From 72f0f30157ec020914ead002ec475963de7c3e15 Mon Sep 17 00:00:00 2001 From: Larry Knox Date: Sat, 28 Sep 2024 12:14:41 -0500 Subject: [PATCH] Hdf5 1 14 5 update (#4895) * Fix issues with large external data files (#4843) (#4847) * Fixed a memory leak from H5FL_blk_malloc (#4882) In H5F__accum_reset(), when H5F__accum_flush() failed, the freeing of f_sh->accum.buf was never reached, causing resource leak. @fortnern added the third argument to H5F__accum_reset() so we can free f_sh->accum.buf when we close the file, that is, when H5F__accum_reset() is called from the H5F__dest() route, and can leave the accumulator in place otherwise. * Added an entry for the GH-4585 fix (#4889) * Fix an incorrect returned value by H5LTfind_dataset() (#4869) H5LTfind_dataset() returns true for non-existing datasets because it only compares up to the length of the searched string, such as "Day" vs "DayNight" (issue GH-4780). This PR applied the user's patch and added tests. * Fix minor spelling in documentation (#4870) * Updated Platforms tested in RELEASE.txt Incremented version subrelease to -3. --- README.md | 2 +- config/cmake/scripts/HDF5config.cmake | 2 +- configure | 22 ++--- configure.ac | 2 +- release_docs/NEWSLETTER.txt | 2 +- release_docs/RELEASE.txt | 122 ++++++++++++-------------- src/H5public.h | 6 +- 7 files changed, 73 insertions(+), 85 deletions(-) diff --git a/README.md b/README.md index 2f4f512f8c4..c2a9f2ea50c 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -HDF5 version 1.14.5-2 currently under development +HDF5 version 1.14.5-3 currently under development ![HDF5 Logo](doxygen/img/HDF5.png) diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index 21f21c9d80c..102e2b94ba2 100644 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -38,7 +38,7 @@ cmake_minimum_required (VERSION 3.18) ############################################################################## set (CTEST_SOURCE_VERSION "1.14.5") -set (CTEST_SOURCE_VERSEXT "-2") +set (CTEST_SOURCE_VERSEXT "-3") ############################################################################## # handle input parameters to script. diff --git a/configure b/configure index c9da1a0298b..f844b15efc3 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.71 for HDF5 1.14.5-2. +# Generated by GNU Autoconf 2.71 for HDF5 1.14.5-3. # # Report bugs to . # @@ -629,8 +629,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='HDF5' PACKAGE_TARNAME='hdf5' -PACKAGE_VERSION='1.14.5-2' -PACKAGE_STRING='HDF5 1.14.5-2' +PACKAGE_VERSION='1.14.5-3' +PACKAGE_STRING='HDF5 1.14.5-3' PACKAGE_BUGREPORT='help@hdfgroup.org' PACKAGE_URL='' @@ -1711,7 +1711,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures HDF5 1.14.5-2 to adapt to many kinds of systems. +\`configure' configures HDF5 1.14.5-3 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1782,7 +1782,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of HDF5 1.14.5-2:";; + short | recursive ) echo "Configuration of HDF5 1.14.5-3:";; esac cat <<\_ACEOF @@ -2098,7 +2098,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -HDF5 configure 1.14.5-2 +HDF5 configure 1.14.5-3 generated by GNU Autoconf 2.71 Copyright (C) 2021 Free Software Foundation, Inc. @@ -2910,7 +2910,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by HDF5 $as_me 1.14.5-2, which was +It was created by HDF5 $as_me 1.14.5-3, which was generated by GNU Autoconf 2.71. Invocation command line was $ $0$ac_configure_args_raw @@ -4410,7 +4410,7 @@ fi # Define the identity of the package. PACKAGE='hdf5' - VERSION='1.14.5-2' + VERSION='1.14.5-3' printf "%s\n" "#define PACKAGE \"$PACKAGE\"" >>confdefs.h @@ -35221,7 +35221,7 @@ Usage: $0 [OPTIONS] Report bugs to ." lt_cl_version="\ -HDF5 config.lt 1.14.5-2 +HDF5 config.lt 1.14.5-3 configured by $0, generated by GNU Autoconf 2.71. Copyright (C) 2011 Free Software Foundation, Inc. @@ -37398,7 +37398,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by HDF5 $as_me 1.14.5-2, which was +This file was extended by HDF5 $as_me 1.14.5-3, which was generated by GNU Autoconf 2.71. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -37470,7 +37470,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config='$ac_cs_config_escaped' ac_cs_version="\\ -HDF5 config.status 1.14.5-2 +HDF5 config.status 1.14.5-3 configured by $0, generated by GNU Autoconf 2.71, with options \\"\$ac_cs_config\\" diff --git a/configure.ac b/configure.ac index 47c41f6f12f..5fa8095103a 100644 --- a/configure.ac +++ b/configure.ac @@ -22,7 +22,7 @@ AC_PREREQ([2.71]) ## NOTE: Do not forget to change the version number here when we do a ## release!!! ## -AC_INIT([HDF5], [1.14.5-2], [help@hdfgroup.org]) +AC_INIT([HDF5], [1.14.5-3], [help@hdfgroup.org]) AC_CONFIG_SRCDIR([src/H5.c]) AC_CONFIG_HEADERS([src/H5config.h]) diff --git a/release_docs/NEWSLETTER.txt b/release_docs/NEWSLETTER.txt index a622e45942f..e114b54af6f 100644 --- a/release_docs/NEWSLETTER.txt +++ b/release_docs/NEWSLETTER.txt @@ -1,4 +1,4 @@ -HDF5 version 1.14.5-2 currently under development +HDF5 version 1.14.5-3 currently under development Features included for the next major release: ---------------------------------------------------------------------------- diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 78ed4d5d8b5..8e425744524 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,4 +1,4 @@ -HDF5 version 1.14.5-2 currently under development +HDF5 version 1.14.5-3 currently under development ================================================================================ @@ -205,7 +205,8 @@ Bug Fixes since HDF5-1.14.4 release Fixes GitHub #4780 - - Fixed a segfault by H5Gmove2, extending to H5Lcopy and H5Lmove + + - Fixed a segfault by H5Gmove2, extended to fix H5Lcopy and H5Lmove A user's application segfaulted when it passed in an invalid location ID to H5Gmove2. The src and dst location IDs must be either a file or a group @@ -224,7 +225,8 @@ Bug Fixes since HDF5-1.14.4 release Fixes GitHub #4730 - - Fixed a segfault by H5Fget_intent(), extending to several other functions + + - Fixed a segfault by H5Fget_intent(), extended to fix several other functions A user's program generated a segfault when the ID passed into H5Fget_intent() was not a file ID. In addition to H5Fget_intent(), a number of APIs also failed @@ -458,64 +460,68 @@ Bug Fixes since HDF5-1.14.4 release Platforms Tested =================== - - HDF5 supports the latest macOS versions, including the current and two - preceding releases. As new major macOS versions become available, HDF5 - will discontinue support for the oldest version and add the latest - version to its list of compatible systems, along with the previous two - releases. - - 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) + - HDF5 is tested with the two latest macOS versions that are available + on github runners. As new major macOS versions become available, HDF5 + will discontinue support for the older version and add the new latest + version to its list of compatible systems, along with the previous + version. + + Linux 6.8.0-1010-aws GNU gcc, gfortran, g++ + #10-Ubuntu SMP 2024 x86_64 (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU/Linux Ubuntu 24.04 Ubuntu clang version 18.1.3 (1ubuntu1) + Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 + ifx (IFX) 2024.2.0 20240602 (cmake and autotools) - 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 + Linux 6.5.0-1018-aws GNU gcc, gfortran, g++ + #18-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 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 + Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2 + ifx (IFX) 2024.0.2 20231213 (cmake and autotools) - Linux 5.14.21-cray_shasta_c cray-mpich/8.1.23 + Linux 5.14.21-cray_shasta_c cray-mpich/8.1.28 #1 SMP x86_64 GNU/Linux cce/15.0.0 - (frontier) gcc/12.2.0 + (frontier) gcc/13.2 (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 + Linux 5.14.0-427.24.1.el9_4 GNU gcc, gfortran, g++ (Red Hat 11.4.1-3) + #1 SMP x86_64 GNU/Linux clang version 17.0.6 + Rocky 9 Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 + ifx (IFX) 2024.2.0 (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) + Linux-4.18.0-553.16.1.1toss.t4 openmpi/4.1.2 + #1 SMP x86_64 GNU/Linux clang 14.0.6 + (corona, dane) GCC 12.1.1 + Intel(R) oneAPI DPC++/C++ Compiler 2023.2.1 + ifx (IFX) 2023.2.1 + + Linux-4.18.0-553.5.1.1toss.t4 openmpi/4.1/4.1.6 + #1 SMP x86_64 GNU/Linux clang 16.0.6 + (eclipse) GCC 12.3.0 + Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2 + ifx (IFX) 2024.0.2 (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 + #1 SMP ppc64le GNU/Linux clang 17.0.6 + (vortex) GCC 12.2.1 + nvhpc 24.1 + XL 2023.06.28 (cmake) - Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 + Linux-4.14.0-115.35.1 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 14.0.5, 15.0.6 (lassen) GCC 8.3.1 - XL 16.1.1.2, 2021.09.22, 2022.08.05 + XL 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++) + Linux 3.10.0-1160.80.1.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, @@ -538,37 +544,19 @@ Platforms Tested (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 + Linux-3.10.0-1160.119.1.1chaos openmpi/4.1.4 + #1 SMP x86_64 GNU/Linux clang 16.0.6 + (skybridge) Intel(R) oneAPI DPC++/C++ Compiler 2023.2.0 + ifx (IFX) 2023.2.0 (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 + #1 SMP x86_64 GNU/Linux clang 16.0.6 + (attaway) GCC 12.1.0 + Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2 + ifx (IFX) 2024.0.2 (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 @@ -581,9 +569,9 @@ Platforms Tested 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 + Visual Studio 2022 w/ clang 17.0.3 with MSVC-like command-line (C/C++ only - cmake) - Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2023 (cmake) + Visual Studio 2022 w/ Intel C/C++ oneAPI 2023 (cmake) Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) diff --git a/src/H5public.h b/src/H5public.h index a03cbbc4b65..b5cb7cca7fe 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -87,15 +87,15 @@ /** * For pre-releases like \c snap0. Empty string for official releases. */ -#define H5_VERS_SUBRELEASE "2" +#define H5_VERS_SUBRELEASE "3" /** * Short version string */ -#define H5_VERS_STR "1.14.5-2" +#define H5_VERS_STR "1.14.5-3" /** * Full version string */ -#define H5_VERS_INFO "HDF5 library version: 1.14.5-2" +#define H5_VERS_INFO "HDF5 library version: 1.14.5-3" #define H5check() H5check_version(H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE)