HDF5 version 1.12.1 released on 2021-07-01 ================================================================================ INTRODUCTION ============ This document describes the new features introduced in the HDF5 1.12.1 release. It contains information on the platforms tested and known problems in this release. For more details check the HISTORY*.txt files in the HDF5 source. Note that documentation in the links below will be updated at the time of the release. Links to HDF5 documentation can be found on The HDF5 web page: https://portal.hdfgroup.org/display/HDF5/HDF5 The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ More information about the new features can be found at: https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12 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 HDF5-1.12.0 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Adds C++ Autotools configuration file for Intel * Checks for icpc as the compiler * Copies most non-warning flags from intel-flags (DER - 2021/06/02) - Adds C++ Autotools configuration file for PGI * Checks for pgc++ as the compiler name (was: pgCC) * Other options basically match new C options (below) (DER - 2021/06/02) - Updates PGI C options * -Minform set to warn (was: inform) to suppress spurious messages * Sets -gopt -O2 as debug options * Sets -O4 as 'high optimization' option * Sets -O0 as 'no optimization' option * Removes specific settings for PGI 9 and 10 (DER - 2021/06/02) - Added an option to make the global thread-safe lock a recursive R/W lock Prior to this release, the HDF5 library supported multi-threaded applications by placing a recursive global lock on the entire library, thus allowing only one thread into the library at a time. While this is still the default, the library can now be built with the recursive global lock replaced with a recursive read / write (R/W) lock that allows recursive writer locks. Currently, this change results in no functional change in the HDF5 library, as all threads will have to acquire a write lock on entry, and thus obtain exclusive access to the HDF5 library as before. However, the addition of the recursive R/W lock is a prerequisite for further work directed at allowing some subset of the HDF5 API calls to enter the library with read locks. CMake: HDF5_USE_RECURSIVE_RW_LOCKS (default: OFF, advanced) Autotools: --enable-recursive-rw-locks [default=no] This feature only works with Pthreads. Win32 threads are not supported. (DER - 2021/05/10) - CMake no longer builds the C++ library by default HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the Autotools build defaults. (DER - 2021/04/20) - Removal of pre-VS2015 work-arounds HDF5 now requires Visual Studio 2015 or greater, so old work-around code and definitions have been removed, including: * <inttypes.h> * snprintf and vsnprintf * llround, llroundf, lround, lroundf, round, roundf * strtoll and strtoull * va_copy * struct timespec (DER - 2021/03/22) - Added CMake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) (RG - 2021/03/22) - On macOS, Universal Binaries can now be built, allowing native execution on both Intel and Apple Silicon (ARM) based Macs. To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" (SAM - 2021/02/07, github-311) - Added a configure-time option to control certain compiler warnings diagnostics A new configure-time option was added that allows some compiler warnings diagnostics to have the default operation. This is mainly intended for library developers and currently only works for gcc 10 and above. The diagnostics flags apply to C, C++ and Fortran compilers and will appear in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They will NOT be exported to h5cc, etc. The default is OFF, which will disable the warnings URL and color attributes for the warnings output. ON will not add the flags and allow default behavior. Autotools: --enable-diags CMake: HDF5_ENABLE_BUILD_DIAGS (ADB - 2021/02/05, HDFFV-11213) - CMake option to build the HDF filter plugins project as an external project The HDF filter plugins project is a collection of registered compression filters that can be dynamically loaded when needed to access data stored in a hdf5 file. This CMake-only option allows the plugins to be built and distributed with the hdf5 library and tools. Like the options for szip and zlib, either a tgz file or a git repository can be specified for the source. The option was refactored to use the CMake FetchContent process. This allows more control over the filter targets, but required external project command options to be moved to a CMake include file, HDF5PluginCache.cmake. Also enabled the filter examples to be used as tests for operation of the filter plugins. (ADB - 2020/12/10, OESS-98) - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did not process C++ options. Since FreeBSD 10, the default compiler has been clang (via 'cc'). The default compilers have been set to 'cc' for C and 'c++' for C++, which will pick up clang and clang++ respectively on FreeBSD 10+. Additionally, clang options are now set correctly for both C and C++ and g++ options will now be set if that compiler is being used (an omission from the former functionality). (DER - 2020/11/28, HDFFV-11193) - Fixed POSIX problems when building w/ gcc on Solaris When building on Solaris using gcc, the POSIX symbols were not being set correctly, which could lead to issues like clock_gettime() not being found. The standard is now set to gnu99 when building with gcc on Solaris, which allows POSIX things to be #defined and linked correctly. This differs slightly from the gcc norm, where we set the standard to c99 and manually set POSIX #define symbols. (DER - 2020/11/25, HDFFV-11191) - Added a configure-time option to consider certain compiler warnings as errors A new configure-time option was added that converts some compiler warnings to errors. This is mainly intended for library developers and currently only works for gcc and clang. The warnings that are considered errors will appear in the generated libhdf5.settings file. These warnings apply to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags", respectively. They will NOT be exported to h5cc, etc. The default is OFF. Building with this option may fail when compiling on operating systems and with compiler versions not commonly used by the library developers. Compilation may also fail when headers not under the control of the library developers (e.g., mpi.h, hdfs.h) raise warnings. Autotools: --enable-warnings-as-errors CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS (DER - 2020/11/23, HDFFV-11189) - Autotools and CMake target added to produce doxygen generated documentation The default is OFF or disabled. Autoconf option is '--enable-doxygen' autotools make target is 'doxygen' and will build all doxygen targets CMake configure option is 'HDF5_BUILD_DOC'. CMake target is 'doxygen' for all available doxygen targets CMake target is 'hdf5lib_doc' for the src subdirectory (ADB - 2020/11/13, HDFFV-11243) - CMake option to use MSVC naming conventions with MinGW HDF5_MSVC_NAMING_CONVENTION option enables the use of MSVC naming conventions when using a MinGW toolchain (xan - 2020/10/30) - CMake option to statically link gcc libs with MinGW HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ with the MinGW toolchain (xan - 2020/10/30) - CMake option to build the HDF filter plugins project as an external project The HDF filter plugins project is a collection of registered compression filters that can be dynamically loaded when needed to access data stored in a hdf5 file. This CMake-only option allows the plugins to be built and distributed with the hdf5 library and tools. Like the options for szip and zlib, either a tgz file or a git repository can be specified for the source. The necessary options are (see the INSTALL_CMake.txt file): HDF5_ENABLE_PLUGIN_SUPPORT PLUGIN_TGZ_NAME or PLUGIN_GIT_URL There are more options necessary for various filters and the plugin project documents should be referenced. (ADB - 2020/10/16, OESS-98) - Added CMake option to format source files HDF5_ENABLE_FORMATTERS option will enable creation of targets using the pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder or tool folder. All sources can be formatted by executing the format target; make format (ADB - 2020/09/24) - Disable memory sanity checks in the Autotools in release branches The library can be configured to use internal memory sanity checking, which replaces C API calls like malloc(3) and free(3) with our own calls which add things like heap canaries. These canaries can cause problems when external filter plugins reallocate canary-marked buffers. For this reason, the default will be to not use the memory allocation sanity check feature in release branches (e.g., hdf5_1_10_7). Debug builds in development branches (e.g., develop, hdf5_1_10) will still use them by default. This change only affects Autotools debug builds. Non-debug autotools builds and all CMake builds do not enable this feature by default. (DER - 2020/08/19) - Add file locking configure and CMake options HDF5 1.10.0 introduced a file locking scheme, primarily to help enforce SWMR setup. Formerly, the only user-level control of the scheme was via the HDF5_USE_FILE_LOCKING environment variable. This change introduces configure-time options that control whether or not file locking will be used and whether or not the library ignores errors when locking has been disabled on the file system (useful on some HPC Lustre installations). In both the Autotools and CMake, the settings have the effect of changing the default property list settings (see the H5Pset/get_file_locking() entry, below). The yes/no/best-effort file locking configure setting has also been added to the libhdf5.settings file. Autotools: An --enable-file-locking=(yes|no|best-effort) option has been added. yes: Use file locking. no: Do not use file locking. best-effort: Use file locking and ignore "disabled" errors. CMake: Two self-explanatory options have been added: HDF5_USE_FILE_LOCKING HDF5_IGNORE_DISABLED_FILE_LOCKS Setting both of these to ON is the equivalent to the Autotools' best-effort setting. NOTE: The precedence order of the various file locking control mechanisms is: 1) HDF5_USE_FILE_LOCKING environment variable (highest) 2) H5Pset_file_locking() 3) configure/CMake options (which set the property list defaults) 4) library defaults (currently best-effort) (DER - 2020/07/30, HDFFV-11092) - CMake option to link the generated Fortran MOD files into the include directory. The Fortran generation of MOD files by a Fortran compile can produce different binary files between SHARED and STATIC compiles with different compilers and/or different platforms. Note that it has been found that different versions of Fortran compilers will produce incompatible MOD files. Currently, CMake will locate these MOD files in subfolders of the include directory and add that path to the Fortran library target in the CMake config file, which can be used by the CMake find library process. For other build systems using the binary from a CMake install, a new CMake configuration can be used to copy the pre-chosen version of the Fortran MOD files into the install include directory. The default will depend on the configuration of BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED The defaults can be overridden by setting the config option HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC (ADB - 2020/07/09, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip The open source AEC library is a replacement library for SZip. In order to use it for hdf5 the libaec CMake source was changed to add "-fPIC" and exclude test files. Autotools does not build the compression libraries within hdf5 builds. New option USE_LIBAEC is required to compensate for the different files produced by AEC build. (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER Some handcrafted tests in HDFTests.c has been removed and the CMake CHECK_STRUCT_HAS_MEMBER module has been used. (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags GNU C, C++ and gfortran warnings flags were moved to files in a config sub-folder named gnu-warnings. Flags that only are available for a specific version of the compiler are in files named with that version. Clang C warnings flags were moved to files in a config sub-folder named clang-warnings. Intel C, Fortran warnings flags were moved to files in a config sub-folder named intel-warnings. There are flags in named "error-xxx" files with warnings that may be promoted to errors. Some source files may still need fixes. There are also pairs of files named "developer-xxx" and "no-developer-xxx" that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the configure option:--enable-developer-warnings. In addition, CMake no longer applies these warnings for examples. (2020/03/24, TRILAB-192) Library: -------- - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX The size_hint value is ultimately stored in a uint32_t struct field, so specifying a value larger than this on a 64-bit machine can cause undefined behavior including crashing the system. The documentation for this API call was also incorrect, stating that passing a negative value would cause the library to use a default value. Instead, passing a "negative" value actually passes a very large value, which is probably not what the user intends and can cause crashes on 64-bit systems. The Doxygen documentation has been updated and passing values larger than UINT32_MAX for size_hint will now produce a normal HDF5 error. (DER - 2021/04/29, HDFFV-11241) - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID When passed an invalid fapl ID, H5Pset_fapl_log() would usually segfault when attempting to free an uninitialized pointer in the error handling code. This behavior is more common in release builds or when the memory sanitization checks were not selected as a build option. The pointer is now correctly initialized and the API call now produces a normal HDF5 error when fed an invalid fapl ID. (DER - 2021/04/28, HDFFV-11240) - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times The call incorrectly attempts to free an internal copy of the previous log location string, which causes a segfault. This only happens when the call is invoked multiple times on the same property list. On the first call to a given fapl, the log location is set to NULL so the segfault does not occur. The string is now handled properly and the segfault no longer occurs. (DER - 2021/04/27, HDFFV-11239) - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows HSYS_GOTO_ERROR is an internal macro that is used to produce error messages when system calls fail. These strings include errno and the the associated strerror() value, which are not particularly useful when a Win32 API call fails. On Windows, this macro has been updated to include the result of GetLastError(). When a system call fails on Windows, usually only one of errno and GetLastError() will be useful, however we emit both for the user to parse. The Windows error message is not emitted as it would be awkward to free the FormatMessage() buffer given the existing HDF5 error framework. Users will have to look up the error codes in MSDN. The format string on Windows has been changed from: "%s, errno = %d, error message = '%s'" to: "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" for those inclined to parse it for error values. (DER - 2021/03/21) - File locking now works on Windows Since version 1.10.0, the HDF5 library has used a file locking scheme to help enforce one reader at a time accessing an HDF5 file, which can be helpful when setting up readers and writers to use the single- writer/multiple-readers (SWMR) access pattern. In the past, this was only functional on POSIX systems where flock() or fcntl() were present. Windows used a no-op stub that always succeeded. HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the same scheme as POSIX systems. We lock the entire file when we set up the locks (by passing DWORDMAX as both size parameters to LockFileEx()). (DER - 2021/03/19, HDFFV-10191) - H5Epush_ret() now requires a trailing semicolon H5Epush_ret() is a function-like macro that has been changed to contain a `do {} while(0)` loop. Consequently, a trailing semicolon is now required to end the `while` statement. Previously, a trailing semi would work, but was not mandatory. This change was made to allow clang-format to correctly format the source code. (SAM - 2021/03/03) - Improved performance of H5Sget_select_elem_pointlist Modified library to cache the point after the last block of points retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the same function to retrieve the next block of points from the list can proceed immediately without needing to iterate over the point list. (NAF - 2021/01/19) - Added H5VL_VERSION macro that indicates the version of the VOL framework implemented by a version of the library. Currently, compatibility checking enforces that the 'version' field in the H5VL_class_t for a VOL connector must match the version of the VOL framework for the library when it is registered or dynamically loaded. (QAK - 2020/12/10) - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that were previously accepted. This option turns on file locking but ignores locking errors when the library detects that file locking has been disabled on a file system (useful on some HPC Lustre installations). The capitalization of BEST_EFFORT is mandatory. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add H5Pset/get_file_locking() API calls This change adds new API calls which can be used to set or get the file locking parameters. The single API call sets both the "use file locking" flag and the "ignore disabled file locking" flag. When opening a file multiple times without closing, the file MUST be opened with the same file locking settings. Opening a file with different file locking settings will fail (this is similar to the behavior of H5Pset_fclose_degree()). See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Added two new API routines for tracking library memory use: H5get_alloc_stats() and H5get_free_list_sizes(). (QAK - 2020/03/25) - Add Mirror VFD Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote machine. Must be used in conjunction with the Splitter VFD. (JOS - 2020/03/13, TBD) - Add Splitter VFD Maintain separate R/W and W/O channels for "concurrent" file writes to two files using a single HDF5 file handle. (JOS - 2020/03/13, TBD) C++ Library: ------------ - Add wrappers for H5Pset/get_file_locking() API calls FileAccPropList::setFileLocking() FileAccPropList::getFileLocking() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Java Library: ------------- - Added new H5S functions. H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, H5Sselect_intersect_block, H5Sselect_project_intersection, H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select wrapper functions added. (ADB - 2020/10/27, HDFFV-10868) - Add wrappers for H5Pset/get_file_locking() API calls H5Pset_file_locking() H5Pget_use_file_locking() H5Pget_ignore_disabled_file_locking() Unlike the C++ and Fortran wrappers, there are separate getters for the two file locking settings, each of which returns a boolean value. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (ADB - 2020/07/30, HDFFV-11092) Tools: ------ - h5repack added help text for user-defined filters. Added help text line that states the valid values of the filter flag for user-defined filters; filter_flag: 1 is OPTIONAL or 0 is MANDATORY (ADB - 2021/01/14, HDFFV-11099) - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2020/08/05, HDFFV-9984) Support for new platforms, languages and compilers ================================================== - Added macOS 11.2 Big Sur Bug Fixes since HDF5-1.12.0 release =================================== Library ------- - Fixed CVE-2018-14460 The tool h5repack produced a segfault when the rank in dataspace message was corrupted, causing invalid read while decoding the dimension sizes. The problem was fixed by ensuring that decoding the dimension sizes and max values will not go beyong the end of the buffer. (BMR - 2021/05/12, HDFFV-11223) - Fixed CVE-2019-9151 h5repack generated a segfault when an invalid memory read occurred on a corrupted file. The issue is now fixed. h5repack produces an error instead of segfault. (BMR - 2021/05/04, HDFFV-10718) - Fixed CVE-2018-11206 The tool h5dump produced a segfault when the size of a fill value message was corrupted and caused a buffer overflow. The problem was fixed by verifying the fill value's size against the buffer size before attempting to access the buffer. (BMR - 2021/03/15, HDFFV-10480) - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) The tool h5dump produced a segfault when the storage size message was corrupted and caused a buffer overflow. The problem was fixed by verifying the storage size against the buffer size before attempting to access the buffer. (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) - Remove underscores on header file guards Header file guards used a variety of underscores at the beginning of the define. Removed all leading (some trailing) underscores from header file guards. (ADB - 2021/03/03, #361) - Fixed issue with MPI communicator and info object not being copied into new FAPL retrieved from H5F_get_access_plist Added logic to copy the MPI communicator and info object into the output FAPL. MPI communicator is retrieved from the VFD, while the MPI info object is retrieved from the file's original FAPL. (JTH - 2021/02/15, HDFFV-11109) - Fixed problems with vlens and refs inside compound using H5VLget_file_type() Modified library to properly ref count H5VL_object_t structs and only consider file vlen and reference types to be equal if their files are the same. (NAF - 2021/01/22) - Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. (QAK - 2020/09/02) - Avoid setting up complex MPI types with 0-length vectors, which some MPI implementations don't handle well. (In particular, IBM SpectrumScale MPI on the Summit system at ORNL) (QAK - 2020/08/21) - Fixed use-of-uninitialized-value error Appropriate initialization of local structs was added to remove the use-of-uninitialized-value errors reported by MemorySanitizer. (BMR - 2020/8/13, HDFFV-11101) - Creation of dataset with optional filter When the combination of type, space, etc doesn't work for filter and the filter is optional, it was supposed to be skipped but it was not skipped and the creation failed. A fix is applied to allow the creation of a dataset in such situation, as specified in the user documentation. (BMR - 2020/8/13, HDFFV-10933) - Explicitly declared dlopen to use RTLD_LOCAL dlopen documentation states that if neither RTLD_GLOBAL nor RTLD_LOCAL are specified, then the default behavior is unspecified. The default on linux is usually RTLD_LOCAL while macos will default to RTLD_GLOBAL. (ADB - 2020/08/12, HDFFV-11127) - Fixed issues CVE-2018-13870 and CVE-2018-13869 When a buffer overflow occurred because a name length was corrupted and became very large, h5dump crashed on memory access violation. A check for reading past the end of the buffer was added to multiple locations to prevent the crashes and h5dump now simply fails with an error message when this error condition occurs. (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. H5S_NO_CLASS is an internal class value that should not have been exposed via a public API call. In debug builds of the library, this can cause assert() function to trip. In non-debug builds, it will produce normal library errors. The new library behavior is for H5Sset_extent_none() to convert the dataspace into one of type H5S_NULL, which is better handled by the library and easier for developers to reason about. (DER - 2020/07/27, HDFFV-11027) - Fixed the segmentation fault when reading attributes with multiple threads It was reported that the reading of attributes with variable length string datatype will crash with segmentation fault particularly when the number of threads is high (>16 threads). The problem was due to the file pointer that was set in the variable length string datatype for the attribute. That file pointer was already closed when the attribute was accessed. The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. (VC - 2020/07/13, HDFFV-11080) - Fixed CVE-2018-17435 The tool h52gif produced a segfault when the size of an attribute message was corrupted and caused a buffer overflow. The problem was fixed by verifying the attribute message's size against the buffer size before accessing the buffer. h52gif was also fixed to display the failure instead of silently exiting after the segfault was eliminated. (BMR - 2020/6/19, HDFFV-10591) - Reduce overhead for H5open(), which is involved in public symbols like H5T_NATIVE_INT, etc. (QAK - 2020/06/18) - Cache last ID looked up for an ID type (dataset, datatype, file, etc), improving performance when accessing the same ID repeatedly. (QAK - 2020/06/11) - Streamline I/O to a single element, improving performance for record appends to chunked datasets. (QAK - 2020/06/11) - Remove redundant tagging of metadata cache entries for some chunked dataset operations, slightly improving performance for chunked datasets. (QAK - 2020/06/10) - Better detect selections with the same shape, improving performance for some uses of H5DOappend (and other situations). (QAK - 2020/06/07) - Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. (QAK - 2020/05/07) Java Library ------------ - JNI utility function does not handle new references. The JNI utility function for converting reference data to string did not use the new APIs. In addition to fixing that function, added new java tests for using the new APIs. (ADB - 2021/02/16, HDFFV-11212) - The H5FArray.java class, in which virtually the entire execution time is spent using the HDFNativeData method that converts from an array of bytes to an array of the destination Java type. 1. Convert the entire byte array into a 1-d array of the desired type, rather than performing 1 conversion per row; 2. Use the Java Arrays method copyOfRange to grab the section of the array from (1) that is desired to be inserted into the destination array. (PGT,ADB - 2020/12/29, HDFFV-10865) Configuration ------------- - Refactor CMake configure for Fortran The Fortran configure tests for KINDs reused a single output file that was read to form the Integer and Real Kinds defines. However, if config was run more then once, the CMake completed variable prevented the tests from executing again and the last value saved in the file was used to create the define. Creating separate files for each KIND solved the issue. In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION correctly for a zero value. This was fixed by supplying the required defines. In addition it was moved from the Fortran specific HDF5UseFortran.camke file to the C centric ConfigureChecks.cmake file. (ADB - 2021/06/03) - Move emscripten flag to compile flags The emscripten flag, -O0, was removed from target_link_libraries command to the correct target_compile_options command. (ADB - 2021/04/26 HDFFV-11083) - Remove arbitrary warning flag groups from CMake builds The arbitrary groups were created to reduce the quantity of warnings being reported that overwhelmed testing report systems. Considerable work has been accomplished to reduce the warning count and these arbitrary groups are no longer needed. Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON. Visual Studio warnings C4100, C4706, and C4127 have been moved to developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. (ADB - 2021/03/22, HDFFV-11228) - Reclassify CMake messages, to allow new modes and --log-level option CMake message commands have a mode argument. By default, STATUS mode was chosen for any non-error message. CMake version 3.15 added additional modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode of STATUS were reviewed and most were reclassified as VERBOSE. The new mode was protected by a check for a CMake version of at least 3.15. If CMake version 3.17 or above is used, the user can use the command line option of "--log-level" to further restrict which message commands are displayed. (ADB - 2021/01/11, HDFFV-11144) - Fixes Autotools determination of the stat struct having an st_blocks field A missing parenthesis in an autoconf macro prevented building the test code used to determine if the stat struct contains the st_blocks field. Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define found in H5pubconf.h will be defined correctly on both the Autotools and CMake. This #define is only used in the tests and does not affect the HDF5 C library. (DER - 2021/01/07, HDFFV-11201) - Add missing ENV variable line to hdfoptions.cmake file Using the build options to use system SZIP/ZLIB libraries need to also specify the library root directory. Setting the {library}_ROOT ENV variable was added to the hdfoptions.cmake file. (ADB - 2020/10/19 HDFFV-11108) - Fixed removal of Java lib files by "make uninstall" "make uninstall" was not removing 5 Java files from the lib directory. (LRK - 2020/08/24, HDFFV-10811) - Stopped addition of szip header and include directory path for incompatible libsz szlib.h is the same for both 32-bit and 64-bit szip, and the header file and its path were added to the HDF5 binary even though the configure check of a function in libsz later failed and szip compression was not enabled. The header file and include path are now added only when the libsz function passes the configure check. (LRK - 2020/08/17, HDFFV-10830) Tools ----- - Changed how h5dump and h5ls identify long double. Long double support is not consistent across platforms. Tools will always identify long double as 128-bit [little/big]-endian float nn-bit precision. New test file created for datasets with attributes for float, double and long double. In addition any unknown integer or float datatype will now also show the number of bits for precision. These files are also used in the java tests. (ADB - 2021/03/24, HDFFV-11229,HDFFV-11113) - Fixed tools argument parsing. Tools parsing used the length of the option from the long array to match the option from the command line. This incorrectly matched a shorter long name option that happened to be a subset of another long option. Changed to match whole names. (ADB - 2021/01/19, HDFFV-11106) - Fixed a bug with h5repack ignoring the "-q" and "-z" command-line options h5repack uses the -q and -z command-line options to specify the indexing options for objects in the file when repacking. Previously, h5repack would simply ignore any setting from these options. This has been fixed so that h5repack will correctly interpret the following settings: -q "name" : Sort objects by name order -q "creation_order" : Sort objects by link creation order -z "ascending" : Sort objects by ascending name/link creation order -z "descending" : Sort objects by descending name/link creation order (JTH - 2020/04/16, HDFFV-11030) - The tools library was updated by standardizing the error stack process. General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); ... process the command-line (check for error-stack enable) ... h5tools_error_report(); ... (do work) ... h5diff_exit(ret); (ADB - 2020/07/20, HDFFV-11066) - h5diff fixed a command line parsing error. h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. (ADB - 2020/07/20, HDFFV-10897) - h5diff added a command line option to ignore attributes. h5diff would ignore all objects with a supplied path if the exclude-path argument is used. Adding the exclude-attribute argument will only exclude attributes, with the supplied path, from comparison. (ADB - 2020/07/20, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names (ADB - 2020/07/20, HDFFV-1005) Fortran API ----------- - Fixed configure issue when building HDF5 with NAG Fortran 7.0. HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033) High-Level Library ------------------ - Eliminated unnecessary code in H5DOappend(), improving its performance. (QAK - 2020/06/05) Fortran High-Level APIs ----------------------- - Documentation ------------- - Updated doxygen comments with changes for release (ADB - 2021/05/03) - Fixed the dimension size description in the layout message table of the file format specification section IV.A.2.i. The layout message table described the dimension sizes starting from Dimension 0 to Dimension #n. This was incorrect because it would mean the rank is n+1. The dimension size entries were changed to starting from Dimension 1 to Dimension #n. (VC – 2020/06/09, HDFFV-11079) F90 APIs -------- - Fixed parallel make build failure due to a missing H5forkit dependency. (MSB, 2021/03/31, HDFFV-11232) C++ APIs -------- - Added DataSet::operator= Some compilers complain if the copy constructor is given explicitly but the assignment operator is implicitly set to default. (LN - 2021/05/19) Testing ------- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. (LRK - 2020/07/02, HDFFV-11063) Supported Platforms =================== Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) Version 4.9.3, 5.2.0, 7.1.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 17.0.0.098 Build 20160721 MPICH 3.2, 3.3 Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) Visual Studio 2017 w/ Intel Fortran 19 (cmake) Visual Studio 2019 w/ Intel Fortran 19 (cmake) Visual Studio 2019 w/ MSMPI 10.1 (cmake) MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) 64-bit gfortran GNU Fortran (GCC) 6.3.0 (bear) Intel icc/icpc/ifort version 19.0.4 MacOS Big Sur 11.2 Apple clang version 12.0.5 (clang-1205.0.22.9) gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 Intel icc/icpc (ICC) 2021.1 Beta 20201112 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 <blank> = testing incomplete on this feature or platform Platform C F90/ F90 C++ zlib SZIP parallel F2003 parallel Windows 10 y y/y n y y y Windows 10 x64 y y/y n y y y MacOS High Sierra 10.13.6 64-bit n y/y n y y y MacOS Big Sur 11.2 64-bit n y/y n y y y CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y CentOS 6.7 Linux 2.6.32 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 3.10.0-1127.10.1.1.ch6.ppc64le n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Windows 10 y y y y Windows 10 x64 y y y y MacOS High Sierra 10.13.6 64-bit y n y y MacOS Big Sur 11.2 64-bit y n y y CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y CentOS 6.7 Linux 2.6.32 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 3.10.0-1127.10.1.1.ch6.ppc64le 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: (platypus) Version 4.4.7 20120313 Version 4.9.3, 5.3.0, 6.2.0 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 19.10-0 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) GCC Version 7.1.0 OpenMPI 3.0.0-GCC-7.2.0-2.29 Intel(R) C (icc) and C++ (icpc) compilers Version 17.0.0.098 Build 20160721 with NAG Fortran Compiler Release 6.1(Tozai) PGI C (pgcc), C++ (pgc++), Fortran (pgf90) compilers: Version 18.4, 19.4 MPICH 3.3 OpenMPI 2.1.5, 3.1.3, 4.0.0 Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3 #1 SMP x86_64 GNU/Linux (moohan) Linux-3.10.0-1127.0.0.1chaos openmpi/4.0.0 #1 SMP x86_64 GNU/Linux clang/6.0.0, 11.0.1 (quartz) gcc/7.3.0, 8.3.0 intel/16.0.4, 18.0.2, 19.0.4 Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang/7.1.0, ibm-11.0.1 (lassen) gcc/4.9.3, 8.3.1 xl/2019.02.07, 2021.03.11 Linux-4.12.14-150.52-default cray-mpich/7.7.10 #1 SMP x86_64 GNU/Linux gcc/8.3.0 (cori) intel/19.0.3 Linux-4.4.180-94.107-default cray-mpich/7.7.16 # 1SMP x86_64 GNU/Linux gcc/7.3.0, 8.3.0, 10.2.0 (mutrino) intel/17.0.4, 18.0.5, 19.1.3 Linux-3.10.0- spectrum-mpi/rolling-release 1127.10.1.1chaos.ch6.ppc64le clang/7.1.0, 11.0.1 #1 SMP ppc64le GNU/Linux gcc/4.9.3,8.3.1 (ray) xl/2019.08.20,2021.03.11 Fedora33 5.11.18-200.fc33.x86_64 #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1) GNU Fortran (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1) clang version 11.0.0 (Fedora 11.0.0-2.fc33) (cmake and autotools) Ubuntu20.04 5.8.0-53-generic-x86_64 #60~20.04-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 9.3.0-17ubuntu1 GNU Fortran (GCC) 9.3.0-17ubuntu1 clang version 10.0.0-4ubuntu1 (cmake and autotools) Ubuntu20.10 5.8.0-53-generic-x86_64 #60-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1 GNU Fortran (GCC) 10.2.0-13ubuntu1 Ubuntu clang version 11.0.0-2 (cmake and autotools) SUSE15sp2 5.3.18-22-default #1 SMP x86_64 GNU/Linux GNU gcc (SUSE Linux) 7.5.0 GNU Fortran (SUSE Linux) 7.5.0 clang version 7.0.1 (tags/RELEASE_701/final 349238) (cmake and autotools) 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 (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 Known Problems ============== testflushrefresh.sh will fail when run with "make check-passthrough-vol" on centos7, with 3 Errors/Segmentation faults. These will not occur when run with "make check". See https://github.com/HDFGroup/hdf5/issues/673 for details. The t_bigio test fails on several HPC platforms, generally by timeout with OpenMPI 4.0.0 or with this error from spectrum-mpi: *** on communicator MPI_COMM_WORLD *** MPI_ERR_COUNT: invalid count argument CMake files do not behave correctly with paths containing spaces. Do not use spaces in paths because the required escaping for handling spaces results in very complex and fragile build files. ADB - 2019/05/07 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. CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. The subsetting option in ph5diff currently will fail and should be avoided. The subsetting option works correctly in serial h5diff. 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. CMake vs. Autotools installations ================================= While both build systems produce similar results, there are differences. Each system produces the same set of folders on linux (only CMake works on standard Windows); bin, include, lib and share. Autotools places the COPYING and RELEASE.txt file in the root folder, CMake places them in the share folder. The bin folder contains the tools and the build scripts. Additionally, CMake creates dynamic versions of the tools with the suffix "-shared". Autotools installs one set of tools depending on the "--enable-shared" configuration option. build scripts ------------- Autotools: h5c++, h5cc, h5fc CMake: h5c++, h5cc, h5hlc++, h5hlcc The include folder holds the header files and the fortran mod files. CMake places the fortran mod files into separate shared and static subfolders, while Autotools places one set of mod files into the include folder. Because CMake produces a tools library, the header files for tools will appear in the include folder. The lib folder contains the library files, and CMake adds the pkgconfig subfolder with the hdf5*.pc files used by the bin/build scripts created by the CMake build. CMake separates the C interface code from the fortran code by creating C-stub libraries for each Fortran library. In addition, only CMake installs the tools library. The names of the szip libraries are different between the build systems. The share folder will have the most differences because CMake builds include a number of CMake specific files for support of CMake's find_package and support for the HDF5 Examples CMake project.