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HDF5 version 1.10.5-snap1 currently under development
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 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 each
final 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/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
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 and languages
- Bug Fixes since HDF5-1.10.3
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Keep stderr and stdout separate in tests
Changed test handling of output capture. Tests now keep the stderr
output separate from the stdout output. It is up to the test to decide
which output to check against a reference. Also added the option
to grep for a string in either output.
(ADB - 2018/12/12, HDFFV-10632)
- 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)
- Incorrectly installed private header files were removed from
CMake installs.
The CMake build files incorrectly flagged the following header files
as public and installed them. They are private and will no longer be
installed.
HDF5 library private package files (H5Xpkg.h)
H5Edefin.h
H5Einit.h
H5Eterm.h
H5LTparse.h
h5diff.h
h5tools_dump.h
h5tools.h
h5tools_ref.h
h5tools_str.h
h5tools_utils.h
h5trav.h
(DER - 2018/10/26, HDFFV-10614, 10609)
- Autotools installs now install H5FDwindows.h
This is simply to align the installed header files between the
autotools and CMake. H5FDwindows.h has no functionality on
non-Windows systems.
(DER - 2018/10/26, HDFFV-10614)
Library:
--------
- 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)
- Several empty public header files where removed from the distribution
The following files were empty placeholders. They are for internal
packages that are unlikely to ever have public functionality and have
thus been removed.
H5Bpublic.h
H5B2public.h
H5FSpublic.h
H5HFpublic.h
H5HGpublic.h
H5HLpublic.h
They were only installed in CMake builds.
(DER - 2018/10/26, HDFFV-10614)
Parallel Library:
-----------------
- All MPI-1 API calls have been replaced with MPI-2 equivalents.
This was done to better support OpenMPI, as default builds no longer
include MPI-1 support (as of OpenMPI 4.0).
(DER - 2018/12/30, HDFFV-10566)
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
----------------
- Duplicate the data read/write functions of Datasets for Attributes.
Region references could not be displayed for attributes as they could
for datasets. Datasets had overloaded read and write functions for different
datatypes that were not available for attributes. After adding similar
functions, attribute region references work normally.
(ADB - 2018/12/12, HDFVIEW-4)
Tools:
------
- The h5repart -family-to-sec2 argument was changed to -family-to-single
In order to better support other single-file VFDs which could work with
h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
This is just a name change and the functionality of the argument has not
changed.
The -family-to-sec2 argument has been kept for backwards-compatibility.
This argument should be considered deprecated.
(DER - 2018/11/14, HDFFV-10633)
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.10.3 release
==================================
Library
-------
- A bug was discovered in the parallel library where an application
would eventually consume all of the available MPI communicators
when continually writing to a compressed dataset in parallel. This
was due to internal copies of an HDF5 File Access Property List,
which each contained a copy of the MPI communicator, not being
closed at the end of each write operation. This problem was
exacerbated by larger numbers of processors.
(JTH - 2018/12/05, HDFFV-10629)
- 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)
- A bug was discovered in the parallel library where an application
would hang if a collective read/write of a chunked dataset occurred
when collective metadata reads were enabled and some of the ranks
had no selection in the dataset's dataspace. The ranks which had no
selection in the dataset's dataspace called H5D__chunk_addrmap() to
retrieve the lowest chunk address in the dataset. This is because we
require reads/writes to be performed in strictly non-decreasing order
of chunk address in the file.
When the chunk index used was a version 1 or 2 B-tree, these
non-participating ranks would issue a collective MPI_Bcast() call
that the participating ranks would not issue, causing the hang. Since
the non-participating ranks are not actually reading/writing anything,
the H5D__chunk_addrmap() call can be safely removed and the address used
for the read/write can be set to an arbitrary number (0 was chosen).
(JTH - 2018/08/25, HDFFV-10501)
Java Library:
----------------
- JNI native library dependencies
The build for the hdf5_java native library used the wrong
hdf5 target library for CMake builds. Correcting the hdf5_java
library to build with the shared hdf5 library required testing
paths to change also.
(ADB - 2018/08/31, HDFFV-10568)
- Java iterator callbacks
Change global callback object to a small stack structure in order
to fix a runtime crash. This crash was discovered when iterating
through a file with nested group members. The global variable
visit_callback is overwritten when recursion starts. When recursion
completes, visit_callback will be pointing to the wrong callback method.
(ADB - 2018/08/15, HDFFV-10536)
- Java HDFLibraryException class
Change parent class from Exception to RuntimeException.
(ADB - 2018/07/30, HDFFV-10534)
- JNI Read and Write
Refactored variable-length functions, H5DreadVL and H5AreadVL,
to correct dataset and attribute reads. New write functions,
H5DwriteVL and H5AwriteVL, are under construction.
(ADB - 2018/06/02, HDFFV-10519)
Fortran
--------
- Made Fortran specific subroutines PRIVATE in generic procedures.
Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
(MSB, 2018/12/04, HDFFV-10511)
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, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
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 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 7 x64 Visual Studio 2013
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 18 (cmake)
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
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 clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(swallow/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
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 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
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
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
Mac OS Sierra 10.12.6 64-bit n y/y n y y y
CentOS 7.2 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/y n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.11 32-bit y y y y
Solaris2.11 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 Mavericks 10.9.5 64-bit y n y y
Mac OS X Yosemite 10.10.5 64-bit y n y y
Mac OS X El Capitan 10.11.6 64-bit y n y y
Mac OS Sierra 10.12.6 64-bit y n y y
CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
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,
3.1.0-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)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
gcc, g++ (Debian 4.9.2-10) 4.9.2
GNU Fortran (Debian 4.9.2-10) 4.9.2
(cmake and autotools)
Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc, g++ (GCC) 6.1.1 20160621
(Red Hat 6.1.1-3)
GNU Fortran (GCC) 6.1.1 20160621
(Red Hat 6.1.1-3)
(cmake and autotools)
Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
5.4.0 20160609
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
5.4.0 20160609
(cmake and autotools)
Known Problems
==============
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.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
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.
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