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Viewing File: /usr/share/doc/hdf5/RELEASE.txt
HDF5 version 1.12.1 released on 2021-07-01
================================================================================
INTRODUCTION
============
This document describes the new features introduced in the HDF5 1.12.1 release.
It contains information on the platforms tested and known problems in this
release. For more details check the HISTORY*.txt files in the HDF5 source.
Note that documentation in the links below will be updated at the time of the
release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
More information about the new features can be found at:
https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.12.0
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Adds C++ Autotools configuration file for Intel
* Checks for icpc as the compiler
* Copies most non-warning flags from intel-flags
(DER - 2021/06/02)
- Adds C++ Autotools configuration file for PGI
* Checks for pgc++ as the compiler name (was: pgCC)
* Other options basically match new C options (below)
(DER - 2021/06/02)
- Updates PGI C options
* -Minform set to warn (was: inform) to suppress spurious messages
* Sets -gopt -O2 as debug options
* Sets -O4 as 'high optimization' option
* Sets -O0 as 'no optimization' option
* Removes specific settings for PGI 9 and 10
(DER - 2021/06/02)
- Added an option to make the global thread-safe lock a recursive R/W lock
Prior to this release, the HDF5 library supported multi-threaded
applications by placing a recursive global lock on the entire library,
thus allowing only one thread into the library at a time.
While this is still the default, the library can now be built with the
recursive global lock replaced with a recursive read / write (R/W) lock
that allows recursive writer locks.
Currently, this change results in no functional change in the HDF5
library, as all threads will have to acquire a write lock on entry, and
thus obtain exclusive access to the HDF5 library as before. However, the
addition of the recursive R/W lock is a prerequisite for further work
directed at allowing some subset of the HDF5 API calls to enter the
library with read locks.
CMake: HDF5_USE_RECURSIVE_RW_LOCKS (default: OFF, advanced)
Autotools: --enable-recursive-rw-locks [default=no]
This feature only works with Pthreads. Win32 threads are not supported.
(DER - 2021/05/10)
- CMake no longer builds the C++ library by default
HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the
Autotools build defaults.
(DER - 2021/04/20)
- Removal of pre-VS2015 work-arounds
HDF5 now requires Visual Studio 2015 or greater, so old work-around
code and definitions have been removed, including:
* <inttypes.h>
* snprintf and vsnprintf
* llround, llroundf, lround, lroundf, round, roundf
* strtoll and strtoull
* va_copy
* struct timespec
(DER - 2021/03/22)
- Added CMake variable HDF5_LIB_INFIX
This infix is added to all library names after 'hdf5'.
e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
This name is used in packages on debian based systems.
(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)
(RG - 2021/03/22)
- On macOS, Universal Binaries can now be built, allowing native execution on
both Intel and Apple Silicon (ARM) based Macs.
To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64"
(SAM - 2021/02/07, github-311)
- Added a configure-time option to control certain compiler warnings
diagnostics
A new configure-time option was added that allows some compiler warnings
diagnostics to have the default operation. This is mainly intended for
library developers and currently only works for gcc 10 and above. The
diagnostics flags apply to C, C++ and Fortran compilers and will appear
in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They
will NOT be exported to h5cc, etc.
The default is OFF, which will disable the warnings URL and color attributes
for the warnings output. ON will not add the flags and allow default behavior.
Autotools: --enable-diags
CMake: HDF5_ENABLE_BUILD_DIAGS
(ADB - 2021/02/05, HDFFV-11213)
- CMake option to build the HDF filter plugins project as an external project
The HDF filter plugins project is a collection of registered compression
filters that can be dynamically loaded when needed to access data stored
in a hdf5 file. This CMake-only option allows the plugins to be built and
distributed with the hdf5 library and tools. Like the options for szip and
zlib, either a tgz file or a git repository can be specified for the source.
The option was refactored to use the CMake FetchContent process. This allows
more control over the filter targets, but required external project command
options to be moved to a CMake include file, HDF5PluginCache.cmake. Also
enabled the filter examples to be used as tests for operation of the
filter plugins.
(ADB - 2020/12/10, OESS-98)
- FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers
On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did
not process C++ options. Since FreeBSD 10, the default compiler has
been clang (via 'cc').
The default compilers have been set to 'cc' for C and 'c++' for C++,
which will pick up clang and clang++ respectively on FreeBSD 10+.
Additionally, clang options are now set correctly for both C and C++
and g++ options will now be set if that compiler is being used (an
omission from the former functionality).
(DER - 2020/11/28, HDFFV-11193)
- Fixed POSIX problems when building w/ gcc on Solaris
When building on Solaris using gcc, the POSIX symbols were not
being set correctly, which could lead to issues like clock_gettime()
not being found.
The standard is now set to gnu99 when building with gcc on Solaris,
which allows POSIX things to be #defined and linked correctly. This
differs slightly from the gcc norm, where we set the standard to c99
and manually set POSIX #define symbols.
(DER - 2020/11/25, HDFFV-11191)
- Added a configure-time option to consider certain compiler warnings
as errors
A new configure-time option was added that converts some compiler warnings
to errors. This is mainly intended for library developers and currently
only works for gcc and clang. The warnings that are considered errors
will appear in the generated libhdf5.settings file. These warnings apply
to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags",
respectively. They will NOT be exported to h5cc, etc.
The default is OFF. Building with this option may fail when compiling
on operating systems and with compiler versions not commonly used by
the library developers. Compilation may also fail when headers not
under the control of the library developers (e.g., mpi.h, hdfs.h) raise
warnings.
Autotools: --enable-warnings-as-errors
CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS
(DER - 2020/11/23, HDFFV-11189)
- Autotools and CMake target added to produce doxygen generated documentation
The default is OFF or disabled.
Autoconf option is '--enable-doxygen'
autotools make target is 'doxygen' and will build all doxygen targets
CMake configure option is 'HDF5_BUILD_DOC'.
CMake target is 'doxygen' for all available doxygen targets
CMake target is 'hdf5lib_doc' for the src subdirectory
(ADB - 2020/11/13, HDFFV-11243)
- CMake option to use MSVC naming conventions with MinGW
HDF5_MSVC_NAMING_CONVENTION option enables the use of MSVC naming
conventions when using a MinGW toolchain
(xan - 2020/10/30)
- CMake option to statically link gcc libs with MinGW
HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++
with the MinGW toolchain
(xan - 2020/10/30)
- CMake option to build the HDF filter plugins project as an external project
The HDF filter plugins project is a collection of registered compression
filters that can be dynamically loaded when needed to access data stored
in a hdf5 file. This CMake-only option allows the plugins to be built and
distributed with the hdf5 library and tools. Like the options for szip and
zlib, either a tgz file or a git repository can be specified for the source.
The necessary options are (see the INSTALL_CMake.txt file):
HDF5_ENABLE_PLUGIN_SUPPORT
PLUGIN_TGZ_NAME or PLUGIN_GIT_URL
There are more options necessary for various filters and the plugin project
documents should be referenced.
(ADB - 2020/10/16, OESS-98)
- Added CMake option to format source files
HDF5_ENABLE_FORMATTERS option will enable creation of targets using the
pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder
or tool folder. All sources can be formatted by executing the format target;
make format
(ADB - 2020/09/24)
- Disable memory sanity checks in the Autotools in release branches
The library can be configured to use internal memory sanity checking,
which replaces C API calls like malloc(3) and free(3) with our own calls
which add things like heap canaries. These canaries can cause problems
when external filter plugins reallocate canary-marked buffers.
For this reason, the default will be to not use the memory allocation
sanity check feature in release branches (e.g., hdf5_1_10_7).
Debug builds in development branches (e.g., develop, hdf5_1_10) will
still use them by default.
This change only affects Autotools debug builds. Non-debug autotools
builds and all CMake builds do not enable this feature by default.
(DER - 2020/08/19)
- Add file locking configure and CMake options
HDF5 1.10.0 introduced a file locking scheme, primarily to help
enforce SWMR setup. Formerly, the only user-level control of the scheme
was via the HDF5_USE_FILE_LOCKING environment variable.
This change introduces configure-time options that control whether
or not file locking will be used and whether or not the library
ignores errors when locking has been disabled on the file system
(useful on some HPC Lustre installations).
In both the Autotools and CMake, the settings have the effect of changing
the default property list settings (see the H5Pset/get_file_locking()
entry, below).
The yes/no/best-effort file locking configure setting has also been
added to the libhdf5.settings file.
Autotools:
An --enable-file-locking=(yes|no|best-effort) option has been added.
yes: Use file locking.
no: Do not use file locking.
best-effort: Use file locking and ignore "disabled" errors.
CMake:
Two self-explanatory options have been added:
HDF5_USE_FILE_LOCKING
HDF5_IGNORE_DISABLED_FILE_LOCKS
Setting both of these to ON is the equivalent to the Autotools'
best-effort setting.
NOTE:
The precedence order of the various file locking control mechanisms is:
1) HDF5_USE_FILE_LOCKING environment variable (highest)
2) H5Pset_file_locking()
3) configure/CMake options (which set the property list defaults)
4) library defaults (currently best-effort)
(DER - 2020/07/30, HDFFV-11092)
- CMake option to link the generated Fortran MOD files into the include
directory.
The Fortran generation of MOD files by a Fortran compile can produce
different binary files between SHARED and STATIC compiles with different
compilers and/or different platforms. Note that it has been found that
different versions of Fortran compilers will produce incompatible MOD
files. Currently, CMake will locate these MOD files in subfolders of
the include directory and add that path to the Fortran library target
in the CMake config file, which can be used by the CMake find library
process. For other build systems using the binary from a CMake install,
a new CMake configuration can be used to copy the pre-chosen version
of the Fortran MOD files into the install include directory.
The default will depend on the configuration of
BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
YES YES Default to SHARED
YES NO Default to STATIC
NO YES Default to SHARED
NO NO Default to SHARED
The defaults can be overridden by setting the config option
HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
(ADB - 2020/07/09, HDFFV-11116)
- CMake option to use AEC (open source SZip) library instead of SZip
The open source AEC library is a replacement library for SZip. In
order to use it for hdf5 the libaec CMake source was changed to add
"-fPIC" and exclude test files. Autotools does not build the
compression libraries within hdf5 builds. New option USE_LIBAEC is
required to compensate for the different files produced by AEC build.
(ADB - 2020/04/22, OESS-65)
- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
Some handcrafted tests in HDFTests.c has been removed and the CMake
CHECK_STRUCT_HAS_MEMBER module has been used.
(ADB - 2020/03/24, TRILAB-24)
- Both build systems use same set of warnings flags
GNU C, C++ and gfortran warnings flags were moved to files in a config
sub-folder named gnu-warnings. Flags that only are available for a specific
version of the compiler are in files named with that version.
Clang C warnings flags were moved to files in a config sub-folder
named clang-warnings.
Intel C, Fortran warnings flags were moved to files in a config sub-folder
named intel-warnings.
There are flags in named "error-xxx" files with warnings that may
be promoted to errors. Some source files may still need fixes.
There are also pairs of files named "developer-xxx" and "no-developer-xxx"
that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
configure option:--enable-developer-warnings.
In addition, CMake no longer applies these warnings for examples.
(2020/03/24, TRILAB-192)
Library:
--------
- H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX
The size_hint value is ultimately stored in a uint32_t struct field,
so specifying a value larger than this on a 64-bit machine can cause
undefined behavior including crashing the system.
The documentation for this API call was also incorrect, stating that
passing a negative value would cause the library to use a default
value. Instead, passing a "negative" value actually passes a very large
value, which is probably not what the user intends and can cause
crashes on 64-bit systems.
The Doxygen documentation has been updated and passing values larger
than UINT32_MAX for size_hint will now produce a normal HDF5 error.
(DER - 2021/04/29, HDFFV-11241)
- H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID
When passed an invalid fapl ID, H5Pset_fapl_log() would usually
segfault when attempting to free an uninitialized pointer in the error
handling code. This behavior is more common in release builds or
when the memory sanitization checks were not selected as a build
option.
The pointer is now correctly initialized and the API call now
produces a normal HDF5 error when fed an invalid fapl ID.
(DER - 2021/04/28, HDFFV-11240)
- Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
The call incorrectly attempts to free an internal copy of the previous
log location string, which causes a segfault. This only happens
when the call is invoked multiple times on the same property list.
On the first call to a given fapl, the log location is set to NULL so
the segfault does not occur.
The string is now handled properly and the segfault no longer occurs.
(DER - 2021/04/27, HDFFV-11239)
- HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows
HSYS_GOTO_ERROR is an internal macro that is used to produce error
messages when system calls fail. These strings include errno and the
the associated strerror() value, which are not particularly useful
when a Win32 API call fails.
On Windows, this macro has been updated to include the result of
GetLastError(). When a system call fails on Windows, usually only
one of errno and GetLastError() will be useful, however we emit both
for the user to parse. The Windows error message is not emitted as
it would be awkward to free the FormatMessage() buffer given the
existing HDF5 error framework. Users will have to look up the error
codes in MSDN.
The format string on Windows has been changed from:
"%s, errno = %d, error message = '%s'"
to:
"%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32""
for those inclined to parse it for error values.
(DER - 2021/03/21)
- File locking now works on Windows
Since version 1.10.0, the HDF5 library has used a file locking scheme
to help enforce one reader at a time accessing an HDF5 file, which can
be helpful when setting up readers and writers to use the single-
writer/multiple-readers (SWMR) access pattern.
In the past, this was only functional on POSIX systems where flock() or
fcntl() were present. Windows used a no-op stub that always succeeded.
HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the
same scheme as POSIX systems. We lock the entire file when we set up the
locks (by passing DWORDMAX as both size parameters to LockFileEx()).
(DER - 2021/03/19, HDFFV-10191)
- H5Epush_ret() now requires a trailing semicolon
H5Epush_ret() is a function-like macro that has been changed to
contain a `do {} while(0)` loop. Consequently, a trailing semicolon
is now required to end the `while` statement. Previously, a trailing
semi would work, but was not mandatory. This change was made to allow
clang-format to correctly format the source code.
(SAM - 2021/03/03)
- Improved performance of H5Sget_select_elem_pointlist
Modified library to cache the point after the last block of points
retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the
same function to retrieve the next block of points from the list can
proceed immediately without needing to iterate over the point list.
(NAF - 2021/01/19)
- Added H5VL_VERSION macro that indicates the version of the VOL framework
implemented by a version of the library. Currently, compatibility
checking enforces that the 'version' field in the H5VL_class_t for
a VOL connector must match the version of the VOL framework for the
library when it is registered or dynamically loaded.
(QAK - 2020/12/10)
- Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable
This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that
were previously accepted. This option turns on file locking but
ignores locking errors when the library detects that file locking
has been disabled on a file system (useful on some HPC Lustre
installations).
The capitalization of BEST_EFFORT is mandatory.
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Add H5Pset/get_file_locking() API calls
This change adds new API calls which can be used to set or get the
file locking parameters. The single API call sets both the "use file
locking" flag and the "ignore disabled file locking" flag.
When opening a file multiple times without closing, the file MUST be
opened with the same file locking settings. Opening a file with different
file locking settings will fail (this is similar to the behavior of
H5Pset_fclose_degree()).
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Added two new API routines for tracking library memory use:
H5get_alloc_stats() and H5get_free_list_sizes().
(QAK - 2020/03/25)
- Add Mirror VFD
Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
machine. Must be used in conjunction with the Splitter VFD.
(JOS - 2020/03/13, TBD)
- Add Splitter VFD
Maintain separate R/W and W/O channels for "concurrent" file writes
to two files using a single HDF5 file handle.
(JOS - 2020/03/13, TBD)
C++ Library:
------------
- Add wrappers for H5Pset/get_file_locking() API calls
FileAccPropList::setFileLocking()
FileAccPropList::getFileLocking()
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
Java Library:
-------------
- Added new H5S functions.
H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
H5Sselect_intersect_block, H5Sselect_project_intersection,
H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
wrapper functions added.
(ADB - 2020/10/27, HDFFV-10868)
- Add wrappers for H5Pset/get_file_locking() API calls
H5Pset_file_locking()
H5Pget_use_file_locking()
H5Pget_ignore_disabled_file_locking()
Unlike the C++ and Fortran wrappers, there are separate getters for the
two file locking settings, each of which returns a boolean value.
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(ADB - 2020/07/30, HDFFV-11092)
Tools:
------
- h5repack added help text for user-defined filters.
Added help text line that states the valid values of the filter flag
for user-defined filters;
filter_flag: 1 is OPTIONAL or 0 is MANDATORY
(ADB - 2021/01/14, HDFFV-11099)
- h5repack added options to control how external links are handled.
Currently h5repack preserves external links and cannot copy and merge
data from the external files. Two options, merge and prune, were added to
control how to merge data from an external link into the resulting file.
--merge Follow external soft link recursively and merge data.
--prune Do not follow external soft links and remove link.
--merge --prune Follow external link, merge data and remove dangling link.
(ADB - 2020/08/05, HDFFV-9984)
Support for new platforms, languages and compilers
==================================================
- Added macOS 11.2 Big Sur
Bug Fixes since HDF5-1.12.0 release
===================================
Library
-------
- Fixed CVE-2018-14460
The tool h5repack produced a segfault when the rank in dataspace
message was corrupted, causing invalid read while decoding the
dimension sizes.
The problem was fixed by ensuring that decoding the dimension sizes
and max values will not go beyong the end of the buffer.
(BMR - 2021/05/12, HDFFV-11223)
- Fixed CVE-2019-9151
h5repack generated a segfault when an invalid memory read occurred on
a corrupted file.
The issue is now fixed. h5repack produces an error instead of segfault.
(BMR - 2021/05/04, HDFFV-10718)
- Fixed CVE-2018-11206
The tool h5dump produced a segfault when the size of a fill value
message was corrupted and caused a buffer overflow.
The problem was fixed by verifying the fill value's size
against the buffer size before attempting to access the buffer.
(BMR - 2021/03/15, HDFFV-10480)
- Fixed CVE-2018-14033 (same issue as CVE-2020-10811)
The tool h5dump produced a segfault when the storage size message
was corrupted and caused a buffer overflow.
The problem was fixed by verifying the storage size against the
buffer size before attempting to access the buffer.
(BMR - 2021/03/15, HDFFV-11159/HDFFV-11049)
- Remove underscores on header file guards
Header file guards used a variety of underscores at the beginning of the define.
Removed all leading (some trailing) underscores from header file guards.
(ADB - 2021/03/03, #361)
- Fixed issue with MPI communicator and info object not being
copied into new FAPL retrieved from H5F_get_access_plist
Added logic to copy the MPI communicator and info object into
the output FAPL. MPI communicator is retrieved from the VFD, while
the MPI info object is retrieved from the file's original FAPL.
(JTH - 2021/02/15, HDFFV-11109)
- Fixed problems with vlens and refs inside compound using
H5VLget_file_type()
Modified library to properly ref count H5VL_object_t structs and only
consider file vlen and reference types to be equal if their files are
the same.
(NAF - 2021/01/22)
- Fix bug and simplify collective metadata write operation when some ranks
have no entries to contribute. This fixes parallel regression test
failures with IBM SpectrumScale MPI on the Summit system at ORNL.
(QAK - 2020/09/02)
- Avoid setting up complex MPI types with 0-length vectors, which some
MPI implementations don't handle well. (In particular, IBM
SpectrumScale MPI on the Summit system at ORNL)
(QAK - 2020/08/21)
- Fixed use-of-uninitialized-value error
Appropriate initialization of local structs was added to remove the
use-of-uninitialized-value errors reported by MemorySanitizer.
(BMR - 2020/8/13, HDFFV-11101)
- Creation of dataset with optional filter
When the combination of type, space, etc doesn't work for filter
and the filter is optional, it was supposed to be skipped but it was
not skipped and the creation failed.
A fix is applied to allow the creation of a dataset in such
situation, as specified in the user documentation.
(BMR - 2020/8/13, HDFFV-10933)
- Explicitly declared dlopen to use RTLD_LOCAL
dlopen documentation states that if neither RTLD_GLOBAL nor
RTLD_LOCAL are specified, then the default behavior is unspecified.
The default on linux is usually RTLD_LOCAL while macos will default
to RTLD_GLOBAL.
(ADB - 2020/08/12, HDFFV-11127)
- Fixed issues CVE-2018-13870 and CVE-2018-13869
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump crashed on memory access violation.
A check for reading past the end of the buffer was added to multiple
locations to prevent the crashes and h5dump now simply fails with an
error message when this error condition occurs.
(BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)
- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
causes asserts/errors when passed to other dataspace API calls.
H5S_NO_CLASS is an internal class value that should not have been
exposed via a public API call.
In debug builds of the library, this can cause assert() function to
trip. In non-debug builds, it will produce normal library errors.
The new library behavior is for H5Sset_extent_none() to convert
the dataspace into one of type H5S_NULL, which is better handled
by the library and easier for developers to reason about.
(DER - 2020/07/27, HDFFV-11027)
- Fixed the segmentation fault when reading attributes with multiple threads
It was reported that the reading of attributes with variable length string
datatype will crash with segmentation fault particularly when the number of
threads is high (>16 threads). The problem was due to the file pointer that
was set in the variable length string datatype for the attribute. That file
pointer was already closed when the attribute was accessed.
The problem was fixed by setting the file pointer to the current opened file pointer
when the attribute was accessed. Similar patch up was done before when reading
dataset with variable length string datatype.
(VC - 2020/07/13, HDFFV-11080)
- Fixed CVE-2018-17435
The tool h52gif produced a segfault when the size of an attribute message
was corrupted and caused a buffer overflow.
The problem was fixed by verifying the attribute message's size against the
buffer size before accessing the buffer. h52gif was also fixed to display
the failure instead of silently exiting after the segfault was eliminated.
(BMR - 2020/6/19, HDFFV-10591)
- Reduce overhead for H5open(), which is involved in public symbols like
H5T_NATIVE_INT, etc.
(QAK - 2020/06/18)
- Cache last ID looked up for an ID type (dataset, datatype, file, etc),
improving performance when accessing the same ID repeatedly.
(QAK - 2020/06/11)
- Streamline I/O to a single element, improving performance for record
appends to chunked datasets.
(QAK - 2020/06/11)
- Remove redundant tagging of metadata cache entries for some chunked
dataset operations, slightly improving performance for chunked
datasets.
(QAK - 2020/06/10)
- Better detect selections with the same shape, improving performance for
some uses of H5DOappend (and other situations).
(QAK - 2020/06/07)
- Don't allocate an empty (0-dimensioned) chunked dataset's chunk
index, until the dataset's dimensions are increased.
(QAK - 2020/05/07)
Java Library
------------
- JNI utility function does not handle new references.
The JNI utility function for converting reference data to string did
not use the new APIs. In addition to fixing that function, added new
java tests for using the new APIs.
(ADB - 2021/02/16, HDFFV-11212)
- The H5FArray.java class, in which virtually the entire execution time
is spent using the HDFNativeData method that converts from an array
of bytes to an array of the destination Java type.
1. Convert the entire byte array into a 1-d array of the desired type,
rather than performing 1 conversion per row;
2. Use the Java Arrays method copyOfRange to grab the section of the
array from (1) that is desired to be inserted into the destination array.
(PGT,ADB - 2020/12/29, HDFFV-10865)
Configuration
-------------
- Refactor CMake configure for Fortran
The Fortran configure tests for KINDs reused a single output file that was
read to form the Integer and Real Kinds defines. However, if config was run
more then once, the CMake completed variable prevented the tests from executing
again and the last value saved in the file was used to create the define.
Creating separate files for each KIND solved the issue.
In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in
defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION
correctly for a zero value. This was fixed by supplying the required defines.
In addition it was moved from the Fortran specific HDF5UseFortran.camke file
to the C centric ConfigureChecks.cmake file.
(ADB - 2021/06/03)
- Move emscripten flag to compile flags
The emscripten flag, -O0, was removed from target_link_libraries command
to the correct target_compile_options command.
(ADB - 2021/04/26 HDFFV-11083)
- Remove arbitrary warning flag groups from CMake builds
The arbitrary groups were created to reduce the quantity of warnings being
reported that overwhelmed testing report systems. Considerable work has
been accomplished to reduce the warning count and these arbitrary groups
are no longer needed.
Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON.
Visual Studio warnings C4100, C4706, and C4127 have been moved to
developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds.
(ADB - 2021/03/22, HDFFV-11228)
- Reclassify CMake messages, to allow new modes and --log-level option
CMake message commands have a mode argument. By default, STATUS mode
was chosen for any non-error message. CMake version 3.15 added additional
modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode
of STATUS were reviewed and most were reclassified as VERBOSE. The new
mode was protected by a check for a CMake version of at least 3.15. If CMake
version 3.17 or above is used, the user can use the command line option
of "--log-level" to further restrict which message commands are displayed.
(ADB - 2021/01/11, HDFFV-11144)
- Fixes Autotools determination of the stat struct having an st_blocks field
A missing parenthesis in an autoconf macro prevented building the test
code used to determine if the stat struct contains the st_blocks field.
Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define
found in H5pubconf.h will be defined correctly on both the Autotools and
CMake. This #define is only used in the tests and does not affect the
HDF5 C library.
(DER - 2021/01/07, HDFFV-11201)
- Add missing ENV variable line to hdfoptions.cmake file
Using the build options to use system SZIP/ZLIB libraries need to also
specify the library root directory. Setting the {library}_ROOT ENV
variable was added to the hdfoptions.cmake file.
(ADB - 2020/10/19 HDFFV-11108)
- Fixed removal of Java lib files by "make uninstall"
"make uninstall" was not removing 5 Java files from the lib directory.
(LRK - 2020/08/24, HDFFV-10811)
- Stopped addition of szip header and include directory path for
incompatible libsz
szlib.h is the same for both 32-bit and 64-bit szip, and the header file
and its path were added to the HDF5 binary even though the configure
check of a function in libsz later failed and szip compression was not
enabled. The header file and include path are now added only when the
libsz function passes the configure check.
(LRK - 2020/08/17, HDFFV-10830)
Tools
-----
- Changed how h5dump and h5ls identify long double.
Long double support is not consistent across platforms. Tools will always
identify long double as 128-bit [little/big]-endian float nn-bit precision.
New test file created for datasets with attributes for float, double and
long double. In addition any unknown integer or float datatype will now
also show the number of bits for precision.
These files are also used in the java tests.
(ADB - 2021/03/24, HDFFV-11229,HDFFV-11113)
- Fixed tools argument parsing.
Tools parsing used the length of the option from the long array to match
the option from the command line. This incorrectly matched a shorter long
name option that happened to be a subset of another long option.
Changed to match whole names.
(ADB - 2021/01/19, HDFFV-11106)
- Fixed a bug with h5repack ignoring the "-q" and "-z" command-line options
h5repack uses the -q and -z command-line options to specify the indexing
options for objects in the file when repacking. Previously, h5repack
would simply ignore any setting from these options. This has been fixed
so that h5repack will correctly interpret the following settings:
-q "name" : Sort objects by name order
-q "creation_order" : Sort objects by link creation order
-z "ascending" : Sort objects by ascending name/link creation order
-z "descending" : Sort objects by descending name/link creation order
(JTH - 2020/04/16, HDFFV-11030)
- The tools library was updated by standardizing the error stack process.
General sequence is:
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
h5tools_init();
... process the command-line (check for error-stack enable) ...
h5tools_error_report();
... (do work) ...
h5diff_exit(ret);
(ADB - 2020/07/20, HDFFV-11066)
- h5diff fixed a command line parsing error.
h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used.
(ADB - 2020/07/20, HDFFV-10897)
- h5diff added a command line option to ignore attributes.
h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
Adding the exclude-attribute argument will only exclude attributes, with the supplied path,
from comparison.
(ADB - 2020/07/20, HDFFV-5935)
- h5diff added another level to the verbose argument to print filenames.
Added verbose level 3 that is level 2 plus the filenames. The levels are:
0 : Identical to '-v' or '--verbose'
1 : All level 0 information plus one-line attribute status summary
2 : All level 1 information plus extended attribute status report
3 : All level 2 information plus file names
(ADB - 2020/07/20, HDFFV-1005)
Fortran API
-----------
- Fixed configure issue when building HDF5 with NAG Fortran 7.0.
HDF5 now accounts for the addition of half-precision floating-point
in NAG 7.0 with a KIND=16.
(MSB - 2020/02/28, HDFFV-11033)
High-Level Library
------------------
- Eliminated unnecessary code in H5DOappend(), improving its performance.
(QAK - 2020/06/05)
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
- Updated doxygen comments with changes for release
(ADB - 2021/05/03)
- Fixed the dimension size description in the layout message table of the
file format specification section IV.A.2.i.
The layout message table described the dimension sizes starting from
Dimension 0 to Dimension #n. This was incorrect because it would mean
the rank is n+1.
The dimension size entries were changed to starting from Dimension 1 to
Dimension #n.
(VC – 2020/06/09, HDFFV-11079)
F90 APIs
--------
- Fixed parallel make build failure due to a missing H5forkit dependency.
(MSB, 2021/03/31, HDFFV-11232)
C++ APIs
--------
- Added DataSet::operator=
Some compilers complain if the copy constructor is given explicitly
but the assignment operator is implicitly set to default.
(LN - 2021/05/19)
Testing
-------
- Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
Lib files needed are now copied to a subdirectory in the java/test
directory, and on Macs the loader path for libhdf5.xxxs.so is changed
in the temporary copy of libhdf5_java.dylib.
(LRK - 2020/07/02, HDFFV-11063)
Supported Platforms
===================
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, 5.2.0, 7.1.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.2, 3.3
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (cmake)
MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(bear) Intel icc/icpc/ifort version 19.0.4
MacOS Big Sur 11.2 Apple clang version 12.0.5 (clang-1205.0.22.9)
gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
Intel icc/icpc (ICC) 2021.1 Beta 20201112
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
MacOS High Sierra 10.13.6 64-bit n y/y n y y y
MacOS Big Sur 11.2 64-bit n y/y n y y y
CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
Linux 3.10.0-1127.10.1.1.ch6.ppc64le n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Windows 10 y y y y
Windows 10 x64 y y y y
MacOS High Sierra 10.13.6 64-bit y n y y
MacOS Big Sur 11.2 64-bit y n y y
CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
Linux 3.10.0-1127.10.1.1.ch6.ppc64le y y y n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 19.10-0
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
PGI C (pgcc), C++ (pgc++), Fortran (pgf90)
compilers:
Version 18.4, 19.4
MPICH 3.3
OpenMPI 2.1.5, 3.1.3, 4.0.0
Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3
#1 SMP x86_64 GNU/Linux
(moohan)
Linux-3.10.0-1127.0.0.1chaos openmpi/4.0.0
#1 SMP x86_64 GNU/Linux clang/6.0.0, 11.0.1
(quartz) gcc/7.3.0, 8.3.0
intel/16.0.4, 18.0.2, 19.0.4
Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang/7.1.0, ibm-11.0.1
(lassen) gcc/4.9.3, 8.3.1
xl/2019.02.07, 2021.03.11
Linux-4.12.14-150.52-default cray-mpich/7.7.10
#1 SMP x86_64 GNU/Linux gcc/8.3.0
(cori) intel/19.0.3
Linux-4.4.180-94.107-default cray-mpich/7.7.16
# 1SMP x86_64 GNU/Linux gcc/7.3.0, 8.3.0, 10.2.0
(mutrino) intel/17.0.4, 18.0.5, 19.1.3
Linux-3.10.0- spectrum-mpi/rolling-release
1127.10.1.1chaos.ch6.ppc64le clang/7.1.0, 11.0.1
#1 SMP ppc64le GNU/Linux gcc/4.9.3,8.3.1
(ray) xl/2019.08.20,2021.03.11
Fedora33 5.11.18-200.fc33.x86_64
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1)
GNU Fortran (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1)
clang version 11.0.0 (Fedora 11.0.0-2.fc33)
(cmake and autotools)
Ubuntu20.04 5.8.0-53-generic-x86_64
#60~20.04-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 9.3.0-17ubuntu1
GNU Fortran (GCC) 9.3.0-17ubuntu1
clang version 10.0.0-4ubuntu1
(cmake and autotools)
Ubuntu20.10 5.8.0-53-generic-x86_64
#60-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1
GNU Fortran (GCC) 10.2.0-13ubuntu1
Ubuntu clang version 11.0.0-2
(cmake and autotools)
SUSE15sp2 5.3.18-22-default
#1 SMP x86_64 GNU/Linux GNU gcc (SUSE Linux) 7.5.0
GNU Fortran (SUSE Linux) 7.5.0
clang version 7.0.1 (tags/RELEASE_701/final 349238)
(cmake and autotools)
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Known Problems
==============
testflushrefresh.sh will fail when run with "make check-passthrough-vol"
on centos7, with 3 Errors/Segmentation faults. These will not occur when
run with "make check". See https://github.com/HDFGroup/hdf5/issues/673
for details.
The t_bigio test fails on several HPC platforms, generally by timeout with
OpenMPI 4.0.0 or with this error from spectrum-mpi:
*** on communicator MPI_COMM_WORLD
*** MPI_ERR_COUNT: invalid count argument
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
ADB - 2019/05/07
At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
Back to Directory
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