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HDF5
1.15.0.f39b228
API Reference
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The target audience for this document has existing applications that use the HDF5 library, and is considering moving to the latest HDF5 release to take advantage of the latest library features and enhancements.
With each major release of HDF5, such as 1.12 or 1.10, certain compatibility issues must be considered when migrating applications from an earlier major release.
This document describes the approach taken by The HDF Group to help existing users of HDF5 address compatibility issues in the HDF5 API.
In response to new and evolving requirements for the library and data format, several basic functions have changed since HDF5 was first released. To allow existing applications to continue to compile and run properly, all versions of these functions have been retained in the later releases of the HDF5 library.
Given the scope of changes available with each major release of HDF5, and recognizing the potentially time-consuming task of editing all the affected calls in user applications, The HDF Group has created a set of macros that can be used to flexibly and easily map existing API calls to previous release functions. We refer to these as the API compatibility macros.
The HDF Group generally encourages users to update applications to work with the latest HDF5 library release so that all new features and enhancements are available to them. At the same time, The HDF Group understands that, under some circumstances, updating applications may not be feasible or necessary. The API compatibility macros, described in this document, provide a bridge from old APIs to new and can be particularly helpful in situations such as these:
As part of latest HDF5 release, several functions that existed in previous versions of the library were updated with new calling parameters and given new names. The updated versions of the functions have a number (for, e.g., '2') at the end of the original function name. The original versions of these functions were retained and renamed to have an earlier number (for, e.g., '1') at the end of the original function name.
For example, consider the function H5Lvisit
in HDF5 release 1.10 as compared with 1.12:
Original function name and signature in 1.10.0 | herr_t H5Lvisit(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data) |
---|---|
Updated function and signature, introduced in release 1.12.0 | herr_t H5Lvisit2(hid_t group_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate2_t op, void *op_data) |
Original function and signature, renamed in release 1.12.0 | herr_t H5Lvisit1(hid_t group_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate1_t op, void *op_data) |
API compatibility macro, introduced in release 1.12.0 |
The macro, The function names ending in '1' or '2' are referred to as versioned names, and the corresponding functions are referred to as versioned functions. For new code development, The HDF Group recommends use of the compatibility macro mapped to the latest version of the function. The original version of the function should be considered deprecated and, in general, should not be used when developing new code. |
To determine the mapping for a given API compatibility macro in a given application, a combination of user-controlled selections, collectively referred to as the compatibility macro mapping options, is considered in the following sequence:
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When the HDF5 library is built, configure
flags can be used to control the API compatibility macro mapping behavior exhibited by the library. This behavior can be overridden by application and function mappings. One configure flag excludes deprecated functions from the HDF5 library, making them unavailable to applications linked with the library.
configure flag | Macros map to release (versioned function; H5Lvisit shown) | Deprecated functions available? ( H5Lvisit1 ) |
---|---|---|
–with-default-api-version=v112 (the default in 1.12) | 1.12.x (H5Lvisit2 ) | yes |
–with-default-api-version=v110 | 1.10.x (H5Lvisit1 ) | yes |
–with-default-api-version=v18 | 1.8.x (H5Lvisit1 ) | yes |
–with-default-api-version=v16 | 1.6.x (H5Lvisit1 ) | yes |
–disable-deprecated-symbols | 1.12.x (H5Lvisit2 ) | no |
Refer to the file libhdf5.settings
in the directory where the HDF5 library is installed to determine the configure
flags used to build the library. In particular, look for the two lines shown here under Features:
Default API mapping: v112
With deprecated public symbols: yes
When an application using HDF5 APIs is built and linked with the HDF5 library, compile-time options to h5cc
can be used to control the API compatibility macro mapping behavior exhibited by the application. The application mapping overrides the behavior specified by the library mapping, and can be overridden on a function-by-function basis by the function mappings.
If the HDF5 library was configured with the –disable-deprecated-symbols
flag, then the deprecated functions will not be available, regardless of the application mapping options.
h5cc option | Macros map to release (versioned function; H5Lvisit shown) | Deprecated functions available? ( H5Lvisit1 ) |
---|---|---|
-DH5_USE_112_API (Default behavior if no option specified.) | 1.12.x (HLvisit2 ) | yes* *if available in library |
-DH5_USE_110_API | 1.10.x (HLvisit1 ) | yes* *if available in library |
-DH5_USE_18_API | 1.8.x (H5Lvisit1 ) | yes* *if available in library |
-DH5_USE_16_API | 1.6.x (H5Lvisit1 ) | yes* *if available in library |
-DH5_NO_DEPRECATED_SYMBOLS | 1.10.x (H5Lvisit1 ) | no |
Function mappings are specified when the application is built. These mappings can be used to control the mapping of the API compatibility macros to underlying functions on a function-by-function basis. The function mappings override the library and application mappings discussed earlier.
If the HDF5 library was configured with the –disable-deprecated-symbols
flag, or -DH5_NO_DEPRECATED_SYMBOLS
is used to compile the application, then the deprecated functions will not be available, regardless of the function mapping options.
For every function with multiple available versions, a compile-time version flag can be defined to selectively map the function macro to the desired versioned function. The function mapping consists of the function name followed by "_vers
" which is mapped by number to a specific function or struct:
Macro | Function Mapping | Mapped to function or struct |
---|---|---|
H5xxx | H5xxx_vers=1 | H5xxx1 |
H5xxx_vers=2 | H5xxx2 |
For example, in version 1.10 the H5Rreference
macro can be mapped to either H5Rreference1
or H5Rreference2
. When used, the value of the H5Rreference_vers
compile-time version flag determines which function will be called:
H5Rreference_vers
is set to 1
, the macro H5Rreference
will be mapped to H5Rreference1
. H5cc ... -DH5Rreference_vers=1 ...
H5Rdereference_vers
is set to 2
, the macro H5Rdereference
will be mapped to H5Rdereference2
. h5cc ... -DH5Rreference_vers=2 ...
H5Rreference_vers
is not set, the macro H5Rreference
will be mapped to either H5Rreference1
or H5Rreference2
, based on the application mapping, if one was specified, or on the library mapping. h5cc ...
application.c
only calls H5Lvisit
, H5Ovisit
, and H5Oget_info_by_name
. To compile this application with 1.10 APIs in 1.12 with the function specific mappings, then not only must H5Lvisit_vers
, H5Ovisit_vers
, and H5Oget_info_by_name_vers
be specified on the command line, but the mapped structures and every function that uses the mapped structures must be included, as well. The full compile line is shown below: Macro ( H5xxx ) | Default function used if no macro specified
| Function used if specifying 1.10
|
---|---|---|
H5Lget_info() | H5Lget_info2()
| H5Lget_info1()
|
H5Lget_info_by_idx() | H5Lget_info_by_idx2()
| H5Lget_info_by_idx1()
|
H5Literate() | H5Literate2()
| H5Literate1()
|
H5Literate_by_name() | H5Literate_by_name2()
| H5Literate_by_name1()
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H5Lvisit() | H5Lvisit2()
| H5Lvisit1()
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H5Lvisit_by_name() | H5Lvisit_by_name2()
| H5Lvisit_by_name1()
|
H5Oget_info() | H5Oget_info3()
| H5Oget_info1()
|
H5Oget_info_by_idx() | H5Oget_info_by_idx3()
| H5Oget_info_by_idx1()
|
H5Oget_info_by_name() | H5Oget_info_by_name3()
| H5Oget_info_by_name1()
|
H5Ovisit() | H5Ovisit3()
| H5Ovisit1()
|
H5Ovisit_by_name() | H5Ovisit_by_name3()
| H5Ovisit_by_name1()
|
H5Pencode() | H5Pencode2()
| H5Pencode1()
|
H5Sencode() | H5Sencode2()
| H5Sencode1()
|
Macro | Default function used (if no macro specified) | Introduced in | h5cc version flag and value | Mapped to function or struct |
---|---|---|---|---|
H5Rdereference() | H5Rdereference2() | HDF5-1.10.0 | -DH5Rdereference_vers=1 | H5Rdereference1() |
-DH5Rdereference_vers=2 | H5Rdereference2() | |||
H5Fget_info() | H5Fget_info2() | HDF5-1.10.0 | -DH5Fget_info_vers=1 | H5Fget_info1() with struct H5F_info1_t |
-DH5Fget_info_vers=2 | H5Fget_info2() with struct H5F_info2_t | |||
H5Oget_info() | H5Oget_info1() | HDF5-1.10.3 | -DH5Oget_info_vers=1 | H5Oget_info1() |
-DH5Oget_info_vers=2 | H5Oget_info2() | |||
H5Oget_info_by_idx() | H5Oget_info_by_idx1() | HDF5-1.10.3 | -DH5Oget_info_by_idx_vers=1 | H5Oget_info_by_idx1() |
-DH5Oget_info_by_idx_vers=2 | H5Oget_info_by_idx2() | |||
H5Oget_info_by_name() | H5Oget_info_by_name1() | HDF5-1.10.3 | -DH5Oget_info_by_name_vers=1 | H5Oget_info_by_name1() |
-DH5Oget_info_by_name_vers=2 | H5Oget_info_by_name2() | |||
H5Ovisit() | H5Ovisit1() | HDF5-1.10.3 | -DH5Ovisit_vers=1 | H5Ovisit1() |
-DH5Ovisit_vers=2 | H5Ovisit2() | |||
H5Ovisit_by_name() | H5Ovisit_by_name1() | HDF5-1.10.3 | -DH5Ovisit_by_name_vers=1 | H5Ovisit_by_name1() |
-DH5Ovisit_by_name_vers=2 | H5Ovisit_by_name2() |
At release 1.8.0, the API compatibility macros, function mapping compile-time version flags and values, and corresponding versioned functions listed in the following table were introduced. If the application being compiled to run with any 1.10.x release was written to use any 1.6.x release of HDF5, you must also consider these macros and mapping options.
Macro | h5cc version flag and value | Mapped to function or struct |
---|---|---|
H5Acreate() | DH5Acreate_vers=1 | H5Acreate1() |
DH5Acreate_vers=2 | H5Acreate2() | |
H5Aiterate() | DH5Aiterate_vers=1 | H5Aiterate1() with struct H5A_operator1_t |
DH5Aiterate_vers=2 | H5Aiterate2() with struct H5A_operator2_t | |
H5Dcreate() | DH5Dcreate_vers=1 | H5Dcreate1() |
DH5Dcreate_vers=2 | H5Dcreate2() | |
H5Dopen() | DH5Dopen_vers=1 | H5Dopen1() |
DH5Dopen_vers=2 | H5Dopen2() | |
H5Eclear() | DH5Eclear_vers=1 | H5Eclear1() |
DH5Eclear_vers=2 | H5Eclear2() | |
H5Eprint() | DH5Eprint_vers=1 | H5Eprint1() |
DH5Eprint_vers=2 | H5Eprint2() | |
H5Epush() | DH5Epush_vers=1 | H5Epush1() |
DH5Epush_vers=2 | H5Epush2() | |
H5Eset_auto() | DH5Eset_auto_vers=1 | H5Eset_auto1() |
DH5Eset_auto_vers=2 | H5Eset_auto2() | |
H5Eget_auto() | DH5Eget_auto_vers=1 | H5Eget_auto1() |
DH5Eget_auto_vers=2 | H5Eget_auto2() | |
H5E_auto_t struct for H5Eset_auto() and H5Eget_auto() | DH5E_auto_t_vers=1 | H5E_auto1_t |
DH5E_auto_t_vers=2 | H5E_auto2_t | |
H5Ewalk() | DH5Ewalk_vers=1 | H5Ewalk1() with callback H5E_walk1_t and struct H5E_error1_t |
DH5Ewalk_vers=2 | H5Ewalk2() with callback H5E_walk2_t and struct H5E_error2_t | |
H5Gcreate() | DH5Gcreate_vers=1 | H5Gcreate1() |
DH5Gcreate_vers=2 | H5Gcreate2() | |
H5Gopen() | DH5Gopen_vers=1 | H5Gopen1() |
DH5Gopen_vers=2 | H5Gopen2() | |
H5Pget_filter() | DH5Pget_filter_vers=1 | H5Pget_filter1() |
DH5Pget_filter_vers=2 | H5Pget_filter2() | |
H5Pget_filter_by_id() | DH5Pget_filter_by_id_vers=1 | H5Pget_filter_by_id1() |
DH5Pget_filter_by_id_vers=2 | H5Pget_filter_by_id2() | |
H5Pinsert() | DH5Pinsert_vers=1 | H5Pinsert1() |
DH5Pinsert_vers=2 | H5Pinsert2() | |
H5Pregister() | DH5Pregister_vers=1 | H5Pregister1() |
DH5Pregister_vers=2 | H5Pregister2() | |
H5Rget_obj_type() | DH5Rget_obj_typevers=1 | H5Rget_obj_type1() |
DH5Rget_obj_type_vers=2 | H5Rget_obj_type2() | |
H5Tarray_create() | DH5Tarray_create_vers=1 | H5Tarray_create1() |
DH5Tarray_create_vers=2 | H5Tarray_create2() | |
H5Tcommit() | DH5Tcommit_vers=1 | H5Tcommit1() |
DH5Tcommit_vers=2 | H5Tcommit2() | |
H5Tget_array_dims() | DH5Tget_array_dims_vers=1 | H5Tget_array_dims1() |
DH5Tget_array_dims_vers=2 | H5Tget_array_dims2() | |
H5Topen() | DH5Topen_vers=1 | H5Topen1() |
DH5Topen_vers=2 | H5Topen2() | |
H5Z_class_t struct for H5Zregister() | DH5Z_class_t_vers=1 | H5Z_class1_t |
DH5Z_class_t_vers=2 | H5Z_class2_t |
It is possible to specify multiple function mappings for a single application build:
As a result of the function and struct mappings in this compile example, all occurrences of the macro H5Rdereference
will be mapped to H5Rdereference1
and all occurrences of the macro H5Fget_info
will be mapped to H5Fget_info2
for the application being built.
The function and struct mappings can be used to guarantee that a given API compatibility macro will be mapped to the desired underlying function or struct version regardless of the library or application mappings. In cases where an application may benefit greatly from features offered by some of the later APIs, or must continue to use some earlier API versions for compatibility reasons, this fine-grained control may be very important.
As noted earlier, the function mappings can only reference versioned functions that are included in the HDF5 library, as determined by the configure flag used to build the library. For example, if the HDF5 library being linked with the application was built with the –disable-deprecated-symbols
option, version 1 of the underlying functions would not be available, and the example above that defined H5Rdereference_vers=1
would not be supported.
The function mappings do not negate any available functions. If H5Rdereference1
is available in the installed version of the HDF5 library, and the application was not compiled with the -DH5_NO_DEPRECATED_SYMBOLS
flag, the function H5Rdereference1
will remain available to the application through its versioned name. Similarly, H5Rdereference2
will remain available to the application as H5Rdereference2
. The function mapping version flag H5Rdereference_vers
only controls the mapping of the API compatibility macro H5Rdereference
to one of the two available functions.
This can be especially useful in any case where the programmer does not have direct control over global macro definitions, such as when writing code meant to be copied to multiple applications or when writing code in a header file.
A series of similar compatibility macros were introduced into the release 1.6 series of the library, starting with release 1.6.8. These macros simply alias the '1' version functions, callbacks, and typedefs listed above to their original non-numbered names.
These macros were strictly a forward-looking feature at that time; they were not necessary for compatibility in 1.6.x. These macros were created at that time to enable writing code that could be used with any version of the library after 1.6.8 and any library compilation options except H5_NO_DEPRECATED_SYMBOLS
, by always using the '1' version of versioned functions and types. For example, H5Dopen1
will always be interpreted in exactly the same manner by any version of the library since 1.6.8.
A common scenario where the API compatibility macros may be helpful is the migration of an existing application to a new HDF5 release. An incremental migration plan is outlined here:
configure
flag. In this default mode, the 1.6.x, 1.8.x, and 1.10.x versions of the underlying functions are available, and the API compatibility macros will be mapped to the current HDF5 versioned functions. -DH5_USE_NN_API
application mapping option if it was written for use with an earlier HDF5 library. Because the application mapping overrides the library mapping, the macros will all be mapped to the earlier versions of the functions. Remap one API compatibility macro at a time (or sets of macros), to use the current HDF5 versions. At each stage, use the function mappings to map the macros being worked on to the current versions. For example, use the -DH5Rdereference_vers=2
version flag setting to remap the H5Rdereference
macro to H5Rdereference2
, the 1.10.x version.
During this step, the application code will need to be modified to change the calling parameters used with the API compatibility macros to match the number and type of the 1.10.x versioned functions. The macro name, for example H5Rdereference
, should continue to be used in the code, to allow for possible re-mappings to later versioned functions in a future release.
-DH5_NO_DEPRECATED_SYMBOLS
, and address any failures to complete the application migration process.