From 88960489604861813b3676bc234f49ca8ee937d3 Mon Sep 17 00:00:00 2001 From: Larry Knox Date: Tue, 9 Feb 2021 15:31:09 -0600 Subject: Hdf5 1 8 (#328) * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Restores maintainer mode in the autotools (#200) Maintainer mode should be enabled in development branches. Also adds helpful commenting. Add script bin/switch_maint_mode. Add file changes generated by bin reconfigure in src/H5Edefin.h src/H5Einit.h src/H5Epubgen.h src/H5Eterm.h * Update MANIFEST for switch_maint_mode. * Update so numbers to match 1.8.22 release. * Updated configure with reconfigure. * Updates and corrections following HDF5 1.8.22 release. * Commit Makefile.ins with so version numbers updated by bin/reconfigure. Co-authored-by: H. Joe Lee Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> --- c++/src/H5CppDoc.h | 4 +- c++/src/H5Library.h | 2 +- c++/src/Makefile.in | 12 +- config/lt_vers.am | 12 +- fortran/src/Makefile.in | 12 +- hl/c++/src/Makefile.in | 12 +- hl/fortran/examples/run-hlfortran-ex.sh.in | 25 +- hl/fortran/src/Makefile.in | 12 +- hl/src/Makefile.in | 12 +- release_docs/HISTORY-1_8.txt | 876 +++++++++++++++++++++++++++++ release_docs/RELEASE.txt | 454 +-------------- src/Makefile.in | 12 +- 12 files changed, 964 insertions(+), 481 deletions(-) diff --git a/c++/src/H5CppDoc.h b/c++/src/H5CppDoc.h index 42ecb45..fc64e33 100644 --- a/c++/src/H5CppDoc.h +++ b/c++/src/H5CppDoc.h @@ -55,8 +55,8 @@ * * The HDF5 C++ API is included with the HDF5 source code and can * be obtained from - * - * https://support.hdfgroup.org/HDF5/release/obtainsrc.html. + * + * * https://portal.hdfgroup.org/display/support/Downloads. * * Please refer to the release_docs/INSTALL file under the top directory * of the HDF5 source code for information about installing, building, diff --git a/c++/src/H5Library.h b/c++/src/H5Library.h index f6571dd..6037539 100644 --- a/c++/src/H5Library.h +++ b/c++/src/H5Library.h @@ -20,7 +20,7 @@ namespace H5 { /*! \class H5Library \brief Class H5Library operates the HDF5 library globably. - It is not neccessary to construct an instance of H5Library to use the + It is not necessary to construct an instance of H5Library to use the methods. */ class H5_DLLCPP H5Library { diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in index 5a6605e..523217a 100644 --- a/c++/src/Makefile.in +++ b/c++/src/Makefile.in @@ -699,23 +699,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 # This is our main target diff --git a/config/lt_vers.am b/config/lt_vers.am index 95ee2b9..1f2646e 100644 --- a/config/lt_vers.am +++ b/config/lt_vers.am @@ -39,27 +39,27 @@ LT_VERS_AGE = 4 ## the effects of the H5_V1_x_COMPAT flag. ## Version numbers for wrapper shared library files. -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 diff --git a/fortran/src/Makefile.in b/fortran/src/Makefile.in index 8eaa893..9e42607 100644 --- a/fortran/src/Makefile.in +++ b/fortran/src/Makefile.in @@ -750,23 +750,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 AM_FCLIBS = $(LIBHDF5) diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in index 564525f..aea6f3f 100644 --- a/hl/c++/src/Makefile.in +++ b/hl/c++/src/Makefile.in @@ -689,23 +689,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 # This is our main target diff --git a/hl/fortran/examples/run-hlfortran-ex.sh.in b/hl/fortran/examples/run-hlfortran-ex.sh.in index 7a21563..30ce8ed 100644 --- a/hl/fortran/examples/run-hlfortran-ex.sh.in +++ b/hl/fortran/examples/run-hlfortran-ex.sh.in @@ -30,9 +30,32 @@ EXIT_SUCCESS=0 EXIT_FAILURE=1 +# +# Try to derive the path to the installation $prefix established +# by ./configure relative to the examples directory established by +# ./configure. If successful, set `prefix_relto_examplesdir` to the +# relative path. Otherwise, set `prefix_relto_examplesdir` to the +# absolute installation $prefix. +# +# This script uses the value of `prefix` in the user's environment, if +# it is set, below. The content of $() is evaluated in a sub-shell, so +# if `prefix` is set in the user's environment, the shell statements in +# $() won't clobbered it. +# +prefix_relto_examplesdir=$( +prefix=@prefix@ +examplesdir=@examplesdir@ +if [ ${examplesdir##${prefix}/} != ${examplesdir} ]; then + echo $(echo ${examplesdir##${prefix}/} | \ + sed 's,[^/][^/]*,..,g') +else + echo $prefix +fi +) + # Where the tool is installed. # default is relative path to installed location of the tools -prefix="${prefix:-@prefix@}" +prefix="${prefix:-../../${prefix_relto_examplesdir}}" PARALLEL=@PARALLEL@ # Am I in parallel mode? AR="@AR@" RANLIB="@RANLIB@" diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in index 3ef6634..c02d331 100644 --- a/hl/fortran/src/Makefile.in +++ b/hl/fortran/src/Makefile.in @@ -707,23 +707,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 # Our main target, the high-level fortran library diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in index cba7048..609b35f 100644 --- a/hl/src/Makefile.in +++ b/hl/src/Makefile.in @@ -688,23 +688,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 # This library is our main target. diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt index da3d849..2009a46 100644 --- a/release_docs/HISTORY-1_8.txt +++ b/release_docs/HISTORY-1_8.txt @@ -3,6 +3,7 @@ HDF5 History This file contains development history of HDF5 1.8 branch +24. Release Information for hdf5-1.8.22 23. Release Information for hdf5-1.8.21 22. Release Information for hdf5-1.8.20 21. Release Information for hdf5-1.8.19 @@ -29,6 +30,881 @@ This file contains development history of HDF5 1.8 branch [Search on the string '%%%%' for section breaks of each release.] +%%%%1.8.22%%%% + + +HDF5 version 1.8.22 released on 2021-02-05 +================================================================================ + +Notice: HDF5 1.8.22 will be followed later in 2021 by HDF5 1.8.23, the final +release of HDF5 1.8. HDF5 1.10 and HDF5 1.12 are currently available. +Detailed information about these releases can be found at: +https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information + +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://portal.hdfgroup.org/display/support/HDF5+1.8.22 + +Changes from Release to Release and New Features in the HDF5-1.8.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, Languages, and Compilers +- Bug Fixes since HDF5-1.8.21 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in an hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The option was refactored to use the CMake FetchContent process. This allows + more control over the filter targets, but required external project command + options to be moved to a CMake include file, HDF5PluginCache.cmake. It also + allows the filter examples to be used as tests for operation of the + filter plugins. + + (ADB - 2020/12/10, OESS-98) + + - CMake option to use MSVC naming conventions with MinGW + + HDF5_MSVC_NAMING_CONVENTION option enables using MSVC naming conventions + when using a MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to statically link gcc libs with MinGW + + HDF5_MINGW_STATIC_GCC_LIBS allows statically linking libg/libstdc++ + with the MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in an hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The necessary options are (see the INSTALL_CMake.txt file): + HDF5_ENABLE_PLUGIN_SUPPORT + PLUGIN_TGZ_NAME or PLUGIN_GIT_URL + There are more options necessary for various filters and the plugin project + documents should be referenced. + + (ADB - 2020/10/16, OESS-98) + + - Added CMake option to format source files + + HDF5_ENABLE_FORMATTERS option will enable creation of targets using the + pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder + or tool folder. All sources can be formatted by executing the format target; + make format + + (ADB - 2020/09/24) + + - CMake option to link the generated Fortran MOD files into the include + directory. + + The Fortran generation of MOD files by a Fortran compile can produce + different binary files between SHARED and STATIC compiles with different + compilers and/or different platforms. Note that it has been found that + different versions of Fortran compilers will produce incompatible MOD + files. Currently, CMake will locate these MOD files in subfolders of + the include directory and add that path to the Fortran library target + in the CMake config file, which can be used by the CMake find library + process. For other build systems using the binary from a CMake install, + a new CMake configuration can be used to copy the pre-chosen version + of the Fortran MOD files into the install include directory. + + The default will depend on the configuration of + BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: + YES YES Default to SHARED + YES NO Default to STATIC + NO YES Default to SHARED + NO NO Default to SHARED + The defaults can be overriden by setting the config option + HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + + (ADB - 2020/07/9, HDFFV-11116) + + - CMake option to use AEC (open source SZip) library instead of SZip + + The open source AEC library is a replacement library for SZip. In + order to use it for hdf5 the libaec CMake source was changed to add + "-fPIC" and exclude test files. Autotools does not build the + compression libraries within hdf5 builds. CMake requires new option + USE_LIBAEC to compensate for the different files produced by AEC build. + + (ADB - 2020/04/22, OESS-65) + + - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER + + Some handcrafted tests in HDFTests.c has been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. + + (ADB - 2020/03/24, TRILAB-24) + + - Both build systems use same set of warnings flags + + GNU C, C++ and gfortran warnings flags were moved to files in a config + sub-folder named gnu-warnings. Flags that only are available for a specific + version of the compiler are in files named with that version. + Clang C warnings flags were moved to files in a config sub-folder + named clang-warnings. + Intel C, Fortran warnings flags were moved to files in a config sub-folder + named intel-warnings. + + There are flags in files named "error-xxx" with warnings that may + be promoted to errors. Some source files may still need fixes. + + There are also pairs of files named "developer-xxx" and "no-developer-xxx" + that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the + configure option:--enable-developer-warnings. + + In addition, CMake no longer applies these warnings for examples. + + (ADB - 2020/03/24, TRILAB-192) + + - Update CMake minimum version to 3.12 + + Updated CMake minimum version to 3.12 and added version checks + for Windows features. + + (ADB - 2020/02/05, TRILABS-142) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + - Added common warnings files for gnu and intel + + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. + + (ADB - 2020/01/17) + + - Added new options to CMake for control of testing + + Added CMake options (default ON); + HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL + combined with: + HDF5_TEST_TOOLS + HDF5_TEST_EXAMPLES + HDF5_TEST_FORTRAN + HDF5_TEST_CPP + + (ADB - 2020/01/15, HDFFV-11001) + + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: + Address + Memory + MemoryWithOrigins + Undefined + Thread + Leak + 'Address;Undefined' + + (ADB - 2019/12/12, TRILAB-135) + + - Update CMake for VS2019 support + + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. + + (ADB - 2019/11/18, HDFFV-10962) + + - Add options to enable or disable building tools and tests + + Configure options --enable-tests and --enable-tools were added for + autotools configure. These options are enabled by default, and can be + disabled with either --disable-tests (or tools) or --enable-tests=no + (or --enable-tools=no). Build time is reduced ~20% when tools are + disabled, 35% when tests are disabled, 45% when both are disabled. + Reenabling them after the initial build requires running configure + again with the option(s) enabled. + + (DAP - 2019/07/24, HDFFV-9976) + + - Update CMake tests to use FIXTURES + + CMake test fixtures allow setup/cleanup tests and other dependency + requirements as properties for tests. This is more flexible for + modern CMake code. + + (ADB - 2019/07/23, HDFFV-10529) + + - Windows PDB files are always installed + + There are build configuration or flag settings for Windows that may not + generate PDB files. If those files are not generated then the install + utility will fail because those PDB files are not found. An optional + variable, DISABLE_PDB_FILES, was added to not install PDB files. + + (ADB - 2019/07/17, HDFFV-10424) + + - Add mingw CMake support with a toolchain file + + There have been a number of mingw issues that have been linked under + HDFFV-10845. It has been decided to implement the CMake cross-compiling + technique of toolchain files. We will use a linux platform with the mingw + compiler stack for testing. Only the C language is fully supported, and + the error tests are skipped. The C++ language works for static but shared + builds have a shared library issue with the mingw Standard Exception Handling + library, which is not available on Windows. Fortran has a common cross-compile + problem with the fortran configure tests. + + (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) + + - Windows PDB files are installed incorrectly + + For static builds, the PDB files for windows should be installed next + to the static libraries in the lib folder. Also the debug versions of + libraries and PDB files are now correctly built using the default + CMAKE_DEBUG_POSTFIX setting. + + (ADB - 2019/07/09, HDFFV-10581) + + - Add option to build only shared libs + + A request was made to prevent building static libraries and only build + shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will + skip building static libraries. Certain utility functions will build with + static libs but are not published. Tests are adjusted to use the correct + libraries depending on SHARED/STATIC settings. + + (ADB - 2019/06/12, HDFFV-10805) + + - Change tools tests to search the error stack + + There are some use cases which can cause the error stack of tools to be + different then the expected output. These tests now use grepTest.cmake; + this was changed to allow the error file to be searched for an expected string. + + (ADB - 2019/04/15, HDFFV-10741) + + - Add toolchain and cross-compile support + + Added info on using a toolchain file to INSTALL_CMAKE.txt. A + toolchain file is also used in cross-compiling, which requires + CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling + the fortran configure process, the HDF5UseFortran.cmake file macros + were improved. Fixed a Fortran configure file issue that incorrectly + used #cmakedefine instead of #define. + + (ADB - 2018/10/04, HDFFV-10594) + + - Add warnings flags for Intel compilers + + Identified Intel compiler specific warnings flags that should be used + instead of GNU flags. + + (ADB - 2018/10/04, TRILABS-21) + + - Add default rpath to targets + + Default rpaths should be set in shared executables and + libraries to allow the use of loading dependent libraries + without requiring LD_LIBRARY_PATH to be set. The default + path should be relative using @rpath on osx and $ORIGIN + on linux. Windows is not affected. + + (ADB - 2018/09/26, HDFFV-10594) + + + Library + ------- + - Improved performance of H5Sget_select_elem_pointlist + + Modified library to cache the point after the last block of points + retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the + same function to retrieve the next block of points from the list can + proceed immediately without needing to iterate over the point list. + + (NAF - 2021/01/19) + + - Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5 + + These new VFDs have been added in HDF5-1.8.22. Instructions to + enable them when configuring HDF5 on Linux and Mac may be found at + https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS. + + Installing on Windows requires CMake 3.13 and the following additional setup. + Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + + PATH should have been updated with the installation dir. + set ENV variable OPENSSL_ROOT_DIR to the installation dir. + set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + Install libcurl library (with dev files); + download the latest released version using git: https://github.com/curl/curl.git + + Open a Visual Studio Command prompt + change to the libcurl root folder + run the "buildconf.bat" batch file + change to the winbuild directory + nmake /f Makefile.vc mode=dll MACHINE=x64 + copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + set ENV variable CURL_ROOT to C:\curl (installation dir) + update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + the aws credentials file should be in %USERPROFILE%\.aws folder + set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + + (ADB - 2019/09/12, HDFFV-10854) + + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + + Rather than always running H5detect and generating H5Tinit.c and + H5make_libsettings.c, supply a location for those files with CMake variables + HDF5_USE_PREGEN and HDF5_USE_PREGEN_DIR. See release_docs/README_HPC + section VI "Other cross compiling options". + + (ADB - 2018/09/18, HDFFV-10332) + + + Parallel Library + ---------------- + - None + + + Tools + ----- + - None + + + High-Level APIs + --------------- + - None + + + Fortran API + ----------- + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + + (MSB - 2020/2/18, HDFFV-11029) + + + C++ API + ------- + - None + + High-Level APIs + --------------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added support for macOS High Sierra 10.13.6 with Apple LLVM version 10.0.0 + (clang-1000.10.44.4) and gfortran GNU Fortran (GCC) 6.3.0 + - Added support for macOS Mojave 10.14.6 with Apple LLVM version 10.0.1 + (clang-1001.0.46.4) and gfortran GNU Fortran (GCC) 6.3.0 + - Added support for Intel icc/icpc/ifort version 19.0.4.233 20190416 + - Added support for MPICH 3.3 compiled with GCC 7.2.0 + - Added support for NAG Fortran Compiler Release 7.0(Yurakuchho) Build 7011 + - Added support for OpenMPI 4.0.0 compiled with GCC 7.2.0 + - Added support for Visual Studio 2019 w/ Intel Fortran 19 (cmake) + - Added support for Visual Studio 2019 w/ MSMPI 10.1 (cmake) + + +Bug Fixes since HDF5-1.8.21 +=========================== + + Configuration + ------------- + - Correct option for default API version + + CMake options for default API version are not mutually exclusive. + Change the multiple BOOL options to a single STRING option with the + strings; v16, v18. + + (ADB - 2019/08/12, HDFFV-10879) + + - Fixes Autotools determination of the stat struct having an st_blocks field + + A missing parenthesis in an autoconf macro prevented building the test + code used to determine if the stat struct contains the st_blocks field. + Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define + found in H5pubconf.h will be defined correctly on both the Autotools and + CMake. This #define is only used in the tests and does not affect the + HDF5 C library. + + (DER - 2021/07/01, HDFFV-11201) + + + Library + ------- + - Fixed issues CVE-2018-14033 and CVE-2018-11206 + + h5dump aborted when buffer size was corrupted, causing buffer over-read. + + Checks for reading past the end of the buffer were added to prevent + the crashes and h5dump now simply fails with an error message when + this error condition occurs. + + (BMR - 2020/12/16, HDFFV-10480 and HDFFV-11159) + + - Fixed a segmentation fault + + A segmentation fault occurred with a Mathworks corrupted file. + + A detection of accessing a null pointer was added to prevent the problem. + + (BMR - 2020/12/14, HDFFV-11150) + + - Explicitly declared dlopen to use RTLD_LOCAL + + dlopen documentation states that if neither RTLD_GLOBAL nor + RTLD_LOCAL are specified, then the default behavior is unspecified. + The default on linux is usually RTLD_LOCAL while macos will default + to RTLD_GLOBAL. + + (ADB - 2020/08/12, HDFFV-11127) + + - Fixed issues CVE-2018-13870 and CVE-2018-13869 + + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. + + A check for reading past the end of the buffer was added to multiple + locations to prevent the crashes and h5dump now simply fails with an + error message when this error condition occurs. + + (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) + + - Fixed the segmentation fault when reading attributes with multiple threads + + It was reported that the reading of attributes with variable length string + datatype will crash with segmentation fault particularly when the number of + threads is high (>16 threads). The problem was due to the file pointer that + was set in the variable length string datatype for the attribute. That file + pointer was already closed when the attribute was accessed. + + The problem was fixed by setting the file pointer to the current opened file pointer + when the attribute was accessed. Similar patch up was done before when reading + dataset with variable length string datatype. + + (VC - 2020/07/13, HDFFV-11080) + + - Fixed CVE-2018-17435 + + The tool h52gif produced a segfault when the size of an attribute + message was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the attribute message's size + against the buffer size before accessing the buffer. h52gif was + also fixed to display the failure instead of silently exiting + after the segfault was eliminated. + + (BMR - 2020/6/19, HDFFV-10591) + + - Fixed user-created data access properties not existing in the property list + returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a + reproducer and a patch. + + (CJH - 2019/12/09, HDFFV-10934) + + - Fixed a bug that could cause an error or cause fill values to be + incorrectly read from a dataset that was written to using H5Dwrite_chunk + if the dataset was not closed after writing. + + (NAF - 2019/03/06, HDFFV-10716) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + + - Allow H5detect and H5make_libsettings to take a file as an argument. + + Rather than only writing to stdout, add a command argument to name + the file that H5detect and H5make_libsettings will use for output. + Without an argument, stdout is still used, so backwards compatibility + is maintained. + + (ADB - 2018/09/05, HDFFV-9059) + + + - Inappropriate linking with deprecated MPI C++ libraries + + HDF5 does not define *_SKIP_MPICXX in the public headers, so applications + can inadvertently wind up linking to the deprecated MPI C++ wrappers. + + MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h + so this should no longer be an issue. HDF5 makes no use of the deprecated + MPI C++ wrappers. + + (DER - 2019/09/17, HDFFV-10893) + + + Parallel Library + ---------------- + - None + + + Performance + ------------- + - None + + + Tools + ----- + - h5repack was fixed to repack the reference attributes properly. + The code line that checks if the update of reference inside a compound + datatype was misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/05, HDFFV-11014) + + + - h5repack was fixed to repack datasets with external storage + to other types of storage. + + New test added to repack files and verify the correct data using h5diff. + + (JS - 2019/09/25, HDFFV-10408) + (ADB - 2019/10/02, HDFFV-10918) + + + Fortran API + ----------- + - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and + libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for + autotools installs. These were added to match the name of the files + installed by CMmake and the general pattern of hl lib files. We will + change the names of the installed lib files to the matching name in + the next major release. + + (LRK - 2019/05/09, HDFFV-10596) + + + C++ API + ------- + - None + + + High-Level APIs: + --------------- + - None + + + Packet Table APIs: + ------------------ + - None + + +Supported Platforms +=================== + + Linux 3.10.0-1127.10.1.el7 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 2.6.32-573.18.1.el6 IBM XL C/C++ V13.1 + #1 SMP ppc64 GNU/Linux IBM XL Fortran V15.1 + (ostrich) + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-39) + Versions 4.9.3, 5.3.0, 6.3.0, 7.2.0 + 8.3.0, 9.1.0, 10.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 4.0.0 compiled with GCC 7.2.0 + NAG Fortran Compiler Release 7.0(Yurakuchho) Build 7011 + + SunOS 5.11 11.4.5.12.5.0 Sun C 5.15 SunOS_sparc 2017/05/30 + 32- and 64-bit Studio 12.6 Fortran 95 8.8 SunOS_sparc 2017/05/30 + (hedgehog) Sun C++ 5.15 SunOS_sparc 2017/05/30 + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (cmake) + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang-1001.0.46.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bobcat) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +Mac OS X High Sierra 10.13.6 64-bit n y/y n y y y +Mac OS X Mojave 10.14.6 64-bit n y/y n y y y +CentOS 7.2 Linux 2.10.0 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +Mac OS X High Sierra 10.13.6 64-bit y n y y +Mac OS X Mojave 10.14.6 64-bit y n y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-573.18.1.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Versions 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 16.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.196 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + OpenMPI 2.0.1 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 2.1.6-GCC-7.2.0-2.29, + 3.1.3-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang/3.9.0, 8.0.1 + (quartz) gcc/7.3.0, 8.1.0 + intel/16.0.4 + + Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang/coral-2018.08.08 + (lassen) gcc/7.3.1 + xl/2019.02.07 + + Linux-4.12.14-150.52-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux gcc/7.3.0, 8.2.0 + (cori) intel/19.0.3 + + Linux-4.4.180-94.107-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux gcc/8.3.0, 9.3.0 + (mutrino) intel/19.0.4 + + Fedora33 5.10.10-200.fc33.x86_64 + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20201125 + (Red Hat 10.2.1-9) + GNU Fortran (GCC) 10.2.1 20201125 + (Red Hat 10.2.1-9) + clang version 11.0.0 (Fedora 11.0.0-2.fc33) + (cmake and autotools) + + Ubuntu20.10 5.8.0-41-generic-x86_64 + #46-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1 + GNU Fortran (GCC) 10.2.0-13ubuntu1 + (cmake and autotools) + + SUSE15sp2 5.3.18-22-default + #1 SMP x86_64 GNU/Linux GNU gcc (SUSE Linux) 7.5.0 + GNU Fortran (SUSE Linux) 7.5.0 + clang version 7.0.1 + (tags/RELEASE_701/final 349238) + (cmake and autotools) + + Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 +l + + + macOS Big Sur 11.1 Apple clang version 12.0.0 (clang-1200.0.32.28) + 64-bit gfortran GNU Fortran )Homebrew GCC 10.2.0) 10.2.0 + (BIGSUR-1) Intel icc/icpc/ifort version 2021.1 + + SunOS 5.11 11.3 Sun C 5.15 SunOS_sparc + 32- and 64-bit Sun Fortran 95 8.8 SunOS_sparc + (emu) + + +Known Problems +============== + HDF5-1.8.22 binaries can replace the previous HDF5 version to run with + applications compiled and linked with HDF5-1.8.21 and possibly HDF5 versions + as early as 1.8.15. However, HDF5 checks versions in lib files against + versions in header files used to compile the application and will cause the + application to abort when they do not match. An environment variable + HDF5_DISABLE_VERSION_CHECK can be set to 2 to skip the check, to 1 to warn + but not abort, or to 0 for the default behavior, aborting when the HDF5 + version in the lib files does not match the version in the header files. + LRK - 2020/02/02 + + 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 + + The dynamically loaded plugin test libraries require undefined references + to HDF5 functions to be resolved at runtime in order to function properly. + With autotools on CYGWIN this results in build errors, and we have not + found a solution that satisfies both. Therefore the dynamically loaded + plugin tests have been disabled on CYGWIN. + + Mac OS X 10.13 added additional subdirectory structure in .libs for shared + libraries. Consequently "make check" will fail testing java and dynamically + loaded plugin test libraries attempting to copy files from the previous + locations in .libs directories. This will be addressed in the next release + when support for the Mac OS X 10.13 platform is added. + + 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. + + Various tests in dt_arith, fillval, and dtypes failed with core dump + during integer conversion on SunOS 5.11 with Sun C 5.15 SunOS_sparc in + 64-bit mode. It appears that these failures were caused by invalid + alignment, which is under investigation. + + 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. + + %%%%1.8.21%%%% diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 5e1d3b2..c6990ec 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -35,7 +35,7 @@ CONTENTS - New Features - Support for New Platforms, Languages, and Compilers -- Bug Fixes since HDF5-1.8.21 +- Bug Fixes since HDF5-1.8.22 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms @@ -48,314 +48,12 @@ New Features Configuration: ------------- - - CMake option to build the HDF filter plugins project as an external project - - The HDF filter plugins project is a collection of registered compression - filters that can be dynamically loaded when needed to access data stored - in a hdf5 file. This CMake-only option allows the plugins to be built and - distributed with the hdf5 library and tools. Like the options for szip and - zlib, either a tgz file or a git repository can be specified for the source. - - The option was refactored to use the CMake FetchContent process. This allows - more control over the filter targets, but required external project command - options to be moved to a CMake include file, HDF5PluginCache.cmake. Also - enabled the filter examples to be used as tests for operation of the - filter plugins. - - (ADB - 2020/12/10, OESS-98) - - - CMake option to use MSVC naming conventions with MinGW - - HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions - when using a MinGW toolchain - - (xan - 2020/10/30) - - - CMake option to statically link gcc libs with MinGW - - HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ - with the MinGW toolchain - - (xan - 2020/10/30) - - - CMake option to build the HDF filter plugins project as an external project - - The HDF filter plugins project is a collection of registered compression - filters that can be dynamically loaded when needed to access data stored - in a hdf5 file. This CMake-only option allows the plugins to be built and - distributed with the hdf5 library and tools. Like the options for szip and - zlib, either a tgz file or a git repository can be specified for the source. - - The necessary options are (see the INSTALL_CMake.txt file): - HDF5_ENABLE_PLUGIN_SUPPORT - PLUGIN_TGZ_NAME or PLUGIN_GIT_URL - There are more options necessary for various filters and the plugin project - documents should be referenced. - - (ADB - 2020/10/16, OESS-98) - - - Added CMake option to format source files - - HDF5_ENABLE_FORMATTERS option will enable creation of targets using the - pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder - or tool folder. All sources can be formatted by executing the format target; - make format - - (ADB - 2020/09/24) - - - CMake option to link the generated Fortran MOD files into the include - directory. - - The Fortran generation of MOD files by a Fortran compile can produce - different binary files between SHARED and STATIC compiles with different - compilers and/or different platforms. Note that it has been found that - different versions of Fortran compilers will produce incompatible MOD - files. Currently, CMake will locate these MOD files in subfolders of - the include directory and add that path to the Fortran library target - in the CMake config file, which can be used by the CMake find library - process. For other build systems using the binary from a CMake install, - a new CMake configuration can be used to copy the pre-chosen version - of the Fortran MOD files into the install include directory. - - The default will depend on the configuration of - BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: - YES YES Default to SHARED - YES NO Default to STATIC - NO YES Default to SHARED - NO NO Default to SHARED - The defaults can be overriden by setting the config option - HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC - - (ADB - 2020/07/9, HDFFV-11116) - - - CMake option to use AEC (open source SZip) library instead of SZip - - The open source AEC library is a replacement library for SZip. In - order to use it for hdf5 the libaec CMake source was changed to add - "-fPIC" and exclude test files. Autotools does not build the - compression libraries within hdf5 builds. New option USE_LIBAEC is - required to compensate for the different files produced by AEC build. - - (ADB - 2020/04/22, OESS-65) - - - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER - - Some handcrafted tests in HDFTests.c has been removed and the CMake - CHECK_STRUCT_HAS_MEMBER module has been used. - - (ADB - 2020/03/24, TRILAB-24) - - - Both build systems use same set of warnings flags - - GNU C, C++ and gfortran warnings flags were moved to files in a config - sub-folder named gnu-warnings. Flags that only are available for a specific - version of the compiler are in files named with that version. - Clang C warnings flags were moved to files in a config sub-folder - named clang-warnings. - Intel C, Fortran warnings flags were moved to files in a config sub-folder - named intel-warnings. - - There are flags in named "error-xxx" files with warnings that may - be promoted to errors. Some source files may still need fixes. - - There are also pairs of files named "developer-xxx" and "no-developer-xxx" - that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the - configure option:--enable-developer-warnings. - - In addition, CMake no longer applies these warnings for examples. - - (ADB - 2020/03/24, TRILAB-192) - - - Update CMake minimum version to 3.12 - - Updated CMake minimum version to 3.12 and added version checks - for Windows features. - - (ADB - 2020/02/05, TRILABS-142) - - - Fixed CMake include properties for Fortran libraries - - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. - - (ADB - 2020/02/04, HDFFV-11012) - - - Added common warnings files for gnu and intel - - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. - - (ADB - 2020/01/17) - - - Added new options to CMake for control of testing - - Added CMake options (default ON); - HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL - combined with: - HDF5_TEST_TOOLS - HDF5_TEST_EXAMPLES - HDF5_TEST_FORTRAN - HDF5_TEST_CPP - - (ADB - 2020/01/15, HDFFV-11001) - - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: - Address - Memory - MemoryWithOrigins - Undefined - Thread - Leak - 'Address;Undefined' - - (ADB - 2019/12/12, TRILAB-135) - - - Update CMake for VS2019 support - - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. - - (ADB - 2019/11/18, HDFFV-10962) - - - Add options to enable or disable building tools and tests - - Configure options --enable-tests and --enable-tools were added for - autotools configure. These options are enabled by default, and can be - disabled with either --disable-tests (or tools) or --enable-tests=no - (or --enable-tools=no). Build time is reduced ~20% when tools are - disabled, 35% when tests are disabled, 45% when both are disabled. - Reenabling them after the initial build requires running configure - again with the option(s) enabled. - - (DAP - 2019/07/24, HDFFV-9976) - - - Update CMake tests to use FIXTURES - - CMake test fixtures allow setup/cleanup tests and other dependency - requirements as properties for tests. This is more flexible for - modern CMake code. - - (ADB - 2019/07/23, HDFFV-10529) - - - Windows PDB files are always installed - - There are build configuration or flag settings for Windows that may not - generate PDB files. If those files are not generated then the install - utility will fail because those PDB files are not found. An optional - variable, DISABLE_PDB_FILES, was added to not install PDB files. - - (ADB - 2019/07/17, HDFFV-10424) - - - Add mingw CMake support with a toolchain file - - There has been a number of mingw issues that has been linked under - HDFFV-10845. It has been decided to implement the CMake cross-compiling - technique of toolchain files. We will use a linux platform with the mingw - compiler stack for testing. Only the C language is fully supported, and - the error tests are skipped. The C++ language works for static but shared - builds has a shared library issue with the mingw Standard Exception Handling - library, which is not available on Windows. Fortran has a common cross-compile - problem with the fortran configure tests. - - (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) - - - Windows PDB files are installed incorrectly - - For static builds, the PDB files for windows should be installed next - to the static libraries in the lib folder. Also the debug versions of - libraries and PDB files are now correctly built using the default - CMAKE_DEBUG_POSTFIX setting. - - (ADB - 2019/07/09, HDFFV-10581) - - - Add option to build only shared libs - - A request was made to prevent building static libraries and only build - shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will - skip building static libraries. Certain utility functions will build with - static libs but are not published. Tests are adjusted to use the correct - libraries depending on SHARED/STATIC settings. - - (ADB - 2019/06/12, HDFFV-10805) - - - Add toolchain and cross-compile support - - Added info on using a toolchain file to INSTALL_CMAKE.txt. A - toolchain file is also used in cross-compiling, which requires - CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling - the fortran configure process, the HDF5UseFortran.cmake file macros - were improved. Fixed a Fortran configure file issue that incorrectly - used #cmakedefine instead of #define. - - (ADB - 2018/10/04, HDFFV-10594) - - - Add warning flags for Intel compilers - - Identified Intel compiler specific warnings flags that should be used - instead of GNU flags. - - (ADB - 2018/10/04, TRILABS-21) - - - Add default rpath to targets - - Default rpaths should be set in shared executables and - libraries to allow the use of loading dependent libraries - without requiring LD_LIBRARY_PATH to be set. The default - path should be relative using @rpath on osx and $ORIGIN - on linux. Windows is not affected. - - (ADB - 2018/09/26, HDFFV-10594) + - None Library ------- - - Improved performance of H5Sget_select_elem_pointlist - - Modified library to cache the point after the last block of points - retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the - same function to retrieve the next block of points from the list can - proceed immediately without needing to iterate over the point list. - - (NAF - 2021/01/19) - - - Add S3 and HDFS VFDs to HDF5 maintenance - - Fix windows requirements and java tests. Windows requires CMake 3.13. - Install openssl library (with dev files); - from "Shining Light Productions". msi package preferred. - - PATH should have been updated with the installation dir. - set ENV variable OPENSSL_ROOT_DIR to the installation dir. - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg - Install libcurl library (with dev files); - download the latest released version using git: https://github.com/curl/curl.git - - Open a Visual Studio Command prompt - change to the libcurl root folder - run the "buildconf.bat" batch file - change to the winbuild directory - nmake /f Makefile.vc mode=dll MACHINE=x64 - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) - set ENV variable CURL_ROOT to C:\curl (installation dir) - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). - the aws credentials file should be in %USERPROFILE%\.aws folder - set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" - - (ADB - 2019/09/12, HDFFV-10854) - - - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. - - Rather than always running H5detect and generating H5Tinit.c and - H5make_libsettings.c, supply a location for those files. - - (ADB - 2018/09/18, HDFFV-10332) + - None Parallel Library @@ -375,15 +73,14 @@ New Features Fortran API ----------- - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - - (MSB - 2020/2/18, HDFFV-11029) + - None C++ API ------- - None + High-Level APIs --------------- - None @@ -399,112 +96,12 @@ Bug Fixes since HDF5-1.8.21 Configuration ------------- - - Correct option for default API version - - CMake options for default API version are not mutually exclusive. - Change the multiple BOOL options to a single STRING option with the - strings; v16, v18. - - (ADB - 2019/08/12, HDFFV-10879) - - - Fixes Autotools determination of the stat struct having an st_blocks field - - A missing parenthesis in an autoconf macro prevented building the test - code used to determine if the stat struct contains the st_blocks field. - Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define - found in H5pubconf.h will be defined correctly on both the Autotools and - CMake. This #define is only used in the tests and does not affect the - HDF5 C library. - - (DER - 2021/07/01, HDFFV-11201) + - None Library ------- - - Explicitly declared dlopen to use RTLD_LOCAL - - dlopen documentation states that if neither RTLD_GLOBAL nor - RTLD_LOCAL are specified, then the default behavior is unspecified. - The default on linux is usually RTLD_LOCAL while macos will default - to RTLD_GLOBAL. - - (ADB - 2020/08/12, HDFFV-11127) - - - Fixed issues CVE-2018-13870 and CVE-2018-13869 - - When a buffer overflow occurred because a name length was corrupted - and became very large, h5dump crashed on memory access violation. - - A check for reading past the end of the buffer was added to multiple - locations to prevent the crashes and h5dump now simply fails with an - error message when this error condition occurs. - - (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - - - Fixed the segmentation fault when reading attributes with multiple threads - - It was reported that the reading of attributes with variable length string - datatype will crash with segmentation fault particularly when the number of - threads is high (>16 threads). The problem was due to the file pointer that - was set in the variable length string datatype for the attribute. That file - pointer was already closed when the attribute was accessed. - - The problem was fixed by setting the file pointer to the current opened file pointer - when the attribute was accessed. Similar patch up was done before when reading - dataset with variable length string datatype. - - (VC - 2020/07/13, HDFFV-11080) - - - Fixed CVE-2018-17435 - - The tool h52gif produced a segfault when the size of an attribute - message was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the attribute message's size - against the buffer size before accessing the buffer. h52gif was - also fixed to display the failure instead of silently exiting - after the segfault was eliminated. - - (BMR - 2020/6/19, HDFFV-10591) - - - Fixed user-created data access properties not existing in the property list - returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a - reproducer and a patch. - - (CJH - 2019/12/09, HDFFV-10934) - - - Fixed a bug that could cause an error or cause fill values to be - incorrectly read from a dataset that was written to using H5Dwrite_chunk - if the dataset was not closed after writing. - - (NAF - 2019/03/06, HDFFV-10716) - - - Fixed a potential invalid memory access and failure that could occur when - decoding an unknown object header message (from a future version of the - library). - - (NAF - 2019/01/07) - - - Allow H5detect and H5make_libsettings to take a file as an argument. - - Rather than only writing to stdout, add a command argument to name - the file that H5detect and H5make_libsettings will use for output. - Without an argument, stdout is still used, so backwards compatibility - is maintained. - - (ADB - 2018/09/05, HDFFV-9059) - - - - Inappropriate linking with deprecated MPI C++ libraries - - HDF5 does not define *_SKIP_MPICXX in the public headers, so applications - can inadvertently wind up linking to the deprecated MPI C++ wrappers. - - MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h - so this should no longer be an issue. HDF5 makes no use of the deprecated - MPI C++ wrappers. - - (DER - 2019/09/17, HDFFV-10893) + - None Performance @@ -514,36 +111,13 @@ Bug Fixes since HDF5-1.8.21 Tools ----- - - h5repack was fixed to repack the reference attributes properly. - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/05, HDFFV-11014) - - - - h5repack was fixed to repack datasets with external storage - to other types of storage. - - New test added to repack files and verify the correct data using h5diff. - - (JS - 2019/09/25, HDFFV-10408) - (ADB - 2019/10/02, HDFFV-10918) + - None Fortran API ----------- - - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and - libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for - autotools installs. These were added to match the name of the files - installed by CMmake and the general pattern of hl lib files. We will - change the names of the installed lib files to the matching name in - the next major release. + - None - (LRK - 2019/05/09, HDFFV-10596) C++ API ------- @@ -725,6 +299,16 @@ The following platforms are not supported but have been tested for this release. Known Problems ============== + HDF5-1.8.22 binaries can replace the previous HDF5 version to run with + applications compiled and linked with HDF5-1.8.21 and possibly HDF5 versions + as early as 1.8.15. However, HDF5 checks versions in lib files against + versions in header files used to compile the application and will cause the + application to abort when they do not match. An environment variable + HDF5_DISABLE_VERSION_CHECK can be set to 2 to skip the check, to 1 to warn + but not abort, or to 0 for the default behavior, aborting when the HDF5 + version in the lib files does not match the version in the header files. + LRK - 2020/02/02 + 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. diff --git a/src/Makefile.in b/src/Makefile.in index fe848eb7..5563d1c 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -795,23 +795,23 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 LT_VERS_INTERFACE = 14 LT_VERS_REVISION = 0 LT_VERS_AGE = 4 -LT_CXX_VERS_INTERFACE = 15 +LT_CXX_VERS_INTERFACE = 16 LT_CXX_VERS_REVISION = 1 LT_CXX_VERS_AGE = 0 LT_F_VERS_INTERFACE = 10 -LT_F_VERS_REVISION = 6 +LT_F_VERS_REVISION = 7 LT_F_VERS_AGE = 0 LT_HL_VERS_INTERFACE = 12 -LT_HL_VERS_REVISION = 2 +LT_HL_VERS_REVISION = 3 LT_HL_VERS_AGE = 2 LT_HL_CXX_VERS_INTERFACE = 12 -LT_HL_CXX_VERS_REVISION = 2 +LT_HL_CXX_VERS_REVISION = 3 LT_HL_CXX_VERS_AGE = 1 LT_HL_F_VERS_INTERFACE = 10 -LT_HL_F_VERS_REVISION = 5 +LT_HL_F_VERS_REVISION = 6 LT_HL_F_VERS_AGE = 0 LT_TOOLS_VERS_INTERFACE = 10 -LT_TOOLS_VERS_REVISION = 7 +LT_TOOLS_VERS_REVISION = 8 LT_TOOLS_VERS_AGE = 0 # Our main target, the HDF5 library -- cgit v0.12