NCWriteGCRM.cpp

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/*
 * NCWriteGCRM.cpp
 *
 *  Created on: April 9, 2014
 */
 
#include "NCWriteGCRM.hpp"
#include "MBTagConventions.hpp"
 
namespace moab
{
 
NCWriteGCRM::~NCWriteGCRM()
{
    // TODO Auto-generated destructor stub
}
 
ErrorCode NCWriteGCRM::collect_mesh_info()
{
    Interface*& mbImpl                   = _writeNC->mbImpl;
    std::vector< std::string >& dimNames = _writeNC->dimNames;
    std::vector< int >& dimLens          = _writeNC->dimLens;
    Tag& mGlobalIdTag                    = _writeNC->mGlobalIdTag;
 
    // Look for time dimension
    std::vector< std::string >::iterator vecIt;
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "Time" ) ) != dimNames.end() )
        tDim = vecIt - dimNames.begin();
    else if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "time" ) ) != dimNames.end() )
        tDim = vecIt - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'Time' or 'time' dimension" );
    }
    nTimeSteps = dimLens[tDim];
 
    // Get number of levels
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "layers" ) ) != dimNames.end() )
        levDim = vecIt - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' dimension" );
    }
    nLevels = dimLens[levDim];
 
    // Get local vertices
    MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 0, localVertsOwned ),
                    "Trouble getting local vertices in current file set" );
    assert( !localVertsOwned.empty() );
 
    // Get local edges
    MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 1, localEdgesOwned ),
                    "Trouble getting local edges in current file set" );
    // There are no edges if NO_EDGES read option is set
 
    // Get local cells
    MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 2, localCellsOwned ),
                    "Trouble getting local cells in current file set" );
    assert( !localCellsOwned.empty() );
 
#ifdef MOAB_HAVE_MPI
    bool& isParallel = _writeNC->isParallel;
    if( isParallel )
    {
        ParallelComm*& myPcomm = _writeNC->myPcomm;
        int rank               = myPcomm->proc_config().proc_rank();
        int procs              = myPcomm->proc_config().proc_size();
        if( procs > 1 )
        {
#ifndef NDEBUG
            unsigned int num_local_verts = localVertsOwned.size();
#endif
            MB_CHK_SET_ERR( myPcomm->filter_pstatus( localVertsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT ),
                            "Trouble getting owned vertices in current file set" );
 
            // Assume that PARALLEL_RESOLVE_SHARED_ENTS option is set
            // Verify that not all local vertices are owned by the last processor
            if( procs - 1 == rank )
                assert( "PARALLEL_RESOLVE_SHARED_ENTS option is set" && localVertsOwned.size() < num_local_verts );
 
            if( !localEdgesOwned.empty() )
            {
                MB_CHK_SET_ERR( myPcomm->filter_pstatus( localEdgesOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT ),
                                "Trouble getting owned edges in current file set" );
            }
 
            MB_CHK_SET_ERR( myPcomm->filter_pstatus( localCellsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT ),
                            "Trouble getting owned cells in current file set" );
        }
    }
#endif
 
    std::vector< int > gids( localVertsOwned.size() );
    MB_CHK_SET_ERR( mbImpl->tag_get_data( mGlobalIdTag, localVertsOwned, &gids[0] ),
                    "Trouble getting global IDs on local vertices" );
 
    // Get localGidVertsOwned
    std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidVertsOwned ) );
 
    if( !localEdgesOwned.empty() )
    {
        gids.resize( localEdgesOwned.size() );
        MB_CHK_SET_ERR( mbImpl->tag_get_data( mGlobalIdTag, localEdgesOwned, &gids[0] ),
                        "Trouble getting global IDs on local edges" );
 
        // Get localGidEdgesOwned
        std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidEdgesOwned ) );
    }
 
    gids.resize( localCellsOwned.size() );
    MB_CHK_SET_ERR( mbImpl->tag_get_data( mGlobalIdTag, localCellsOwned, &gids[0] ),
                    "Trouble getting global IDs on local cells" );
 
    // Get localGidCellsOwned
    std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidCellsOwned ) );
 
    return MB_SUCCESS;
}
 
ErrorCode NCWriteGCRM::collect_variable_data( std::vector< std::string >& var_names, std::vector< int >& tstep_nums )
{
    NCWriteHelper::collect_variable_data( var_names, tstep_nums );
 
    std::vector< std::string >& dimNames = _writeNC->dimNames;
    std::vector< int >& dimLens          = _writeNC->dimLens;
 
    // Dimension indices for other optional levels
    std::vector< unsigned int > opt_lev_dims;
 
    unsigned int lev_idx;
    std::vector< std::string >::iterator vecIt;
 
    // Get index of interface levels
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "interfaces" ) ) != dimNames.end() )
    {
        lev_idx = vecIt - dimNames.begin();
        opt_lev_dims.push_back( lev_idx );
    }
 
    std::map< std::string, WriteNC::VarData >& varInfo = _writeNC->varInfo;
 
    for( size_t i = 0; i < var_names.size(); i++ )
    {
        std::string varname                                     = var_names[i];
        std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( varname );
        if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find variable " << varname );
 
        WriteNC::VarData& currentVarData = vit->second;
        std::vector< int >& varDims      = currentVarData.varDims;
 
        // Skip edge variables, if there are no edges
        if( localEdgesOwned.empty() && currentVarData.entLoc == WriteNC::ENTLOCEDGE ) continue;
 
        // If layers dimension is not found, try other optional levels such as interfaces
        if( std::find( varDims.begin(), varDims.end(), levDim ) == varDims.end() )
        {
            for( unsigned int j = 0; j < opt_lev_dims.size(); j++ )
            {
                if( std::find( varDims.begin(), varDims.end(), opt_lev_dims[j] ) != varDims.end() )
                {
                    currentVarData.numLev = dimLens[opt_lev_dims[j]];
                    break;
                }
            }
        }
 
        // Skip set variables, which were already processed in
        // NCWriteHelper::collect_variable_data()
        if( WriteNC::ENTLOCSET == currentVarData.entLoc ) continue;
 
        // Set up writeStarts and writeCounts (maximum number of dimensions is 3)
        currentVarData.writeStarts.resize( 3 );
        currentVarData.writeCounts.resize( 3 );
        unsigned int dim_idx = 0;
 
        // First: time
        if( currentVarData.has_tsteps )
        {
            // Non-set variables with timesteps
            // 3 dimensions like (time, cells, layers)
            // 2 dimensions like (time, cells)
            assert( 3 == varDims.size() || 2 == varDims.size() );
 
            // Time should be the first dimension
            assert( tDim == varDims[0] );
 
            currentVarData.writeStarts[dim_idx] = 0;  // This value is timestep dependent, will be set later
            currentVarData.writeCounts[dim_idx] = 1;
            dim_idx++;
        }
        else
        {
            // Non-set variables without timesteps
            // 2 dimensions like (cells, layers)
            // 1 dimension like (cells)
            assert( 2 == varDims.size() || 1 == varDims.size() );
        }
 
        // Next: corners / cells / edges
        switch( currentVarData.entLoc )
        {
            case WriteNC::ENTLOCVERT:
                // Vertices
                // Start from the first localGidVerts
                // Actually, this will be reset later for writing
                currentVarData.writeStarts[dim_idx] = localGidVertsOwned[0] - 1;
                currentVarData.writeCounts[dim_idx] = localGidVertsOwned.size();
                break;
            case WriteNC::ENTLOCFACE:
                // Faces
                // Start from the first localGidCells
                // Actually, this will be reset later for writing
                currentVarData.writeStarts[dim_idx] = localGidCellsOwned[0] - 1;
                currentVarData.writeCounts[dim_idx] = localGidCellsOwned.size();
                break;
            case WriteNC::ENTLOCEDGE:
                // Edges
                // Start from the first localGidEdges
                // Actually, this will be reset later for writing
                currentVarData.writeStarts[dim_idx] = localGidEdgesOwned[0] - 1;
                currentVarData.writeCounts[dim_idx] = localGidEdgesOwned.size();
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << varname );
        }
        dim_idx++;
 
        // Finally: layers or other optional levels, it is possible that there is no
        // level dimension (numLev is 0) for this non-set variable
        if( currentVarData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (time, cells, layers)
            // 2 dimensions like (cells, layers)
            assert( 3 == varDims.size() || 2 == varDims.size() );
 
            currentVarData.writeStarts[dim_idx] = 0;
            currentVarData.writeCounts[dim_idx] = currentVarData.numLev;
            dim_idx++;
        }
        else
        {
            // Non-set variables without levels
            // 2 dimensions like (time, cells)
            // 1 dimension like (cells)
            assert( 2 == varDims.size() || 1 == varDims.size() );
        }
 
        // Get variable size
        currentVarData.sz = 1;
        for( std::size_t idx = 0; idx < dim_idx; idx++ )
            currentVarData.sz *= currentVarData.writeCounts[idx];
    }  // for (size_t i = 0; i < var_names.size(); i++)
 
    return MB_SUCCESS;
}
 
ErrorCode NCWriteGCRM::write_nonset_variables( std::vector< WriteNC::VarData >& vdatas, std::vector< int >& tstep_nums )
{
    Interface*& mbImpl = _writeNC->mbImpl;
 
    int success;
 
    // For each indexed variable tag, write a time step data
    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        WriteNC::VarData& variableData = vdatas[i];
 
        // Skip edge variables, if there are no edges
        if( localEdgesOwned.empty() && variableData.entLoc == WriteNC::ENTLOCEDGE ) continue;
 
        // Get local owned entities of this variable
        Range* pLocalEntsOwned    = NULL;
        Range* pLocalGidEntsOwned = NULL;
        switch( variableData.entLoc )
        {
            case WriteNC::ENTLOCVERT:
                // Vertices
                pLocalEntsOwned    = &localVertsOwned;
                pLocalGidEntsOwned = &localGidVertsOwned;
                break;
            case WriteNC::ENTLOCEDGE:
                // Edges
                pLocalEntsOwned    = &localEdgesOwned;
                pLocalGidEntsOwned = &localGidEdgesOwned;
                break;
            case WriteNC::ENTLOCFACE:
                // Cells
                pLocalEntsOwned    = &localCellsOwned;
                pLocalGidEntsOwned = &localGidCellsOwned;
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << variableData.varName );
        }
 
        unsigned int num_timesteps;
        unsigned int ents_idx = 0;
        if( variableData.has_tsteps )
        {
            // Non-set variables with timesteps
            // 3 dimensions like (time, cells, layers)
            // 2 dimensions like (time, cells)
            num_timesteps = tstep_nums.size();
            ents_idx++;
        }
        else
        {
            // Non-set variables without timesteps
            // 2 dimensions like (cells, layers)
            // 1 dimension like (cells)
            num_timesteps = 1;
        }
 
        unsigned int num_lev;
        if( variableData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (time, cells, layers)
            // 2 dimensions like (cells, layers)
            num_lev = variableData.numLev;
        }
        else
        {
            // Non-set variables without levels
            // 2 dimensions like (time, cells)
            // 1 dimension like (cells)
            num_lev = 1;
        }
 
        for( unsigned int t = 0; t < num_timesteps; t++ )
        {
            // We will write one time step, and count will be one; start will be different
            // Use tag_get_data instead of tag_iterate to copy tag data, as localEntsOwned
            // might not be contiguous.
            if( tDim == variableData.varDims[0] ) variableData.writeStarts[0] = t;  // This is start for time
            std::vector< double > tag_data( pLocalEntsOwned->size() * num_lev );
            MB_CHK_SET_ERR( mbImpl->tag_get_data( variableData.varTags[t], *pLocalEntsOwned, &tag_data[0] ),
                            "Trouble getting tag data on owned entities" );
 
#ifdef MOAB_HAVE_PNETCDF
            size_t nb_writes = pLocalGidEntsOwned->psize();
            std::vector< int > requests( nb_writes ), statuss( nb_writes );
            size_t idxReq = 0;
#endif
 
            // Now write copied tag data
            // Use nonblocking put (request aggregation)
            switch( variableData.varDataType )
            {
                case NC_DOUBLE: {
                    size_t indexInDoubleArray = 0;
                    size_t ic                 = 0;
                    for( Range::pair_iterator pair_iter = pLocalGidEntsOwned->pair_begin();
                         pair_iter != pLocalGidEntsOwned->pair_end(); ++pair_iter, ic++ )
                    {
                        EntityHandle starth                = pair_iter->first;
                        EntityHandle endh                  = pair_iter->second;
                        variableData.writeStarts[ents_idx] = (NCDF_SIZE)( starth - 1 );
                        variableData.writeCounts[ents_idx] = (NCDF_SIZE)( endh - starth + 1 );
 
                        // Do a partial write, in each subrange
#ifdef MOAB_HAVE_PNETCDF
                        // Wait outside this loop
                        success =
                            NCFUNCREQP( _vara_double )( _fileId, variableData.varId, &( variableData.writeStarts[0] ),
                                                        &( variableData.writeCounts[0] ),
                                                        &( tag_data[indexInDoubleArray] ), &requests[idxReq++] );
#else
                        success = NCFUNCAP(
                            _vara_double )( _fileId, variableData.varId, &( variableData.writeStarts[0] ),
                                            &( variableData.writeCounts[0] ), &( tag_data[indexInDoubleArray] ) );
#endif
                        if( success )
                            MB_SET_ERR( MB_FAILURE,
                                        "Failed to write double data in a loop for variable " << variableData.varName );
                        // We need to increment the index in double array for the
                        // next subrange
                        indexInDoubleArray += ( endh - starth + 1 ) * num_lev;
                    }
                    assert( ic == pLocalGidEntsOwned->psize() );
#ifdef MOAB_HAVE_PNETCDF
                    success = ncmpi_wait_all( _fileId, requests.size(), &requests[0], &statuss[0] );
                    if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
                    break;
                }
                default:
                    MB_SET_ERR( MB_NOT_IMPLEMENTED, "Writing non-double data is not implemented yet" );
            }
        }
    }
 
    return MB_SUCCESS;
}
 
} /* namespace moab */