Cppcheck report - MOAB: src/io/NCWriteHOMME.cpp

/*
 * NCWriteHOMME.cpp
 *
 *  Created on: April 9, 2014
 */

#include "NCWriteHOMME.hpp"
#include "MBTagConventions.hpp"

namespace moab
{

NCWriteHOMME::~NCWriteHOMME()
{
    // TODO Auto-generated destructor stub
}

ErrorCode NCWriteHOMME::collect_mesh_info()
{
    Interface*& mbImpl                   = _writeNC->mbImpl;
    std::vector< std::string >& dimNames = _writeNC->dimNames;
    std::vector< int >& dimLens          = _writeNC->dimLens;<--- Variable 'dimLens' can be declared with const
    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
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'time' dimension" );
    }
    nTimeSteps = dimLens[tDim];

    // Get number of levels
    if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "lev" ) ) != dimNames.end() )
        levDim = vecIt - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'lev' 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() );

#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 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 );
        }
    }
#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 ) );

    return MB_SUCCESS;
}

ErrorCode NCWriteHOMME::collect_variable_data( std::vector< std::string >& var_names, std::vector< int >& tstep_nums )
{
    NCWriteHelper::collect_variable_data( var_names, tstep_nums );

    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;
#ifndef NDEBUG
        std::vector< int >& varDims = currentVarData.varDims;
#endif

        // 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, lev, ncol)
            // 2 dimensions like (time, ncol)
            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 (lev, ncol)
            // 1 dimension like (ncol)
            assert( 2 == varDims.size() || 1 == varDims.size() );
        }

        // Next: lev
        if( currentVarData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (time, lev, ncol)
            // 2 dimensions like (lev, ncol)
            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, ncol)
            // 1 dimension like (ncol)
            assert( 2 == varDims.size() || 1 == varDims.size() );
        }

        // Finally: ncol
        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;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << varname );
        }
        dim_idx++;

        // Get variable size
        currentVarData.sz = 1;
        for( std::size_t idx = 0; idx < dim_idx; idx++ )
            currentVarData.sz *= currentVarData.writeCounts[idx];
    }

    return MB_SUCCESS;
}

ErrorCode NCWriteHOMME::write_nonset_variables( std::vector< WriteNC::VarData >& vdatas,
                                                std::vector< int >& tstep_nums )
{
    Interface*& mbImpl = _writeNC->mbImpl;

    int success;
    int num_local_verts_owned = localVertsOwned.size();

    // For each indexed variable tag, write a time step data
    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        WriteNC::VarData& variableData = vdatas[i];

        // Assume this variable is on vertices for the time being
        switch( variableData.entLoc )
        {
            case WriteNC::ENTLOCVERT:
                // Vertices
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << variableData.varName );
        }

        unsigned int num_timesteps;
        unsigned int ncol_idx = 0;
        if( variableData.has_tsteps )
        {
            // Non-set variables with timesteps
            // 3 dimensions like (time, lev, ncol)
            // 2 dimensions like (time, ncol)
            num_timesteps = tstep_nums.size();
            ncol_idx++;
        }
        else
        {
            // Non-set variables without timesteps
            // 2 dimensions like (lev, ncol)
            // 1 dimension like (ncol)
            num_timesteps = 1;
        }

        unsigned int num_lev;
        if( variableData.numLev > 0 )
        {
            // Non-set variables with levels
            // 3 dimensions like (time, lev, ncol)
            // 2 dimensions like (lev, ncol)
            num_lev = variableData.numLev;
            ncol_idx++;
        }
        else
        {
            // Non-set variables without levels
            // 2 dimensions like (time, ncol)
            // 1 dimension like (ncol)
            num_lev = 1;
        }

        // At each timestep, we need to transpose tag format (ncol, lev) back
        // to NC format (lev, ncol) for writing
        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 localVertsOwned
            // might not be contiguous. We should also transpose for level so that means
            // deep copy for transpose
            if( tDim == variableData.varDims[0] ) variableData.writeStarts[0] = t;  // This is start for time
            std::vector< double > tag_data( num_local_verts_owned * num_lev );
            ErrorCode rval = mbImpl->tag_get_data( variableData.varTags[t], localVertsOwned, &tag_data[0] );MB_CHK_SET_ERR( rval, "Trouble getting tag data on owned vertices" );

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

            // Now transpose and write copied tag data
            // Use nonblocking put (request aggregation)
            switch( variableData.varDataType )
            {
                case NC_DOUBLE: {
                    std::vector< double > tmpdoubledata( num_local_verts_owned * num_lev );
                    if( num_lev > 1 )
                    {
                        // Transpose (ncol, lev) back to (lev, ncol)
                        // Note, num_local_verts_owned is not used by jik_to_kji_stride()
                        jik_to_kji_stride( num_local_verts_owned, 1, num_lev, &tmpdoubledata[0], &tag_data[0],
                                           localGidVertsOwned );
                    }

                    size_t indexInDoubleArray = 0;
                    size_t ic                 = 0;
                    for( Range::pair_iterator pair_iter = localGidVertsOwned.pair_begin();
                         pair_iter != localGidVertsOwned.pair_end(); ++pair_iter, ic++ )
                    {
                        EntityHandle starth                = pair_iter->first;
                        EntityHandle endh                  = pair_iter->second;
                        variableData.writeStarts[ncol_idx] = (NCDF_SIZE)( starth - 1 );
                        variableData.writeCounts[ncol_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] ),
                                                        &( tmpdoubledata[indexInDoubleArray] ), &requests[idxReq++] );
#else
                        success = NCFUNCAP(
                            _vara_double )( _fileId, variableData.varId, &( variableData.writeStarts[0] ),
                                            &( variableData.writeCounts[0] ), &( tmpdoubledata[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 == localGidVertsOwned.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 */