diff options
| author | Larry Knox <lrknox@hdfgroup.org> | 2022-11-01 21:14:52 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-11-01 21:14:52 (GMT) |
| commit | e4fb9aa96ef805e2dada8a78c32aab8cf8c34f4a (patch) | |
| tree | d2cb6c0511922333187ed12ac5dcb783e0967a4d | |
| parent | 94119211a74ce966380d0013efd48c6effe01f10 (diff) | |
| download | hdf5-e4fb9aa96ef805e2dada8a78c32aab8cf8c34f4a.zip hdf5-e4fb9aa96ef805e2dada8a78c32aab8cf8c34f4a.tar.gz hdf5-e4fb9aa96ef805e2dada8a78c32aab8cf8c34f4a.tar.bz2 | |
Update link for Software Changes in RELEASE.txt. (#2205)
* Update link for Software Changes in RELEASE.txt.
Add RELEASE.txt contents from 1.13.3 release to HISTORY-1_13.txt.
* Reverse order of entries in HISTORY-1_13.txt to match the order in previous HISTORY
files.
| -rw-r--r-- | release_docs/HISTORY-1_13.txt | 2384 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 2 |
2 files changed, 1428 insertions, 958 deletions
diff --git a/release_docs/HISTORY-1_13.txt b/release_docs/HISTORY-1_13.txt index 9a2f6e2..73b7feb 100644 --- a/release_docs/HISTORY-1_13.txt +++ b/release_docs/HISTORY-1_13.txt @@ -4,12 +4,1437 @@ 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 +04. Release Information for hdf5-1.13.3 03. Release Information for hdf5-1.13.2 +02. Release Information for hdf5-1.13.1 +01. Release Information for hdf5-1.13.0 [Search on the string '%%%%' for section breaks of each release.] + +%%%%1.13.3%%%% + +HDF5 version 1.13.3 released on 2022-10-28 +================================================================================ + + +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 HDF5-1.13.2 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + +New features and bug fixes previously added in 1.13.0 - 1.13.2 releases can be +found in release_docs/HISTORY-1_13.txt in the HDF5 source code. + + +New Features +============ + + Configuration: + ------------- + - Add new CMake configuration variable HDF5_USE_GNU_DIRS + + HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install + directory variables by including the CMake module, GNUInstallDirs(see CMake + documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file + sets various PATH variables for use during the build, test and install processes. + By default, the historical settings for these variables will be used. + + (ADB - 2022/10/21, GH-2175, GH-1716) + + - Update CMake minimum version to 3.18 + + Updated CMake minimum version from 3.12 to 3.18 and removed version checks + which were added for Windows features not yet available in version 3.12. Also + removed configure macros and code checks for old style code compile checks. + + (ADB - 2022/08/29, HDFFV-11329) + + + Library: + -------- + - Added multi dataset I/O feature + + Added H5Dread_multi, H5Dread_multi_async, H5Dwrite_multi, and + H5Dwrite_multi_async API routines to allow I/O on multiple datasets with a + single API call. Added H5Dread_multi_f and H5Dwrite_multi_f Fortran + wrappers. Updated VOL callbacks for dataset I/O to support multi dataset + I/O. + + (NAF - 2022/10/19) + + + Parallel Library: + ----------------- + - + + + Fortran Library: + ---------------- + - Added pointer based H5Dfill_f API + + Added Fortran H5Dfill_f, which is fully equivalent to the C API. It accepts pointers, + fill value datatype and datatype of dataspace elements. + + (MSB - 2022/10/10, HDFFV-10734.) + + C++ Library: + ------------ + - + + + Java Library: + ------------- + - + + + Tools: + ------ + - + + + High-Level APIs: + ---------------- + - + + + C Packet Table API: + ------------------- + - + + + Internal header file: + --------------------- + - + + + Documentation: + -------------- + - Doxygen User Guide documentation is available when configured and generated. + The resulting documentation files will be in the share/html subdirectory + of the HDF5 install directory. + + (ADB - 2022/08/09) + + +Support for new platforms, languages and compilers +================================================== + - + + +Bug Fixes since HDF5-1.13.2 release +=================================== + Library + ------- + - Fixed an issue with variable length attributes + + Previously, if a variable length attribute was held open while its file + was opened through another handle, the same attribute was opened through + the second file handle, and the second file and attribute handles were + closed, attempting to write to the attribute through the first handle + would cause an error. + + (NAF - 2022/10/24) + + - Memory leak + + A memory leak was observed with variable-length fill value in + H5O_fill_convert() function in H5Ofill.c. The leak is + manifested by running valgrind on test/set_extent.c. + + Previously, fill->buf is used for datatype conversion + if it is large enough and the variable-length information + is therefore lost. A buffer is now allocated regardless + so that the element in fill->buf can later be reclaimed. + + (VC - 2022/10/10, HDFFV-10840) + + - Fixed an issue with hyperslab selections + + Previously, when combining hyperslab selections, it was possible for the + library to produce an incorrect combined selection. + + (NAF - 2022/09/25) + + - Fixed an issue with attribute type conversion with compound datatypes + + Previously, when performing type conversion for attribute I/O with a + compound datatype, the library would not fill the background buffer with + the contents of the destination, potentially causing data to be lost when + only writing to a subset of the compound fields. + + (NAF - 2022/08/22, GitHub #2016) + + + Java Library + ------------ + - Improve variable-length datatype handling in JNI. + + The existing JNI read-write functions could handle variable-length datatypes + that were simple variable-length datatype with an atomic sub-datatype. More + complex combinations could not be handled. Reworked the JNI read-write functions + to recursively inspect datatypes for variable-length sub-datatypes. + + (ADB - 2022/10/12, HDFFV-8701,10375) + + + Configuration + ------------- + - + + + Tools + ----- + - + + + Performance + ------------- + - + + + Fortran API + ----------- + - + + 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 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 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 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-3.10.0-1160.0.0.1chaos 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-3.10.0-1160.71.1.1chaos 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 +============== + + ************************************************************ + * _ * + * (_) * + * __ ____ _ _ __ _ __ _ _ __ __ _ * + * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * + * \ V V / (_| | | | | | | | | | | (_| | * + * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * + * __/ | * + * |___/ * + * * + * Please refrain from running any program (including * + * HDF5 tests) which uses the subfiling VFD on Perlmutter * + * at the National Energy Research Scientific Computing * + * Center, NERSC. * + * Doing so may cause a system disruption due to subfiling * + * crashing Lustre. The sytem's Lustre bug is expected * + * to be resolved by 2023. * + * * + ************************************************************ + + 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 + + +%%%%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 + + +%%%%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 + + %%%%1.13.0%%%% HDF5 version 1.13.0 released on 2021-12-01 @@ -1766,959 +3191,4 @@ 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 diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 25e4e6e..5945e22 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -24,7 +24,7 @@ The official HDF5 releases can be obtained from: 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 + https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information If you have any questions or comments, please send them to the HDF Help Desk: |