NCHelperGCRM.cpp

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#include "NCHelperGCRM.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/FileOptions.hpp"
#include "moab/SpectralMeshTool.hpp"
#include "MBTagConventions.hpp"

#ifdef MOAB_HAVE_ZOLTAN
#include "moab/ZoltanPartitioner.hpp"
#endif

#include <cmath>

namespace moab
{

// GCRM cells are either pentagons or hexagons, and pentagons are always padded to hexagons
const int EDGES_PER_CELL = 6;

NCHelperGCRM::NCHelperGCRM( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
    : UcdNCHelper( readNC, fileId, opts, fileSet ), createGatherSet( false )
{
    // Ignore variables containing topological information
    ignoredVarNames.insert( "grid" );
    ignoredVarNames.insert( "cell_corners" );
    ignoredVarNames.insert( "cell_edges" );
    ignoredVarNames.insert( "edge_corners" );
    ignoredVarNames.insert( "cell_neighbors" );
}

bool NCHelperGCRM::can_read_file( ReadNC* readNC )
{
    std::vector< std::string >& dimNames = readNC->dimNames;

    // If dimension name "cells" exists then it should be the GCRM grid
    if( std::find( dimNames.begin(), dimNames.end(), std::string( "cells" ) ) != dimNames.end() ) return true;

    return false;
}

ErrorCode NCHelperGCRM::init_mesh_vals()
{
    std::vector< std::string >& dimNames              = _readNC->dimNames;
    std::vector< int >& dimLens                       = _readNC->dimLens;
    std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;

    ErrorCode rval;
    unsigned int idx;
    std::vector< std::string >::iterator vit;

    // Look for time dimension
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "Time" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else if( ( vit = std::find( dimNames.begin(), dimNames.end(), "time" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'Time' or 'time' dimension" );
    }
    tDim       = idx;
    nTimeSteps = dimLens[idx];

    // Get number of cells
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "cells" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'cells' dimension" );
    }
    cDim   = idx;
    nCells = dimLens[idx];

    // Get number of edges
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "edges" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'edges' dimension" );
    }
    eDim   = idx;
    nEdges = dimLens[idx];

    // Get number of vertices
    vDim = -1;
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "corners" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'corners' dimension" );
    }
    vDim      = idx;
    nVertices = dimLens[idx];

    // Get number of layers
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "layers" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' dimension" );
    }
    levDim  = idx;
    nLevels = dimLens[idx];

    // Dimension indices for other optional levels
    std::vector< unsigned int > opt_lev_dims;

    // Get index of interface levels
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "interfaces" ) ) != dimNames.end() )
    {
        idx = vit - dimNames.begin();
        opt_lev_dims.push_back( idx );
    }

    std::map< std::string, ReadNC::VarData >::iterator vmit;

    // Store time coordinate values in tVals
    if( nTimeSteps > 0 )
    {
        if( ( vmit = varInfo.find( "time" ) ) != varInfo.end() )
        {
            rval = read_coordinate( "time", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 'time' variable" );
        }
        else if( ( vmit = varInfo.find( "t" ) ) != varInfo.end() )
        {
            rval = read_coordinate( "t", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 't' variable" );
        }
        else
        {
            // If expected time variable is not available, set dummy time coordinate values to tVals
            for( int t = 0; t < nTimeSteps; t++ )
                tVals.push_back( (double)t );
        }
    }

    // For each variable, determine the entity location type and number of levels
    for( vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit )
    {
        ReadNC::VarData& vd = ( *vmit ).second;

        // Default entLoc is ENTLOCSET
        if( std::find( vd.varDims.begin(), vd.varDims.end(), tDim ) != vd.varDims.end() )
        {
            if( std::find( vd.varDims.begin(), vd.varDims.end(), vDim ) != vd.varDims.end() )
                vd.entLoc = ReadNC::ENTLOCVERT;
            else if( std::find( vd.varDims.begin(), vd.varDims.end(), eDim ) != vd.varDims.end() )
                vd.entLoc = ReadNC::ENTLOCEDGE;
            else if( std::find( vd.varDims.begin(), vd.varDims.end(), cDim ) != vd.varDims.end() )
                vd.entLoc = ReadNC::ENTLOCFACE;
        }

        // Default numLev is 0
        if( std::find( vd.varDims.begin(), vd.varDims.end(), levDim ) != vd.varDims.end() )
            vd.numLev = nLevels;
        else
        {
            // If layers dimension is not found, try other optional levels such as interfaces
            for( unsigned int i = 0; i < opt_lev_dims.size(); i++ )
            {
                if( std::find( vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i] ) != vd.varDims.end() )
                {
                    vd.numLev = dimLens[opt_lev_dims[i]];
                    break;
                }
            }
        }
    }

    // Hack: create dummy variables for dimensions (like cells) with no corresponding coordinate
    // variables
    rval = create_dummy_variables();MB_CHK_SET_ERR( rval, "Failed to create dummy variables" );

    return MB_SUCCESS;
}

// When noMesh option is used on this read, the old ReadNC class instance for last read can get out
// of scope (and deleted). The old instance initialized some variables properly when the mesh was
// created, but they are now lost. The new instance (will not create the mesh with noMesh option)
// has to restore them based on the existing mesh from last read
ErrorCode NCHelperGCRM::check_existing_mesh()
{
    Interface*& mbImpl = _readNC->mbImpl;
    Tag& mGlobalIdTag  = _readNC->mGlobalIdTag;
    bool& noMesh       = _readNC->noMesh;

    if( noMesh )
    {
        ErrorCode rval;

        if( localGidVerts.empty() )
        {
            // Get all vertices from current file set (it is the input set in no_mesh scenario)
            Range local_verts;
            rval = mbImpl->get_entities_by_dimension( _fileSet, 0, local_verts );MB_CHK_SET_ERR( rval, "Trouble getting local vertices in current file set" );

            if( !local_verts.empty() )
            {
                std::vector< int > gids( local_verts.size() );

                // !IMPORTANT : this has to be the GLOBAL_ID tag
                rval = mbImpl->tag_get_data( mGlobalIdTag, local_verts, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of vertices" );

                // Restore localGidVerts
                std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidVerts ) );
                nLocalVertices = localGidVerts.size();
            }
        }

        if( localGidEdges.empty() )
        {
            // Get all edges from current file set (it is the input set in no_mesh scenario)
            Range local_edges;
            rval = mbImpl->get_entities_by_dimension( _fileSet, 1, local_edges );MB_CHK_SET_ERR( rval, "Trouble getting local edges in current file set" );

            if( !local_edges.empty() )
            {
                std::vector< int > gids( local_edges.size() );

                // !IMPORTANT : this has to be the GLOBAL_ID tag
                rval = mbImpl->tag_get_data( mGlobalIdTag, local_edges, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of edges" );

                // Restore localGidEdges
                std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidEdges ) );
                nLocalEdges = localGidEdges.size();
            }
        }

        if( localGidCells.empty() )
        {
            // Get all cells from current file set (it is the input set in no_mesh scenario)
            Range local_cells;
            rval = mbImpl->get_entities_by_dimension( _fileSet, 2, local_cells );MB_CHK_SET_ERR( rval, "Trouble getting local cells in current file set" );

            if( !local_cells.empty() )
            {
                std::vector< int > gids( local_cells.size() );

                // !IMPORTANT : this has to be the GLOBAL_ID tag
                rval = mbImpl->tag_get_data( mGlobalIdTag, local_cells, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of cells" );

                // Restore localGidCells
                std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidCells ) );
                nLocalCells = localGidCells.size();
            }
        }
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_mesh( Range& faces )
{
    bool& noEdges       = _readNC->noEdges;
    DebugOutput& dbgOut = _readNC->dbgOut;

#ifdef MOAB_HAVE_MPI
    int rank         = 0;
    int procs        = 1;
    bool& isParallel = _readNC->isParallel;
    if( isParallel )
    {
        ParallelComm*& myPcomm = _readNC->myPcomm;
        rank                   = myPcomm->proc_config().proc_rank();
        procs                  = myPcomm->proc_config().proc_size();
    }

    // Need to know whether we'll be creating gather mesh
    if( rank == _readNC->gatherSetRank ) createGatherSet = true;

    if( procs >= 2 )
    {
        // Shift rank to obtain a rotated trivial partition
        int shifted_rank           = rank;
        int& trivialPartitionShift = _readNC->trivialPartitionShift;
        if( trivialPartitionShift > 0 ) shifted_rank = ( rank + trivialPartitionShift ) % procs;

        // Compute the number of local cells on this proc
        nLocalCells = int( std::floor( 1.0 * nCells / procs ) );

        // The starting global cell index in the GCRM file for this proc
        int start_cell_idx = shifted_rank * nLocalCells;

        // Number of extra cells after equal split over procs
        int iextra = nCells % procs;

        // Allocate extra cells over procs
        if( shifted_rank < iextra ) nLocalCells++;
        start_cell_idx += std::min( shifted_rank, iextra );

        start_cell_idx++;  // 0 based -> 1 based

        // Redistribute local cells after trivial partition (e.g. apply Zoltan partition)
        ErrorCode rval = redistribute_local_cells( start_cell_idx );MB_CHK_SET_ERR( rval, "Failed to redistribute local cells after trivial partition" );
    }
    else
    {
        nLocalCells = nCells;
        localGidCells.insert( 1, nLocalCells );
    }
#else
    nLocalCells = nCells;
    localGidCells.insert( 1, nLocalCells );
#endif
    dbgOut.tprintf( 1, " localGidCells.psize() = %d\n", (int)localGidCells.psize() );
    dbgOut.tprintf( 1, " localGidCells.size() = %d\n", (int)localGidCells.size() );

    // Read vertices on each local cell, to get localGidVerts and cell connectivity later
    int verticesOnCellVarId;
    int success = NCFUNC( inq_varid )( _fileId, "cell_corners", &verticesOnCellVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_corners" );
    std::vector< int > vertices_on_local_cells( nLocalCells * EDGES_PER_CELL );
    dbgOut.tprintf( 1, " nLocalCells = %d\n", (int)nLocalCells );
    dbgOut.tprintf( 1, " vertices_on_local_cells.size() = %d\n", (int)vertices_on_local_cells.size() );
#ifdef MOAB_HAVE_PNETCDF
    size_t nb_reads = localGidCells.psize();
    std::vector< int > requests( nb_reads );
    std::vector< int > statuss( nb_reads );
    size_t idxReq = 0;
#endif
    size_t indexInArray = 0;
    for( Range::pair_iterator pair_iter = localGidCells.pair_begin(); pair_iter != localGidCells.pair_end();
         ++pair_iter )
    {
        EntityHandle starth = pair_iter->first;
        EntityHandle endh   = pair_iter->second;
        dbgOut.tprintf( 1, " cell_corners starth = %d\n", (int)starth );
        dbgOut.tprintf( 1, " cell_corners   endh = %d\n", (int)endh );
        NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
        NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ),
                                     static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };

        // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
        success = NCFUNCREQG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts,
                                           &( vertices_on_local_cells[indexInArray] ), &requests[idxReq++] );
#else
        success = NCFUNCAG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts,
                                         &( vertices_on_local_cells[indexInArray] ) );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data in a loop" );

        // Increment the index for next subrange
        indexInArray += ( endh - starth + 1 ) * EDGES_PER_CELL;
    }

#ifdef MOAB_HAVE_PNETCDF
    // Wait outside the loop
    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif

    // Correct vertices_on_local_cells array. Pentagons as hexagons should have
    // a connectivity like 123455 and not 122345
    for( int local_cell_idx = 0; local_cell_idx < nLocalCells; local_cell_idx++ )
    {
        int* pvertex = &vertices_on_local_cells[local_cell_idx * EDGES_PER_CELL];
        for( int k = 0; k < EDGES_PER_CELL - 2; k++ )
        {
            if( *( pvertex + k ) == *( pvertex + k + 1 ) )
            {
                // Shift the connectivity
                for( int kk = k + 1; kk < EDGES_PER_CELL - 1; kk++ )
                    *( pvertex + kk ) = *( pvertex + kk + 1 );
                // No need to try next k
                break;
            }
        }
    }

    // GCRM is 0 based, convert vertex indices from 0 to 1 based
    for( std::size_t idx = 0; idx < vertices_on_local_cells.size(); idx++ )
        vertices_on_local_cells[idx] += 1;

    // Create local vertices
    EntityHandle start_vertex;
    ErrorCode rval = create_local_vertices( vertices_on_local_cells, start_vertex );MB_CHK_SET_ERR( rval, "Failed to create local vertices for GCRM mesh" );

    // Create local edges (unless NO_EDGES read option is set)
    if( !noEdges )
    {
        rval = create_local_edges( start_vertex );MB_CHK_SET_ERR( rval, "Failed to create local edges for GCRM mesh" );
    }

    // Create local cells, padded
    rval = create_padded_local_cells( vertices_on_local_cells, start_vertex, faces );MB_CHK_SET_ERR( rval, "Failed to create padded local cells for GCRM mesh" );

    if( createGatherSet )
    {
        EntityHandle gather_set;
        rval = _readNC->readMeshIface->create_gather_set( gather_set );MB_CHK_SET_ERR( rval, "Failed to create gather set" );

        // Create gather set vertices
        EntityHandle start_gather_set_vertex;
        rval = create_gather_set_vertices( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create gather set vertices for GCRM mesh" );

        // Create gather set edges (unless NO_EDGES read option is set)
        if( !noEdges )
        {
            rval = create_gather_set_edges( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create gather set edges for GCRM mesh" );
        }

        // Create gather set cells with padding
        rval = create_padded_gather_set_cells( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create padded gather set cells for GCRM mesh" );
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::read_ucd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
                                                               std::vector< int >& tstep_nums )
{
    Interface*& mbImpl          = _readNC->mbImpl;
    std::vector< int >& dimLens = _readNC->dimLens;
    bool& noEdges               = _readNC->noEdges;
    DebugOutput& dbgOut         = _readNC->dbgOut;

    Range* range = NULL;

    // Get vertices
    Range verts;
    ErrorCode rval = mbImpl->get_entities_by_dimension( _fileSet, 0, verts );MB_CHK_SET_ERR( rval, "Trouble getting vertices in current file set" );
    assert( "Should only have a single vertex subrange, since they were read in one shot" && verts.psize() == 1 );

    // Get edges
    Range edges;
    rval = mbImpl->get_entities_by_dimension( _fileSet, 1, edges );MB_CHK_SET_ERR( rval, "Trouble getting edges in current file set" );

    // Get faces
    Range faces;
    rval = mbImpl->get_entities_by_dimension( _fileSet, 2, faces );MB_CHK_SET_ERR( rval, "Trouble getting faces in current file set" );
    assert( "Should only have a single face subrange, since they were read in one shot" && faces.psize() == 1 );

#ifdef MOAB_HAVE_MPI
    bool& isParallel = _readNC->isParallel;
    if( isParallel )
    {
        ParallelComm*& myPcomm = _readNC->myPcomm;
        rval                   = myPcomm->filter_pstatus( faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &facesOwned );MB_CHK_SET_ERR( rval, "Trouble getting owned faces in current file set" );
    }
    else
        facesOwned = faces;  // not running in parallel, but still with MPI
#else
    facesOwned = faces;
#endif

    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        // Skip edge variables, if specified by the read options
        if( noEdges && vdatas[i].entLoc == ReadNC::ENTLOCEDGE ) continue;

        // Support non-set variables with 3 dimensions like (time, cells, layers), or
        // 2 dimensions like (time, cells)
        assert( 3 == vdatas[i].varDims.size() || 2 == vdatas[i].varDims.size() );

        // For a non-set variable, time should be the first dimension
        assert( tDim == vdatas[i].varDims[0] );

        // Set up readStarts and readCounts
        vdatas[i].readStarts.resize( 3 );
        vdatas[i].readCounts.resize( 3 );

        // First: Time
        vdatas[i].readStarts[0] = 0;  // This value is timestep dependent, will be set later
        vdatas[i].readCounts[0] = 1;

        // Next: nVertices / nCells / nEdges
        switch( vdatas[i].entLoc )
        {
            case ReadNC::ENTLOCVERT:
                // Vertices
                // Start from the first localGidVerts
                // Actually, this will be reset later on in a loop
                vdatas[i].readStarts[1] = localGidVerts[0] - 1;
                vdatas[i].readCounts[1] = nLocalVertices;
                range                   = &verts;
                break;
            case ReadNC::ENTLOCFACE:
                // Faces
                // Start from the first localGidCells
                // Actually, this will be reset later on in a loop
                vdatas[i].readStarts[1] = localGidCells[0] - 1;
                vdatas[i].readCounts[1] = nLocalCells;
                range                   = &facesOwned;
                break;
            case ReadNC::ENTLOCEDGE:
                // Edges
                // Start from the first localGidEdges
                // Actually, this will be reset later on in a loop
                vdatas[i].readStarts[1] = localGidEdges[0] - 1;
                vdatas[i].readCounts[1] = nLocalEdges;
                range                   = &edges;
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
        }

        // Finally: layers or other optional levels, it is possible that there is no
        // level dimension (numLev is 0) for this non-set variable
        if( vdatas[i].numLev < 1 ) vdatas[i].numLev = 1;
        vdatas[i].readStarts[2] = 0;
        vdatas[i].readCounts[2] = vdatas[i].numLev;

        // Get variable size
        vdatas[i].sz = 1;
        for( std::size_t idx = 0; idx != 3; idx++ )
            vdatas[i].sz *= vdatas[i].readCounts[idx];

        for( unsigned int t = 0; t < tstep_nums.size(); t++ )
        {
            dbgOut.tprintf( 2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t] );

            if( tstep_nums[t] >= dimLens[tDim] )
            {
                MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number " << tstep_nums[t] );
            }

            // Get the tag to read into
            if( !vdatas[i].varTags[t] )
            {
                rval = get_tag_to_nonset( vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev );MB_CHK_SET_ERR( rval, "Trouble getting tag for variable " << vdatas[i].varName );
            }

            // Get ptr to tag space
            assert( 1 == range->psize() );
            void* data;
            int count;
            rval = mbImpl->tag_iterate( vdatas[i].varTags[t], range->begin(), range->end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate tag for variable " << vdatas[i].varName );
            assert( (unsigned)count == range->size() );
            vdatas[i].varDatas[t] = data;
        }
    }

    return rval;
}

#ifdef MOAB_HAVE_PNETCDF
ErrorCode NCHelperGCRM::read_ucd_variables_to_nonset_async( std::vector< ReadNC::VarData >& vdatas,
                                                            std::vector< int >& tstep_nums )
{
    bool& noEdges       = _readNC->noEdges;
    DebugOutput& dbgOut = _readNC->dbgOut;

    ErrorCode rval = read_ucd_variables_to_nonset_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read non-set variables" );

    // Finally, read into that space
    int success;
    Range* pLocalGid = NULL;

    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        // Skip edge variables, if specified by the read options
        if( noEdges && vdatas[i].entLoc == ReadNC::ENTLOCEDGE ) continue;

        switch( vdatas[i].entLoc )
        {
            case ReadNC::ENTLOCVERT:
                pLocalGid = &localGidVerts;
                break;
            case ReadNC::ENTLOCFACE:
                pLocalGid = &localGidCells;
                break;
            case ReadNC::ENTLOCEDGE:
                pLocalGid = &localGidEdges;
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
        }

        std::size_t sz = vdatas[i].sz;

        for( unsigned int t = 0; t < tstep_nums.size(); t++ )
        {
            // We will synchronize all these reads with the other processors,
            // so the wait will be inside this double loop; is it too much?
            size_t nb_reads = pLocalGid->psize();
            std::vector< int > requests( nb_reads ), statuss( nb_reads );
            size_t idxReq = 0;

            // Set readStart for each timestep along time dimension
            vdatas[i].readStarts[0] = tstep_nums[t];

            switch( vdatas[i].varDataType )
            {
                case NC_FLOAT:
                case NC_DOUBLE: {
                    // Read float as double
                    std::vector< double > tmpdoubledata( sz );

                    // In the case of ucd mesh, and on multiple proc,
                    // we need to read as many times as subranges we have in the
                    // localGid range;
                    // basically, we have to give a different point
                    // for data to start, for every subrange :(
                    size_t indexInDoubleArray = 0;
                    size_t ic                 = 0;
                    for( Range::pair_iterator pair_iter = pLocalGid->pair_begin(); pair_iter != pLocalGid->pair_end();
                         ++pair_iter, ic++ )
                    {
                        EntityHandle starth     = pair_iter->first;
                        EntityHandle endh       = pair_iter->second;  // inclusive
                        vdatas[i].readStarts[1] = ( NCDF_SIZE )( starth - 1 );
                        vdatas[i].readCounts[1] = ( NCDF_SIZE )( endh - starth + 1 );

                        // Do a partial read, in each subrange
                        // wait outside this loop
                        success =
                            NCFUNCREQG( _vara_double )( _fileId, vdatas[i].varId, &( vdatas[i].readStarts[0] ),
                                                        &( vdatas[i].readCounts[0] ),
                                                        &( tmpdoubledata[indexInDoubleArray] ), &requests[idxReq++] );
                        if( success )
                            MB_SET_ERR( MB_FAILURE,
                                        "Failed to read double data in a loop for variable " << vdatas[i].varName );
                        // We need to increment the index in double array for the
                        // next subrange
                        indexInDoubleArray += ( endh - starth + 1 ) * 1 * vdatas[i].numLev;
                    }
                    assert( ic == pLocalGid->psize() );

                    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
                    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );

                    void* data = vdatas[i].varDatas[t];
                    for( std::size_t idx = 0; idx != tmpdoubledata.size(); idx++ )
                        ( (double*)data )[idx] = tmpdoubledata[idx];

                    break;
                }
                default:
                    MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
            }
        }
    }

    // Debug output, if requested
    if( 1 == dbgOut.get_verbosity() )
    {
        dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
        for( unsigned int i = 1; i < vdatas.size(); i++ )
            dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
        dbgOut.tprintf( 1, "\n" );
    }

    return rval;
}
#else
ErrorCode NCHelperGCRM::read_ucd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas,
                                                      std::vector< int >& tstep_nums )
{
    bool& noEdges = _readNC->noEdges;
    DebugOutput& dbgOut = _readNC->dbgOut;

    ErrorCode rval = read_ucd_variables_to_nonset_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read non-set variables" );

    // Finally, read into that space
    int success;
    Range* pLocalGid = NULL;

    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        // Skip edge variables, if specified by the read options
        if( noEdges && vdatas[i].entLoc == ReadNC::ENTLOCEDGE ) continue;

        switch( vdatas[i].entLoc )
        {
            case ReadNC::ENTLOCVERT:
                pLocalGid = &localGidVerts;
                break;
            case ReadNC::ENTLOCFACE:
                pLocalGid = &localGidCells;
                break;
            case ReadNC::ENTLOCEDGE:
                pLocalGid = &localGidEdges;
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
        }

        std::size_t sz = vdatas[i].sz;

        for( unsigned int t = 0; t < tstep_nums.size(); t++ )
        {
            // Set readStart for each timestep along time dimension
            vdatas[i].readStarts[0] = tstep_nums[t];

            switch( vdatas[i].varDataType )
            {
                case NC_FLOAT:
                case NC_DOUBLE: {
                    // Read float as double
                    std::vector< double > tmpdoubledata( sz );

                    // In the case of ucd mesh, and on multiple proc,
                    // we need to read as many times as subranges we have in the
                    // localGid range;
                    // basically, we have to give a different point
                    // for data to start, for every subrange :(
                    size_t indexInDoubleArray = 0;
                    size_t ic = 0;
                    for( Range::pair_iterator pair_iter = pLocalGid->pair_begin(); pair_iter != pLocalGid->pair_end();
                         ++pair_iter, ic++ )
                    {
                        EntityHandle starth = pair_iter->first;
                        EntityHandle endh = pair_iter->second;  // Inclusive
                        vdatas[i].readStarts[1] = ( NCDF_SIZE )( starth - 1 );
                        vdatas[i].readCounts[1] = ( NCDF_SIZE )( endh - starth + 1 );

                        success = NCFUNCAG( _vara_double )( _fileId, vdatas[i].varId, &( vdatas[i].readStarts[0] ),
                                                            &( vdatas[i].readCounts[0] ),
                                                            &( tmpdoubledata[indexInDoubleArray] ) );
                        if( success )
                            MB_SET_ERR( MB_FAILURE,
                                        "Failed to read double data in a loop for variable " << vdatas[i].varName );
                        // We need to increment the index in double array for the
                        // next subrange
                        indexInDoubleArray += ( endh - starth + 1 ) * 1 * vdatas[i].numLev;
                    }
                    assert( ic == pLocalGid->psize() );

                    void* data = vdatas[i].varDatas[t];
                    for( std::size_t idx = 0; idx != tmpdoubledata.size(); idx++ )
                        ( (double*)data )[idx] = tmpdoubledata[idx];

                    break;
                }
                default:
                    MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
            }
        }
    }

    // Debug output, if requested
    if( 1 == dbgOut.get_verbosity() )
    {
        dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
        for( unsigned int i = 1; i < vdatas.size(); i++ )
            dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
        dbgOut.tprintf( 1, "\n" );
    }

    return rval;
}
#endif

#ifdef MOAB_HAVE_MPI
ErrorCode NCHelperGCRM::redistribute_local_cells( int start_cell_idx )
{
    // If possible, apply Zoltan partition
#ifdef MOAB_HAVE_ZOLTAN
    if( _readNC->partMethod == ScdParData::RCBZOLTAN )
    {
        // Read lat/lon coordinates of cell centers, then convert spherical to
        // Cartesian, and use them as input to Zoltan partition
        int xCellVarId;
        int success = NCFUNC( inq_varid )( _fileId, "grid_center_lat", &xCellVarId );
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_center_lat" );
        std::vector< double > xCell( nLocalCells );
        NCDF_SIZE read_start = static_cast< NCDF_SIZE >( start_cell_idx - 1 );
        NCDF_SIZE read_count = static_cast< NCDF_SIZE >( nLocalCells );
        success              = NCFUNCAG( _vara_double )( _fileId, xCellVarId, &read_start, &read_count, &xCell[0] );
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_center_lat data" );

        // Read y coordinates of cell centers
        int yCellVarId;
        success = NCFUNC( inq_varid )( _fileId, "grid_center_lon", &yCellVarId );
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_center_lon" );
        std::vector< double > yCell( nLocalCells );
        success = NCFUNCAG( _vara_double )( _fileId, yCellVarId, &read_start, &read_count, &yCell[0] );
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_center_lon data" );

        // Convert lon/lat/rad to x/y/z
        std::vector< double > zCell( nLocalCells );
        double rad = 8000.0;  // This is just a approximate radius
        for( int i = 0; i < nLocalCells; i++ )
        {
            double cosphi = cos( xCell[i] );
            double zmult  = sin( xCell[i] );
            double xmult  = cosphi * cos( yCell[i] );
            double ymult  = cosphi * sin( yCell[i] );
            xCell[i]      = rad * xmult;
            yCell[i]      = rad * ymult;
            zCell[i]      = rad * zmult;
        }

        // Zoltan partition using RCB; maybe more studies would be good, as to which partition
        // is better
        Interface*& mbImpl         = _readNC->mbImpl;
        DebugOutput& dbgOut        = _readNC->dbgOut;
        ZoltanPartitioner* mbZTool = new ZoltanPartitioner( mbImpl, false, 0, NULL );
        ErrorCode rval             = mbZTool->repartition( xCell, yCell, zCell, start_cell_idx, "RCB", localGidCells );MB_CHK_SET_ERR( rval, "Error in Zoltan partitioning" );
        delete mbZTool;

        dbgOut.tprintf( 1, "After Zoltan partitioning, localGidCells.psize() = %d\n", (int)localGidCells.psize() );
        dbgOut.tprintf( 1, "                           localGidCells.size() = %d\n", (int)localGidCells.size() );

        // This is important: local cells are now redistributed, so nLocalCells might be different!
        nLocalCells = localGidCells.size();

        return MB_SUCCESS;
    }
#endif

    // By default, apply trivial partition
    localGidCells.insert( start_cell_idx, start_cell_idx + nLocalCells - 1 );

    return MB_SUCCESS;
}
#endif

ErrorCode NCHelperGCRM::create_local_vertices( const std::vector< int >& vertices_on_local_cells,
                                               EntityHandle& start_vertex )
{
    Interface*& mbImpl                                = _readNC->mbImpl;
    Tag& mGlobalIdTag                                 = _readNC->mGlobalIdTag;
    const Tag*& mpFileIdTag                           = _readNC->mpFileIdTag;
    DebugOutput& dbgOut                               = _readNC->dbgOut;
    std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;

    // Make a copy of vertices_on_local_cells for sorting (keep original one to set cell
    // connectivity later)
    std::vector< int > vertices_on_local_cells_sorted( vertices_on_local_cells );
    std::sort( vertices_on_local_cells_sorted.begin(), vertices_on_local_cells_sorted.end() );
    std::copy( vertices_on_local_cells_sorted.rbegin(), vertices_on_local_cells_sorted.rend(),
               range_inserter( localGidVerts ) );
    nLocalVertices = localGidVerts.size();

    dbgOut.tprintf( 1, "   localGidVerts.psize() = %d\n", (int)localGidVerts.psize() );
    dbgOut.tprintf( 1, "   localGidVerts.size() = %d\n", (int)localGidVerts.size() );

    // Create local vertices
    std::vector< double* > arrays;
    ErrorCode rval =
        _readNC->readMeshIface->get_node_coords( 3, nLocalVertices, 0, start_vertex, arrays,
                                                 // Might have to create gather mesh later
                                                 ( createGatherSet ? nLocalVertices + nVertices : nLocalVertices ) );MB_CHK_SET_ERR( rval, "Failed to create local vertices" );

    // Add local vertices to current file set
    Range local_verts_range( start_vertex, start_vertex + nLocalVertices - 1 );
    rval = _readNC->mbImpl->add_entities( _fileSet, local_verts_range );MB_CHK_SET_ERR( rval, "Failed to add local vertices to current file set" );

    // Get ptr to GID memory for local vertices
    int count  = 0;
    void* data = NULL;
    rval       = mbImpl->tag_iterate( mGlobalIdTag, local_verts_range.begin(), local_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local vertices" );
    assert( count == nLocalVertices );
    int* gid_data = (int*)data;
    std::copy( localGidVerts.begin(), localGidVerts.end(), gid_data );

    // Duplicate GID data, which will be used to resolve sharing
    if( mpFileIdTag )
    {
        rval = mbImpl->tag_iterate( *mpFileIdTag, local_verts_range.begin(), local_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate file id tag on local vertices" );
        assert( count == nLocalVertices );
        int bytes_per_tag = 4;
        rval              = mbImpl->tag_get_bytes( *mpFileIdTag, bytes_per_tag );MB_CHK_SET_ERR( rval, "can't get number of bytes for file id tag" );
        if( 4 == bytes_per_tag )
        {
            gid_data = (int*)data;
            std::copy( localGidVerts.begin(), localGidVerts.end(), gid_data );
        }
        else if( 8 == bytes_per_tag )
        {  // Should be a handle tag on 64 bit machine?
            long* handle_tag_data = (long*)data;
            std::copy( localGidVerts.begin(), localGidVerts.end(), handle_tag_data );
        }
    }

#ifdef MOAB_HAVE_PNETCDF
    size_t nb_reads = localGidVerts.psize();
    std::vector< int > requests( nb_reads );
    std::vector< int > statuss( nb_reads );
    size_t idxReq = 0;
#endif

    // Store lev values in levVals
    std::map< std::string, ReadNC::VarData >::iterator vmit;
    if( ( vmit = varInfo.find( "layers" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
    {
        rval = read_coordinate( "layers", 0, nLevels - 1, levVals );MB_CHK_SET_ERR( rval, "Trouble reading 'layers' variable" );
    }
    else if( ( vmit = varInfo.find( "interfaces" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
    {
        rval = read_coordinate( "interfaces", 0, nLevels - 1, levVals );MB_CHK_SET_ERR( rval, "Trouble reading 'interfaces' variable" );
    }
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' or 'interfaces' variable" );
    }

    // Decide whether down is positive
    char posval[10] = { 0 };
    int success     = NCFUNC( get_att_text )( _fileId, ( *vmit ).second.varId, "positive", posval );
    if( 0 == success && !strncmp( posval, "down", 4 ) )
    {
        for( std::vector< double >::iterator dvit = levVals.begin(); dvit != levVals.end(); ++dvit )
            ( *dvit ) *= -1.0;
    }

    // Read x coordinates for local vertices
    double* xptr = arrays[0];
    int xVertexVarId;
    success = NCFUNC( inq_varid )( _fileId, "grid_corner_lon", &xVertexVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lon" );
    size_t indexInArray = 0;
    for( Range::pair_iterator pair_iter = localGidVerts.pair_begin(); pair_iter != localGidVerts.pair_end();
         ++pair_iter )
    {
        EntityHandle starth  = pair_iter->first;
        EntityHandle endh    = pair_iter->second;
        NCDF_SIZE read_start = ( NCDF_SIZE )( starth - 1 );
        NCDF_SIZE read_count = ( NCDF_SIZE )( endh - starth + 1 );

        // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
        success = NCFUNCREQG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, &( xptr[indexInArray] ),
                                              &requests[idxReq++] );
#else
        success = NCFUNCAG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, &( xptr[indexInArray] ) );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data in a loop" );

        // Increment the index for next subrange
        indexInArray += ( endh - starth + 1 );
    }

#ifdef MOAB_HAVE_PNETCDF
    // Wait outside the loop
    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif

    // Read y coordinates for local vertices
    double* yptr = arrays[1];
    int yVertexVarId;
    success = NCFUNC( inq_varid )( _fileId, "grid_corner_lat", &yVertexVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lat" );
#ifdef MOAB_HAVE_PNETCDF
    idxReq = 0;
#endif
    indexInArray = 0;
    for( Range::pair_iterator pair_iter = localGidVerts.pair_begin(); pair_iter != localGidVerts.pair_end();
         ++pair_iter )
    {
        EntityHandle starth  = pair_iter->first;
        EntityHandle endh    = pair_iter->second;
        NCDF_SIZE read_start = ( NCDF_SIZE )( starth - 1 );
        NCDF_SIZE read_count = ( NCDF_SIZE )( endh - starth + 1 );

        // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
        success = NCFUNCREQG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, &( yptr[indexInArray] ),
                                              &requests[idxReq++] );
#else
        success = NCFUNCAG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, &( yptr[indexInArray] ) );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data in a loop" );

        // Increment the index for next subrange
        indexInArray += ( endh - starth + 1 );
    }

#ifdef MOAB_HAVE_PNETCDF
    // Wait outside the loop
    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif

    // Convert lon/lat/rad to x/y/z
    double* zptr = arrays[2];
    double rad   = 8000.0 + levVals[0];
    for( int i = 0; i < nLocalVertices; i++ )
    {
        double cosphi = cos( yptr[i] );
        double zmult  = sin( yptr[i] );
        double xmult  = cosphi * cos( xptr[i] );
        double ymult  = cosphi * sin( xptr[i] );
        xptr[i]       = rad * xmult;
        yptr[i]       = rad * ymult;
        zptr[i]       = rad * zmult;
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_local_edges( EntityHandle start_vertex )
{
    Interface*& mbImpl  = _readNC->mbImpl;
    Tag& mGlobalIdTag   = _readNC->mGlobalIdTag;
    DebugOutput& dbgOut = _readNC->dbgOut;

    // Read edges on each local cell, to get localGidEdges
    int edgesOnCellVarId;
    int success = NCFUNC( inq_varid )( _fileId, "cell_edges", &edgesOnCellVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_edges" );

    std::vector< int > edges_on_local_cells( nLocalCells * EDGES_PER_CELL );
    dbgOut.tprintf( 1, "   edges_on_local_cells.size() = %d\n", (int)edges_on_local_cells.size() );

#ifdef MOAB_HAVE_PNETCDF
    size_t nb_reads = localGidCells.psize();
    std::vector< int > requests( nb_reads );
    std::vector< int > statuss( nb_reads );
    size_t idxReq = 0;
#endif
    size_t indexInArray = 0;
    for( Range::pair_iterator pair_iter = localGidCells.pair_begin(); pair_iter != localGidCells.pair_end();
         ++pair_iter )
    {
        EntityHandle starth = pair_iter->first;
        EntityHandle endh   = pair_iter->second;
        dbgOut.tprintf( 1, "   starth = %d\n", (int)starth );
        dbgOut.tprintf( 1, "   endh = %d\n", (int)endh );
        NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
        NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ),
                                     static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };

        // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
        success = NCFUNCREQG( _vara_int )( _fileId, edgesOnCellVarId, read_starts, read_counts,
                                           &( edges_on_local_cells[indexInArray] ), &requests[idxReq++] );
#else
        success = NCFUNCAG( _vara_int )( _fileId, edgesOnCellVarId, read_starts, read_counts,
                                         &( edges_on_local_cells[indexInArray] ) );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_edges data in a loop" );

        // Increment the index for next subrange
        indexInArray += ( endh - starth + 1 ) * EDGES_PER_CELL;
    }

#ifdef MOAB_HAVE_PNETCDF
    // Wait outside the loop
    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif

    // GCRM is 0 based, convert edge indices from 0 to 1 based
    for( std::size_t idx = 0; idx < edges_on_local_cells.size(); idx++ )
        edges_on_local_cells[idx] += 1;

    // Collect local edges
    std::sort( edges_on_local_cells.begin(), edges_on_local_cells.end() );
    std::copy( edges_on_local_cells.rbegin(), edges_on_local_cells.rend(), range_inserter( localGidEdges ) );
    nLocalEdges = localGidEdges.size();

    dbgOut.tprintf( 1, "   localGidEdges.psize() = %d\n", (int)localGidEdges.psize() );
    dbgOut.tprintf( 1, "   localGidEdges.size() = %d\n", (int)localGidEdges.size() );

    // Create local edges
    EntityHandle start_edge;
    EntityHandle* conn_arr_edges = NULL;
    ErrorCode rval =
        _readNC->readMeshIface->get_element_connect( nLocalEdges, 2, MBEDGE, 0, start_edge, conn_arr_edges,
                                                     // Might have to create gather mesh later
                                                     ( createGatherSet ? nLocalEdges + nEdges : nLocalEdges ) );MB_CHK_SET_ERR( rval, "Failed to create local edges" );

    // Add local edges to current file set
    Range local_edges_range( start_edge, start_edge + nLocalEdges - 1 );
    rval = _readNC->mbImpl->add_entities( _fileSet, local_edges_range );MB_CHK_SET_ERR( rval, "Failed to add local edges to current file set" );

    // Get ptr to GID memory for edges
    int count  = 0;
    void* data = NULL;
    rval       = mbImpl->tag_iterate( mGlobalIdTag, local_edges_range.begin(), local_edges_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local edges" );
    assert( count == nLocalEdges );
    int* gid_data = (int*)data;
    std::copy( localGidEdges.begin(), localGidEdges.end(), gid_data );

    int verticesOnEdgeVarId;

    // Read vertices on each local edge, to get edge connectivity
    success = NCFUNC( inq_varid )( _fileId, "edge_corners", &verticesOnEdgeVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of edge_corners" );
    // Utilize the memory storage pointed by conn_arr_edges
    int* vertices_on_local_edges = (int*)conn_arr_edges;
#ifdef MOAB_HAVE_PNETCDF
    nb_reads = localGidEdges.psize();
    requests.resize( nb_reads );
    statuss.resize( nb_reads );
    idxReq = 0;
#endif
    indexInArray = 0;
    for( Range::pair_iterator pair_iter = localGidEdges.pair_begin(); pair_iter != localGidEdges.pair_end();
         ++pair_iter )
    {
        EntityHandle starth      = pair_iter->first;
        EntityHandle endh        = pair_iter->second;
        NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
        NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ), 2 };

        // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
        success = NCFUNCREQG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts,
                                           &( vertices_on_local_edges[indexInArray] ), &requests[idxReq++] );
#else
        success = NCFUNCAG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts,
                                         &( vertices_on_local_edges[indexInArray] ) );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data in a loop" );

        // Increment the index for next subrange
        indexInArray += ( endh - starth + 1 ) * 2;
    }

#ifdef MOAB_HAVE_PNETCDF
    // Wait outside the loop
    success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif

    // Populate connectivity data for local edges
    // Convert in-place from int (stored in the first half) to EntityHandle
    // Reading backward is the trick
    for( int edge_vert = nLocalEdges * 2 - 1; edge_vert >= 0; edge_vert-- )
    {
        // Note, indices stored in vertices_on_local_edges are 0 based
        int global_vert_idx = vertices_on_local_edges[edge_vert] + 1;  // Global vertex index, 1 based
        int local_vert_idx  = localGidVerts.index( global_vert_idx );  // Local vertex index, 0 based
        assert( local_vert_idx != -1 );
        conn_arr_edges[edge_vert] = start_vertex + local_vert_idx;
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_padded_local_cells( const std::vector< int >& vertices_on_local_cells,
                                                   EntityHandle start_vertex, Range& faces )
{
    Interface*& mbImpl = _readNC->mbImpl;
    Tag& mGlobalIdTag  = _readNC->mGlobalIdTag;

    // Create cells
    EntityHandle start_element;
    EntityHandle* conn_arr_local_cells = NULL;
    ErrorCode rval =
        _readNC->readMeshIface->get_element_connect( nLocalCells, EDGES_PER_CELL, MBPOLYGON, 0, start_element,
                                                     conn_arr_local_cells,
                                                     // Might have to create gather mesh later
                                                     ( createGatherSet ? nLocalCells + nCells : nLocalCells ) );MB_CHK_SET_ERR( rval, "Failed to create local cells" );
    faces.insert( start_element, start_element + nLocalCells - 1 );

    // Add local cells to current file set
    Range local_cells_range( start_element, start_element + nLocalCells - 1 );
    rval = _readNC->mbImpl->add_entities( _fileSet, local_cells_range );MB_CHK_SET_ERR( rval, "Failed to add local cells to current file set" );

    // Get ptr to GID memory for local cells
    int count  = 0;
    void* data = NULL;
    rval       = mbImpl->tag_iterate( mGlobalIdTag, local_cells_range.begin(), local_cells_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local cells" );
    assert( count == nLocalCells );
    int* gid_data = (int*)data;
    std::copy( localGidCells.begin(), localGidCells.end(), gid_data );

    // Set connectivity array with proper local vertices handles
    // vertices_on_local_cells array was already corrected to have
    // the last vertices repeated for pentagons, e.g. 122345 => 123455
    for( int local_cell_idx = 0; local_cell_idx < nLocalCells; local_cell_idx++ )
    {
        for( int i = 0; i < EDGES_PER_CELL; i++ )
        {
            // Note, indices stored in vertices_on_local_cells are 1 based
            EntityHandle global_vert_idx =
                vertices_on_local_cells[local_cell_idx * EDGES_PER_CELL + i];  // Global vertex index, 1 based
            int local_vert_idx = localGidVerts.index( global_vert_idx );       // Local vertex index, 0 based
            assert( local_vert_idx != -1 );
            conn_arr_local_cells[local_cell_idx * EDGES_PER_CELL + i] = start_vertex + local_vert_idx;
        }
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_gather_set_vertices( EntityHandle gather_set, EntityHandle& gather_set_start_vertex )
{
    Interface*& mbImpl      = _readNC->mbImpl;
    Tag& mGlobalIdTag       = _readNC->mGlobalIdTag;
    const Tag*& mpFileIdTag = _readNC->mpFileIdTag;

    // Create gather set vertices
    std::vector< double* > arrays;
    // Don't need to specify allocation number here, because we know enough vertices were created
    // before
    ErrorCode rval = _readNC->readMeshIface->get_node_coords( 3, nVertices, 0, gather_set_start_vertex, arrays );MB_CHK_SET_ERR( rval, "Failed to create gather set vertices" );

    // Add vertices to the gather set
    Range gather_set_verts_range( gather_set_start_vertex, gather_set_start_vertex + nVertices - 1 );
    rval = mbImpl->add_entities( gather_set, gather_set_verts_range );MB_CHK_SET_ERR( rval, "Failed to add vertices to the gather set" );

    // Read x coordinates for gather set vertices
    double* xptr = arrays[0];
    int xVertexVarId;
    int success = NCFUNC( inq_varid )( _fileId, "grid_corner_lon", &xVertexVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lon" );
    NCDF_SIZE read_start = 0;
    NCDF_SIZE read_count = static_cast< NCDF_SIZE >( nVertices );
#ifdef MOAB_HAVE_PNETCDF
    // Enter independent I/O mode, since this read is only for the gather processor
    success = NCFUNC( begin_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
    success = NCFUNCG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, xptr );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data" );
    success = NCFUNC( end_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
    success = NCFUNCG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, xptr );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data" );
#endif

    // Read y coordinates for gather set vertices
    double* yptr = arrays[1];
    int yVertexVarId;
    success = NCFUNC( inq_varid )( _fileId, "grid_corner_lat", &yVertexVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lat" );
#ifdef MOAB_HAVE_PNETCDF
    // Enter independent I/O mode, since this read is only for the gather processor
    success = NCFUNC( begin_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
    success = NCFUNCG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, yptr );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data" );
    success = NCFUNC( end_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
    success = NCFUNCG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, yptr );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data" );
#endif

    // Convert lon/lat/rad to x/y/z
    double* zptr = arrays[2];
    double rad   = 8000.0 + levVals[0];
    for( int i = 0; i < nVertices; i++ )
    {
        double cosphi = cos( yptr[i] );
        double zmult  = sin( yptr[i] );
        double xmult  = cosphi * cos( xptr[i] );
        double ymult  = cosphi * sin( xptr[i] );
        xptr[i]       = rad * xmult;
        yptr[i]       = rad * ymult;
        zptr[i]       = rad * zmult;
    }

    // Get ptr to GID memory for gather set vertices
    int count  = 0;
    void* data = NULL;
    rval =
        mbImpl->tag_iterate( mGlobalIdTag, gather_set_verts_range.begin(), gather_set_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on gather set vertices" );
    assert( count == nVertices );
    int* gid_data = (int*)data;
    for( int j = 1; j <= nVertices; j++ )
        gid_data[j - 1] = j;

    // Set the file id tag too, it should be bigger something not interfering with global id
    if( mpFileIdTag )
    {
        rval = mbImpl->tag_iterate( *mpFileIdTag, gather_set_verts_range.begin(), gather_set_verts_range.end(), count,
                                    data );MB_CHK_SET_ERR( rval, "Failed to iterate file id tag on gather set vertices" );
        assert( count == nVertices );
        int bytes_per_tag = 4;
        rval              = mbImpl->tag_get_bytes( *mpFileIdTag, bytes_per_tag );MB_CHK_SET_ERR( rval, "Can't get number of bytes for file id tag" );
        if( 4 == bytes_per_tag )
        {
            gid_data = (int*)data;
            for( int j = 1; j <= nVertices; j++ )
                gid_data[j - 1] = nVertices + j;  // Bigger than global id tag
        }
        else if( 8 == bytes_per_tag )
        {  // Should be a handle tag on 64 bit machine?
            long* handle_tag_data = (long*)data;
            for( int j = 1; j <= nVertices; j++ )
                handle_tag_data[j - 1] = nVertices + j;  // Bigger than global id tag
        }
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_gather_set_edges( EntityHandle gather_set, EntityHandle gather_set_start_vertex )
{
    Interface*& mbImpl = _readNC->mbImpl;

    // Create gather set edges
    EntityHandle start_edge;
    EntityHandle* conn_arr_gather_set_edges = NULL;
    // Don't need to specify allocation number here, because we know enough edges were created
    // before
    ErrorCode rval =
        _readNC->readMeshIface->get_element_connect( nEdges, 2, MBEDGE, 0, start_edge, conn_arr_gather_set_edges );MB_CHK_SET_ERR( rval, "Failed to create gather set edges" );

    // Add edges to the gather set
    Range gather_set_edges_range( start_edge, start_edge + nEdges - 1 );
    rval = mbImpl->add_entities( gather_set, gather_set_edges_range );MB_CHK_SET_ERR( rval, "Failed to add edges to the gather set" );

    // Read vertices on each edge
    int verticesOnEdgeVarId;
    int success = NCFUNC( inq_varid )( _fileId, "edge_corners", &verticesOnEdgeVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of edge_corners" );
    // Utilize the memory storage pointed by conn_arr_gather_set_edges
    int* vertices_on_gather_set_edges = (int*)conn_arr_gather_set_edges;
    NCDF_SIZE read_starts[2]          = { 0, 0 };
    NCDF_SIZE read_counts[2]          = { static_cast< NCDF_SIZE >( nEdges ), 2 };
#ifdef MOAB_HAVE_PNETCDF
    // Enter independent I/O mode, since this read is only for the gather processor
    success = NCFUNC( begin_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
    success =
        NCFUNCG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts, vertices_on_gather_set_edges );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data" );
    success = NCFUNC( end_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
    success =
        NCFUNCG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts, vertices_on_gather_set_edges );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data" );
#endif

    // Populate connectivity data for gather set edges
    // Convert in-place from int (stored in the first half) to EntityHandle
    // Reading backward is the trick
    for( int edge_vert = nEdges * 2 - 1; edge_vert >= 0; edge_vert-- )
    {
        // Note, indices stored in vertices_on_gather_set_edges are 0 based
        int gather_set_vert_idx = vertices_on_gather_set_edges[edge_vert];  // Global vertex index, 0 based
        // Connectivity array is shifted by where the gather set vertices start
        conn_arr_gather_set_edges[edge_vert] = gather_set_start_vertex + gather_set_vert_idx;
    }

    return MB_SUCCESS;
}

ErrorCode NCHelperGCRM::create_padded_gather_set_cells( EntityHandle gather_set, EntityHandle gather_set_start_vertex )
{
    Interface*& mbImpl = _readNC->mbImpl;

    // Create gather set cells
    EntityHandle start_element;
    EntityHandle* conn_arr_gather_set_cells = NULL;
    // Don't need to specify allocation number here, because we know enough cells were created
    // before
    ErrorCode rval = _readNC->readMeshIface->get_element_connect( nCells, EDGES_PER_CELL, MBPOLYGON, 0, start_element,
                                                                  conn_arr_gather_set_cells );MB_CHK_SET_ERR( rval, "Failed to create gather set cells" );

    // Add cells to the gather set
    Range gather_set_cells_range( start_element, start_element + nCells - 1 );
    rval = mbImpl->add_entities( gather_set, gather_set_cells_range );MB_CHK_SET_ERR( rval, "Failed to add cells to the gather set" );

    // Read vertices on each gather set cell (connectivity)
    int verticesOnCellVarId;
    int success = NCFUNC( inq_varid )( _fileId, "cell_corners", &verticesOnCellVarId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_corners" );
    // Utilize the memory storage pointed by conn_arr_gather_set_cells
    int* vertices_on_gather_set_cells = (int*)conn_arr_gather_set_cells;
    NCDF_SIZE read_starts[2]          = { 0, 0 };
    NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( nCells ), static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };
#ifdef MOAB_HAVE_PNETCDF
    // Enter independent I/O mode, since this read is only for the gather processor
    success = NCFUNC( begin_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
    success =
        NCFUNCG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts, vertices_on_gather_set_cells );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data" );
    success = NCFUNC( end_indep_data )( _fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
    success =
        NCFUNCG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts, vertices_on_gather_set_cells );
    if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data" );
#endif

    // Correct gather set cell vertices array in the same way as local cell vertices array
    // Pentagons as hexagons should have a connectivity like 123455 and not 122345
    for( int gather_set_cell_idx = 0; gather_set_cell_idx < nCells; gather_set_cell_idx++ )
    {
        int* pvertex = vertices_on_gather_set_cells + gather_set_cell_idx * EDGES_PER_CELL;
        for( int k = 0; k < EDGES_PER_CELL - 2; k++ )
        {
            if( *( pvertex + k ) == *( pvertex + k + 1 ) )
            {
                // Shift the connectivity
                for( int kk = k + 1; kk < EDGES_PER_CELL - 1; kk++ )
                    *( pvertex + kk ) = *( pvertex + kk + 1 );
                // No need to try next k
                break;
            }
        }
    }

    // Populate connectivity data for gather set cells
    // Convert in-place from int (stored in the first half) to EntityHandle
    // Reading backward is the trick
    for( int cell_vert = nCells * EDGES_PER_CELL - 1; cell_vert >= 0; cell_vert-- )
    {
        // Note, indices stored in vertices_on_gather_set_cells are 0 based
        int gather_set_vert_idx = vertices_on_gather_set_cells[cell_vert];  // Global vertex index, 0 based
        // Connectivity array is shifted by where the gather set vertices start
        conn_arr_gather_set_cells[cell_vert] = gather_set_start_vertex + gather_set_vert_idx;
    }

    return MB_SUCCESS;
}

}  // namespace moab