Export NC files. More...

#include <WriteNC.hpp>

Inheritance diagram for moab::WriteNC:

Collaboration diagram for moab::WriteNC:

Classes
class	AttData
class	VarData
Public Member Functions
	WriteNC (Interface *impl=NULL)
	Constructor.
virtual	~WriteNC ()
	Destructor.
ErrorCode	write_file (const char file_name, const bool overwrite, const FileOptions &opts, const EntityHandle output_list, const int num_sets, const std::vector< std::string > &qa_list, const Tag *tag_list=NULL, int num_tags=0, int export_dimension=3)
	Writes out a file.
Static Public Member Functions
static WriterIface *	factory (Interface *)
	Factory method.
Private Types
enum	EntityLocation { ENTLOCVERT = 0, ENTLOCNSEDGE, ENTLOCEWEDGE, ENTLOCFACE, ENTLOCSET, ENTLOCEDGE, ENTLOCREGION }
	ENTLOCNSEDGE for north/south edge ENTLOCWEEDGE for west/east edge. More...
Private Member Functions
ErrorCode	parse_options (const FileOptions &opts, std::vector< std::string > &var_names, std::vector< std::string > &desired_names, std::vector< int > &tstep_nums, std::vector< double > &tstep_vals)
ErrorCode	process_conventional_tags (EntityHandle fileSet)
ErrorCode	process_concatenated_attribute (const void *attPtr, int attSz, std::vector< int > &attLen, std::map< std::string, AttData > &attributes)
Private Attributes
std::vector< std::string >	dimNames
	This info will be reconstructed from metadata stored on conventional fileSet tags Dimension names.
std::vector< int >	dimLens
	Dimension lengths.
std::set< std::string >	usedCoordinates
	Will collect used dimensions (coordinate variables)
std::set< std::string >	dummyVarNames
	Dummy variables (for dimensions that have no corresponding coordinate variables)
std::map< std::string, AttData >	globalAtts
	Global attribs.
std::map< std::string, VarData >	varInfo
	Variable info.
Interface *	mbImpl
	Interface instance.
WriteUtilIface *	mWriteIface
const char *	fileName
	File var.
int	fileId
	File numbers assigned by (p)netcdf.
DebugOutput	dbgOut
	Debug stuff.
bool	noMesh
	Write options.
bool	noVars
bool	append
Tag	mGlobalIdTag
	Cached tags for writing. This will be important for ordering the data, in parallel.
bool	isParallel
	Are we writing in parallel? (probably in the future)
std::string	grid_type
	CAM Euler, etc,.
NCWriteHelper *	myHelper
	Helper class instance.
Friends
class	NCWriteHelper
class	ScdNCWriteHelper
class	UcdNCWriteHelper
class	NCWriteEuler
class	NCWriteFV
class	NCWriteHOMME
class	NCWriteMPAS
class	NCWriteGCRM

Detailed Description

Export NC files.

Definition at line 70 of file WriteNC.hpp.

Member Enumeration Documentation

enum moab::WriteNC::EntityLocation [private]

ENTLOCNSEDGE for north/south edge ENTLOCWEEDGE for west/east edge.

Enumerator:

ENTLOCVERT
ENTLOCNSEDGE
ENTLOCEWEDGE
ENTLOCFACE
ENTLOCSET
ENTLOCEDGE
ENTLOCREGION

Definition at line 105 of file WriteNC.hpp.

    {
        ENTLOCVERT = 0,
        ENTLOCNSEDGE,
        ENTLOCEWEDGE,
        ENTLOCFACE,
        ENTLOCSET,
        ENTLOCEDGE,
        ENTLOCREGION
    };

Constructor & Destructor Documentation

moab::WriteNC::WriteNC ( Interface * impl = NULL )

Constructor.

Definition at line 32 of file WriteNC.cpp.

References mWriteIface, and moab::Interface::query_interface().

Referenced by factory().

    : mbImpl( impl ), dbgOut( stderr ),
#ifdef MOAB_HAVE_MPI
      myPcomm( NULL ),
#endif
      noMesh( false ), noVars( false ), append( false ), mGlobalIdTag( 0 ), isParallel( false ), myHelper( NULL )
{
    assert( impl != NULL );
    impl->query_interface( mWriteIface );
}

moab::WriteNC::~WriteNC ( ) [virtual]

Destructor.

Definition at line 43 of file WriteNC.cpp.

References mbImpl, mWriteIface, myHelper, and moab::Interface::release_interface().

{
    mbImpl->release_interface( mWriteIface );
    if( myHelper != NULL ) delete myHelper;
}

Member Function Documentation

WriterIface * moab::WriteNC::factory ( Interface * iface ) [static]

Factory method.

Definition at line 27 of file WriteNC.cpp.

References WriteNC().

Referenced by moab::ReaderWriterSet::ReaderWriterSet().

{
    return new WriteNC( iface );
}

ErrorCode moab::WriteNC::parse_options	(	const FileOptions &	opts,
		std::vector< std::string > &	var_names,
		std::vector< std::string > &	desired_names,
		std::vector< int > &	tstep_nums,
		std::vector< double > &	tstep_vals
	)		`[private]`

Definition at line 140 of file WriteNC.cpp.

References append, dbgOut, ErrorCode, moab::FileOptions::get_int_option(), moab::FileOptions::get_ints_option(), moab::FileOptions::get_null_option(), moab::ParallelComm::get_pcomm(), moab::FileOptions::get_reals_option(), moab::FileOptions::get_strs_option(), moab::DebugOutput::get_verbosity(), isParallel, moab::FileOptions::match_option(), MB_ENTITY_NOT_FOUND, MB_SET_ERR, MB_SUCCESS, MB_TYPE_OUT_OF_RANGE, MB_UNSUPPORTED_OPERATION, mbImpl, noMesh, noVars, moab::DebugOutput::set_prefix(), moab::DebugOutput::set_rank(), and moab::DebugOutput::set_verbosity().

Referenced by write_file().

{
    int tmpval;
    if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
    {
        dbgOut.set_verbosity( tmpval );
        dbgOut.set_prefix( "NCWrite" );
    }

    ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
    if( MB_TYPE_OUT_OF_RANGE == rval )
        noVars = true;
    else
        noVars = false;

    rval = opts.get_strs_option( "RENAME", desired_names );
    if( MB_ENTITY_NOT_FOUND == rval )
    {
        if( !noVars )
        {
            desired_names.resize( var_names.size() );
            std::copy( var_names.begin(), var_names.end(), desired_names.begin() );
        }
    }
    // Either way
    assert( desired_names.size() == var_names.size() );

    opts.get_ints_option( "TIMESTEP", tstep_nums );
    opts.get_reals_option( "TIMEVAL", tstep_vals );
    rval = opts.get_null_option( "NOMESH" );
    if( MB_SUCCESS == rval ) noMesh = true;

    rval = opts.get_null_option( "APPEND" );
    if( MB_SUCCESS == rval ) append = true;

    if( 2 <= dbgOut.get_verbosity() )
    {
        if( !var_names.empty() )
        {
            std::cerr << "Variables requested: ";
            for( unsigned int i = 0; i < var_names.size(); i++ )
                std::cerr << var_names[i];
            std::cerr << std::endl;
        }
        if( !tstep_nums.empty() )
        {
            std::cerr << "Timesteps requested: ";
            for( unsigned int i = 0; i < tstep_nums.size(); i++ )
                std::cerr << tstep_nums[i];
            std::cerr << std::endl;
        }
        if( !tstep_vals.empty() )
        {
            std::cerr << "Time vals requested: ";
            for( unsigned int i = 0; i < tstep_vals.size(); i++ )
                std::cerr << tstep_vals[i];
            std::cerr << std::endl;
        }
    }

// FIXME: copied from ReadNC, may need revise
#ifdef MOAB_HAVE_MPI
    isParallel = ( opts.match_option( "PARALLEL", "WRITE_PART" ) != MB_ENTITY_NOT_FOUND );

    if( !isParallel )
        // Return success here, since rval still has _NOT_FOUND from not finding option
        // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
        // before any use for myPcomm
        return MB_SUCCESS;

    int pcomm_no = 0;
    rval         = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
    if( MB_TYPE_OUT_OF_RANGE == rval )
    {
        MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
    }

    myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
    if( 0 == myPcomm )
    {
        myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
    }

#ifndef MOAB_HAVE_PNETCDF
    const int procs = myPcomm->proc_config().proc_size();
    if( procs > 1 )
    {
        MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Attempt to launch NC writer in parallel without pnetcdf support" );
    }
#endif

    const int rank = myPcomm->proc_config().proc_rank();
    dbgOut.set_rank( rank );
#endif

    return MB_SUCCESS;
}

ErrorCode moab::WriteNC::process_concatenated_attribute	(	const void *	attPtr,
		int	attSz,
		std::vector< int > &	attLen,
		std::map< std::string, AttData > &	attributes
	)		`[private]`

Definition at line 455 of file WriteNC.cpp.

References moab::WriteNC::AttData::attDataType, moab::WriteNC::AttData::attLen, moab::WriteNC::AttData::attValue, dbgOut, MB_SET_ERR, MB_SUCCESS, and moab::DebugOutput::tprintf().

Referenced by process_conventional_tags().

{
    std::size_t start       = 0;
    std::size_t att_counter = 0;
    std::string concatString( (char*)attPtr, (char*)attPtr + attSz );

    for( std::size_t i = 0; i != (size_t)attSz; i++ )
    {
        if( concatString[i] == '\0' )
        {
            std::string att_name( &concatString[start], i - start );
            start = i + 1;
            while( concatString[i] != ';' )
                ++i;
            std::string data_type( &concatString[start], i - start );
            ++i;
            start = i;
            i     = attLen[att_counter];
            if( concatString[i] != ';' ) MB_SET_ERR( MB_FAILURE, "Error parsing attributes" );

            std::string data_val( &concatString[start], i - start );
            start = i + 1;

            AttData& attrib = attributes[att_name];
            attrib.attValue = data_val;
            attrib.attLen   = data_val.size();

            if( data_type == "char" )
                attrib.attDataType = NC_CHAR;
            else if( data_type == "double" )
                attrib.attDataType = NC_DOUBLE;
            else if( data_type == "float" )
                attrib.attDataType = NC_FLOAT;
            else if( data_type == "int" )
                attrib.attDataType = NC_INT;
            else if( data_type == "short" )
                attrib.attDataType = NC_SHORT;

            ++att_counter;
            dbgOut.tprintf( 2, "       Process attribute %s with value %s \n", att_name.c_str(), data_val.c_str() );
        }
    }

    return MB_SUCCESS;
}

ErrorCode moab::WriteNC::process_conventional_tags ( EntityHandle fileSet ) [private]

Definition at line 244 of file WriteNC.cpp.

References dbgOut, dimLens, dimNames, dummyVarNames, moab::WriteNC::VarData::entLoc, ErrorCode, globalAtts, grid_type, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_ANY, MB_TAG_NOT_FOUND, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, mbImpl, moab::WriteNC::VarData::numAtts, process_concatenated_attribute(), moab::Interface::tag_get_by_ptr(), moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), moab::Interface::tag_get_length(), moab::Interface::tag_get_name(), moab::DebugOutput::tprintf(), moab::WriteNC::VarData::varAtts, moab::WriteNC::VarData::varDims, varInfo, and moab::WriteNC::VarData::varName.

Referenced by write_file().

{
    ErrorCode rval;

    // Start copy
    Tag dimNamesTag      = 0;
    std::string tag_name = "__DIM_NAMES";
    const void* data     = NULL;
    int dimNamesSz       = 0;
    rval                 = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( dimNamesTag, &fileSet, 1, &data, &dimNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    const char* p = static_cast< const char* >( data );
    dbgOut.tprintf( 1, "__DIM_NAMES tag has string length %d\n", dimNamesSz );

    std::size_t start = 0;

    Tag dimLensTag = 0;
    tag_name       = "__DIM_LENS";
    data           = NULL;
    int dimLensSz  = 0;
    rval           = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( dimLensTag, &fileSet, 1, &data, &dimLensSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    const int* int_p = static_cast< const int* >( data );
    dbgOut.tprintf( 1, "__DIM_LENS tag has %d values\n", dimLensSz );

    int idxDim = 0;
    // Dim names are separated by '\0' in the string of __DIM_NAMES tag
    for( std::size_t i = 0; i != static_cast< std::size_t >( dimNamesSz ); i++ )
    {
        if( p[i] == '\0' )
        {
            std::string dim_name( &p[start], i - start );
            int len = int_p[idxDim];
            dimNames.push_back( dim_name );
            dimLens.push_back( len );
            dbgOut.tprintf( 2, "Dimension %s has length %d\n", dim_name.c_str(), len );
            // FIXME: Need info from moab to set unlimited dimension
            // Currently assume each file has the same number of time dimensions
            /*if ((dim_name == "time") || (dim_name == "Time"))
              insert(dim_name, *(new pcdim(dim_name, len * m_file_names.size(), true)));
            else
              insert(dim_name, *(new pcdim(dim_name, len)));*/
            start = i + 1;
            idxDim++;
        }
    }

    Tag meshTypeTag = 0;
    tag_name        = "__MESH_TYPE";
    data            = NULL;
    int meshTypeSz  = 0;
    rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( meshTypeTag, &fileSet, 1, &data, &meshTypeSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    p         = static_cast< const char* >( data );
    grid_type = std::string( &p[0], meshTypeSz );
    dbgOut.tprintf( 2, "Mesh type: %s\n", grid_type.c_str() );

    // Read <__VAR_NAMES_LOCATIONS> tag
    Tag varNamesLocsTag = 0;
    tag_name            = "__VAR_NAMES_LOCATIONS";
    data                = NULL;
    int varNamesLocsSz  = 0;
    rval                = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varNamesLocsTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( varNamesLocsTag, &fileSet, 1, &data, &varNamesLocsSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    int_p = static_cast< const int* >( data );
    std::vector< int > varNamesLocs( varNamesLocsSz );
    std::copy( int_p, int_p + varNamesLocsSz, varNamesLocs.begin() );

    Tag varNamesTag = 0;
    tag_name        = "__VAR_NAMES";
    rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    data           = NULL;
    int varNamesSz = 0;
    rval           = mbImpl->tag_get_by_ptr( varNamesTag, &fileSet, 1, &data, &varNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    dbgOut.tprintf( 2, "__VAR_NAMES tag has string length %d\n", varNamesSz );
    p = static_cast< const char* >( data );

    start      = 0;
    int idxVar = 0;
    int sz;
    // Var names are separated by '\0' in the string of __VAR_NAMES tag
    for( std::size_t i = 0; i != static_cast< std::size_t >( varNamesSz ); i++ )
    {
        if( p[i] == '\0' )
        {
            std::string var_name( &p[start], i - start );

            dbgOut.tprintf( 2, "var name: %s index %d \n", var_name.c_str(), idxVar );
            // Process var name:
            // This will create/initiate map; we will populate variableDataStruct with info about
            // dims, tags, etc reference & is important; otherwise variableDataStruct will go out of
            // scope, and deleted :(
            VarData& variableDataStruct = varInfo[var_name];
            variableDataStruct.varName  = var_name;
            variableDataStruct.entLoc   = varNamesLocs[idxVar];

            dbgOut.tprintf( 2, "at var name %s varInfo size %d \n", var_name.c_str(), (int)varInfo.size() );

            sz                    = 0;
            Tag dims_tag          = 0;
            std::string dim_names = "__" + var_name + "_DIMS";
            rval = mbImpl->tag_get_handle( dim_names.c_str(), 0, MB_TYPE_OPAQUE, dims_tag, MB_TAG_ANY );
            if( MB_SUCCESS != rval )
            {
                if( MB_TAG_NOT_FOUND == rval )
                {
                    dbgOut.tprintf( 2, "tag : %s not found, continue \n", dim_names.c_str() );
                    start = i + 1;
                    idxVar++;
                    continue;
                }
                MB_SET_ERR( rval, "Trouble getting conventional tag " << dim_names );
            }
            rval = mbImpl->tag_get_length( dims_tag, sz );MB_CHK_SET_ERR( rval, "Trouble getting size of dimensions for variable " << var_name );
            sz /= sizeof( Tag );  // The type is MB_TYPE_OPAQUE, but it is a list of tags, so we
                                  // need to divide by the size of Tag
            // sz is used for number of dimension tags in this list
            dbgOut.tprintf( 2, "var name: %s has %d dimensions \n", var_name.c_str(), sz );

            variableDataStruct.varDims.resize( sz );
            const void* ptr = NULL;
            rval            = mbImpl->tag_get_by_ptr( dims_tag, &fileSet, 1, &ptr );

            const Tag* ptags = static_cast< const moab::Tag* >( ptr );
            for( std::size_t j = 0; j != static_cast< std::size_t >( sz ); j++ )
            {
                std::string dim_name;
                rval = mbImpl->tag_get_name( ptags[j], dim_name );MB_CHK_SET_ERR( rval, "Trouble getting dimension of variable " << var_name );
                dbgOut.tprintf( 2, "var name: %s has %s as dimension \n", var_name.c_str(), dim_name.c_str() );
                std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), dim_name );
                if( vit == dimNames.end() )
                    MB_SET_ERR( MB_FAILURE, "Dimension " << dim_name << " not found for variable " << var_name );
                variableDataStruct.varDims[j] = (int)( vit - dimNames.begin() );  // Will be used for writing
                // This will have to change to actual file dimension, for writing
            }

            // Attributes for this variable
            std::stringstream ssTagName;
            ssTagName << "__" << var_name << "_ATTRIBS";
            tag_name      = ssTagName.str();
            Tag varAttTag = 0;
            rval =
                mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
            const void* varAttPtr = NULL;
            int varAttSz          = 0;
            rval                  = mbImpl->tag_get_by_ptr( varAttTag, &fileSet, 1, &varAttPtr, &varAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
            if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );

            std::string attribString( (char*)varAttPtr, (char*)varAttPtr + varAttSz );
            if( attribString == "NO_ATTRIBS" )
            {
                // This variable has no attributes
                variableDataStruct.numAtts = 0;
            }
            else if( attribString == "DUMMY_VAR" )
            {
                // This variable is a dummy coordinate variable
                variableDataStruct.numAtts = 0;
                dummyVarNames.insert( variableDataStruct.varName );
            }
            else
            {
                ssTagName << "_LEN";
                tag_name         = ssTagName.str();
                Tag varAttLenTag = 0;
                rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
                int varAttLenSz = 0;
                rval            = mbImpl->tag_get_length( varAttLenTag, varAttLenSz );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
                std::vector< int > varAttLen( varAttLenSz );
                rval = mbImpl->tag_get_data( varAttLenTag, &fileSet, 1, &varAttLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );

                rval = process_concatenated_attribute( varAttPtr, varAttSz, varAttLen, variableDataStruct.varAtts );MB_CHK_SET_ERR( rval, "Trouble processing attributes of variable " << var_name );

                if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag metadata for variable %s\n", tag_name.c_str() );
            }
            // End attribute

            start = i + 1;
            idxVar++;
        }  // if (p[i] == '\0')
    }

    // Global attributes
    tag_name         = "__GLOBAL_ATTRIBS";
    Tag globalAttTag = 0;
    rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    std::vector< int > gattLen;

    const void* gattptr = NULL;
    int globalAttSz     = 0;
    rval                = mbImpl->tag_get_by_ptr( globalAttTag, &fileSet, 1, &gattptr, &globalAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );

    if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag value retrieved for %s size %d\n", tag_name.c_str(), globalAttSz );

    // <__GLOBAL_ATTRIBS_LEN>
    tag_name            = "__GLOBAL_ATTRIBS_LEN";
    Tag globalAttLenTag = 0;

    rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, globalAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    int sizeGAtt = 0;
    rval         = mbImpl->tag_get_length( globalAttLenTag, sizeGAtt );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
    gattLen.resize( sizeGAtt );
    rval = mbImpl->tag_get_data( globalAttLenTag, &fileSet, 1, &gattLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );

    rval = process_concatenated_attribute( gattptr, globalAttSz, gattLen, globalAtts );MB_CHK_SET_ERR( rval, "Trouble processing global attributes" );

    return MB_SUCCESS;
}

ErrorCode moab::WriteNC::write_file	(	const char *	file_name,
		const bool	overwrite,
		const FileOptions &	opts,
		const EntityHandle *	output_list,
		const int	num_sets,
		const std::vector< std::string > &	qa_list,
		const Tag *	tag_list = `NULL`,
		int	num_tags = `0`,
		int	export_dimension = `3`
	)		`[virtual]`

Writes out a file.

Implements moab::WriterIface.

Definition at line 50 of file WriteNC.cpp.

References append, moab::NCWriteHelper::collect_mesh_info(), moab::NCWriteHelper::collect_variable_data(), dbgOut, ErrorCode, fileId, fileName, moab::NCWriteHelper::get_nc_helper(), moab::Interface::globalId_tag(), moab::NCWriteHelper::init_file(), isParallel, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, mbImpl, mGlobalIdTag, myHelper, NCFUNC, parse_options(), process_conventional_tags(), moab::DebugOutput::tprintf(), and moab::NCWriteHelper::write_values().

{
    ErrorCode rval;
    // See if opts has variable(s) specified
    std::vector< std::string > var_names;
    std::vector< std::string > desired_names;
    std::vector< int > tstep_nums;
    std::vector< double > tstep_vals;

    // Get and cache predefined tag handles
    mGlobalIdTag = mbImpl->globalId_tag();

    // num set has to be 1, we will write only one set, the original file set used to load
    if( num_set != 1 ) MB_SET_ERR( MB_FAILURE, "We should write only one set (the file set used to read data into)" );

    rval = parse_options( options, var_names, desired_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );

    // Important to create some data that will be used to write the file; dimensions, variables, etc
    // new variables still need to have some way of defining their dimensions
    // maybe it will be passed as write options
    rval = process_conventional_tags( *file_set );MB_CHK_SET_ERR( rval, "Trouble processing conventional tags" );

    // Create or append the file
    if( append )
        dbgOut.tprintf( 1, "opening file %s for appending \n", file_name );
    else
        dbgOut.tprintf( 1, "creating file %s\n", file_name );
    fileName = file_name;
    int success;

    if( append )
    {
        int omode = NC_WRITE;
#ifdef MOAB_HAVE_PNETCDF
        if( isParallel )
            success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, omode, MPI_INFO_NULL, &fileId );
        else
            success = NCFUNC( open )( MPI_COMM_SELF, file_name, omode, MPI_INFO_NULL, &fileId );
#else
        // This is a regular netcdf file, open in write mode
        success = NCFUNC( open )( file_name, omode, &fileId );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name << " for appending" );
    }
    else
    {  // Case when the file is new, will be overwritten, most likely
        int cmode = overwrite ? NC_CLOBBER : NC_NOCLOBBER;
#ifdef MOAB_HAVE_PNETCDF
        if( isParallel )
            success = NCFUNC( create )( myPcomm->proc_config().proc_comm(), file_name, cmode, MPI_INFO_NULL, &fileId );
        else
            success = NCFUNC( create )( MPI_COMM_SELF, file_name, cmode, MPI_INFO_NULL, &fileId );
#else
        // This is a regular netcdf file
        success = NCFUNC( create )( file_name, cmode, &fileId );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble creating file " << file_name << " for writing" );
    }

    if( NULL != myHelper ) delete myHelper;

    // Get appropriate helper instance for WriteNC class based on some info in the file set
    myHelper = NCWriteHelper::get_nc_helper( this, fileId, options, *file_set );
    if( NULL == myHelper )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to get NCWriteHelper class instance" );
    }

    rval = myHelper->collect_mesh_info();MB_CHK_SET_ERR( rval, "Trouble collecting mesh information" );

    rval = myHelper->collect_variable_data( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble collecting variable data" );

    rval = myHelper->init_file( var_names, desired_names, append );MB_CHK_SET_ERR( rval, "Trouble initializing file" );

    rval = myHelper->write_values( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble writing values to file" );

    success = NCFUNC( close )( fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );

    return MB_SUCCESS;
}