TempestOnlineMapIO.cpp

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/*
 * =====================================================================================
 *
 * Filename: TempestOnlineMapIO.cpp
 *
 * Description: All I/O implementations related to TempestOnlineMap
 *
 * Version: 1.0
 * Created: 02/06/2021 02:35:41
 *
 * Author: Vijay S. Mahadevan (vijaysm), [email protected]
 * Company: Argonne National Lab
 *
 * =====================================================================================
 */
 
#include "FiniteElementTools.h"
#include "moab/Remapping/TempestOnlineMap.hpp"
#include "moab/TupleList.hpp"
 
#ifdef MOAB_HAVE_NETCDFPAR
#include "netcdfcpp_par.hpp"
#else
#include "netcdfcpp.h"
#endif
 
#ifdef MOAB_HAVE_PNETCDF
#include <pnetcdf.h>
 
#define ERR_PARNC( err ) \
 if( err != NC_NOERR ) \
 { \
 fprintf( stderr, "Error at line %d: %s\n", __LINE__, ncmpi_strerror( err ) ); \
 MPI_Abort( MPI_COMM_WORLD, 1 ); \
 }
 
#endif
 
#ifdef MOAB_HAVE_MPI
 
#define MPI_CHK_ERR( err ) \
 if( err ) \
 { \
 std::cout << "MPI Failure. ErrorCode (" << ( err ) << ") "; \
 std::cout << "\nMPI Aborting... \n"; \
 return moab::MB_FAILURE; \
 }
 
int moab::TempestOnlineMap::rearrange_arrays_by_dofs( const std::vector< unsigned int >& gdofmap,
 DataArray1D< double >& vecFaceArea,
 DataArray1D< double >& dCenterLon,
 DataArray1D< double >& dCenterLat,
 DataArray2D< double >& dVertexLon,
 DataArray2D< double >& dVertexLat,
 std::vector< int >& masks,
 unsigned& N, // will have the local, after
 int nv,
 int& maxdof )
{
 // first decide maxdof, for partitioning
 unsigned int localmax = 0;
 for( unsigned i = 0; i < N; i++ )
 if( gdofmap[i] > localmax ) localmax = gdofmap[i];
 
 // decide partitioning based on maxdof/size
 MPI_Allreduce( &localmax, &maxdof, 1, MPI_INT, MPI_MAX, m_pcomm->comm() );
 // maxdof is 0 based, so actual number is +1
 // maxdof
 int size_per_task = ( maxdof + 1 ) / size; // based on this, processor to process dof x is x/size_per_task
 // so we decide to reorder by actual dof, such that task 0 has dofs from [0 to size_per_task), etc
 moab::TupleList tl;
 unsigned numr = 2 * nv + 3; // doubles: area, centerlon, center lat, nv (vertex lon, vertex lat)
 tl.initialize( 3, 0, 0, numr, N ); // to proc, dof, then
 tl.enableWriteAccess();
 // populate
 for( unsigned i = 0; i < N; i++ )
 {
 int gdof = gdofmap[i];
 int to_proc = gdof / size_per_task;
 int mask = masks[i];
 if( to_proc >= size ) to_proc = size - 1; // the last ones go to last proc
 int n = tl.get_n();
 tl.vi_wr[3 * n] = to_proc;
 tl.vi_wr[3 * n + 1] = gdof;
 tl.vi_wr[3 * n + 2] = mask;
 tl.vr_wr[n * numr] = vecFaceArea[i];
 tl.vr_wr[n * numr + 1] = dCenterLon[i];
 tl.vr_wr[n * numr + 2] = dCenterLat[i];
 for( int j = 0; j < nv; j++ )
 {
 tl.vr_wr[n * numr + 3 + j] = dVertexLon[i][j];
 tl.vr_wr[n * numr + 3 + nv + j] = dVertexLat[i][j];
 }
 tl.inc_n();
 }
 
 // now do the heavy communication
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tl, 0 );
 
 // after communication, on each processor we should have tuples coming in
 // still need to order by global dofs; then rearrange input vectors
 moab::TupleList::buffer sort_buffer;
 sort_buffer.buffer_init( tl.get_n() );
 tl.sort( 1, &sort_buffer );
 // count how many are unique, and collapse
 int nb_unique = 1;
 for( unsigned i = 0; i < tl.get_n() - 1; i++ )
 {
 if( tl.vi_wr[3 * i + 1] != tl.vi_wr[3 * i + 4] ) nb_unique++;
 }
 vecFaceArea.Allocate( nb_unique );
 dCenterLon.Allocate( nb_unique );
 dCenterLat.Allocate( nb_unique );
 dVertexLon.Allocate( nb_unique, nv );
 dVertexLat.Allocate( nb_unique, nv );
 masks.resize( nb_unique );
 int current_size = 1;
 vecFaceArea[0] = tl.vr_wr[0];
 dCenterLon[0] = tl.vr_wr[1];
 dCenterLat[0] = tl.vr_wr[2];
 masks[0] = tl.vi_wr[2];
 for( int j = 0; j < nv; j++ )
 {
 dVertexLon[0][j] = tl.vr_wr[3 + j];
 dVertexLat[0][j] = tl.vr_wr[3 + nv + j];
 }
 for( unsigned i = 0; i < tl.get_n() - 1; i++ )
 {
 int i1 = i + 1;
 if( tl.vi_wr[3 * i + 1] != tl.vi_wr[3 * i + 4] )
 {
 vecFaceArea[current_size] = tl.vr_wr[i1 * numr];
 dCenterLon[current_size] = tl.vr_wr[i1 * numr + 1];
 dCenterLat[current_size] = tl.vr_wr[i1 * numr + 2];
 for( int j = 0; j < nv; j++ )
 {
 dVertexLon[current_size][j] = tl.vr_wr[i1 * numr + 3 + j];
 dVertexLat[current_size][j] = tl.vr_wr[i1 * numr + 3 + nv + j];
 }
 masks[current_size] = tl.vi_wr[3 * i1 + 2];
 current_size++;
 }
 else
 {
 vecFaceArea[current_size - 1] += tl.vr_wr[i1 * numr]; // accumulate areas; will come here only for cgll ?
 }
 }
 
 N = current_size; // or nb_unique, should be the same
 return 0;
}
#endif
 
///////////////////////////////////////////////////////////////////////////////
 
moab::ErrorCode moab::TempestOnlineMap::WriteParallelMap( const std::string& strFilename,
 const std::map< std::string, std::string >& attrMap )
{
 moab::ErrorCode rval;
 
 size_t lastindex = strFilename.find_last_of( "." );
 std::string extension = strFilename.substr( lastindex + 1, strFilename.size() );
 
 // Write the map file to disk in parallel
 if( extension == "nc" )
 {
 /* Invoke the actual call to write the parallel map to disk in SCRIP format */
 rval = this->WriteSCRIPMapFile( strFilename.c_str(), attrMap );MB_CHK_ERR( rval );
 }
 else
 {
 /* Write to the parallel H5M format */
 rval = this->WriteHDF5MapFile( strFilename.c_str() );MB_CHK_ERR( rval );
 }
 
 return rval;
}
 
///////////////////////////////////////////////////////////////////////////////
 
moab::ErrorCode moab::TempestOnlineMap::WriteSCRIPMapFile( const std::string& strFilename,
 const std::map< std::string, std::string >& attrMap )
{
 NcError error( NcError::silent_nonfatal );
 
#ifdef MOAB_HAVE_NETCDFPAR
 bool is_independent = true;
 ParNcFile ncMap( m_pcomm->comm(), MPI_INFO_NULL, strFilename.c_str(), NcFile::Replace, NcFile::Netcdf4 );
 // ParNcFile ncMap( m_pcomm->comm(), MPI_INFO_NULL, strFilename.c_str(), NcmpiFile::replace, NcmpiFile::classic5 );
#else
 NcFile ncMap( strFilename.c_str(), NcFile::Replace );
#endif
 
 if( !ncMap.is_valid() )
 {
 _EXCEPTION1( "Unable to open output map file \"%s\"", strFilename.c_str() );
 }
 
 // Attributes
 // ncMap.add_att( "Title", "MOAB-TempestRemap Online Regridding Weight Generator" );
 auto it = attrMap.begin();
 while( it != attrMap.end() )
 {
 // set the map attributes
 ncMap.add_att( it->first.c_str(), it->second.c_str() );
 // increment iterator
 it++;
 }
 
 /**
 * Need to get the global maximum of number of vertices per element
 * Key issue is that when calling InitializeCoordinatesFromMeshFV, the allocation for
 *dVertexLon/dVertexLat are made based on the maximum vertices in the current process. However,
 *when writing this out, other processes may have a different size for the same array. This is
 *hence a mess to consolidate in h5mtoscrip eventually.
 **/
 
 /* Let us compute all relevant data for the current original source mesh on the process */
 DataArray1D< double > vecSourceFaceArea, vecTargetFaceArea;
 DataArray1D< double > dSourceCenterLon, dSourceCenterLat, dTargetCenterLon, dTargetCenterLat;
 DataArray2D< double > dSourceVertexLon, dSourceVertexLat, dTargetVertexLon, dTargetVertexLat;
 if( m_srcDiscType == DiscretizationType_FV || m_srcDiscType == DiscretizationType_PCLOUD )
 {
 this->InitializeCoordinatesFromMeshFV(
 *m_meshInput, dSourceCenterLon, dSourceCenterLat, dSourceVertexLon, dSourceVertexLat,
 ( this->m_remapper->m_source_type == moab::TempestRemapper::RLL ), /* fLatLon = false */
 m_remapper->max_source_edges );
 
 vecSourceFaceArea.Allocate( m_meshInput->vecFaceArea.GetRows() );
 for( unsigned i = 0; i < m_meshInput->vecFaceArea.GetRows(); ++i )
 vecSourceFaceArea[i] = m_meshInput->vecFaceArea[i];
 }
 else
 {
 DataArray3D< double > dataGLLJacobianSrc;
 this->InitializeCoordinatesFromMeshFE( *m_meshInput, m_nDofsPEl_Src, dataGLLNodesSrc, dSourceCenterLon,
 dSourceCenterLat, dSourceVertexLon, dSourceVertexLat );
 
 // Generate the continuous Jacobian for input mesh
 GenerateMetaData( *m_meshInput, m_nDofsPEl_Src, false /* fBubble */, dataGLLNodesSrc, dataGLLJacobianSrc );
 
 if( m_srcDiscType == DiscretizationType_CGLL )
 {
 GenerateUniqueJacobian( dataGLLNodesSrc, dataGLLJacobianSrc, vecSourceFaceArea );
 }
 else
 {
 GenerateDiscontinuousJacobian( dataGLLJacobianSrc, vecSourceFaceArea );
 }
 }
 
 if( m_destDiscType == DiscretizationType_FV || m_destDiscType == DiscretizationType_PCLOUD )
 {
 this->InitializeCoordinatesFromMeshFV(
 *m_meshOutput, dTargetCenterLon, dTargetCenterLat, dTargetVertexLon, dTargetVertexLat,
 ( this->m_remapper->m_target_type == moab::TempestRemapper::RLL ), /* fLatLon = false */
 m_remapper->max_target_edges );
 
 vecTargetFaceArea.Allocate( m_meshOutput->vecFaceArea.GetRows() );
 for( unsigned i = 0; i < m_meshOutput->vecFaceArea.GetRows(); ++i )
 {
 vecTargetFaceArea[i] = m_meshOutput->vecFaceArea[i];
 }
 }
 else
 {
 DataArray3D< double > dataGLLJacobianDest;
 this->InitializeCoordinatesFromMeshFE( *m_meshOutput, m_nDofsPEl_Dest, dataGLLNodesDest, dTargetCenterLon,
 dTargetCenterLat, dTargetVertexLon, dTargetVertexLat );
 
 // Generate the continuous Jacobian for input mesh
 GenerateMetaData( *m_meshOutput, m_nDofsPEl_Dest, false /* fBubble */, dataGLLNodesDest, dataGLLJacobianDest );
 
 if( m_destDiscType == DiscretizationType_CGLL )
 {
 GenerateUniqueJacobian( dataGLLNodesDest, dataGLLJacobianDest, vecTargetFaceArea );
 }
 else
 {
 GenerateDiscontinuousJacobian( dataGLLJacobianDest, vecTargetFaceArea );
 }
 }
 
 // Map dimensions
 unsigned nA = ( vecSourceFaceArea.GetRows() );
 unsigned nB = ( vecTargetFaceArea.GetRows() );
 
 std::vector< int > masksA, masksB;
 ErrorCode rval = m_remapper->GetIMasks( moab::Remapper::SourceMesh, masksA );MB_CHK_SET_ERR( rval, "Trouble getting masks for source" );
 rval = m_remapper->GetIMasks( moab::Remapper::TargetMesh, masksB );MB_CHK_SET_ERR( rval, "Trouble getting masks for target" );
 
 // Number of nodes per Face
 int nSourceNodesPerFace = dSourceVertexLon.GetColumns();
 int nTargetNodesPerFace = dTargetVertexLon.GetColumns();
 
 // if source or target cells have triangles at poles, center of those triangles need to come from
 // the original quad, not from center in 3d, converted to 2d again
 // start copy OnlineMap.cpp tempestremap
 // right now, do this only for source mesh; copy the logic for target mesh
 for( unsigned i = 0; i < nA; i++ )
 {
 const Face& face = m_meshInput->faces[i];
 
 int nNodes = face.edges.size();
 int indexNodeAtPole = -1;
 if( 3 == nNodes ) // check if one node at the poles
 {
 for( int j = 0; j < nNodes; j++ )
 if( fabs( fabs( dSourceVertexLat[i][j] ) - 90.0 ) < 1.0e-12 )
 {
 indexNodeAtPole = j;
 break;
 }
 }
 if( indexNodeAtPole < 0 ) continue; // continue i loop, do nothing
 // recompute center of cell, from 3d data; add one 2 nodes at pole, and average
 int nodeAtPole = face[indexNodeAtPole]; // use the overloaded operator
 Node nodePole = m_meshInput->nodes[nodeAtPole];
 Node newCenter = nodePole * 2;
 for( int j = 1; j < nNodes; j++ )
 {
 int indexi = ( indexNodeAtPole + j ) % nNodes; // nNodes is 3 !
 const Node& node = m_meshInput->nodes[face[indexi]];
 newCenter = newCenter + node;
 }
 newCenter = newCenter * 0.25;
 newCenter = newCenter.Normalized();
 
#ifdef VERBOSE
 double iniLon = dSourceCenterLon[i], iniLat = dSourceCenterLat[i];
#endif
 // dSourceCenterLon, dSourceCenterLat
 XYZtoRLL_Deg( newCenter.x, newCenter.y, newCenter.z, dSourceCenterLon[i], dSourceCenterLat[i] );
#ifdef VERBOSE
 std::cout << " modify center of triangle from " << iniLon << " " << iniLat << " to " << dSourceCenterLon[i]
 << " " << dSourceCenterLat[i] << "\n";
#endif
 }
 
 // first move data if in parallel
#if defined( MOAB_HAVE_MPI )
 int max_row_dof, max_col_dof; // output; arrays will be re-distributed in chunks [maxdof/size]
 // if (size > 1)
 {
 int ierr = rearrange_arrays_by_dofs( srccol_gdofmap, vecSourceFaceArea, dSourceCenterLon, dSourceCenterLat,
 dSourceVertexLon, dSourceVertexLat, masksA, nA, nSourceNodesPerFace,
 max_col_dof ); // now nA will be close to maxdof/size
 if( ierr != 0 )
 {
 _EXCEPTION1( "Unable to arrange source data %d ", nA );
 }
 // rearrange target data: (nB)
 //
 ierr = rearrange_arrays_by_dofs( row_gdofmap, vecTargetFaceArea, dTargetCenterLon, dTargetCenterLat,
 dTargetVertexLon, dTargetVertexLat, masksB, nB, nTargetNodesPerFace,
 max_row_dof ); // now nA will be close to maxdof/size
 if( ierr != 0 )
 {
 _EXCEPTION1( "Unable to arrange target data %d ", nB );
 }
 }
#endif
 
 // Number of non-zeros in the remap matrix operator
 int nS = m_weightMatrix.nonZeros();
 
#if defined( MOAB_HAVE_MPI ) && defined( MOAB_HAVE_NETCDFPAR )
 int locbuf[5] = { (int)nA, (int)nB, nS, nSourceNodesPerFace, nTargetNodesPerFace };
 int offbuf[3] = { 0, 0, 0 };
 int globuf[5] = { 0, 0, 0, 0, 0 };
 MPI_Scan( locbuf, offbuf, 3, MPI_INT, MPI_SUM, m_pcomm->comm() );
 MPI_Allreduce( locbuf, globuf, 3, MPI_INT, MPI_SUM, m_pcomm->comm() );
 MPI_Allreduce( &locbuf[3], &globuf[3], 2, MPI_INT, MPI_MAX, m_pcomm->comm() );
 
 // MPI_Scan is inclusive of data in current rank; modify accordingly.
 offbuf[0] -= nA;
 offbuf[1] -= nB;
 offbuf[2] -= nS;
 
#else
 int offbuf[3] = { 0, 0, 0 };
 int globuf[5] = { (int)nA, (int)nB, nS, nSourceNodesPerFace, nTargetNodesPerFace };
#endif
 
 std::vector< std::string > srcdimNames, tgtdimNames;
 std::vector< int > srcdimSizes, tgtdimSizes;
 {
 if( m_remapper->m_source_type == moab::TempestRemapper::RLL && m_remapper->m_source_metadata.size() )
 {
 srcdimNames.push_back( "lat" );
 srcdimNames.push_back( "lon" );
 srcdimSizes.resize( 2, 0 );
 srcdimSizes[0] = m_remapper->m_source_metadata[0];
 srcdimSizes[1] = m_remapper->m_source_metadata[1];
 }
 else
 {
 srcdimNames.push_back( "num_elem" );
 srcdimSizes.push_back( globuf[0] );
 }
 
 if( m_remapper->m_target_type == moab::TempestRemapper::RLL && m_remapper->m_target_metadata.size() )
 {
 tgtdimNames.push_back( "lat" );
 tgtdimNames.push_back( "lon" );
 tgtdimSizes.resize( 2, 0 );
 tgtdimSizes[0] = m_remapper->m_target_metadata[0];
 tgtdimSizes[1] = m_remapper->m_target_metadata[1];
 }
 else
 {
 tgtdimNames.push_back( "num_elem" );
 tgtdimSizes.push_back( globuf[1] );
 }
 }
 
 // Write output dimensions entries
 unsigned nSrcGridDims = ( srcdimSizes.size() );
 unsigned nDstGridDims = ( tgtdimSizes.size() );
 
 NcDim* dimSrcGridRank = ncMap.add_dim( "src_grid_rank", nSrcGridDims );
 NcDim* dimDstGridRank = ncMap.add_dim( "dst_grid_rank", nDstGridDims );
 
 NcVar* varSrcGridDims = ncMap.add_var( "src_grid_dims", ncInt, dimSrcGridRank );
 NcVar* varDstGridDims = ncMap.add_var( "dst_grid_dims", ncInt, dimDstGridRank );
 
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varSrcGridDims, is_independent );
 ncMap.enable_var_par_access( varDstGridDims, is_independent );
#endif
 
 // write dimension names
 {
 char szDim[64];
 for( unsigned i = 0; i < srcdimSizes.size(); i++ )
 {
 varSrcGridDims->set_cur( nSrcGridDims - i - 1 );
 varSrcGridDims->put( &( srcdimSizes[nSrcGridDims - i - 1] ), 1 );
 }
 
 for( unsigned i = 0; i < srcdimSizes.size(); i++ )
 {
 snprintf( szDim, 64, "name%i", i );
 varSrcGridDims->add_att( szDim, srcdimNames[nSrcGridDims - i - 1].c_str() );
 }
 
 for( unsigned i = 0; i < tgtdimSizes.size(); i++ )
 {
 varDstGridDims->set_cur( nDstGridDims - i - 1 );
 varDstGridDims->put( &( tgtdimSizes[nDstGridDims - i - 1] ), 1 );
 }
 
 for( unsigned i = 0; i < tgtdimSizes.size(); i++ )
 {
 snprintf( szDim, 64, "name%i", i );
 varDstGridDims->add_att( szDim, tgtdimNames[nDstGridDims - i - 1].c_str() );
 }
 }
 
 // Source and Target mesh resolutions
 NcDim* dimNA = ncMap.add_dim( "n_a", globuf[0] );
 NcDim* dimNB = ncMap.add_dim( "n_b", globuf[1] );
 
 // Number of nodes per Face
 NcDim* dimNVA = ncMap.add_dim( "nv_a", globuf[3] );
 NcDim* dimNVB = ncMap.add_dim( "nv_b", globuf[4] );
 
 // Write coordinates
 NcVar* varYCA = ncMap.add_var( "yc_a", ncDouble, dimNA );
 NcVar* varYCB = ncMap.add_var( "yc_b", ncDouble, dimNB );
 
 NcVar* varXCA = ncMap.add_var( "xc_a", ncDouble, dimNA );
 NcVar* varXCB = ncMap.add_var( "xc_b", ncDouble, dimNB );
 
 NcVar* varYVA = ncMap.add_var( "yv_a", ncDouble, dimNA, dimNVA );
 NcVar* varYVB = ncMap.add_var( "yv_b", ncDouble, dimNB, dimNVB );
 
 NcVar* varXVA = ncMap.add_var( "xv_a", ncDouble, dimNA, dimNVA );
 NcVar* varXVB = ncMap.add_var( "xv_b", ncDouble, dimNB, dimNVB );
 
 // Write masks
 NcVar* varMaskA = ncMap.add_var( "mask_a", ncInt, dimNA );
 NcVar* varMaskB = ncMap.add_var( "mask_b", ncInt, dimNB );
 
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varYCA, is_independent );
 ncMap.enable_var_par_access( varYCB, is_independent );
 ncMap.enable_var_par_access( varXCA, is_independent );
 ncMap.enable_var_par_access( varXCB, is_independent );
 ncMap.enable_var_par_access( varYVA, is_independent );
 ncMap.enable_var_par_access( varYVB, is_independent );
 ncMap.enable_var_par_access( varXVA, is_independent );
 ncMap.enable_var_par_access( varXVB, is_independent );
 ncMap.enable_var_par_access( varMaskA, is_independent );
 ncMap.enable_var_par_access( varMaskB, is_independent );
#endif
 
 varYCA->add_att( "units", "degrees" );
 varYCB->add_att( "units", "degrees" );
 
 varXCA->add_att( "units", "degrees" );
 varXCB->add_att( "units", "degrees" );
 
 varYVA->add_att( "units", "degrees" );
 varYVB->add_att( "units", "degrees" );
 
 varXVA->add_att( "units", "degrees" );
 varXVB->add_att( "units", "degrees" );
 
 // Verify dimensionality
 if( dSourceCenterLon.GetRows() != nA )
 {
 _EXCEPTIONT( "Mismatch between dSourceCenterLon and nA" );
 }
 if( dSourceCenterLat.GetRows() != nA )
 {
 _EXCEPTIONT( "Mismatch between dSourceCenterLat and nA" );
 }
 if( dTargetCenterLon.GetRows() != nB )
 {
 _EXCEPTIONT( "Mismatch between dTargetCenterLon and nB" );
 }
 if( dTargetCenterLat.GetRows() != nB )
 {
 _EXCEPTIONT( "Mismatch between dTargetCenterLat and nB" );
 }
 if( dSourceVertexLon.GetRows() != nA )
 {
 _EXCEPTIONT( "Mismatch between dSourceVertexLon and nA" );
 }
 if( dSourceVertexLat.GetRows() != nA )
 {
 _EXCEPTIONT( "Mismatch between dSourceVertexLat and nA" );
 }
 if( dTargetVertexLon.GetRows() != nB )
 {
 _EXCEPTIONT( "Mismatch between dTargetVertexLon and nB" );
 }
 if( dTargetVertexLat.GetRows() != nB )
 {
 _EXCEPTIONT( "Mismatch between dTargetVertexLat and nB" );
 }
 
 varYCA->set_cur( (long)offbuf[0] );
 varYCA->put( &( dSourceCenterLat[0] ), nA );
 varYCB->set_cur( (long)offbuf[1] );
 varYCB->put( &( dTargetCenterLat[0] ), nB );
 
 varXCA->set_cur( (long)offbuf[0] );
 varXCA->put( &( dSourceCenterLon[0] ), nA );
 varXCB->set_cur( (long)offbuf[1] );
 varXCB->put( &( dTargetCenterLon[0] ), nB );
 
 varYVA->set_cur( (long)offbuf[0] );
 varYVA->put( &( dSourceVertexLat[0][0] ), nA, nSourceNodesPerFace );
 varYVB->set_cur( (long)offbuf[1] );
 varYVB->put( &( dTargetVertexLat[0][0] ), nB, nTargetNodesPerFace );
 
 varXVA->set_cur( (long)offbuf[0] );
 varXVA->put( &( dSourceVertexLon[0][0] ), nA, nSourceNodesPerFace );
 varXVB->set_cur( (long)offbuf[1] );
 varXVB->put( &( dTargetVertexLon[0][0] ), nB, nTargetNodesPerFace );
 
 varMaskA->set_cur( (long)offbuf[0] );
 varMaskA->put( &( masksA[0] ), nA );
 varMaskB->set_cur( (long)offbuf[1] );
 varMaskB->put( &( masksB[0] ), nB );
 
 // Write areas
 NcVar* varAreaA = ncMap.add_var( "area_a", ncDouble, dimNA );
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varAreaA, is_independent );
#endif
 varAreaA->set_cur( (long)offbuf[0] );
 varAreaA->put( &( vecSourceFaceArea[0] ), nA );
 
 NcVar* varAreaB = ncMap.add_var( "area_b", ncDouble, dimNB );
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varAreaB, is_independent );
#endif
 varAreaB->set_cur( (long)offbuf[1] );
 varAreaB->put( &( vecTargetFaceArea[0] ), nB );
 
 // Write SparseMatrix entries
 DataArray1D< int > vecRow( nS );
 DataArray1D< int > vecCol( nS );
 DataArray1D< double > vecS( nS );
 DataArray1D< double > dFracA( nA );
 DataArray1D< double > dFracB( nB );
 
 moab::TupleList tlValRow, tlValCol;
 unsigned numr = 1; //
 // value has to be sent to processor row/nB for for fracA and col/nA for fracB
 // vecTargetArea (indexRow ) has to be sent for fracA (index col?)
 // vecTargetFaceArea will have to be sent to col index, with its index !
 tlValRow.initialize( 2, 0, 0, numr, nS ); // to proc(row), global row , value
 tlValCol.initialize( 3, 0, 0, numr, nS ); // to proc(col), global row / col, value
 tlValRow.enableWriteAccess();
 tlValCol.enableWriteAccess();
 /*
 *
 dFracA[ col ] += val / vecSourceFaceArea[ col ] * vecTargetFaceArea[ row ];
 dFracB[ row ] += val ;
 */
 int offset = 0;
#if defined( MOAB_HAVE_MPI )
 int nAbase = ( max_col_dof + 1 ) / size; // it is nA, except last rank ( == size - 1 )
 int nBbase = ( max_row_dof + 1 ) / size; // it is nB, except last rank ( == size - 1 )
#endif
 for( int i = 0; i < m_weightMatrix.outerSize(); ++i )
 {
 for( WeightMatrix::InnerIterator it( m_weightMatrix, i ); it; ++it )
 {
 vecRow[offset] = 1 + this->GetRowGlobalDoF( it.row() ); // row index
 vecCol[offset] = 1 + this->GetColGlobalDoF( it.col() ); // col index
 vecS[offset] = it.value(); // value
 
#if defined( MOAB_HAVE_MPI )
 {
 // value M(row, col) will contribute to procRow and procCol values for fracA and fracB
 int procRow = ( vecRow[offset] - 1 ) / nBbase;
 if( procRow >= size ) procRow = size - 1;
 int procCol = ( vecCol[offset] - 1 ) / nAbase;
 if( procCol >= size ) procCol = size - 1;
 int nrInd = tlValRow.get_n();
 tlValRow.vi_wr[2 * nrInd] = procRow;
 tlValRow.vi_wr[2 * nrInd + 1] = vecRow[offset] - 1;
 tlValRow.vr_wr[nrInd] = vecS[offset];
 tlValRow.inc_n();
 int ncInd = tlValCol.get_n();
 tlValCol.vi_wr[3 * ncInd] = procCol;
 tlValCol.vi_wr[3 * ncInd + 1] = vecRow[offset] - 1;
 tlValCol.vi_wr[3 * ncInd + 2] = vecCol[offset] - 1; // this is column
 tlValCol.vr_wr[ncInd] = vecS[offset];
 tlValCol.inc_n();
 }
 
#endif
 offset++;
 }
 }
#if defined( MOAB_HAVE_MPI )
 // need to send values for their row and col processors, to compute fractions there
 // now do the heavy communication
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tlValCol, 0 );
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tlValRow, 0 );
 
 // we have now, for example, dFracB[ row ] += val ;
 // so we know that on current task, we received tlValRow
 // reminder dFracA[ col ] += val / vecSourceFaceArea[ col ] * vecTargetFaceArea[ row ];
 // dFracB[ row ] += val ;
 for( unsigned i = 0; i < tlValRow.get_n(); i++ )
 {
 // int fromProc = tlValRow.vi_wr[2 * i];
 int gRowInd = tlValRow.vi_wr[2 * i + 1];
 int localIndexRow = gRowInd - nBbase * rank; // modulo nBbase rank is from 0 to size - 1;
 double wgt = tlValRow.vr_wr[i];
 assert( localIndexRow >= 0 );
 assert( nB - localIndexRow > 0 );
 dFracB[localIndexRow] += wgt;
 }
 // to compute dFracA we need vecTargetFaceArea[ row ]; we know the row, and we can get the proc we need it from
 
 std::set< int > neededRows;
 for( unsigned i = 0; i < tlValCol.get_n(); i++ )
 {
 int rRowInd = tlValCol.vi_wr[3 * i + 1];
 neededRows.insert( rRowInd );
 // we need vecTargetFaceAreaGlobal[ rRowInd ]; this exists on proc procRow
 }
 moab::TupleList tgtAreaReq;
 tgtAreaReq.initialize( 2, 0, 0, 0, neededRows.size() );
 tgtAreaReq.enableWriteAccess();
 for( std::set< int >::iterator sit = neededRows.begin(); sit != neededRows.end(); sit++ )
 {
 int neededRow = *sit;
 int procRow = neededRow / nBbase;
 if( procRow >= size ) procRow = size - 1;
 int nr = tgtAreaReq.get_n();
 tgtAreaReq.vi_wr[2 * nr] = procRow;
 tgtAreaReq.vi_wr[2 * nr + 1] = neededRow;
 tgtAreaReq.inc_n();
 }
 
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tgtAreaReq, 0 );
 // we need to send back the tgtArea corresponding to row
 moab::TupleList tgtAreaInfo; // load it with tgtArea at row
 tgtAreaInfo.initialize( 2, 0, 0, 1, tgtAreaReq.get_n() );
 tgtAreaInfo.enableWriteAccess();
 for( unsigned i = 0; i < tgtAreaReq.get_n(); i++ )
 {
 int from_proc = tgtAreaReq.vi_wr[2 * i];
 int row = tgtAreaReq.vi_wr[2 * i + 1];
 int locaIndexRow = row - rank * nBbase;
 double areaToSend = vecTargetFaceArea[locaIndexRow];
 // int remoteIndex = tgtAreaReq.vi_wr[3*i + 2] ;
 
 tgtAreaInfo.vi_wr[2 * i] = from_proc; // send back requested info
 tgtAreaInfo.vi_wr[2 * i + 1] = row;
 tgtAreaInfo.vr_wr[i] = areaToSend; // this will be tgt area at row
 tgtAreaInfo.inc_n();
 }
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tgtAreaInfo, 0 );
 
 std::map< int, double > areaAtRow;
 for( unsigned i = 0; i < tgtAreaInfo.get_n(); i++ )
 {
 // we have received from proc, value for row !
 int row = tgtAreaInfo.vi_wr[2 * i + 1];
 areaAtRow[row] = tgtAreaInfo.vr_wr[i];
 }
 
 // we have now for rows the
 // it is ordered by index, so:
 // now compute reminder dFracA[ col ] += val / vecSourceFaceArea[ col ] * vecTargetFaceArea[ row ];
 // tgtAreaInfo will have at index i the area we need (from row)
 // there should be an easier way :(
 for( unsigned i = 0; i < tlValCol.get_n(); i++ )
 {
 int rRowInd = tlValCol.vi_wr[3 * i + 1];
 int colInd = tlValCol.vi_wr[3 * i + 2];
 double val = tlValCol.vr_wr[i];
 int localColInd = colInd - rank * nAbase; // < local nA
 // we need vecTargetFaceAreaGlobal[ rRowInd ]; this exists on proc procRow
 auto itMap = areaAtRow.find( rRowInd ); // it should be different from end
 if( itMap != areaAtRow.end() )
 {
 double areaRow = itMap->second; // we fished a lot for this !
 dFracA[localColInd] += val / vecSourceFaceArea[localColInd] * areaRow;
 }
 }
 
#endif
 // Load in data
 NcDim* dimNS = ncMap.add_dim( "n_s", globuf[2] );
 
 NcVar* varRow = ncMap.add_var( "row", ncInt, dimNS );
 NcVar* varCol = ncMap.add_var( "col", ncInt, dimNS );
 NcVar* varS = ncMap.add_var( "S", ncDouble, dimNS );
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varRow, is_independent );
 ncMap.enable_var_par_access( varCol, is_independent );
 ncMap.enable_var_par_access( varS, is_independent );
#endif
 
 varRow->set_cur( (long)offbuf[2] );
 varRow->put( vecRow, nS );
 
 varCol->set_cur( (long)offbuf[2] );
 varCol->put( vecCol, nS );
 
 varS->set_cur( (long)offbuf[2] );
 varS->put( &( vecS[0] ), nS );
 
 // Calculate and write fractional coverage arrays
 NcVar* varFracA = ncMap.add_var( "frac_a", ncDouble, dimNA );
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varFracA, is_independent );
#endif
 varFracA->add_att( "name", "fraction of target coverage of source dof" );
 varFracA->add_att( "units", "unitless" );
 varFracA->set_cur( (long)offbuf[0] );
 varFracA->put( &( dFracA[0] ), nA );
 
 NcVar* varFracB = ncMap.add_var( "frac_b", ncDouble, dimNB );
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varFracB, is_independent );
#endif
 varFracB->add_att( "name", "fraction of source coverage of target dof" );
 varFracB->add_att( "units", "unitless" );
 varFracB->set_cur( (long)offbuf[1] );
 varFracB->put( &( dFracB[0] ), nB );
 
 // Add global attributes
 // std::map<std::string, std::string>::const_iterator iterAttributes =
 // mapAttributes.begin();
 // for (; iterAttributes != mapAttributes.end(); iterAttributes++) {
 // ncMap.add_att(
 // iterAttributes->first.c_str(),
 // iterAttributes->second.c_str());
 // }
 
 ncMap.close();
 
 return moab::MB_SUCCESS;
}
 
///////////////////////////////////////////////////////////////////////////////
 
moab::ErrorCode moab::TempestOnlineMap::WriteHDF5MapFile( const std::string& strOutputFile )
{
 moab::ErrorCode rval;
 
 /**
 * Need to get the global maximum of number of vertices per element
 * Key issue is that when calling InitializeCoordinatesFromMeshFV, the allocation for
 *dVertexLon/dVertexLat are made based on the maximum vertices in the current process. However,
 *when writing this out, other processes may have a different size for the same array. This is
 *hence a mess to consolidate in h5mtoscrip eventually.
 **/
 
 /* Let us compute all relevant data for the current original source mesh on the process */
 DataArray1D< double > vecSourceFaceArea, vecTargetFaceArea;
 DataArray1D< double > dSourceCenterLon, dSourceCenterLat, dTargetCenterLon, dTargetCenterLat;
 DataArray2D< double > dSourceVertexLon, dSourceVertexLat, dTargetVertexLon, dTargetVertexLat;
 if( m_srcDiscType == DiscretizationType_FV || m_srcDiscType == DiscretizationType_PCLOUD )
 {
 this->InitializeCoordinatesFromMeshFV(
 *m_meshInput, dSourceCenterLon, dSourceCenterLat, dSourceVertexLon, dSourceVertexLat,
 ( this->m_remapper->m_source_type == moab::TempestRemapper::RLL ) /* fLatLon = false */,
 m_remapper->max_source_edges );
 
 vecSourceFaceArea.Allocate( m_meshInput->vecFaceArea.GetRows() );
 for( unsigned i = 0; i < m_meshInput->vecFaceArea.GetRows(); ++i )
 vecSourceFaceArea[i] = m_meshInput->vecFaceArea[i];
 }
 else
 {
 DataArray3D< double > dataGLLJacobianSrc;
 this->InitializeCoordinatesFromMeshFE( *m_meshInput, m_nDofsPEl_Src, dataGLLNodesSrc, dSourceCenterLon,
 dSourceCenterLat, dSourceVertexLon, dSourceVertexLat );
 
 // Generate the continuous Jacobian for input mesh
 GenerateMetaData( *m_meshInput, m_nDofsPEl_Src, false /* fBubble */, dataGLLNodesSrc, dataGLLJacobianSrc );
 
 if( m_srcDiscType == DiscretizationType_CGLL )
 {
 GenerateUniqueJacobian( dataGLLNodesSrc, dataGLLJacobianSrc, vecSourceFaceArea );
 }
 else
 {
 GenerateDiscontinuousJacobian( dataGLLJacobianSrc, vecSourceFaceArea );
 }
 }
 
 if( m_destDiscType == DiscretizationType_FV || m_destDiscType == DiscretizationType_PCLOUD )
 {
 this->InitializeCoordinatesFromMeshFV(
 *m_meshOutput, dTargetCenterLon, dTargetCenterLat, dTargetVertexLon, dTargetVertexLat,
 ( this->m_remapper->m_target_type == moab::TempestRemapper::RLL ) /* fLatLon = false */,
 m_remapper->max_target_edges );
 
 vecTargetFaceArea.Allocate( m_meshOutput->vecFaceArea.GetRows() );
 for( unsigned i = 0; i < m_meshOutput->vecFaceArea.GetRows(); ++i )
 vecTargetFaceArea[i] = m_meshOutput->vecFaceArea[i];
 }
 else
 {
 DataArray3D< double > dataGLLJacobianDest;
 this->InitializeCoordinatesFromMeshFE( *m_meshOutput, m_nDofsPEl_Dest, dataGLLNodesDest, dTargetCenterLon,
 dTargetCenterLat, dTargetVertexLon, dTargetVertexLat );
 
 // Generate the continuous Jacobian for input mesh
 GenerateMetaData( *m_meshOutput, m_nDofsPEl_Dest, false /* fBubble */, dataGLLNodesDest, dataGLLJacobianDest );
 
 if( m_destDiscType == DiscretizationType_CGLL )
 {
 GenerateUniqueJacobian( dataGLLNodesDest, dataGLLJacobianDest, vecTargetFaceArea );
 }
 else
 {
 GenerateDiscontinuousJacobian( dataGLLJacobianDest, vecTargetFaceArea );
 }
 }
 
 moab::EntityHandle& m_meshOverlapSet = m_remapper->m_overlap_set;
 int tot_src_ents = m_remapper->m_source_entities.size();
 int tot_tgt_ents = m_remapper->m_target_entities.size();
 int tot_src_size = dSourceCenterLon.GetRows();
 int tot_tgt_size = m_dTargetCenterLon.GetRows();
 int tot_vsrc_size = dSourceVertexLon.GetRows() * dSourceVertexLon.GetColumns();
 int tot_vtgt_size = m_dTargetVertexLon.GetRows() * m_dTargetVertexLon.GetColumns();
 
 const int weightMatNNZ = m_weightMatrix.nonZeros();
 moab::Tag tagMapMetaData, tagMapIndexRow, tagMapIndexCol, tagMapValues, srcEleIDs, tgtEleIDs;
 rval = m_interface->tag_get_handle( "SMAT_DATA", 13, moab::MB_TYPE_INTEGER, tagMapMetaData,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SMAT_ROWS", weightMatNNZ, moab::MB_TYPE_INTEGER, tagMapIndexRow,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SMAT_COLS", weightMatNNZ, moab::MB_TYPE_INTEGER, tagMapIndexCol,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SMAT_VALS", weightMatNNZ, moab::MB_TYPE_DOUBLE, tagMapValues,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SourceGIDS", tot_src_size, moab::MB_TYPE_INTEGER, srcEleIDs,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetGIDS", tot_tgt_size, moab::MB_TYPE_INTEGER, tgtEleIDs,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 moab::Tag srcAreaValues, tgtAreaValues;
 rval = m_interface->tag_get_handle( "SourceAreas", tot_src_size, moab::MB_TYPE_DOUBLE, srcAreaValues,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetAreas", tot_tgt_size, moab::MB_TYPE_DOUBLE, tgtAreaValues,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 moab::Tag tagSrcCoordsCLon, tagSrcCoordsCLat, tagTgtCoordsCLon, tagTgtCoordsCLat;
 rval = m_interface->tag_get_handle( "SourceCoordCenterLon", tot_src_size, moab::MB_TYPE_DOUBLE, tagSrcCoordsCLon,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SourceCoordCenterLat", tot_src_size, moab::MB_TYPE_DOUBLE, tagSrcCoordsCLat,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetCoordCenterLon", tot_tgt_size, moab::MB_TYPE_DOUBLE, tagTgtCoordsCLon,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetCoordCenterLat", tot_tgt_size, moab::MB_TYPE_DOUBLE, tagTgtCoordsCLat,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 moab::Tag tagSrcCoordsVLon, tagSrcCoordsVLat, tagTgtCoordsVLon, tagTgtCoordsVLat;
 rval = m_interface->tag_get_handle( "SourceCoordVertexLon", tot_vsrc_size, moab::MB_TYPE_DOUBLE, tagSrcCoordsVLon,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "SourceCoordVertexLat", tot_vsrc_size, moab::MB_TYPE_DOUBLE, tagSrcCoordsVLat,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetCoordVertexLon", tot_vtgt_size, moab::MB_TYPE_DOUBLE, tagTgtCoordsVLon,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 rval = m_interface->tag_get_handle( "TargetCoordVertexLat", tot_vtgt_size, moab::MB_TYPE_DOUBLE, tagTgtCoordsVLat,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 moab::Tag srcMaskValues, tgtMaskValues;
 if( m_iSourceMask.IsAttached() )
 {
 rval = m_interface->tag_get_handle( "SourceMask", m_iSourceMask.GetRows(), moab::MB_TYPE_INTEGER, srcMaskValues,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 }
 if( m_iTargetMask.IsAttached() )
 {
 rval = m_interface->tag_get_handle( "TargetMask", m_iTargetMask.GetRows(), moab::MB_TYPE_INTEGER, tgtMaskValues,
 moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE | moab::MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Retrieving tag handles failed" );
 }
 
 std::vector< int > smatrowvals( weightMatNNZ ), smatcolvals( weightMatNNZ );
 std::vector< double > smatvals( weightMatNNZ );
 // const double* smatvals = m_weightMatrix.valuePtr();
 // Loop over the matrix entries and find the max global ID for rows and columns
 for( int k = 0, offset = 0; k < m_weightMatrix.outerSize(); ++k )
 {
 for( moab::TempestOnlineMap::WeightMatrix::InnerIterator it( m_weightMatrix, k ); it; ++it, ++offset )
 {
 smatrowvals[offset] = this->GetRowGlobalDoF( it.row() );
 smatcolvals[offset] = this->GetColGlobalDoF( it.col() );
 smatvals[offset] = it.value();
 }
 }
 
 /* Set the global IDs for the DoFs */
 ////
 // col_gdofmap [ col_ldofmap [ 0 : local_ndofs ] ] = GDOF
 // row_gdofmap [ row_ldofmap [ 0 : local_ndofs ] ] = GDOF
 ////
 int maxrow = 0, maxcol = 0;
 std::vector< int > src_global_dofs( tot_src_size ), tgt_global_dofs( tot_tgt_size );
 for( int i = 0; i < tot_src_size; ++i )
 {
 src_global_dofs[i] = srccol_gdofmap[i];
 maxcol = ( src_global_dofs[i] > maxcol ) ? src_global_dofs[i] : maxcol;
 }
 
 for( int i = 0; i < tot_tgt_size; ++i )
 {
 tgt_global_dofs[i] = row_gdofmap[i];
 maxrow = ( tgt_global_dofs[i] > maxrow ) ? tgt_global_dofs[i] : maxrow;
 }
 
 ///////////////////////////////////////////////////////////////////////////
 // The metadata in H5M file contains the following data:
 //
 // 1. n_a: Total source entities: (number of elements in source mesh)
 // 2. n_b: Total target entities: (number of elements in target mesh)
 // 3. nv_a: Max edge size of elements in source mesh
 // 4. nv_b: Max edge size of elements in target mesh
 // 5. maxrows: Number of rows in remap weight matrix
 // 6. maxcols: Number of cols in remap weight matrix
 // 7. nnz: Number of total nnz in sparse remap weight matrix
 // 8. np_a: The order of the field description on the source mesh: >= 1
 // 9. np_b: The order of the field description on the target mesh: >= 1
 // 10. method_a: The type of discretization for field on source mesh: [0 = FV, 1 = cGLL, 2 =
 // dGLL]
 // 11. method_b: The type of discretization for field on target mesh: [0 = FV, 1 = cGLL, 2 =
 // dGLL]
 // 12. conserved: Flag to specify whether the remap operator has conservation constraints: [0,
 // 1]
 // 13. monotonicity: Flags to specify whether the remap operator has monotonicity constraints:
 // [0, 1, 2]
 //
 ///////////////////////////////////////////////////////////////////////////
 int map_disc_details[6];
 map_disc_details[0] = m_nDofsPEl_Src;
 map_disc_details[1] = m_nDofsPEl_Dest;
 map_disc_details[2] = ( m_srcDiscType == DiscretizationType_FV || m_srcDiscType == DiscretizationType_PCLOUD
 ? 0
 : ( m_srcDiscType == DiscretizationType_CGLL ? 1 : 2 ) );
 map_disc_details[3] = ( m_destDiscType == DiscretizationType_FV || m_destDiscType == DiscretizationType_PCLOUD
 ? 0
 : ( m_destDiscType == DiscretizationType_CGLL ? 1 : 2 ) );
 map_disc_details[4] = ( m_bConserved ? 1 : 0 );
 map_disc_details[5] = m_iMonotonicity;
 
#ifdef MOAB_HAVE_MPI
 int loc_smatmetadata[13] = { tot_src_ents,
 tot_tgt_ents,
 m_remapper->max_source_edges,
 m_remapper->max_target_edges,
 maxrow + 1,
 maxcol + 1,
 weightMatNNZ,
 map_disc_details[0],
 map_disc_details[1],
 map_disc_details[2],
 map_disc_details[3],
 map_disc_details[4],
 map_disc_details[5] };
 rval = m_interface->tag_set_data( tagMapMetaData, &m_meshOverlapSet, 1, &loc_smatmetadata[0] );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 int glb_smatmetadata[13] = { 0,
 0,
 0,
 0,
 0,
 0,
 0,
 map_disc_details[0],
 map_disc_details[1],
 map_disc_details[2],
 map_disc_details[3],
 map_disc_details[4],
 map_disc_details[5] };
 int loc_buf[7] = {
 tot_src_ents, tot_tgt_ents, weightMatNNZ, m_remapper->max_source_edges, m_remapper->max_target_edges,
 maxrow, maxcol };
 int glb_buf[4] = { 0, 0, 0, 0 };
 MPI_Reduce( &loc_buf[0], &glb_buf[0], 3, MPI_INT, MPI_SUM, 0, m_pcomm->comm() );
 glb_smatmetadata[0] = glb_buf[0];
 glb_smatmetadata[1] = glb_buf[1];
 glb_smatmetadata[6] = glb_buf[2];
 MPI_Reduce( &loc_buf[3], &glb_buf[0], 4, MPI_INT, MPI_MAX, 0, m_pcomm->comm() );
 glb_smatmetadata[2] = glb_buf[0];
 glb_smatmetadata[3] = glb_buf[1];
 glb_smatmetadata[4] = glb_buf[2];
 glb_smatmetadata[5] = glb_buf[3];
#else
 int glb_smatmetadata[13] = { tot_src_ents,
 tot_tgt_ents,
 m_remapper->max_source_edges,
 m_remapper->max_target_edges,
 maxrow,
 maxcol,
 weightMatNNZ,
 map_disc_details[0],
 map_disc_details[1],
 map_disc_details[2],
 map_disc_details[3],
 map_disc_details[4],
 map_disc_details[5] };
#endif
 // These values represent number of rows and columns. So should be 1-based.
 glb_smatmetadata[4]++;
 glb_smatmetadata[5]++;
 
 if( this->is_root )
 {
 std::cout << " " << this->rank << " Writing remap weights with size [" << glb_smatmetadata[4] << " X "
 << glb_smatmetadata[5] << "] and NNZ = " << glb_smatmetadata[6] << std::endl;
 EntityHandle root_set = 0;
 rval = m_interface->tag_set_data( tagMapMetaData, &root_set, 1, &glb_smatmetadata[0] );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 }
 
 int dsize;
 const int numval = weightMatNNZ;
 const void* smatrowvals_d = smatrowvals.data();
 const void* smatcolvals_d = smatcolvals.data();
 const void* smatvals_d = smatvals.data();
 rval = m_interface->tag_set_by_ptr( tagMapIndexRow, &m_meshOverlapSet, 1, &smatrowvals_d, &numval );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagMapIndexCol, &m_meshOverlapSet, 1, &smatcolvals_d, &numval );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagMapValues, &m_meshOverlapSet, 1, &smatvals_d, &numval );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 
 /* Set the global IDs for the DoFs */
 const void* srceleidvals_d = src_global_dofs.data();
 const void* tgteleidvals_d = tgt_global_dofs.data();
 dsize = src_global_dofs.size();
 rval = m_interface->tag_set_by_ptr( srcEleIDs, &m_meshOverlapSet, 1, &srceleidvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 dsize = tgt_global_dofs.size();
 rval = m_interface->tag_set_by_ptr( tgtEleIDs, &m_meshOverlapSet, 1, &tgteleidvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 
 /* Set the source and target areas */
 const void* srcareavals_d = vecSourceFaceArea;
 const void* tgtareavals_d = vecTargetFaceArea;
 dsize = tot_src_size;
 rval = m_interface->tag_set_by_ptr( srcAreaValues, &m_meshOverlapSet, 1, &srcareavals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 dsize = tot_tgt_size;
 rval = m_interface->tag_set_by_ptr( tgtAreaValues, &m_meshOverlapSet, 1, &tgtareavals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 
 /* Set the coordinates for source and target center vertices */
 const void* srccoordsclonvals_d = &dSourceCenterLon[0];
 const void* srccoordsclatvals_d = &dSourceCenterLat[0];
 dsize = dSourceCenterLon.GetRows();
 rval = m_interface->tag_set_by_ptr( tagSrcCoordsCLon, &m_meshOverlapSet, 1, &srccoordsclonvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagSrcCoordsCLat, &m_meshOverlapSet, 1, &srccoordsclatvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 const void* tgtcoordsclonvals_d = &m_dTargetCenterLon[0];
 const void* tgtcoordsclatvals_d = &m_dTargetCenterLat[0];
 dsize = vecTargetFaceArea.GetRows();
 rval = m_interface->tag_set_by_ptr( tagTgtCoordsCLon, &m_meshOverlapSet, 1, &tgtcoordsclonvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagTgtCoordsCLat, &m_meshOverlapSet, 1, &tgtcoordsclatvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 
 /* Set the coordinates for source and target element vertices */
 const void* srccoordsvlonvals_d = &( dSourceVertexLon[0][0] );
 const void* srccoordsvlatvals_d = &( dSourceVertexLat[0][0] );
 dsize = dSourceVertexLon.GetRows() * dSourceVertexLon.GetColumns();
 rval = m_interface->tag_set_by_ptr( tagSrcCoordsVLon, &m_meshOverlapSet, 1, &srccoordsvlonvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagSrcCoordsVLat, &m_meshOverlapSet, 1, &srccoordsvlatvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 const void* tgtcoordsvlonvals_d = &( m_dTargetVertexLon[0][0] );
 const void* tgtcoordsvlatvals_d = &( m_dTargetVertexLat[0][0] );
 dsize = m_dTargetVertexLon.GetRows() * m_dTargetVertexLon.GetColumns();
 rval = m_interface->tag_set_by_ptr( tagTgtCoordsVLon, &m_meshOverlapSet, 1, &tgtcoordsvlonvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 rval = m_interface->tag_set_by_ptr( tagTgtCoordsVLat, &m_meshOverlapSet, 1, &tgtcoordsvlatvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 
 /* Set the masks for source and target meshes if available */
 if( m_iSourceMask.IsAttached() )
 {
 const void* srcmaskvals_d = m_iSourceMask;
 dsize = m_iSourceMask.GetRows();
 rval = m_interface->tag_set_by_ptr( srcMaskValues, &m_meshOverlapSet, 1, &srcmaskvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 }
 
 if( m_iTargetMask.IsAttached() )
 {
 const void* tgtmaskvals_d = m_iTargetMask;
 dsize = m_iTargetMask.GetRows();
 rval = m_interface->tag_set_by_ptr( tgtMaskValues, &m_meshOverlapSet, 1, &tgtmaskvals_d, &dsize );MB_CHK_SET_ERR( rval, "Setting local tag data failed" );
 }
 
#ifdef MOAB_HAVE_MPI
 const char* writeOptions = ( this->size > 1 ? "PARALLEL=WRITE_PART" : "" );
#else
 const char* writeOptions = "";
#endif
 
 // EntityHandle sets[3] = {m_remapper->m_source_set, m_remapper->m_target_set, m_remapper->m_overlap_set};
 EntityHandle sets[1] = { m_remapper->m_overlap_set };
 rval = m_interface->write_file( strOutputFile.c_str(), NULL, writeOptions, sets, 1 );MB_CHK_ERR( rval );
 
#ifdef WRITE_SCRIP_FILE
 sstr.str( "" );
 sstr << ctx.outFilename.substr( 0, lastindex ) << "_" << proc_id << ".nc";
 std::map< std::string, std::string > mapAttributes;
 mapAttributes["Creator"] = "MOAB mbtempest workflow";
 if( !ctx.proc_id ) std::cout << "Writing offline map to file: " << sstr.str() << std::endl;
 this->Write( strOutputFile.c_str(), mapAttributes, NcFile::Netcdf4 );
 sstr.str( "" );
#endif
 
 return moab::MB_SUCCESS;
}
 
///////////////////////////////////////////////////////////////////////////////
 
void print_progress( const int barWidth, const float progress, const char* message )
{
 std::cout << message << " [";
 int pos = barWidth * progress;
 for( int i = 0; i < barWidth; ++i )
 {
 if( i < pos )
 std::cout << "=";
 else if( i == pos )
 std::cout << ">";
 else
 std::cout << " ";
 }
 std::cout << "] " << int( progress * 100.0 ) << " %\r";
 std::cout.flush();
}
 
///////////////////////////////////////////////////////////////////////////////
moab::ErrorCode moab::TempestOnlineMap::ReadParallelMap( const char* strSource,
 const std::vector< int >& owned_dof_ids,
 bool row_partition )
{
 NcError error( NcError::silent_nonfatal );
 
 NcVar *varRow = NULL, *varCol = NULL, *varS = NULL;
 int nS = 0, nA = 0, nB = 0;
#ifdef MOAB_HAVE_PNETCDF
 // some variables will be used just in the case netcdfpar reader fails
 int ncfile = -1, ret = 0;
 int ndims, nvars, ngatts, unlimited;
#endif
#ifdef MOAB_HAVE_NETCDFPAR
 bool is_independent = true;
 ParNcFile ncMap( m_pcomm->comm(), MPI_INFO_NULL, strSource, NcFile::ReadOnly, NcFile::Netcdf4 );
 // ParNcFile ncMap( m_pcomm->comm(), MPI_INFO_NULL, strFilename.c_str(), NcmpiFile::replace, NcmpiFile::classic5 );
#else
 NcFile ncMap( strSource, NcFile::ReadOnly );
#endif
 
#define CHECK_EXCEPTION( obj, type, varstr ) \
 { \
 if( obj == NULL ) \
 { \
 _EXCEPTION3( "Map file \"%s\" does not contain %s \"%s\"", strSource, type, varstr ); \
 } \
 }
 
 // Read SparseMatrix entries
 
 if( ncMap.is_valid() )
 {
 NcDim* dimNS = ncMap.get_dim( "n_s" );
 CHECK_EXCEPTION( dimNS, "dimension", "n_s" );
 
 NcDim* dimNA = ncMap.get_dim( "n_a" );
 CHECK_EXCEPTION( dimNA, "dimension", "n_a" );
 
 NcDim* dimNB = ncMap.get_dim( "n_b" );
 CHECK_EXCEPTION( dimNB, "dimension", "n_b" );
 
 // store total number of nonzeros
 nS = dimNS->size();
 nA = dimNA->size();
 nB = dimNB->size();
 
 varRow = ncMap.get_var( "row" );
 CHECK_EXCEPTION( varRow, "variable", "row" );
 
 varCol = ncMap.get_var( "col" );
 CHECK_EXCEPTION( varCol, "variable", "col" );
 
 varS = ncMap.get_var( "S" );
 CHECK_EXCEPTION( varS, "variable", "S" );
 
#ifdef MOAB_HAVE_NETCDFPAR
 ncMap.enable_var_par_access( varRow, is_independent );
 ncMap.enable_var_par_access( varCol, is_independent );
 ncMap.enable_var_par_access( varS, is_independent );
#endif
 }
 else
 {
#ifdef MOAB_HAVE_PNETCDF
 // read the file using pnetcdf directly, in parallel; need to have MPI, we do not check that anymore
 // why build wth pnetcdf without MPI ?
 // ParNcFile ncMap( m_pcomm->comm(), MPI_INFO_NULL, strSource, NcFile::ReadOnly, NcFile::Netcdf4 );
 ret = ncmpi_open( m_pcomm->comm(), strSource, NC_NOWRITE, MPI_INFO_NULL, &ncfile );
 ERR_PARNC( ret ); // bail out completely
 ret = ncmpi_inq( ncfile, &ndims, &nvars, &ngatts, &unlimited );
 ERR_PARNC( ret );
 // find dimension ids for n_S
 int ins;
 ret = ncmpi_inq_dimid( ncfile, "n_s", &ins );
 ERR_PARNC( ret );
 MPI_Offset leng;
 ret = ncmpi_inq_dimlen( ncfile, ins, &leng );
 ERR_PARNC( ret );
 nS = (int)leng;
 ret = ncmpi_inq_dimid( ncfile, "n_b", &ins );
 ERR_PARNC( ret );
 ret = ncmpi_inq_dimlen( ncfile, ins, &leng );
 ERR_PARNC( ret );
 nB = (int)leng;
#else
 _EXCEPTION1( "cannot read the file %s", strSource );
#endif
 }
 
 // Let us declare the map object for every process
 SparseMatrix< double >& sparseMatrix = this->GetSparseMatrix();
 
 int localSize = nS / size;
 long offsetRead = rank * localSize;
 // leftovers on last rank
 if( rank == size - 1 )
 {
 localSize += nS % size;
 }
 
 std::vector< int > vecRow, vecCol;
 std::vector< double > vecS;
 vecRow.resize( localSize );
 vecCol.resize( localSize );
 vecS.resize( localSize );
 
 if( ncMap.is_valid() )
 {
 varRow->set_cur( (long)( offsetRead ) );
 varRow->get( &( vecRow[0] ), localSize );
 
 varCol->set_cur( (long)( offsetRead ) );
 varCol->get( &( vecCol[0] ), localSize );
 
 varS->set_cur( (long)( offsetRead ) );
 varS->get( &( vecS[0] ), localSize );
 
 ncMap.close();
 }
 else
 {
#ifdef MOAB_HAVE_PNETCDF
 // fill the local vectors with the variables from pnetcdf file; first inquire, then fill
 MPI_Offset start = (MPI_Offset)offsetRead;
 MPI_Offset count = (MPI_Offset)localSize;
 int varid;
 ret = ncmpi_inq_varid( ncfile, "S", &varid );
 ERR_PARNC( ret );
 ret = ncmpi_get_vara_double_all( ncfile, varid, &start, &count, &vecS[0] );
 ERR_PARNC( ret );
 ret = ncmpi_inq_varid( ncfile, "row", &varid );
 ERR_PARNC( ret );
 ret = ncmpi_get_vara_int_all( ncfile, varid, &start, &count, &vecRow[0] );
 ERR_PARNC( ret );
 ret = ncmpi_inq_varid( ncfile, "col", &varid );
 ERR_PARNC( ret );
 ret = ncmpi_get_vara_int_all( ncfile, varid, &start, &count, &vecCol[0] );
 ERR_PARNC( ret );
 ret = ncmpi_close( ncfile );
 ERR_PARNC( ret );
#endif
 }
 
 // Now let us set the necessary global-to-local ID maps so that A*x operations
 // can be performed cleanly as if map was computed online
 row_dtoc_dofmap.clear();
 // row_dtoc_dofmap.reserve( nB / size );
 col_dtoc_dofmap.clear();
 rowMap.clear();
 colMap.clear();
 // col_dtoc_dofmap.reserve( 2 * nA / size );
 // row_dtoc_dofmap.resize( m_nTotDofs_Dest, UINT_MAX );
 // col_dtoc_dofmap.resize( m_nTotDofs_SrcCov, UINT_MAX );
 
#ifdef MOAB_HAVE_MPI
 // bother with tuple list only if size > 1
 // otherwise, just fill the sparse matrix
 if( size > 1 )
 {
 std::vector< int > ownership;
 // the default trivial partitioning scheme
 int nDofs = nB; // this is for row partitioning
 if( !row_partition ) nDofs = nA; // column partitioning
 
 // assert(row_major_ownership == true); // this block is valid only for row-based partitioning
 ownership.resize( size );
 int nPerPart = nDofs / size;
 int nRemainder = nDofs % size; // Keep the remainder in root
 ownership[0] = nPerPart + nRemainder;
 for( int ip = 1, roffset = ownership[0]; ip < size; ++ip )
 {
 roffset += nPerPart;
 ownership[ip] = roffset;
 }
 moab::TupleList* tl = new moab::TupleList;
 unsigned numr = 1; //
 tl->initialize( 3, 0, 0, numr, localSize ); // to proc, row, col, value
 tl->enableWriteAccess();
 // populate
 for( int i = 0; i < localSize; i++ )
 {
 int rowval = vecRow[i] - 1; // dofs are 1 based in the file
 int colval = vecCol[i] - 1;
 int to_proc = -1;
 int dof_val = colval;
 if( row_partition ) dof_val = rowval;
 
 if( ownership[0] > dof_val )
 to_proc = 0;
 else
 {
 for( int ip = 1; ip < size; ++ip )
 {
 if( ownership[ip - 1] <= dof_val && ownership[ip] > dof_val )
 {
 to_proc = ip;
 break;
 }
 }
 }
 
 int n = tl->get_n();
 tl->vi_wr[3 * n] = to_proc;
 tl->vi_wr[3 * n + 1] = rowval;
 tl->vi_wr[3 * n + 2] = colval;
 tl->vr_wr[n] = vecS[i];
 tl->inc_n();
 }
 // heavy communication
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, *tl, 0 );
 
 if( owned_dof_ids.size() > 0 )
 {
 // we need to send desired dof to the rendez_vous point
 moab::TupleList tl_re; //
 tl_re.initialize( 2, 0, 0, 0, owned_dof_ids.size() ); // to proc, value
 tl_re.enableWriteAccess();
 // send first to rendez_vous point, decided by trivial partitioning
 
 for( size_t i = 0; i < owned_dof_ids.size(); i++ )
 {
 int to_proc = -1;
 int dof_val = owned_dof_ids[i] - 1; // dofs are 1 based in the file, partition from 0 ?
 
 if( ownership[0] > dof_val )
 to_proc = 0;
 else
 {
 for( int ip = 1; ip < size; ++ip )
 {
 if( ownership[ip - 1] <= dof_val && ownership[ip] > dof_val )
 {
 to_proc = ip;
 break;
 }
 }
 }
 
 int n = tl_re.get_n();
 tl_re.vi_wr[2 * n] = to_proc;
 tl_re.vi_wr[2 * n + 1] = dof_val;
 
 tl_re.inc_n();
 }
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, tl_re, 0 );
 // now we know in tl_re where do we need to send back dof_val
 moab::TupleList::buffer sort_buffer;
 sort_buffer.buffer_init( tl_re.get_n() );
 tl_re.sort( 1, &sort_buffer ); // so now we order by value
 
 sort_buffer.buffer_init( tl->get_n() );
 int indexOrder = 2; // colVal
 if( row_partition ) indexOrder = 1; // rowVal
 //tl->sort( indexOrder, &sort_buffer );
 
 std::map< int, int > startDofIndex, endDofIndex; // indices in tl_re for values we want
 int dofVal = -1;
 if( tl_re.get_n() > 0 ) dofVal = tl_re.vi_rd[1]; // first dof val on this rank
 startDofIndex[dofVal] = 0;
 endDofIndex[dofVal] = 0; // start and end
 for( unsigned k = 1; k < tl_re.get_n(); k++ )
 {
 int newDof = tl_re.vi_rd[2 * k + 1];
 if( dofVal == newDof )
 {
 endDofIndex[dofVal] = k; // increment by 1 actually
 }
 else
 {
 dofVal = newDof;
 startDofIndex[dofVal] = k;
 endDofIndex[dofVal] = k;
 }
 }
 
 // basically, for each value we are interested in, index in tl_re with those values are
 // tl_re.vi_rd[2*startDofIndex+1] == valDof == tl_re.vi_rd[2*endDofIndex+1]
 // so now we have ordered
 // tl_re shows to what proc do we need to send the tuple (row, col, val)
 moab::TupleList* tl_back = new moab::TupleList;
 unsigned numr = 1; //
 // localSize is a good guess, but maybe it should be bigger ?
 // this could be bigger for repeated dofs
 tl_back->initialize( 3, 0, 0, numr, tl->get_n() ); // to proc, row, col, value
 tl_back->enableWriteAccess();
 // now loop over tl and tl_re to see where to send
 // form the new tuple, which will contain the desired dofs per task, per row or column distribution
 
 for( unsigned k = 0; k < tl->get_n(); k++ )
 {
 int valDof = tl->vi_rd[3 * k + indexOrder]; // 1 for row, 2 for column // first value, it should be
 for( int ire = startDofIndex[valDof]; ire <= endDofIndex[valDof]; ire++ )
 {
 int to_proc = tl_re.vi_rd[2 * ire];
 int n = tl_back->get_n();
 tl_back->vi_wr[3 * n] = to_proc;
 tl_back->vi_wr[3 * n + 1] = tl->vi_rd[3 * k + 1]; // row
 tl_back->vi_wr[3 * n + 2] = tl->vi_rd[3 * k + 2]; // col
 tl_back->vr_wr[n] = tl->vr_rd[k];
 tl_back->inc_n();
 }
 }
 
 // now communicate to the desired tasks:
 ( m_pcomm->proc_config().crystal_router() )->gs_transfer( 1, *tl_back, 0 );
 
 tl_re.reset(); // clear memory, although this will go out of scope
 tl->reset();
 tl = tl_back;
 }
 
 int rindexMax = 0, cindexMax = 0;
 // populate the sparsematrix, using rowMap and colMap
 int n = tl->get_n();
 for( int i = 0; i < n; i++ )
 {
 int rindex, cindex;
 const int& vecRowValue = tl->vi_wr[3 * i + 1];
 const int& vecColValue = tl->vi_wr[3 * i + 2];
 
 std::map< int, int >::iterator riter = rowMap.find( vecRowValue );
 if( riter == rowMap.end() )
 {
 rowMap[vecRowValue] = rindexMax;
 rindex = rindexMax;
 row_gdofmap.push_back( vecRowValue );
 // row_dtoc_dofmap.push_back( vecRowValue );
 rindexMax++;
 }
 else
 rindex = riter->second;
 
 std::map< int, int >::iterator citer = colMap.find( vecColValue );
 if( citer == colMap.end() )
 {
 colMap[vecColValue] = cindexMax;
 cindex = cindexMax;
 col_gdofmap.push_back( vecColValue );
 // col_dtoc_dofmap.push_back( vecColValue );
 cindexMax++;
 }
 else
 cindex = citer->second;
 
 sparseMatrix( rindex, cindex ) = tl->vr_wr[i];
 }
 tl->reset();
 }
 else
#endif
 {
 int rindexMax = 0, cindexMax = 0;
 
 for( int i = 0; i < nS; i++ )
 {
 int rindex, cindex;
 const int& vecRowValue = vecRow[i] - 1; // the rows, cols are 1 based in the file
 const int& vecColValue = vecCol[i] - 1;
 
 std::map< int, int >::iterator riter = rowMap.find( vecRowValue );
 if( riter == rowMap.end() )
 {
 rowMap[vecRowValue] = rindexMax;
 rindex = rindexMax;
 row_gdofmap.push_back( vecRowValue );
 // row_dtoc_dofmap.push_back( vecRowValue );
 rindexMax++;
 }
 else
 rindex = riter->second;
 
 std::map< int, int >::iterator citer = colMap.find( vecColValue );
 if( citer == colMap.end() )
 {
 colMap[vecColValue] = cindexMax;
 cindex = cindexMax;
 col_gdofmap.push_back( vecColValue );
 // col_dtoc_dofmap.push_back( vecColValue );
 cindexMax++;
 }
 else
 cindex = citer->second;
 
 sparseMatrix( rindex, cindex ) = vecS[i];
 }
 }
 
 m_nTotDofs_SrcCov = sparseMatrix.GetColumns();
 m_nTotDofs_Dest = sparseMatrix.GetRows();
 
#ifdef MOAB_HAVE_EIGEN3
 this->copy_tempest_sparsemat_to_eigen3();
#endif
 
 // Reset the source and target data first
 m_rowVector.setZero();
 m_colVector.setZero();
 
 return moab::MB_SUCCESS;
}
 
///////////////////////////////////////////////////////////////////////////////