NCWriteHOMME.cpp

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/*
 * 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;
 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 */