moab::NCWriteGCRM Class Reference

#include <NCWriteGCRM.hpp>

Inheritance diagram for moab::NCWriteGCRM:

Collaboration diagram for moab::NCWriteGCRM:

Public Member Functions
	NCWriteGCRM (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~NCWriteGCRM ()
Private Member Functions
virtual ErrorCode	collect_mesh_info ()
	Implementation of NCWriteHelper::collect_mesh_info()
virtual ErrorCode	collect_variable_data (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Collect data for specified variables.
virtual ErrorCode	write_nonset_variables (std::vector< WriteNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Implementation of NCWriteHelper::write_nonset_variables()

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Detailed Description

Definition at line 17 of file NCWriteGCRM.hpp.

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Constructor & Destructor Documentation

moab::NCWriteGCRM::NCWriteGCRM	(	WriteNC *	writeNC,
		int	fileId,
		const FileOptions &	opts,
		EntityHandle	fileSet
	)		[inline]

Definition at line 20 of file NCWriteGCRM.hpp.

        : UcdNCWriteHelper( writeNC, fileId, opts, fileSet )
    {
    }

moab::NCWriteGCRM::~NCWriteGCRM

(

)

[virtual]

Definition at line 13 of file NCWriteGCRM.cpp.

{
    // TODO Auto-generated destructor stub
}

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Member Function Documentation

ErrorCode moab::NCWriteGCRM::collect_mesh_info

(

)

[private, virtual]

Implementation of NCWriteHelper::collect_mesh_info()

Implements moab::NCWriteHelper.

Definition at line 18 of file NCWriteGCRM.cpp.

References moab::NCWriteHelper::_fileSet, moab::NCWriteHelper::_writeNC, moab::WriteNC::dimLens, moab::WriteNC::dimNames, moab::Range::empty(), ErrorCode, moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_dimension(), moab::WriteNC::isParallel, moab::NCWriteHelper::levDim, moab::NCWriteHelper::localCellsOwned, moab::NCWriteHelper::localEdgesOwned, moab::UcdNCWriteHelper::localGidCellsOwned, moab::UcdNCWriteHelper::localGidEdgesOwned, moab::UcdNCWriteHelper::localGidVertsOwned, moab::NCWriteHelper::localVertsOwned, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, moab::WriteNC::mbImpl, moab::WriteNC::mGlobalIdTag, moab::NCWriteHelper::nLevels, moab::NCWriteHelper::nTimeSteps, moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ProcConfig::proc_size(), PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::Range::size(), moab::Interface::tag_get_data(), and moab::NCWriteHelper::tDim.

{
    Interface*& mbImpl                   = _writeNC->mbImpl;
    std::vector< std::string >& dimNames = _writeNC->dimNames;
    std::vector< int >& dimLens          = _writeNC->dimLens;
    Tag& mGlobalIdTag                    = _writeNC->mGlobalIdTag;

    ErrorCode rval;

    // 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
    rval = mbImpl->get_entities_by_dimension( _fileSet, 0, localVertsOwned );MB_CHK_SET_ERR( rval, "Trouble getting local vertices in current file set" );
    assert( !localVertsOwned.empty() );

    // Get local edges
    rval = mbImpl->get_entities_by_dimension( _fileSet, 1, localEdgesOwned );MB_CHK_SET_ERR( rval, "Trouble getting local edges in current file set" );
    // There are no edges if NO_EDGES read option is set

    // Get local cells
    rval = mbImpl->get_entities_by_dimension( _fileSet, 2, localCellsOwned );MB_CHK_SET_ERR( rval, "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
            rval = myPcomm->filter_pstatus( localVertsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "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() )
            {
                rval = myPcomm->filter_pstatus( localEdgesOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Trouble getting owned edges in current file set" );
            }

            rval = myPcomm->filter_pstatus( localCellsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Trouble getting owned cells in current file set" );
        }
    }
#endif

    std::vector< int > gids( localVertsOwned.size() );
    rval = mbImpl->tag_get_data( mGlobalIdTag, localVertsOwned, &gids[0] );MB_CHK_SET_ERR( rval, "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() );
        rval = mbImpl->tag_get_data( mGlobalIdTag, localEdgesOwned, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting global IDs on local edges" );

        // Get localGidEdgesOwned
        std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidEdgesOwned ) );
    }

    gids.resize( localCellsOwned.size() );
    rval = mbImpl->tag_get_data( mGlobalIdTag, localCellsOwned, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting global IDs on local cells" );

    // Get localGidCellsOwned
    std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidCellsOwned ) );

    return MB_SUCCESS;
}

ErrorCode moab::NCWriteGCRM::collect_variable_data	(	std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums
	)		[private, virtual]

Collect data for specified variables.

Reimplemented from moab::NCWriteHelper.

Definition at line 113 of file NCWriteGCRM.cpp.

References moab::NCWriteHelper::_writeNC, moab::WriteNC::dimLens, moab::WriteNC::dimNames, moab::Range::empty(), moab::WriteNC::VarData::entLoc, moab::WriteNC::ENTLOCEDGE, moab::WriteNC::ENTLOCFACE, moab::WriteNC::ENTLOCSET, moab::WriteNC::ENTLOCVERT, moab::WriteNC::VarData::has_tsteps, moab::NCWriteHelper::levDim, moab::NCWriteHelper::localEdgesOwned, moab::UcdNCWriteHelper::localGidCellsOwned, moab::UcdNCWriteHelper::localGidEdgesOwned, moab::UcdNCWriteHelper::localGidVertsOwned, MB_SET_ERR, MB_SUCCESS, moab::WriteNC::VarData::numLev, moab::Range::size(), moab::WriteNC::VarData::sz, moab::NCWriteHelper::tDim, moab::WriteNC::VarData::varDims, moab::WriteNC::varInfo, moab::WriteNC::VarData::writeCounts, and moab::WriteNC::VarData::writeStarts.

{
    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 moab::NCWriteGCRM::write_nonset_variables	(	std::vector< WriteNC::VarData > &	vdatas,
		std::vector< int > &	tstep_nums
	)		[private, virtual]

Implementation of NCWriteHelper::write_nonset_variables()

Implements moab::NCWriteHelper.

Definition at line 251 of file NCWriteGCRM.cpp.

References moab::NCWriteHelper::_fileId, moab::NCWriteHelper::_writeNC, moab::Range::empty(), moab::WriteNC::VarData::entLoc, moab::WriteNC::ENTLOCEDGE, moab::WriteNC::ENTLOCFACE, moab::WriteNC::ENTLOCVERT, ErrorCode, moab::WriteNC::VarData::has_tsteps, moab::NCWriteHelper::localCellsOwned, moab::NCWriteHelper::localEdgesOwned, moab::UcdNCWriteHelper::localGidCellsOwned, moab::UcdNCWriteHelper::localGidEdgesOwned, moab::UcdNCWriteHelper::localGidVertsOwned, moab::NCWriteHelper::localVertsOwned, MB_CHK_SET_ERR, MB_NOT_IMPLEMENTED, MB_SET_ERR, MB_SUCCESS, moab::WriteNC::mbImpl, NCDF_SIZE, NCFUNCAP, moab::WriteNC::VarData::numLev, moab::Range::pair_begin(), moab::Range::pair_end(), moab::Range::psize(), moab::Range::size(), t, moab::Interface::tag_get_data(), moab::NCWriteHelper::tDim, moab::WriteNC::VarData::varDataType, moab::WriteNC::VarData::varDims, moab::WriteNC::VarData::varId, moab::WriteNC::VarData::varName, moab::WriteNC::VarData::varTags, moab::WriteNC::VarData::writeCounts, and moab::WriteNC::VarData::writeStarts.

{
    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 );
            ErrorCode rval = mbImpl->tag_get_data( variableData.varTags[t], *pLocalEntsOwned, &tag_data[0] );MB_CHK_SET_ERR( rval, "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;
}

List of all members.

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The documentation for this class was generated from the following files:

• NCWriteGCRM.hpp
• NCWriteGCRM.cpp