ReadNC.cpp

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#include "ReadNC.hpp"
#include "NCHelper.hpp"
 
#include "moab/ReadUtilIface.hpp"
#include "MBTagConventions.hpp"
#include "moab/FileOptions.hpp"
 
namespace moab
{
 
ReaderIface* ReadNC::factory( Interface* iface )
{
    return new ReadNC( iface );
}
 
ReadNC::ReadNC( Interface* impl )
    : mbImpl( impl ), fileId( -1 ), mGlobalIdTag( 0 ), mpFileIdTag( NULL ), dbgOut( stderr ), isParallel( false ),
      partMethod( ScdParData::ALLJORKORI ), scdi( NULL ),
#ifdef MOAB_HAVE_MPI
      myPcomm( NULL ),
#endif
      noMesh( false ), noVars( false ), spectralMesh( false ), noMixedElements( false ), noEdges( false ),
      culling( true ), repartition( false ), gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ),
      myHelper( NULL )
{
    assert( impl != NULL );
    impl->query_interface( readMeshIface );
}
 
ReadNC::~ReadNC()
{
    mbImpl->release_interface( readMeshIface );
    if( myHelper != NULL ) delete myHelper;
}
 
ErrorCode ReadNC::load_file( const char* file_name,
                             const EntityHandle* file_set,
                             const FileOptions& opts,
                             const ReaderIface::SubsetList* /*subset_list*/,
                             const Tag* file_id_tag )
{
    // See if opts has variable(s) specified
    std::vector< std::string > var_names;
    std::vector< int > tstep_nums;
    std::vector< double > tstep_vals;
 
    // Get and cache predefined tag handles
    mGlobalIdTag = mbImpl->globalId_tag();
    // Store the pointer to the tag; if not null, set when global id tag
    // is set too, with the same data, duplicated
    mpFileIdTag = file_id_tag;
 
    MB_CHK_SET_ERR( parse_options( opts, var_names, tstep_nums, tstep_vals ), "Trouble parsing option string" );
 
    // Open the file
    dbgOut.tprintf( 1, "Opening file %s\n", file_name );
    fileName = std::string( file_name );
    int success;
 
    // Probe on-disk format and select the backend that can actually read it.
    // This replaces the old compile-time choice between nc_open and ncmpi_open
    // (which silently failed on NetCDF-4/HDF5 files under PNetCDF-only builds).
    // For parallel reads the probe runs on rank 0 and the answer is
    // broadcast; the file header read is cheap (8 bytes) so the cost is
    // negligible vs. doing the probe collectively on every rank.
    int fileFormat = NCFMT_UNKNOWN;
#ifdef MOAB_HAVE_MPI
    if( isParallel )
    {
        int rank = myPcomm->proc_config().proc_rank();
        if( rank == 0 ) fileFormat = mbnc_detect_format( file_name );
        MPI_Bcast( &fileFormat, 1, MPI_INT, 0, myPcomm->proc_config().proc_comm() );
    }
    else
#endif
    {
        fileFormat = mbnc_detect_format( file_name );
    }
 
#ifdef MOAB_HAVE_MPI
    const int mpi_size = isParallel ? myPcomm->proc_config().proc_size() : 1;
#else
    const int mpi_size = 1;
#endif
 
    const NcBackend backend = mbnc_choose_backend_for_read( fileFormat, mpi_size );
    if( backend == NCB_NONE )
    {
        const char* fmtName = ( fileFormat == NCFMT_CLASSIC )  ? "classic CDF-1/2/5"
                              : ( fileFormat == NCFMT_NETCDF4 ) ? "NetCDF-4 / HDF5"
                                                                : "unrecognized / non-NetCDF";
        MB_SET_ERR( MB_FAILURE,
                    "Cannot find a compatible parallel reader for file '"
                        << file_name << "' (detected format: " << fmtName
                        << "). PNetCDF cannot read NetCDF-4 files; libnetcdf parallel "
                           "must be configured for that case. Classic-format files require "
                           "either PNetCDF or libnetcdf built with --enable-pnetcdf." );
    }
 
#ifdef MOAB_HAVE_MPI
    if( backend == NCB_NETCDF_SERIAL || mpi_size == 1 )
    {
        success = mbnc_open( file_name, 0, &fileId );
    }
    else
    {
        success = mbnc_open_par( backend, myPcomm->proc_config().proc_comm(), MPI_INFO_NULL, file_name, 0, &fileId );
    }
#else
    success = mbnc_open( file_name, 0, &fileId );
#endif
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name );
 
    // Read the header (num dimensions, dimensions, num variables, global attribs)
    MB_CHK_SET_ERR( read_header(), "Trouble reading file header" );
 
    // Make sure there's a file set to put things in
    EntityHandle tmp_set;
    if( noMesh && !file_set )
    {
        MB_SET_ERR( MB_FAILURE, "NOMESH option requires non-NULL file set on input" );
    }
    else if( !file_set || ( file_set && *file_set == 0 ) )
    {
        MB_CHK_SET_ERR( mbImpl->create_meshset( MESHSET_SET, tmp_set ), "Trouble creating file set" );
    }
    else
        tmp_set = *file_set;
 
    // Get the scd interface
    scdi = nullptr;
    MB_CHK_SET_ERR( mbImpl->query_interface( scdi ), "failed to get SCD interface from query" );
    if( nullptr == scdi ) return MB_FAILURE;
 
    if( nullptr != myHelper ) delete myHelper;
 
    // Get appropriate NC helper instance based on information read from the header
    myHelper = NCHelper::get_nc_helper( this, fileId, opts, tmp_set );
    if( nullptr == myHelper )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
    }
 
    // Initialize mesh values
    MB_CHK_SET_ERR( myHelper->init_mesh_vals(), "Trouble initializing mesh values" );
 
    // Check existing mesh from last read
    if( noMesh && !noVars )
    {
        MB_CHK_SET_ERR( myHelper->check_existing_mesh(), "Trouble checking mesh from last read" );
    }
 
    // Create some conventional tags, e.g. __NUM_DIMS
    // For multiple reads to a specified file set, we assume a single file, or a series of
    // files with separated timesteps. Keep a flag on the file set to prevent conventional
    // tags from being created again on a second read
    Tag convTagsCreated = 0;
    int def_val         = 0;
    MB_CHK_SET_ERR( mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
                                            MB_TAG_SPARSE | MB_TAG_CREAT, &def_val ),
                    "Trouble getting _CONV_TAGS_CREATED tag" );
    int create_conv_tags_flag = 0;
    MB_CHK_SET_ERR( mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag ),
                    "failed to get conventional tags" );
    // The first read to the file set
    if( 0 == create_conv_tags_flag )
    {
        // Read dimensions (coordinate variables) by default to create tags like __<var_name>_DIMS
        // This is done only once (assume that all files read to the file set have the same
        // dimensions)
        MB_CHK_SET_ERR( myHelper->read_variables( dimNames, tstep_nums ), "Trouble reading dimensions" );
 
        MB_CHK_SET_ERR( myHelper->create_conventional_tags( tstep_nums ), "Trouble creating NC conventional tags" );
 
        create_conv_tags_flag = 1;
        MB_CHK_SET_ERR( mbImpl->tag_set_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag ),
                        "Trouble setting data to _CONV_TAGS_CREATED tag" );
    }
    else  // Another read to the file set
    {
        if( tStepBase > -1 )
        {
            // If timesteps spread across files, merge time values read
            // from current file to existing time tag
            MB_CHK_SET_ERR( myHelper->update_time_tag_vals(), "Trouble updating time tag values" );
        }
    }
 
    // Create mesh vertex/edge/face sequences
    Range faces;
    if( !noMesh )
    {
        MB_CHK_SET_ERR( myHelper->create_mesh( faces ), "Trouble creating mesh" );
    }
 
    // Read specified variables onto grid
    if( !noVars )
    {
        if( var_names.empty() )
        {
            // If VARIABLE option is missing, read all variables
            MB_CHK_SET_ERR( myHelper->read_variables( var_names, tstep_nums ), "Trouble reading all variables" );
        }
        else
        {
            // Exclude dimensions that are read to the file set by default
            std::vector< std::string > non_dim_var_names;
            for( unsigned int i = 0; i < var_names.size(); i++ )
            {
                if( std::find( dimNames.begin(), dimNames.end(), var_names[i] ) == dimNames.end() )
                    non_dim_var_names.push_back( var_names[i] );
            }
 
            if( !non_dim_var_names.empty() )
            {
                MB_CHK_SET_ERR( myHelper->read_variables( non_dim_var_names, tstep_nums ),
                                "Trouble reading specified variables" );
            }
        }
    }
 
#ifdef MOAB_HAVE_MPI
    // Create partition set, and populate with elements
    if( isParallel )
    {
        // Write partition tag name on partition set
        Tag part_tag = myPcomm->partition_tag();
        int dum_rank = myPcomm->proc_config().proc_rank();
        // the tmp_set is the file_set
        MB_CHK_SET_ERR( mbImpl->tag_set_data( part_tag, &tmp_set, 1, &dum_rank ),
                        "Trouble writing partition tag name on partition set" );
    }
#endif
 
    mbImpl->release_interface( scdi );
    scdi = NULL;
 
    // Close the file
    success = NCFUNC( close )( fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::parse_options( const FileOptions& opts,
                                 std::vector< std::string >& var_names,
                                 std::vector< int >& tstep_nums,
                                 std::vector< double >& tstep_vals )
{
    int tmpval;
    if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
    {
        dbgOut.set_verbosity( tmpval );
        dbgOut.set_prefix( "NC " );
    }
 
    ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
    if( MB_TYPE_OUT_OF_RANGE == rval )
        noVars = true;
    else
        noVars = false;
 
    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( "SPECTRAL_MESH" );
    if( MB_SUCCESS == rval ) spectralMesh = true;
 
    rval = opts.get_null_option( "NO_MIXED_ELEMENTS" );
    if( MB_SUCCESS == rval ) noMixedElements = true;
 
    rval = opts.get_null_option( "NO_EDGES" );
    if( MB_SUCCESS == rval ) noEdges = true;
 
    rval = opts.get_null_option( "NO_CULLING" );  // used now only for domain nc convention
    if( MB_SUCCESS == rval ) culling = false;
 
    rval = opts.get_null_option( "REPARTITION" );  // used now only for domain nc, to repartition with zoltan
    if( MB_SUCCESS == rval ) repartition = 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;
        }
    }
 
    rval = opts.get_int_option( "GATHER_SET", 0, gatherSetRank );
    if( MB_TYPE_OUT_OF_RANGE == rval )
    {
        MB_SET_ERR( rval, "Invalid value for GATHER_SET option" );
    }
 
    rval = opts.get_int_option( "TIMESTEPBASE", 0, tStepBase );
    if( MB_TYPE_OUT_OF_RANGE == rval )
    {
        MB_SET_ERR( rval, "Invalid value for TIMESTEPBASE option" );
    }
 
    rval = opts.get_int_option( "TRIVIAL_PARTITION_SHIFT", 1, trivialPartitionShift );
    if( MB_TYPE_OUT_OF_RANGE == rval )
    {
        MB_SET_ERR( rval, "Invalid value for TRIVIAL_PARTITION_SHIFT option" );
    }
 
#ifdef MOAB_HAVE_MPI
    isParallel = ( opts.match_option( "PARALLEL", "READ_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 );
    }
    const int rank = myPcomm->proc_config().proc_rank();
    dbgOut.set_rank( rank );
 
    int dum;
    rval = opts.match_option( "PARTITION_METHOD", ScdParData::PartitionMethodNames, dum );
    if( MB_FAILURE == rval )
    {
        MB_SET_ERR( rval, "Unknown partition method specified" );
    }
    else if( MB_ENTITY_NOT_FOUND == rval )
        partMethod = ScdParData::ALLJORKORI;
    else
        partMethod = dum;
#endif
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::read_header()
{
    dbgOut.tprint( 1, "Reading header...\n" );
 
    // Get the global attributes
    int numgatts;
    int success;
    success = NCFUNC( inq_natts )( fileId, &numgatts );
    if( success ) MB_SET_ERR( MB_FAILURE, "Couldn't get number of global attributes" );
 
    // Read attributes into globalAtts
    ErrorCode result = get_attributes( NC_GLOBAL, numgatts, globalAtts );
    MB_CHK_SET_ERR( result, "Trouble getting global attributes" );
    dbgOut.tprintf( 1, "Read %u attributes\n", (unsigned int)globalAtts.size() );
 
    // Read in dimensions into dimNames and dimLens
    result = get_dimensions( fileId, dimNames, dimLens );
    MB_CHK_SET_ERR( result, "Trouble getting dimensions" );
    dbgOut.tprintf( 1, "Read %u dimensions\n", (unsigned int)dimNames.size() );
 
    // Read in variables into varInfo
    result = get_variables();
    MB_CHK_SET_ERR( result, "Trouble getting variables" );
    dbgOut.tprintf( 1, "Read %u variables\n", (unsigned int)varInfo.size() );
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_attributes( int var_id, int num_atts, std::map< std::string, AttData >& atts, const char* prefix )
{
    char dum_name[120];
 
    for( int i = 0; i < num_atts; i++ )
    {
        // Get the name
        int success = NCFUNC( inq_attname )( fileId, var_id, i, dum_name );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting attribute name" );
 
        AttData& data = atts[std::string( dum_name )];
        data.attName  = std::string( dum_name );
        success       = NCFUNC( inq_att )( fileId, var_id, dum_name, &data.attDataType, &data.attLen );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting info for attribute " << data.attName );
        data.attVarId = var_id;
 
        dbgOut.tprintf( 2, "%sAttribute %s: length=%u, varId=%d, type=%d\n", ( prefix ? prefix : "" ),
                        data.attName.c_str(), (unsigned int)data.attLen, data.attVarId, data.attDataType );
    }
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_dimensions( int file_id, std::vector< std::string >& dim_names, std::vector< int >& dim_lens )
{
    // Get the number of dimensions
    int num_dims;
    int success = NCFUNC( inq_ndims )( file_id, &num_dims );
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dimensions" );
 
    if( num_dims > NC_MAX_DIMS )
    {
        MB_SET_ERR( MB_FAILURE,
                    "ReadNC: File contains " << num_dims << " dims but NetCDF library supports only " << NC_MAX_DIMS );
    }
 
    char dim_name[NC_MAX_NAME + 1];
    NCDF_SIZE dim_len;
    dim_names.resize( num_dims );
    dim_lens.resize( num_dims );
 
    for( int i = 0; i < num_dims; i++ )
    {
        success = NCFUNC( inq_dim )( file_id, i, dim_name, &dim_len );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimension info" );
 
        dim_names[i] = std::string( dim_name );
        dim_lens[i]  = dim_len;
 
        dbgOut.tprintf( 2, "Dimension %s, length=%u\n", dim_name, (unsigned int)dim_len );
    }
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_variables()
{
    // First cache the number of time steps
    std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), "time" );
    if( vit == dimNames.end() ) vit = std::find( dimNames.begin(), dimNames.end(), "t" );
 
    int ntimes = 0;
    if( vit != dimNames.end() ) ntimes = dimLens[vit - dimNames.begin()];
    if( !ntimes ) ntimes = 1;
 
    // Get the number of variables
    int num_vars;
    int success = NCFUNC( inq_nvars )( fileId, &num_vars );
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of variables" );
 
    if( num_vars > NC_MAX_VARS )
    {
        MB_SET_ERR( MB_FAILURE,
                    "ReadNC: File contains " << num_vars << " vars but NetCDF library supports only " << NC_MAX_VARS );
    }
 
    char var_name[NC_MAX_NAME + 1];
    int var_ndims;
 
    for( int i = 0; i < num_vars; i++ )
    {
        // Get the name first, so we can allocate a map iterate for this var
        success = NCFUNC( inq_varname )( fileId, i, var_name );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting variable name" );
        VarData& data = varInfo[std::string( var_name )];
        data.varName  = std::string( var_name );
        data.varId    = i;
        data.varTags.resize( ntimes, 0 );
 
        // Get the data type
        success = NCFUNC( inq_vartype )( fileId, i, &data.varDataType );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting data type for variable " << data.varName );
 
        // Get the number of dimensions, then the dimensions
        success = NCFUNC( inq_varndims )( fileId, i, &var_ndims );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
        data.varDims.resize( var_ndims );
 
        success = NCFUNC( inq_vardimid )( fileId, i, &data.varDims[0] );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimensions for variable " << data.varName );
 
        // Finally, get the number of attributes, then the attributes
        success = NCFUNC( inq_varnatts )( fileId, i, &data.numAtts );
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
 
        // Print debug info here so attribute info comes afterwards
        dbgOut.tprintf( 2, "Variable %s: Id=%d, numAtts=%d, datatype=%d, num_dims=%u\n", data.varName.c_str(),
                        data.varId, data.numAtts, data.varDataType, (unsigned int)data.varDims.size() );
 
        MB_CHK_SET_ERR( get_attributes( i, data.numAtts, data.varAtts, "   " ),
                        "Trouble getting attributes for variable " << data.varName );
    }
 
    return MB_SUCCESS;
}
 
ErrorCode ReadNC::read_tag_values( const char*,
                                   const char*,
                                   const FileOptions&,
                                   std::vector< int >&,
                                   const SubsetList* )
{
    return MB_FAILURE;
}
 
}  // namespace moab