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HDF5 version 1.8.22-snap6 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.21 and HDF5 1.10.22, and
contains information on the platforms tested and known problems in HDF5-1.10.21.
For more details check the HISTORY*.txt files in the HDF5 source.
Links to the HDF5 1.8.21 source code, documentation, and additional materials
can be found on the HDF5 web page at:
https://support.hdfgroup.org/HDF5/
The HDF5 1.8.21 release can be obtained from:
https://support.hdfgroup.org/HDF5/release/obtain518.html
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
New features in the HDF5-1.8.x release series, including brief general
descriptions of some new and modified APIs, are described in the "What's New
in 1.8.0?" document:
https://www.hdfgroup.org/downloads/hdf5/
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.22 (current
release) versus Release 1.8.21
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
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, Languages, and Compilers
- Bug Fixes since HDF5-1.8.20
- Supported Platforms
- Supported Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration
-------------
- 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_FORTRAN
HDF5_TEST_CPP
(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)
- Add options to enable or disable building tools and tests
Configure options --enable-tests and --enable-tools were added for
autotools configure. These options are enabled by default, and can be
disabled with either --disable-tests (or tools) or --enable-tests=no
(or --enable-tools=no). Build time is reduced ~20% when tools are
disabled, 35% when tests are disabled, 45% when both are disabled.
Reenabling them after the initial build requires running configure
again with the option(s) enabled.
(DAP - 2019/07/24, HDFFV-9976)
- Update CMake tests to use FIXTURES
CMake test fixtures allow setup/cleanup tests and other dependency
requirements as properties for tests. This is more flexible for
modern CMake code.
(ADB - 2019/07/23, HDFFV-10529)
- Windows PDB files are always installed
There are build configuration or flag settings for Windows that may not
generate PDB files. If those files are not generated then the install
utility will fail because those PDB files are not found. An optional
variable, DISABLE_PDB_FILES, was added to not install PDB files.
(ADB - 2019/07/17, HDFFV-10424)
- Add mingw CMake support with a toolchain file
There has been a number of mingw issues that has been linked under
HDFFV-10845. It has been decided to implement the CMake cross-compiling
technique of toolchain files. We will use a linux platform with the mingw
compiler stack for testing. Only the C language is fully supported, and
the error tests are skipped. The C++ language works for static but shared
builds has a shared library issue with the mingw Standard Exception Handling
library, which is not available on Windows. Fortran has a common cross-compile
problem with the fortran configure tests.
(ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
- Windows PDB files are installed incorrectly
For static builds, the PDB files for windows should be installed next
to the static libraries in the lib folder. Also the debug versions of
libraries and PDB files are now correctly built using the default
CMAKE_DEBUG_POSTFIX setting.
(ADB - 2019/07/09, HDFFV-10581)
- Add option to build only shared libs
A request was made to prevent building static libraries and only build
shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
skip building static libraries. Certain utility functions will build with
static libs but are not published. Tests are adjusted to use the correct
libraries depending on SHARED/STATIC settings.
(ADB - 2019/06/12, HDFFV-10805)
- Add toolchain and cross-compile support
Added info on using a toolchain file to INSTALL_CMAKE.txt. A
toolchain file is also used in cross-compiling, which requires
CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
the fortran configure process, the HDF5UseFortran.cmake file macros
were improved. Fixed a Fortran configure file issue that incorrectly
used #cmakedefine instead of #define.
(ADB - 2018/10/04, HDFFV-10594)
- Add warning flags for Intel compilers
Identified Intel compiler specific warnings flags that should be used
instead of GNU flags.
(ADB - 2018/10/04, TRILABS-21)
- Add default rpath to targets
Default rpaths should be set in shared executables and
libraries to allow the use of loading dependent libraries
without requiring LD_LIBRARY_PATH to be set. The default
path should be relative using @rpath on osx and $ORIGIN
on linux. Windows is not affected.
(ADB - 2018/09/26, HDFFV-10594)
Library
-------
- Add S3 and HDFS VFDs to HDF5 maintenance
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=https://s3.us-east-2.amazonaws.com/hdf5ros3"
(ADB - 2019/09/12, HDFFV-10854)
- Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
Rather than always running H5detect and generating H5Tinit.c and
H5make_libsettings.c, supply a location for those files.
(ADB - 2018/09/18, HDFFV-10332)
Parallel Library
----------------
- None
Tools
-----
- None
High-Level APIs
---------------
- None
Fortran API
-----------
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/2/18, HDFFV-11029)
C++ API
-------
- None
High-Level APIs
---------------
- None
Support for New Platforms, Languages, and Compilers
===================================================
Bug Fixes since HDF5-1.8.21
===========================
Configuration
-------------
- Correct option for default API version
CMake options for default API version are not mutually exclusive.
Change the multiple BOOL options to a single STRING option with the
strings; v16, v18.
(ADB - 2019/08/12, HDFFV-10879)
Library
-------
- 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 a bug that could cause an error or cause fill values to be
incorrectly read from a dataset that was written to using H5Dwrite_chunk
if the dataset was not closed after writing.
(NAF - 2019/03/06, HDFFV-10716)
- Fixed a potential invalid memory access and failure that could occur when
decoding an unknown object header message (from a future version of the
library).
(NAF - 2019/01/07)
- Allow H5detect and H5make_libsettings to take a file as an argument.
Rather than only writing to stdout, add a command argument to name
the file that H5detect and H5make_libsettings will use for output.
Without an argument, stdout is still used, so backwards compatibility
is maintained.
(ADB - 2018/09/05, HDFFV-9059)
- Inappropriate linking with deprecated MPI C++ libraries
HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
can inadvertently wind up linking to the deprecated MPI C++ wrappers.
MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
so this should no longer be an issue. HDF5 makes no use of the deprecated
MPI C++ wrappers.
(DER - 2019/09/17, HDFFV-10893)
Parallel Library
----------------
- None
Performance
-------------
- None
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 -2020/02/05, HDFFV-11014)
- h5repack was fixed to repack datasets with external storage
to other types of storage.
New test added to repack files and verify the correct data using h5diff.
(JS - 2019/09/25, HDFFV-10408)
(ADB - 2019/10/02, HDFFV-10918)
Fortran API
-----------
- Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
autotools installs. These were added to match the name of the files
installed by CMmake and the general pattern of hl lib files. We will
change the names of the installed lib files to the matching name in
the next major release.
(LRK - 2019/05/09, HDFFV-10596)
C++ API
-------
- None
High-Level APIs:
---------------
- None
Packet Table APIs:
------------------
- None
Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(platypus/mayll) Version 4.4.7 20120313
Versions 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 16.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.196 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
OpenMPI 2.0.1 compiled with GCC 4.9.3
Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
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/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Versions 4.9.3, 5.3.0, 6.2.0
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
NAG Fortran Compiler Release 6.1(Tozai) Build 6116
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)
Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29)
64-bit gfortran GNU Fortran (GCC) 5.2.0
(VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(kite) Intel icc/icpc/ifort version 17.0.2
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/y 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
Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
AIX 6.1 32- and 64-bit n y/n n y y y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.1 Linux 3.10.0 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
Mac OS X Mountain Lion 10.8.5 64-bit y n y y
Mac OS X Mavericks 10.9.5 64-bit y n y y
Mac OS X Yosemite 10.10.5 64-bit y n y y
AIX 6.1 32- and 64-bit y n n y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
Linux 2.6.32-573.18.1.el6.ppc64 y y y y
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 g95 (GCC 4.0.3 (g95 0.94!)
#1 SMP x86_64 GNU/Linux
(mayll)
Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
gcc (Debian 4.9.2-10) 4.9.2
GNU Fortran (Debian 4.9.2-10) 4.9.2
(cmake and autotools)
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)
Known Problems
==============
The dynamically loaded plugin test libraries require undefined references
to HDF5 functions to be resolved at runtime in order to function properly.
With autotools on CYGWIN this results in build errors, and we have not
found a solution that satisfies both. Therefore the dynamically loaded
plugin tests have been disabled on CYGWIN.
Mac OS X 10.13 added additional subdirectory structure in .libs for shared
libraries. Consequently "make check" will fail testing java and dynamically
loaded plugin test libraries attempting to copy files from the previous
locations in .libs directories. This will be addressed in the next release
when support for the Mac OS X 10.13 platform is added.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. 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.
|