HDF5 version 1.12.1-3 currently under development ================================================================================ 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 CMake option to format source files HDF5_ENABLE_FORMATTERS option will enable creation of targets using the pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder or tool folder. All sources can be formatted by executing the format target; make format (ADB - 2020/09/24) - CMake option to link the generated Fortran MOD files into the include directory. The Fortran generation of MOD files by a Fortran compile can produce different binary files between SHARED and STATIC compiles with different compilers and/or different platforms. Note that it has been found that different versions of Fortran compilers will produce incompatible MOD files. Currently, CMake will locate these MOD files in subfolders of the include directory and add that path to the Fortran library target in the CMake config file, which can be used by the CMake find library process. For other build systems using the binary from a CMake install, a new CMake configuration can be used to copy the pre-chosen version of the Fortran MOD files into the install include directory. The default will depend on the configuration of BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED The defaults can be overriden by setting the config option HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC (ADB - 2020/07/9, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip The open source AEC library is a replacement library for SZip. In order to use it for hdf5 the libaec CMake source was changed to add "-fPIC" and exclude test files. Autotools does not build the compression libraries within hdf5 builds. New option USE_LIBAEC is required to compensate for the different files produced by AEC build. (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER Some handcrafted tests in HDFTests.c has been removed and the CMake CHECK_STRUCT_HAS_MEMBER module has been used. (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags GNU C, C++ and gfortran warnings flags were moved to files in a config sub-folder named gnu-warnings. Flags that only are available for a specific version of the compiler are in files named with that version. Clang C warnings flags were moved to files in a config sub-folder named clang-warnings. Intel C, Fortran warnings flags were moved to files in a config sub-folder named intel-warnings. There are flags in named "error-xxx" files with warnings that may be promoted to errors. Some source files may still need fixes. There are also pairs of files named "developer-xxx" and "no-developer-xxx" that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the configure option:--enable-developer-warnings. In addition, CMake no longer applies these warnings for examples. (ADB - 2020/03/24, TRILAB-192) Library: -------- - Added two new API routines for tracking library memory use: H5get_alloc_stats() and H5get_free_list_sizes(). (QAK - 2020/03/25) Java Library: ---------------- Tools: ------ - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2020/08/05, HDFFV-9984) Support for new platforms, languages and compilers. ======================================= Bug Fixes since HDF5-1.12.0 release ================================== Library ------- - Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. (QAK - 2020/09/02) - Avoid setting up complex MPI types with 0-length vectors, which some MPI implementations don't handle well. (In particular, IBM SpectrumScale MPI on the Summit system at ORNL) (QAK - 2020/08/21) - Explicitly declared dlopen to use RTLD_LOCAL dlopen documentation states that if neither RTLD_GLOBAL nor RTLD_LOCAL are specified, then the default behavior is unspecified. The default on linux is usually RTLD_LOCAL while macos will default to RTLD_GLOBAL. (ADB - 2020/08/12, HDFFV-11127) - Fixed the segmentation fault when reading attributes with multiple threads It was reported that the reading of attributes with variable length string datatype will crash with segmentation fault particularly when the number of threads is high (>16 threads). The problem was due to the file pointer that was set in the variable length string datatype for the attribute. That file pointer was already closed when the attribute was accessed. The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. (VC - 2020/07/13, HDFFV-11080) - Reduce overhead for H5open(), which is involved in public symbols like H5T_NATIVE_INT, etc. (QAK - 2020/06/18) - Cache last ID looked up for an ID type (dataset, datatype, file, etc), improving performance when accessing the same ID repeatedly. (QAK - 2020/06/11) - Streamline I/O to a single element, improving performance for record appends to chunked datasets. (QAK - 2020/06/11) - Remove redundant tagging of metadata cache entries for some chunked dataset operations, slightly improving performance for chunked datasets. (QAK - 2020/06/10) - Better detect selections with the same shape, improving performance for some uses of H5DOappend (and other situations). (QAK - 2020/06/07) - Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. (QAK - 2020/05/07) - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. H5S_NO_CLASS is an internal class value that should not have been exposed via a public API call. In debug builds of the library, this can cause asserts to trip. In non-debug builds, it will produce normal library errors. The new library behavior is for H5Sset_extent_none() to convert the dataspace into one of type H5S_NULL, which is better handled by the library and easier for developers to reason about. (DER - 2020/07/27, HDFFV-11027) Tools: ------ Fortran API ----------- - Fixed configure issue when building HDF5 with NAG Fortran 7.0. HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033) High-Level Library ------------------ - Eliminated unnecessary code in H5DOappend(), improving its performance. (QAK - 2020/06/05) Testing ------- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. (LRK, 2020/7/2, HDFFV-11063) 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) 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 High Sierra 10.13.6 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 Mac OS Mojave 10.14.6 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 = 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 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 ? Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ? Mac OS X El Capitan 10.11.6 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 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 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 Mac OS X El Capitan 10.11.6 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) 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. 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.