HDF5 version 1.8.21-snap13 currently under development ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.20 and HDF5-1.8.21, and contains information on the platforms tested and known problems in HDF5-1.8.21. 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 1.8.21 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 User documentation for 1.8.21 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 1.8.21 (current release) versus Release 1.8.20 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 HDF5-1.8.20 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - CMake Change minimum version to 3.10. This change removes the need to support a copy of the FindMPI.cmake module, which has been removed, along with its subfolder in the config/cmake_ext_mod location. (ADB - 2018/03/09) - CMake Add pkg-config file generation Added pkg-config file generation for the C, C++, HL, and HL C++ libraries. In addition, builds on linux will create h5cXXX scripts that use the pkg-config files. This is a limited implementation of a script like autotools h5cc. (ADB - 2018/03/08, HDFFV-4359) - CMake Refactor use of CMAKE_BUILD_TYPE for new variable, which understands the type of generator in use. Added new configuration macros to use new HDF_BUILD_TYPE variable. This variable is set correctly for the type of generator being used for the build. (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296) - None Library ------- - None 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 HDF5-1.8.20 =========================== - If an HDF5 file contains a filter pipeline message with a 'number of filters' field that exceeds the maximum number of allowed filters, the error handling code will attempt to dereference a NULL pointer. This issue was reported to The HDF Group as issue #CVE-2017-17505. NOTE: The HDF5 C library cannot produce such a file. This condition should only occur in a corrupt (or deliberately altered) file or a file created by third-party software. This problem arose because the error handling code assumed that the 'number of filters' field implied that a dynamic array of that size had already been created and that the cleanup code should iterate over that array and clean up each element's resources. If an error occurred before the array has been allocated, this will not be true. This has been changed so that the number of filters is set to zero on errors. Additionally, the filter array traversal in the error handling code now requires that the filter array not be NULL. (DER - 2018/02/06, HDFFV-10354) - If an HDF5 file contains a filter pipeline message which contains a 'number of filters' field that exceeds the actual number of filters in the message, the HDF5 C library will read off the end of the read buffer. This issue was reported to The HDF Group as issue #CVE-2017-17506. NOTE: The HDF5 C library cannot produce such a file. This condition should only occur in a corrupt (or deliberately altered) file or a file created by third-party software. The problem was fixed by passing the buffer size with the buffer and ensuring that the pointer cannot be incremented off the end of the buffer. A mismatch between the number of filters declared and the actual number of filters will now invoke normal HDF5 error handling. (DER - 2018/02/26, HDFFV-10355) - If an HDF5 file contains a malformed compound datatype with a suitably large offset, the type conversion code can run off the end of the type conversion buffer, causing a segmentation fault. This issue was reported to The HDF Group as issue #CVE-2017-17507. NOTE: The HDF5 C library cannot produce such a file. This condition should only occur in a corrupt (or deliberately altered) file or a file created by third-party software. THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME Fixing this problem would involve updating the publicly visible H5T_conv_t function pointer typedef and versioning the API calls which use it. We normally only modify the public API during major releases, so this bug will not be fixed at this time. (DER - 2018/02/26, HDFFV-10356) - If an HDF5 file contains a malformed compound type which contains a member of size zero, a division by zero error will occur while processing the type. This issue was reported to The HDF Group as issue #CVE-2017-17508. NOTE: The HDF5 C library cannot produce such a file. This condition should only occur in a corrupt (or deliberately altered) file or a file created by third-party software. Checking for zero before dividing fixes the problem. Instead of the division by zero, the normal HDF5 error handling is invoked. (DER - 2018/02/26, HDFFV-10357) - If an HDF5 file contains a malformed symbol table node that declares it contains more symbols than it actually contains, the library can run off the end of the metadata cache buffer while processing the symbol table node. This issue was reported to The HDF Group as issue #CVE-2017-17509. NOTE: The HDF5 C library cannot produce such a file. This condition should only occur in a corrupt (or deliberately altered) file or a file created by third-party software. Performing bounds checks on the buffer while processing fixes the problem. Instead of the segmentation fault, the normal HDF5 error handling is invoked. (DER - 2018/03/12, HDFFV-10358) Configuration ------------- - CMake Update CMake commands configuration. A number of improvements were made to the CMake commands. Most changes simplify usage or eliminate unused constructs. Also, some changes support better cross-platform support. (ADB - 2018/02/01, HDFFV-10398) - CMake Correct usage of CMAKE_BUILD_TYPE variable. The use of the CMAKE_BUILD_TYPE is incorrect for multi-config generators (Visual Studio and XCode) and is optional for single config generators. Created a new macro to check GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE. Defaults for these variables is "Release". (ADB - 2018/01/10, HDFFV-10385) - CMake Add replacement of fortran flags if using static CRT. Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in config/cmake_ext_mod folder. (ADB - 2018/01/08, HDFFV-10334) Library ------- - Utility function can not handle lowercase Windows drive letters Added call to toupper function for drive letter. (ADB - 2017/12/18, HDFFV-10307) Parallel Library ---------------- - None Performance ------------- - None Tools ----- - h5repack h5repack changes the chunk parameters when a change of layout is not specified and a filter is applied. HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code in the tools library. The check for an existing layout was incorrectly placed into an if block and not executed. The check was moved into the normal path of the function. (ADB - 2018/02/21, HDFFV-10412) - h5dump the tools library will hide the error stack during file open. While this is preferable almost always, there are reasons to enable display of the error stack when a tool will not open a file. Adding an optional argument to the --enable-error-stack will provide this use case. As an optional argument it will not affect the operation of the --enable-error-stack. h5dump is the only tool to implement this change. (ADB - 2018/02/15, HDFFV-10384) - h5dump h5dump would output an indented blank line in the filters section. h5dump overused the h5tools_simple_prefix function, which is a function intended to account for the data index (x,y,z) option. Removed the function call for header information. (ADB - 2018/01/25, HDFFV-10396) - h5repack h5repack incorrectly searched internal object table for name. h5repack would search the table of objects for a name, if the name did not match it tried to determine if the name without a leading slash would match. The logic was flawed! The table stored names(paths) without a leading slash and did a strstr of the table path to the name. The assumption was that if there was a difference of one then it was a match, however "pressure" would match "/pressure" as well as "/pressure1", "/pressure2", etc. Changed logic to remove any leading slash and then do a full compare of the name. (ADB - 2018/01/18, HDFFV-10393) - h5repack h5repack failed to handle more then 9 chars for int conversion. User defined filter parameter conversions would fail for integers larger then 9 characters. Increased local variable array for storing the current command line parameter to prevent buffer overflows. (ADB - 2018/01/17, HDFFV-10392) - h5diff h5diff seg-faulted if comparing VL strings against fixed strings. Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check for string objects of same type in the diff_can_type function by adding an if(tclass1 == H5T_STRING) block. This if block moves the same check that was added for attributes to this function, which is used by all object types. This function also handles complex type structures. Also added a new test file in h5diffgenttest for testing this issue and removed the temporary files used in the test scripts. (ADB - 2018/01/04, HDFFV-8745) Fortran API ----------- - None 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 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Visual Studio 2015 w/ Intel Fortran 16 (cmake) 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) Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) Visual Studio 2015 w/ MSMPI 8 (cmake) Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) gcc and gfortran compilers (GCC 5.4.0) (cmake and autotools) Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) gcc and gfortran compilers (GCC 5.4.0) (cmake and autotools) Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (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 n 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.