HDF5Interface Class Reference

This class provides an interface to some HDF5 functionality. More...

#include <HDF5Interface.h>

Static Public Member Functions
static hid_t	open_file (MPI_Comm comm, const std::filesystem::path &filename, const std::string &mode, const bool use_mpi_io)
	Open HDF5 and return file descriptor. More...
static void	close_file (const hid_t handle)
	Close HDF5 file. More...
static void	flush_file (const hid_t handle)
	Flush data to file to improve data integrity after interruption. More...
static std::filesystem::path	get_filename (hid_t handle)
	Get filename. More...
template<typename T >
static void	write_dataset (const hid_t handle, const std::string &dataset_path, const T *data, const std::array< std::int64_t, 2 > &range, const std::vector< std::int64_t > &global_size, bool use_mpi_io, bool use_chunking)
	Write data to existing HDF file as defined by range blocks on each process. More...
template<typename T >
static std::vector< T >	read_dataset (const hid_t handle, const std::string &dataset_path, const std::array< std::int64_t, 2 > &range)
	Read data from a HDF5 dataset "dataset_path" as defined by range blocks on each process. More...
static bool	has_dataset (const hid_t handle, const std::string &dataset_path)
	Check for existence of dataset in HDF5 file. More...
static std::vector< std::int64_t >	get_dataset_shape (const hid_t handle, const std::string &dataset_path)
	Get dataset shape (size of each dimension) More...
static void	set_mpi_atomicity (const hid_t handle, const bool atomic)
	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.
static bool	get_mpi_atomicity (const hid_t handle)
	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.

Detailed Description

This class provides an interface to some HDF5 functionality.

Member Function Documentation

close_file()

void close_file ( const hid_t  handle )

static

Close HDF5 file.

Parameters

[in]

handle

HDF5 file handle

flush_file()

void flush_file ( const hid_t  handle )

static

Flush data to file to improve data integrity after interruption.

Parameters

[in]

handle

HDF5 file handle

get_dataset_shape()

std::vector< std::int64_t > get_dataset_shape ( const hid_t  handle, const std::string &  dataset_path  )

static

Get dataset shape (size of each dimension)

Parameters

[in]	handle	HDF5 file handle
[in]	dataset_path	Dataset path

Returns

The shape of the dataset (row-major)

get_filename()

std::filesystem::path get_filename ( hid_t  handle )

static

Get filename.

Parameters

[in]

handle

HDF5 file handle return The filename

has_dataset()

bool has_dataset ( const hid_t  handle, const std::string &  dataset_path  )

static

Check for existence of dataset in HDF5 file.

Parameters

[in]	handle	HDF5 file handle
[in]	dataset_path	Data set path

Returns

True if dataset_path is in the file

open_file()

hid_t open_file ( MPI_Comm  comm, const std::filesystem::path &  filename, const std::string &  mode, const bool  use_mpi_io  )

static

Open HDF5 and return file descriptor.

Parameters

[in]	comm	MPI communicator
[in]	filename	Name of the HDF5 file to open
[in]	mode	Mode in which to open the file (w, r, a)
[in]	use_mpi_io	True if MPI-IO should be used

read_dataset()

static std::vector<T> read_dataset ( const hid_t  handle, const std::string &  dataset_path, const std::array< std::int64_t, 2 > &  range  )

static

Read data from a HDF5 dataset "dataset_path" as defined by range blocks on each process.

Parameters

[in]	handle	HDF5 file handle
[in]	dataset_path	Path for the dataset in the HDF5 file
[in]	range	The local range on this processor

Returns

Flattened 1D array of values. If range = {-1, -1}, then all data is read on this process.

write_dataset()

static void write_dataset ( const hid_t  handle, const std::string &  dataset_path, const T *  data, const std::array< std::int64_t, 2 > &  range, const std::vector< std::int64_t > &  global_size, bool  use_mpi_io, bool  use_chunking  )

static

Write data to existing HDF file as defined by range blocks on each process.

Parameters

[in]	handle	HDF5 file handle
[in]	dataset_path	Path for the dataset in the HDF5 file
[in]	data	Data to be written, flattened into 1D vector (row-major storage)
[in]	range	The local range on this processor
[in]	global_size	The global shape shape of the array
[in]	use_mpi_io	True if MPI-IO should be used
[in]	use_chunking	True if chunking should be used

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

• /__w/dolfinx/dolfinx/cpp/dolfinx/io/HDF5Interface.h
• /__w/dolfinx/dolfinx/cpp/dolfinx/io/HDF5Interface.cpp