Migrating from HDF5 1.10 to HDF5 1.12

Also see the video presentation: Moving Applications from 1.10 to 1.12

There were many existing functions that were modified in 1.12. Applications created with 1.10 or earlier that use these functions will encounter errors when compiled with 1.12. This page describes how to compile 1.10 and earlier applications with 1.12 without modifying an application, and provides details on the functions that changed for users who wish to update their applications.

For further information, see:

Compiling 1.10 and earlier applications with 1.12

Applications that were created with earlier HDF5 releases may not compile with 1.12 by default. The API Compatibility Macros allow users to work around this issue. Users can specify a compatibility macro mapping for the version of HDF5 that an application was built with. For example, a 1.10 application can be built with 1.12 using either an application or library mapping as follows:

To compile an application built with a version of HDF5 that includes deprecated symbols (the default), make sure to pass -DH5_USE_110_API to the compiler. For example:
- Autotools: h5cc -DH5_USE_110_API (C)
- CMake: cmake -DCMAKE_C_FLAGS="-DH5_USE_110_API" (and likewise for other CMAKE_<LANG>_FLAGS)
To build an HDF5 library with the 1.10 APIs specify:
- Autotools: –with-default-api-version=v110
  execute: ./configure –with-default-api-version=v110
- CMake: -DDEFAULT_API_VERSION:STRING=v110
  If using the source code packaged with CMake configuration files (CMake-hdf5-1.12.0*), edit HDF5options.cmake, and add this line:
  set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DDEFAULT_API_VERSION:STRING=v110")

View the libhdf5.settings file to verify that the library was built with the 1.10 APIs:

Default API mapping: v110 (under Features:)

Note: However, users will not be able to take advantage of some of the new features in 1.12 if using these compatibility mappings.

Functions that changed

Functions were modified in HDF5 version 1.12 to support a token type used in the Virtual Object Layer (VOL) and to enable 64-bit selection encodings. These changes are described below.

Remarks

The updated versions of the functions have a number (for eg '2' or '3') 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.
A macro was created with the name of the original function.
Please read API Compatibility Macros for more details on how the function names changed in version 1.12.

Token Type

In HDF5 1.12, a token type, H5O_token_t, replaced the address type, haddr_t, for representing locations in an HDF5 file. This change better supports the Virtual Object Layer (VOL), as the concept of an "address" does not make sense for many connectors. A token type is a more generic type that can function as both a connector and address location.

This change affected the following functions:

Original Function in 1.10/Macro in 1.12 (H5xxx)	Deprecated Function in 1.12 (H5xxx1)	New Function (using token type) (H5xxx2 or H5xxx3

H5Lget_info	H5Lget_info1	H5Lget_info2
H5Lget_info_by_idx	H5Lget_info_by_idx1	H5Lget_info_by_idx2
H5Literate	H5Literate1	H5Literate2
H5Literate_by_name	H5Literate_by_name1	H5Literate_by_name2
H5Lvisit	H5Lvisit1	H5Lvisit2
H5Lvisit_by_name	H5Lvisit_by_name1	H5Lvisit_by_name2
H5Oget_info	H5Oget_info1	H5Oget_info3
H5Oget_info_by_idx	H5Oget_info_by_idx1	H5Oget_info_by_idx3
H5Oget_info_by_name	H5Oget_info_by_name1	H5Oget_info_by_name3
H5Ovisit	H5Ovisit1	H5Ovisit3
H5Ovisit_by_name	H5Ovisit_by_name1	H5Ovisit_by_name3

Encoding Properties

These functions were introduced in HDF5 version 1.12 as part of the H5Sencode format change to enable 64-bit selection encodings and a dataspace selection that is tied to a file. See the RFC H5Sencode() / H5Sdecode() Format Change RFC for details.

Original Function in 1.10/Macro in 1.12 (H5xxx)	Deprecated Function in 1.12 (H5xxx1)	New Function (using token type)

H5Pencode	H5Pencode1	H5Pencode2
H5Sencode	H5Sencode1	H5Sencode2

New Features in HDF5 Release 1.12

This release includes changes in the HDF5 storage format.

Note: PLEASE NOTE that HDF5-1.10 and earlier releases cannot read files created with the new features described below that are marked with a *.

HDF5 1.12 introduces several new features in the HDF5 library:

Virtual Object Layer (VOL)

See the Virtual Object Layer for more information.

The Virtual Object Layer (VOL) is an abstraction layer within the HDF5 library that enables different methods for accessing data and objects that conform to the HDF5 data model. The VOL intercepts all HDF5 API calls that potentially modify data on disk and forwards those calls to a plugin "object driver". The data on disk can be a different format than the HDF5 format.

The plugins can actually store the objects in variety of ways. A plugin could, for example, have objects be distributed remotely over different platforms, provide a raw mapping of the model to the file system, or even store the data in other file formats (like native netCDF or HDF4 format). The user still gets the same data model where access is done to a single HDF5 "container"; however the plugin object driver translates from what the user sees to how the data is actually stored. Having this abstraction layer maintains the object model of HDF5 and allows better usage of new object storage file systems that are targeted for Exascale systems.

Hyperslab Performance Improvements

In 1.12.0 the hyperslab selection code was optimized to achieve better performance. In general, performance improved by an order of a magnitude. In the case of reading a regular selection from a 20 GB dataset into a one dimensional array, performance improved by a factor of 6000. If you are interested in the benchmark we ran, please see issue HDFFV-10930 by logging into jira.hdfgroup.org with your hdfgroup.org login.

Update to References (RFC) *

See the Update to References page for details on the changes in HDF5-1.12.

HDF5 references were extended to support attributes, as well as object and dataset selections that reside in another HDF5 file. In order to support these features several functions were introduced:

Create (H5Rcreate*) functions were added for each reference type: object, dataset region and attribute.
A function was added to release a reference (H5Rdestroy). This is required because a region reference no longer modifies the original file.
Functions were added to query references (H5Rget*).
Other functions were added to simplify or clarify the API.

Update to Selections

Several new H5S APIs were introduced to allow a user to more flexibly operate on two hyperslab selections. See Update to Selections for more details.

RFCs

Release Software Changes for HDF5 1.12