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-rw-r--r--MANIFEST1
-rw-r--r--release_docs/HISTORY-1_13.txt1758
-rw-r--r--release_docs/RELEASE.txt1435
3 files changed, 1775 insertions, 1419 deletions
diff --git a/MANIFEST b/MANIFEST
index a7ab9c7..bc967be 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -620,6 +620,7 @@
./release_docs/HISTORY-1_8.txt
./release_docs/HISTORY-1_10.txt
./release_docs/HISTORY-1_12.txt
+./release_docs/HISTORY-1_13.txt
./release_docs/INSTALL
./release_docs/INSTALL_CMake.txt
./release_docs/INSTALL_Cygwin.txt
diff --git a/release_docs/HISTORY-1_13.txt b/release_docs/HISTORY-1_13.txt
new file mode 100644
index 0000000..06be75b
--- /dev/null
+++ b/release_docs/HISTORY-1_13.txt
@@ -0,0 +1,1758 @@
+HDF5 History
+============
+
+This file contains development history of the HDF5 1.13 releases from
+the develop branch
+
+01. Release Information for hdf5-1.13.0
+
+[Search on the string '%%%%' for section breaks of each release.]
+
+%%%%1.13.0%%%%
+
+HDF5 version 1.13.0 released on 2021-12-01
+================================================================================
+
+
+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 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/
+
+Changes from Release to Release and New Features in the HDF5-1.13.x release series
+can be found at:
+
+ https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
+
+If you have any questions or comments, please send them to the HDF Help Desk:
+
+ help@hdfgroup.org
+
+
+CONTENTS
+========
+
+- New Features
+- New platforms, languages and compilers tested
+- Bug Fixes since HDF5-1.12.0
+- Platforms Tested
+- Known Problems
+- CMake vs. Autotools installations
+
+
+New Features
+============
+
+ Configuration:
+ -------------
+ - Added new configure option to support building parallel tools.
+ See Tools below (autotools - CMake):
+ --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS
+
+ (RAW - 2021/10/25)
+
+ - Added new configure options to enable dimension scales APIs (H5DS*) to
+ use new object references with the native VOL connector (aka native HDF5
+ library). New references are always used for non-native terminal VOL
+ connectors (e.g., DAOS).
+
+ Autotools --enable-dimension-scales-with-new-ref
+ CMake HDF5_DIMENSION_SCALES_NEW_REF=ON
+
+ (EIP - 2021/10/25, HDFFV-11180)
+
+ - Refactored the utils folder.
+
+ Added subfolder test and moved the 'swmr_check_compat_vfd.c file'
+ from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c
+ file in hl/tools/h5watch folder. Also fixed vfd check options.
+
+ (ADB - 2021/10/18)
+
+ - Changed autotools and CMake configurations to derive both
+ compilation warnings-as-errors and warnings-only-warn configurations
+ from the same files, 'config/*/*error*'. Removed redundant files
+ 'config/*/*noerror*'.
+
+ (DCY - 2021/09/29)
+
+ - Added new option to control the build of High-Level tools
+ that default ON/enabled.
+
+ Add configure options (autotools - CMake):
+ --enable-hltools HDF5_BUILD_HL_TOOLS
+
+ Disabling this option prevents building the gif tool which
+ contains the following CVEs:
+ HDFFV-10592 CVE-2018-17433
+ HDFFV-10593 CVE-2018-17436
+ HDFFV-11048 CVE-2020-10809
+
+ (ADB - 2021/09/16, HDFFV-11266)
+
+ - Adds C++ Autotools configuration file for Intel
+
+ * Checks for icpc as the compiler
+ * Sets std=c++11
+ * 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)
+ * Sets -std=c++11
+ * 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)
+
+ - A C++11-compliant compiler is now required to build the C++ wrappers
+
+ CMAKE_CXX_STANDARD is now set to 11 when building with CMake and
+ -std=c++11 is added when building with clang/gcc via the Autotools.
+
+ (DER - 2021/05/27)
+
+ - CMake will now run the shell script tests in test/ by default
+
+ The test directory includes several shell script tests that previously
+ were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS
+ has been set to ON and SH_PROGRAM has been set to bash (some test
+ scripts use bash-isms). Platforms without bash (e.g., Windows) will
+ ignore the script tests.
+
+ (DER - 2021/05/23)
+
+ - Removed unused HDF5_ENABLE_HSIZET option from CMake
+
+ This has been unused for some time and has no effect.
+
+ (DER - 2021/05/23)
+
+ - 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)
+
+ - Add 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)
+
+ (barcode - 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 - 2020/11/03)
+
+ - CMake option to use MSVC naming conventions with MinGW
+
+ HDF5_MSVC_NAMING_CONVENTION option enable to use 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 - 2020/09/27, 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 - 2020/08/24)
+
+ - 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.
+
+ (ADB - 2020/03/24, TRILAB-192)
+
+ - Added test script for file size compare
+
+ If CMake minimum version is at least 3.14, the fileCompareTest.cmake
+ script will compare file sizes.
+
+ (ADB - 2020/02/24, HDFFV-11036)
+
+ - Update CMake minimum version to 3.12
+
+ Updated CMake minimum version to 3.12 and added version checks
+ for Windows features.
+
+ (ADB - 2020/02/05, TRILABS-142)
+
+ - Fixed CMake include properties for Fortran libraries
+
+ Corrected the library properties for Fortran to use the
+ correct path for the Fortran module files.
+
+ (ADB - 2020/02/04, HDFFV-11012)
+
+ - Added common warnings files for gnu and intel
+
+ Added warnings files to use one common set of flags
+ during configure for both autotools and CMake build
+ systems. The initial implementation only affects a
+ general set of flags for gnu and intel compilers.
+
+ (ADB - 2020/01/17)
+
+ - Added new options to CMake for control of testing
+
+ Added CMake options (default ON);
+ HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
+ combined with:
+ HDF5_TEST_TOOLS
+ HDF5_TEST_EXAMPLES
+ HDF5_TEST_SWMR
+ HDF5_TEST_FORTRAN
+ HDF5_TEST_CPP
+ HDF5_TEST_JAVA
+
+ (ADB - 2020/01/15, HDFFV-11001)
+
+ - Added Clang sanitizers to CMake for analyzer support if compiler is clang.
+
+ Added CMake code and files to execute the Clang sanitizers if
+ HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
+ is set to one of the following:
+ Address
+ Memory
+ MemoryWithOrigins
+ Undefined
+ Thread
+ Leak
+ 'Address;Undefined'
+
+ (ADB - 2019/12/12, TRILAB-135)
+
+ - Update CMake for VS2019 support
+
+ CMake added support for VS2019 in version 3.15. Changes to the CMake
+ generator setting required changes to scripts. Also updated version
+ references in CMake files as necessary.
+
+ (ADB - 2019/11/18, HDFFV-10962)
+
+ - Update CMake options to match new autotools options
+
+ Add configure options (autotools - CMake):
+ enable-asserts HDF5_ENABLE_ASSERTS
+ enable-symbols HDF5_ENABLE_SYMBOLS
+ enable-profiling HDF5_ENABLE_PROFILING
+ enable-optimization HDF5_ENABLE_OPTIMIZATION
+ In addition NDEBUG is no longer forced defined and relies on the CMake
+ process.
+
+ (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
+
+
+ Library:
+ --------
+ - Adds new file driver-level memory copy operation for
+ "ctl" callback and updates compact dataset I/O routines
+ to utilize it
+
+ When accessing an HDF5 file with a file driver that uses
+ memory allocated in special ways (e.g., without standard
+ library's `malloc`), a crash could be observed when HDF5
+ tries to perform `memcpy` operations on such a memory
+ region.
+
+ These changes add a new H5FD_FEAT_MEMMANAGE VFD feature
+ flag, which, if specified as supported by a VFD, will
+ inform HDF5 that the VFD either uses special memory
+ management routines or wishes to perform memory management
+ in a specific way. Therefore, this flag instructs HDF5 to
+ ask the file driver to perform memory management for
+ certain operations.
+
+ These changes also introduce a new "ctl" callback
+ operation identified by the H5FD_CTL__MEM_COPY op code.
+ This operation simply asks a VFD to perform a memory copy.
+ The arguments to this operation are passed to the "ctl"
+ callback's "input" parameter as a pointer to a struct
+ defined as:
+
+ struct H5FD_ctl_memcpy_args_t {
+ void * dstbuf; /**< Destination buffer */
+ hsize_t dst_off; /**< Offset within destination buffer */
+ const void *srcbuf; /**< Source buffer */
+ hsize_t src_off; /**< Offset within source buffer */
+ size_t len; /**< Length of data to copy from source buffer */
+ } H5FD_ctl_memcpy_args_t;
+
+ Further, HDF5's compact dataset I/O routines were
+ identified as a problematic area that could cause a crash
+ for VFDs that make use of special memory management. Those
+ I/O routines were therefore updated to make use of this new
+ "ctl" callback operation in order to ask the underlying
+ file driver to correctly handle memory copies.
+
+ (JTH - 2021/09/28)
+
+ - Adds new "ctl" callback to VFD H5FD_class_t structure
+ with the following prototype:
+
+ herr_t (*ctl)(H5FD_t *file, uint64_t op_code,
+ uint64_t flags, const void *input,
+ void **output);
+
+ This newly-added "ctl" callback allows Virtual File
+ Drivers to intercept and handle arbitrary operations
+ identified by an operation code. Its parameters are
+ as follows:
+
+ `file` [in] - A pointer to the file to be operated on
+ `op_code` [in] - The operation code identifying the
+ operation to be performed
+ `flags` [in] - Flags governing the behavior of the
+ operation performed (see H5FDpublic.h
+ for a list of valid flags)
+ `input` [in] - A pointer to arguments passed to the
+ VFD performing the operation
+ `output` [out] - A pointer for the receiving VFD to
+ use for output from the operation
+
+ (JRM - 2021/08/16)
+
+ - Change how the release part of version, in major.minor.release is checked
+ for compatibility
+
+ The HDF5 library uses a function, H5check_version, to check that
+ the version defined in the header files, which is used to compile an
+ application is compatible with the version codified in the library, which
+ the application loads at runtime. This previously required an exact match
+ or the library would print a warning, dump the build settings and then
+ abort or continue. An environment variable controlled the logic.
+
+ Now the function first checks that the library release version, in
+ major.minor.release, is not older than the version in the headers.
+ Secondly, if the release version is different, it checks if either
+ the library version or the header version is in the exception list, in
+ which case the release part of version, in major.minor.release, must
+ be exact. An environment variable still controls the logic.
+
+ (ADB - 2021/07/27)
+
+ - gcc warning suppression macros were moved out of H5public.h
+
+ The HDF5 library uses a set of macros to suppress warnings on gcc.
+ These warnings were originally located in H5public.h so that the
+ multi VFD (which only uses public headers) could also make use of them
+ but internal macros should not be publicly exposed like this.
+
+ These macros have now been moved to H5private.h. Pending future multi
+ VFD refactoring, the macros have been duplicated in H5FDmulti.c to
+ suppress the format string warnings there.
+
+ (DER - 2021/06/03)
+
+ - 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)
+
+ - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h
+
+ The term "atom" is archaic and not in line with current HDF5 library
+ terminology, which uses "ID" instead. "Atom" has mostly been purged
+ from the library internals and this change removes H5E_ATOM from
+ the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with
+ H5E_ID.
+
+ (DER - 2020/11/24, HDFFV-11190)
+
+ - Add a new public function H5Ssel_iter_reset
+
+ This function resets a dataspace selection iterator back to an
+ initial state so that it may be used for iteration once more.
+ This can be useful when needing to iterate over a selection
+ multiple times without having to repeatedly create/destroy
+ a selection iterator for that dataspace selection.
+
+ (JTH - 2020/09/18)
+
+ - Remove HDFS VFD stubs
+
+ The original implementation of the HDFS VFD included non-functional
+ versions of the following public API calls when the HDFS VFD is
+ not built as a part of the HDF5 library:
+
+ * H5FD_hdfs_init()
+ * H5Pget_fapl_hdfs()
+ * H5Pset_fapl_hdfs()
+
+ They will remain present in HDF5 1.10 and HDF5 1.12 releases
+ for binary compatibility purposes but have been removed as of 1.14.0.
+
+ Note that this has nothing to do with the real HDFS VFD API calls
+ that are fully functional when the HDFS VFD is configured and built.
+
+ We simply changed:
+
+ #ifdef LIBHDFS
+ <real API call>
+ #else
+ <useless stub>
+ #endif
+
+ to:
+
+ #ifdef LIBHDFS
+ <real API call>
+ #endif
+
+ Which is how the other optional VFDs are handled.
+
+ (DER - 2020/08/27)
+
+ - 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)
+
+ - Refactored public exposure of haddr_t type in favor of "object tokens"
+
+ To better accommodate HDF5 VOL connectors where "object addresses in a file"
+ may not make much sense, the following changes were made to the library:
+
+ * Introduced new H5O_token_t "object token" type, which represents a
+ unique and permanent identifier for referencing an HDF5 object within
+ a container; these "object tokens" are meant to replace object addresses.
+ Along with the new type, a new H5Oopen_by_token API call was introduced
+ to open an object by a token, similar to how object addresses were
+ previously used with H5Oopen_by_addr.
+
+ * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
+ H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
+ struct and H5L_iterate2_t callback function, which work with the newly-introduced
+ object tokens, instead of object addresses. The original functions have been
+ renamed to version 1 functions and are deprecated in favor of the new version 2
+ functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
+ types and are now deprecated in favor of their version 2 counterparts. For each of
+ the functions and types, compatibility macros take place of the original symbols.
+
+ * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
+ H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
+ struct and H5O_iterate2_t callback function, which work with the newly-introduced
+ object tokens, instead of object addresses. The version 2 functions are now
+ deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
+ types have been renamed to version 1 types and are now deprecated in favor of their
+ version 2 counterparts. For each, compatibility macros take place of the original
+ symbols.
+
+ * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
+ H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
+ struct, which are used to retrieve the native HDF5 file format-specific information
+ about an object. This information (such as object header info and B-tree/heap info)
+ has been removed from the new H5O_info2_t struct so that the more generic
+ H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
+ VOL connectors.
+
+ * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
+ two object tokens, convert an object token into a nicely-readable string format and
+ to convert an object token string back into a real object token, respectively.
+
+ (DER, QAK, JTH - 2020/01/16)
+
+ - Add new public function H5Sselect_adjust.
+
+ This function shifts a dataspace selection by a specified logical offset
+ within the dataspace extent. This can be useful for VOL developers to
+ implement chunked datasets.
+
+ (NAF - 2019/11/18)
+
+ - Add new public function H5Sselect_project_intersection.
+
+ This function computes the intersection between two dataspace selections
+ and projects that intersection into a third selection. This can be useful
+ for VOL developers to implement chunked or virtual datasets.
+
+ (NAF - 2019/11/13, ID-148)
+
+ - Add new public function H5VLget_file_type.
+
+ This function returns a datatype equivalent to the supplied datatype but
+ with the location set to be in the file. This datatype can then be used
+ with H5Tconvert to convert data between file and in-memory representation.
+ This function is intended for use only by VOL connector developers.
+
+ (NAF - 2019/11/08, ID-127)
+
+
+ Parallel Library:
+ -----------------
+ -
+
+
+ Fortran Library:
+ ----------------
+ - H5Fget_name_f fixed to handle correctly trailing whitespaces and
+ newly allocated buffers.
+
+ (MSB - 2021/08/30, github-826,972)
+
+ - Add wrappers for H5Pset/get_file_locking() API calls
+
+ h5pget_file_locking_f()
+ h5pset_file_locking_f()
+
+ 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)
+
+ 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:
+ -------------
+ - Replaced HDF5AtomException with HDF5IdException
+
+ Since H5E_ATOM changed to H5E_ID in the C library, the Java exception
+ that wraps the error category was also renamed. Its functionality
+ remains unchanged aside from the name.
+
+ (See also the HDFFV-11190 note in the C library section)
+
+ (DER - 2020/11/24, HDFFV-11190)
+
+ - 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.
+
+ (DER - 2020/07/30, HDFFV-11092)
+
+ - Added ability to test java library with VOLs.
+
+ Created a new CMake script that combines the java and vol test scripts.
+
+ (ADB - 2020/02/03, HDFFV-10996)
+
+ - Tests fail for non-English locales.
+
+ In the JUnit tests with a non-English locale, only the part before
+ the decimal comma is replaced by XXXX and this leads to a comparison
+ error. Changed the regex for the Time substitution.
+
+ (ADB - 2020/01/09, HDFFV-10995)
+
+
+ Tools:
+ ------
+ - Added a new (unix ONLY) parallel meta tool 'h5dwalk', which utilizes the
+ mpifileutils (https://hpc.github.io/mpifileutils) open source utility
+ library to enable parallel execution of other HDF5 tools.
+ This approach can greatly enhance the serial hdf5 tool performance over large
+ collections of files by utilizing MPI parallelism to distribute an application
+ load over many independent MPI ranks and files.
+
+ An introduction to the mpifileutils library and initial 'User Guide' for
+ the new 'h5dwalk" tool can be found at:
+ https://github.com/HDFGroup/hdf5doc/tree/master/RFCs/HDF5/tools/parallel_tools
+
+ (RAW - 2021/10/25)
+
+ - Refactored the perform tools and removed depends on test library.
+
+ Moved the perf and h5perf tools from tools/test/perform to
+ tools/src/h5perf so that they can be installed. This required
+ that the test library dependency be removed by copying the
+ needed functions from h5test.c.
+ The standalone scripts and other perform tools remain in the
+ tools/test/perform folder.
+
+ (ADB - 2021/08/10)
+
+ - Removed partial long exceptions
+
+ Some of the tools accepted shortened versions of the long options
+ (ex: --datas instead of --dataset). These were implemented inconsistently,
+ are difficult to maintian, and occasionally block useful long option
+ names. These partial long options have been removed from all the tools.
+
+ (DER - 2021/08/03)
+
+ - 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)
+
+ - Added h5delete tool
+
+ Deleting HDF5 storage when using the VOL can be tricky when the VOL
+ does not create files. The h5delete tool is a simple wrapper around
+ the H5Fdelete() API call that uses the VOL specified in the
+ HDF5_VOL_CONNECTOR environment variable to delete a "file". If
+ the call to H5Fdelete() fails, the tool will attempt to use
+ the POSIX remove(3) call to remove the file.
+
+ Note that the HDF5 library does currently have support for
+ H5Fdelete() in the native VOL connector.
+
+ (DER - 2020/12/16)
+
+ - 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)
+
+ - h5repack was fixed to repack the reference attributes properly.
+ The code line that checks if the update of reference inside a compound
+ datatype is misplaced outside the code block loop that carries out the
+ check. In consequence, the next attribute that is not the reference
+ type was repacked again as the reference type and caused the failure of
+ repacking. The fix is to move the corresponding code line to the correct
+ code block.
+
+ (KY -2020/02/07, HDFFV-11014)
+
+ - h5diff was updated to use the new reference APIs.
+
+ h5diff uses the new reference APIs to compare references.
+ Attribute references can also be compared.
+
+ (ADB - 2019/12/19, HDFFV-10980)
+
+ - h5dump and h5ls were updated to use the new reference APIs.
+
+ The tools library now use the new reference APIs to inspect a
+ file. Also the DDL spec was updated to reflect the format
+ changes produced with the new APIs. The export API and support
+ functions in the JNI were updated to match.
+
+ (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
+
+
+ High-Level APIs:
+ ----------------
+ - added set/get for unsigned long long attributes
+
+ The attribute writing high-level API has been expanded to include
+ public set/get functions for ULL attributes, analogously to the
+ existing set/get for other types.
+
+ (AF - 2021/09/08)
+
+ C Packet Table API:
+ -------------------
+ -
+
+ Internal header file:
+ ---------------------
+ -
+
+ Documentation:
+ --------------
+ -
+
+
+New platforms, languages and compilers tested
+=============================================
+ - Linux 5.13.14-200.fc34 #1 SMP x86_64 GNU/Linux Fedora34
+ - Linux 5.11.0-34-generic #36-Ubuntu SMP x86_64 GNU/Linux Ubuntu 20.04
+ - Linux 5.3.18-22-default #1 SMP x86_64 GNU/Linux SUSE15sp2
+ - Linux-4.14.0-115.21.2 #1 SMP ppc64le GNU/Linux
+ - Linux-4.12.14-150.75-default #1 SMP x86_64 GNU/Linux
+ - macOS Apple M1 11.6 Darwin 20.6.0 arm64
+ - macOS Big Sur 11.3.1 Darwin 20.4.0 x86_64
+ - clang versions 11.0.1, 12.0.5
+ - Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line
+
+
+Bug Fixes since HDF5-1.12.0 release
+===================================
+ Library
+ -------
+ - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs
+
+ Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which
+ could trip as assert in debug versions of the library. The library now
+ returns a normal HDF5 error when the filter ID is out of range.
+
+ (DER - 2021/11/23, HDFFV-11286)
+
+ - Fixed an issue with collective metadata reads being permanently disabled
+ after a dataset chunk lookup operation. This would usually cause a
+ mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for
+ simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate().
+
+ (JTH - 2021/11/08, HDFFV-11090)
+
+ - Fixed cross platform incompatibility of references within variable length
+ types
+
+ Reference types within variable length types previously could not be
+ read on a platform with different endianness from where they were
+ written. Fixed so cross platform portability is restored.
+
+ (NAF - 2021/09/30)
+
+ - Detection of simple data transform function "x"
+
+ In the case of the simple data transform function "x" the (parallel)
+ library recognizes this is the same as not applying this data transform
+ function. This improves the I/O performance. In the case of the parallel
+ library, it also avoids breaking to independent I/O, which makes it
+ possible to apply a filter when writing or reading data to or from
+ the HDF5 file.
+
+ (JWSB - 2021/09/13)
+
+ - Fixed an invalid read and memory leak when parsing corrupt file space
+ info messages
+
+ When the corrupt file from CVE-2020-10810 was parsed by the library,
+ the code that imports the version 0 file space info object header
+ message to the version 1 struct could read past the buffer read from
+ the disk, causing an invalid memory read. Not catching this error would
+ cause downstream errors that eventually resulted in a previously
+ allocated buffer to be unfreed when the library shut down. In builds
+ where the free lists are in use, this could result in an infinite loop
+ and SIGABRT when the library shuts down.
+
+ We now track the buffer size and raise an error on attempts to read
+ past the end of it.
+
+ (DER - 2021/08/12, HDFFV-11053)
+
+
+ - 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 beyond the end of the buffer.
+
+ (BMR - 2021/05/12, HDFFV-11223)
+
+ - 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 a segmentation fault
+
+ A segmentation fault occurred with a Mathworks corrupted file.
+
+ A detection of accessing a null pointer was added to prevent the problem.
+
+ (BMR - 2021/02/19, HDFFV-11150)
+
+ - 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)
+
+ - Fixed CVE-2018-17432
+
+ The tool h5repack produced a segfault on a corrupted file which had
+ invalid rank for scalar or NULL datatype.
+
+ The problem was fixed by modifying the dataspace encode and decode
+ functions to detect and report invalid rank. h5repack now fails
+ with an error message for the corrupted file.
+
+ (BMR - 2020/10/26, HDFFV-10590)
+
+ - 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.
+
+ Allowed the creation of the dataset in such a situation.
+
+ (BMR - 2020/08/13, 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)
+
+ - 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 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 pass 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 - 2020/07/22, HDFFV-11120 and HDFFV-11121)
+
+ - 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-2020-10810
+
+ The tool h5clear produced a segfault during an error recovery in
+ the superblock decoding. An internal pointer was reset to prevent
+ further accessing when it is not assigned with a value.
+
+ (BMR - 2020/06/29, HDFFV-11053)
+
+ - 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 - 2020/06/19, HDFFV-10591)
+
+
+ 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 - 2020/12/13, HDFFV-10865)
+
+ - Added ability to test java library with VOLs.
+
+ Created a new CMake script that combines the java and vol test scripts.
+
+ (ADB - 2020/02/03, HDFFV-10996)
+
+ - Tests fail for non-English locales.
+
+ In the JUnit tests with a non-English locale, only the part before
+ the decimal comma is replaced by XXXX and this leads to a comparison
+ error. Changed the regex for the Time substitution.
+
+ (ADB - 2020/01/09, HDFFV-10995)
+
+
+ Configuration
+ -------------
+ - Corrected path searched by CMake find_package command
+
+ The install path for cmake find_package files had been changed to use
+ "share/cmake"
+ for all platforms. However the trailing "hdf5" directory was not removed.
+ This "hdf5" additional directory has been removed.
+
+ (ADB - 2021/09/27)
+
+ - Corrected pkg-config compile script
+
+ It was discovered that the position of the "$@" argument for the command
+ in the compile script may fail on some platforms and configurations. The
+ position of the "$@"command argument was moved before the pkg-config sub command.
+
+ (ADB - 2021/08/30)
+
+ - Fixed CMake C++ compiler flags
+
+ A recent refactoring of the C++ configure files accidentally removed the
+ file that executed the enable_language command for C++ needed by the
+ HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files,
+ including adding support for windows platforms.
+
+ (ADB - 2021/08/10)
+
+ - Better support for libaec (open-source Szip library) in CMake
+
+ Implemented better support for libaec 1.0.5 (or later) library. This version
+ of libaec contains improvements for better integration with HDF5. Furthermore,
+ the variable USE_LIBAEC_STATIC has been introduced to allow to make use of
+ static version of libaec library. Use libaec_DIR or libaec_ROOT to set
+ the location in which libaec can be found.
+
+ Be aware, the Szip library of libaec 1.0.4 depends on another library within
+ libaec library. This dependency is not specified in the current CMake
+ configuration which means that one can not use the static Szip library of
+ libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5.
+
+ (JWSB - 2021/06/22)
+
+ - 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)
+
+
+ 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)
+
+ - 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 comparison 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)
+
+ - h5repack was fixed to repack the reference attributes properly.
+
+ The code line that checks if the update of reference inside a compound
+ datatype is misplaced outside the code block loop that carries out the
+ check. In consequence, the next attribute that is not the reference
+ type was repacked again as the reference type and caused the failure of
+ repacking. The fix is to move the corresponding code line to the correct
+ code block.
+
+ (KY -2020/02/10, HDFFV-11014)
+
+ - h5diff was updated to use the new reference APIs.
+
+ h5diff uses the new reference APIs to compare references.
+ Attribute references can also be compared.
+
+ (ADB - 2019/12/19, HDFFV-10980)
+
+ - h5dump and h5ls were updated to use the new reference APIs.
+
+ The tools library now use the new reference APIs to inspect a
+ file. Also the DDL spec was updated to reflect the format
+ changes produced with the new APIs. The export API and support
+ functions in the JNI were updated to match.
+
+ (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
+
+
+ Performance
+ -------------
+ -
+
+
+ Fortran API
+ -----------
+ - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
+
+ (MSB - 2020/02/18, HDFFV-11029)
+
+
+ High-Level Library
+ ------------------
+ - Fixed HL_test_packet, test for packet table vlen of vlen.
+
+ Incorrect length assignment.
+
+ (ADB - 2021/10/14)
+
+
+ Fortran High-Level APIs
+ -----------------------
+ -
+
+
+ Documentation
+ -------------
+ -
+
+
+ F90 APIs
+ --------
+ -
+
+
+ C++ APIs
+ --------
+ - Added DataSet::operator=
+
+ Some compilers complain if the copy constructor is given explicitly
+ but the assignment operator is implicitly set to default.
+
+ (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)
+
+
+Platforms Tested
+===================
+
+ Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1)
+ #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1)
+ Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34)
+ (cmake and autotools)
+
+ Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
+ #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1
+ Ubuntu 20.04 Ubuntu clang version 10.0.0-4
+ (cmake and autotools)
+
+ Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1
+ #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1
+ Ubuntu20.10 Ubuntu clang version 11.0.0-2
+ (cmake and autotools)
+
+ Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0
+ #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0
+ SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238)
+ (cmake and autotools)
+
+ Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
+ #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1
+ (lassen) GCC 7.3.1
+ XL 16.1.1.2
+ (cmake)
+
+ Linux-4.12.14-150.75-default cray-mpich/7.7.10
+ #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0
+ (cori) Intel (R) Version 19.0.3.199
+ (cmake)
+
+ Linux-4.12.14-197.86-default cray-mpich/7.7.6
+ # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0
+ (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3
+ (cmake)
+
+ 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 5.3.0, Version 6.3.0,
+ Version 7.2.0, Version 8.3.0, Version 9.1.0
+ 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 6.1(Tozai)
+ Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
+ with NAG Fortran Compiler Release 6.1(Tozai)
+ MPICH 3.1.4 compiled with GCC 4.9.3
+ MPICH 3.3 compiled with GCC 7.2.0
+ OpenMPI 2.1.6 compiled with icc 18.0.1
+ OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0
+ PGI C, Fortran, C++ for 64-bit target on
+ x86_64;
+ Version 19.10-0
+
+ 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, 8.1.0
+ Intel 16.0.4, 18.0.2, 19.0.4
+
+ 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
+
+ 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 19.0.4.233 20190416
+
+ macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
+ 64-bit gfortran GNU Fortran (GCC) 7.4.0
+ (kite) Intel icc/icpc/ifort version 17.0.2
+
+ 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 2015 w/ Intel C/C++/Fortran 18 (cmake)
+ Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake)
+ Visual Studio 2019 w/ clang 12.0.0
+ with MSVC-like command-line (C/C++ only - cmake)
+ Visual Studio 2019 w/ Intel Fortran 19 (cmake)
+ Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
+
+
+Known Problems
+==============
+ Setting a variable-length dataset fill value will leak the memory allocated
+ for the p field of the hvl_t struct. A fix is in progress for this.
+ HDFFV-10840
+
+ 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.
+
+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 can be avoided by not building
+the gif tool. Disable building the High-Level tools with these options:
+ autotools: --disable-hltools
+ cmake: HDF5_BUILD_HL_TOOLS=OFF
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 045d594..160675f 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -36,7 +36,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
-- Bug Fixes since HDF5-1.12.0
+- Bug Fixes since HDF5-1.13.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
@@ -73,462 +73,6 @@ New Features
(ADB - 2021/11/23)
- - Added new configure option to support building parallel tools.
- See Tools below (autotools - CMake):
- --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS
-
- (RAW - 2021/10/25)
-
- - Added new configure options to enable dimension scales APIs (H5DS*) to
- use new object references with the native VOL connector (aka native HDF5
- library). New references are always used for non-native terminal VOL
- connectors (e.g., DAOS).
-
- Autotools --enable-dimension-scales-with-new-ref
- CMake HDF5_DIMENSION_SCALES_NEW_REF=ON
-
- (EIP - 2021/10/25, HDFFV-11180)
-
- - Refactored the utils folder.
-
- Added subfolder test and moved the 'swmr_check_compat_vfd.c file'
- from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c
- file in hl/tools/h5watch folder. Also fixed vfd check options.
-
- (ADB - 2021/10/18)
-
- - Changed autotools and CMake configurations to derive both
- compilation warnings-as-errors and warnings-only-warn configurations
- from the same files, 'config/*/*error*'. Removed redundant files
- 'config/*/*noerror*'.
-
- (DCY - 2021/09/29)
-
- - Added new option to control the build of High-Level tools
- that default ON/enabled.
-
- Add configure options (autotools - CMake):
- --enable-hltools HDF5_BUILD_HL_TOOLS
-
- Disabling this option prevents building the gif tool which
- contains the following CVEs:
- HDFFV-10592 CVE-2018-17433
- HDFFV-10593 CVE-2018-17436
- HDFFV-11048 CVE-2020-10809
-
- (ADB - 2021/09/16, HDFFV-11266)
-
- - Adds C++ Autotools configuration file for Intel
-
- * Checks for icpc as the compiler
- * Sets std=c++11
- * 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)
- * Sets -std=c++11
- * 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)
-
- - A C++11-compliant compiler is now required to build the C++ wrappers
-
- CMAKE_CXX_STANDARD is now set to 11 when building with CMake and
- -std=c++11 is added when building with clang/gcc via the Autotools.
-
- (DER - 2021/05/27)
-
- - CMake will now run the shell script tests in test/ by default
-
- The test directory includes several shell script tests that previously
- were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS
- has been set to ON and SH_PROGRAM has been set to bash (some test
- scripts use bash-isms). Platforms without bash (e.g., Windows) will
- ignore the script tests.
-
- (DER - 2021/05/23)
-
- - Removed unused HDF5_ENABLE_HSIZET option from CMake
-
- This has been unused for some time and has no effect.
-
- (DER - 2021/05/23)
-
- - 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)
-
- - Add 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)
-
- (barcode - 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 - 2020/11/03)
-
- - CMake option to use MSVC naming conventions with MinGW
-
- HDF5_MSVC_NAMING_CONVENTION option enable to use 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 - 2020/09/27, 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 - 2020/08/24)
-
- - 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.
-
- (ADB - 2020/03/24, TRILAB-192)
-
- - Added test script for file size compare
-
- If CMake minimum version is at least 3.14, the fileCompareTest.cmake
- script will compare file sizes.
-
- (ADB - 2020/02/24, HDFFV-11036)
-
- - Update CMake minimum version to 3.12
-
- Updated CMake minimum version to 3.12 and added version checks
- for Windows features.
-
- (ADB - 2020/02/05, TRILABS-142)
-
- - Fixed CMake include properties for Fortran libraries
-
- Corrected the library properties for Fortran to use the
- correct path for the Fortran module files.
-
- (ADB - 2020/02/04, HDFFV-11012)
-
- - Added common warnings files for gnu and intel
-
- Added warnings files to use one common set of flags
- during configure for both autotools and CMake build
- systems. The initial implementation only affects a
- general set of flags for gnu and intel compilers.
-
- (ADB - 2020/01/17)
-
- - Added new options to CMake for control of testing
-
- Added CMake options (default ON);
- HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
- combined with:
- HDF5_TEST_TOOLS
- HDF5_TEST_EXAMPLES
- HDF5_TEST_SWMR
- HDF5_TEST_FORTRAN
- HDF5_TEST_CPP
- HDF5_TEST_JAVA
-
- (ADB - 2020/01/15, HDFFV-11001)
-
- - Added Clang sanitizers to CMake for analyzer support if compiler is clang.
-
- Added CMake code and files to execute the Clang sanitizers if
- HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
- is set to one of the following:
- Address
- Memory
- MemoryWithOrigins
- Undefined
- Thread
- Leak
- 'Address;Undefined'
-
- (ADB - 2019/12/12, TRILAB-135)
-
- - Update CMake for VS2019 support
-
- CMake added support for VS2019 in version 3.15. Changes to the CMake
- generator setting required changes to scripts. Also updated version
- references in CMake files as necessary.
-
- (ADB - 2019/11/18, HDFFV-10962)
-
- - Update CMake options to match new autotools options
-
- Add configure options (autotools - CMake):
- enable-asserts HDF5_ENABLE_ASSERTS
- enable-symbols HDF5_ENABLE_SYMBOLS
- enable-profiling HDF5_ENABLE_PROFILING
- enable-optimization HDF5_ENABLE_OPTIMIZATION
- In addition NDEBUG is no longer forced defined and relies on the CMake
- process.
-
- (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
-
Library:
--------
@@ -539,347 +83,6 @@ New Features
(NAF - 2022/01/11)
- - Adds new file driver-level memory copy operation for
- "ctl" callback and updates compact dataset I/O routines
- to utilize it
-
- When accessing an HDF5 file with a file driver that uses
- memory allocated in special ways (e.g., without standard
- library's `malloc`), a crash could be observed when HDF5
- tries to perform `memcpy` operations on such a memory
- region.
-
- These changes add a new H5FD_FEAT_MEMMANAGE VFD feature
- flag, which, if specified as supported by a VFD, will
- inform HDF5 that the VFD either uses special memory
- management routines or wishes to perform memory management
- in a specific way. Therefore, this flag instructs HDF5 to
- ask the file driver to perform memory management for
- certain operations.
-
- These changes also introduce a new "ctl" callback
- operation identified by the H5FD_CTL__MEM_COPY op code.
- This operation simply asks a VFD to perform a memory copy.
- The arguments to this operation are passed to the "ctl"
- callback's "input" parameter as a pointer to a struct
- defined as:
-
- struct H5FD_ctl_memcpy_args_t {
- void * dstbuf; /**< Destination buffer */
- hsize_t dst_off; /**< Offset within destination buffer */
- const void *srcbuf; /**< Source buffer */
- hsize_t src_off; /**< Offset within source buffer */
- size_t len; /**< Length of data to copy from source buffer */
- } H5FD_ctl_memcpy_args_t;
-
- Further, HDF5's compact dataset I/O routines were
- identified as a problematic area that could cause a crash
- for VFDs that make use of special memory management. Those
- I/O routines were therefore updated to make use of this new
- "ctl" callback operation in order to ask the underlying
- file driver to correctly handle memory copies.
-
- (JTH - 2021/09/28)
-
- - Adds new "ctl" callback to VFD H5FD_class_t structure
- with the following prototype:
-
- herr_t (*ctl)(H5FD_t *file, uint64_t op_code,
- uint64_t flags, const void *input,
- void **output);
-
- This newly-added "ctl" callback allows Virtual File
- Drivers to intercept and handle arbitrary operations
- identified by an operation code. Its parameters are
- as follows:
-
- `file` [in] - A pointer to the file to be operated on
- `op_code` [in] - The operation code identifying the
- operation to be performed
- `flags` [in] - Flags governing the behavior of the
- operation performed (see H5FDpublic.h
- for a list of valid flags)
- `input` [in] - A pointer to arguments passed to the
- VFD performing the operation
- `output` [out] - A pointer for the receiving VFD to
- use for output from the operation
-
- (JRM - 2021/08/16)
-
- - Change how the release part of version, in major.minor.release is checked
- for compatibility
-
- The HDF5 library uses a function, H5check_version, to check that
- the version defined in the header files, which is used to compile an
- application is compatible with the version codified in the library, which
- the application loads at runtime. This previously required an exact match
- or the library would print a warning, dump the build settings and then
- abort or continue. An environment variable controlled the logic.
-
- Now the function first checks that the library release version, in
- major.minor.release, is not older than the version in the headers.
- Secondly, if the release version is different, it checks if either
- the library version or the header version is in the exception list, in
- which case the release part of version, in major.minor.release, must
- be exact. An environment variable still controls the logic.
-
- (ADB - 2021/07/27)
-
- - gcc warning suppression macros were moved out of H5public.h
-
- The HDF5 library uses a set of macros to suppress warnings on gcc.
- These warnings were originally located in H5public.h so that the
- multi VFD (which only uses public headers) could also make use of them
- but internal macros should not be publicly exposed like this.
-
- These macros have now been moved to H5private.h. Pending future multi
- VFD refactoring, the macros have been duplicated in H5FDmulti.c to
- suppress the format string warnings there.
-
- (DER - 2021/06/03)
-
- - 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)
-
- - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h
-
- The term "atom" is archaic and not in line with current HDF5 library
- terminology, which uses "ID" instead. "Atom" has mostly been purged
- from the library internals and this change removes H5E_ATOM from
- the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with
- H5E_ID.
-
- (DER - 2020/11/24, HDFFV-11190)
-
- - Add a new public function H5Ssel_iter_reset
-
- This function resets a dataspace selection iterator back to an
- initial state so that it may be used for iteration once more.
- This can be useful when needing to iterate over a selection
- multiple times without having to repeatedly create/destroy
- a selection iterator for that dataspace selection.
-
- (JTH - 2020/09/18)
-
- - Remove HDFS VFD stubs
-
- The original implementation of the HDFS VFD included non-functional
- versions of the following public API calls when the HDFS VFD is
- not built as a part of the HDF5 library:
-
- * H5FD_hdfs_init()
- * H5Pget_fapl_hdfs()
- * H5Pset_fapl_hdfs()
-
- They will remain present in HDF5 1.10 and HDF5 1.12 releases
- for binary compatibility purposes but have been removed as of 1.14.0.
-
- Note that this has nothing to do with the real HDFS VFD API calls
- that are fully functional when the HDFS VFD is configured and built.
-
- We simply changed:
-
- #ifdef LIBHDFS
- <real API call>
- #else
- <useless stub>
- #endif
-
- to:
-
- #ifdef LIBHDFS
- <real API call>
- #endif
-
- Which is how the other optional VFDs are handled.
-
- (DER - 2020/08/27)
-
- - 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)
-
- - Refactored public exposure of haddr_t type in favor of "object tokens"
-
- To better accommodate HDF5 VOL connectors where "object addresses in a file"
- may not make much sense, the following changes were made to the library:
-
- * Introduced new H5O_token_t "object token" type, which represents a
- unique and permanent identifier for referencing an HDF5 object within
- a container; these "object tokens" are meant to replace object addresses.
- Along with the new type, a new H5Oopen_by_token API call was introduced
- to open an object by a token, similar to how object addresses were
- previously used with H5Oopen_by_addr.
-
- * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
- H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
- struct and H5L_iterate2_t callback function, which work with the newly-introduced
- object tokens, instead of object addresses. The original functions have been
- renamed to version 1 functions and are deprecated in favor of the new version 2
- functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
- types and are now deprecated in favor of their version 2 counterparts. For each of
- the functions and types, compatibility macros take place of the original symbols.
-
- * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
- H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
- struct and H5O_iterate2_t callback function, which work with the newly-introduced
- object tokens, instead of object addresses. The version 2 functions are now
- deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
- types have been renamed to version 1 types and are now deprecated in favor of their
- version 2 counterparts. For each, compatibility macros take place of the original
- symbols.
-
- * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
- H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
- struct, which are used to retrieve the native HDF5 file format-specific information
- about an object. This information (such as object header info and B-tree/heap info)
- has been removed from the new H5O_info2_t struct so that the more generic
- H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
- VOL connectors.
-
- * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
- two object tokens, convert an object token into a nicely-readable string format and
- to convert an object token string back into a real object token, respectively.
-
- (DER, QAK, JTH - 2020/01/16)
-
- - Add new public function H5Sselect_adjust.
-
- This function shifts a dataspace selection by a specified logical offset
- within the dataspace extent. This can be useful for VOL developers to
- implement chunked datasets.
-
- (NAF - 2019/11/18)
-
- - Add new public function H5Sselect_project_intersection.
-
- This function computes the intersection between two dataspace selections
- and projects that intersection into a third selection. This can be useful
- for VOL developers to implement chunked or virtual datasets.
-
- (NAF - 2019/11/13, ID-148)
-
- - Add new public function H5VLget_file_type.
-
- This function returns a datatype equivalent to the supplied datatype but
- with the location set to be in the file. This datatype can then be used
- with H5Tconvert to convert data between file and in-memory representation.
- This function is intended for use only by VOL connector developers.
-
- (NAF - 2019/11/08, ID-127)
-
Parallel Library:
-----------------
@@ -926,205 +129,49 @@ New Features
Fortran Library:
----------------
- - H5Fget_name_f fixed to handle correctly trailing whitespaces and
- newly allocated buffers.
-
- (MSB - 2021/08/30, github-826,972)
-
- - Add wrappers for H5Pset/get_file_locking() API calls
-
- h5pget_file_locking_f()
- h5pset_file_locking_f()
-
- 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)
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:
-------------
- - Replaced HDF5AtomException with HDF5IdException
-
- Since H5E_ATOM changed to H5E_ID in the C library, the Java exception
- that wraps the error category was also renamed. Its functionality
- remains unchanged aside from the name.
-
- (See also the HDFFV-11190 note in the C library section)
-
- (DER - 2020/11/24, HDFFV-11190)
-
- - 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.
-
- (DER - 2020/07/30, HDFFV-11092)
-
- - Added ability to test java library with VOLs.
-
- Created a new CMake script that combines the java and vol test scripts.
-
- (ADB - 2020/02/03, HDFFV-10996)
-
- - Tests fail for non-English locales.
-
- In the JUnit tests with a non-English locale, only the part before
- the decimal comma is replaced by XXXX and this leads to a comparison
- error. Changed the regex for the Time substitution.
-
- (ADB - 2020/01/09, HDFFV-10995)
+ -
Tools:
------
- - Added a new (unix ONLY) parallel meta tool 'h5dwalk', which utilizes the
- mpifileutils (https://hpc.github.io/mpifileutils) open source utility
- library to enable parallel execution of other HDF5 tools.
- This approach can greatly enhance the serial hdf5 tool performance over large
- collections of files by utilizing MPI parallelism to distribute an application
- load over many independent MPI ranks and files.
-
- An introduction to the mpifileutils library and initial 'User Guide' for
- the new 'h5dwalk" tool can be found at:
- https://github.com/HDFGroup/hdf5doc/tree/master/RFCs/HDF5/tools/parallel_tools
-
- (RAW - 2021/10/25)
-
- - Refactored the perform tools and removed depends on test library.
-
- Moved the perf and h5perf tools from tools/test/perform to
- tools/src/h5perf so that they can be installed. This required
- that the test library dependency be removed by copying the
- needed functions from h5test.c.
- The standalone scripts and other perform tools remain in the
- tools/test/perform folder.
-
- (ADB - 2021/08/10)
-
- - Removed partial long exceptions
-
- Some of the tools accepted shortened versions of the long options
- (ex: --datas instead of --dataset). These were implemented inconsistently,
- are difficult to maintian, and occasionally block useful long option
- names. These partial long options have been removed from all the tools.
-
- (DER - 2021/08/03)
-
- - 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)
-
- - Added h5delete tool
-
- Deleting HDF5 storage when using the VOL can be tricky when the VOL
- does not create files. The h5delete tool is a simple wrapper around
- the H5Fdelete() API call that uses the VOL specified in the
- HDF5_VOL_CONNECTOR environment variable to delete a "file". If
- the call to H5Fdelete() fails, the tool will attempt to use
- the POSIX remove(3) call to remove the file.
-
- Note that the HDF5 library does currently have support for
- H5Fdelete() in the native VOL connector.
-
- (DER - 2020/12/16)
-
- - 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)
-
- - h5repack was fixed to repack the reference attributes properly.
- The code line that checks if the update of reference inside a compound
- datatype is misplaced outside the code block loop that carries out the
- check. In consequence, the next attribute that is not the reference
- type was repacked again as the reference type and caused the failure of
- repacking. The fix is to move the corresponding code line to the correct
- code block.
-
- (KY -2020/02/07, HDFFV-11014)
-
- - h5diff was updated to use the new reference APIs.
-
- h5diff uses the new reference APIs to compare references.
- Attribute references can also be compared.
-
- (ADB - 2019/12/19, HDFFV-10980)
-
- - h5dump and h5ls were updated to use the new reference APIs.
-
- The tools library now use the new reference APIs to inspect a
- file. Also the DDL spec was updated to reflect the format
- changes produced with the new APIs. The export API and support
- functions in the JNI were updated to match.
-
- (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
+ -
High-Level APIs:
----------------
- - added set/get for unsigned long long attributes
-
- The attribute writing high-level API has been expanded to include
- public set/get functions for ULL attributes, analogously to the
- existing set/get for other types.
+ -
- (AF - 2021/09/08)
C Packet Table API:
-------------------
-
+
Internal header file:
---------------------
-
+
Documentation:
--------------
-
+
Support for new platforms, languages and compilers
==================================================
-
+
Bug Fixes since HDF5-1.12.0 release
===================================
Library
@@ -1163,14 +210,6 @@ Bug Fixes since HDF5-1.12.0 release
(ADB - 2022/02/24, #1438)
- - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs
-
- Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which
- could trip as assert in debug versions of the library. The library now
- returns a normal HDF5 error when the filter ID is out of range.
-
- (DER - 2021/11/23, HDFFV-11286)
-
- Unified handling of collective metadata reads to correctly fix old bugs
Due to MPI-related issues occurring in HDF5 from mismanagement of the
@@ -1204,440 +243,20 @@ Bug Fixes since HDF5-1.12.0 release
(JTH - 2021/11/09)
- - Fixed an issue with collective metadata reads being permanently disabled
- after a dataset chunk lookup operation. This would usually cause a
- mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for
- simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate().
-
- (JTH - 2021/11/08, HDFFV-11090)
-
- - Fixed cross platform incompatibility of references within variable length
- types
-
- Reference types within variable length types previously could not be
- read on a platform with different endianness from where they were
- written. Fixed so cross platform portability is restored.
-
- (NAF - 2021/09/30)
-
- - Detection of simple data transform function "x"
-
- In the case of the simple data transform function "x" the (parallel)
- library recognizes this is the same as not applying this data transform
- function. This improves the I/O performance. In the case of the parallel
- library, it also avoids breaking to independent I/O, which makes it
- possible to apply a filter when writing or reading data to or from
- the HDF5 file.
-
- (JWSB - 2021/09/13)
-
- - Fixed an invalid read and memory leak when parsing corrupt file space
- info messages
-
- When the corrupt file from CVE-2020-10810 was parsed by the library,
- the code that imports the version 0 file space info object header
- message to the version 1 struct could read past the buffer read from
- the disk, causing an invalid memory read. Not catching this error would
- cause downstream errors that eventually resulted in a previously
- allocated buffer to be unfreed when the library shut down. In builds
- where the free lists are in use, this could result in an infinite loop
- and SIGABRT when the library shuts down.
-
- We now track the buffer size and raise an error on attempts to read
- past the end of it.
-
- (DER - 2021/08/12, HDFFV-11053)
-
-
- - 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 beyond the end of the buffer.
-
- (BMR - 2021/05/12, HDFFV-11223)
-
- - 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 a segmentation fault
-
- A segmentation fault occurred with a Mathworks corrupted file.
-
- A detection of accessing a null pointer was added to prevent the problem.
-
- (BMR - 2021/02/19, HDFFV-11150)
-
- - 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)
-
- - Fixed CVE-2018-17432
-
- The tool h5repack produced a segfault on a corrupted file which had
- invalid rank for scalar or NULL datatype.
-
- The problem was fixed by modifying the dataspace encode and decode
- functions to detect and report invalid rank. h5repack now fails
- with an error message for the corrupted file.
-
- (BMR - 2020/10/26, HDFFV-10590)
-
- - 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.
-
- Allowed the creation of the dataset in such a situation.
-
- (BMR - 2020/08/13, 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)
-
- - 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 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 pass 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 - 2020/07/22, HDFFV-11120 and HDFFV-11121)
-
- - 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-2020-10810
-
- The tool h5clear produced a segfault during an error recovery in
- the superblock decoding. An internal pointer was reset to prevent
- further accessing when it is not assigned with a value.
-
- (BMR - 2020/06/29, HDFFV-11053)
-
- - 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 - 2020/06/19, HDFFV-10591)
-
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 - 2020/12/13, HDFFV-10865)
-
- - Added ability to test java library with VOLs.
-
- Created a new CMake script that combines the java and vol test scripts.
-
- (ADB - 2020/02/03, HDFFV-10996)
-
- - Tests fail for non-English locales.
-
- In the JUnit tests with a non-English locale, only the part before
- the decimal comma is replaced by XXXX and this leads to a comparison
- error. Changed the regex for the Time substitution.
-
- (ADB - 2020/01/09, HDFFV-10995)
+ -
Configuration
-------------
- - Corrected path searched by CMake find_package command
-
- The install path for cmake find_package files had been changed to use
- "share/cmake"
- for all platforms. However the trailing "hdf5" directory was not removed.
- This "hdf5" additional directory has been removed.
-
- (ADB - 2021/09/27)
-
- - Corrected pkg-config compile script
-
- It was discovered that the position of the "$@" argument for the command
- in the compile script may fail on some platforms and configurations. The
- position of the "$@"command argument was moved before the pkg-config sub command.
-
- (ADB - 2021/08/30)
-
- - Fixed CMake C++ compiler flags
-
- A recent refactoring of the C++ configure files accidentally removed the
- file that executed the enable_language command for C++ needed by the
- HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files,
- including adding support for windows platforms.
-
- (ADB - 2021/08/10)
-
- - Better support for libaec (open-source Szip library) in CMake
-
- Implemented better support for libaec 1.0.5 (or later) library. This version
- of libaec contains improvements for better integration with HDF5. Furthermore,
- the variable USE_LIBAEC_STATIC has been introduced to allow to make use of
- static version of libaec library. Use libaec_DIR or libaec_ROOT to set
- the location in which libaec can be found.
-
- Be aware, the Szip library of libaec 1.0.4 depends on another library within
- libaec library. This dependency is not specified in the current CMake
- configuration which means that one can not use the static Szip library of
- libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5.
-
- (JWSB - 2021/06/22)
-
- - 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)
+ -
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)
-
- - 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 comparison 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)
-
- - h5repack was fixed to repack the reference attributes properly.
-
- The code line that checks if the update of reference inside a compound
- datatype is misplaced outside the code block loop that carries out the
- check. In consequence, the next attribute that is not the reference
- type was repacked again as the reference type and caused the failure of
- repacking. The fix is to move the corresponding code line to the correct
- code block.
-
- (KY -2020/02/10, HDFFV-11014)
-
- - h5diff was updated to use the new reference APIs.
-
- h5diff uses the new reference APIs to compare references.
- Attribute references can also be compared.
-
- (ADB - 2019/12/19, HDFFV-10980)
-
- - h5dump and h5ls were updated to use the new reference APIs.
-
- The tools library now use the new reference APIs to inspect a
- file. Also the DDL spec was updated to reflect the format
- changes produced with the new APIs. The export API and support
- functions in the JNI were updated to match.
-
- (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
+ -
Performance
@@ -1647,18 +266,12 @@ Bug Fixes since HDF5-1.12.0 release
Fortran API
-----------
- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
-
- (MSB - 2020/02/18, HDFFV-11029)
+ -
High-Level Library
------------------
- - Fixed HL_test_packet, test for packet table vlen of vlen.
-
- Incorrect length assignment.
-
- (ADB - 2021/10/14)
+ -
Fortran High-Level APIs
@@ -1678,23 +291,7 @@ Bug Fixes since HDF5-1.12.0 release
C++ APIs
--------
- - Added DataSet::operator=
-
- Some compilers complain if the copy constructor is given explicitly
- but the assignment operator is implicitly set to default.
-
- (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)
+ -
Platforms Tested