HDF5 version 1.11.2 currently under development ================================================================================ INTRODUCTION This document describes the differences between HDF5-1.10.1 and HDF5 1.10.2, and contains information on the platforms tested and known problems in HDF5-1.10.1. For more details check the HISTORY*.txt files in the HDF5 source. Links to HDF5 1.10.1 source code, documentation, and additional materials can be found on The HDF5 web page at: https://support.hdfgroup.org/HDF5/ The HDF5 1.10.1 release can be obtained from: https://support.hdfgroup.org/HDF5/release/obtain5.html User documentation for the snapshot can be accessed directly at this location: https://support.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.10.x release series, including brief general descriptions of some new and modified APIs, are described in the "New Features in HDF5 1.10" document: https://support.hdfgroup.org/HDF5/docNewFeatures/index.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.10.1 (current release) versus Release 1.10.0 https://support.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 and languages - Bug Fixes since HDF5-1.10.1 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration: ------------- - 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) Library: -------- - Add prefix option to VDS files. Currently, VDS source files must be in the active directory to be found by the virtual file. Adding the option of a prefix to be set on the virtual file, using a data access property list (DAPL), allows the source files to located at an absolute or relative path to the virtual file. Private utility functions in H5D and H5L packages merged into single function in H5F package. New public APIs: herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix); ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size); The prefix can also be set with an environment variable, HDF5_VDS_PREFIX. (ADB - 2017/12/12, HDFFV-9724, HDFFV-10361) Parallel Library: ----------------- - Optimize parallel open/location of the HDF5 super-block Previous releases of PHDF5 required all parallel ranks to search for the HDF5 superblock signature when opening the file. As this is accomplished more or less as a synchronous operation, a large number of processes can experience a slowdown in the file open due to filesystem contention. As a first step in improving the startup/file-open performance, we allow MPI rank 0 of the associated MPI communicator to locate the base offset of the super-block and then broadcast that result to the remaining ranks in the parallel group. Note that this approach is utilized ONLY during file opens which employ the MPIO file driver in HDF5 by previously having called H5Pset_fapl_mpio(). HDF5 parallel file operations which do not employ multiple ranks e.g. specifiying MPI_COMM_SELF (whose MPI_Comm_size == 1) as opposed to MPI_COMM_WORLD, will not be affected by this optimization. Conversely, parallel file operations on subgroups of MPI_COMM_WORLD are allowed to be run in parallel with each subgroup operating as an independant collection of processes. (RAW - 2017/10/10, HDFFV-10294) - Large MPI-IO transfers Previous releases of PHDF5 would fail when attempting to read or write greater than 2GB of data in a single IO operation. This issue stems principally from an MPI API whose definitions utilize 32 bit integers to describe the number of data elements and datatype that MPI should use to effect a data transfer. Historically, HDF5 has invoked MPI-IO with the number of elements in a contiguous buffer represented as the length of that buffer in bytes. Resolving the issue and thus enabling larger MPI-IO transfers is accomplished first, by detecting when a user IO request would exceed the 2GB limit as described above. Once a transfer request is identified as requiring special handling, PHDF5 now creates a derived datatype consisting of a vector of fixed sized blocks which is in turn wrapped within a single MPI_Type_struct to contain the vector and any remaining data. The newly created datatype is then used in place of MPI_BYTE and can be used to fulfill the original user request without encountering API errors. (RAW - 2017/07/11, HDFFV-8839) Fortran Library: ---------------- - C++ Library: ------------ - Java Library: ---------------- - Wrappers added for the following APIs: H5Pset_evict_on_close H5Pget_evict_on_close H5Pset_chunk_opts H5Pget_chunk_opts H5Pset_efile_prefix H5Pget_efile_prefix H5Pset_virtual_prefix H5Pget_virtual_prefix (ADB - 2017/12/20) Tools: ------ - h5diff h5diff has new option enable-error-stack. Updated h5diff with the --enable-error-stack argument, which enables the display of the hdf5 error stack. This completes the improvement to the main tools; h5copy, h5diff, h5dump, h5ls and h5repack. (ADB - 2017/08/30, HDFFV-9774) High-Level APIs: --------------- - C Packet Table API ------------------ - Internal header file -------------------- - Documentation ------------- - Support for new platforms, languages and compilers. ======================================= - Bug Fixes since HDF5-1.10.1 release ================================== Library ------- - H5Pset_evict_on_close in H5Pfapl.c Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for parallel library. (ADB - 2018/03/6, HDFFV-10414) - Utility function can not handle lowercase Windows drive letters Added call to toupper function for drive letter. (ADB - 2017/12/18, HDFFV-10307) - filter plugin handling in H5PL.c and H5Z.c It was discovered that the dynamic loading process used by filter plugins had issues with library dependencies. CMake build process changed to use LINK INTERFACE keywords, which allowed HDF5 C library to make dependent libraries private. The filter plugin libraries no longer require dependent libraries (such as szip or zlib) to be available. (ADB - 2017/11/16, HDFFV-10328) - H5Zfilter_avail in H5Z.c The public function checked for plugins, while the private function did not. Modified H5Zfilter_avail and private function, H5Z_filter_avail. Moved check for plugin from public to private function. Updated H5P__set_filter due to change in H5Z_filter_avail. Updated tests. (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - An uninitialized struct could cause a memory access error when using variable-length or reference types in a compressed, chunked dataset. A struct containing a callback function pointer and a pointer to some associated data was used before initialization. This could cause a memory access error and system crash. This could only occur under unusual conditions when using variable-lenth and reference types in a compressed, chunked dataset. On recent versions of Visual Studio, when built in debug mode, the debug heap will complain and cause a crash if the code in question is executed (this will cause the objcopy test to fail). (DER - 2017/11/21, HDFFV-10330) - 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 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) 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) - CMake The hdf5 library used shared szip and zlib, which needlessly required applications to link with the same szip and zlib libraries. Changed the target_link_libraries commands to use the static libs. Removed improper link duplication of szip and zlib. Adjusted the link dependencies and the link interface values of the target_link_libraries commands. (ADB - 2017/11/14, HDFFV-10329) - CMake MPI CMake implementation for MPI was problematic and would create incorrect MPI library references in the hdf5 libraries. Reworked the CMake MPI code to properly create CMake targets. Also merged the latest CMake FindMPI.cmake changes to the local copy. This is necessary until HDF changes the CMake minimum to 3.9 or greater. (ADB - 2017/11/02, HDFFV-10321) - CMake Too many commands for POST_BUILD step caused command line to be too big on windows. Changed foreach of copy command to use a custom command with the use of the HDFTEST_COPY_FILE macro. (ADB - 2017/07/12, HDFFV-10254) Performance ------------- - Fortran -------- - Fixed compilation errors when using Intel 18 Fortran compilers (MSB - 2017/11/3, HDFFV-10322) 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) - h5repack h5repack failed to copy a dataset with existing filter. Reworked code for h5repack and h5diff code in tools library. Added improved error handling, cleanup of resources and checks of calls. Modified H5Zfilter_avail and private function, H5Z_filter_avail. Moved check for plugin from public to private function. Updated H5P__set_filter due to change in H5Z_filter_avail. Updated tests. Note, h5repack output display has changed to clarify the individual steps of the repack process. The output indicates if an operation applies to all objects. Lines with notation and no information have been removed. (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - h5repack h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY. Added another parameter to the 'UD=' option to set the flag by default to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL. (ADB - 2017/08/31, HDFFV-10269) - h5ls h5ls generated error on stack when it encountered a H5S_NULL dataspace. Adding checks for H5S_NULL before calling H5Sis_simple (located in the h5tools_dump_mem function) fixed the issue. (ADB - 2017/08/17, HDFFV-10188) - h5dump h5dump segfaulted on output of XML file. Function that escape'd strings used the full buffer length instead of just the length of the replacement string in a strncpy call. Using the correct length fixed the issue. (ADB - 2017/08/01, HDFFV-10256) - h5diff h5diff segfaulted on compare of a NULL variable length string. Improved h5diff compare of strings by adding a check for NULL strings and setting the lengths to zero. (ADB - 2017/07/25, HDFFV-10246) - h5import h5import crashed trying to import data from a subset of a dataset. Improved h5import by adding the SUBSET keyword. h5import understands to use the Count times the Block as the size of the dimensions. Added INPUT_B_ORDER keyword to old-style configuration files. The import from h5dump function expects the binary files to use native types (FILE '-b' option) in the binary file. (ADB - 2017/06/15, HDFFV-10219) - h5repack h5repack did not maintain the creation order flag of the root group. Improved h5repack by reading the creation order and applying the flag to the new root group. Also added arguments to set the order and index direction, which applies to the traversing of the original file, on the command line. (ADB - 2017/05/26, HDFFV-8611) - h5diff h5diff failed to account for strpad type and null terminators of char strings. Also, h5diff failed to account for string length differences and would give a different result depending on file order in the command line. Improved h5diff compare of strings and arrays by adding a check for string lengths and if the strpad was null filled. (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) High-Level APIs: ------ - Fortran High-Level APIs: ------ - Documentation ------------- - F90 APIs -------- - C++ APIs -------- - Testing ------- - Supported Platforms =================== 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 4.8.4 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 15.0.3.187 (Build 20150407) MPICH 3.1.4 compiled with GCC 4.9.3 Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) 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, 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) 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 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 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 6.1 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 (osx1010dev/osx1010test) 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 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 4.8.4 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 15.0.3.187 (Build 20150407) 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) Intel(R) C (icc) and C++ (icpc) compilers Version 15.0.3.187 (Build 20150407) with NAG Fortran Compiler Release 6.1(Tozai) Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 (ostrich) and IBM XL Fortran for Linux, V15.1 Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux gcc, g++ (Debian 4.9.2-10) 4.9.2 GNU Fortran (Debian 4.9.2-10) 4.9.2 (cmake and autotools) Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc, g++ (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) Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609 GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609 (cmake and autotools) Known Problems ============== 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.