moab::NCWriteMPAS Class Reference

#include <NCWriteMPAS.hpp>

Inheritance diagram for moab::NCWriteMPAS:

Collaboration diagram for moab::NCWriteMPAS:

Public Member Functions
	NCWriteMPAS (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~NCWriteMPAS ()
Public Member Functions inherited from moab::UcdNCWriteHelper
	UcdNCWriteHelper (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~UcdNCWriteHelper ()
Public Member Functions inherited from moab::NCWriteHelper
	NCWriteHelper (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~NCWriteHelper ()
ErrorCode	init_file (std::vector< std::string > &var_names, std::vector< std::string > &desired_names, bool _append)
	Initialize file: this is where all defines are done The VarData dimension ids are filled up after define. More...
ErrorCode	write_values (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Take the info from VarData and write first non-set variables, then set variables. More...

Private Member Functions
virtual ErrorCode	collect_mesh_info ()
	Implementation of NCWriteHelper::collect_mesh_info() More...
virtual ErrorCode	collect_variable_data (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Collect data for specified variables. More...
virtual ErrorCode	write_nonset_variables (std::vector< WriteNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Implementation of NCWriteHelper::write_nonset_variables() More...

Additional Inherited Members
Static Public Member Functions inherited from moab::NCWriteHelper
static NCWriteHelper *	get_nc_helper (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
	Get appropriate helper instance for WriteNC class based on some info in the file set. More...
Protected Member Functions inherited from moab::UcdNCWriteHelper
template<typename T >
void	jik_to_kji_stride (size_t, size_t nj, size_t nk, T *dest, T *source, Range &localGid)
	This version takes as input the moab range, from which we actually need just the size of each sequence, for a proper transpose of the data. More...
Protected Attributes inherited from moab::UcdNCWriteHelper
int	cDim
	Dimension numbers for nCells, nEdges and nVertices. More...
int	eDim
int	vDim
Range	localGidCellsOwned
	Local global ID for owned cells, edges and vertices. More...
Range	localGidEdgesOwned
Range	localGidVertsOwned
Protected Attributes inherited from moab::NCWriteHelper
WriteNC *	_writeNC
	Allow NCWriteHelper to directly access members of WriteNC. More...
int	_fileId
	Cache some information from WriteNC. More...
const FileOptions &	_opts
EntityHandle	_fileSet
int	nTimeSteps
	Dimensions of time and level. More...
int	nLevels
int	tDim
	Dimension numbers for time and level. More...
int	levDim
Range	localCellsOwned
	Local owned cells, edges and vertices. More...
Range	localEdgesOwned
Range	localVertsOwned
std::vector< double >	timeStepVals
	Time values of output timesteps. More...

Detailed Description

Definition at line 17 of file NCWriteMPAS.hpp.

Constructor & Destructor Documentation

NCWriteMPAS()

moab::NCWriteMPAS::NCWriteMPAS ( WriteNC *  writeNC, int  fileId, const FileOptions &  opts, EntityHandle  fileSet  )

inline

Definition at line 20 of file NCWriteMPAS.hpp.

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

~NCWriteMPAS()

moab::NCWriteMPAS::~NCWriteMPAS ( )

virtual

Definition at line 13 of file NCWriteMPAS.cpp.

{
    // TODO Auto-generated destructor stub
}

Member Function Documentation

collect_mesh_info()

ErrorCode moab::NCWriteMPAS::collect_mesh_info ( )

privatevirtual

Implementation of NCWriteHelper::collect_mesh_info()

Implements moab::NCWriteHelper.

Definition at line 18 of file NCWriteMPAS.cpp.

{
    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(), "nVertLevels" ) ) != dimNames.end() )
        levDim = vecIt - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'nVertLevels' 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;
}

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.

collect_variable_data()

ErrorCode moab::NCWriteMPAS::collect_variable_data ( std::vector< std::string > &  var_names, std::vector< int > &  tstep_nums  )

privatevirtual

Collect data for specified variables.

Reimplemented from moab::NCWriteHelper.

Definition at line 113 of file NCWriteMPAS.cpp.

{
    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 vertex levels P1
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "nVertLevelsP1" ) ) != dimNames.end() )
    {
        lev_idx = vecIt - dimNames.begin();
        opt_lev_dims.push_back( lev_idx );
    }
 
    // Get index of vertex levels P2
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "nVertLevelsP2" ) ) != dimNames.end() )
    {
        lev_idx = vecIt - dimNames.begin();
        opt_lev_dims.push_back( lev_idx );
    }
 
    // Get index of soil levels
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "nSoilLevels" ) ) != 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 nVertLevels dimension is not found, try other optional levels such as nVertLevelsP1
        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, nCells, nVertLevels)
            // 2 dimensions like (Time, nCells)
            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 (nCells, nVertLevels)
            // 1 dimension like (nCells)
            assert( 2 == varDims.size() || 1 == varDims.size() );
        }
 
        // Next: nVertices / nCells / nEdges
        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: nVertLevels or other optional levels, it is possible that there is no
        // level dimension (numLev is 0) for this non-set variable, e.g. (Time, nCells)
        if( currentVarData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (Time, nCells, nVertLevels)
            // 2 dimensions like (nCells, nVertLevels)
            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, nCells)
            // 1 dimension like (nCells)
            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];
    }
 
    return MB_SUCCESS;
}

References moab::NCWriteHelper::_writeNC, moab::NCWriteHelper::collect_variable_data(), 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.

write_nonset_variables()

ErrorCode moab::NCWriteMPAS::write_nonset_variables ( std::vector< WriteNC::VarData > &  vdatas, std::vector< int > &  tstep_nums  )

privatevirtual

Implementation of NCWriteHelper::write_nonset_variables()

Implements moab::NCWriteHelper.

Definition at line 265 of file NCWriteMPAS.cpp.

{
    Interface*& mbImpl = _writeNC->mbImpl;
 
    int success;
 
    // For each variable tag in the indexed lists, 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, nCells, nVertLevels)
            // 2 dimensions like (Time, nCells)
            num_timesteps = tstep_nums.size();
            ents_idx++;
        }
        else
        {
            // Non-set variables without timesteps
            // 2 dimensions like (nCells, nVertLevels)
            // 1 dimension like (nCells)
            num_timesteps = 1;
        }
 
        unsigned int num_lev;
        if( variableData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (Time, nCells, nVertLevels)
            // 2 dimensions like (nCells, nVertLevels)
            num_lev = variableData.numLev;
        }
        else
        {
            // Non-set variables without levels
            // 2 dimensions like (Time, nCells)
            // 1 dimension like (nCells)
            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;
}

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(), 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.

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

• NCWriteMPAS.hpp
• NCWriteMPAS.cpp