Reading/Writing in HDF5 format. More...

#include <arcane/hdf5/Hdf5ReaderWriter.h>

Inheritance diagram for Arcane::Hdf5ReaderWriter:

Collaboration diagram for Arcane::Hdf5ReaderWriter:

Public Types
enum	eOpenMode { OpenModeRead , OpenModeTruncate , OpenModeAppend }

Public Member Functions
	Hdf5ReaderWriter (ISubDomain *sd, const String &filename, const String &m_sub_group_name, Integer fileset_size, Integer write_index, Integer index_modulo, eOpenMode om, bool do_verif=false)
virtual void	initialize ()
virtual void	beginWrite (const VariableCollection &vars)
virtual void	endWrite ()
virtual void	beginRead (const VariableCollection &vars)
virtual void	endRead ()
virtual void	setMetaData (const String &meta_data)
	Sets the metadata information.
virtual String	metaData ()
	Metadata.
virtual void	write (IVariable v, IData data)
	Writes the data data of the variable var.
virtual void	read (IVariable v, IData data)
	Reads the data data of the variable var.
herr_t	iterateMe (hid_t group_id, const char *member_name)
Public Member Functions inherited from Arcane::TraceAccessor
	TraceAccessor (ITraceMng *m)
	Constructs an accessor via the trace manager m.
	TraceAccessor (const TraceAccessor &rhs)
	Copy constructor.
TraceAccessor &	operator= (const TraceAccessor &rhs)
	Copy assignment operator.
virtual	~TraceAccessor ()
	Frees resources.
ITraceMng *	traceMng () const
	Trace manager.
TraceMessage	info () const
	Flow for an information message.
TraceMessage	pinfo () const
	Flow for a parallel information message.
TraceMessage	info (char category) const
	Flow for an information message of a given category.
TraceMessage	pinfo (char category) const
	Flow for a parallel information message of a given category.
TraceMessage	info (bool v) const
	Flow for an information message.
TraceMessage	warning () const
	Flow for a warning message.
TraceMessage	pwarning () const
TraceMessage	error () const
	Flow for an error message.
TraceMessage	perror () const
TraceMessage	log () const
	Flow for a log message.
TraceMessage	plog () const
	Flow for a log message.
TraceMessage	logdate () const
	Flow for a log message preceded by the date.
TraceMessage	fatal () const
	Flow for a fatal error message.
TraceMessage	pfatal () const
	Flow for a parallel fatal error message.
TraceMessageDbg	debug (Trace::eDebugLevel=Trace::Medium) const
	Flow for a debug message.
Trace::eDebugLevel	configDbgLevel () const
	Debug level of the configuration file.
TraceMessage	info (Int32 verbose_level) const
	Flow for an information message of a given level.
TraceMessage	linfo () const
	Flow for an information message with the local information level of this instance.
TraceMessage	linfo (Int32 relative_level) const
	Flow for an information message with the local information level of this instance.
void	fatalMessage (const StandaloneTraceMessage &o) const
Public Member Functions inherited from Arcane::IDataReader
virtual	~IDataReader ()=default
	Frees resources.
Public Member Functions inherited from Arcane::IDataWriter
virtual	~IDataWriter ()=default
	Frees resources.

Private Member Functions
void	_writeVal (const String &var_group_name, const String &sub_group_name, const ISerializedData *sdata, const Int32 from_rank=0)
void	_writeValParallel (IVariable v, const ISerializedData sdata)
	Parallel writing.
void	_readVal (IVariable var, IData data)
Ref< ISerializedData >	_readDim2 (IVariable *v)
void	_directReadVal (IVariable v, IData data)
void	_directWriteVal (IVariable v, IData data)
void	_checkValid ()
String	_variableGroupName (IVariable *var)
void	_receiveRemoteVariables ()
void	_writeRemoteVariable (ISerializer *sb)
void	_setMetaData (const String &meta_data, const String &sub_group_name)

Private Attributes
IParallelMng *	m_parallel_mng
	Parallelism manager;.
eOpenMode	m_open_mode
	Open mode.
String	m_filename
	Filename.
String	m_sub_group_name
	Subgroup name.
bool	m_is_initialized
	True if already initialized.
Hdf5Utils::StandardTypes	m_types
Hdf5Utils::HFile	m_file_id
	HDF file identifier.
Hdf5Utils::HGroup	m_sub_group_id
	HDF group identifier containing the protection.
Hdf5Utils::HGroup	m_variable_group_id
	HDF group identifier containing the variables.
StringList	m_variables_name
	List of names of saved variables.
Timer	m_io_timer
bool	m_is_parallel
	Active parallel mode: WARNING: for testing only.
Int32	m_my_rank
Int32	m_send_rank
Int32	m_last_recv_rank
Integer	m_fileset_size
Integer	m_index_write
Integer	m_index_modulo

Additional Inherited Members
Protected Member Functions inherited from Arcane::TraceAccessor
void	_setLocalVerboseLevel (Int32 v)
Int32	_localVerboseLevel () const

Detailed Description

Reading/Writing in HDF5 format.

The HDF5 version used is at least version 1.4.3.

Regarding real numbers, only double precision is supported. They are therefore stored in 8 bytes as well.

For Real2, Real2x2, Real3, and Real3x3, a composite type is used.

The structure of the saved information is as follows:

* all variables are saved in a group called "Variables". * .
* for each variable, a subgroup named after the variable is created. This subgroup contains the following attributes and datasets:
- * An attribute named "Dims" which is an array of 1 or 2 Integer elements containing information about the sizes and dimensions of the variable. This attribute is always present and is used, among other things, to determine if the other two datasets are present. The first value (index 0) is always the number of elements in the array. If the variable is a one-dimensional array, there are no other values. If the array is two-dimensional, the second value is equal to the size of the first dimension of the array, while the sizes of the second dimensions are given by the "Dim2" attribute.
- * A dataset named "Dim2". This dataset is only present if the variable is a two-dimensional array, when the first dimension is not zero and the number of elements is not zero. In this case, this dataset is an array of Integer type whose size is equal to the size of the first dimension of the variable, and thus each value is equal to the size of the second dimension.
- * A dataset named "Values" containing the values of the variable. This dataset is not present in the case of an array variable whose number of elements is zero or when the variable is temporary (IVariable::PNoDump property). *

Todo: save/read the list of mesh entity groups.

Warning: * The handling of reading/writing in this format is currently at the experimental stage and cannot be used to ensure long-term data persistence.

Definition at line 76 of file hdf5/Hdf5ReaderWriter.h.

Member Enumeration Documentation

◆ eOpenMode

enum Arcane::Hdf5ReaderWriter::eOpenMode

Definition at line 84 of file hdf5/Hdf5ReaderWriter.h.

Constructor & Destructor Documentation

◆ Hdf5ReaderWriter()

Arcane::Hdf5ReaderWriter::Hdf5ReaderWriter	(	ISubDomain *	sd,
		const String &	filename,
		const String &	m_sub_group_name,
		Integer	fileset_size,
		Integer	write_index,
		Integer	index_modulo,
		eOpenMode	om,
		bool	do_verif = false )

Definition at line 94 of file Hdf5ReaderWriter.cc.

◆ ~Hdf5ReaderWriter()

Arcane::Hdf5ReaderWriter::~Hdf5ReaderWriter ( )

Definition at line 235 of file Hdf5ReaderWriter.cc.

Member Function Documentation

◆ _checkValid()

void Arcane::Hdf5ReaderWriter::_checkValid ( )

private

Definition at line 243 of file Hdf5ReaderWriter.cc.

◆ _directReadVal()

void Arcane::Hdf5ReaderWriter::_directReadVal	(	IVariable *	v,
		IData *	data )

private

Definition at line 290 of file Hdf5ReaderWriter.cc.

◆ _directWriteVal()

void Arcane::Hdf5ReaderWriter::_directWriteVal	(	IVariable *	v,
		IData *	data )

private

Definition at line 301 of file Hdf5ReaderWriter.cc.

◆ _readDim2()

Ref< ISerializedData > Arcane::Hdf5ReaderWriter::_readDim2 ( IVariable * v )

private

Definition at line 469 of file Hdf5ReaderWriter.cc.

◆ _readVal()

void Arcane::Hdf5ReaderWriter::_readVal	(	IVariable *	var,
		IData *	data )

private

Definition at line 603 of file Hdf5ReaderWriter.cc.

◆ _receiveRemoteVariables()

void Arcane::Hdf5ReaderWriter::_receiveRemoteVariables ( )

private

Definition at line 777 of file Hdf5ReaderWriter.cc.

◆ _setMetaData()

void Arcane::Hdf5ReaderWriter::_setMetaData	(	const String &	meta_data,
		const String &	sub_group_name )

private

Definition at line 683 of file Hdf5ReaderWriter.cc.

◆ _variableGroupName()

String Arcane::Hdf5ReaderWriter::_variableGroupName ( IVariable * var )

private

Definition at line 254 of file Hdf5ReaderWriter.cc.

◆ _writeRemoteVariable()

void Arcane::Hdf5ReaderWriter::_writeRemoteVariable ( ISerializer * sb )

private

Definition at line 802 of file Hdf5ReaderWriter.cc.

◆ _writeVal()

void Arcane::Hdf5ReaderWriter::_writeVal	(	const String &	var_group_name,
		const String &	sub_group_name,
		const ISerializedData *	sdata,
		const Int32	from_rank = 0 )

private

Definition at line 338 of file Hdf5ReaderWriter.cc.

◆ _writeValParallel()

void Arcane::Hdf5ReaderWriter::_writeValParallel	(	IVariable *	v,
		const ISerializedData *	sdata )

private

Parallel writing.

Warning: Under test, not usable.

< Group name.

Definition at line 267 of file Hdf5ReaderWriter.cc.

References Arcane::BasicSerializer::allocateBuffer(), Arcane::DT_Int32, Arcane::IVariable::fullName(), m_parallel_mng, m_sub_group_name, Arcane::ISerializer::ModePut, Arcane::BasicSerializer::put(), Arcane::BasicSerializer::putInt32(), Arcane::BasicSerializer::reserve(), Arcane::ISerializedData::serialize(), and Arcane::BasicSerializer::setMode().

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◆ beginRead()

virtual void Arcane::Hdf5ReaderWriter::beginRead ( const VariableCollection & vars )

inlinevirtual

Implements Arcane::IDataReader.

Definition at line 108 of file hdf5/Hdf5ReaderWriter.h.

◆ beginWrite()

virtual void Arcane::Hdf5ReaderWriter::beginWrite ( const VariableCollection & vars )

inlinevirtual

Implements Arcane::IDataWriter.

Definition at line 103 of file hdf5/Hdf5ReaderWriter.h.

◆ endRead()

virtual void Arcane::Hdf5ReaderWriter::endRead ( )

inlinevirtual

Implements Arcane::IDataReader.

Definition at line 112 of file hdf5/Hdf5ReaderWriter.h.

◆ endWrite()

void Arcane::Hdf5ReaderWriter::endWrite ( )

virtual

Implements Arcane::IDataWriter.

Definition at line 750 of file Hdf5ReaderWriter.cc.

◆ initialize()

void Arcane::Hdf5ReaderWriter::initialize ( )

virtual

Definition at line 138 of file Hdf5ReaderWriter.cc.

◆ iterateMe()

herr_t Arcane::Hdf5ReaderWriter::iterateMe	(	hid_t	group_id,
		const char *	member_name )

Definition at line 327 of file Hdf5ReaderWriter.cc.

◆ metaData()

String Arcane::Hdf5ReaderWriter::metaData ( )

virtual

Metadata.

Implements Arcane::IDataReader.

Definition at line 719 of file Hdf5ReaderWriter.cc.

References Arcane::Array< T >::data(), and m_sub_group_id.

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◆ read()

void Arcane::Hdf5ReaderWriter::read	(	IVariable *	var,
		IData *	data )

virtual

Reads the data data of the variable var.

Implements Arcane::IDataReader.

Definition at line 635 of file Hdf5ReaderWriter.cc.

◆ setMetaData()

void Arcane::Hdf5ReaderWriter::setMetaData ( const String & meta_data )

virtual

Sets the metadata information.

Implements Arcane::IDataWriter.

Definition at line 644 of file Hdf5ReaderWriter.cc.

References Arcane::BasicSerializer::allocateBuffer(), Arcane::BasicSerializer::get(), m_is_parallel, m_parallel_mng, m_sub_group_name, Arcane::ISerializer::ModeGet, Arcane::ISerializer::ModePut, Arcane::BasicSerializer::put(), Arcane::BasicSerializer::reserve(), and Arcane::BasicSerializer::setMode().

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◆ write()

void Arcane::Hdf5ReaderWriter::write	(	IVariable *	var,
		IData *	data )

virtual

Writes the data data of the variable var.

Implements Arcane::IDataWriter.

Definition at line 594 of file Hdf5ReaderWriter.cc.

Member Data Documentation

◆ m_file_id

Hdf5Utils::HFile Arcane::Hdf5ReaderWriter::m_file_id

private

HDF file identifier.

Definition at line 134 of file hdf5/Hdf5ReaderWriter.h.

◆ m_filename

String Arcane::Hdf5ReaderWriter::m_filename

private

Filename.

Definition at line 128 of file hdf5/Hdf5ReaderWriter.h.

◆ m_fileset_size

Integer Arcane::Hdf5ReaderWriter::m_fileset_size

private

Definition at line 149 of file hdf5/Hdf5ReaderWriter.h.

◆ m_index_modulo

Integer Arcane::Hdf5ReaderWriter::m_index_modulo

private

Definition at line 151 of file hdf5/Hdf5ReaderWriter.h.

◆ m_index_write

Integer Arcane::Hdf5ReaderWriter::m_index_write

private

Definition at line 150 of file hdf5/Hdf5ReaderWriter.h.

◆ m_io_timer

Timer Arcane::Hdf5ReaderWriter::m_io_timer

private

Definition at line 139 of file hdf5/Hdf5ReaderWriter.h.

◆ m_is_initialized

bool Arcane::Hdf5ReaderWriter::m_is_initialized

private

True if already initialized.

Definition at line 130 of file hdf5/Hdf5ReaderWriter.h.

◆ m_is_parallel

bool Arcane::Hdf5ReaderWriter::m_is_parallel

private

Active parallel mode: WARNING: for testing only.

Definition at line 144 of file hdf5/Hdf5ReaderWriter.h.

Referenced by setMetaData().

◆ m_last_recv_rank

Int32 Arcane::Hdf5ReaderWriter::m_last_recv_rank

private

Definition at line 147 of file hdf5/Hdf5ReaderWriter.h.

◆ m_my_rank

Int32 Arcane::Hdf5ReaderWriter::m_my_rank

private

Definition at line 145 of file hdf5/Hdf5ReaderWriter.h.

◆ m_open_mode

eOpenMode Arcane::Hdf5ReaderWriter::m_open_mode

private

Open mode.

Definition at line 127 of file hdf5/Hdf5ReaderWriter.h.

◆ m_parallel_mng

IParallelMng* Arcane::Hdf5ReaderWriter::m_parallel_mng

private

Parallelism manager;.

Definition at line 126 of file hdf5/Hdf5ReaderWriter.h.

Referenced by _writeValParallel(), and setMetaData().

◆ m_send_rank

Int32 Arcane::Hdf5ReaderWriter::m_send_rank

private

Definition at line 146 of file hdf5/Hdf5ReaderWriter.h.

◆ m_sub_group_id

Hdf5Utils::HGroup Arcane::Hdf5ReaderWriter::m_sub_group_id

private

HDF group identifier containing the protection.

Definition at line 135 of file hdf5/Hdf5ReaderWriter.h.

Referenced by metaData().

◆ m_sub_group_name

String Arcane::Hdf5ReaderWriter::m_sub_group_name

private

Subgroup name.

Definition at line 129 of file hdf5/Hdf5ReaderWriter.h.

Referenced by _writeValParallel(), and setMetaData().

◆ m_types

Hdf5Utils::StandardTypes Arcane::Hdf5ReaderWriter::m_types

private

Definition at line 132 of file hdf5/Hdf5ReaderWriter.h.

◆ m_variable_group_id

Hdf5Utils::HGroup Arcane::Hdf5ReaderWriter::m_variable_group_id

private

HDF group identifier containing the variables.

Definition at line 136 of file hdf5/Hdf5ReaderWriter.h.

◆ m_variables_name

StringList Arcane::Hdf5ReaderWriter::m_variables_name

private

List of names of saved variables.

Definition at line 138 of file hdf5/Hdf5ReaderWriter.h.

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ eOpenMode

Constructor & Destructor Documentation

◆ Hdf5ReaderWriter()

◆ ~Hdf5ReaderWriter()

Member Function Documentation

◆ _checkValid()

◆ _directReadVal()

◆ _directWriteVal()

◆ _readDim2()

◆ _readVal()

◆ _receiveRemoteVariables()

◆ _setMetaData()

◆ _variableGroupName()

◆ _writeRemoteVariable()

◆ _writeVal()

◆ _writeValParallel()

◆ beginRead()

◆ beginWrite()

◆ endRead()

◆ endWrite()

◆ initialize()

◆ iterateMe()

◆ metaData()

◆ read()

◆ setMetaData()

◆ write()

Member Data Documentation

◆ m_file_id

◆ m_filename

◆ m_fileset_size

◆ m_index_modulo

◆ m_index_write

◆ m_io_timer

◆ m_is_initialized

◆ m_is_parallel

◆ m_last_recv_rank

◆ m_my_rank

◆ m_open_mode

◆ m_parallel_mng

◆ m_send_rank

◆ m_sub_group_id

◆ m_sub_group_name

◆ m_types

◆ m_variable_group_id

◆ m_variables_name