HDF5 version 1.10.7 released on 2020-09-11
================================================================================
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/
HDF5 binaries provided are fully tested with ZLIB and the free
Open Source SZIP successor Libaec (with BSD license).
The official ZLIB and SZIP/Libaec pages are at:
ZLIB: http://www.zlib.net/http://www.zlib.net/zlib_license.html
SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaechttps://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt
Changes from Release to Release and New Features in the HDF5-1.10.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 HDF5-1.10.6
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- 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 overriden 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. A new option USE_LIBAEC is required
to compensate for the different files produced by AEC build.
Autotools does not build the compression libraries within hdf5 builds,
but will use an installed libaec when configured as before with the
option --with-libsz=<path to libaec directory>.
(ADB - 2020/04/22, OESS-65)
- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
Some handcrafted tests in HDFTests.c have 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)
- 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)
Library:
--------
- Add metadata cache optimization to reduce skip list usage
On file flush or close, the metadata cache attempts to write out
all dirty entries in increasing address order. To do this, it needs
an address sorted list of metadata entries. Further, since flushing
one metadata cache entry can dirty another, this list must support
efficient insertion and deletion.
The metadata cache uses a skip list of all dirty entries for this
purpose. Before this release, this skip list was maintained at all
times. However, since profiling indicates that this imposes a
significant cost, we now construct and maintain the skip list only
when needed. Specifically, we enable the skip list and load it with
a list of all dirty entries in the metadata cache just before a flush,
and disable it after the flush.
(JRM - 2020/08/17, HDFFV-11034)
- 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)
- 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)
- Fixed an assertion failure in the parallel library when collectively
filling chunks. As it is required that chunks be written in
monotonically non-decreasing order of offset in the file, this assertion
was being triggered when the list of chunk file space allocations being
passed to the collective chunk filling routine was not sorted according
to this particular requirement.
The addition of a sort of the out of order chunks trades a bit of
performance for the elimination of this assertion and of any complaints
from MPI implementations about the file offsets used being out of order.
(JTH - 2019/10/07)
Fortran Library:
----------------
- 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)
- Added new Fortran parameters:
H5F_LIBVER_ERROR_F
H5F_LIBVER_NBOUNDS_F
H5F_LIBVER_V18_F
H5F_LIBVER_V110_F
- Added new Fortran API: h5pget_libver_bounds_f
(MSB - 2020/02/11, HDFFV-11018)
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:
----------------
- 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)
Tools:
------
- 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)
High-Level APIs:
---------------
- None
C Packet Table API
------------------
- None
Internal header file
--------------------
- None
Documentation
-------------
- None
Support for new platforms, languages and compilers.
=======================================
- None
Bug Fixes since HDF5-1.10.6 release
==================================
Library
-------
- 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 asserts 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 issue CVE-2018-17438
A division by zero was discovered in H5D__select_io() of H5Dselect.c.
https://security-tracker.debian.org/tracker/CVE-2018-17438
A check was added to protect against division by zero. When such
situation occurs again, the normal HDF5 error handling will be invoked,
instead of segmentation fault.
(BMR, DER - 2020/07/09, HDFFV-10587)
- 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)
- Don't allocate an empty (0-dimensioned) chunked dataset's chunk
index, until the dataset's dimensions are increased.
(QAK - 2020/05/07)
Configuration
-------------
- 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)
- Added -fsanitize=address autotools configure option for Clang compiler
Clang sanitizer options were also added for Clang compilers with CMake.
(LRK, 2020/08/05, HDFFV-10836)
- Updated testh5cc.sh.in for functions versioned in HDF5 1.10.
testh5cc.sh previously tested that the correct version of a function
versioned in HDF5 1.6 or 1.8 was compiled when one of
H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This
test was extended for additional testing with H5_USE_18_API_DEFAULT.
(LRK, 2020/06/22, HDFFV-11000)
- 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)
Performance
-------------
- None
Java Library:
----------------
- None
Fortran
--------
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/2/18, HDFFV-11029)
- 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)
Tools
-----
- 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 eclude attributes, with the supplied path,
from comparision.
(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-10005)
- 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)
High-Level APIs:
------
- The H5DSis_scale function was updated to return "not a dimension scale" (0)
instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
not written according to Dimension Scales Specification.
(EIP - 2020/08/12, HDFFV-10436)
Fortran High-Level APIs:
------
- None
Documentation
-------------
- None
F90 APIs
--------
- None
C++ APIs
--------
- None
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, 2020/7/2, HDFFV-11063)
a0d717d510