocalElement(*r)];
          globalColPtr[j] = targetQcols[j][reducedMap->getLocalElement(*r)];
        }
        Ptentative->insertGlobalValues(*r, globalColPtr.view(0,NSDim), valPtr.view(0,NSDim));
      } //if (targetQvalues->getLocalLength() > 0)
    }
 
    Ptentative->fillComplete(coarseMap, A->getDomainMap());
  }
 
  template <class Scalar,class LocalOrdinal, class GlobalOrdinal, class Node>
  bool TentativePFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::isGoodMap(const Map& rowMap, const Map& colMap) const {
    ArrayView<const GO> rowElements = rowMap.getNodeElementList();
    ArrayView<const GO> colElements = colMap.getNodeElementList();
 
    const size_t numElements = rowElements.size();
 
    bool goodMap = true;
    for (size_t i = 0; i < numElements; i++)
      if (rowElements[i] != colElements[i]) {
        goodMap = false;
        break;
      }
 
    return goodMap;
  }
 
} //namespace MueLu
 
// TODO ReUse: If only P or Nullspace is missing, TentativePFactory can be smart and skip part of the computation.
 
#define MUELU_TENTATIVEPFACTORY_SHORT
#endif // MUELU_TENTATIVEPFACTORY_DEF_HPP