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 ()
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 NCWriteGCRM.hpp.

Constructor & Destructor Documentation

NCWriteGCRM()

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 )
 {
 }

~NCWriteGCRM()

moab::NCWriteGCRM::~NCWriteGCRM ( )

virtual

Definition at line 13 of file NCWriteGCRM.cpp.

{
 // TODO Auto-generated destructor stub
}

Member Function Documentation

collect_mesh_info()

ErrorCode moab::NCWriteGCRM::collect_mesh_info ( )

privatevirtual

Implementation of NCWriteHelper::collect_mesh_info()

Implements moab::NCWriteHelper.

Definition at line 18 of file NCWriteGCRM.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(), "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;
}

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::NCWriteGCRM::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 NCWriteGCRM.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 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;
}

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::NCWriteGCRM::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 251 of file NCWriteGCRM.cpp.

{
 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;
}

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.

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

• NCWriteGCRM.hpp
• NCWriteGCRM.cpp