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Code Issues Packages Projects Releases Wiki Activity

Update release_docs HISTORY scheme (#2443)

Browse Source 
We will no longer maintain HISTORY files for other maintenance branches,
so those have been removed. Adds a README.md explaining the purpose
and procedures of HDF5 HISTORY. Also adds a newsletter template and
updates the RELEASE.txt note part of CONTRIBUTING.md.

Also cleans out RELEASE.txt post-HDF5-1.14.0
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CONTRIBUTING.md
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@ -86,36 +86,7 @@ application developers, library developers, and system administrators.
# Release Note <A NAME="releasenote"></A>
* **Entry Syntax**
The release note entry syntax is shown below.
```
- Title/Problem
Problem/Solution
Signature
```
* **Entry Elements** - The elements of the entry - title, problem, solution, and signature - are described in more detail in the table
below. Descriptions of the problem and the solution should be clear without any ambiguities and should be short without losing clarity or specifics.
* **Title** - The title or tag should identify one or more categories that will help readers decide if the entry is something they need to study. Can be combined with the `Problem` element
* **Problem** - Describe the problem and how users might see the problem in a paragraph.
You might also consider the following as you describe the problem:
* Under what specific conditions does this issue arise?
* Under what specific conditions are we sure this issue will not arise?
* For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is?
* **Solution** - Describe the solution in another paragraph.
You might also consider the following as you describe the solution:
* What was done to resolve the issue?
* What is the functional impact?
* Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround?
* For a performance fix, how has the performance improved? Links to published documentation would be good.
* **Signature** - Each entry must be signed with the initials of the author, the date in YYYY/MM/DD format, and the JIRA ticket number. The
following is an example entry written by developer Xavier Zolo on April 16, 2014 about JIRA ticket HDFFV-5555: (XYZ - 2014/04/16, HDFFV-5555). The
signature is enclosed in parentheses. JIRA or Github numbers should not be used in the description of the problem or the solution. They are like
abbreviations that customers and external users will not be able to interpret.
The use and format of release notes is described in `doc/release_txt_notes.md` in this source code tree
# Checklist <A NAME="checklist"></A>

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# Writing Notes in a RELEASE.txt File
## Introduction
We have been challenged to write more helpful entries in our RELEASE.txt file
for new features, improvements, and bug fixes. To help users determine the
effects of our software changes on their applications, we have developed a
template that can be used to write release notes. The template is described on
the rest of this page.
Some of our users face scrutiny from regulatory agencies for their use of
software they did not develop (aka SOUP). When they use our software, they have
to be aware of every change we make. For every change we make, they need to
investigate the effect the change will have on their software. If our change
affects their application, they may have to have their software retested or
re-certified.
[SOUP](https://en.wikipedia.org/wiki/Software_of_unknown_pedigree) stands for Software Of Unknown/Uncertain Pedigree/Provenance
## When to write a RELEASE.txt note
Generally, a release note must be written for every change that is made to the
code for which users might see a change in the way the software works. In other
words, if a user might see a difference in the way the software works, a note
should be written. By code we mean the text that will be compiled into one of
the company's software products. The code includes configuration changes and
changes to tools users might work with to configure and build our software.
A release note does not need to be written for changes to the code that users
will not see.
These things DO require a release note:
* New features
* Changes in functionality/semantics
* Anything that changes functionality or symbols in a public header file
* Command-line tool option changes
* Adding or dropping support for compilers or operating systems
* Build system (Autotools, CMake) changes that users will encounter
These things do NOT require a release note:
* Internal comments
* Refactoring that does not change behavior or public headers (`H5XYpublic.h`)
* Minor build system changes (adding warning flags)
Notes should also be added for known problems. Known problems are issues that
we know about and have not yet been able to fix.
## RELEASE.txt entry format
```
- Title
Problem
Solution
Signature
```
## RELEASE.txt entry elements
### Title
The title or tag should identify one or more categories that will help readers
decide if the entry is something they need to study. Categories include problem
areas, tool names, and code file names. Two examples are "Memory Leak" and
"h5repack". A code file such as H5R.c or H5Z.c can be used as the title if the
problem is located in the code file. If both a title and one or more tags are
used, separate each with a period. For example, "Changed Autotools Build Behavior. Fortran."
adds the Fortran tag to the title Changed Autotools Build Behavior. Use
standard capitalization rules.
### Problem
Describe the problem and how users might see the problem in a paragraph.
You might also consider the following as you describe the problem:
* Under what specific conditions does this issue arise?
* Under what specific conditions are we sure this issue will not arise?
* For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is?
### Solution
Describe the solution in another paragraph.
You might also consider the following as you describe the solution:
* What was done to resolve the issue?
* What is the functional impact?
* Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround?
* For a performance fix, how has the performance improved? Links to published documentation would be good.
### Signature
Each entry must be signed with the initials of the author, the date in
YYYY/MM/DD format, and the JIRA ticket number. The signature is enclosed in
parentheses.
Example:
```
(ABC - 2023/02/28, JIRA-12345, GitHub #1234)
```

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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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@ -0,0 +1,25 @@
INTRODUCTION
============
This purpose of this document is to contain entries that can be used to quickly
produce a release newsletter. When something is added to the library that is
"newsletter worthy" (i.e., new feature, CVE fix, etc.) a summary note should
be added here.
The format should look like this:
* SUMMARY OF NEWSLETTER-WORTHY THING
Here is where you describe the summary. Summarize the feature, fix, or
change in general language. Remember, RELEASE.txt is for communicating
technical specifics. Text entered here is more like advertising.
(GitHub #123, #125)
The GitHub #s could be relevant issues or PRs. They will probably not appear
in the final newsletter, but are so that the person writing the newsletter
has easy access to context if they have questions.
Every entry in RELEASE.txt does NOT require an entry here. The newsletter is
for communicating major changes that are of interest to anyone. Minor bugfixes,
memory leak fixes, etc. do not require entries.

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@ -0,0 +1,102 @@
# The `release_docs` directory
## Intro
This directory contains instructions for building and using the library as
well as the HDF5 history files.
## HISTORY files
The `HISTORY` files contain the history of this branch of HDF5. They fall into
three categories.
### HISTORY-\[VERSION 1\]-\[VERSION 2\].txt
These files are created when we release a new major version and include all
the changes that were made to the `develop` branch while creating a major release.
### HISTORY-\[VERSION\].txt
This file contains the changes that were made to a maintenance branch since
it split off from `develop`. It will also be found in the `develop` branch
when experimental releases have been created.
### RELEASE.txt
This is the changelog for the current version of the library.
For a MAJOR release (or in `develop`) this files lists all the changes since the
last major version. For a MINOR release (or in a maintenance branch), this file
lists all the changes since the last release in the maintenance branch.
Examples:
* The file for HDF5 1.14.0 includes all the changes since HDF5 1.12.0
* The file for HDF5 1.10.9 includes all the changes since HDF5 1.10.8
* The file in `develop` includes all the changes since the last major release
* The file in `hdf5_1_14` includes all the changes since the last minor HDF5 1.14 release
Note that we make no effort to bring maintenance branch `HISTORY` files back to
develop. If you want to compare, say, 1.10.4 with 1.12.3, you'd have to get
the history files from those releases and compare them by hand.
## Creating new releases
### MAJOR release
* If there were experimental releases, merge the experimental `HISTORY` file
and the current `RELEASE.txt` by category to create a separate, unified
file that ignores the experimental releases. Don't check this in yet or
clobber any existing `HISTORY`/`RELEASE` files, but put it someplace handy for
use in later steps.
* Create the new maintenance branch
In develop:
* Create the new `HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file
* If there is an experimental `HISTORY` file, add `RELEASE.txt` to the beginning of it and use that
* Otherwise, start with `RELEASE.txt`
* Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.)
* Delete any experimental `HISTORY` file
* Clear out `RELEASE.txt`
Note that we're KEEPING any experimental release history information in the
`HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file, so do NOT use the merged file in
the above steps!
In the new maintenance branch:
* Create the new `HISTORY-\[VERSION\].txt` file
* If there is an experimental `HISTORY` file use the combined file you created earlier
* Otherwise, start with `RELEASE.txt`
* Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.)
* Delete any experimental `HISTORY` file
* Clear out `RELEASE.txt`
* Create the new release branch
In the new release branch:
* If there were experimental releases, use the combined file you created earlier as `RELEASE.txt`
* Otherwise the `RELEASE.txt` will be used as-is
### MINOR release
* Create the release branch
In the maintenance branch:
* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt`
* Clear out `RELEASE.txt`
### EXPERIMENTAL release
* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt`
* Clear out `RELEASE.txt`
## INSTALL files
These files include instructions for building and installing HDF5 on various
platforms.
## USING files
These files document how to build HDF5 applications with an installed HDF5
library.

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@ -21,7 +21,7 @@ The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.13.x release series
Changes from release to release and new features in the HDF5-1.14.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information
@ -36,7 +36,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.13.3
- Bug Fixes since HDF5-1.14.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
@ -47,108 +47,13 @@ New Features
Configuration:
-------------
- Removal of MPE support
-
The ability to build with MPE instrumentation has been removed along with
the following configure options:
Autotools:
--with-mpe=
CMake has never supported building with MPE support.
(DER - 2022/11/08)
- Removal of dmalloc support
The ability to build with dmalloc support has been removed along with
the following configure options:
Autotools:
--with-dmalloc=
CMake:
HDF5_ENABLE_USING_DMALLOC
(DER - 2022/11/08)
- Removal of memory allocation sanity checks configure options
With the removal of the memory allocation sanity checks feature, the
following configure options are no longer necessary and have been
removed:
Autotools:
--enable-memory-alloc-sanity-check
CMake:
HDF5_MEMORY_ALLOC_SANITY_CHECK
HDF5_ENABLE_MEMORY_STATS
(DER - 2022/11/03)
Library:
--------
- Overhauled the Virtual Object Layer (VOL)
-
The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial
implementation required API-breaking changes to better support optional
operations and pass-through VOL connectors. The original VOL API is
now considered deprecated and VOL users and connector authors should
target the 1.14 VOL API.
The specific changes are too extensive to document in a release note, so
VOL users and connector authors should consult the updated VOL connector
author's guide and the 1.12-1.14 VOL migration guide.
(DER - 2022/12/28)
- H5VLquery_optional() signature change
The last parameter of this API call has changed from a pointer to hbool_t
to a pointer to uint64_t. Due to the changes in how optional operations
are handled in the 1.14 VOL API, we cannot make the old API call work
with the new scheme, so there is no API compatibility macro for it.
(DER - 2022/12/28)
- H5I_free_t callback signature change
In order to support asynchronous operations and future IDs, the signature
of the H5I_free_t callback has been modified to take a second 'request'
parameter. Due to the nature of the internal library changes, no API
compatibility macro is available for this change.
(DER - 2022/12/28)
- Fix for CVE-2019-8396
Malformed HDF5 files may have truncated content which does not match
the expected size. When H5O__pline_decode() attempts to decode these it
may read past the end of the allocated space leading to heap overflows
as bounds checking is incomplete.
The fix ensures each element is within bounds before reading.
(2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209)
- Removal of memory allocation sanity checks feature
This feature added heap canaries and statistics tracking for internal
library memory operations. Unfortunately, the heap canaries caused
problems when library memory operations were mixed with standard C
library memory operations (such as in the filter pipeline, where
buffers may have to be reallocated). Since any platform with a C
compiler also usually has much more sophisticated memory sanity
checking tools than the HDF5 library provided (e.g., valgrind), we
have decided to to remove the feature entirely.
In addition to the configure changes described above, this also removes
the following from the public API:
H5get_alloc_stats()
H5_alloc_stats_t
(DER - 2022/11/03)
Parallel Library:
-----------------
@ -198,132 +103,13 @@ New Features
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-1.13.3 release
Bug Fixes since HDF5-1.14.0 release
===================================
Library
-------
- Seg fault on file close
h5debug fails at file close with core dump on a file that has an
illegal file size in its cache image. In H5F_dest(), the library
performs all the closing operations for the file and keeps track of
the error encountered when reading the file cache image.
At the end of the routine, it frees the file's file structure and
returns error. Due to the error return, the file object is not removed
from the ID node table. This eventually causes assertion failure in
H5VL__native_file_close() when the library finally exits and tries to
access that file object in the table for closing.
The closing routine, H5F_dest(), will not free the file structure if
there is error, keeping a valid file structure in the ID node table.
It will be freed later in H5VL__native_file_close() when the
library exits and terminates the file package.
(VC - 2022/12/14, HDFFV-11052, CVE-2020-10812)
- Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf
Validate location (offset) of the accumulated metadata when comparing.
Initially, the accumulated metadata location is initialized to HADDR_UNDEF
- the highest available address. Bogus input files may provide a location
or size matching this value. Comparing this address against such bogus
values may provide false positives. Thus make sure, the value has been
initialized or fail the comparison early and let other parts of the
code deal with the bogus address/size.
Note: To avoid unnecessary checks, it is assumed that if the 'dirty'
member in the same structure is true the location is valid.
(EFE - 2022/10/10 GH-2230)
- Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx
Make sure info block for external links has at least 3 bytes.
According to the specification, the information block for external links
contains 1 byte of version/flag information and two 0 terminated strings
for the object linked to and the full path.
Although not very useful, the minimum string length for each (with
terminating 0) would be one byte.
Checking this helps to avoid SEGVs triggered by bogus files.
(EFE - 2022/10/09 GH-2233)
- CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm
Compound datatypes may not have members of size 0
A member size of 0 may lead to an FPE later on as reported in
CVE-2021-46244. To avoid this, check for this as soon as the
member is decoded.
(EFE - 2022/10/05 GEH-2242)
- Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2
Make H5O__fsinfo_decode() more resilient to out-of-bound reads.
When decoding a file space info message in H5O__fsinfo_decode() make
sure each element to be decoded is still within the message. Malformed
hdf5 files may have trunkated content which does not match the
expected size. Checking this will prevent attempting to decode
unrelated data and heap overflows. So far, only free space manager
address data was checked before decoding.
(EFE - 2022/10/05 GH-2228)
- Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf
When evicting driver info block, NULL the corresponding entry.
Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag
H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing
the pointer in f->shared->drvinfo will prevent use-after-free when it is
used in other functions (like H5F__dest()) - as other places will check
whether the pointer is initialized before using its value.
(EFE - 2022/09/29 GH-2254)
- Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79
Report error if dimensions of chunked storage in data layout < 2
For Data Layout Messages version 1 & 2 the specification state
that the value stored in the data field is 1 greater than the
number of dimensions in the dataspace. For version 3 this is
not explicitly stated but the implementation suggests it to be
the case.
Thus the set value needs to be at least 2. For dimensionality
< 2 an out-of-bounds access occurs.
(EFE - 2022/09/28 GH-2240)
- Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j
Parent of enum datatype message must have the same size as the
enum datatype message itself.
Functions accessing the enumeration values use the size of the
enumeration datatype to determine the size of each element and
how much data to copy.
Thus the size of the enumeration and its parent need to match.
Check in H5O_dtype_decode_helper() to avoid unpleasant surprises
later.
(EFE - 2022/09/28 GH-2236)
- Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7
H5IMget_image_info(): Make sure to not exceed local array size
Malformed hdf5 files may provide more dimensions than the array dim[] in
H5IMget_image_info() is able to hold. Check number of elements first by calling
H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
This will cause the function to return only the number of dimensions.
The fix addresses a stack overflow on write.
(EFE - 2022/09/27 HDFFV-10589, GH-2226)
-
Java Library
@ -333,49 +119,12 @@ Bug Fixes since HDF5-1.13.3 release
Configuration
-------------
- Remove Javadoc generation
The use of doxygen now supersedes the requirement to build javadocs. We do not
have the resources to continue to support two documentation methods and have
chosen doxygen as our standard.
(ADB - 2022/12/19)
- Change the default for building the high-level tools
The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed
in a future release. The default build setting for them have been changed from enabled
to disabled. A user can enable the build of these tools if needed.
autotools: --enable-hlgiftools
cmake: HDF5_BUILD_HL_GIF_TOOLS=ON
(ADB - 2022/12/16)
- Change the settings of the *pc files to use the correct format
The pkg-config files generated by CMake uses incorrect syntax for the 'Requires'
settings. Changing the set to use 'lib-name = version' instead 'lib-name-version'
fixes the issue
(ADB - 2022/12/06 HDFFV-11355)
- Move MPI libraries link from PRIVATE to PUBLIC
The install dependencies were not including the need for MPI libraries when
an application or library was built with the C library. Also updated the
CMake target link command to use the newer style MPI::MPI_C link variable.
(ADB - 2022/10/27)
-
Tools
-----
- Fix h5repack to only print output when verbose option is selected
When timing option was added to h5repack, the check for verbose was
incorrectly implemented.
(ADB - 2022/12/02, GH #2270)
-
Performance
@ -387,6 +136,7 @@ Bug Fixes since HDF5-1.13.3 release
-----------
-
High-Level Library
------------------
-