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.

  : closeDataSet( close_data_set ), dataSet( data_set_handle ), dataSpace( -1 ), dataType( -1 ), fileType( -1 ),
  ioProp( H5P_DEFAULT ), dataSpaceRank( 0 ), rowsInTable( 0 ), doConversion( false ), nativeParallel( parallel ),
  readCount( 0 ), bufferSize( 0 ), mpiComm( communicator ), mpeDesc( debug_desc )
 {
  if( !haveMPEEvents )
  {
  haveMPEEvents = true;
  mpeReadEvent = allocate_mpe_state( "ReadHDF5Dataset::read", "yellow" );
  mpeReduceEvent = allocate_mpe_state( "ReadHDF5Dataset::all_reduce", "yellow" );
  }
  
  init( data_set_handle, close_data_set );
  
 #ifndef MOAB_HAVE_HDF5_PARALLEL
  if( nativeParallel ) throw Exception( __LINE__ );
 #else
  if( nativeParallel && !mpiComm ) throw Exception( __LINE__ );
  
  if( mpiComm )
  {
  ioProp = H5Pcreate( H5P_DATASET_XFER );
  H5Pset_dxpl_mpio( ioProp, H5FD_MPIO_COLLECTIVE );
  }
 #endif
 }

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.

  : closeDataSet( false ), dataSet( -1 ), dataSpace( -1 ), dataType( -1 ), fileType( -1 ), ioProp( H5P_DEFAULT ),
  dataSpaceRank( 0 ), rowsInTable( 0 ), doConversion( false ), nativeParallel( parallel ), readCount( 0 ),
  bufferSize( 0 ), mpiComm( communicator ), mpeDesc( debug_desc )
 {
  if( !haveMPEEvents )
  {
  haveMPEEvents = true;
  mpeReadEvent = allocate_mpe_state( "ReadHDF5Dataset::read", "yellow" );
  mpeReduceEvent = allocate_mpe_state( "ReadHDF5Dataset::all_reduce", "yellow" );
  }
  
 #ifndef MOAB_HAVE_HDF5_PARALLEL
  if( nativeParallel ) throw Exception( __LINE__ );
 #else
  if( nativeParallel && !mpiComm ) throw Exception( __LINE__ );
  
  if( mpiComm )
  {
  ioProp = H5Pcreate( H5P_DATASET_XFER );
  H5Pset_dxpl_mpio( ioProp, H5FD_MPIO_COLLECTIVE );
  }
 #endif
 }

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

◆ ~ReadHDF5Dataset()

moab::ReadHDF5Dataset::~ReadHDF5Dataset ( )

Definition at line 231 of file ReadHDF5Dataset.cpp.

 {
  if( fileType >= 0 ) H5Tclose( fileType );
  if( dataSpace >= 0 ) H5Sclose( dataSpace );
  if( closeDataSet && dataSet >= 0 ) H5Dclose( dataSet );
  dataSpace = dataSet = -1;
  if( ioProp != H5P_DEFAULT ) H5Pclose( ioProp );
 }

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.

  {
  hyperslabSelectOp = H5S_SELECT_APPEND;
  }

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.

  {
  closeDataSet = val;
  }

References closeDataSet.

◆ columns()

unsigned moab::ReadHDF5Dataset::columns ( ) const

Definition at line 137 of file ReadHDF5Dataset.cpp.

 {
  if( dataSpaceRank == 1 )
  return 1;
  else if( dataSpaceRank == 2 )
  return dataSetCount[1];
  
  throw Exception( __LINE__ );
 }

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.

 {
  hyperslabSelectionLimit = DEFAULT_HYPERSLAB_SELECTION_LIMIT;
 }

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.

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

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.

  {
  return mpeDesc.c_str();
  }

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.

  {
  return readCount;
  }

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.

 {
  closeDataSet = close_data_set;
  dataSet = data_set_handle;
  
  fileType = H5Dget_type( data_set_handle );
  if( fileType < 0 ) throw Exception( __LINE__ );
  
  dataSpace = H5Dget_space( dataSet );
  if( dataSpace < 0 ) throw Exception( __LINE__ );
  
  dataSpaceRank = H5Sget_simple_extent_dims( dataSpace, dataSetCount, dataSetOffset );
  if( dataSpaceRank < 0 ) throw Exception( __LINE__ );
  rowsInTable = dataSetCount[0];
  
  for( int i = 0; i < dataSpaceRank; ++i )
  dataSetOffset[i] = 0;
  
  currOffset = rangeEnd = internalRange.end();
 }

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.

 {
  size_t slabs_remaining = hyperslabSelectionLimit;
  size_t avail = bufferSize;
  while( iter != rangeEnd && slabs_remaining )
  {
  size_t count = *( iter.end_of_block() ) - *iter + 1;
  if( count >= avail )
  {
  iter += avail;
  break;
  }
  
  avail -= count;
  iter += count;
  --slabs_remaining;
  }
  return iter;
 }

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.

  {
  return currOffset;
  }

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.

 {
  herr_t err;
  err = H5Sselect_none( dataSpace );
  if( err < 0 ) throw Exception( __LINE__ );
  
  //#if HDF5_16API
  hsize_t one = 1;
  hid_t mem_id = H5Screate_simple( 1, &one, NULL );
  if( mem_id < 0 ) throw Exception( __LINE__ );
  err = H5Sselect_none( mem_id );
  if( err < 0 )
  {
  H5Sclose( mem_id );
  throw Exception( __LINE__ );
  }
  //#else
  // hid_t mem_id = H5Screate(H5S_NULL);
  // if (mem_id < 0)
  // throw Exception(__LINE__);
  //#endif
  
  err = H5Dread( dataSet, fileType, mem_id, dataSpace, ioProp, 0 );
  H5Sclose( mem_id );
  if( err < 0 ) throw Exception( __LINE__ );
 }

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.

  {
  hyperslabSelectOp = H5S_SELECT_OR;
  }

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.

 {
  herr_t err;
  rows_read = 0;
  
  MPE_Log_event( mpeReadEvent.first, (int)readCount, mpeDesc.c_str() );
  if( currOffset != rangeEnd )
  {
  
  // Build H5S hyperslab selection describing the portions of the
  // data set to read
  H5S_seloper_t sop = H5S_SELECT_SET;
  Range::iterator new_end = next_end( currOffset );
  while( currOffset != new_end )
  {
  size_t count = *( currOffset.end_of_block() ) - *currOffset + 1;
  if( new_end != rangeEnd && *currOffset + count > *new_end )
  {
  count = *new_end - *currOffset;
  }
  rows_read += count;
  
  dataSetOffset[0] = *currOffset - startID;
  dataSetCount[0] = count;
  err = H5Sselect_hyperslab( dataSpace, sop, dataSetOffset, NULL, dataSetCount, 0 );
  if( err < 0 ) throw Exception( __LINE__ );
  sop = hyperslabSelectOp; // subsequent calls to select_hyperslab append
  
  currOffset += count;
  }
  
  // Create a data space describing the memory in which to read the data
  dataSetCount[0] = rows_read;
  hid_t mem_id = H5Screate_simple( dataSpaceRank, dataSetCount, NULL );
  if( mem_id < 0 ) throw Exception( __LINE__ );
  
  // Do the actual read
  err = H5Dread( dataSet, fileType, mem_id, dataSpace, ioProp, buffer );
  H5Sclose( mem_id );
  if( err < 0 ) throw Exception( __LINE__ );
  
  if( readCount ) --readCount;
  
  if( doConversion )
  {
  err = H5Tconvert( fileType, dataType, rows_read * columns(), buffer, 0, H5P_DEFAULT );
  if( err < 0 ) throw Exception( __LINE__ );
  }
  }
  else if( readCount )
  {
  null_read();
  --readCount;
  }
  MPE_Log_event( mpeReadEvent.second, (int)readCount, mpeDesc.c_str() );
 }

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.

 {
  internalRange.clear();
  internalRange.insert( (EntityHandle)1, (EntityHandle)( rowsInTable ) );
  set_file_ids( internalRange, 1, row_count, data_type );
 }

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.

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

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.

 {
  startID = start_id;
  currOffset = file_ids.begin();
  rangeEnd = file_ids.end();
  readCount = 0;
  bufferSize = row_count;
  
  // if a) user specified buffer size and b) we're doing a true
  // parallel partial read and c) we're doing collective I/O, then
  // we need to know the maximum number of reads that will be done.
 #ifdef MOAB_HAVE_HDF5_PARALLEL
  if( nativeParallel )
  {
  Range::const_iterator iter = currOffset;
  while( iter != rangeEnd )
  {
  ++readCount;
  iter = next_end( iter );
  }
  
  MPE_Log_event( mpeReduceEvent.first, (int)readCount, mpeDesc.c_str() );
  unsigned long recv = readCount, send = readCount;
  MPI_Allreduce( &send, &recv, 1, MPI_UNSIGNED_LONG, MPI_MAX, *mpiComm );
  readCount = recv;
  MPE_Log_event( mpeReduceEvent.second, (int)readCount, mpeDesc.c_str() );
  }
 #endif
  
  dataType = data_type;
  htri_t equal = H5Tequal( fileType, dataType );
  if( equal < 0 ) throw Exception( __LINE__ );
  doConversion = !equal;
  
  // We always read in the format of the file to avoid stupind HDF5
  // library behavior when reading in parallel. We call H5Tconvert
  // ourselves to do the data conversion. If the type we're reading
  // from the file is larger than the type we want in memory, then
  // we need to reduce num_rows so that we can read the larger type
  // from the file into the passed buffer mean to accomodate num_rows
  // of values of the smaller in-memory type.
  if( doConversion )
  {
  size_t mem_size, file_size;
  mem_size = H5Tget_size( dataType );
  file_size = H5Tget_size( fileType );
  if( file_size > mem_size ) bufferSize = bufferSize * mem_size / file_size;
  }
 }

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.

  {
  hyperslabSelectionLimit = val;
  }

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.

  {
  return closeDataSet;
  }

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