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 In the HDF5 Reference Manual 
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H5: General Library Functions

These functions and macros serve general-purpose needs of the HDF5 library and its users.

The C Interfaces:

Alphabetical Listing

The Fortran Interface:
In general, each Fortran subroutine performs exactly the same task as the corresponding C function.

Last modified: 1 May 2015

Name: H5allocate_memory

Signature:
void * H5allocate_memory( size_t size, hbool_t clear )

Purpose:
Allocates memory that will later be freed internally by the HDF5 Library.

Description:
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).

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.


Notes:
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 allocate memory in Microsoft Windows envrionments. 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.


Parameters:
size_t size   IN: Specifies the size in bytes of the buffer to be allocated.
hbool_t clear   IN: Specifies whether the new buffer is to be initialized to 0 (zero).

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

Fortran Interface:
None

See Also:

History:
Release     Change
1.8.15 C function introduced with this release.



Last modified: 25 October 2011
Name: H5check_version
Signature:
herr_t H5check_version( unsigned majnum, unsigned minnum, unsigned relnum )

Purpose:
Verifies that HDF5 library versions are consistent.

Description:
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 illustration:

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 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.

Parameters:

Returns:
Returns a non-negative value if successful. Upon failure, this function causes the application to abort.

Fortran90 Interface: h5check_version_f
Signature:

  SUBROUTINE h5check_version_f(majnum, minnum, relnum, error)
    INTEGER, INTENT(IN)  :: majnum, minnum, relnum
    INTEGER, INTENT(OUT) :: error

Inputs:

  majnum - major version of the library
  minum  - minor version of the library
  relnum - release version of the library

Outputs:

  error - Returns 0 if successful and -1 if fails

History:
Last modified: 25 October 2011
Name: H5close
Signature:
herr_t H5close(void)

Purpose:
Flushes all data to disk, closes all open identifiers, and cleans up memory.

Description:
H5close flushes all data to disk, closes all open HDF5 identifiers, 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.

When the HDF5 Library is employed in a Fortran90 application, h5close_f closes the HDF5 Fortran interface but does not shut down the HDF5 Library, leaving HDF5 available to other software that may require the resource. h5open_f and h5close_f are required calls in HDF5 Fortran applications.

Parameters:
None.

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

Fortran90 Interface: h5close_f
Signature:

  SUBROUTINE h5close_f(error)
    INTEGER, INTENT(OUT) :: error

Outputs:

  error - Returns 0 if successful and -1 if fails

History:
Release     Change
1.8.8 Fortran subroutine updated modified so that it does not shut down the HDF5 Library.
Last modified: 25 October 2011
Name: H5dont_atexit
Signature:
herr_t H5dont_atexit(void)

Purpose:
Instructs library not to install atexit cleanup routine.

Description:
H5dont_atexit indicates to the library that an atexit() cleanup routine should not be installed. The major purpose for this 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 which was no longer in memory, causing errors.

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

Parameters:
None.

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

Fortran90 Interface: h5dont_atexit_f
Signature:

  SUBROUTINE h5dont_atexit_f(error)
    INTEGER, INTENT(OUT) :: error

Outputs:

  error - Returns 0 if successful and -1 if fails

History:
Release     Change
1.4.5 Fortran subroutine introduced in this release.
1.8.8 Fortran subroutine updated in this release.
Last modified: 19 May 2016

Name: H5free_memory

Signature:
herr_t H5free_memory(void *buf)

Purpose:
Frees memory allocated by the HDF5 Library.

Description:
H5free_memory frees memory that has been allocated by the caller with H5alloc_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.


Notes:
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.


Parameters:
void *mem    IN: Buffer to be freed. Can be NULL.

Returns:
Returns a non-negative value if successful. Otherwise returns a negative value.

Fortran Interface:
None

See Also:

History:
Release Change
1.8.13 C function introduced with this release.



Last modified: 25 October 2011
Name: H5garbage_collect
Signature:
herr_t H5garbage_collect(void)

Purpose:
Garbage collects on all free-lists of all types.

Description:
H5garbage_collect walks through all the 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 in 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.

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

Parameters:
None.

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

Fortran90 Interface: h5garbage_collect_f
Signature:

  SUBROUTINE h5garbage_collect_f(error)
    INTEGER, INTENT(OUT) :: error

Outputs:

  error - Returns 0 if successful and -1 if fails

History:
Release     Fortran90
1.4.5 Function introduced in this release.
1.8.8 Fortran subroutine updated in this release.
Last modified: 25 October 2011
Name: H5get_libversion
Signature:
herr_t H5get_libversion( unsigned *majnum, unsigned *minnum, unsigned *relnum )

Purpose:
Returns the HDF library release number.

Description:
H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF library which is linked to the application.

Parameters:
unsigned *majnum OUT: The major version of the library.
unsigned *minnum     OUT: The minor version of the library.
unsigned *relnum OUT: The release number of the library.

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

Fortran90 Interface: h5get_libversion_f
Signature:

  SUBROUTINE h5get_libversion_f(majnum, minnum, relnum, error)
    INTEGER, INTENT(OUT) :: majnum, minnum, relnum, error

Outputs:

  majnum - major version of the library
  minum  - minor version of the library
  relnum - release version of the library
  error  - Returns 0 if successful and -1 if fails

History:
Release     Change
1.4.5 Fortran subroutine introduced in this release.
1.8.8 Fortran subroutine updated in this release.
Last modified: 29 September 2015

Name: H5is_library_threadsafe

Signature:
herr_t H5is_library_threadsafe(/*OUT*/ hbool_t* is_ts)

Purpose:
Determine whether the HDF5 Library was built with the thread-safety feature enabled.

Description:
The HDF5 Library, although not internally multithreaded, can optionally 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 this thread-safety feature enabled.

Parameters:
hbool_t* is_ts     OUT: 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.

Fortran Interface:
None

History:
Release     Change
1.8.16 C function introduced with this release.




Last modified: 25 October 2011
Name: H5open
Signature:
herr_t H5open(void)

Purpose:
Initializes the HDF5 library.

Description:
H5open initialize the library.

When the HDF5 Library is employed in a C application, this function is normally called automatically, but if you find that an HDF5 library function is failing inexplicably, try calling this function first. If you wish to elimnate this possibility, it is safe to routinely call H5open before an application starts working with the library as there are no damaging side-effects in calling it more than once.

When the HDF5 Library is employed in a Fortran90 application, h5open_f initializes global variables (for example, predefined types) and performs other tasks required to initialize the HDF5 Fortran Library. h5open_f and h5close_f are required calls in HDF5 Fortran applications.

Parameters:
None.

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

Fortran90 Interface: h5open_f
Signature:

  SUBROUTINE h5open_f(error)
    INTEGER, INTENT(OUT) :: error

Outputs:

  error - Returns 0 if successful and -1 if fails

History:
Release     Change
1.8.8 Fortran subroutine updated in this release.
Last modified: 1 May 2015

Name: H5resize_memory

Signature:
void * H5resize_memory( void *mem, size_t size )

Purpose:
Resizes and possibly re-allocates memory that will later be freed internally by the HDF5 Library.

Description:
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).

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.


Notes:
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.


Parameters:
void *mem   IN: Pointer to a buffer to be resized.
May be NULL.
size_t size   IN: 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.

Fortran Interface:
None

See Also:

History:
Release     Change
1.8.15 C function introduced with this release.



Last modified: 6 May 2010
Name: H5set_free_list_limits
Signature:
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 )

Purpose:
Sets free-list size limits.

Description:
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.

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

Fortran90 Interface:
None.

History:
    Release     C
    1.6.0 Function introduced in this release.
    1.8.3 Function changed in this release to set factory free list memory limits.
Last modified: 22 April 2011
Name: H5_VERSION_GE
Signature:
H5_VERSION_GE( int maj, int min, int rel )

Purpose:
Determines whether the version of the library being used is greater than or equal to the specified version.

Motivation:
The H5_VERSION_GE and H5_VERSION_LE macros are used at compile time to conditionally include or exclude code based on the version of the HDF5 library against which an application will be linked.

Description:
The H5_VERSION_GE macro compares the version of the HDF5 library being used against the version number specified in the parameters.

For more information, see “HDF5 Software Updates” at www.hdfgroup.org/HDF5/doc/TechNotes/Version.html.

Parameters:
int maj     IN: Major version number
A non-negative integer value
int min IN: Minor version number
A non-negative integer value
int rel IN: Release number
A non-negative integer value

Returns:
TRUE If the library version is greater than or equal to the version number specified
FALSE     If the library version is less than the version number specified

A library version is greater than the specified version number if its major version is larger than the specified major version number. If the major version numbers are the same, it is greater than the specified version number if its minor version is larger than the specified minor version number. If the minor version numbers are the same, then a library version would be greater than the specified version number if its release number is larger than the specified release number.

Fortran Interface:
None

Example Usage:
Suppose an application wants to call different functions based on the version of the HDF5 library to which an application will be linked. For example, the link functions, H5Lxxx, are new in the 1.8 versions of HDF5, and some group functions, H5Gxxx, are deprecated in the 1.8 versions. The following code uses H5Ldelete if the library version is 1.8.0 or greater or uses H5Gunlink if the library version is not greater than 1.8.0. Similarly, the code calls H5Lexists or H5Gopen to make sure the group has been deleted. 

    #if H5_VERSION_GE(1,8,0)
        ret = H5Ldelete(file, "Group", H5P_DEFAULT);
        CHECK(ret, FAIL, "H5Lunlink");

        status = H5Lexists(file, "Group", H5P_DEFAULT);
        VERIFY(status, FALSE, "H5Lexists");
    #else
        ret = H5Gunlink(file, "Group");
        CHECK(ret, FAIL, "H5Gunlink");

        H5E_BEGIN_TRY {
            grp = H5Gopen(file, "Group");
        } H5E_END_TRY;
        VERIFY(grp, FAIL, "H5Gopen");
    #endif

History:
Release     Change
1.8.7 C macro introduced in this release.
Last modified: 22 April 2011
Name: H5_VERSION_LE
Signature:
H5_VERSION_LE( int maj, int min, int rel )

Purpose:
Determines whether the version of the library being used is less than or equal to the specified version.

Motivation:
The H5_VERSION_GE and H5_VERSION_LE macros are used at compile time to conditionally include or exclude code based on the version of the HDF5 library against which an application will be linked.

Description:
The H5_VERSION_LE macro compares the version of the HDF5 library being used against the version number specified in the parameters.

For more information, see “HDF5 Software Updates” at www.hdfgroup.org/HDF5/doc/TechNotes/Version.html.

Parameters:
int maj     IN: Major version number
A non-negative integer value
int min IN: Minor version number
A non-negative integer value
int rel IN: Release number
A non-negative integer value

Returns:
TRUE If the library version is less than or equal to the version number specified
FALSE     If the library version is greater than the version number specified

A library version is less than the specified version number if its major version is smaller than the specified major version number. If the major version numbers are the same, it is less than the specified version number if its minor version is smaller than the specified minor version number. If the minor version numbers are the same, then a library version would be less than the specified version number if its release number is smaller than the specified release number.

Fortran Interface:
None

Example Usage:
Suppose an application wants to call different functions based on the version of the HDF5 library to which an application will be linked. For example, the link functions, H5Lxxx, are new in the 1.8 versions of HDF5, and some group functions, H5Gxxx, are deprecated in the 1.8 versions. The following code uses H5Gunlink if the library version is 1.6.10 or earlier or uses H5Ldelete if the library version is not 1.6.10 or earlier. Similarly, the code calls H5Gopen or H5Lexists to make sure the group has been deleted. 

    #if H5_VERSION_LE(1,6,10)
        ret = H5Gunlink(file, "Group");
        CHECK(ret, FAIL, "H5Gunlink");

        H5E_BEGIN_TRY {
            grp = H5Gopen(file, "Group");
        } H5E_END_TRY;
        VERIFY(grp, FAIL, "H5Gopen");
    #else
        ret = H5Ldelete(file, "Group", H5P_DEFAULT);
        CHECK(ret, FAIL, "H5Lunlink");

        status = H5Lexists(file, "Group", H5P_DEFAULT);
        VERIFY(status, FALSE, "H5Lexists");
    #endif

History:
Release     Change
1.8.7 C macro introduced in this release.
HDF5 documents and links 
Introduction to HDF5 
HDF5 User’s Guide 
 In the HDF5 Reference Manual 
H5DS   H5IM   H5LT   H5PT   H5TB  Optimized 
H5   H5A   H5D   H5E   H5F   H5G   H5I   H5L 
H5O   H5P   H5PL   H5R   H5S   H5T   H5Z 
Tools   Datatypes   Fortran   Compatibility Macros 
Collective Calls in Parallel 
The HDF Group Help Desk:
Describes HDF5 Release 1.8.18, November 2016.
  Copyright by The HDF Group
and the Board of Trustees of the University of Illinois