dolfin::HDF5Interface Class Reference

#include <HDF5Interface.h>

Public Member Functions
template<typename T >
void	write_dataset (const hid_t file_handle, const std::string dataset_path, const std::vector< T > &data, const std::pair< std::int64_t, std::int64_t > range, const std::vector< int64_t > global_size, bool use_mpi_io, bool use_chunking)
template<>
void	add_attribute_value (const hid_t dset_id, const std::string attribute_name, const std::string &attribute_value)
template<>
void	get_attribute_value (const hid_t attr_type, const hid_t attr_id, std::string &attribute_value)

Static Public Member Functions
static hid_t	open_file (MPI_Comm mpi_comm, const std::string filename, const std::string mode, const bool use_mpi_io)
	Open HDF5 and return file descriptor.
static void	close_file (const hid_t hdf5_file_handle)
	Close HDF5 file.
static void	flush_file (const hid_t hdf5_file_handle)
static std::string	get_filename (hid_t hdf5_file_handle)
template<typename T >
static void	write_dataset (const hid_t file_handle, const std::string dataset_path, const std::vector< T > &data, const std::pair< std::int64_t, std::int64_t > range, const std::vector< std::int64_t > global_size, bool use_mpio, bool use_chunking)
template<typename T >
static void	read_dataset (const hid_t file_handle, const std::string dataset_path, const std::pair< std::int64_t, std::int64_t > range, std::vector< T > &data)
static bool	has_group (const hid_t hdf5_file_handle, const std::string group_name)
	Check for existence of group in HDF5 file.
static bool	has_dataset (const hid_t hdf5_file_handle, const std::string dataset_path)
	Check for existence of dataset in HDF5 file.
static void	add_group (const hid_t hdf5_file_handle, const std::string dataset_path)
	Add group to HDF5 file.
static int	dataset_rank (const hid_t hdf5_file_handle, const std::string dataset_path)
	Get dataset rank.
static int	num_datasets_in_group (const hid_t hdf5_file_handle, const std::string group_name)
	Return number of data sets in a group.
static std::vector< std::int64_t >	get_dataset_shape (const hid_t hdf5_file_handle, const std::string dataset_path)
	Get dataset shape (size of each dimension)
static std::vector< std::string >	dataset_list (const hid_t hdf5_file_handle, const std::string group_name)
	Return list all datasets in named group of file.
static const std::string	get_attribute_type (const hid_t hdf5_file_handle, const std::string dataset_path, const std::string attribute_name)
	Get type of attribute.
template<typename T >
static void	get_attribute (const hid_t hdf5_file_handle, const std::string dataset_path, const std::string attribute_name, T &attribute_value)
	Get a named attribute of a dataset of known type.
template<typename T >
static void	add_attribute (const hid_t hdf5_file_handle, const std::string dataset_path, const std::string attribute_name, const T &attribute_value)
	Add attribute to dataset or group.
static void	delete_attribute (const hid_t hdf5_file_handle, const std::string dataset_path, const std::string attribute_name)
	Delete an attribute from a dataset or group.
static bool	has_attribute (const hid_t hdf5_file_handle, const std::string dataset_path, const std::string attribute_name)
	Check if an attribute exists on a dataset or group.
static const std::vector< std::string >	list_attributes (const hid_t hdf5_file_handle, const std::string dataset_path)
static void	set_mpi_atomicity (const hid_t hdf5_file_handle, const bool atomic)
static bool	get_mpi_atomicity (const hid_t hdf5_file_handle)

Detailed Description

This class wraps HDF5 function calls. HDF5 function calls should only appear in a member function of this class and not elsewhere in the library.

Member Function Documentation

flush_file()

void HDF5Interface::flush_file ( const hid_t  hdf5_file_handle )

static

Flush data to file to improve data integrity after interruption

get_mpi_atomicity()

bool HDF5Interface::get_mpi_atomicity ( const hid_t  hdf5_file_handle )

static

Get MPI atomicity. See https://support.hdfgroup.org/HDF5/doc/RM/RM_H5F.html#File-GetMpiAtomicity and https://www.open-mpi.org/doc/v2.0/man3/MPI_File_get_atomicity.3.php

read_dataset()

template<typename T >

void dolfin::HDF5Interface::read_dataset ( const hid_t  file_handle, const std::string  dataset_path, const std::pair< std::int64_t, std::int64_t >  range, std::vector< T > &  data  )

inlinestatic

Read data from a HDF5 dataset "dataset_path" as defined by range blocks on each process range: the local range on this processor data: a flattened 1D array of values. If range = {-1, -1}, then all data is read on this process.

set_mpi_atomicity()

void HDF5Interface::set_mpi_atomicity ( const hid_t  hdf5_file_handle, const bool  atomic  )

static

Set MPI atomicity. See https://support.hdfgroup.org/HDF5/doc/RM/RM_H5F.html#File-SetMpiAtomicity and https://www.open-mpi.org/doc/v2.0/man3/MPI_File_set_atomicity.3.php Writes must be followed by an MPI_Barrier on the communicator before any subsequent reads are guaranteed to return the same data.

write_dataset()

template<typename T >

static void dolfin::HDF5Interface::write_dataset ( const hid_t  file_handle, const std::string  dataset_path, const std::vector< T > &  data, const std::pair< std::int64_t, std::int64_t >  range, const std::vector< std::int64_t >  global_size, bool  use_mpio, bool  use_chunking  )

static

Write data to existing HDF file as defined by range blocks on each process data: data to be written, flattened into 1D vector range: the local range on this processor global_size: the global multidimensional shape of the array use_mpio: whether using MPI or not use_chunking: whether using chunking or not

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

• /home/fenics/shared/dolfin/dolfin/io/HDF5Interface.h
• /home/fenics/shared/dolfin/dolfin/io/HDF5Interface.cpp