Audience
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.
Compatibility Issues
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.
Summary and Motivation
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:
- Source code is not available - only binaries are available; updating the application is not feasible.
- Source code is available, but there are no resources to update it.
- Source code is available, as are resources to update it, but the old version works quite well so updates are not a priority. At the same time, it is desirable to take advantage of certain efficiencies in the newer HDF5 release that do not require code changes.
- Source code is available, as are resources to update it, but the applications are large or complex, and must continue to run while the code updates are carried out.
Understanding and Using the Macros
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 eg '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 eg '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:
Compatibility Macro Mapping Options
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:
Library Mapping Options
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.
Table 1: Library Mapping Options
configure flag | Macros map to release (versioned function; H5Lvisit shown) | Deprecated functions available? ( H5Lvisit1 ) |
---|---|---|
(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
Application Mapping Options
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.
Table 2: Application Mapping Options
h5cc option | Macros map to release (versioned function; H5Lvisit shown) | Deprecated functions available? ( H5Lvisit1 ) |
---|---|---|
(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 Mapping Options
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:
- When
H5Rreference_vers
is set to1
, the macroH5Rreference
will be mapped toH5Rreference1
.
h5cc ... -DH5Rreference_vers=1 ...
- When
H5Rdereference_vers
is set to2
, the macroH5Rdereference
will be mapped toH5Rdereference2
.
h5cc ... -DH5Rreference_vers=2 ...
- When
H5Rreference_vers
is not set, the macroH5Rreference
will be mapped to eitherH5Rreference1
orH5Rreference2
, based on the application mapping, if one was specified, or on the library mapping.
h5cc ...
Please be aware that some function mappings use mapped structures, as well. If compiling an application with a function mapping that uses a mapped structure, you must include each function and mapped structure plus EVERY function that uses the mapped structure, whether or not that function is used in the application. In 1.12, mappings of structures are used by the H5L and H5O function mappings.
For example, the application h5ex_g_iterate.c
(found on the Examples by API page under "Groups") only calls
, H5Lvisit
, andH5Ovisit
. To compile this application with 1.10 APIs in 1.12 with the function specific mappings, then not only must H5Oget_info_by_name
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:
h5cc -DH5Lvisit_vers=1 -DH5Ovisit_vers=1 -DH5Oget_info_by_name_vers=1 -DH5Lvisit_by_name_vers=1 -DH5Literate_vers=1 -DH5Literate_by_name_vers=1 -DH5O_info_t_vers=1 -DH5L_info_t_vers=1 -DH5L_iterate_t_vers=1 -DH5Lget_info_by_idx_vers=1 -DH5Lget_info_vers=1 h5ex_g_visit.c
Function Mapping Options in Releases 1.12.x
Macro ( | Default function used if no macro specified
| Function used if specifying 1.10
|
---|---|---|
H5L_GET_INFO | H5L_GET_INFO2
| H5L_GET_INFO1
|
H5L_GET_INFO_BY_IDX | H5L_GET_INFO_BY_IDX2
| H5L_GET_INFO_BY_IDX1
|
H5L_ITERATE | H5L_ITERATE2
| H5L_ITERATE1
|
H5L_ITERATE_BY_NAME | H5L_ITERATE_BY_NAME2
| H5L_ITERATE_BY_NAME1
|
H5L_VISIT | H5L_VISIT2
| H5L_VISIT1
|
H5L_VISIT_BY_NAME | H5L_VISIT_BY_NAME2
| H5L_VISIT_BY_NAME1
|
H5O_GET_INFO | H5O_GET_INFO3
| H5O_GET_INFO1
|
H5O_GET_INFO_BY_IDX | H5O_GET_INFO_BY_IDX3
| H5O_GET_INFO_BY_IDX1
|
H5O_GET_INFO_BY_NAME | H5O_GET_INFO_BY_NAME3
| H5O_GET_INFO_BY_NAME1
|
H5O_VISIT | H5O_VISIT3
| H5O_VISIT1
|
H5O_VISIT_BY_NAME | H5O_VISIT_BY_NAME3
| H5O_VISIT_BY_NAME1
|
H5P_ENCODE | H5P_ENCODE2
| H5P_ENCODE1
|
H5S_ENCODE | H5S_ENCODE2
| H5S_ENCODE1
|
Function Mapping Options in Releases 1.10.x
The versioned H5Oget_info
functions (H5Oget_info1
and H5Oget_info2
) were added in 1.10.3, and H5Oget_info
was replaced by a macro to invoke H5Oget_info1
or H5Oget_info2
. However, this broke compatibility and caused problems for users because there was no longer a function H5Oget_info
. In 1.10.4 and subsequent 1.10.x versions the macro was removed, H5Oget_info1
was deprecated, and H5Oget_info
was resurrected as a function. H5Oget_info2
remained as a function, but is not a versioned alternative to the original H5Oget_info
. The same is true for H5Oget_info_by name
, H5Oget_info_by_idx
, H5Ovisit
, and H5Ovisit_by_name
. The version 2 functions were added to improve performance.
The unversioned originals and version 2 of those functions exist in 1.10 because having released them in 1.10.3, it would break compatibility to remove them, so the original and version 2 functions remained in the source but without any macro to map to one or the other. Therefore, version 2 functions are available, but only when invoked directly.
In 1.12 there is a version 3 of all 5 functions which uses version 2 H5Oinfo2_t or H5Oiterate2_t structures. Both versions 1 and 2 are deprecated and macros replace the unversioned functions, mapping to version 1 for 18 and 110 default apis and to version 3 for 112 default api. Version 2 is available, but will only be invoked if invoked directly.
Macro | Default function used (if no macro specified) | Introduced in | h5cc version flag and value | Mapped to function or struct |
---|---|---|---|---|
| H5Rdereference2 | HDF5-1.10.0 | -DH5Rdereference_vers=1 | H5Rdereference1 |
-DH5Rdereference_vers=2 | H5Rdereference2 | |||
| 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_info1 | HDF5-1.10.3 | -DH5Oget_info_vers=1 | H5Oget_info1 |
-DH5Oget_info_vers=2 | H5Oget_info2 | |||
| 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 |
| |||
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 |
Function Mapping Options in Releases 1.8.x
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.
Table 5: Function Mapping Options in Releases 1.8.x
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 |
Further Information
See the HDF5 Reference Manual for complete descriptions of all API compatibility macros and versioned functions shown.
It is possible to specify multiple function mappings for a single application build:
h5cc ... -DH5Rdereference_vers=1 -DH5Fget_info_vers=2 ...
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.
Compatibility Macros in HDF5 1.6.8 and Later
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.
Common Use Case
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:
- Build the HDF5 library without specifying any library mapping
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. - Compile the application with the
-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 theH5Rdereference
macro toH5Rdereference2
, 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. - After all macros have been migrated to the latest versioned functions in step 3, compile the application without any application or function mappings. This build uses the library mappings set in step 1, and maps API compatibility macros to the latest versions.
- Finally, compile the application with the application mapping
-DH5_NO_DEPRECATED_SYMBOLS
, and address any failures to complete the application migration process.
--- Last Modified: March 22, 2021 | 02:16 PM