HDF5 version 1.8.22-snap1 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 ------------- - 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 ------- - 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 ----------- - None C++ API ------- - None High-Level APIs --------------- - None Support for New Platforms, Languages, and Compilers =================================================== Bug Fixes since HDF5-1.8.21 =========================== Configuration ------------- - None Library ------- - 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) Parallel Library ---------------- - None Performance ------------- - None Tools ----- - None 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 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 Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) 64-bit gfortran GNU Fortran (GCC) 4.9.2 (wren/quail) Intel icc/icpc/ifort version 15.0.3 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 = 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) Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (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) CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) (cmake and autotools) Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 (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.