#include <NCWriteHelper.hpp>

Inheritance diagram for moab::NCWriteHelper:

Collaboration diagram for moab::NCWriteHelper:

Public Member Functions
	NCWriteHelper (WriteNC *writeNC, int fileId, const FileOptions &opts, EntityHandle fileSet)

virtual	~NCWriteHelper ()

virtual ErrorCode	collect_mesh_info ()=0
	Collect necessary info about local mesh (implemented in child classes) More...

virtual ErrorCode	collect_variable_data (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Collect data for specified variables (partially implemented in child classes) More...

virtual 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. Virtual so that grid-output writers (NCWriteScrip / NCWriteESMF / NCWriteDomain) can synthesize a fresh schema from mesh state instead of going through the climate var_names plumbing. More...

virtual 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. Virtual for the same reason as init_file. More...

Static Public Member Functions
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
virtual ErrorCode	write_nonset_variables (std::vector< WriteNC::VarData > &vdatas, std::vector< int > &tstep_nums)=0

Protected Attributes
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...

Private Member Functions
ErrorCode	write_set_variables (std::vector< WriteNC::VarData > &vsetdatas, std::vector< int > &tstep_nums)

Detailed Description

Definition at line 22 of file NCWriteHelper.hpp.

Constructor & Destructor Documentation

◆ NCWriteHelper()

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

inline

Definition at line 25 of file NCWriteHelper.hpp.

         : _writeNC( writeNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
           tDim( -1 ), levDim( -1 )
     {
     }

◆ ~NCWriteHelper()

virtual moab::NCWriteHelper::~NCWriteHelper ( )

inlinevirtual

Definition at line 30 of file NCWriteHelper.hpp.

30 {};

Member Function Documentation

◆ collect_mesh_info()

virtual ErrorCode moab::NCWriteHelper::collect_mesh_info ( )

pure virtual

Collect necessary info about local mesh (implemented in child classes)

Implemented in moab::NCWriteScrip, moab::ScdNCWriteHelper, moab::NCWriteESMF, moab::NCWriteDomain, moab::NCWriteMPAS, moab::NCWriteHOMME, and moab::NCWriteGCRM.

Referenced by moab::WriteNC::write_file().

◆ collect_variable_data()

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

virtual

Collect data for specified variables (partially implemented in child classes)

Reimplemented in moab::ScdNCWriteHelper, moab::NCWriteMPAS, moab::NCWriteHOMME, and moab::NCWriteGCRM.

Definition at line 60 of file NCWriteHelper.cpp.

 {
     Interface*& mbImpl                                 = _writeNC->mbImpl;
     std::vector< std::string >& dimNames               = _writeNC->dimNames;
     std::vector< int >& dimLens                        = _writeNC->dimLens;
     std::set< std::string >& usedCoordinates           = _writeNC->usedCoordinates;
     std::set< std::string >& dummyVarNames             = _writeNC->dummyVarNames;
     std::map< std::string, WriteNC::VarData >& varInfo = _writeNC->varInfo;
     DebugOutput& dbgOut                                = _writeNC->dbgOut;
  
     usedCoordinates.clear();
     if( tstep_nums.empty() && nTimeSteps > 0 )
     {
         // No timesteps input, get them all
         for( int i = 0; i < nTimeSteps; i++ )
             tstep_nums.push_back( i );
     }
  
     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;
  
         dbgOut.tprintf( 2, "    for variable %s varDims.size %d \n", varname.c_str(),
                         (int)currentVarData.varDims.size() );
         for( size_t j = 0; j < currentVarData.varDims.size(); j++ )
         {
             std::string dimName = dimNames[currentVarData.varDims[j]];
             vit                 = varInfo.find( dimName );
             if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find coordinate variable " << dimName );
  
             usedCoordinates.insert( dimName );  // Collect those used, we will need to write them to the file
             dbgOut.tprintf( 2, "    for variable %s need dimension %s with length %d\n", varname.c_str(),
                             dimName.c_str(), dimLens[currentVarData.varDims[j]] );
         }
  
         // Process coordinate variables later
         if( usedCoordinates.find( varname ) != usedCoordinates.end() ) continue;
  
         // Default has_tsteps is false
         if( std::find( currentVarData.varDims.begin(), currentVarData.varDims.end(), tDim ) !=
             currentVarData.varDims.end() )
             currentVarData.has_tsteps = true;
  
         // Default numLev is 0
         if( ( std::find( currentVarData.varDims.begin(), currentVarData.varDims.end(), levDim ) !=
               currentVarData.varDims.end() ) )
             currentVarData.numLev = nLevels;
  
         // Process set variables
         if( WriteNC::ENTLOCSET == currentVarData.entLoc )
         {
             if( currentVarData.has_tsteps )
             {
                 // Set variables with timesteps, e.g. xtime(Time) or xtime(Time, StrLen)
                 // TBD
                 MB_SET_ERR( MB_NOT_IMPLEMENTED, "Writing set variables with timesteps is not implemented yet" );
             }
             else
             {
                 // Get the tag with varname
                 Tag tag = 0;
                 MB_CHK_SET_ERR( mbImpl->tag_get_handle( varname.c_str(), tag ), "Can't find tag " << varname );
                 currentVarData.varTags.push_back( tag );  // Really, only one for these
                 const void* data;
                 int size;
                 MB_CHK_SET_ERR( mbImpl->tag_get_by_ptr( tag, &_fileSet, 1, &data, &size ),
                                 "Can't get data of tag " << varname );
  
                 // Find the type of tag, and use it
                 DataType type;
                 MB_CHK_SET_ERR( mbImpl->tag_get_data_type( tag, type ), "Can't get data type of tag " << varname );
  
                 currentVarData.varDataType = NC_DOUBLE;
                 if( MB_TYPE_INTEGER == type ) currentVarData.varDataType = NC_INT;
  
                 assert( 0 == currentVarData.memoryHogs.size() );  // Nothing so far
                 currentVarData.memoryHogs.push_back( (void*)data );
  
                 if( currentVarData.varDims.empty() )
                 {
                     // Scalar variable
                     currentVarData.writeStarts.push_back( 0 );
                     currentVarData.writeCounts.push_back( 1 );
                 }
                 else
                 {
                     for( size_t j = 0; j < currentVarData.varDims.size(); j++ )
                     {
                         currentVarData.writeStarts.push_back( 0 );
                         currentVarData.writeCounts.push_back( dimLens[currentVarData.varDims[j]] );
                     }
                 }
  
                 // Get variable size
                 currentVarData.sz = 1;
                 for( std::size_t idx = 0; idx != currentVarData.writeCounts.size(); idx++ )
                     currentVarData.sz *= currentVarData.writeCounts[idx];
             }
         }  // if (WriteNC::ENTLOCSET == currentVarData.entLoc)
         // Process non-set variables
         else
         {
             Tag indexedTag = 0;
  
             if( currentVarData.has_tsteps )
             {
                 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
                 {
                     std::stringstream ssTagNameWithIndex;
                     ssTagNameWithIndex << varname << tstep_nums[t];
                     MB_CHK_SET_ERR( mbImpl->tag_get_handle( ssTagNameWithIndex.str().c_str(), indexedTag ),
                                     "Can't find tag " << ssTagNameWithIndex.str() );
                     dbgOut.tprintf( 2, "    found indexed tag %d with name %s\n", tstep_nums[t],
                                     ssTagNameWithIndex.str().c_str() );
                     currentVarData.varTags.push_back( indexedTag );
                 }
             }
             else
             {
                 // This should be a user-created non-set variable without timesteps
                 // Treat it like having one, 0th, timestep
                 std::stringstream ssTagNameWithIndex;
                 ssTagNameWithIndex << varname << 0;
                 MB_CHK_SET_ERR( mbImpl->tag_get_handle( ssTagNameWithIndex.str().c_str(), indexedTag ),
                                 "Can't find tag " << ssTagNameWithIndex.str() << " for a user-created variable" );
                 dbgOut.tprintf( 2, "    found indexed tag 0 with name %s\n", ssTagNameWithIndex.str().c_str() );
                 currentVarData.varTags.push_back( indexedTag );
             }
  
             // The type of the tag is fixed though
             DataType type;
             MB_CHK_SET_ERR( mbImpl->tag_get_data_type( indexedTag, type ), "Can't get data type of tag " << varname );
  
             currentVarData.varDataType = NC_DOUBLE;
             if( MB_TYPE_INTEGER == type ) currentVarData.varDataType = NC_INT;
         }
     }  // for (size_t i = 0; i < var_names.size(); i++)
  
     // Process coordinate variables here
     // Check that for used coordinates we have found the tags
     for( std::set< std::string >::iterator setIt = usedCoordinates.begin(); setIt != usedCoordinates.end(); ++setIt )
     {
         const std::string& coordName = *setIt;
  
         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( coordName );
         if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find coordinate variable " << coordName );
  
         WriteNC::VarData& varCoordData = vit->second;
         Tag coordTag                   = 0;
         MB_CHK_SET_ERR( mbImpl->tag_get_handle( coordName.c_str(), coordTag ), "Can't find tag " << coordName );
         varCoordData.varTags.push_back( coordTag );  // Really, only one for these
  
         const void* data;
         int sizeCoordinate;
         MB_CHK_SET_ERR( mbImpl->tag_get_by_ptr( coordTag, &_fileSet, 1, &data, &sizeCoordinate ),
                         "Can't get coordinate values of " << coordName );
         dbgOut.tprintf( 2, "    found coordinate tag with name %s and length %d\n", coordName.c_str(), sizeCoordinate );
  
         // Find the type of tag, and use it
         DataType type;
         MB_CHK_SET_ERR( mbImpl->tag_get_data_type( coordTag, type ), "Can't get data type of tag " << coordName );
         varCoordData.varDataType = NC_DOUBLE;
         if( MB_TYPE_INTEGER == type ) varCoordData.varDataType = NC_INT;
  
         // Get dimension length (the only dimension of this coordinate variable, with the same name)
         assert( 1 == varCoordData.varDims.size() );
         int coordDimLen = dimLens[varCoordData.varDims[0]];
  
         if( dummyVarNames.find( coordName ) != dummyVarNames.end() )
         {
             // For a dummy coordinate variable, the tag size is always 1
             // The number of coordinates should be set to dimension length, instead of 1
             assert( 1 == sizeCoordinate );
             sizeCoordinate = coordDimLen;
  
             // No variable data to write
             data = NULL;
         }
         else
         {
             // The number of coordinates should be exactly the same as dimension length
             // However, if timesteps spread across files and time tag has been updated,
             // sizeCoordinate will be larger
             if( varCoordData.varDims[0] != tDim ) assert( sizeCoordinate == coordDimLen );
         }
  
         // For time, the actual output size and values are determined by tstep_nums
         if( varCoordData.varDims[0] == tDim )
         {
             // Does not apply to dummy time tag (e.g. 'Time' tag of MPAS), when timesteps
             // spread across files
             if( NULL != data ) assert( tstep_nums.size() > 0 && tstep_nums.size() <= (size_t)sizeCoordinate );
  
             sizeCoordinate = tstep_nums.size();
  
             if( NULL != data )
             {
                 assert( NC_DOUBLE == varCoordData.varDataType );
                 timeStepVals.resize( sizeCoordinate );
                 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
                     timeStepVals[t] = ( (double*)data )[tstep_nums[t]];
  
                 data = &timeStepVals[0];
             }
         }
  
         // This is the length
         varCoordData.sz = sizeCoordinate;
         varCoordData.writeStarts.resize( 1 );
         varCoordData.writeStarts[0] = 0;
         varCoordData.writeCounts.resize( 1 );
         varCoordData.writeCounts[0] = sizeCoordinate;
  
         assert( 0 == varCoordData.memoryHogs.size() );  // Nothing so far
         varCoordData.memoryHogs.push_back( (void*)data );
     }  // for (std::set<std::string>::iterator setIt ...
  
     return MB_SUCCESS;
 }

Referenced by moab::NCWriteGCRM::collect_variable_data(), moab::NCWriteHOMME::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::ScdNCWriteHelper::collect_variable_data(), and moab::WriteNC::write_file().

◆ get_nc_helper()

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

static

Get appropriate helper instance for WriteNC class based on some info in the file set.

Get appropriate helper instance for WriteNC class; based on some info in the file set.

Definition at line 33 of file NCWriteHelper.cpp.

 {
     std::string& grid_type = writeNC->grid_type;
     if( grid_type == "CAM_EUL" )
         return new( std::nothrow ) NCWriteEuler( writeNC, fileId, opts, fileSet );
     else if( grid_type == "CAM_FV" )
         return new( std::nothrow ) NCWriteFV( writeNC, fileId, opts, fileSet );
     else if( grid_type == "CAM_SE" )
         return new( std::nothrow ) NCWriteHOMME( writeNC, fileId, opts, fileSet );
     else if( grid_type == "MPAS" )
         return new( std::nothrow ) NCWriteMPAS( writeNC, fileId, opts, fileSet );
     else if( grid_type == "GCRM" )
         return new( std::nothrow ) NCWriteGCRM( writeNC, fileId, opts, fileSet );
     else if( grid_type == "SCRIP" )
         return new( std::nothrow ) NCWriteScrip( writeNC, fileId, opts, fileSet );
     else if( grid_type == "ESMF" )
         return new( std::nothrow ) NCWriteESMF( writeNC, fileId, opts, fileSet );
     else if( grid_type == "DOMAIN" )
         return new( std::nothrow ) NCWriteDomain( writeNC, fileId, opts, fileSet );
  
     // Unknown NetCDF grid
     return NULL;
 }

References moab::WriteNC::grid_type.

Referenced by moab::WriteNC::write_file().

◆ init_file()

ErrorCode moab::NCWriteHelper::init_file	(	std::vector< std::string > &	var_names,
		std::vector< std::string > &	desired_names,
		bool	_append
	)

virtual

Initialize file: this is where all defines are done. Virtual so that grid-output writers (NCWriteScrip / NCWriteESMF / NCWriteDomain) can synthesize a fresh schema from mesh state instead of going through the climate var_names plumbing.

Reimplemented in moab::NCWriteScrip, moab::NCWriteESMF, and moab::NCWriteDomain.

Definition at line 284 of file NCWriteHelper.cpp.

 {
     std::vector< std::string >& dimNames                  = _writeNC->dimNames;
     std::set< std::string >& usedCoordinates              = _writeNC->usedCoordinates;
     std::set< std::string >& dummyVarNames                = _writeNC->dummyVarNames;
     std::map< std::string, WriteNC::VarData >& varInfo    = _writeNC->varInfo;
     std::map< std::string, WriteNC::AttData >& globalAtts = _writeNC->globalAtts;
     DebugOutput& dbgOut                                   = _writeNC->dbgOut;
  
     int tDim_in_dimNames   = tDim;
     int levDim_in_dimNames = levDim;
  
     // If append mode, make sure we are in define mode; a simple open will not allow creation of new
     // variables
     if( append )
     {
         int errcode = NCFUNC( redef )( _fileId );
         if( errcode != NC_NOERR ) MB_SET_ERR( MB_FAILURE, "Can't open file in redefine mode" );
     }
  
     // First initialize all coordinates, then fill VarData for actual variables (and dimensions)
     // Check that for used coordinates we have found the tags
     for( std::set< std::string >::iterator setIt = usedCoordinates.begin(); setIt != usedCoordinates.end(); ++setIt )
     {
         const std::string& coordName = *setIt;
  
         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( coordName );
         if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find coordinate variable " << coordName );
  
         WriteNC::VarData& varCoordData = vit->second;
         varCoordData.varDims.resize( 1 );
  
         // If not append, create it for sure
         // If append, we might already have it, including the tag / variable with the same name
         /*
          * int ncmpi_inq_dimid(int ncid, const char *name, int *idp);
          */
         if( append )
         {
             int dimId;
             if( NCFUNC( inq_dimid )( _fileId, coordName.c_str(), &dimId ) == NC_NOERR )
             {  // If not found, create it later
                 varCoordData.varDims[0] = dimId;
                 dbgOut.tprintf( 2, "    file already has coordName %s dim id is %d \n", coordName.c_str(),
                                 (int)varCoordData.varDims[0] );
  
                 // Update tDim and levDim to actual dimension id
                 if( coordName == dimNames[tDim_in_dimNames] )
                     tDim = varCoordData.varDims[0];
                 else if( coordName == dimNames[levDim_in_dimNames] )
                     levDim = varCoordData.varDims[0];
  
                 // Skip dummy coordinate variables (e.g. ncol)
                 if( dummyVarNames.find( coordName ) != dummyVarNames.end() ) continue;
  
                 // Check that the coordinate is a variable too
                 // Inquire for a variable with the same name
                 int varId;
                 if( NCFUNC( inq_varid )( _fileId, coordName.c_str(), &varId ) != NC_NOERR )
                     MB_SET_ERR( MB_FAILURE, "We do not have a variable with the same name " << coordName );
                 // We should also check that this variable has one dimension, and it is dimId
                 varCoordData.varId = varId;
                 dbgOut.tprintf( 2, "    file already has coordinate %s and varId is %d \n", coordName.c_str(), varId );
  
                 continue;  // Maybe more checks are needed here
             }
         }
  
         /* int nc_def_dim (int ncid, const char *name, size_t len, int *dimidp);
          * example:  status = nc_def_dim(fileId, "lat", 18L, &latid);
          */
  
         // Actually define a dimension
         if( NCFUNC( def_dim )( _fileId, coordName.c_str(), (size_t)varCoordData.sz, &varCoordData.varDims[0] ) !=
             NC_NOERR )
             MB_SET_ERR( MB_FAILURE, "Failed to generate dimension " << coordName );
         dbgOut.tprintf( 2, "    for coordName %s dim id is %d \n", coordName.c_str(), (int)varCoordData.varDims[0] );
  
         // Update tDim and levDim to actual dimension id
         if( coordName == dimNames[tDim_in_dimNames] )
             tDim = varCoordData.varDims[0];
         else if( coordName == dimNames[levDim_in_dimNames] )
             levDim = varCoordData.varDims[0];
  
         // Create a variable with the same name, and its only dimension the one we just defined
         /*
          * int nc_def_var (int ncid, const char *name, nc_type xtype,
                            int ndims, const int dimids[], int *varidp);
            example:
          http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-c/nc_005fdef_005fvar.html#nc_005fdef_005fvar
          */
  
         // Skip dummy coordinate variables (e.g. ncol)
         if( dummyVarNames.find( coordName ) != dummyVarNames.end() ) continue;
  
         // Define a coordinate variable
         if( NCFUNC( def_var )( _fileId, coordName.c_str(), varCoordData.varDataType, 1, &( varCoordData.varDims[0] ),
                                &varCoordData.varId ) != NC_NOERR )
             MB_SET_ERR( MB_FAILURE, "Failed to create coordinate variable " << coordName );
  
         dbgOut.tprintf( 2, "    for coordName %s variable id is %d \n", coordName.c_str(), varCoordData.varId );
     }
  
     // Now look at requested variables, and update from the index in dimNames to the actual
     // dimension id
     for( size_t i = 0; i < var_names.size(); i++ )
     {
         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( var_names[i] );
         if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find requested variable " << var_names[i] );
  
         // Skip coordinate variables
         if( usedCoordinates.find( var_names[i] ) != usedCoordinates.end() ) continue;
  
         WriteNC::VarData& variableData = vit->second;
  
         // The index is for dimNames; we need to find out the actual dimension id (from above)
         int numDims = (int)variableData.varDims.size();
         for( int j = 0; j < numDims; j++ )
         {
             std::string dimName                                      = dimNames[variableData.varDims[j]];
             std::map< std::string, WriteNC::VarData >::iterator vit2 = varInfo.find( dimName );
             if( vit2 == varInfo.end() )
                 MB_SET_ERR( MB_FAILURE, "Can't find requested coordinate variable " << dimName );
  
             WriteNC::VarData& coordData = vit2->second;
             // Index in dimNames to actual dimension id
             variableData.varDims[j] = coordData.varDims[0];  // This one, being a coordinate, is the only one
             dbgOut.tprintf( 2, "          dimension with index %d name %s has ID %d \n", j, dimName.c_str(),
                             variableData.varDims[j] );
         }
  
         // Define the variable now:
         int errCode =
             NCFUNC( def_var )( _fileId, desired_names[i].c_str(), variableData.varDataType,
                                (int)variableData.varDims.size(), &( variableData.varDims[0] ), &variableData.varId );
         if( errCode != NC_NOERR ) MB_SET_ERR( MB_FAILURE, "Failed to create requested variable " << desired_names[i] );
  
         dbgOut.tprintf( 2, "    for variable %s with desired name %s variable id is %d \n", var_names[i].c_str(),
                         desired_names[i].c_str(), variableData.varId );
         // Now define the variable, with all dimensions
     }
  
     // Define global attributes (exactly copied from the original file for the time being)
     // Should we modify some of them (e.g. revision_Id) later?
     std::map< std::string, WriteNC::AttData >::iterator attIt;
     for( attIt = globalAtts.begin(); attIt != globalAtts.end(); ++attIt )
     {
         const std::string& attName  = attIt->first;
         WriteNC::AttData& attData   = attIt->second;
         NCDF_SIZE& attLen           = attData.attLen;
         nc_type& attDataType        = attData.attDataType;
         const std::string& attValue = attData.attValue;
  
         switch( attDataType )
         {
             case NC_BYTE:
             case NC_CHAR:
                 if( NC_NOERR !=
                     NCFUNC( put_att_text )( _fileId, NC_GLOBAL, attName.c_str(), attLen, attValue.c_str() ) )
                     MB_SET_ERR( MB_FAILURE, "Failed to define text type attribute" );
                 break;
             case NC_DOUBLE:
                 if( NC_NOERR != NCFUNC( put_att_double )( _fileId, NC_GLOBAL, attName.c_str(), NC_DOUBLE, 1,
                                                           (double*)attValue.c_str() ) )
                     MB_SET_ERR( MB_FAILURE, "Failed to define double type attribute" );
                 break;
             case NC_FLOAT:
                 if( NC_NOERR != NCFUNC( put_att_float )( _fileId, NC_GLOBAL, attName.c_str(), NC_FLOAT, 1,
                                                          (float*)attValue.c_str() ) )
                     MB_SET_ERR( MB_FAILURE, "Failed to define float type attribute" );
                 break;
             case NC_INT:
                 if( NC_NOERR !=
                     NCFUNC( put_att_int )( _fileId, NC_GLOBAL, attName.c_str(), NC_INT, 1, (int*)attValue.c_str() ) )
                     MB_SET_ERR( MB_FAILURE, "Failed to define int type attribute" );
                 break;
             case NC_SHORT:
                 if( NC_NOERR != NCFUNC( put_att_short )( _fileId, NC_GLOBAL, attName.c_str(), NC_SHORT, 1,
                                                          (short*)attValue.c_str() ) )
                     MB_SET_ERR( MB_FAILURE, "Failed to define short type attribute" );
                 break;
             default:
                 MB_SET_ERR( MB_FAILURE, "Unknown attribute data type" );
         }
     }
  
     // Take it out of define mode
     if( NC_NOERR != NCFUNC( enddef )( _fileId ) ) MB_SET_ERR( MB_FAILURE, "Failed to close define mode" );
  
     return MB_SUCCESS;
 }

References _fileId, _writeNC, moab::WriteNC::AttData::attDataType, moab::WriteNC::AttData::attLen, moab::WriteNC::AttData::attValue, moab::WriteNC::dbgOut, moab::WriteNC::dimNames, moab::WriteNC::dummyVarNames, moab::WriteNC::globalAtts, levDim, MB_SET_ERR, MB_SUCCESS, NCDF_SIZE, NCFUNC, moab::WriteNC::VarData::sz, tDim, moab::DebugOutput::tprintf(), moab::WriteNC::usedCoordinates, moab::WriteNC::VarData::varDataType, moab::WriteNC::VarData::varDims, moab::WriteNC::VarData::varId, and moab::WriteNC::varInfo.

Referenced by moab::WriteNC::write_file().

◆ write_nonset_variables()

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

protectedpure virtual

Implemented in moab::NCWriteScrip, moab::ScdNCWriteHelper, moab::NCWriteESMF, moab::NCWriteDomain, moab::NCWriteMPAS, moab::NCWriteHOMME, and moab::NCWriteGCRM.

Referenced by write_values().

◆ write_set_variables()

ErrorCode moab::NCWriteHelper::write_set_variables	(	std::vector< WriteNC::VarData > &	vsetdatas,
		std::vector< int > &	tstep_nums
	)

private

Definition at line 535 of file NCWriteHelper.cpp.

 {
     int success;
  
     // CAUTION: if the NetCDF ID is from a previous call to ncmpi_create rather than ncmpi_open,
     // all processors need to call ncmpi_begin_indep_data(). If only the root processor does so,
     // ncmpi_begin_indep_data() call will be blocked forever :(
 #ifdef MOAB_HAVE_PNETCDF
     // Enter independent I/O mode
     success = NCFUNC( begin_indep_data )( _fileId );
     if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
 #endif
  
     int rank = 0;
 #ifdef MOAB_HAVE_MPI
     bool& isParallel = _writeNC->isParallel;
     if( isParallel )
     {
         ParallelComm*& myPcomm = _writeNC->myPcomm;
         rank                   = myPcomm->proc_config().proc_rank();
     }
 #endif
     if( 0 == rank )
     {
         for( unsigned int i = 0; i < vsetdatas.size(); i++ )
         {
             WriteNC::VarData& variableData = vsetdatas[i];
  
             // Set variables with timesteps, e.g. xtime(Time) or xtime(Time, StrLen)
             if( variableData.has_tsteps )
             {
                 MB_SET_ERR( MB_NOT_IMPLEMENTED, "Writing set variables with timesteps is not implemented yet" );
             }
  
             switch( variableData.varDataType )
             {
                 case NC_DOUBLE:
                     // Independent I/O mode put
                     success = NCFUNCP( _vara_double )( _fileId, variableData.varId, &variableData.writeStarts[0],
                                                        &variableData.writeCounts[0],
                                                        (double*)( variableData.memoryHogs[0] ) );
                     if( success )
                         MB_SET_ERR( MB_FAILURE, "Failed to write double data for variable " << variableData.varName );
                     break;
                 case NC_INT:
                     // Independent I/O mode put
                     success =
                         NCFUNCP( _vara_int )( _fileId, variableData.varId, &variableData.writeStarts[0],
                                               &variableData.writeCounts[0], (int*)( variableData.memoryHogs[0] ) );
                     if( success )
                         MB_SET_ERR( MB_FAILURE, "Failed to write int data for variable " << variableData.varName );
                     break;
                 default:
                     MB_SET_ERR( MB_NOT_IMPLEMENTED, "Writing non-double or non-int data is not implemented yet" );
             }
         }
     }
  
 #ifdef MOAB_HAVE_PNETCDF
     // End independent I/O mode
     success = NCFUNC( end_indep_data )( _fileId );
     if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
 #endif
  
     return MB_SUCCESS;
 }

References _fileId, _writeNC, moab::WriteNC::VarData::has_tsteps, moab::WriteNC::isParallel, MB_NOT_IMPLEMENTED, MB_SET_ERR, MB_SUCCESS, moab::WriteNC::VarData::memoryHogs, NCFUNC, NCFUNCP, moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::WriteNC::VarData::varDataType, moab::WriteNC::VarData::varId, moab::WriteNC::VarData::varName, moab::WriteNC::VarData::writeCounts, and moab::WriteNC::VarData::writeStarts.

Referenced by write_values().

◆ write_values()

ErrorCode moab::NCWriteHelper::write_values	(	std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums
	)

virtual

Take the info from VarData and write first non-set variables, then set variables. Virtual for the same reason as init_file.

Reimplemented in moab::NCWriteScrip, moab::NCWriteESMF, and moab::NCWriteDomain.

Definition at line 478 of file NCWriteHelper.cpp.

 {
     std::set< std::string >& usedCoordinates           = _writeNC->usedCoordinates;
     std::set< std::string >& dummyVarNames             = _writeNC->dummyVarNames;
     std::map< std::string, WriteNC::VarData >& varInfo = _writeNC->varInfo;
  
     std::vector< WriteNC::VarData > vdatas;
     std::vector< WriteNC::VarData > vsetdatas;
  
     // For set variables, include coordinates used by requested var_names
     for( std::set< std::string >::iterator setIt = usedCoordinates.begin(); setIt != usedCoordinates.end(); ++setIt )
     {
         const std::string& coordName = *setIt;
  
         // Skip dummy coordinate variables (if any)
         if( dummyVarNames.find( coordName ) != dummyVarNames.end() ) continue;
  
         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( coordName );
         if( vit == varInfo.end() )
         {
             MB_SET_ERR( MB_FAILURE, "Can't find coordinate variable " << coordName );
         }
  
         vsetdatas.push_back( vit->second );
     }
  
     // Collect non-set and set variables from requested var_names
     for( unsigned int i = 0; i < var_names.size(); i++ )
     {
         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( var_names[i] );
         if( vit == varInfo.end() )
         {
             MB_SET_ERR( MB_FAILURE, "Can't find requested variable " << var_names[i] );
         }
  
         WriteNC::VarData& variableData = vit->second;
         if( WriteNC::ENTLOCSET == variableData.entLoc )
         {
             // Used coordinates has all ready been included
             if( usedCoordinates.find( var_names[i] ) != usedCoordinates.end() ) continue;
  
             vsetdatas.push_back( variableData );
         }
         else
             vdatas.push_back( variableData );
     }
  
     // Assume that the data ranges do not overlap across processors
     // While overlapped writing might still work, we should better not take that risk
     write_nonset_variables( vdatas, tstep_nums );
  
     // Use independent I/O mode put, since this write is only for the root processor
     write_set_variables( vsetdatas, tstep_nums );
  
     return MB_SUCCESS;
 }

References _writeNC, moab::WriteNC::dummyVarNames, moab::WriteNC::VarData::entLoc, moab::WriteNC::ENTLOCSET, MB_SET_ERR, MB_SUCCESS, moab::WriteNC::usedCoordinates, moab::WriteNC::varInfo, write_nonset_variables(), and write_set_variables().

Referenced by moab::WriteNC::write_file().

Member Data Documentation

◆ _fileId

int moab::NCWriteHelper::_fileId

protected

Cache some information from WriteNC.

Definition at line 66 of file NCWriteHelper.hpp.

Referenced by init_file(), moab::NCWriteDomain::init_file(), moab::NCWriteESMF::init_file(), moab::NCWriteScrip::init_file(), moab::NCWriteGCRM::write_nonset_variables(), moab::NCWriteHOMME::write_nonset_variables(), moab::NCWriteMPAS::write_nonset_variables(), moab::ScdNCWriteHelper::write_nonset_variables(), write_set_variables(), moab::NCWriteDomain::write_values(), moab::NCWriteESMF::write_values(), and moab::NCWriteScrip::write_values().

◆ _fileSet

EntityHandle moab::NCWriteHelper::_fileSet

protected

Definition at line 68 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteDomain::collect_mesh_info(), moab::NCWriteESMF::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteScrip::collect_mesh_info(), and collect_variable_data().

◆ _opts

const FileOptions& moab::NCWriteHelper::_opts

protected

Definition at line 67 of file NCWriteHelper.hpp.

◆ _writeNC

WriteNC* moab::NCWriteHelper::_writeNC

protected

Allow NCWriteHelper to directly access members of WriteNC.

Definition at line 63 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteDomain::collect_mesh_info(), moab::NCWriteESMF::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteScrip::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), collect_variable_data(), moab::NCWriteHOMME::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::ScdNCWriteHelper::collect_variable_data(), init_file(), moab::NCWriteGCRM::write_nonset_variables(), moab::NCWriteHOMME::write_nonset_variables(), moab::NCWriteMPAS::write_nonset_variables(), moab::ScdNCWriteHelper::write_nonset_variables(), write_set_variables(), write_values(), moab::NCWriteDomain::write_values(), moab::NCWriteESMF::write_values(), and moab::NCWriteScrip::write_values().

◆ levDim

int moab::NCWriteHelper::levDim

protected

Definition at line 74 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), and init_file().

◆ localCellsOwned

Range moab::NCWriteHelper::localCellsOwned

protected

Local owned cells, edges and vertices.

Definition at line 77 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteDomain::collect_mesh_info(), moab::NCWriteESMF::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteScrip::collect_mesh_info(), moab::NCWriteGCRM::write_nonset_variables(), moab::NCWriteMPAS::write_nonset_variables(), and moab::ScdNCWriteHelper::write_nonset_variables().

◆ localEdgesOwned

Range moab::NCWriteHelper::localEdgesOwned

protected

Definition at line 77 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::NCWriteGCRM::write_nonset_variables(), and moab::NCWriteMPAS::write_nonset_variables().

◆ localVertsOwned

Range moab::NCWriteHelper::localVertsOwned

protected

Definition at line 77 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteGCRM::write_nonset_variables(), moab::NCWriteHOMME::write_nonset_variables(), and moab::NCWriteMPAS::write_nonset_variables().

◆ nLevels

int moab::NCWriteHelper::nLevels

protected

Definition at line 71 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), and collect_variable_data().

◆ nTimeSteps

int moab::NCWriteHelper::nTimeSteps

protected

Dimensions of time and level.

Definition at line 71 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), and collect_variable_data().

◆ tDim

int moab::NCWriteHelper::tDim

protected

Dimension numbers for time and level.

Definition at line 74 of file NCWriteHelper.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), collect_variable_data(), moab::NCWriteHOMME::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::ScdNCWriteHelper::collect_variable_data(), init_file(), moab::NCWriteGCRM::write_nonset_variables(), moab::NCWriteHOMME::write_nonset_variables(), moab::NCWriteMPAS::write_nonset_variables(), and moab::ScdNCWriteHelper::write_nonset_variables().

◆ timeStepVals

std::vector< double > moab::NCWriteHelper::timeStepVals

protected

Time values of output timesteps.

Definition at line 80 of file NCWriteHelper.hpp.

Referenced by collect_variable_data().

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ NCWriteHelper()

◆ ~NCWriteHelper()

Member Function Documentation

◆ collect_mesh_info()

◆ collect_variable_data()

◆ get_nc_helper()

◆ init_file()

◆ write_nonset_variables()

◆ write_set_variables()

◆ write_values()

Member Data Documentation

◆ _fileId

◆ _fileSet

◆ _opts

◆ _writeNC

◆ levDim

◆ localCellsOwned

◆ localEdgesOwned

◆ localVertsOwned

◆ nLevels

◆ nTimeSteps

◆ tDim

◆ timeStepVals