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hdf5/release_docs/HISTORY-1_13.txt
Larry Knox 9dfcca0bbb
Release updates (#2033) 
* Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
2022-08-18 08:35:21 -05:00

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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
02. Release Information for hdf5-1.13.1
03. Release Information for hdf5-1.13.2
[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:
------
- h5repack added an optional verbose value for reporting R/W timing.
In addition to adding timing capture around the read/write calls in
h5repack, added help text to indicate how to show timing for read/write;
-v N, --verbose=N Verbose mode, print object information.
N - is an integer greater than 1, 2 displays read/write timing
(ADB - 2021/11/08)
- 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
%%%%1.13.1%%%%
HDF5 version 1.13.1 released on 2022-03-02
================================================================================
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
- Support for new platforms and languages
- Bug Fixes since HDF5-1.13.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Reworked 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 setting the HDF5_ROOT variable failed to locate
the configuration files. The build variable HDF5_INSTALL_CMAKE_DIR is now
set to the <INSTALL_DIR>/cmake folder. The location of the configuration
files can still be specified by the "HDF5_DIR" variable.
(ADB - 2022/02/02)
- CPack will now generate RPM/DEB packages.
Enabled the RPM and DEB CPack generators on linux. In addition to
generating STGZ and TGZ packages, CPack will try to package the
library for RPM and DEB packages. This is the initial attempt and
may change as issues are resolved.
(ADB - 2022/01/27)
- Added new option to the h5cc scripts produced by CMake.
Add -showconfig option to h5cc scripts to cat the
libhdf5.settings file to the standard output.
(ADB - 2022/01/25)
- CMake will now run the PowerShell script tests in test/ by default
on Windows.
The test directory includes several shell script tests that previously
were not run by CMake on Windows. These are now run by default.
If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts
will execute. Similar to the bash scripts on unix platforms.
(ADB - 2021/11/23)
Library:
--------
- Add a new public function, H5ESget_requests()
This function allows the user to retrieve request pointers from an event
set. It is intended for use primarily by VOL plugin developers.
(NAF - 2022/01/11)
Parallel Library:
-----------------
- Several improvements to parallel compression feature, including:
* Improved support for collective I/O (for both writes and reads)
* Significant reduction of memory usage for the feature as a whole
* Reduction of copying of application data buffers passed to H5Dwrite
* Addition of support for incremental file space allocation for filtered
datasets created in parallel. Incremental file space allocation is the
default for these types of datasets (early file space allocation is
also still supported), while early file space allocation is still the
default (and only supported at allocation time) for unfiltered datasets
created in parallel. Incremental file space allocation should help with
parallel HDF5 applications that wish to use fill values on filtered
datasets, but would typically avoid doing so since dataset creation in
parallel would often take an excessive amount of time. Since these
datasets previously used early file space allocation, HDF5 would
allocate space for and write fill values to every chunk in the dataset
at creation time, leading to noticeable overhead. Instead, with
incremental file space allocation, allocation of file space for chunks
and writing of fill values to those chunks will be delayed until each
individual chunk is initially written to.
* Addition of support for HDF5's "don't filter partial edge chunks" flag
(https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS)
* Addition of proper support for HDF5 fill values with the feature
* Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h
so HDF5 applications can determine at compile-time whether the feature
is available
* Addition of simple examples (ph5_filtered_writes.c and
ph5_filtered_writes_no_sel.c) under examples directory to demonstrate
usage of the feature
* Improved coverage of regression testing for the feature
(JTH - 2022/2/23)
Support for new platforms, languages and compilers
==================================================
- None
Bug Fixes since HDF5-1.13.0 release
===================================
Library
-------
- Fixed a metadata cache bug when resizing a pinned/protected cache entry
When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This
caused H5C_resize_entry to mark the entry as dirty and made
H5AC_resize_entry think that it didn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needed to allocate a new entry for insertion into the dirty
entry skip list, since the entry didGn't exist on that list.
This caused an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
(JRM - 2022/02/28)
- Issue #1436 identified a problem with the H5_VERS_RELEASE check in the
H5check_version function.
Investigating the original fix, #812, we discovered some inconsistencies
with a new block added to check H5_VERS_RELEASE for incompatibilities.
This new block was not using the new warning text dealing with the
H5_VERS_RELEASE check and would cause the warning to be duplicated.
By removing the H5_VERS_RELEASE argument in the first check for
H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
the H5_VERS_RELEASE for incompatible release versions. This adheres
to the statement that except for the develop branch, all release versions
in a major.minor maintenance branch should be compatible. The prerequisite
is that an application will not use any APIs not present in all release versions.
(ADB - 2022/02/24, #1438)
- Unified handling of collective metadata reads to correctly fix old bugs
Due to MPI-related issues occurring in HDF5 from mismanagement of the
status of collective metadata reads, they were forced to be disabled
during chunked dataset raw data I/O in the HDF5 1.10.5 release. This
wouldn't generally have affected application performance because HDF5
already disables collective metadata reads during chunk lookup, since
it is generally unlikely that the same chunks will be read by all MPI
ranks in the I/O operation. However, this was only a partial solution
that wasn't granular enough.
This change now unifies the handling of the file-global flag and the
API context-level flag for collective metadata reads in order to
simplify querying of the true status of collective metadata reads. Thus,
collective metadata reads are once again enabled for chunked dataset
raw data I/O, but manually controlled at places where some processing
occurs on MPI rank 0 only and would cause issues when collective
metadata reads are enabled.
(JTH - 2021/11/16, HDFFV-10501/HDFFV-10562)
- Fixed several potential MPI deadlocks in library failure conditions
In the parallel library, there were several places where MPI rank 0
could end up skipping past collective MPI operations when some failure
occurs in rank 0-specific processing. This would lead to deadlocks
where rank 0 completes an operation while other ranks wait in the
collective operation. These places have been rewritten to have rank 0
push an error and try to cleanup after the failure, then continue to
participate in the collective operation to the best of its ability.
(JTH - 2021/11/09)
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-3.10.0-1160.49.1 openmpi-intel/4.1
#1 SMP x86_64 GNU/Linux Intel(R) Version 18.0.5, 19.1.2
(chama) (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
%%%%1.13.2%%%%
HDF5 version 1.13.2 released on 2022-08-15
================================================================================
INTRODUCTION
============
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on 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
- Support for new platforms and languages
- Bug Fixes since HDF5-1.13.1
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Correct the usage of CMAKE_Fortran_MODULE_DIRECTORY and where to
install Fortran mod files.
The Fortran modules files, ending in .mod are files describing a
Fortran 90 (and above) module API and ABI. These are not like C
header files describing an API, they are compiler dependent and
arch dependent, and not easily readable by a human being. They are
nevertheless searched for in the includes directories by gfortran
(in directories specified with -I).
Autotools configure uses the -fmoddir option to specify the folder.
CMake will use "mod" folder by default unless overridden by the CMake
variable; HDF5_INSTALL_MODULE_DIR.
(ADB - 2022/07/21)
- HDF5 memory allocation sanity checking is now off by default for
Autotools debug builds
HDF5 can be configured to perform sanity checking on internal memory
allocations by adding heap canaries to these allocations. However,
enabling this option can cause issues with external filter plugins
when working with (reallocating/freeing/allocating and passing back)
buffers.
Previously, this option was off by default for all CMake build types,
but only off by default for non-debug Autotools builds. Since debug
is the default build mode for HDF5 when built from source with
Autotools, this can result in surprising segfaults that don't occur
when an application is built against a release version of HDF5.
Therefore, this option is now off by default for all build types
across both CMake and Autotools.
(JTH - 2022/03/01)
Library:
--------
- Onion VFD
The onion VFD allows creating "versioned" HDF5 files. File open/close
operations after initial file creation will add changes to an external
"onion" file (.onion extension by default) instead of the original file.
Each written revision can be opened independently.
To open a file with the onion VFD, use the H5Pset_fapl_onion() API call
(does not need to be used for the initial creation of the file). The
options for the H5FD_onion_fapl_info_t struct are described in H5FDonion.h.
The H5FDonion_get_revision_count() API call can be used to query a file
to find out how many revisions have been created.
(DER - 2022/08/02)
- Subfiling VFD
The HDF5 Subfiling VFD is a new MPI-based file driver that allows an
HDF5 application to distribute an HDF5 file across a collection of
"sub-files" in equal-sized data segment "stripes". I/O to the logical
HDF5 file is then directed to the appropriate "sub-file" according to
the Subfiling configuration and a system of I/O concentrators, which
are MPI ranks operating worker threads.
By allowing a configurable stripe size, number of I/O concentrators and
method for selecting MPI ranks as I/O concentrators, the Subfiling VFD
aims to enable an HDF5 application to find a middle ground between the
single shared file and file-per-process approaches to parallel file I/O
for the particular machine the application is running on. In general, the
goal is to avoid some of the complexity of the file-per-process approach
while also minimizing the locking issues of the single shared file approach
on a parallel file system.
Also included with the Subfiling VFD is a new h5fuse.sh script which
reads a Subfiling configuration file and then combines the various
sub-files back into a single HDF5 file. By default, the h5fuse.sh script
looks in the current directory for the Subfiling configuration file,
but can also be pointed to the configuration file with a command-line
option.
The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a
File Access Property List and using that FAPL for file operations. Note
that the Subfiling VFD currently has the following limitations:
* Does not currently support HDF5 collective I/O, other than collective
metadata writes and reads as set by H5Pset_coll_metadata_write() and
H5Pset_all_coll_metadata_ops()
* The Subfiling VFD should not currently be used with an HDF5 library
that has been built with thread-safety enabled. This can cause deadlocks
when failures occur due to interactions between the VFD's internal
threads and HDF5's global lock.
(JTH - 2022/07/22)
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
- Added two new constructors to H5::H5File class
Two new constructors were added to allow opening a file with non-default
access property list.
Java Library:
-------------
- Added version of H5Rget_name to return the name as a Java string.
Other functions that get_name process the get_size then get the name
within the JNI implementation. Now H5Rget_name has a H5Rget_name_string.
(ADB - 2022/07/12)
- Added reference support to H5A and H5D read write vlen JNI functions.
Added the implementation to handle VL references as an Array of Lists
of byte arrays.
The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
structures. The wrappers use the specified datatype arguments for the
List type translation, it is expected that the Java type is correct.
(ADB - 2022/07/11, HDFFV-11318)
- H5A and H5D read write vlen JNI functions were incorrect.
Corrected the vlen function implementations for the basic primitive types.
The VLStrings functions now correctly use the implementation that had been
the VL functions. (VLStrings functions did not have an implementation.)
The new VL functions implementation now expect an Array of Lists between
Java and the JNI wrapper.
The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
structures. The wrappers use the specified datatype arguments for the
List type translation, it is expected that the Java type is correct.
(ADB - 2022/07/07, HDFFV-11310)
- H5A and H5D read write JNI functions had flawed vlen datatype check.
Adapted tools function for JNI utils file. This reduced multiple calls
to a single check and variable. The variable can then be used to call
the H5Treclaim function. Adjusted existing test and added new test.
(ADB - 2022/06/22)
Tools:
------
- Building h5perf/h5perf_serial in "standalone mode" has been removed
Building h5perf separately from the library was added circa 2008
in HDF5 1.6.8. It's unclear what purpose this serves and the current
implementation is currently broken. The existing files require
H5private.h and the symbols we use to determine how the copied
platform-independence scheme should be used come from H5pubconf.h,
which may not match the compiler being used to build standalone h5perf.
Due to the maintenance overhead and lack of a clear use case, support
for building h5perf and h5perf_serial separately from the HDF5 library
has been removed.
(DER - 2022/07/15)
- The perf tool has been removed
The small `perf` tool didn't really do anything special and the name
conflicts with gnu's perf tool.
(DER - 2022/07/15, GitHub #1787)
- 1.10 References in containers were not displayed properly by h5dump.
Ported 1.10 tools display function to provide ability to inspect and
display 1.10 reference data.
(ADB - 2022/06/22)
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
- All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore.
Documentation:
--------------
-
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-1.13.1 release
===================================
Library
-------
- The offset parameter in H5Dchunk_iter() is now scaled properly
In earlier HDF5 1.13.x versions, the chunk offset was not scaled by the
chunk dimensions. This offset parameter in the callback now matches
that of H5Dget_chunk_info().
(@mkitti - 2022/08/06, GitHub #1419)
- Converted an assertion on (possibly corrupt) file contents to a normal
error check
Previously, the library contained an assertion check that a read superblock
doesn't contain a superblock extension message when the superblock
version < 2. When a corrupt HDF5 file is read, this assertion can be triggered
in debug builds of HDF5. In production builds, this situation could cause
either a library error or a crash, depending on the platform.
(JTH - 2022/07/08, HDFFV-11316/HDFFV-11317)
Java Library
------------
-
Configuration
-------------
-
Tools
-----
-
Performance
-------------
-
Fortran API
-----------
- h5open_f and h5close_f fixes
* Fixed it so both h5open_f and h5close_f can be called multiple times.
* Fixed an issue with open objects remaining after h5close_f was called.
* Added additional tests.
(MSB, 2022/04/19, HDFFV-11306)
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
-
Platforms Tested
===================
Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35)
(cmake and autotools)
Linux 5.11.0-34-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 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
#1 SMP x86_64 GNU/Linux Cray clang 14.0.0
(crusher) GCC 11.2.0
(cmake)
Linux 5.3.18-24-cray_shasta_c cray-mpich/8.1.12
#1 SMP x86_64 GNU/Linux Cray clang 13.0.0
(spock) AMD clang 13.0.0
GCC 8.2.0, 11.2.0
(cmake)
Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5
#1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5)
(stria) GCC 7.2.0 (Spack GCC)
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 12.0.1
(vortex) GCC 8.3.1
XL 16.1.1
(cmake)
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 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
(autotools and cmake)
Linux-3.10.0-1160.71.1.1chaos 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
(cmake)
Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(skybridge) Intel/19.1
(cmake)
Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(attaway) Intel/19.1
(cmake)
Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux Intel/19.1
(chama) (cmake)
macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
(macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
(bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
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 C/C++/Fortran oneAPI 2021 (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.
Several tests currently fail on certain platforms:
MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
cray-mpich on theta and with XL compilers on ppc64le platforms.
MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
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
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