AMP::IO Namespace Reference

Classes
class	AsciiWriter
	A class used to abstract away reading/writing files. More...
class	HDF5data
	Class to wrap HDF5 data. More...
class	HDF5writer
	A class used to abstract away reading/writing files for visualization. More...
class	NullWriter
	A class used to abstract away reading/writing files for visualization. More...
class	RestartManager
	Class to manage reading/writing restart data. More...
class	SiloIO
	A class used to abstract away reading/writing files for visualization. More...
class	Writer
	A class used to abstract away reading/writing files. More...

Enumerations
enum class	Compression : uint8_t { None , GZIP , SZIP }

Functions
void	closeDataset (hid_t fid)
	Close a dataset.
void	closeDataspace (hid_t fid)
	Close a dataspace.
void	closeDatatype (hid_t fid)
	Close a datatype.
void	closeGroup (hid_t fid)
	Close a group.
void	closeHDF5 (hid_t fid, bool printLeaks=false)
	Open an HDF5 file.
hid_t	createChunk (AMP::ArraySize dims, Compression compress, size_t objSize=0)
	Open an HDF5 file.
hid_t	createGroup (hid_t fid, const std::string &name)
	Create a group.
Compression	defaultCompression (hid_t fid)
	Retrun the the default compression.
void	deleteFile (const std::string &filename)
	Delete a file. If the file does not exist, nothing will happen.
bool	exists (const std::string &filename)
	Check if a file exists and return true if it does.
bool	fileExists (const std::string &)
std::string	filename (const std::string &filename)
	Return the filename (strip the path)
size_t	fileSize (const std::string &filename)
	Return the file size.
template<class T >
hid_t	getHDF5datatype ()
	Get HDF5 data type.
hid_t	getHDF5datatype (hid_t fid, const std::string &name)
	Get the type of a dataset.
std::string	getSuffix (const std::string &filename)
	Get the lower case suffix for a file.
bool	H5Dexists (hid_t fid, const std::string &name)
	Check if dataset exists.
bool	H5Gexists (hid_t fid, const std::string &name)
	Check if group exists.
bool	HDF5enabled ()
	Is HDF5 enabled.
hid_t	openGroup (hid_t fid, const std::string &name, bool create=false)
	Open a group.
hid_t	openHDF5 (const std::string &filename, const char *mode, Compression compress=Compression::None)
	Open an HDF5 file.
std::tuple< std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t > >	openObjects (hid_t fid)
	list open objects
std::string	path (const std::string &filename)
	Return the path to the file.
void	permissions (const std::string &filename, std::filesystem::perms mode)
	Set the permissions for the file or directory.
template<class T >
std::unique_ptr< T >	readHDF5 (hid_t fid, const std::string &name, AMP_MPI comm=AMP_COMM_SELF)
	Read a structure from HDF5.
void	readHDF5 (hid_t fid, const std::string &name, size_t N_bytes, void *data)
	Read data from HDF5.
template<class T >
void	readHDF5 (hid_t fid, const std::string &name, T &data)
	Read a structure from HDF5.
std::unique_ptr< HDF5data >	readHDF5 (hid_t fid, const std::string_view &name)
	Read data from HDF5.
void	recursiveMkdir (const std::string &, mode_t)
void	recursiveMkdir (const std::string &, mode_t, bool)
void	recursiveMkdir (const std::string &path)
void	rename (const std::string &old_filename, const std::string &new_filename)
	Rename a file from old file name to new file name.
void	renameFile (const std::string &old_filename, const std::string &new_filename)
template<class T >
void	writeHDF5 (hid_t fid, const std::string &name, const T &data)
	Write a structure to HDF5.
void	writeHDF5 (hid_t fid, const std::string &name, size_t N_bytes, const void *data)
	Write data to HDF5.

Enumeration Type Documentation

Compression

enum class AMP::IO::Compression : uint8_t

strong

Enumerator
None
GZIP
SZIP

Definition at line 31 of file HDF.h.

Function Documentation

closeDataset()

void AMP::IO::closeDataset

(

hid_t

fid

)

Close a dataset.

This function closes an HDF5 dataset

Parameters

[in]

fid

Dataset to close

closeDataspace()

void AMP::IO::closeDataspace

(

hid_t

fid

)

Close a dataspace.

This function closes an HDF5 dataspace

Parameters

[in]

fid

closeDataspace to close

closeDatatype()

void AMP::IO::closeDatatype

(

hid_t

fid

)

Close a datatype.

This function closes an HDF5 datatype

Parameters

[in]

fid

Datatype to close

closeGroup()

void AMP::IO::closeGroup

(

hid_t

fid

)

Close a group.

This function closes an HDF5 group

Parameters

[in]

fid

Group to close

closeHDF5()

void AMP::IO::closeHDF5	(	hid_t	fid,
		bool	printLeaks = false
	)

Open an HDF5 file.

This function opens and HDF5 file for reading/writing

Parameters

[in]	fid	File to open
[in]	printLeaks	Print the resource leaks

createChunk()

hid_t AMP::IO::createChunk	(	AMP::ArraySize	dims,
		Compression	compress,
		size_t	objSize = 0
	)

Open an HDF5 file.

This function create a chunk for HDF5

Parameters

[in]	dims	Chunk size
[in]	compress	Compression to use
[in]	objSize	Optional number of bytes of an object

Returns

Return a handle to the file.

createGroup()

hid_t AMP::IO::createGroup	(	hid_t	fid,
		const std::string &	name
	)

Create a group.

This function creates a new HDF5 group

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the group

defaultCompression()

Compression AMP::IO::defaultCompression

(

hid_t

fid

)

Retrun the the default compression.

This function returns the default compression used when the file was created

Parameters

[in]

fid

File/Group id

deleteFile()

void AMP::IO::deleteFile

(

const std::string &

filename

)

Delete a file. If the file does not exist, nothing will happen.

exists()

bool AMP::IO::exists

(

const std::string &

filename

)

Check if a file exists and return true if it does.

fileExists()

bool AMP::IO::fileExists

(

const std::string &

)

filename()

std::string AMP::IO::filename

(

const std::string &

filename

)

Return the filename (strip the path)

fileSize()

size_t AMP::IO::fileSize

(

const std::string &

filename

)

Return the file size.

getHDF5datatype() [1/2]

template<class T >

hid_t AMP::IO::getHDF5datatype

(

)

Get HDF5 data type.

This function returns the id of the data type

getHDF5datatype() [2/2]

hid_t AMP::IO::getHDF5datatype	(	hid_t	fid,
		const std::string &	name
	)

Get the type of a dataset.

This function returns the type of a dataset

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the group

getSuffix()

std::string AMP::IO::getSuffix

(

const std::string &

filename

)

Get the lower case suffix for a file.

H5Dexists()

bool AMP::IO::H5Dexists	(	hid_t	fid,
		const std::string &	name
	)

Check if dataset exists.

This function checks if an HDF5 dataset exists in the file

Parameters

[in]	fid	File to open
[in]	name	The name of the dataset

H5Gexists()

bool AMP::IO::H5Gexists	(	hid_t	fid,
		const std::string &	name
	)

Check if group exists.

This function checks if an HDF5 group exists in the file

Parameters

[in]	fid	ID of group or database to read
[in]	name	The name of the group

HDF5enabled()

bool AMP::IO::HDF5enabled

(

)

Is HDF5 enabled.

This function returns true if HDF5 support is enabled (AMP was compiled with HDF5)

openGroup()

hid_t AMP::IO::openGroup	(	hid_t	fid,
		const std::string &	name,
		bool	create = false
	)

Open a group.

This function opens an HDF5 group

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the group
[in]	create	Create the group if it does not exist?

openHDF5()

hid_t AMP::IO::openHDF5	(	const std::string &	filename,
		const char *	mode,
		Compression	compress = Compression::None
	)

Open an HDF5 file.

This function opens and HDF5 file for reading/writing. Once complete, we must close the file using closeHDF5

Parameters

[in]	filename	File to open
[in]	mode	C string containing a file access mode. It can be: "r" read: Open file for input operations. The file must exist. "w" write: Create an empty file for output operations. If a file with the same name already exists, its contents are discarded and the file is treated as a new empty file. "rw" read+write: Open file for reading and writing. The file must exist.
[in]	compress	Default compression

Returns

Return a handle to the file.

openObjects()

std::tuple< std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t >, std::vector< hid_t > > AMP::IO::openObjects

(

hid_t

fid

)

list open objects

This function closes an HDF5 group

Returns

Returns the list of open objects associated with the file: [files,datasets,groups,datatypes,attributes]

Parameters

[in]

fid

Group to close

path()

std::string AMP::IO::path

(

const std::string &

filename

)

Return the path to the file.

permissions()

void AMP::IO::permissions	(	const std::string &	filename,
		std::filesystem::perms	mode
	)

Set the permissions for the file or directory.

readHDF5() [1/4]

template<class T >

std::unique_ptr< T > AMP::IO::readHDF5	(	hid_t	fid,
		const std::string &	name,
		AMP_MPI	comm = AMP_COMM_SELF
	)

Read a structure from HDF5.

This function reads a C++ class/struct from HDF5. This is a templated function and users can implement their own data types by creating explicit instantiations for a given type. There is no default instantiation except when compiled without HDF5 which is a no-op.

Parameters

[in]	fid	File or group to read from
[in]	name	The name of the variable
[in]	comm	The communicator of the object

readHDF5() [2/4]

void AMP::IO::readHDF5	(	hid_t	fid,
		const std::string &	name,
		size_t	N_bytes,
		void *	data
	)

Read data from HDF5.

This function reads a fixed number of bytes from HDF5.

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the variable
[in]	N_bytes	The number of bytes to write
[out]	data	The data to read

readHDF5() [3/4]

template<class T >

void AMP::IO::readHDF5	(	hid_t	fid,
		const std::string &	name,
		T &	data
	)

Read a structure from HDF5.

This function reads a C++ class/struct from HDF5. This is a templated function and users can implement their own data types by creating explicit instantiations for a given type. There is no default instantiation except when compiled without HDF5 which is a no-op.

Parameters

[in]	fid	File or group to read from
[in]	name	The name of the variable
[out]	data	The structure to read

readHDF5() [4/4]

std::unique_ptr< HDF5data > AMP::IO::readHDF5	(	hid_t	fid,
		const std::string_view &	name
	)

Read data from HDF5.

This function reads arbitrary from HDF5. The user then requests the individual data from the class.

Parameters

[in]	fid	File or group to read from
[in]	name	The name of the variable

Returns

The structure to read

recursiveMkdir() [1/3]

void AMP::IO::recursiveMkdir	(	const std::string &	,
		mode_t
	)

recursiveMkdir() [2/3]

void AMP::IO::recursiveMkdir	(	const std::string &	,
		mode_t	,
		bool
	)

recursiveMkdir() [3/3]

void AMP::IO::recursiveMkdir

(

const std::string &

path

)

rename()

void AMP::IO::rename	(	const std::string &	old_filename,
		const std::string &	new_filename
	)

Rename a file from old file name to new file name.

renameFile()

void AMP::IO::renameFile	(	const std::string &	old_filename,
		const std::string &	new_filename
	)

writeHDF5() [1/2]

template<class T >

void AMP::IO::writeHDF5	(	hid_t	fid,
		const std::string &	name,
		const T &	data
	)

Write a structure to HDF5.

This function writes a C++ class/struct to HDF5. This is a templated function and users can implement their own data types by creating explicit instantiations for a given type. There is no default instantiation except when compiled without HDF5 which is a no-op.

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the variable
[in]	data	The structure to write

writeHDF5() [2/2]

void AMP::IO::writeHDF5	(	hid_t	fid,
		const std::string &	name,
		size_t	N_bytes,
		const void *	data
	)

Write data to HDF5.

This function writes a fixed number of bytes from HDF5.

Parameters

[in]	fid	File or group to write to
[in]	name	The name of the variable
[in]	N_bytes	The number of bytes to write
[in]	data	The data to write