HDF5 version 1.8.17-snap14 currently under development ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.15 and HDF5-1.8.16-*, and contains information on the platforms tested and known problems in HDF5-1.8.16-*. 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 1.8.15 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.15 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.15 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ 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: http://www.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 1.8.16 (current release) versus Release 1.8.15 http://www.hdfgroup.org/HDF5/doc/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 HDF5-1.8.15 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - Cmakehdf5: added ability to run multiple make commands. Added option --njobs to specific up to homw many jobs to launch during build (cmamke) and testing (ctest). (AKC, 2015/12/13, HDFFV-9612) - Cmakehdf5: added --with-szlib to support szip library support; and --enable/disable-verbose to display all cmake process output. (AKC, 2015/11/16, HDFFV-8932 and DAILYTEST-195) - CMake minimum is now 3.1.0. (ADB 2015/11/14) - Large file system (LFS) support has changed in the autotools * We assume that fseeko and ftello exist. * The *64 I/O functions and types are no longer explicitly used. We now rely on a mapping provided by _FILE_OFFSET_BITS (or its equivalent). * _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS. (DER, 2016/03/29, HDFFV-9626) Library ------- - None Parallel Library ---------------- - None Tools ----- - None High-Level APIs --------------- - None Fortran API ----------- - None C++ API ------- - New function: ArrayType::setArrayInfo() ArrayType::setArrayInfo() was added to retrieve rank and dimensions of an array and store them in memory for easy access. (BMR, 2016/01/13, part of fixing a user's problem) Support for New Platforms, Languages, and Compilers =================================================== - - Bug Fixes since HDF5-1.8.16 =========================== Configuration ------------- - Updated Linux language level flags to match the Autotools. Removed Linux-specific flags from OS X. An addition to the flags simply being out of sync with the Autotools, the Linux flags were used on OS X builds which led to symbols not being found. Although this was non-fatal and compilation continued (implicit definitions were used by the compiler and the symbols resolved at link time), a large number of warnings were raised. Linux changes: * CHANGED: _POSIX_C_SOURCE (from 199605 to 200112L) * ADDED: _GNU_SOURCE * REMOVED: _BSD_SOURCE * REMOVED: _DEFAULT_SOURCE (DER, 2015/12/08, HDFFV-9627) - The --enable-clear-file-buffers configure option was non-functional so the feature was always enabled (its default value). Regardless of the configure flag, the setting was always enabled when the autotools were used to configure HDF5. This was due to the "no" option being processed after the "*" option in configure.ac so "*" matched first. CMake was unaffected. The option now works correctly. NOTE that builders are always advised to leave this option enabled. When disabled, buffers that are written to disk may contain the memory's previous contents, which may include secure information. The performance overhead of the feature (a single memset call per allocation) is minimal. (DER, 2016/02/03, HDFFV-9676) Library ------- - Fixed some format string warnings that prevent compiling with -Werror=format-security on gcc. These only appeared in error messages and would not cause problems under normal operation. (DER, 2016/01/13, HDFFV-9640) Parallel Library ---------------- - None Performance ------------- - None Tools ----- - h5dump subsetting fixed for dims greater then two. When a dataset has more then two dimensions, subsetting would incorrectly calculate the data that needed to be displayed. Added in block and stride calculation that account for dimensions greater then two. NOTE: lines that have line breaks inserted because of display length calculations, may have index info that is incorrect until the next dimension break. (ADB, 2016/03/07, HDFFV-9698) - h5dump issue with argument segfault. When an argument with an optional value was at the end of the command line with a value, h5dump would crash. Reworked check for remaining arguments. (ADB, 2016/03/07, HDFFV-9570) - h5dump issue with default fill value. Added all default cases of fill value to display of fill value.. (ADB, 2016/03/07, HDFFV-9241) Fortran API ------------ - None C++ API ------ - The member function AbstractDs::getArrayType() caused failure in user's program. This problem was caused by missing initialization of the ArrayType's members. The problem is now fixed. (BMR, 2016/01/13, User's report) High-Level APIs: ------ - None 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. AIX 6.1 xlc/xlc_r 10.1.0.5 (NASA G-ADA) xlC/xlC_r 10.1.0.5 xlf90/xlf90_r 12.1.0.6 Linux 2.6.32-573.3.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (platypus) Version 4.4.7 20120313 Version 4.8.4, Version 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 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) IBM XL C/C++ V13.1 IBM XL Fortran V15.1 Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (kituo/moohan) Version 4.8.3 20140911 (Red Hat 4.8.3-9) Version 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 (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 (cmake) Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 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 clang/clang++ version 6.0 from Xcode 6.2.0 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 clang/clang++ version 6.0 from Xcode 7.0.0 64-bit gfortran GNU Fortran (GCC) 4.9.2 (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 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 8.1 n y/y n y y y Windows 8.1 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 Yosemeti 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 8.1 y y y y Windows 8.1 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 Yosemeti 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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) #1 SMP x86_64 GNU/Linux (platypus) Mac OS X El Capitan 10.11 Apple clang/clang++ version 7.0.0 from Xcode 7.0.1 64-bit gfortran GNU Fortran (GCC) 5.2.0 (VM) Windows 7 Visual Studio 2008 (cmake) Windows 7 x64 Visual Studio 2008 (cmake) Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux gcc (Debian 4.7.2-5) 4.7.2 GNU Fortran (Debian 4.7.2-5) 4.7.2 (cmake and autotools) Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) (cmake and autotools) SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.8.1 GNU Fortran (SUSE Linux) 4.8.1 (cmake and autotools) Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 (cmake and autotools) hopper.nersc.gov PrgEnv-gnu/5.2.40 gcc (GCC) 4.9.2 20141030 (Cray Inc.) GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) g++ (GCC) 4.9.2 20141030 (Cray Inc.) 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)