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HDF5 History
============
This file contains development history of the HDF5 1.12 branch
01. Release Information for hdf5-1.12.0
[Search on the string '%%%%' for section breaks of each release.]
%%%%1.12.0%%%%
HDF5 version 1.12.0 released on 2020-02-28
================================================================================
INTRODUCTION
This document describes the new features introduced in the HDF5 1.12.0 release.
It contains information on the platforms tested and known problems in this
release. For more details check the HISTORY*.txt files in the HDF5 source.
Note that documentation in the links below will be updated at the time of the
release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
More information about the new features can be found at:
https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.12.0-alpha1
- Major Bug Fixes since HDF5-1.10.0
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Added test script for file size compare
If CMake minimum version is at least 3.14, the fileCompareTest.cmake
script will compare file sizes.
(ADB - 2020/02/24, HDFFV-11036)
- Update CMake minimum version to 3.12
Updated CMake minimum version to 3.12 and added version checks
for Windows features.
(ADB - 2020/02/05, TRILABS-142)
- Fixed CMake include properties for Fortran libraries
Corrected the library properties for Fortran to use the
correct path for the Fortran module files.
(ADB - 2020/02/04, HDFFV-11012)
- Added common warnings files for gnu and intel
Added warnings files to use one common set of flags
during configure for both autotools and CMake build
systems. The initial implementation only affects a
general set of flags for gnu and intel compilers.
(ADB - 2020/01/17)
- Added new options to CMake for control of testing
Added CMake options (default ON);
HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
combined with:
HDF5_TEST_TOOLS
HDF5_TEST_EXAMPLES
HDF5_TEST_SWMR
HDF5_TEST_FORTRAN
HDF5_TEST_CPP
HDF5_TEST_JAVA
(ADB - 2020/01/15, HDFFV-11001)
- Added Clang sanitizers to CMake for analyzer support if compiler is clang.
Added CMake code and files to execute the Clang sanitizers if
HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
is set to one of the following:
Address
Memory
MemoryWithOrigins
Undefined
Thread
Leak
'Address;Undefined'
(ADB - 2019/12/12, TRILAB-135)
- Update CMake for VS2019 support
CMake added support for VS2019 in version 3.15. Changes to the CMake
generator setting required changes to scripts. Also updated version
references in CMake files as necessary.
(ADB - 2019/11/18, HDFFV-10962)
Library:
--------
- Refactored public exposure of haddr_t type in favor of "object tokens"
To better accommodate HDF5 VOL connectors where "object addresses in a file"
may not make much sense, the following changes were made to the library:
* Introduced new H5O_token_t "object token" type, which represents a
unique and permanent identifier for referencing an HDF5 object within
a container; these "object tokens" are meant to replace object addresses.
Along with the new type, a new H5Oopen_by_token API call was introduced
to open an object by a token, similar to how object addresses were
previously used with H5Oopen_by_addr.
* Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
struct and H5L_iterate2_t callback function, which work with the newly-introduced
object tokens, instead of object addresses. The original functions have been
renamed to version 1 functions and are deprecated in favor of the new version 2
functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
types and are now deprecated in favor of their version 2 counterparts. For each of
the functions and types, compatibility macros take place of the original symbols.
* Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
struct and H5O_iterate2_t callback function, which work with the newly-introduced
object tokens, instead of object addresses. The version 2 functions are now
deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
types have been renamed to version 1 types and are now deprecated in favor of their
version 2 counterparts. For each, compatibility macros take place of the original
symbols.
* Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
struct, which are used to retrieve the native HDF5 file format-specific information
about an object. This information (such as object header info and B-tree/heap info)
has been removed from the new H5O_info2_t struct so that the more generic
H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
VOL connectors.
* Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
two object tokens, convert an object token into a nicely-readable string format and
to convert an object token string back into a real object token, respectively.
(DER, QAK, JTH - 2020/01/16)
- Virtual Object Layer (VOL)
In this major HDF5 release we introduce HDF5 Virtual Object Layer (VOL).
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 layer 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. For more information
about VOL we refer the reader to the following documents (under review):
VOL HDF5 APIs
https://portal.hdfgroup.org/display/HDF5/Virtual+Object++Layer
VOL Documentation
https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5/VOL
Repository with VOL plugins
https://bitbucket.hdfgroup.org/projects/HDF5VOL
- Enhancements to HDF5 References
HDF5 references were extended to support attributes, and object and dataset
selections that reside in another HDF5 file. For more information including
a list of new APIs, see
https://portal.hdfgroup.org/display/HDF5/Update+to+References
- Add new public function H5Sselect_adjust.
This function shifts a dataspace selection by a specified logical offset
within the dataspace extent. This can be useful for VOL developers to
implement chunked datasets.
(NAF - 2019/11/18)
- Add new public function H5Sselect_project_intersection.
This function computes the intersection between two dataspace selections
and projects that intersection into a third selection. This can be useful
for VOL developers to implement chunked or virtual datasets.
(NAF - 2019/11/13, ID-148)
- Add new public function H5VLget_file_type.
This function returns a datatype equivalent to the supplied datatype but
with the location set to be in the file. This datatype can then be used
with H5Tconvert to convert data between file and in-memory representation.
This funcition is intended for use only by VOL connector developers.
(NAF - 2019/11/08, ID-127)
- New S3 and HDFS Virtual File Drivers (VFDs)
This release has two new VFDs. The S3 VFD allows accessing HDF5 files on
AWS S3 buckets. HDFS VFD allows accessing HDF5 files stored on Apache HDFS.
See https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS
for information on enabling those drivers and using those APIs.
Below are specific instructions for enabling S3 VFD on Windows:
Fix windows requirements and java tests. Windows requires CMake 3.13.
- Install openssl library (with dev files);
from "Shining Light Productions". msi package preferred.
- PATH should have been updated with the installation dir.
- set ENV variable OPENSSL_ROOT_DIR to the installation dir.
- set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
- Install libcurl library (with dev files);
- download the latest released version using git: https://github.com/curl/curl.git
- Open a Visual Studio Command prompt
- change to the libcurl root folder
- run the "buildconf.bat" batch file
- change to the winbuild directory
- nmake /f Makefile.vc mode=dll MACHINE=x64
- copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
- set ENV variable CURL_ROOT to C:\curl (installation dir)
- update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
- the aws credentials file should be in %USERPROFILE%\.aws folder
- set the ENV variable HDF5_ROS3_TEST_BUCKET_URL to the s3 url for the
s3 bucket containing the HDF5 files to be accessed.
FORTRAN Library:
----------------
- Added new Fortran parameters:
H5F_LIBVER_ERROR_F
H5F_LIBVER_NBOUNDS_F
H5F_LIBVER_V18_F
H5F_LIBVER_V110_F
H5F_LIBVER_V112_F
- Added new Fortran API: h5pget_libver_bounds_f
(MSB - 2020/02/11, HDFFV-11018)
Java Library:
----------------
- Added ability to test java library with VOLs.
Created new CMake script that combines the java and vol test scripts.
(ADB - 2020/02/03, HDFFV-10996)
- Tests fail for non-English locale.
In the JUnit tests with a non-English locale, only the part before
the decimal comma is replaced by XXXX and this leads to a comparison
error. Changed the regex for the Time substitution.
(ADB - 2020/01/09, HDFFV-10995)
Tools:
------
- h5diff was updated to use the new reference APIs.
h5diff uses the new reference APIs to compare references.
Attribute references can also be compared.
(ADB - 2019/12/19, HDFFV-10980)
- h5dump and h5ls were updated to use the new reference APIs.
The tools library now use the new reference APIs to inspect a
file. Also the DDL spec was updated to reflect the format
changes produced with the new APIs. The export API and support
functions in the JNI were updated to match.
Other improvements and changes:
- Hyperslab selection code was reworked to improve performance, getting more
than 10x speedup in some cases.
- The HDF5 Library was enhanced to open files with Unicode names on Windows.
- Deprecated H5Dvlen_reclaim() and replaced it with H5Treclaim().
This routine is meant to be used when resources are internally allocated
when reading data, i.e. when using either vlen or new reference types.
This is applicable to both attribute and dataset reads.
- h5repack was fixed to repack datasets with external storage
to other types of storage.
Support for new platforms, languages and compilers.
=======================================
- Added spectrum-mpi with clang, gcc and xl compilers on Linux 3.10.0
- Added OpenMPI 3.1 and 4.0 with clang, gcc and Intel compilers on Linux 3.10.0
- Added cray-mpich/PrgEnv with gcc and Intel compilers on Linux 4.14.180
- Added spectrum mpi with clang, gcc and xl compilers on Linux 4.14.0
Bug Fixes since HDF5-1.12.0-alpha1 release
==========================================
Library
-------
- Improved performance when creating a large number of small datasets by
retrieving default property values from the API context instead of doing
skip list searches.
(CJH - 2019/12/10, HDFFV-10658)
- Fixed user-created data access properties not existing in the property list
returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
reproducer and a patch.
(CJH - 2019/12/09, HDFFV-10934)
- Fixed an assertion failure in the parallel library when collectively
filling chunks. As it is required that chunks be written in
monotonically non-decreasing order of offset in the file, this assertion
was being triggered when the list of chunk file space allocations being
passed to the collective chunk filling routine was not sorted according
to this particular requirement.
The addition of a sort of the out of order chunks trades a bit of
performance for the elimination of this assertion and of any complaints
from MPI implementations about the file offsets used being out of order.
(JTH - 2019/10/07, HDFFV-10792)
FORTRAN library:
----------------
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/2/18, HDFFV-11029)
Java Library:
----------------
- Added ability to test java library with VOLs.
Created new CMake script that combines the java and vol test scripts.
(ADB - 2020/02/03, HDFFV-10996)
- Tests fail for non-English locale.
In the JUnit tests with a non-English locale, only the part before
the decimal comma is replaced by XXXX and this leads to a comparison
error. Changed the regex for the Time substitution.
(ADB - 2020/01/09, HDFFV-10995)
Tools:
------
- h5repack was fixed to repack the reference attributes properly.
The code line that checks if the update of reference inside a compound
datatype is misplaced outside the code block loop that carries out the
check. In consequence, the next attribute that is not the reference
type was repacked again as the reference type and caused the failure of
repacking. The fix is to move the corresponding code line to the correct
code block.
(KY -2020/02/10, HDFFV-11014)
- h5diff was updated to use the new reference APIs.
h5diff uses the new reference APIs to compare references.
Attribute references can also be compared.
(ADB - 2019/12/19, HDFFV-10980)
- h5dump and h5ls were updated to use the new reference APIs.
The tools library now use the new reference APIs to inspect a
file. Also the DDL spec was updated to reflect the format
changes produced with the new APIs. The export API and support
functions in the JNI were updated to match.
(ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
Major Bug Fixes since HDF5-1.10.0 release
=========================================
- For major bug fixes please see HISTORY-1_10_0-1_12_0.txt file
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, 5.2.0, 7.1.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4
Linux-3.10.0- spectrum-mpi/rolling-release with cmake>3.10 and
862.14.4.1chaos.ch6.ppc64le clang/3.9,8.0
#1 SMP ppc64le GNU/Linux gcc/7.3
(ray) xl/2016,2019
Linux 3.10.0- openmpi/3.1,4.0 with cmake>3.10 and
957.12.2.1chaos.ch6.x86_64 clang 5.0
#1 SMP x86_64 GNU/Linux gcc/7.3,8.2
(serrano) intel/17.0,18.0/19.0
Linux 3.10.0- openmpi/3.1/4.0 with cmake>3.10 and
1062.1.1.1chaos.ch6.x86_64 clang/3.9,5.0,8.0
#1 SMP x86_64 GNU/Linux gcc/7.3,8.1,8.2
(chama,quartz) intel/16.0,18.0,19.0
Linux 4.4.180-94.100-default cray-mpich/7.7.6 with PrgEnv-*/6.0.5, cmake>3.10 and
#1 SMP x86_64 GNU/Linux gcc/7.2.0,8.2.0
(mutrino) intel/17.0,18.0
Linux 4.14.0- spectrum-mpi/rolling-release with cmake>3.10 and
49.18.1.bl6.ppc64le clang/6.0,8.0
#1 SMP ppc64le GNU/Linux gcc/7.3
(lassen) xl/2019
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 10 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
macOS 10.13.6 High Sierra Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(bear) Intel icc/icpc/ifort version 19.0.4
macOS 10.14.6 Mohave Apple LLVM version 10.0.1 (clang/clang++-1001.0.46.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(bobcat) Intel icc/icpc/ifort version 19.0.4
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
SunOS 5.11 32-bit n y/y n y y y
SunOS 5.11 64-bit n y/n n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y y y y y
Windows 7 Cygwin n y/n n y y y
Windows 7 x64 Cygwin n y/n n y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
macOS 10.13.6 64-bit n y/y n y y ?
macOS 10.14.6 64-bit n y/y n y y ?
CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
SunOS 5.11 32-bit y y y y
SunOS 5.11 64-bit y y y y
Windows 7 y y y y
Windows 7 x64 y y y y
Windows 7 Cygwin n n n y
Windows 7 x64 Cygwin n n n y
Windows 10 y y y y
Windows 10 x64 y y y y
macOS 10.13.6 64-bit y n y y
macOS 10.14.6 64-bit y n y y
CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
PGI C (pgcc), C++ (pgc++), Fortran (pgf90)
compilers:
Version 18.4, 19.4
MPICH 3.3
OpenMPI 2.1.5, 3.1.3, 4.0.0
Fedora30 5.3.11-200.fc30.x86_64
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
(cmake and autotools)
Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang/clang++-703.0.29)
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
macOS 10.12.6 Sierra Apple LLVM version 9.0.0 (clang/clang++-900.0.39.2)
64-bit gfortran GNU Fortran (GCC) 7.4.0
(kite) Intel icc/icpc/ifort version 17.0.8
Known Problems
==============
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
ADB - 2019/05/07
At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source, and in the HDF5 Jira database, available at
https://jira.hdfgroup.org/. Please register at https://www.hdfgroup.org to
create a free account for accessing the Jira database. Please report any
new problems found to help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
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