HDF5 version 1.14.4-2 released on 2024-04-15 ================================================================================ INTRODUCTION ============ This document describes the differences between this release and the previous HDF5 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 each final release. Links to HDF5 documentation can be found on: https://portal.hdfgroup.org/documentation/ The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ Changes from release to release and new features in the HDF5-1.14.x release series can be found at: https://portal.hdfgroup.org/documentation/hdf5-docs/release_specific_info.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 HDF5-1.14.3 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Added configure options for enabling/disabling non-standard programming language features * Added a new configuration option that allows enabling or disabling of support for features that are extensions to programming languages, such as support for the _Float16 datatype: CMake: HDF5_ENABLE_NONSTANDARD_FEATURES (ON/OFF) (Default: ON) Autotools: --enable-nonstandard-features (yes/no) (Default: yes) When this option is enabled, configure time checks are still performed to ensure that a feature can be used properly, but these checks may not be sufficient when compiler support for a feature is incomplete or broken, resulting in library build failures. When set to OFF/no, this option provides a way to disable support for all non-standard features to avoid these issues. Individual features can still be re-enabled with their respective configuration options. * Added a new configuration option that allows enabling or disabling of support for the _Float16 C datatype: CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16 (ON/OFF) (Default: ON) Autotools: --enable-nonstandard-feature-float16 (yes/no) (Default: yes) While support for the _Float16 C datatype can generally be detected and used properly, some compilers have incomplete support for the datatype and will pass configure time checks while still failing to build HDF5. This option provides a way to disable support for the _Float16 datatype when the compiler doesn't have the proper support for it. - Deprecate bin/cmakehdf5 script With the improvements made in CMake since version 3.23 and the addition of CMake preset files, this script is no longer necessary. See INSTALL_CMake.txt file, Section X: Using CMakePresets.json for compiling - Overhauled LFS support checks In 2024, we can assume that Large File Support (LFS) exists on all systems we support, though it may require flags to enable it, particularly when building 32-bit binaries. The HDF5 source does not use any of the 64-bit specific API calls (e.g., ftello64) or explicit 64-bit offsets via off64_t. Autotools * We now use AC_SYS_LARGEFILE to determine how to support LFS. We previously used a custom m4 script for this. CMake * The HDF_ENABLE_LARGE_FILE option (advanced) has been removed * We no longer run a test program to determine if LFS works, which will help with cross-compiling * On Linux we now unilaterally set -D_LARGEFILE_SOURCE and -D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since those options do nothing on 64-bit systems, this seems safe and covers all our bases. We don't set -D_LARGEFILE64_SOURCE since we don't use any of the POSIX 64-bit specific API calls like ftello64, as noted above. * We didn't test for LFS support on non-Linux platforms. We've added comments for how LFS should probably be supported on AIX and Solaris, which seem to be alive, though uncommon. PRs would be appreciated if anyone wishes to test this. This overhaul also fixes GitHub #2395, which points out that the LFS flags used when building with CMake differ based on whether CMake has been run before. The LFS check program that caused this problem no longer exists. - The CMake HDF5_ENABLE_DEBUG_H5B option has been removed This enabled some additional version-1 B-tree checks. These have been removed so the option is no longer necessary. This option was CMake-only and marked as advanced. - New option for building with static CRT in Windows The following option has been added: HDF5_BUILD_STATIC_CRT_LIBS "Build With Static Windows CRT Libraries" OFF Because our minimum CMake is 3.18, the macro to change runtime flags no longer works as CMake changed the default behavior in CMake 3.15. Fixes GitHub issue #3984 - Added support for the new MSVC preprocessor Microsoft added support for a new, standards-conformant preprocessor to MSVC, which can be enabled with the /Zc:preprocessor option. This preprocessor would trip over our HDopen() variadic function-like macro, which uses a feature that only works with the legacy preprocessor. ifdefs have been added that select the correct HDopen() form and allow building HDF5 with the /Zc:preprocessor option. The HDopen() macro is located in an internal header file and only affects building the HDF5 library from source. Fixes GitHub #2515 - Renamed HDF5_ENABLE_USING_MEMCHECKER to HDF5_USING_ANALYSIS_TOOL The HDF5_USING_ANALYSIS_TOOL is used to indicate to test macros that an analysis tool is being used and that the tests should not use the runTest.cmake macros and it's variations. The analysis tools, like valgrind, test the macro code instead of the program under test. HDF5_ENABLE_USING_MEMCHECKER is still used for controlling the HDF5 define, H5_USING_MEMCHECKER. - New option for building and naming tools in CMake The following option has been added: HDF5_BUILD_STATIC_TOOLS "Build Static Tools Not Shared Tools" OFF The default will build shared tools unless BUILD_SHARED_LIBS = OFF. Tools will no longer have "-shared" as only one set of tools will be created. - Incorporated HDF5 examples repository into HDF5 library. The HDF5Examples folder is equivalent to the hdf5-examples repository. This enables building and testing the examples during the library build process or after the library has been installed. Previously, the hdf5-examples archives were downloaded for packaging with the library. Now the examples can be built and tested without a packaged install of the library. However, to maintain the ability to use the HDF5Examples with an installed library, it is necessary to map the option names used by the library to those used by the examples. The typical pattern is: = HDF_BUILD_FORTRAN = ${HDF5_BUILD_FORTRAN} - Added new option for CMake to mark tests as SKIPPED. HDF5_DISABLE_TESTS_REGEX is a REGEX string that will be checked with test names and if there is a match then that test's property will be set to DISABLED. HDF5_DISABLE_TESTS_REGEX can be initialized on the command line: "-DHDF5_DISABLE_TESTS_REGEX:STRING=" See CMake documentation for regex-specification. - Added defaults to CMake for long double conversion checks HDF5 performs a couple of checks at build time to see if long double values can be converted correctly (IBM's Power architecture uses a special format for long doubles). These checks were performed using TRY_RUN, which is a problem when cross-compiling. These checks now use default values appropriate for most non-Power systems when cross-compiling. The cache values can be pre-set if necessary, which will preempt both the TRY_RUN and the default. Affected values: H5_LDOUBLE_TO_LONG_SPECIAL (default no) H5_LONG_TO_LDOUBLE_SPECIAL (default no) H5_LDOUBLE_TO_LLONG_ACCURATE (default yes) H5_LLONG_TO_LDOUBLE_CORRECT (default yes) H5_DISABLE_SOME_LDOUBLE_CONV (default no) Fixes GitHub #3585 Library: -------- - Relaxed behavior of H5Pset_page_buffer_size() when opening files This API call sets the size of a file's page buffer cache. This call was extremely strict about matching its parameters to the file strategy and page size used to create the file, requiring a separate open of the file to obtain these parameters. These requirements have been relaxed when using the fapl to open a previously-created file: * When opening a file that does not use the H5F_FSPACE_STRATEGY_PAGE strategy, the setting is ignored and the file will be opened, but without a page buffer cache. This was previously an error. * When opening a file that has a page size larger than the desired page buffer cache size, the page buffer cache size will be increased to the file's page size. This was previously an error. The behavior when creating a file using H5Pset_page_buffer_size() is unchanged. Fixes GitHub issue #3382 - Added support for _Float16 16-bit half-precision floating-point datatype Support for the _Float16 C datatype has been added on platforms where: - The _Float16 datatype and its associated macros (FLT16_MIN, FLT16_MAX, FLT16_EPSILON, etc.) are available - A simple test program that converts between the _Float16 datatype and other datatypes with casts can be successfully compiled and run at configure time. Some compilers appear to be buggy or feature-incomplete in this regard and will generate calls to compiler-internal functions for converting between the _Float16 datatype and other datatypes, but will not link these functions into the build, resulting in build failures. The following new macros have been added: H5_HAVE__FLOAT16 - This macro is defined in H5pubconf.h and will have the value 1 if support for the _Float16 datatype is available. It will not be defined otherwise. H5_SIZEOF__FLOAT16 - This macro is defined in H5pubconf.h and will have a value corresponding to the size of the _Float16 datatype, as computed by sizeof(). It will have the value 0 if support for the _Float16 datatype is not available. H5_HAVE_FABSF16 - This macro is defined in H5pubconf.h and will have the value 1 if the fabsf16 function is available for use. H5_LDOUBLE_TO_FLOAT16_CORRECT - This macro is defined in H5pubconf.h and will have the value 1 if the platform can correctly convert long double values to _Float16. Some compilers have issues with this. H5T_NATIVE_FLOAT16 - This macro maps to the ID of an HDF5 datatype representing the native C _Float16 datatype for the platform. If support for the _Float16 datatype is not available, the macro will map to H5I_INVALID_HID and should not be used. H5T_IEEE_F16BE - This macro maps to the ID of an HDF5 datatype representing a big-endian IEEE 754 16-bit floating-point datatype. This datatype is available regardless of whether _Float16 support is available or not. H5T_IEEE_F16LE - This macro maps to the ID of an HDF5 datatype representing a little-endian IEEE 754 16-bit floating-point datatype. This datatype is available regardless of whether _Float16 support is available or not. The following new hard datatype conversion paths have been added, but will only be used when _Float16 support is available: H5T_NATIVE_SCHAR <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_UCHAR <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_SHORT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_USHORT <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_INT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_UINT <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_LONG <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_ULONG <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_LLONG <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_ULLONG <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_FLOAT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_DOUBLE <-> H5T_NATIVE_FLOAT16 H5T_NATIVE_LDOUBLE <-> H5T_NATIVE_FLOAT16 The H5T_NATIVE_LDOUBLE -> H5T_NATIVE_FLOAT16 hard conversion path will only be available and used if H5_LDOUBLE_TO_FLOAT16_CORRECT has a value of 1. Otherwise, the conversion will be emulated in software by the library. Note that in the absence of any compiler flags for architecture-specific tuning, the generated code for datatype conversions with the _Float16 type may perform conversions by first promoting the type to float. Use of architecture-specific tuning compiler flags may instead allow for the generation of specialized instructions, such as AVX512-FP16 instructions, if available. - Made several improvements to the datatype conversion code * The datatype conversion code was refactored to use pointers to H5T_t datatype structures internally rather than IDs wrapping the pointers to those structures. These IDs are needed if an application-registered conversion function or conversion exception function are involved during the conversion process. For simplicity, the conversion code simply passed these IDs down and let the internal code unwrap the IDs as necessary when needing to access the wrapped H5T_t structures. However, this could cause a significant amount of repeated ID lookups for compound datatypes and other container-like datatypes. The code now passes down pointers to the datatype structures and only creates IDs to wrap those pointers as necessary. Quick testing showed an average ~3x to ~10x improvement in performance of conversions on container-like datatypes, depending on the complexity of the datatype. * A conversion "context" structure was added to hold information about the current conversion being performed. This allows conversions on container-like datatypes to be optimized better by skipping certain portions of the conversion process that remain relatively constant when multiple elements of the container-like datatype are being converted. * After refactoring the datatype conversion code to use pointers internally rather than IDs, several copies of datatypes that were made by higher levels of the library were able to be removed. The internal IDs that were previously registered to wrap those copied datatypes were also able to be removed. - Implemented optimized support for vector I/O in the Subfiling VFD Previously, the Subfiling VFD would handle vector I/O requests by breaking them down into individual I/O requests, one for each entry in the I/O vectors provided. This could result in poor I/O performance for features in HDF5 that utilize vector I/O, such as parallel I/O to filtered datasets. The Subfiling VFD now properly handles vector I/O requests in their entirety, resulting in fewer I/O calls, improved vector I/O performance and improved vector I/O memory efficiency. - Added support for in-place type conversion in most cases In-place type conversion allows the library to perform type conversion without an intermediate type conversion buffer. This can improve performance by allowing I/O in a single operation over the entire selection instead of being limited by the size of the intermediate buffer. Implemented for I/O on contiguous and chunked datasets when the selection is contiguous in memory and when the memory datatype is not smaller than the file datatype. - Changed selection I/O to be on by default when using the MPIO file driver - Added support for selection I/O in the MPIO file driver Previously, only vector I/O operations were supported. Support for selection I/O should improve performance and reduce memory uses in some cases. - Changed the error handling for a not found path in the find plugin process. While attempting to load a plugin the HDF5 library will fail if one of the directories in the plugin paths does not exist, even if there are more paths to check. Instead of exiting the function with an error, just logged the error and continue processing the list of paths to check. - Implemented support for temporary security credentials for the Read-Only S3 (ROS3) file driver. When using temporary security credentials, one also needs to specify a session/security token next to the access key id and secret access key. This token can be specified by the new API function H5Pset_fapl_ros3_token(). The API function H5Pget_fapl_ros3_token() can be used to retrieve the currently set token. - Added a Subfiling VFD configuration file prefix environment variable The Subfiling VFD now checks for values set in a new environment variable "H5FD_SUBFILING_CONFIG_FILE_PREFIX" to determine if the application has specified a pathname prefix to apply to the file path for its configuration file. For example, this can be useful for cases where the application wishes to write subfiles to a machine's node-local storage while placing the subfiling configuration file on a file system readable by all machine nodes. - Added H5Pset_selection_io(), H5Pget_selection_io(), and H5Pget_no_selection_io_cause() API functions to manage the selection I/O feature. This can be used to enable collective I/O with type conversion, or it can be used with custom VFDs that support vector or selection I/O. - Added H5Pset_modify_write_buf() and H5Pget_modify_write_buf() API functions to allow the library to modify the contents of write buffers, in order to avoid malloc/memcpy. Currently only used for type conversion with selection I/O. Parallel Library: ----------------- - Fortran Library: ---------------- - Added Fortran H5E APIs: h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f, h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f, h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature) - Added API support for Fortran MPI_F08 module definitions: Adds support for MPI's MPI_F08 module datatypes: type(MPI_COMM) and type(MPI_INFO) for HDF5 APIs: H5PSET_FAPL_MPIO_F, H5PGET_FAPL_MPIO_F, H5PSET_MPI_PARAMS_F, H5PGET_MPI_PARAMS_F Ref. #3951 - Added Fortran APIs: H5FGET_INTENT_F, H5SSEL_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F, H5SSEL_ITER_CLOSE_F, H5S_mp_H5SSEL_ITER_RESET_F - Added Fortran Parameters: H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F - Added Fortran Parameters: H5S_BLOCK_F and H5S_PLIST_F - The configuration definitions file, H5config_f.inc, is now installed and the HDF5 version number has been added to it. - Added Fortran APIs: h5fdelete_f - Added Fortran APIs: h5vlnative_addr_to_token_f and h5vlnative_token_to_address_f C++ Library: ------------ - Java Library: ------------- - Tools: ------ - High-Level APIs: ---------------- - C Packet Table API: ------------------- - Internal header file: --------------------- - Documentation: -------------- - Support for new platforms, languages and compilers ================================================== - Bug Fixes since HDF5-1.14.3 release =================================== Configuration: ------------- - Fix Autotools -Werror cleanup The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc. so configure checks don't trip over warnings generated by configure check programs. The sed line originally only scrubbed -Werror but not -Werror=something, which would cause errors when the '=something' was left behind in CFLAGS. The sed line has been updated to handle -Werror=something lines. Fixes one issue raised in #3872 Library ------- - Fixed many (future) CVE issues A partner organization corrected many potential security issues, which were fixed and reported to us before submission to MITRE. These do not have formal CVE issues assigned to them yet, so the numbers assigned here are just placeholders. We will update the HDF5 1.14 CVE list (link below) when official MITRE CVE tracking numbers are assigned. These CVE issues are generally of the same form as other reported HDF5 CVE issues, and rely on the library failing while attempting to read a malformed file. Most of them cause the library to segfault and will probably be assigned "medium (~5/10)" scores by NIST, like the other HDF5 CVE issues. The issues that were reported to us have all been fixed in this release, so HDF5 will continue to have no unfixed public CVE issues. NOTE: HDF5 versions earlier than 1.14.4 should be considered vulnerable to these issues and users should upgrade to 1.14.4 as soon as possible. Note that it's possible to build the 1.14 library with HDF5 1.8, 1.10, etc. API bindings for people who wish to enjoy the benefits of a more secure library but don't want to upgrade to the latest API. We will not be bringing the CVE fixes to earlier versions of the library (they are no longer supported). LIST OF CVE ISSUES FIXED IN THIS RELEASE: * CVE-2024-0116-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5D__scatter_mem resulting in causing denial of service or potential code execution * CVE-2024-0112-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5S__point_deserialize resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2024-0111-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5T__conv_struct_opt resulting in causing denial of service or potential code execution * CVE-2023-1208-002 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5O__mtime_new_encode resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1208-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5O__layout_encode resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1207-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5O__dtype_encode_helper causing denial of service or potential code execution * CVE-2023-1205-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5VM_array_fill resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1202-002 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5T__get_native_type resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1202-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5T__ref_mem_setnull resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1130-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5T_copy_reopen resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1125-001 HDF5 versions <= 1.14.3 contain a heap buffer overflow in H5Z__nbit_decompress_one_byte caused by the earlier use of an initialized pointer. This may result in Denial of Service or potential code execution * CVE-2023-1114-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5HG_read resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1113-002 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5F_addr_decode_len resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1113-001 HDF5 versions <= 1.14.3 contain a heap buffer overflow caused by the unsafe use of strdup in H5MM_xstrdup, resulting in denial of service or potential code execution * CVE-2023-1108-001 HDF5 versions <= 1.14.3 contain a out-of-bounds read operation in H5FL_arr_malloc resulting in denial of service or potential code execution * CVE-2023-1104-004 HDF5 versions <= 1.14.3 contain a out-of-bounds read operation in H5T_close_real resulting in denial of service or potential code execution * CVE-2023-1104-003 HDF5 library versions <=1.14.3 contain a heap buffer overflow flaw in the function H5HL__fl_deserialize resulting in denial of service or potential code execution * CVE-2023-1104-002 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5HL__fl_deserialize resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1104-001 HDF5 library versions <=1.14.3 contains a stack overflow in the function H5E_printf_stack resulting in denial of service or potential code execution * CVE-2023-1023-001 HDF5 library versions <=1.14.3 heap buffer overflow in H5VM_memcpyvv which may result in denial of service or code execution * CVE-2023-1019-001 HDF5 library versions <=1.14.3 contain a stack buffer overflow in H5VM_memcpyvv resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1018-001 HDF5 library versions <=1.14.3 contain a memory corruption in H5A__close resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1017-002 HDF5 library versions <=1.14.3 may use an uninitialized value H5A__attr_release_table resulting in denial of service * CVE-2023-1017-001 HDF5 library versions <=1.14.3 may attempt to dereference uninitialized values in h5tools_str_sprint, which will lead to denial of service * CVE-2023-1013-004 HDF5 versions <= 1.13.3 contain a stack buffer overflow in H5HG_read resulting in denial of service or potential code execution * CVE-2023-1013-003 HDF5 library versions <=1.14.3 contain a buffer overrun in H5Z__filter_fletcher32 resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1013-002 HDF5 library versions <=1.14.3 contain a buffer overrun in H5O__linfo_decode resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1013-001 HDF5 library versions <=1.14.3 contain a buffer overrun in H5Z__filter_scaleoffset resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1012-001 HDF5 library versions <=1.14.3 contain a stack buffer overflow in H5R__decode_heap resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1010-001 HDF5 library versions <=1.14.3 contain a stack buffer overflow in H5FL_arr_malloc resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1009-001 HDF5 library versions <=1.14.3 contain a stack buffer overflow in H5FL_arr_malloc resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1006-004 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5A__attr_release_table resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1006-003 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5T__bit_find resulting in the corruption of the instruction pointer and causing denial of service or potential code execution. * CVE-2023-1006-002 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5HG_read resulting in the corruption of the instruction pointer and causing denial of service or potential code execution * CVE-2023-1006-001 HDF5 library versions <=1.14.3 contain a heap buffer overflow in H5HG__cache_heap_deserialize resulting in the corruption of the instruction pointer and causing denial of service or potential code execution FULL OFFICIAL HDF5 CVE list (from mitre.org): https://cve.mitre.org/cgi-bin/cvekey.cgi?keyword=HDF5 1.14.x CVE tracking list: https://github.com/HDFGroup/hdf5/blob/hdf5_1_14/CVE_list_1_14.md HDF5 CVE regression test suite (includes proof-of-concept files): https://github.com/HDFGroup/cve_hdf5 - Fixed a divide-by-zero issue when a corrupt file sets the page size to 0 If a corrupt file sets the page buffer size in the superblock to zero, the library could attempt to divide by zero when allocating space in the file. The library now checks for valid page buffer sizes when reading the superblock message. Fixes oss-fuzz issue 58762 - Fixed a bug when using array datatypes with certain parent types Array datatype conversion would never use a background buffer, even if the array's parent type (what the array is an array of) required a background buffer for conversion. This resulted in crashes in some cases when using an array of compound, variable length, or reference datatypes. Array types now use a background buffer if needed by the parent type. - Fixed potential buffer read overflows in H5PB_read H5PB_read previously did not account for the fact that the size of the read it's performing could overflow the page buffer pointer, depending on the calculated offset for the read. This has been fixed by adjusting the size of the read if it's determined that it would overflow the page. - Fixed CVE-2017-17507 This CVE was previously declared fixed, but later testing with a static build of HDF5 showed that it was not fixed. When parsing a malformed (fuzzed) compound type containing variable-length string members, the library could produce a segmentation fault, crashing the library. This was fixed after GitHub PR #4234 Fixes GitHub issue #3446 - Fixed a cache assert with very large metadata objects If the library tries to load a metadata object that is above a certain size, this would trip an assert in debug builds. This could happen if you create a very large number of links in an old-style group that uses local heaps. There is no need for this assert. The library's metadata cache can handle large objects. The assert has been removed. Fixes GitHub #3762 - Fixed an issue with the Subfiling VFD and multiple opens of a file An issue with the way the Subfiling VFD handles multiple opens of the same file caused the file structures for the extra opens to occasionally get mapped to an incorrect subfiling context object. The VFD now correctly maps the file structures for additional opens of an already open file to the same context object. - Fixed a bug that causes the library to incorrectly identify the endian-ness of 16-bit and smaller C floating-point datatypes When detecting the endian-ness of an in-memory C floating-point datatype, the library previously always assumed that the type was at least 32 bits in size. This resulted in invalid memory accesses and would usually cause the library to identify the datatype as having an endian-ness of H5T_ORDER_VAX. This has now been fixed. - Fixed a bug that causes an invalid memory access issue when converting 16-bit floating-point values to integers with the library's software conversion function The H5T__conv_f_i function previously always assumed that floating-point values were at least 32 bits in size and would access invalid memory when attempting to convert 16-bit floating-point values to integers. To fix this, parts of the H5T__conv_f_i function had to be rewritten, which also resulted in a significant speedup when converting floating-point values to integers where the library does not have a hard conversion path. This is the case for any floating-point values with a datatype not represented by H5T_NATIVE_FLOAT16 (if _Float16 is supported), H5T_NATIVE_FLOAT, H5T_NATIVE_DOUBLE or H5T_NATIVE_LDOUBLE. - Fixed a bug that can cause incorrect data when overflows occur while converting integer values to floating-point values with the library's software conversion function The H5T__conv_i_f function had a bug which previously caused it to return incorrect data when an overflow occurs and an application's conversion exception callback function decides not to handle the overflow. Rather than return positive infinity, the library would return truncated data. This has now been fixed. - Corrected H5Soffset_simple() when offset is NULL The reference manual states that the offset parameter of H5Soffset_simple() can be set to NULL to reset the offset of a simple dataspace to 0. This has never been true, and passing NULL was regarded as an error. The library will now accept NULL for the offset parameter and will correctly set the offset to zero. Fixes HDFFV-9299 - Fixed an issue where the Subfiling VFD's context object cache could grow too large The Subfiling VFD keeps a cache of its internal context objects to speed up access to a context object for a particular file, as well as access to that object across multiple opens of the same file. However, opening a large amount of files with the Subfiling VFD over the course of an application's lifetime could cause this cache to grow too large and result in the application running out of available MPI communicator objects. On file close, the Subfiling VFD now simply evicts context objects out of its cache and frees them. It is assumed that multiple opens of a file will be a less common use case for the Subfiling VFD, but this can be revisited if it proves to be an issue for performance. - Fixed error when overwriting certain nested variable length types Previously, when using a datatype that included a variable length type within a compound or array within another variable length type, and overwriting data with a shorter (top level) variable length sequence, an error could occur. This has been fixed. - Take user block into account in H5Dchunk_iter() and H5Dget_chunk_info() The address reported by the following functions did not correctly take the user block into account: * H5Dchunk_iter() <-- addr passed to callback * H5Dget_chunk_info() <-- addr parameter * H5Dget_chunk_info_by_coord() <-- addr parameter This means that these functions reported logical HDF5 file addresses, which would only be equal to the physical addresses when there is no user block prepended to the HDF5 file. This is unfortunate, as the primary use of these functions is to get physical addresses in order to directly access the chunks. The listed functions now correctly take the user block into account, so they will emit physical addresses that can be used to directly access the chunks. Fixes #3003 - Fixed asserts raised by large values of H5Pset_est_link_info() parameters If large values for est_num_entries and/or est_name_len were passed to H5Pset_est_link_info(), the library would attempt to create an object header NIL message to reserve enough space to hold the links in compact form (i.e., concatenated), which could exceed allowable object header message size limits and trip asserts in the library. This bug only occurred when using the HDF5 1.8 file format or later and required the product of the two values to be ~64k more than the size of any links written to the group, which would cause the library to write out a too-large NIL spacer message to reserve the space for the unwritten links. The library now inspects the phase change values to see if the dataset is likely to be compact and checks the size to ensure any NIL spacer messages won't be larger than the library allows. Fixes GitHub #1632 - Fixed a bug where H5Tset_fields does not account for any offset set for a floating-point datatype when determining if values set for spos, epos, esize, mpos and msize make sense for the datatype Previously, H5Tset_fields did not take datatype offsets into account when determining if the values set make sense for the datatype. This would cause the function to fail when the precision for a datatype is correctly set such that the offset bits are not included. This has now been fixed. - Fixed H5Fget_access_plist so that it returns the file locking settings for a file When H5Fget_access_plist (and the internal H5F_get_access_plist) is called on a file, the returned File Access Property List has the library's default file locking settings rather than any settings set for the file. This causes two problems: - Opening an HDF5 file through an external link using H5Gopen, H5Dopen, etc. with H5P_DEFAULT for the Dataset/Group/etc. Access Property List will cause the external file to be opened with the library's default file locking settings rather than inheriting them from the parent file. This can be surprising when a file is opened with file locking disabled, but its external files are opened with file locking enabled. - An application cannot make use of the H5Pset_elink_fapl function to match file locking settings between an external file and its parent file without knowing the correct setting ahead of time, as calling H5Fget_access_plist on the parent file will not return the correct settings. This has been fixed by copying a file's file locking settings into the newly-created File Access Property List in H5F_get_access_plist. This fix partially addresses GitHub issue #4011 - Memory usage growth issue Starting with the HDF5 1.12.1 release, an issue (GitHub issue #1256) was observed where running a simple program that has a loop of opening a file, reading from an object with a variable-length datatype and then closing the file would result in the process fairly quickly running out of memory. Upon further investigation, it was determined that this memory was being kept around in the library's datatype conversion pathway cache that is used to speed up datatype conversions which are repeatedly used within an HDF5 application's lifecycle. For conversions involving variable-length or reference datatypes, each of these cached pathway entries keeps a reference to its associated file for later use. Since the file was being closed and reopened on each loop iteration, and since the library compares for equality between instances of opened files (rather than equality of the actual files) when determining if it can reuse a cached conversion pathway, it was determining that no cached conversion pathways could be reused and was creating a new cache entry on each loop iteration during I/O. This would lead to constant growth of that cache and the memory it consumed, as well as constant growth of the memory consumed by each cached entry for the reference to its associated file. To fix this issue, the library now removes any cached datatype conversion path entries for variable-length or reference datatypes associated with a particular file when that file is closed. Fixes GitHub #1256 - Suppressed floating-point exceptions in H5T init code The floating-point datatype initialization code in H5Tinit_float.c could raise FE_INVALID exceptions while munging bits and performing comparisons that might involve NaN. This was not a problem when the initialization code was executed in H5detect at compile time (prior to 1.14.3), but now that the code is executed at library startup (1.14.3+), these exceptions can be caught by user code, as is the default in the NAG Fortran compiler. Starting in 1.14.4, we now suppress floating-point exceptions while initializing the floating-point types and clear FE_INVALID before restoring the original environment. Fixes GitHub #3831 - Fixed a file handle leak in the core VFD When opening a file with the core VFD and a file image, if the file already exists, the file check would leak the POSIX file handle. Fixes GitHub issue #635 - Dropped support for MPI-2 The MPI-2 supporting artifacts have been removed due to the cessation of MPI-2 maintenance and testing since version HDF5 1.12. - Fixed a segfault when using a user-defined conversion function between compound datatypes During type info initialization for compound datatype conversion, the library checked if the datatypes are subsets of one another in order to perform special conversion handling. This check uses information that is only defined if a library conversion function is in use. The library now skips this check for user-defined conversion functions. Fixes Github issue #3840 Java Library ------------ - Configuration ------------- - Changed default of 'Error on HDF5 doxygen warnings' DOXYGEN_WARN_AS_ERROR option. The default setting of DOXYGEN_WARN_AS_ERROR to 'FAIL_ON_WARNINGS' has been changed to 'NO'. It was decided that the setting was too aggressive and should be a user choice. The github actions and scripts have been updated to reflect this. * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: OFF) * --enable-doxygen-errors: enable/disable (Default: disable) - Removed an Autotools configure hack that causes problems on MacOS A sed line in configure.ac was added in the past to paper over some problems with older versions of the Autotools that would add incorrect linker flags. This hack is not needed with recent versions of the Autotools and the sed line errors on MacOS (though this was a silent error that didn't break the build) so the hack has been removed. Fixes GitHub issue #3843 - Fixed an issue where the h5tools_test_utils test program was being installed on the system for Autotools builds of HDF5 The h5tools_test_utils test program was mistakenly added to bin_PROGRAMS in its Makefile.am configuration file, causing the executable to be installed on the system. The executable is now added to noinst_PROGRAMS instead and will no longer be installed on the system for Autotools builds of HDF5. The CMake configuration code already avoids installing the executable on the system. Tools ----- - Renamed h5fuse.sh to h5fuse Addresses Discussion #3791 Performance ------------- - Fortran API ----------- - Fixed: HDF5 fails to compile with -Werror=lto-type-mismatch Removed the use of the offending C stub wrapper. Fixes GitHub issue #3987 High-Level Library ------------------ - Fixed a memory leak in H5LTopen_file_image with H5LT_FILE_IMAGE_DONT_COPY flag When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the internally-allocated udata structure gets leaked as the core file driver doesn't have a way to determine when or if it needs to call the "udata_free" callback. This has been fixed by freeing the udata structure when the "image_free" callback gets made during file close, where the file is holding the last reference to the udata structure. Fixes GitHub issue #827 Fortran High-Level APIs ----------------------- - Documentation ------------- - F90 APIs -------- - C++ APIs -------- - Testing ------- - Fixed a bug in the dt_arith test when H5_WANT_DCONV_EXCEPTION is not defined The dt_arith test program's test_particular_fp_integer sub-test tries to ensure that the library correctly raises a datatype conversion exception when converting a floating-point value to an integer overflows. However, this test would run even when H5_WANT_DCONV_EXCEPTION isn't defined, causing the test to fail due to the library not raising datatype conversion exceptions. This has now been fixed by not running the test when H5_WANT_DCONV_EXCEPTION is not defined. - Fixed a testing failure in testphdf5 on Cray machines On some Cray machines, what appears to be a bug in Cray MPICH was causing calls to H5Fis_accessible to create a 0-byte file with strange Unix permissions. This was causing an H5Fdelete file deletion test in the testphdf5 program to fail due to a just-deleted HDF5 file appearing to still be accessible on the file system. The issue in Cray MPICH has been worked around for the time being by resetting the MPI_Info object on the File Access Property List used to MPI_INFO_NULL before passing it to the H5Fis_accessible call. - A bug was fixed in the HDF5 API test random datatype generation code A bug in the random datatype generation code could cause test failures when trying to generate an enumeration datatype that has duplicated name/value pairs in it. This has now been fixed. - A bug was fixed in the HDF5 API test VOL connector registration checking code The HDF5 API test code checks to see if the VOL connector specified by the HDF5_VOL_CONNECTOR environment variable (if any) is registered with the library before attempting to run tests with it so that testing can be skipped and an error can be returned when a VOL connector fails to register successfully. Previously, this code didn't account for VOL connectors that specify extra configuration information in the HDF5_VOL_CONNECTOR environment variable and would incorrectly report that the specified VOL connector isn't registered due to including the configuration information as part of the VOL connector name being checked for registration status. This has now been fixed. - Fixed Fortran 2003 test with gfortran-v13, optimization levels O2,O3 Fixes failing Fortran 2003 test with gfortran, optimization level O2,O3 with -fdefault-real-16. Fixes GH #2928. Platforms Tested =================== - HDF5 supports the latest macOS versions, including the current and two preceding releases. As new major macOS versions become available, HDF5 will discontinue support for the oldest version and add the latest version to its list of compatible systems, along with the previous two releases. Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) (cmake and autotools) Linux 5.19.0-1023-aws GNU gcc, gfortran, g++ #24-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1 Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0 ifort (IFORT) 2021.9.0 20230302 (cmake and autotools) Linux 5.14.21-cray_shasta_c cray-mpich/8.1.23 #1 SMP x86_64 GNU/Linux cce/15.0.0 (frontier) gcc/12.2.0 (cmake) Linux 5.11.0-34-generic GNU gcc (GCC) 9.4.0-1ubuntu1 #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1 Ubuntu 20.04 Ubuntu clang version 10.0.0-4ubuntu1 Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0 ifort (IFORT) 2021.9.0 20230302 (cmake and autotools) Linux 4.14.0-115.35.1.1chaos aue/openmpi/4.1.4-arm-22.1.0.12 #1 SMP aarch64 GNU/Linux Arm C/C++/Fortran Compiler version 22.1 (stria) (based on LLVM 13.0.1) (cmake) Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang 12.0.1 (vortex) GCC 8.3.1 XL 2021.09.22 (cmake) Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 (lassen) GCC 8.3.1 XL 16.1.1.2, 2021.09.22, 2022.08.05 (cmake) Linux-4.12.14-197.99-default cray-mpich/7.7.14 #1 SMP x86_64 GNU/Linux cce 12.0.3 (theta) GCC 11.2.0 llvm 9.0 Intel 19.1.2 Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) (jelly/kituo/moohan) Version 4.9.3, Version 7.2.0, Version 8.3.0, Version 9.1.0, Version 10.2.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 17.0.0.098 Build 20160721 GNU C (gcc) and C++ (g++) 4.8.5 compilers with NAG Fortran Compiler Release 7.1(Hanzomon) Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers with NAG Fortran Compiler Release 7.1(Hanzomon) MPICH 3.1.4 compiled with GCC 4.9.3 MPICH 3.3 compiled with GCC 7.2.0 OpenMPI 3.1.3 compiled with GCC 7.2.0 and 4.1.2 compiled with GCC 9.1.0 PGI C, Fortran, C++ for 64-bit target on x86_64; Versions 18.4.0 and 19.10-0 NVIDIA nvc, nvfortran and nvc++ version 22.5-0 (autotools and cmake) Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 7.3.0, 8.1.0 Intel 19.0.4, 2022.2, oneapi.2022.2 Linux-3.10.0-1160.90.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (skybridge) Intel/19.1 (cmake) Linux-3.10.0-1160.90.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (attaway) Intel/19.1 (cmake) Linux-3.10.0-1160.90.1.1chaos openmpi-intel/4.1 #1 SMP x86_64 GNU/Linux Intel/19.1.2, 21.3.0 and 22.2.0 (chama) (cmake) macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 64-bit gfortran GNU Fortran (GCC) 5.2.0 (osx1011test) Intel icc/icpc/ifort version 16.0.2 Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: Centos6 Version 4.4.7 20120313 (platypus) Version 4.9.3, 5.3.0, 6.2.0 MPICH 3.1.4 compiled with GCC 4.9.3 PGI C, Fortran, C++ for 64-bit target on x86_64; Version 19.10-0 Windows 10 x64 Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2019 w/ Intel (C/C++ only - cmake) Visual Studio 2022 w/ clang 15.0.1 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2023 (cmake) Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) Known Problems ============== - When building with the NAG Fortran compiler using the Autotools and libtool 2.4.2 or earlier, the -shared flag will be missing '-Wl,', which will cause compilation to fail. This is due to a bug in libtool that was fixed in 2012 and released in 2.4.4 in 2014. - When the library detects and builds in support for the _Float16 datatype, an issue has been observed on at least one MacOS 14 system where the library fails to initialize due to not being able to detect the byte order of the _Float16 type (https://github.com/HDFGroup/hdf5/issues/4310): #5: H5Tinit_float.c line 308 in H5T__fix_order(): failed to detect byte order major: Datatype minor: Unable to initialize object If this issue is encountered, support for the _Float16 type can be disabled with a configuration option: CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16=OFF Autotools: --disable-nonstandard-feature-float16 - When HDF5 is compiled with NVHPC versions 23.5 - 23.9 (additional versions may also be applicable) and with -O2 (or higher) and -DNDEBUG, test failures occur in the following tests: H5PLUGIN-filter_plugin H5TEST-flush2 H5TEST-testhdf5-base MPI_TEST_t_filters_parallel Sporadic failures (even with lower -O levels): Java JUnit-TestH5Pfapl Java JUnit-TestH5D Also, NVHPC will fail to compile the test/tselect.c test file with a compiler error of 'use of undefined value' when the optimization level is -O2 or higher. This is confirmed to be a bug in the nvc compiler that has been fixed as of 23.11. If you are using an affected version of the NVidia compiler, the work-around is to set the optimization level to -O1. https://forums.developer.nvidia.com/t/hdf5-no-longer-compiles-with-nv-23-9/269045 - 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. - 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. - The subsetting option in ph5diff currently will fail and should be avoided. The subsetting option works correctly in serial h5diff. - Flang Fortran compilation will fail (last check version 17) due to not yet implemented: (1) derived type argument passed by value (H5VLff.F90), and (2) support for REAL with KIND = 2 in intrinsic SPACING used in testing. - Fortran tests HDF5_1_8.F90 and HDF5_F03.F90 will fail with Cray compilers greater than version 16.0 due to a compiler bug. The latest version verified as failing was version 17.0. - Several tests currently fail on certain platforms: MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with cray-mpich on theta and with XL compilers on ppc64le platforms. MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. - File space may not be released when overwriting or deleting certain nested variable length or reference types. - 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. The issues with the gif tool are: HDFFV-10592 CVE-2018-17433 HDFFV-10593 CVE-2018-17436 HDFFV-11048 CVE-2020-10809 These CVE issues have not yet been addressed and are avoided by not building the gif tool by default. Enable building the High-Level tools with these options: autotools: --enable-hlgiftools cmake: HDF5_BUILD_HL_GIF_TOOLS=ON