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RELEASE.txt
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HDF5 version 1.10.11 released on 2023-09-25
================================================================================
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 HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5-1.10+Release
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, Languages and Compilers
- Bug Fixes Since HDF5-1.10.10 Release
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools Installations
New Features
============
Configuration:
-------------
- Added support for CMake presets file.
CMake supports two main files, CMakePresets.json and CMakeUserPresets.json,
that allow users to specify common configure options and share them with
others. This release added a CMakePresets.json file of a typical
configuration and support file, config/cmake-presets/hidden-presets.json.
It also added a section to INSTALL_CMake.txt with a very basic explanation
of the process to use CMakePresets.
- Enabled instrumentation of the library by default in CMake for parallel
debug builds
HDF5 can be configured to instrument portions of the parallel library to
aid in debugging. Autotools builds of HDF5 turn this capability on by
default for parallel debug builds and off by default for other build types.
CMake has been updated to match this behavior.
Library:
--------
- Changed the error handling for a not found path in the find plugin process.
While attempting to load a plugin the HDF5 library will fail if one of the
directories in the plugin paths does not exist, even if there are more paths
to check. Instead of exiting the function with an error, it now just logs
the error and continues processing the list of paths to check.
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
-------------
- Deprecated the HDF5GroupInfo class.
This class assumes that an object can contain four values which uniquely
identify an object among those HDF5 files which are open. This is no
longer valid in future HDF5 releases.
Tools:
------
-
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
-
Support for New Platforms, Languages and Compilers
==================================================
-
Bug Fixes Since HDF5-1.10.10 Release
===================================
Library
-------
- Fixed CVE-2018-11202, a malformed file could result in chunk index
memory leaks.
Under most conditions (i.e., when the --enable-using-memchecker option is
NOT used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be due
to the "free list" package not being able to clear its resources so the
library couldn't shut down. When the "using a memory checker" option is
used, the free lists are disabled so there is just a memory leak with no
abort on library shutdown.
The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.
- Fixed a file space allocation bug in the parallel library for chunked
datasets
With the addition of support for incremental file space allocation for
chunked datasets with filters applied to them that are created/accessed
in parallel, a bug was introduced to the library's parallel file space
allocation code. This could cause file space to not be allocated correctly
for datasets without filters applied to them that are created with serial
file access and later opened with parallel file access. In turn, this could
cause parallel writes to those datasets to place incorrect data in the file.
- Fixed an assertion failure in Parallel HDF5 when a file can't be created
due to an invalid library version bounds setting
An assertion failure could occur in H5MF_settle_raw_data_fsm when a file
can't be created with Parallel HDF5 due to specifying the use of a paged,
persistent file free space manager
(H5Pset_file_space_strategy(..., H5F_FSPACE_STRATEGY_PAGE, 1, ...)) with
an invalid library version bounds combination
(H5Pset_libver_bounds(..., H5F_LIBVER_EARLIEST, H5F_LIBVER_V18)). This
has now been fixed.
- Fixed an assertion in a previous fix for CVE-2016-4332
An assert could fail when processing corrupt files that have invalid
shared message flags (as in CVE-2016-4332).
The assert statement in question has been replaced with pointer checks
that don't raise errors. Since the function is in cleanup code, we do
our best to close and free things, even when presented with partially
initialized structs.
Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
- Fixed segfault on file close
h5debug fails at file close with core dump on a file that has an
illegal file size in its cache image. In H5F__dest(), the library
performs all the closing operations for the file and keeps track of
the error encountered when reading the file cache image.
At the end of the routine, it frees the file's file structure and
returns an error. Due to the error return, the file object is not removed
from the ID node table. This eventually causes assertion failure in
H5F__close_cb() when the library finally exits and tries to
access that file object in the table for closing.
The closing routine, H5F__dest(), will not free the file structure if
there is an error, keeping a valid file structure in the ID node table.
It will be freed later in H5F__close_cb() when the library exits and
terminates the file package.
Fixes HDFFV-11052, CVE-2020-10812
- Fixed memory leaks that could occur when reading a dataset from a
malformed file
When attempting to read layout, pline, and efl information for a
dataset, memory leaks could occur if attempting to read pline/efl
information throws an error. The leaks would occur because the memory
that was allocated for pline and efl was not properly cleaned up by
error handling.
Fixes Github issue #2602
- Fixed a bug in H5Ocopy that could generate invalid HDF5 files
H5Ocopy was missing a check to determine whether the new object's
object header version is greater than version 1. Without this check,
copying an object with an object header that is smaller than a
certain size would cause H5Ocopy to create an object header for the
new object that has a gap in the header data. According to the
HDF5 File Format Specification, this is not allowed for version
1 of the object header format.
Fixes GitHub issue #2653
- Fixed potential heap buffer overflow in decoding of link info message
Detections of buffer overflow were added for decoding version, index
flags, link creation order value, and the next three addresses. The
checks will remove the potential invalid read of any of these
values that could be triggered by a malformed file.
Fixes GitHub issue #2603
- Fixed potential buffer overrun issues in some object header decode routines
Several checks were added to H5O__layout_decode and H5O__sdspace_decode to
ensure that memory buffers are not overrun when decoding buffers read from
a possibly corrupted HDF5 file.
- Fixed a heap buffer overflow that occurs when reading from
a dataset with a compact layout within a malformed HDF5 file.
During opening of a dataset that has a compact layout, the
library allocates a buffer that stores the dataset's raw data.
The dataset's object header that gets written to the file
contains information about how large of a buffer the library
should allocate. If this object header is malformed such that
it causes the library to allocate a buffer that is too small
to hold the dataset's raw data, future I/O to the dataset can
result in heap buffer overflows. To fix this issue, an extra
check is now performed for compact datasets to ensure that
the size of the allocated buffer matches the expected size
of the dataset's raw data (as calculated from the dataset's
dataspace and datatype information). If the two sizes do not
match, opening of the dataset will fail.
Fixes GitHub issue #2606
- Fixed CVE-2019-8396, malformed HDF5 files where content does not match
expected size.
Malformed HDF5 files may have truncated content which does not match
the expected size. When H5O__pline_decode() attempts to decode these it
may read past the end of the allocated space leading to heap overflows
as bounds checking is incomplete.
The fix ensures each element is within bounds before reading.
Fixes Jira issue HDFFV-10712, CVE-2019-8396, GitHub issue #2209
- Fixed memory leak when running h5dump with proof of vulnerability file.
The fuzzed file "pov" was an HDF5 file containing an illegal continuation
message. When deserializing the object header chunks for the file, memory
was allocated for the array of continuation messages, but this memory was
never freed when an error occurred.
The allocated memory is now properly released.
Fixes GitHub issue #2599
Java Library
------------
- Fixed switch case 'L' block missing a break statement.
The HDF5Array.arrayify method is missing a break statement in the
case 'L': section which causes it to fall through and throw an
HDF5JavaException when attempting to read an Array[Array[Long]].
The error was fixed by inserting a break statement at the end of
the case 'L': sections.
Fixes GitHub issue #3056
Configuration
-------------
- Fixed syntax of generator expressions used by CMake
Adding quotes around the generator expression should allow CMake to
correctly parse the expression. Generator expressions are typically
parsed after command arguments. If a generator expression contains
spaces, new lines, semicolons or other characters that may be
interpreted as command argument separators, the whole expression
should be surrounded by quotes when passed to a command. Failure to
do so may result in the expression being split and it may no longer
be recognized as a generator expression.
Fixes GitHub issue #2906
Tools
-----
- Added option --no-compact-subset to h5diff
When the name of an object contains square brackets, h5diff was not able
to parse it correctly because “[ ]” were interpreted as the compact form
of subsetting.
h5dump has the special argument, --no-compact-subset to allow the use of
‘[‘ and ‘]’ in dataset names. h5diff now has this option as well.
Fixes GitHub issue #2682
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
-
Platforms Tested
===================
Linux 5.19.0-1023-aws GNU gcc, gfortran, g++
#24-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1
Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0
ifort (IFORT) 2021.9.0 20230302
(cmake and autotools)
Linux 5.16.14-200.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 5.14.21-cray_shasta_c cray-mpich/8.1.23
#1 SMP x86_64 GNU/Linux cce/15.0.0
(frontier) gcc/12.2.0
(cmake)
Linux 5.11.0-34-generic GNU gcc (GCC) 9.4.0-1ubuntu1
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1
Ubuntu 20.04 Ubuntu clang version 10.0.0-4ubuntu1
Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0
ifort (IFORT) 2021.9.0 20230302
(cmake and autotools)
Linux 4.14.0-115.35.1.1chaos aue/openmpi/4.1.4-arm-22.1.0.12
#1 SMP aarch64 GNU/Linux Arm C/C++/Fortran Compiler version 22.1
(stria) (based on LLVM 13.0.1)
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 12.0.1
(vortex) GCC 8.3.1
XL 2021.09.22
(cmake)
Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5
(lassen) GCC 8.3.1
XL 16.1.1.2, 2021.09.22, 2022.08.05
(cmake)
Linux-4.12.14-197.99-default cray-mpich/7.7.14
#1 SMP x86_64 GNU/Linux cce 12.0.3
(theta) GCC 11.2.0
llvm 9.0
Intel 19.1.2
Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
#1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly/kituo/moohan) Version 4.9.3, Version 7.2.0, Version 8.3.0,
Version 9.1.0, Version 10.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
GNU C (gcc) and C++ (g++) 4.8.5 compilers
with NAG Fortran Compiler Release 7.1(Hanzomon)
Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
with NAG Fortran Compiler Release 7.1(Hanzomon)
MPICH 3.1.4 compiled with GCC 4.9.3
MPICH 3.3 compiled with GCC 7.2.0
OpenMPI 3.1.3 compiled with GCC 7.2.0 and 4.1.2
compiled with GCC 9.1.0
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Versions 18.4.0 and 19.10-0
NVIDIA nvc, nvfortran and nvc++ version 22.5-0
(autotools and cmake)
Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2
#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
(quartz) GCC 7.3.0, 8.1.0
Intel 19.0.4, 2022.2, oneapi.2022.2
Linux-3.10.0-1160.90.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(skybridge) Intel/19.1
(cmake)
Linux-3.10.0-1160.90.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(attaway) Intel/19.1
(cmake)
Linux-3.10.0-1160.90.1.1chaos openmpi-intel/4.1
#1 SMP x86_64 GNU/Linux Intel/19.1.2, 21.3.0 and 22.2.0
(chama) (cmake)
macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
(macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
(bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011test) Intel icc/icpc/ifort version 16.0.2
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos6 Version 4.4.7 20120313
(platypus) Version 4.9.3, 5.3.0, 6.2.0
MPICH 3.1.4 compiled with GCC 4.9.3
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Version 19.10-0
Windows 10 x64 Visual Studio 2019 w/ clang 12.0.0
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2019 w/ Intel C/C++ only cmake)
Visual Studio 2022 w/ clang 15.0.1
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2023 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
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.
Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
CPP ptable test fails on both VS2017 and VS2019 with Intel and Clang compilers,
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-hlgiftools
cmake: HDF5_BUILD_HL_GIF_TOOLS=OFF