Utility used for reading portions of an HDF5 dataset. More...

#include <ReadHDF5Dataset.hpp>

Collaboration diagram for moab::ReadHDF5Dataset:

Classes
class	Exception

Public Types
typedef int	Comm

Public Member Functions
	ReadHDF5Dataset (const char debug_desc, hid_t data_set_handle, bool parallel, const Comm communicator=0, bool close_data_set_on_destruct=true)
	Setup to read entire table. More...

	ReadHDF5Dataset (const char debug_desc, bool parallel, const Comm communicator=0)

void	init (hid_t data_set_handle, bool close_data_set_on_destruct=true)

bool	will_close_data_set () const

void	close_data_set_on_destruct (bool val)

	~ReadHDF5Dataset ()

void	set_file_ids (const Range &file_ids, EntityHandle start_id, hsize_t row_cout, hid_t data_type)
	Change file ids to read from. More...

void	set_all_file_ids (hsize_t row_count, hid_t data_type)
	Read all values in dataset (undo set_file_ids) More...

bool	done () const
	Return false if more data to read, true otherwise. More...

void	read (void *buffer, size_t &rows_read)
	Read rows of table. More...

Range::const_iterator	next_file_id () const
	Return position in `Range` of file IDs at which next read will start. More...

void	null_read ()
	Do null read operation. More...

unsigned	columns () const

void	set_column (unsigned c)

unsigned long	get_read_count () const

const char *	get_debug_desc () const

Static Public Member Functions
static void	set_hyperslab_selection_limit (size_t val)

static void	default_hyperslab_selection_limit ()

static void	append_hyperslabs ()

static void	or_hyperslabs ()

Private Member Functions
Range::const_iterator	next_end (Range::const_iterator iter)

Private Attributes
Range	internalRange
	used when reading entire dataset More...

bool	closeDataSet
	close dataset in destructor More...

hsize_t	dataSetOffset [64]

hsize_t	dataSetCount [64]

hid_t	dataSet
	Handle for HDF5 data set. More...

hid_t	dataSpace
	Data space for data set. More...

hid_t	dataType
	Data type client code wants for data. More...

hid_t	fileType
	Data type as stored in data set. More...

hid_t	ioProp
	Used to specify collective IO. More...

int	dataSpaceRank
	Rank of data set. More...

hsize_t	rowsInTable
	Total number of rows in dataset. More...

bool	doConversion
	True if dataType != fileType. More...

bool	nativeParallel
	If true then reading different data on different procs. More...

hsize_t	readCount
	Number of actual reads to do. More...

hsize_t	bufferSize
	size of buffer passed to `read`, in number of rows More...

const Comm *	mpiComm

Range::const_iterator	currOffset

Range::const_iterator	rangeEnd

EntityHandle	startID

std::string	mpeDesc

Static Private Attributes
static bool	haveMPEEvents = false

static std::pair< int, int >	mpeReadEvent

static std::pair< int, int >	mpeReduceEvent

static size_t	hyperslabSelectionLimit = DEFAULT_HYPERSLAB_SELECTION_LIMIT

static H5S_seloper_t	hyperslabSelectOp = H5S_SELECT_OR

Detailed Description

Utility used for reading portions of an HDF5 dataset.

Implement iterative read of table where:

subset of rows to be read can be specified usign an Range of offsets
each read fills as much as possible of a passed buffer
each read call reads a subsequent set of rows of the data set in an iterator-like fashion.

NOTE: This class also implements an RAII pattern for the data set handle: It will close the data set in its destructor unless it is specified to the constructor that only a single column should be read.

NOTE: This class will always do collective IO for parallel reads.

Definition at line 38 of file ReadHDF5Dataset.hpp.

Member Typedef Documentation

◆ Comm

typedef int moab::ReadHDF5Dataset::Comm

Definition at line 44 of file ReadHDF5Dataset.hpp.

Constructor & Destructor Documentation

◆ ReadHDF5Dataset() [1/2]

moab::ReadHDF5Dataset::ReadHDF5Dataset	(	const char *	debug_desc,
		hid_t	data_set_handle,
		bool	parallel,
		const Comm *	communicator = `0`,
		bool	close_data_set_on_destruct = `true`
	)

Setup to read entire table.

Parameters

data_set_handle	The HDF5 DataSet to read.
parallel	Doing true partial-read parallel read (as opposed to read and delete where collective IO is done for everything because all procs read the same stuff.)
communictor	If `parallel` is `true` and `io_prop` is `H5FD_MPIO_COLLECTIVE`, then this must be a pointer to the MPI_Communicator value.
close_data_set_on_destruct	Call `H5Dclose` on passed `data_set_handle` in desturctor.

\NOTE If parallel is true and io_prop is H5FD_MPIO_COLLECTIVE, then not only must communicator be non-null, but this call must be made collectively!

\NOTE Class instance will not be usable until one of either set_file_ids or set_all_file_ids is called.

Definition at line 85 of file ReadHDF5Dataset.cpp.

   90     : closeDataSet( close_data_set ), dataSet( data_set_handle ), dataSpace( -1 ), dataType( -1 ), fileType( -1 ),
   91       ioProp( H5P_DEFAULT ), dataSpaceRank( 0 ), rowsInTable( 0 ), doConversion( false ), nativeParallel( parallel ),
   92       readCount( 0 ), bufferSize( 0 ), mpiComm( communicator ), mpeDesc( debug_desc )
   93 {
   94     if( !haveMPEEvents )
   95     {
   96         haveMPEEvents  = true;
   97         mpeReadEvent   = allocate_mpe_state( "ReadHDF5Dataset::read", "yellow" );
   98         mpeReduceEvent = allocate_mpe_state( "ReadHDF5Dataset::all_reduce", "yellow" );
   99     }
  100  
  101     init( data_set_handle, close_data_set );
  102  
  103 #ifndef MOAB_HAVE_HDF5_PARALLEL
  104     if( nativeParallel ) throw Exception( __LINE__ );
  105 #else
  106     if( nativeParallel && !mpiComm ) throw Exception( __LINE__ );
  107  
  108     if( mpiComm )
  109     {
  110         ioProp = H5Pcreate( H5P_DATASET_XFER );
  111         H5Pset_dxpl_mpio( ioProp, H5FD_MPIO_COLLECTIVE );
  112     }
  113 #endif
  114 }

References moab::allocate_mpe_state(), haveMPEEvents, init(), ioProp, mpeReadEvent, mpeReduceEvent, mpiComm, and nativeParallel.

◆ ReadHDF5Dataset() [2/2]

moab::ReadHDF5Dataset::ReadHDF5Dataset	(	const char *	debug_desc,
		bool	parallel,
		const Comm *	communicator = `0`
	)

Definition at line 60 of file ReadHDF5Dataset.cpp.

   61     : closeDataSet( false ), dataSet( -1 ), dataSpace( -1 ), dataType( -1 ), fileType( -1 ), ioProp( H5P_DEFAULT ),
   62       dataSpaceRank( 0 ), rowsInTable( 0 ), doConversion( false ), nativeParallel( parallel ), readCount( 0 ),
   63       bufferSize( 0 ), mpiComm( communicator ), mpeDesc( debug_desc )
   64 {
   65     if( !haveMPEEvents )
   66     {
   67         haveMPEEvents  = true;
   68         mpeReadEvent   = allocate_mpe_state( "ReadHDF5Dataset::read", "yellow" );
   69         mpeReduceEvent = allocate_mpe_state( "ReadHDF5Dataset::all_reduce", "yellow" );
   70     }
   71  
   72 #ifndef MOAB_HAVE_HDF5_PARALLEL
   73     if( nativeParallel ) throw Exception( __LINE__ );
   74 #else
   75     if( nativeParallel && !mpiComm ) throw Exception( __LINE__ );
   76  
   77     if( mpiComm )
   78     {
   79         ioProp = H5Pcreate( H5P_DATASET_XFER );
   80         H5Pset_dxpl_mpio( ioProp, H5FD_MPIO_COLLECTIVE );
   81     }
   82 #endif
   83 }

References moab::allocate_mpe_state(), haveMPEEvents, ioProp, mpeReadEvent, mpeReduceEvent, mpiComm, and nativeParallel.

◆ ~ReadHDF5Dataset()

moab::ReadHDF5Dataset::~ReadHDF5Dataset ( )

Definition at line 231 of file ReadHDF5Dataset.cpp.

  232 {
  233     if( fileType >= 0 ) H5Tclose( fileType );
  234     if( dataSpace >= 0 ) H5Sclose( dataSpace );
  235     if( closeDataSet && dataSet >= 0 ) H5Dclose( dataSet );
  236     dataSpace = dataSet = -1;
  237     if( ioProp != H5P_DEFAULT ) H5Pclose( ioProp );
  238 }

References closeDataSet, dataSet, dataSpace, fileType, and ioProp.

Member Function Documentation

◆ append_hyperslabs()

static void moab::ReadHDF5Dataset::append_hyperslabs ( )

inlinestatic

Use non-standard 'APPEND' operation for hyperslab selection

Definition at line 166 of file ReadHDF5Dataset.hpp.

  167     {
  168         hyperslabSelectOp = H5S_SELECT_APPEND;
  169     }

References hyperslabSelectOp.

Referenced by moab::ReadHDF5::set_up_read().

◆ close_data_set_on_destruct()

void moab::ReadHDF5Dataset::close_data_set_on_destruct ( bool val )

inline

Definition at line 85 of file ReadHDF5Dataset.hpp.

   86     {
   87         closeDataSet = val;
   88     }

References closeDataSet.

◆ columns()

unsigned moab::ReadHDF5Dataset::columns ( ) const

Definition at line 137 of file ReadHDF5Dataset.cpp.

  138 {
  139     if( dataSpaceRank == 1 )
  140         return 1;
  141     else if( dataSpaceRank == 2 )
  142         return dataSetCount[1];
  143  
  144     throw Exception( __LINE__ );
  145 }

References dataSetCount, and dataSpaceRank.

Referenced by read().

◆ default_hyperslab_selection_limit()

void moab::ReadHDF5Dataset::default_hyperslab_selection_limit ( )

static

Definition at line 33 of file ReadHDF5Dataset.cpp.

   34 {
   35     hyperslabSelectionLimit = DEFAULT_HYPERSLAB_SELECTION_LIMIT;
   36 }

References moab::DEFAULT_HYPERSLAB_SELECTION_LIMIT, and hyperslabSelectionLimit.

Referenced by moab::ReadHDF5::set_up_read().

◆ done()

bool moab::ReadHDF5Dataset::done ( ) const

inline

Return false if more data to read, true otherwise.

Test if the iterative read has reached the end.

Definition at line 116 of file ReadHDF5Dataset.hpp.

  117     {
  118         return ( currOffset == rangeEnd ) && ( readCount == 0 );
  119     }

References currOffset, rangeEnd, and readCount.

Referenced by moab::ReadHDF5VarLen::read_data(), moab::ReadHDF5::read_dense_tag(), moab::ReadHDF5::read_elems(), moab::ReadHDF5::read_nodes(), moab::ReadHDF5VarLen::read_offsets(), moab::ReadHDF5::read_set_data(), moab::ReadHDF5::read_sparse_tag(), moab::ReadHDF5::read_sparse_tag_indices(), and moab::ReadHDF5::read_tag_values_partial().

◆ get_debug_desc()

const char* moab::ReadHDF5Dataset::get_debug_desc ( ) const

inline

Definition at line 154 of file ReadHDF5Dataset.hpp.

  155     {
  156         return mpeDesc.c_str();
  157     }

References mpeDesc.

Referenced by moab::ReadHDF5VarLen::read_data(), moab::ReadHDF5VarLen::read_offsets(), and moab::ReadHDF5::read_set_data().

◆ get_read_count()

unsigned long moab::ReadHDF5Dataset::get_read_count ( ) const

inline

Definition at line 150 of file ReadHDF5Dataset.hpp.

  151     {
  152         return readCount;
  153     }

References readCount.

Referenced by moab::ReadHDF5VarLen::read_data(), moab::ReadHDF5::read_dense_tag(), moab::ReadHDF5::read_elems(), moab::ReadHDF5::read_nodes(), moab::ReadHDF5VarLen::read_offsets(), moab::ReadHDF5::read_sparse_tag(), moab::ReadHDF5::read_sparse_tag_indices(), and moab::ReadHDF5::read_tag_values_partial().

◆ init()

void moab::ReadHDF5Dataset::init	(	hid_t	data_set_handle,
		bool	close_data_set_on_destruct = `true`
	)

Definition at line 116 of file ReadHDF5Dataset.cpp.

  117 {
  118     closeDataSet = close_data_set;
  119     dataSet      = data_set_handle;
  120  
  121     fileType = H5Dget_type( data_set_handle );
  122     if( fileType < 0 ) throw Exception( __LINE__ );
  123  
  124     dataSpace = H5Dget_space( dataSet );
  125     if( dataSpace < 0 ) throw Exception( __LINE__ );
  126  
  127     dataSpaceRank = H5Sget_simple_extent_dims( dataSpace, dataSetCount, dataSetOffset );
  128     if( dataSpaceRank < 0 ) throw Exception( __LINE__ );
  129     rowsInTable = dataSetCount[0];
  130  
  131     for( int i = 0; i < dataSpaceRank; ++i )
  132         dataSetOffset[i] = 0;
  133  
  134     currOffset = rangeEnd = internalRange.end();
  135 }

References closeDataSet, currOffset, dataSet, dataSetCount, dataSetOffset, dataSpace, dataSpaceRank, moab::Range::end(), fileType, internalRange, rangeEnd, and rowsInTable.

Referenced by moab::ReadHDF5::read_set_ids_recursive(), and ReadHDF5Dataset().

◆ next_end()

Range::const_iterator moab::ReadHDF5Dataset::next_end ( Range::const_iterator iter )

private

Definition at line 154 of file ReadHDF5Dataset.cpp.

  155 {
  156     size_t slabs_remaining = hyperslabSelectionLimit;
  157     size_t avail           = bufferSize;
  158     while( iter != rangeEnd && slabs_remaining )
  159     {
  160         size_t count = *( iter.end_of_block() ) - *iter + 1;
  161         if( count >= avail )
  162         {
  163             iter += avail;
  164             break;
  165         }
  166  
  167         avail -= count;
  168         iter += count;
  169         --slabs_remaining;
  170     }
  171     return iter;
  172 }

References bufferSize, moab::Range::const_iterator::end_of_block(), hyperslabSelectionLimit, and rangeEnd.

Referenced by read(), and set_file_ids().

◆ next_file_id()

Range::const_iterator moab::ReadHDF5Dataset::next_file_id ( ) const

inline

Return position in Range of file IDs at which next read will start.

Definition at line 132 of file ReadHDF5Dataset.hpp.

  133     {
  134         return currOffset;
  135     }

References currOffset.

◆ null_read()

void moab::ReadHDF5Dataset::null_read ( )

Do null read operation.

Do a read call requesting no data. This functionality is provided so as to allow collective IO when not all processes need to make the same number of read calls. To prevent deadlock in this case, processes that have finished their necessary read calls can call this function so that all processes are calling the read method collectively.

Definition at line 297 of file ReadHDF5Dataset.cpp.

  298 {
  299     herr_t err;
  300     err = H5Sselect_none( dataSpace );
  301     if( err < 0 ) throw Exception( __LINE__ );
  302  
  303     //#if HDF5_16API
  304     hsize_t one  = 1;
  305     hid_t mem_id = H5Screate_simple( 1, &one, NULL );
  306     if( mem_id < 0 ) throw Exception( __LINE__ );
  307     err = H5Sselect_none( mem_id );
  308     if( err < 0 )
  309     {
  310         H5Sclose( mem_id );
  311         throw Exception( __LINE__ );
  312     }
  313     //#else
  314     //  hid_t mem_id = H5Screate(H5S_NULL);
  315     //  if (mem_id < 0)
  316     //    throw Exception(__LINE__);
  317     //#endif
  318  
  319     err = H5Dread( dataSet, fileType, mem_id, dataSpace, ioProp, 0 );
  320     H5Sclose( mem_id );
  321     if( err < 0 ) throw Exception( __LINE__ );
  322 }

References dataSet, dataSpace, fileType, and ioProp.

Referenced by read(), and moab::ReadHDF5::read_set_data().

◆ or_hyperslabs()

static void moab::ReadHDF5Dataset::or_hyperslabs ( )

inlinestatic

Revert to default select behavior for standard HDF5 library

Definition at line 171 of file ReadHDF5Dataset.hpp.

  172     {
  173         hyperslabSelectOp = H5S_SELECT_OR;
  174     }

References hyperslabSelectOp.

◆ read()

void moab::ReadHDF5Dataset::read	(	void *	buffer,
		size_t &	rows_read
	)

Read rows of table.

Read up to max_num_rows from data set.

Parameters

buffer	Memory in which to store values read from data set
rows_read	The actual number of rows read from the table. Will never exceed `max_rows` .

Definition at line 240 of file ReadHDF5Dataset.cpp.

  241 {
  242     herr_t err;
  243     rows_read = 0;
  244  
  245     MPE_Log_event( mpeReadEvent.first, (int)readCount, mpeDesc.c_str() );
  246     if( currOffset != rangeEnd )
  247     {
  248  
  249         // Build H5S hyperslab selection describing the portions of the
  250         // data set to read
  251         H5S_seloper_t sop       = H5S_SELECT_SET;
  252         Range::iterator new_end = next_end( currOffset );
  253         while( currOffset != new_end )
  254         {
  255             size_t count = *( currOffset.end_of_block() ) - *currOffset + 1;
  256             if( new_end != rangeEnd && *currOffset + count > *new_end )
  257             {
  258                 count = *new_end - *currOffset;
  259             }
  260             rows_read += count;
  261  
  262             dataSetOffset[0] = *currOffset - startID;
  263             dataSetCount[0]  = count;
  264             err              = H5Sselect_hyperslab( dataSpace, sop, dataSetOffset, NULL, dataSetCount, 0 );
  265             if( err < 0 ) throw Exception( __LINE__ );
  266             sop = hyperslabSelectOp;  // subsequent calls to select_hyperslab append
  267  
  268             currOffset += count;
  269         }
  270  
  271         // Create a data space describing the memory in which to read the data
  272         dataSetCount[0] = rows_read;
  273         hid_t mem_id    = H5Screate_simple( dataSpaceRank, dataSetCount, NULL );
  274         if( mem_id < 0 ) throw Exception( __LINE__ );
  275  
  276         // Do the actual read
  277         err = H5Dread( dataSet, fileType, mem_id, dataSpace, ioProp, buffer );
  278         H5Sclose( mem_id );
  279         if( err < 0 ) throw Exception( __LINE__ );
  280  
  281         if( readCount ) --readCount;
  282  
  283         if( doConversion )
  284         {
  285             err = H5Tconvert( fileType, dataType, rows_read * columns(), buffer, 0, H5P_DEFAULT );
  286             if( err < 0 ) throw Exception( __LINE__ );
  287         }
  288     }
  289     else if( readCount )
  290     {
  291         null_read();
  292         --readCount;
  293     }
  294     MPE_Log_event( mpeReadEvent.second, (int)readCount, mpeDesc.c_str() );
  295 }

References buffer, columns(), currOffset, dataSet, dataSetCount, dataSetOffset, dataSpace, dataSpaceRank, dataType, doConversion, moab::Range::const_iterator::end_of_block(), fileType, hyperslabSelectOp, ioProp, MPE_Log_event, mpeDesc, mpeReadEvent, next_end(), null_read(), rangeEnd, readCount, and startID.

Referenced by moab::ReadHDF5VarLen::read_data(), moab::ReadHDF5::read_dense_tag(), moab::ReadHDF5::read_elems(), moab::ReadHDF5::read_nodes(), moab::ReadHDF5VarLen::read_offsets(), moab::ReadHDF5::read_set_data(), moab::ReadHDF5::read_sparse_tag(), moab::ReadHDF5::read_sparse_tag_indices(), and moab::ReadHDF5::read_tag_values_partial().

◆ set_all_file_ids()

void moab::ReadHDF5Dataset::set_all_file_ids	(	hsize_t	row_count,
		hid_t	data_type
	)

Read all values in dataset (undo set_file_ids)

Parameters

row_count	Read buffer size in number of table rows.
data_type	The data type of the buffer into which table values are to be read.

Definition at line 224 of file ReadHDF5Dataset.cpp.

  225 {
  226     internalRange.clear();
  227     internalRange.insert( (EntityHandle)1, (EntityHandle)( rowsInTable ) );
  228     set_file_ids( internalRange, 1, row_count, data_type );
  229 }

References moab::Range::clear(), moab::Range::insert(), internalRange, rowsInTable, and set_file_ids().

Referenced by moab::ReadHDF5::read_sparse_tag_indices(), and moab::ReadHDF5::read_tag_values_partial().

◆ set_column()

void moab::ReadHDF5Dataset::set_column ( unsigned c )

Definition at line 147 of file ReadHDF5Dataset.cpp.

  148 {
  149     if( dataSpaceRank != 2 || column >= dataSetCount[1] ) throw Exception( __LINE__ );
  150     dataSetCount[1]  = 1;
  151     dataSetOffset[1] = column;
  152 }

References dataSetCount, dataSetOffset, and dataSpaceRank.

Referenced by moab::ReadHDF5::read_nodes().

◆ set_file_ids()

void moab::ReadHDF5Dataset::set_file_ids	(	const Range &	file_ids,
		EntityHandle	start_id,
		hsize_t	row_cout,
		hid_t	data_type
	)

Change file ids to read from.

Parameters

file_ids	List of rows to read from dataset
start_id	Rows of dataset are enumerating beginning with this value. Thus the offset row to be read from dataset will be `file_ids.begin()` - `start_id` .
row_count	Read buffer size in number of table rows.
data_type	The data type of the buffer into which table values are to be read.

Definition at line 174 of file ReadHDF5Dataset.cpp.

  175 {
  176     startID    = start_id;
  177     currOffset = file_ids.begin();
  178     rangeEnd   = file_ids.end();
  179     readCount  = 0;
  180     bufferSize = row_count;
  181  
  182     // if a) user specified buffer size and b) we're doing a true
  183     // parallel partial read and c) we're doing collective I/O, then
  184     // we need to know the maximum number of reads that will be done.
  185 #ifdef MOAB_HAVE_HDF5_PARALLEL
  186     if( nativeParallel )
  187     {
  188         Range::const_iterator iter = currOffset;
  189         while( iter != rangeEnd )
  190         {
  191             ++readCount;
  192             iter = next_end( iter );
  193         }
  194  
  195         MPE_Log_event( mpeReduceEvent.first, (int)readCount, mpeDesc.c_str() );
  196         unsigned long recv = readCount, send = readCount;
  197         MPI_Allreduce( &send, &recv, 1, MPI_UNSIGNED_LONG, MPI_MAX, *mpiComm );
  198         readCount = recv;
  199         MPE_Log_event( mpeReduceEvent.second, (int)readCount, mpeDesc.c_str() );
  200     }
  201 #endif
  202  
  203     dataType     = data_type;
  204     htri_t equal = H5Tequal( fileType, dataType );
  205     if( equal < 0 ) throw Exception( __LINE__ );
  206     doConversion = !equal;
  207  
  208     // We always read in the format of the file to avoid stupind HDF5
  209     // library behavior when reading in parallel.  We call H5Tconvert
  210     // ourselves to do the data conversion.  If the type we're reading
  211     // from the file is larger than the type we want in memory, then
  212     // we need to reduce num_rows so that we can read the larger type
  213     // from the file into the passed buffer mean to accomodate num_rows
  214     // of values of the smaller in-memory type.
  215     if( doConversion )
  216     {
  217         size_t mem_size, file_size;
  218         mem_size  = H5Tget_size( dataType );
  219         file_size = H5Tget_size( fileType );
  220         if( file_size > mem_size ) bufferSize = bufferSize * mem_size / file_size;
  221     }
  222 }

References moab::Range::begin(), bufferSize, currOffset, dataType, doConversion, moab::Range::end(), fileType, MPE_Log_event, mpeDesc, mpeReduceEvent, mpiComm, nativeParallel, next_end(), rangeEnd, readCount, and startID.

Referenced by moab::ReadHDF5VarLen::read_data(), moab::ReadHDF5::read_dense_tag(), moab::ReadHDF5::read_elems(), moab::ReadHDF5::read_nodes(), moab::ReadHDF5VarLen::read_offsets(), moab::ReadHDF5::read_set_data(), moab::ReadHDF5::read_sparse_tag(), moab::ReadHDF5::read_tag_values_partial(), and set_all_file_ids().

◆ set_hyperslab_selection_limit()

static void moab::ReadHDF5Dataset::set_hyperslab_selection_limit ( size_t val )

inlinestatic

Definition at line 159 of file ReadHDF5Dataset.hpp.

  160     {
  161         hyperslabSelectionLimit = val;
  162     }

References hyperslabSelectionLimit.

Referenced by moab::ReadHDF5::set_up_read().

◆ will_close_data_set()

bool moab::ReadHDF5Dataset::will_close_data_set ( ) const

inline

Definition at line 81 of file ReadHDF5Dataset.hpp.

   82     {
   83         return closeDataSet;
   84     }

References closeDataSet.

Member Data Documentation

◆ bufferSize

hsize_t moab::ReadHDF5Dataset::bufferSize

private

size of buffer passed to read, in number of rows

Definition at line 194 of file ReadHDF5Dataset.hpp.

Referenced by next_end(), and set_file_ids().

◆ closeDataSet

bool moab::ReadHDF5Dataset::closeDataSet

private

close dataset in destructor

Definition at line 181 of file ReadHDF5Dataset.hpp.

Referenced by close_data_set_on_destruct(), init(), will_close_data_set(), and ~ReadHDF5Dataset().

◆ currOffset

Range::const_iterator moab::ReadHDF5Dataset::currOffset

private

Definition at line 197 of file ReadHDF5Dataset.hpp.

Referenced by done(), init(), next_file_id(), read(), and set_file_ids().

◆ dataSet

hid_t moab::ReadHDF5Dataset::dataSet

private

Handle for HDF5 data set.

Definition at line 183 of file ReadHDF5Dataset.hpp.

Referenced by init(), null_read(), read(), and ~ReadHDF5Dataset().

◆ dataSetCount

hsize_t moab::ReadHDF5Dataset::dataSetCount[64]

private

Definition at line 182 of file ReadHDF5Dataset.hpp.

Referenced by columns(), init(), read(), and set_column().

◆ dataSetOffset

hsize_t moab::ReadHDF5Dataset::dataSetOffset[64]

private

Definition at line 182 of file ReadHDF5Dataset.hpp.

Referenced by init(), read(), and set_column().

◆ dataSpace

hid_t moab::ReadHDF5Dataset::dataSpace

private

Data space for data set.

Definition at line 184 of file ReadHDF5Dataset.hpp.

Referenced by init(), null_read(), read(), and ~ReadHDF5Dataset().

◆ dataSpaceRank

int moab::ReadHDF5Dataset::dataSpaceRank

private

Rank of data set.

Definition at line 188 of file ReadHDF5Dataset.hpp.

Referenced by columns(), init(), read(), and set_column().

◆ dataType

hid_t moab::ReadHDF5Dataset::dataType

private

Data type client code wants for data.

Definition at line 185 of file ReadHDF5Dataset.hpp.

Referenced by read(), and set_file_ids().

◆ doConversion

bool moab::ReadHDF5Dataset::doConversion

private

True if dataType != fileType.

Definition at line 190 of file ReadHDF5Dataset.hpp.

Referenced by read(), and set_file_ids().

◆ fileType

hid_t moab::ReadHDF5Dataset::fileType

private

Data type as stored in data set.

Definition at line 186 of file ReadHDF5Dataset.hpp.

Referenced by init(), null_read(), read(), set_file_ids(), and ~ReadHDF5Dataset().

◆ haveMPEEvents

bool moab::ReadHDF5Dataset::haveMPEEvents = false

staticprivate

Definition at line 200 of file ReadHDF5Dataset.hpp.

Referenced by ReadHDF5Dataset().

◆ hyperslabSelectionLimit

size_t moab::ReadHDF5Dataset::hyperslabSelectionLimit = DEFAULT_HYPERSLAB_SELECTION_LIMIT

staticprivate

Definition at line 205 of file ReadHDF5Dataset.hpp.

Referenced by default_hyperslab_selection_limit(), next_end(), and set_hyperslab_selection_limit().

◆ hyperslabSelectOp

H5S_seloper_t moab::ReadHDF5Dataset::hyperslabSelectOp = H5S_SELECT_OR

staticprivate

Definition at line 206 of file ReadHDF5Dataset.hpp.

Referenced by append_hyperslabs(), or_hyperslabs(), and read().

◆ internalRange

Range moab::ReadHDF5Dataset::internalRange

private

used when reading entire dataset

Definition at line 179 of file ReadHDF5Dataset.hpp.

Referenced by init(), and set_all_file_ids().

◆ ioProp

hid_t moab::ReadHDF5Dataset::ioProp

private

Used to specify collective IO.

Definition at line 187 of file ReadHDF5Dataset.hpp.

Referenced by null_read(), read(), ReadHDF5Dataset(), and ~ReadHDF5Dataset().

◆ mpeDesc

std::string moab::ReadHDF5Dataset::mpeDesc

private

Definition at line 203 of file ReadHDF5Dataset.hpp.

Referenced by get_debug_desc(), read(), and set_file_ids().

◆ mpeReadEvent

std::pair< int, int > moab::ReadHDF5Dataset::mpeReadEvent

staticprivate

Definition at line 201 of file ReadHDF5Dataset.hpp.

Referenced by read(), and ReadHDF5Dataset().

◆ mpeReduceEvent

std::pair< int, int > moab::ReadHDF5Dataset::mpeReduceEvent

staticprivate

Definition at line 202 of file ReadHDF5Dataset.hpp.

Referenced by ReadHDF5Dataset(), and set_file_ids().

◆ mpiComm

const Comm* moab::ReadHDF5Dataset::mpiComm

private

Definition at line 195 of file ReadHDF5Dataset.hpp.

Referenced by ReadHDF5Dataset(), and set_file_ids().

◆ nativeParallel

bool moab::ReadHDF5Dataset::nativeParallel

private

If true then reading different data on different procs.

Definition at line 191 of file ReadHDF5Dataset.hpp.

Referenced by ReadHDF5Dataset(), and set_file_ids().

◆ rangeEnd

Range::const_iterator moab::ReadHDF5Dataset::rangeEnd

private

Definition at line 197 of file ReadHDF5Dataset.hpp.

Referenced by done(), init(), next_end(), read(), and set_file_ids().

◆ readCount

hsize_t moab::ReadHDF5Dataset::readCount

private

Number of actual reads to do.

Definition at line 193 of file ReadHDF5Dataset.hpp.

Referenced by done(), get_read_count(), read(), and set_file_ids().

◆ rowsInTable

hsize_t moab::ReadHDF5Dataset::rowsInTable

private

Total number of rows in dataset.

Definition at line 189 of file ReadHDF5Dataset.hpp.

Referenced by init(), and set_all_file_ids().

◆ startID

EntityHandle moab::ReadHDF5Dataset::startID

private

Definition at line 198 of file ReadHDF5Dataset.hpp.

Referenced by read(), and set_file_ids().

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ Comm

Constructor & Destructor Documentation

◆ ReadHDF5Dataset() [1/2]

◆ ReadHDF5Dataset() [2/2]

◆ ~ReadHDF5Dataset()

Member Function Documentation

◆ append_hyperslabs()

◆ close_data_set_on_destruct()

◆ columns()

◆ default_hyperslab_selection_limit()

◆ done()

◆ get_debug_desc()

◆ get_read_count()

◆ init()

◆ next_end()

◆ next_file_id()

◆ null_read()

◆ or_hyperslabs()

◆ read()

◆ set_all_file_ids()

◆ set_column()

◆ set_file_ids()

◆ set_hyperslab_selection_limit()

◆ will_close_data_set()

Member Data Documentation

◆ bufferSize

◆ closeDataSet

◆ currOffset

◆ dataSet

◆ dataSetCount

◆ dataSetOffset

◆ dataSpace

◆ dataSpaceRank

◆ dataType

◆ doConversion

◆ fileType

◆ haveMPEEvents

◆ hyperslabSelectionLimit

◆ hyperslabSelectOp

◆ internalRange

◆ ioProp

◆ mpeDesc

◆ mpeReadEvent

◆ mpeReduceEvent

◆ mpiComm

◆ nativeParallel

◆ rangeEnd

◆ readCount

◆ rowsInTable

◆ startID