HDF5 version 1.10.4 released on 2018-10-05 ================================================================================ 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 - 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: ------------- - 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: -------- - 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) Bug Fixes since HDF5-1.10.3 release ================================== Library ------- - 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) 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 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Visual Studio 2015 w/ Intel Fortran 16 (cmake) Visual Studio 2015 w/ Intel C, Fortran 2017 (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 (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 = 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 3.10.0 x86_64 PGI n y/y n y y y CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y CentOS 7.2 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/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 3.10.0 x86_64 PGI y y y n CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y CentOS 7.2 Linux 3.10.0 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.