HDF5 version 1.8.16 released on 2015-11-10 ================================================================================ 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 1.8.16 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.16 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.16 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 and Build ------------- - The thread-safety + high-level library combination has been marked as "unsupported" in the Autotools The global lock used by the thread-safety feature has never been raised to the high-level library level, making it possible that the library state could change if a context switch were to occur in a high-level library call. Because of this, the combination of thread-safety and high-level library is officially unsupported by The HDF Group. In the past, although this combination has never been supported, this was not enforced by the build systems. These changes will cause an Autotools configure step to fail if --enable-threadsafe and --enable-hl are combined unless additional options are specified. Since the high-level library is built by default, this means that these extra configuration options will need to be used any time --enable-threadsafe is selected. To build with --enable-threadsafe, either: 1) Use --disable-hl to disable the high-level library (recommended) 2) Use --enable-unsupported to build the high-level library with the thread-safety feature. (DER - 2015/09/10 HDFFV-8719) - Using CMake now builds both static and shared libraries. The CMake files have been updated to build both static and shared libraries, with tools only built statically. The packaging of the libraries and tools will include cmake-config files that allows projects to choose either shared or static (default) libraries to be found with the find_package command using the COMPONENTS keyword and a list of components. The imported libraries will include any interface specific settings and dependent libraries. The default setting for BUILD_SHARED_LIBS has changed from OFF to ON, which builds both static and shared libraries. The static libraries are always built because of tools requirements. (ADB - 2015/08/24 HDFFV-5881) - Inline functions now correctly annotated with Autotools builds. The method used to detect the appropriate inline markup scheme was nonfunctional in Autotools builds. The Autotools have been modified to correctly detect the compiler's inline markup symbol and apply it to the source. Note that only a very small number of internal functions are marked inline so this was not a very big change or likely to significantly affect performance. As a part of this change, the H5_inline symbol no longer appears in H5pubconf.h. (DER - 2015/08/13 HDFFV-9119, HDFFV-9421) - Removed obsolete/unmaintained files from config/ Several files were removed from the config directory. These files represent old operating systems, were no longer necessary, and/or were no longer maintained. configure.ac was updated to reflect the removed files. Removed: craynv dec-flags hpux11.23 ia64-linux-gnu nec-superux14.1 sv1-cray x86_64-redstorm-linux-gnu powerpc-ibm-aix5.x As a part of this work, a few lines that deal with locating the sys/fpu.h header on SGI machines and some OSF/1 configure lines were also removed. The Solaris config was also renamed to not have a version number since the version number was ignored by configure as it applies to all Solaris versions. (DER - 2015/09/04 HDFFV-9116) - Removed the FP_TO_INTEGER_OVERFLOW_WORKS macro/defines from the library This was for working around bugs in the Cray X1 compiler, which is no longer supported. (DER - 2015/09/09 HDFFV-9191) - Removed the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS symbols and associated code. H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS was a work-around on old 64-bit SGI and Solaris systems. H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS was a work-around for old PGI compilers on Linux. Neither of these were used in any current library code and only appeared in the dt_arith test. (DER - 2015/09/09 HDFFV-9187) - Removed CONVERT_DENORMAL_FLOAT symbol and associated code from the library. This was only set in configure files for Cray and NEC computers. These config files no longer exist so there is no effect on currently supported platforms. (DER - 2015/09/09 HDFFV-9188) - Removed _BSD_SOURCE and _DEFAULT_SOURCE from configure.ac These are old BSD-compatibility symbols that are no longer needed by the library. (DER - 2015/09/10 HDFFV-9079) - Removed HW_FP_TO_LLONG_NOT_WORKS symbol and associated code from the library. This was part of a work-around for the VS.NET 2003 compiler, which is no longer supported. (DER - 2015/09/10 HDFFV-9189) - Removed the BAD_LOG2_CODE_GENERATED symbol and associated code from the library. This was an IRIX work-around. (DER - 2015/09/11 HDFFV-9195) - Decoupled shared object version numbers for wrapper libraries from the shared object version number for the HDF5 library. These will be maintained on an individual basis according to the interface changes specific to these wrapper libraries. For HDF5 1.8.16 the shared object version numbers were changed from 10.0.1 to 10.1.0 for the HDF5 library due to added APIs. For the C++ wrapper library they were changed from 10.0.1 to 11.0.0 due to changes in existing APIs. For all other wrapper libraries the versions were changed from 10.0.1 to 10.0.2 because while the APIs had no changes there have been changes in code that did not result in changes to their interfaces. (LRK - 2015/10/28) Library ------- - H5F_ACC_DEBUG flag for H5Fopen/create: functionality removed The symbol was used to emit some extra debugging information for HDF Group developers in the multi VFD. The underlying functionality has been removed due to disuse. The symbol remains defined since it was visible in H5Fpublic.h but it has been set to zero and has no effect anywhere in the library. (DER - 2015-05-02, HDFFV-1074) - New public API call: H5is_library_threadsafe() This API call indicates if the library was built with thread- safety enabled. (DER - 2015-09-01, HDFFV-9496) Parallel Library ---------------- - None Tools ----- - None High-Level APIs --------------- - None Fortran API ----------- - None C++ API ------- - Class H5::ObjCreatPropList is added for the object creation property list class. Class H5::ObjCreatPropList is derived from H5::PropList and is a baseclass of H5::DSetCreatPropList. Additional property list classes will be derived from H5::ObjCreatPropList when they are added to the library in future releases. (BMR, 2015/10/13, Part of HDFFV-9169) - New Wrappers for C Functions H5P[s/g]et_attr_phase_change and H5P[s/g]et_attr_creation_order. Wrappers were added to class H5::ObjCreatPropList for the C Functions H5Pset_attr_phase_change: H5::ObjCreatPropList::setAttrPhaseChange H5Pget_attr_phase_change: H5::ObjCreatPropList::getAttrPhaseChange H5Pset_attr_creation_order: H5::ObjCreatPropList::setAttrCrtOrder H5Pget_attr_creation_order: H5::ObjCreatPropList::getAttrCrtOrder (BMR, 2015/10/13, Part of HDFFV-9167 and HDFFV-9169) Support for New Platforms, Languages, and Compilers =================================================== - Added VS2015 with Intel Fortran 16 to supported Windows 7 platforms Bug Fixes since HDF5-1.8.15 =========================== Configuration ------------- - CMake test for long long printf format improved The CMake configuration test for determining the printf format string for printing a long long integer was fixed. The test would crash when executed with VS2015. (ADB - 2015-10-21 HDFFV-9488) Library ------- - VS2015 removed global variable timezone The usage of the global variable timezone was modified for VS2015 by adding an alias to Windows builds. (ADB - 2015-10-23 HDFFV-9550) - Fix potential error in H5Iclear_type If the ID type's close callback could close another ID of the same type, H5Iclear_type could occasionally run into problems due to the inner workings of the skip list package. This could potentially cause an error on library shutdown without calling H5Iclear_type directly. This issue has been fixed. (NAF - 2015-08-12) - Fix uninitialized memory in dataspace selection code When creating a dataspace with H5Screate and setting the extent with H5Sextent_copy, the selection offset was not initialized, potentially causing invalid I/O. There may be other cases where this happened. Modified the library to always initialize the offset. (NAF - 2015-09-08) - Truncate file in H5Fflush() if EOA != EOF to avoid file corruption in certain scenarios In the following scenario, the resulting HDF5 file would be incorrectly corrupted because the truncate operation was at some point wrongly moved out of the flush operation: - Create a new file with a single dataset. - Write parts of the dataset (make sure that some values at the end of the dataset are not initialized). - Flush the file. - Crash the program. - Try to open the file with h5dump or h5debug, but the resulting file is corrupted. (MSC - 2015-06-15 HDFFV-9418) Parallel Library ---------------- - (XYZ - YYYY/MM/DD HDFFV-####) Performance ------------- - None Tools ----- - VS2015 changed the default format for printing of exponents VS2015 default format for exponents changed with the elimination of the leading '0'. CMake now tests for the VS2015 compiler and adjusts which reference files are used by tests. (ADB - 2015-10-23 HDFFV-9550) - Fixed h5repack with user-defined filters h5repack would throw a buffer overrun exception on Windows when parsing a user-defined filter ID of 5 digits. A local variable in the parse routine was not of sufficient size. (ADB - 2015/09/01 HDFFV-9515) Fortran API ------------ - None C++ API ------ - Removed memory leaks The static global constant objects were changed to constant references referencing dynamically allocated objects. This ensures that the clean-up process in the C++ library occurs before the termination of the C library and prevents memory leaks because the previous global constants were not properly deleted before the C library termination. (BMR, 2015/10/13, HDFFV-9529) - Fixed the problem about identifiers being closed prematurely. The C++ library needs to increment the ID's reference counter when it is duplicated in the form of C++ objects, but not when the ID is obtained from a C function. With this approach, both problems, prematurely closing ID's and memory leaks due to ID's not being closed, should be eliminated. (BMR, 2015/10/15, HDFFV-7947) 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 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 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. 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 of 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 systems. 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)