HDF5 version 1.8.18 released on 2016-11-14 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.17 and HDF5-1.8.18, and contains information on the platforms tested and known problems in HDF5-1.8.18. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.18 source code, documentation, and additional materials can be found on the HDF5 web page at: https://support.hdfgroup.org/HDF5/ The HDF5 1.8.18 release can be obtained from: https://support.hdfgroup.org/HDF5/release/obtain518.html User documentation for 1.8.18 can be accessed directly at this location: https://support.hdfgroup.org/HDF5/doc1.8/ 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://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.18 (current release) versus Release 1.8.17 https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html 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 HDF5-1.8.17 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - CMake: Added NAMESPACE hdf5:: to package configuration files to allow projects using installed HDF5 binaries built with CMake to link with them without specifying the HDF5 library location via IMPORTED_LOCATION. (ADB, 2016/10/17, HDFFV-10003) - CMake: Changed the CTEST_BUILD_CONFIGURATION option to CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. (ADB, 2016/10/17, HDFFV-9971) - CMake: Added support for GIT (ADB, 2016/07/12) Library ------- - None Parallel Library ---------------- - None Tools ----- - None High-Level APIs --------------- - None Fortran API ----------- - None C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== Bug Fixes since HDF5-1.8.17 =========================== Configuration ------------- - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by condensing cygwin configuration files into a single file and removing outdated compiler settings. (ABD, 2016/07/12, HDFFV-9946) - CMake: Fixed a command length overflow error by converting custom commands inside CMakeTest.cmake files into regular dependencies and targets. (ABD, 2016/07/12, HDFFV-9939) - CMake: Fixed a timeout error that would occasionally occur when running the virtual file driver tests simultaneously due to test directory and file name collisions. (ABD, 2016/09/19, HDFFV-9431) Library ------- - Fixed a memory leak that would occur when the library allocated memory for an external file prefix (H5Pset_efile_prefix) and failed to free it. (DER, 2016/04/29) - Fixed an error that would occur when calling H5Adelete on an attribute which is attached to an externally linked object in the target file and whose datatype is a committed datatype in the main file. (VC, 2016-07-04, HDFFV-9940) - Fixed a problem where a plugin compiled into a DLL in the default plugin directory could not be found by the HDF5 library at runtime on Windows when the HDF5_PLUGIN_PATH environment variable was not set. (ABD, 2016/08/01, HDFFV-9706) - Fixed an issue where H5Pset_alignment could result in misaligned blocks with some input combinations, causing an assertion failure in debug mode. (NAF, 2016/08/11, HDFFV-9948) - A number of issues were fixed when reading/writing from/to corrupted files to ensure that the library fails gracefully in these cases: * Writing to a corrupted file that has an object message which is incorrectly marked as sharable on disk results in a buffer overflow / invalid write instead of a clean error message. * Decoding data from a corrupted file with a dataset encoded with the H5Z_NBIT decoding can result in a code execution vulnerability under the context of the application using the HDF5 library. * When decoding an array datatype from a corrupted file, the HDF5 library fails to return an error in production if the number of dimensions decoded is greater than the maximum rank. * When decoding an "old style" array datatype from a corrupted file, the HDF5 library fails to return an error in production if the number of dimensions decoded is greater than the maximum rank. (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) - Fixed an error that would occur when copying an object with an attribute which is a compound datatype consisting of a variable length string. (VC, 2016-10-17, HDFFV-7991) Parallel Library ---------------- - Fixed a bug that could occur when allocating a chunked dataset in parallel with an alignment set and an alignment threshold greater than the chunk size but less than or equal to the raw data aggregator size. (NAF, 2016/08/11, HDFFV-9969) Performance ------------- - None Tools ----- - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) in which they would erroneously drop the file argument specified via the -o flag when the -o flag was specified before the -c flag on the command line, resulting in a failure to compile. (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530) - h5repack User Defined (UD) filter parameters were not parsed correctly. The UD filter parameters were not being parsed correctly. Reworked coding section to parse the correct values and verify number of parameters. (ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) Fortran API ----------- - Fortran library fails to compile and fails tests with NAG compiler. * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5 configure programs. * Removed Fortran 66 character/integer conversions from tests. * Removed the use of C_SIZEOF in the test programs * Changed to using STORAGE_SIZE in the test programs if available. Otherwise, uses C_SIZEOF or SIZEOF. (MSB, 2016/9/22, HDFFV-9973) - Fortran segfaults for F03 tests with NAG compiler * Removed INTENT(OUT) from 'fillvalue' in F2003 interface for H5Pget_fill_value_f. (MSB, 2016/9/22, HDFFV-9980) C++ API ------- - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library. In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may also be removed. (BMR, 2016/10/27, HDFFV-9532) High-Level APIs: --------------- - The high-level API Packet Table (PT) did not write data correctly when the datatype is a compound type that has string type as one of the members. This problem started in 1.8.15, after the fix of HDFFV-9042 was applied, which caused the Packet Table to use native type to access the data. It should be up to the application to specify whether the buffer to be read into memory in the machine’s native architecture. Thus, the PT is fixed to not use native type but to make a copy of the user's provided datatype during creation or the packet table's datatype during opening. If an application wishes to use native type to read the data, then the application will request that. However, the Packet Table doesn't provide a way to specify memory datatype in this release. This feature will be available in future releases, HDFFV-10023. (BMR, 2016/10/27, HDFFV-9758) Fortran High-Level APIs: ------------------------ - None Testing ------- - 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 4.8.4, 4.9.3, 5.2.0 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 15.7-0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 15.0.3.187 Build 20150407 MPICH 3.1.4 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) Version 4.8.5 20150623 (Red Hat 4.8.5-4) Versions 4.9.3, 5.2.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 15.0.3.187 Build 20150407 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 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Visual Studio 2015 w/ Intel Fortran 16 (cmake) Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) (cmake and autotools) 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) Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) 64-bit gfortran GNU Fortran (GCC) 4.8.2 (swallow/kite) Intel icc/icpc/ifort version 15.0.3 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 10.11.4 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 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 n y y y Windows 7 Cygwin n y/y n y y n Windows 10 n y/y n y y y Windows 10 x64 n 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 2.6.32-431.11.2.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 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 2.6.32-431.11.2.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 (platypus) 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 ============== * On windows platforms in debug configurations, the VFD flush1 tests will fail with the split and multi VFD drivers. These tests will display a modal debug dialog which must be answered or wait for the test timeout to expire. (ADB - 2014/06/23 - HDFFV-8851) * CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv catches some undefined behavior in the alignment algorithm of the macro DETECT_I in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for H5detect.c. In the future, we can separate flags for H5detect.c from the rest of the library. (SLU - 2013/10/16) * Make provided by Solaris fails in "make check". Solaris users should use gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. (SLU - 2005/06/30)