Library General (H5)

Detailed Description

Use the functions in this module to manage the life cycle of HDF5 library instances.

Create	Read
{ // an HDF5 library instance is automatically initialized as // part of the first HDF5 API call, but there's no harm in // calling H5open(). if (H5open() < 0) { ret_val = EXIT_FAILURE; } }	{ __label__ fail_read; unsigned majnum, minnum, relnum; hbool_t flag; // retrieve the library version if (H5get_libversion(&majnum, &minnum, &relnum) < 0) { ret_val = EXIT_FAILURE; goto fail_read; } // is this a thread-safe library build? if (H5is_library_threadsafe(&flag) < 0) { ret_val = EXIT_FAILURE; goto fail_read; } printf("Welcome to HDF5 %d.%d.%d\n", majnum, minnum, relnum); printf("Thread-safety %s\n", (flag > 0) ? "enabled" : "disabled"); fail_read:; }
Update	Delete
{ // update the library instance free list limits if (H5set_free_list_limits(512 * 1024, 32 * 1024, 2048 * 1024, 128 * 1024, 8192 * 1024, 512 * 1024) < 0) { ret_val = EXIT_FAILURE; } }	void closing_shop(void *ctx) { printf("GoodBye, Cruel World!\n"); } { #if H5_VERSION_GE(1, 13, 0) // install a finalization routine if (H5atclose(&closing_shop, NULL) < 0) { ret_val = EXIT_FAILURE; } #endif // close shop if (H5close() < 0) { ret_val = EXIT_FAILURE; } }

Functions
herr_t	H5open (void)
	Initializes the HDF5 library. More...
herr_t	H5atclose (H5_atclose_func_t func, void *ctx)
	Registers a callback for the library to invoke when it's closing. More...
herr_t	H5close (void)
	Flushes all data to disk, closes all open objects, and releases memory. More...
herr_t	H5dont_atexit (void)
	Instructs library not to install atexit() cleanup routine. More...
herr_t	H5garbage_collect (void)
	Garbage collects on all free-lists of all types. More...
herr_t	H5set_free_list_limits (int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim)
	Sets free-list size limits. More...
herr_t	H5get_free_list_sizes (size_t *reg_size, size_t *arr_size, size_t *blk_size, size_t *fac_size)
	Gets the current size of the free lists used to manage memory. More...
herr_t	H5get_libversion (unsigned *majnum, unsigned *minnum, unsigned *relnum)
	Returns the HDF library release number. More...
herr_t	H5check_version (unsigned majnum, unsigned minnum, unsigned relnum)
	Verifies that HDF5 library versions are consistent. More...
herr_t	H5is_library_terminating (hbool_t *is_terminating)
	Checks whether the HDF5 library is closing. More...
herr_t	H5is_library_threadsafe (hbool_t *is_ts)
	Determines whether the HDF5 library was built with the thread-safety feature enabled. More...
herr_t	H5free_memory (void *mem)
	Frees memory allocated by the HDF5 library. More...
void *	H5allocate_memory (size_t size, hbool_t clear)
	Allocates memory that will be freed later internally. More...
void *	H5resize_memory (void *mem, size_t size)
	Resizes and, if required, re-allocates memory that will later be freed internally by the HDF5 library. More...

Function Documentation

H5allocate_memory()

void* H5allocate_memory	(	size_t	size,
		hbool_t	clear
	)

Allocates memory that will be freed later internally.

Parameters

[in]	size	The size in bytes of the buffer to be allocated
[in]	clear	Flag whether the new buffer is to be initialized with 0

Returns

On success, returns pointer to newly allocated buffer or returns NULL if size is 0 (zero).
Returns NULL on failure.

H5allocate_memory() allocates a memory buffer of size bytes that will later be freed internally by the HDF5 library.

The boolean clear parameter specifies whether the buffer should be initialized. If clear is true, all bits in the buffer are to be set to 0 (zero); if clear is false, the buffer will not be initialized.

This function is intended to have the semantics of malloc() and calloc(). However, unlike malloc() and calloc(), which allow for a "special" pointer to be returned instead of NULL, this function always returns NULL on failure or when size is set to 0 (zero).

Note

At this time, the only intended use for this function is to allocate memory that will be returned to the library as a data buffer from a third-party filter.

Attention

To avoid heap corruption, allocated memory should be freed using the same library that initially allocated it. In most cases, the HDF5 API uses resources that are allocated and freed either entirely by the user or entirely by the library, so this is not a problem. In rare cases, however, HDF5 API calls will free the memory that the user allocated. This function allows the user to safely allocate this memory.
It is particularly important to use this function to allocate memory in Microsoft Windows environments. In Windows, the C standard library is implemented in dynamic link libraries (DLLs) known as the C run-time (CRT). Each version of Visual Studio comes with multiple versions of the CRT DLLs (debug, release, et cetera) and allocating and freeing memory across DLL boundaries can cause resource leaks and subtle bugs due to heap corruption.
Even when using this function, it is best where possible to ensure that all components of a C application are built with the same version of Visual Studio and configuration (Debug or Release), and thus linked against the same CRT.
Use this function only to allocate memory inside third-party HDF5 filters. It will generally not be safe to use this function to allocate memory for any other purpose.

See also

H5free_memory(), H5resize_memory()

Since

1.8.15

H5atclose()

herr_t H5atclose	(	H5_atclose_func_t	func,
		void *	ctx
	)

Registers a callback for the library to invoke when it's closing.

Parameters

[in]	func	The function pointer to invoke
[in]	ctx	Context to pass to func when invoked

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5atclose() registers a callback that the HDF5 library will invoke when closing. The full capabilities of the HDF5 library are available to callbacks invoked through this mechanism, and library shutdown will only begin in earnest when all callbacks have been invoked and have returned.

Registered callbacks are invoked in LIFO order, similar to the Standard C 'atexit' routine. For example, if 'func1' is registered, then 'func2', when the library is closing 'func2', will be invoked first, then 'func1'.

The ctx pointer will be passed to func when it's invoked. NULL is allowed for ctx.

If the HDF5 library is initialized and closed more than once, the func callback must be registered within each open/close cycle.

Since

1.14.0

H5check_version()

herr_t H5check_version	(	unsigned	majnum,
		unsigned	minnum,
		unsigned	relnum
	)

Verifies that HDF5 library versions are consistent.

Parameters

[in]	majnum	HDF5 library major version number
[in]	minnum	HDF5 library minor version number
[in]	relnum	HDF5 library release number

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5check_version() verifies that the version of the HDF5 library with which an application was compiled, as indicated by the passed parameters, matches the version of the HDF5 library against which the application is currently linked.

majnum is the major version number of the HDF library with which the application was compiled, minnum is the minor version number, and relnum is the release number. Consider the following example:

An official HDF5 release is labelled as follows: HDF5 Release <majnum>.<minnum>.<relnum>
For example, in HDF5 Release 1.8.5:

• 1 is the major version number, majnum.
• 8 is the minor version number, minnum.
• 5 is the release number, relnum.

As stated above, H5check_version() first verifies that the version of the HDF5 library with which an application was compiled matches the version of the HDF5 library against which the application is currently linked. If this check fails, H5check_version() causes the application to abort (by means of a standard C abort() call) and prints information that is usually useful for debugging. This precaution is taken to avoid the risks of data corruption or segmentation faults.

The most common cause of this failure is that an application was compiled with one version of HDF5 and is dynamically linked with a different version different version.

If the above test passes, H5check_version() proceeds to verify the consistency of additional library version information. This is designed to catch source code inconsistencies that do not normally cause failures; if this check reveals an inconsistency, an informational warning is printed but the application is allowed to run.

H5close()

herr_t H5close

(

void

)

Flushes all data to disk, closes all open objects, and releases memory.

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5close() flushes all data to disk, closes all open HDF5 objects, and cleans up all memory used by the HDF5 library. This function is generally called when the application calls exit(), but may be called earlier in the event of an emergency shutdown or out of a desire to free all resources used by the HDF5 library.

H5dont_atexit()

herr_t H5dont_atexit

(

void

)

Instructs library not to install atexit() cleanup routine.

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5dont_atexit() indicates to the library that an atexit() cleanup routine should not be installed. The major purpose for using this function is in situations where the library is dynamically linked into an application and is un-linked from the application before exit() gets called. In those situations, a routine installed with atexit() would jump to a routine that was no longer in memory, causing errors.

Attention

In order to be effective, this routine must be called before any other HDF5 function calls, and must be called each time the library is loaded/linked into the application (the first time and after it's been unloaded).

H5free_memory()

herr_t H5free_memory

(

void *

mem

)

Frees memory allocated by the HDF5 library.

Parameters

[in]

mem

Buffer to be freed. Can be NULL

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5free_memory() frees the memory that has been allocated by the caller with H5allocate_memory() or by the HDF5 library on behalf of the caller.

H5Tget_member_name() provides an example of memory allocation on behalf of the caller: The function returns a buffer containing the name of a compound datatype member. It is the caller's responsibility to eventually free that buffer with H5free_memory().

Attention

It is especially important to use this function to free memory allocated by the library on Windows. The C standard library is implemented in dynamic link libraries (DLLs) known as the C run-time (CRT). Each version of Visual Studio comes with two CRT DLLs (debug and release) and allocating and freeing across DLL boundaries can cause resource leaks and subtle bugs due to heap corruption.
Only use this function to free memory allocated by the HDF5 Library. It will generally not be safe to use this function to free memory allocated by any other means.
Even when using this function, it is still best to ensure that all components of a C application are built with the same version of Visual Studio and build (debug or release) and thus linked against the same CRT.

See also

H5allocate_memory(), H5resize_memory()

Since

1.8.13

H5garbage_collect()

herr_t H5garbage_collect

(

void

)

Garbage collects on all free-lists of all types.

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5garbage_collect() walks through all garbage collection routines of the library, freeing any unused memory.

It is not required that H5garbage_collect() be called at any particular time; it is only necessary for certain situations where the application has performed actions that cause the library to allocate many objects. The application should call H5garbage_collect() if it eventually releases those objects and wants to reduce the memory used by the library from the peak usage required.

Note

The library automatically garbage collects all the free lists when the application ends.

H5get_free_list_sizes()

herr_t H5get_free_list_sizes	(	size_t *	reg_size,
		size_t *	arr_size,
		size_t *	blk_size,
		size_t *	fac_size
	)

Gets the current size of the free lists used to manage memory.

Parameters

[out]	reg_size	The current size of all "regular" free list memory used
[out]	arr_size	The current size of all "array" free list memory used
[out]	blk_size	The current size of all "block" free list memory used
[out]	fac_size	The current size of all "factory" free list memory used

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5get_free_list_sizes() obtains the current size of the different kinds of free lists that the library uses to manage memory. The free list sizes can be set with H5set_free_list_limits() and garbage collected with H5garbage_collect(). These lists are global for the entire library.

Since

1.10.7

H5get_libversion()

herr_t H5get_libversion	(	unsigned *	majnum,
		unsigned *	minnum,
		unsigned *	relnum
	)

Returns the HDF library release number.

Parameters

[out]	majnum	The major version number of the library
[out]	minnum	The minor version number of the library
[out]	relnum	The release version number of the library

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5get_libversion() retrieves the major, minor, and release numbers of the version of the HDF5 library which is linked to the application.

H5is_library_terminating()

herr_t H5is_library_terminating

(

hbool_t *

is_terminating

)

Checks whether the HDF5 library is closing.

Parameters

[out]

is_terminating

Flag indicating whether library is shutting down

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5is_library_terminating() queries whether the HDF5 library is in the process of shutting down. The is_terminating flag will only be set to true after shutdown starts, it will be false before the library has been initialized, while the library is initialized, and after it has been closed. The value of is_terminating is undefined if this routine fails.

Since

1.14.0

H5is_library_threadsafe()

herr_t H5is_library_threadsafe

(

hbool_t *

is_ts

)

Determines whether the HDF5 library was built with the thread-safety feature enabled.

Parameters

[out]

is_ts

Boolean value indicating whether the library was built with thread-safety enabled

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

The HDF5 library, although not internally multi-threaded, can be built with a thread-safety feature enabled that protects internal data structures with a mutex. In certain circumstances, it may be useful to determine, at run-time, whether the linked HDF5 library was built with the thread-safety feature enabled.

H5open()

herr_t H5open

(

void

)

Initializes the HDF5 library.

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5open() initializes the HDF5 library.

When the HDF5 library is used in a C application, the library is automatically initialized when the first HDf5 function call is issued. If one finds that an HDF5 library function is failing inexplicably, H5open() can be called first. It is safe to call H5open() before an application issues any other function calls to the HDF5 library, as there are no damaging side effects in calling it more than once.

H5resize_memory()

void* H5resize_memory	(	void *	mem,
		size_t	size
	)

Resizes and, if required, re-allocates memory that will later be freed internally by the HDF5 library.

Parameters

[in]	mem	Pointer to a buffer to be resized. May be NULL
[in]	size	New size of the buffer, in bytes

Returns

On success, returns pointer to resized or reallocated buffer or returns NULL if size is 0 (zero).
Returns NULL on failure.

H5resize_memory() takes a pointer to an existing buffer and resizes the buffer to match the value in size. If necessary, the buffer is reallocated. If size is 0, the buffer is released.

The input buffer must either be NULL or have been allocated by H5allocate_memory() since the input buffer may be freed by the library.

For certain behaviors, the pointer mem may be passed in as NULL.

This function is intended to have the semantics of realloc():

H5resize_memory(buffer, size)	Resizes buffer. Returns pointer to resized buffer.
H5resize_memory(NULL, size)	Allocates memory using HDF5 Library allocator. Returns pointer to new buffer
H5resize_memory(buffer, 0)	Frees memory using HDF5 Library allocator. Returns NULL.
H5resize_memory(NULL, 0)	Returns NULL (undefined in C standard).

Unlike realloc(), which allows for a "special pointer to be returned instead of NULL, this function always returns NULL on failure or when size is 0 (zero).

Note

At this time, the only intended use for this function is to resize or reallocate memory that will be returned to the library (and eventually to the user) as a data buffer from a third-party HDF5 filter.

Attention

To avoid heap corruption, allocated memory should be freed using the same library that initially allocated it. In most cases, the HDF5 API uses resources that are allocated and freed either entirely by the user or entirely by the library, so this is not a problem. In rare cases, however, HDF5 API calls will free memory that the user allocated. This function allows the user to safely allocate this memory.
It is particularly important to use this function to resize memory on Microsoft Windows systems. In Windows, the C standard library is implemented in dynamic link libraries (DLLs) known as the C run-time (CRT). Each version of Visual Studio comes with multiple versions of the CRT DLLs (debug, release, et cetera) and allocating and freeing memory across DLL boundaries can cause resource leaks and subtle bugs due to heap corruption.
Even when using this function, it is still best to ensure that all components of a C application are built with the same version of Visual Studio and the same configuration (Debug or Release), and thus linked against the same CRT.
Only use this function to resize memory inside third-party HDF5 filters. It will generally not be safe to use this function to resize memory for any other purpose.

See also

H5allocate_memory(), H5free_memory()

Since

1.8.15

H5set_free_list_limits()

herr_t H5set_free_list_limits	(	int	reg_global_lim,
		int	reg_list_lim,
		int	arr_global_lim,
		int	arr_list_lim,
		int	blk_global_lim,
		int	blk_list_lim
	)

Sets free-list size limits.

Parameters

[in]	reg_global_lim	The cumulative limit, in bytes, on memory used for all regular free lists (Default: 1MB)
[in]	reg_list_lim	The limit, in bytes, on memory used for each regular free list (Default: 64KB)
[in]	arr_global_lim	The cumulative limit, in bytes, on memory used for all array free lists (Default: 4MB)
[in]	arr_list_lim	The limit, in bytes, on memory used for each array free list (Default: 256KB)
[in]	blk_global_lim	The cumulative limit, in bytes, on memory used for all block free lists and, separately, for all factory free lists (Default: 16MB)
[in]	blk_list_lim	The limit, in bytes, on memory used for each block or factory free list (Default: 1MB)

Returns

Returns a non-negative value if successful; otherwise, returns a negative value.

H5set_free_list_limits() sets size limits on all types of free lists. The HDF5 library uses free lists internally to manage memory. The types of free lists used are as follows:

• Regular free lists manage memory for single internal data structures.
• Array free lists manage memory for arrays of internal data structures.
• Block free lists manage memory for arbitrarily-sized blocks of bytes.
• Factory free lists manage memory for fixed-size blocks of bytes.

The parameters specify global and per-list limits; for example, reg_global_limit and reg_list_limit limit the accumulated size of all regular free lists and the size of each individual regular free list, respectively. Therefore, if an application sets a 1Mb limit on each of the global lists, up to 4Mb of total storage might be allocated, 1Mb for each of the regular, array, block, and factory type lists.

The settings specified for block free lists are duplicated for factory free lists. Therefore, increasing the global limit on block free lists by x bytes will increase the potential free list memory usage by 2x bytes.

Using a value of -1 for a limit means that no limit is set for the specified type of free list.

Version

1.8.3 Function changed in this release to set factory free list memory limits.

Since

1.6.0