883 lines
36 KiB
Plaintext
883 lines
36 KiB
Plaintext
HDF5 version 1.10.7-1 currently under development
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================================================================================
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INTRODUCTION
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This document describes the differences between this release and the previous
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HDF5 release. It contains information on the platforms tested and known
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problems in this release. For more details check the HISTORY*.txt files in the
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HDF5 source.
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Note that documentation in the links below will be updated at the time of each
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final release.
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Links to HDF5 documentation can be found on The HDF5 web page:
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https://portal.hdfgroup.org/display/HDF5/HDF5
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The official HDF5 releases can be obtained from:
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https://www.hdfgroup.org/downloads/hdf5/
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Changes from Release to Release and New Features in the HDF5-1.10.x release series
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can be found at:
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https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.10.5
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- Supported Platforms
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- Tested Configuration Features Summary
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- More Tested Platforms
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- Known Problems
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- CMake vs. Autotools installations
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New Features
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============
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Configuration:
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-------------
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- CMake option to link the generated Fortran MOD files into the include
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directory.
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The Fortran generation of MOD files by a Fortran compile can produce
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different binary files between SHARED and STATIC compiles with different
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compilers and/or different platforms. Note that it has been found that
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different versions of Fortran compilers will produce incompatible MOD
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files. Currently, CMake will locate these MOD files in subfolders of
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the include directory and add that path to the Fortran library target
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in the CMake config file, which can be used by the CMake find library
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process. For other build systems using the binary from a CMake install,
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a new CMake configuration can be used to copy the pre-chosen version
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of the Fortran MOD files into the install include directory.
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The default will depend on the configuration of
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BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
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YES YES Default to SHARED
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YES NO Default to STATIC
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NO YES Default to SHARED
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NO NO Default to SHARED
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The defaults can be overriden by setting the config option
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HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
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(ADB - 2020/07/9, HDFFV-11116)
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- CMake option to use AEC (open source SZip) library instead of SZip
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The open source AEC library is a replacement library for SZip. In
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order to use it for hdf5 the libaec CMake source was changed to add
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"-fPIC" and exclude test files. Autotools does not build the
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compression libraries within hdf5 builds. New option USE_LIBAEC is
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required to compensate for the different files produced by AEC build.
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(ADB - 2020/04/22, OESS-65)
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- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
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Some handcrafted tests in HDFTests.c has been removed and the CMake
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CHECK_STRUCT_HAS_MEMBER module has been used.
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(ADB - 2020/03/24, TRILAB-24)
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- Both build systems use same set of warnings flags
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GNU C, C++ and gfortran warnings flags were moved to files in a config
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sub-folder named gnu-warnings. Flags that only are available for a specific
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version of the compiler are in files named with that version.
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Clang C warnings flags were moved to files in a config sub-folder
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named clang-warnings.
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Intel C, Fortran warnings flags were moved to files in a config sub-folder
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named intel-warnings.
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There are flags in named "error-xxx" files with warnings that may
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be promoted to errors. Some source files may still need fixes.
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There are also pairs of files named "developer-xxx" and "no-developer-xxx"
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that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
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configure option:--enable-developer-warnings.
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In addition, CMake no longer applies these warnings for examples.
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(ADB - 2020/03/24, TRILAB-192)
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- Update CMake minimum version to 3.12
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Updated CMake minimum version to 3.12 and added version checks
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for Windows features.
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(ADB - 2020/02/05, TRILABS-142)
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- Fixed CMake include properties for Fortran libraries
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Corrected the library properties for Fortran to use the
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correct path for the Fortran module files.
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(ADB - 2020/02/04, HDFFV-11012)
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- Added common warnings files for gnu and intel
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Added warnings files to use one common set of flags
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during configure for both autotools and CMake build
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systems. The initial implementation only affects a
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general set of flags for gnu and intel compilers.
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(ADB - 2020/01/17)
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- Added new options to CMake for control of testing
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Added CMake options (default ON);
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HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
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combined with:
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HDF5_TEST_TOOLS
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HDF5_TEST_EXAMPLES
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HDF5_TEST_SWMR
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HDF5_TEST_FORTRAN
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HDF5_TEST_CPP
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HDF5_TEST_JAVA
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(ADB - 2020/01/15, HDFFV-11001)
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- Added Clang sanitizers to CMake for analyzer support if compiler is clang.
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Added CMake code and files to execute the Clang sanitizers if
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HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
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is set to one of the following:
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Address
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Memory
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MemoryWithOrigins
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Undefined
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Thread
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Leak
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'Address;Undefined'
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(ADB - 2019/12/12, TRILAB-135)
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- Update CMake for VS2019 support
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CMake added support for VS2019 in version 3.15. Changes to the CMake
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generator setting required changes to scripts. Also updated version
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references in CMake files as necessary.
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(ADB - 2019/11/18, HDFFV-10962)
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- Update CMake options to match new autotools options
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Add configure options (autotools - CMake):
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enable-asserts HDF5_ENABLE_ASSERTS
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enable-symbols HDF5_ENABLE_SYMBOLS
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enable-profiling HDF5_ENABLE_PROFILING
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enable-optimization HDF5_ENABLE_OPTIMIZATION
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In addition NDEBUG is no longer forced defined and relies on the CMake
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process.
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(ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
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- Update CMake tests to use FIXTURES
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CMake test fixtures allow setup/cleanup tests and other dependency
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requirements as properties for tests. This is more flexible for
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modern CMake code.
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(ADB - 2019/07/23, HDFFV-10529)
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- Windows PDB files are always installed
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There are build configuration or flag settings for Windows that may not
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generate PDB files. If those files are not generated then the install
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utility will fail because those PDB files are not found. An optional
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variable, DISABLE_PDB_FILES, was added to not install PDB files.
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(ADB - 2019/07/17, HDFFV-10424)
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- Add mingw CMake support with a toolchain file
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There has been a number of mingw issues that has been linked under
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HDFFV-10845. It has been decided to implement the CMake cross-compiling
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technique of toolchain files. We will use a linux platform with the mingw
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compiler stack for testing. Only the C language is fully supported, and
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the error tests are skipped. The C++ language works for static but shared
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builds has a shared library issue with the mingw Standard Exception Handling
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library, which is not available on Windows. Fortran has a common cross-compile
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problem with the fortran configure tests.
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(ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
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- Windows PDB files are installed incorrectly
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For static builds, the PDB files for windows should be installed next
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to the static libraries in the lib folder. Also the debug versions of
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libraries and PDB files are now correctly built using the default
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CMAKE_DEBUG_POSTFIX setting.
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(ADB - 2019/07/09, HDFFV-10581)
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- Add option to build only shared libs
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A request was made to prevent building static libraries and only build
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shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
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skip building static libraries. Certain utility functions will build with
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static libs but are not published. Tests are adjusted to use the correct
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libraries depending on SHARED/STATIC settings.
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(ADB - 2019/06/12, HDFFV-10805)
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- Add options to enable or disable building tools and tests
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Configure options --enable-tests and --enable-tools were added for
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autotools configure. These options are enabled by default, and can be
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disabled with either --disable-tests (or tools) or --enable-tests=no
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(or --enable-tools=no). Build time is reduced ~20% when tools are
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disabled, 35% when tests are disabled, 45% when both are disabled.
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Reenabling them after the initial build requires running configure
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again with the option(s) enabled.
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(LRK - 2019/06/12, HDFFV-9976)
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- Change tools test that test the error stack
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There are some use cases which can cause the error stack of tools to be
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different then the expected output. These tests now use grepTest.cmake,
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this was changed to allow the error file to be searched for an expected string.
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(ADB - 2019/04/15, HDFFV-10741)
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Library:
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--------
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- Add S3 and HDFS VFDs to HDF5 maintenance
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Fix windows requirements and java tests. Windows requires CMake 3.13.
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Install openssl library (with dev files);
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from "Shining Light Productions". msi package preferred.
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PATH should have been updated with the installation dir.
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set ENV variable OPENSSL_ROOT_DIR to the installation dir.
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set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
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Install libcurl library (with dev files);
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download the latest released version using git: https://github.com/curl/curl.git
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Open a Visual Studio Command prompt
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change to the libcurl root folder
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run the "buildconf.bat" batch file
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change to the winbuild directory
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nmake /f Makefile.vc mode=dll MACHINE=x64
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copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
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set ENV variable CURL_ROOT to C:\curl (installation dir)
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update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
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the aws credentials file should be in %USERPROFILE%\.aws folder
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set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3"
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(ADB - 2019/09/12, HDFFV-10854)
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- Fixed an assertion failure in the parallel library when collectively
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filling chunks. As it is required that chunks be written in
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monotonically non-decreasing order of offset in the file, this assertion
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was being triggered when the list of chunk file space allocations being
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passed to the collective chunk filling routine was not sorted according
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to this particular requirement.
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The addition of a sort of the out of order chunks trades a bit of
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performance for the elimination of this assertion and of any complaints
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from MPI implementations about the file offsets used being out of order.
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(JTH - 2019/10/07)
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Parallel Library:
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-----------------
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-
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C++ Library:
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------------
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- Added new wrappers for H5Pset/get_create_intermediate_group()
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LinkCreatPropList::setCreateIntermediateGroup()
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LinkCreatPropList::getCreateIntermediateGroup()
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(BMR - 2019/04/22, HDFFV-10622)
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Java Library:
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----------------
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- Fix a failure in JUnit-TestH5P on 32-bit architectures
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(JTH - 2019/04/30)
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Tools:
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------
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-
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High-Level APIs:
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---------------
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-
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C Packet Table API
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------------------
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-
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Internal header file
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--------------------
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-
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Documentation
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-------------
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-
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Support for new platforms, languages and compilers.
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=======================================
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-
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Bug Fixes since HDF5-1.10.5 release
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==================================
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Library
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-------
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- Explicitly declared dlopen to use RTLD_LOCAL
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dlopen documentation states that if neither RTLD_GLOBAL nor
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RTLD_LOCAL are specified, then the default behavior is unspecified.
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The default on linux is usually RTLD_LOCAL while macos will default
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to RTLD_GLOBAL.
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(ADB - 2020/08/12, HDFFV-11127)
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- Fixed issues CVE-2018-13870 and CVE-2018-13869
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When a buffer overflow occurred because a name length was corrupted
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and became very large, h5dump crashed on memory access violation.
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A check for reading past the end of the buffer was added to multiple
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locations to prevent the crashes and h5dump now simply fails with an
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error message when this error condition occurs.
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(BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)
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- Fixed the segmentation fault when reading attributes with multiple threads
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It was reported that the reading of attributes with variable length string
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datatype will crash with segmentation fault particularly when the number of
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threads is high (>16 threads). The problem was due to the file pointer that
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was set in the variable length string datatype for the attribute. That file
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pointer was already closed when the attribute was accessed.
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The problem was fixed by setting the file pointer to the current opened file pointer
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when the attribute was accessed. Similar patch up was done before when reading
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dataset with variable length string datatype.
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(VC - 2020/07/13, HDFFV-11080)
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- Fixed CVE-2018-17435
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The tool h52gif produced a segfault when the size of an attribute
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message was corrupted and caused a buffer overflow.
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The problem was fixed by verifying the attribute message's size
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against the buffer size before accessing the buffer. h52gif was
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also fixed to display the failure instead of silently exiting
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after the segfault was eliminated.
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(BMR - 2020/6/19, HDFFV-10591)
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- Improved peformance when creating a large number of small datasets by
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retrieving default property values from the API context instead of doing
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skip list searches.
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(CJH - 2019/12/10, HDFFV-10658)
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- Fixed user-created data access properties not existing in the property list
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returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
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reproducer and a patch.
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(CJH - 2019/12/9, HDFFV-10934)
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- Fixed a bug caused by bad tag value when condensing object header
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messages
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There was an assertion failure when moving meessages from running a
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user test program with library release hdf5.1.10.4. It was because
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the tag value (object header's address) was not set up when entering
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the library routine H5O__chunk_update_idx(), which will eventually
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verifies the metadata tag value when protecting the object header.
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The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx()
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with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.
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(VC - 2019/08/23, HDFFV-10873)
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- Fixed the test failure from test_metadata_read_retry_info() in
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test/swmr.c
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The test failure is due to the incorrect number of bins returned for
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retry info (info.nbins). The # of bins expected for 101 read attempts
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is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c
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calculates the # of bins by first obtaining the log10 value for
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(read attempts - 1). For PGI/19, the log10 value for 100 read attempts
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is 1.9999999999999998 instead of 2.00000. When casting the log10 value
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to unsigned later on, the decimal part is chopped off causing the test
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failure.
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This was fixed by obtaining the rounded integer value (HDceil) for the
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log10 value of read attempts first before casting the result to unsigned.
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(VC - 2019/8/14, HDFFV-10813)
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- Fixed an issue where creating a file with non-default file space info
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together with library high bound setting to H5F_LIBVER_V18.
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When setting non-default file space info in fcpl via
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H5Pset_file_space_strategy() and then creating a file with
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both high and low library bounds set to
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H5F_LIBVER_V18 in fapl, the library succeeds in creating the file.
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File creation should fail because the feature of setting non-default
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file space info does not exist in library release 1.8 or earlier.
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This was fixed by setting and checking the proper version in the
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file space info message based on the library low and high bounds
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when creating and opening the HDF5 file.
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(VC - 2019/6/25, HDFFV-10808)
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- Fixed an issue where copying a version 1.8 dataset between files using
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H5Ocopy fails due to an incompatible fill version
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When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
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dataset to a file created with both high and low library bounds set to
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H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
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that the fill value version is out of bounds.
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This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
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(from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.
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(VC - 2019/6/14, HDFFV-10800)
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- Fixed a bug that would cause an error or cause fill values to be
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incorrectly read from a chunked dataset using the "single chunk" index if
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the data was held in cache and there was no data on disk.
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(NAF - 2019/03/06)
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- Fixed a bug that could cause an error or cause fill values to be
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incorrectly read from a dataset that was written to using H5Dwrite_chunk
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if the dataset was not closed after writing.
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(NAF - 2019/03/06, HDFFV-10716)
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- Fixed memory leak in scale offset filter
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In a special case where the MinBits is the same as the number of bits in
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the datatype's precision, the filter's data buffer was not freed, causing
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the memory usage to grow. In general the buffer was freed correctly. The
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Minbits are the minimal number of bits to store the data values. Please
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see the reference manual for H5Pset_scaleoffset for the detail.
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(RL - 2019/3/4, HDFFV-10705)
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- fcntl(2)-based file locking incorrectly passed the lock argument struct
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instead of a pointer to the struct, causing errors on systems where
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flock(2) is not available.
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File locking is used when files are opened to enforce SWMR semantics. A
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lock operation takes place on all file opens unless the
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HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
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flock(2) is preferentially used, with fcntl(2) locks as a backup if
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flock(2) is unavailable on a system (if neither is available, the lock
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operation fails). On these systems, the file lock will often fail, which
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causes HDF5 to not open the file and report an error.
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This bug only affects POSIX systems. Win32 builds on Windows use a no-op
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locking call which always succeeds. Systems which exhibit this bug will
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have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.
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This bug affects HDF5 1.10.0 through 1.10.5.
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fcntl(2)-based file locking now correctly passes the struct pointer.
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|
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(DER - 2019/08/27, HDFFV-10892)
|
|
|
|
- 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)
|
|
|
|
- Don't allocate an empty (0-dimensioned) chunked dataset's chunk
|
|
index, until the dataset's dimensions are increased.
|
|
|
|
(QAK - 2020/05/07)
|
|
|
|
- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
|
|
causes asserts/errors when passed to other dataspace API calls.
|
|
|
|
H5S_NO_CLASS is an internal class value that should not have been
|
|
exposed via a public API call.
|
|
|
|
In debug builds of the library, this can cause asserts to trip. In
|
|
non-debug builds, it will produce normal library errors.
|
|
|
|
The new library behavior is for H5Sset_extent_none() to convert
|
|
the dataspace into one of type H5S_NULL, which is better handled
|
|
by the library and easier for developers to reason about.
|
|
|
|
(DER - 2020/07/27, HDFFV-11027)
|
|
|
|
|
|
Java Library:
|
|
----------------
|
|
-
|
|
|
|
Configuration
|
|
-------------
|
|
- 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)
|
|
|
|
- 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, v110.
|
|
|
|
(ADB - 2019/08/12, HDFFV-10879)
|
|
|
|
Performance
|
|
-------------
|
|
-
|
|
|
|
Fortran
|
|
--------
|
|
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
|
|
|
|
(MSB - 2020/2/18, HDFFV-11029)
|
|
|
|
- Fixed configure issue when building HDF5 with NAG Fortran 7.0.
|
|
|
|
HDF5 now accounts for the addition of half-precision floating-point
|
|
in NAG 7.0 with a KIND=16.
|
|
|
|
(MSB - 2020/02/28, HDFFV-11033)
|
|
|
|
Tools
|
|
-----
|
|
- The tools library was updated by standardizing the error stack process.
|
|
|
|
General sequence is:
|
|
h5tools_setprogname(PROGRAMNAME);
|
|
h5tools_setstatus(EXIT_SUCCESS);
|
|
h5tools_init();
|
|
... process the command-line (check for error-stack enable) ...
|
|
h5tools_error_report();
|
|
... (do work) ...
|
|
h5diff_exit(ret);
|
|
|
|
(ADB - 2020/07/20, HDFFV-11066)
|
|
|
|
- h5diff fixed a command line parsing error.
|
|
|
|
h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
|
|
The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used.
|
|
|
|
(ADB - 2020/07/20, HDFFV-10897)
|
|
|
|
- h5diff added a command line option to ignore attributes.
|
|
|
|
h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
|
|
Adding the exclude-attribute argument will only eclude attributes, with the supplied path,
|
|
from comparision.
|
|
|
|
(ADB - 2020/07/20, HDFFV-5935)
|
|
|
|
- h5diff added another level to the verbose argument to print filenames.
|
|
|
|
Added verbose level 3 that is level 2 plus the filenames. The levels are:
|
|
0 : Identical to '-v' or '--verbose'
|
|
1 : All level 0 information plus one-line attribute status summary
|
|
2 : All level 1 information plus extended attribute status report
|
|
3 : All level 2 information plus file names
|
|
|
|
(ADB - 2020/07/20, HDFFV-10005)
|
|
|
|
- h5repack was fixed to repack the reference attributes properly.
|
|
The code line that checks if the update of reference inside a compound
|
|
datatype is misplaced outside the code block loop that carries out the
|
|
check. In consequence, the next attribute that is not the reference
|
|
type was repacked again as the reference type and caused the failure of
|
|
repacking. The fix is to move the corresponding code line to the correct
|
|
code block.
|
|
|
|
(KY -2020/02/10, HDFFV-11014)
|
|
|
|
- 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)
|
|
|
|
|
|
High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Fortran High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Documentation
|
|
-------------
|
|
-
|
|
|
|
F90 APIs
|
|
--------
|
|
-
|
|
|
|
C++ APIs
|
|
--------
|
|
-
|
|
|
|
Testing
|
|
-------
|
|
- Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
|
|
|
|
Lib files needed are now copied to a subdirectory in the java/test
|
|
directory, and on Macs the loader path for libhdf5.xxxs.so is changed
|
|
in the temporary copy of libhdf5_java.dylib.
|
|
|
|
(LRK, 2020/7/2, HDFFV-11063)
|
|
|
|
|
|
Supported Platforms
|
|
===================
|
|
|
|
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
|
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
|
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
|
IBM XL C/C++ V13.1
|
|
IBM XL Fortran V15.1
|
|
|
|
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
|
|
Version 4.9.3, Version 5.2.0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 17.0.0.098 Build 20160721
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
|
|
(emu) Sun Fortran 95 8.6 SunOS_sparc
|
|
Sun C++ 5.12 SunOS_sparc
|
|
|
|
Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
|
|
Visual Studio 2015 w/ MSMPI 10 (cmake)
|
|
|
|
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)
|
|
|
|
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
|
|
64-bit gfortran GNU Fortran (GCC) 4.9.2
|
|
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
|
|
|
|
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
|
|
|
|
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
|
|
64-bit gfortran GNU Fortran (GCC) 7.1.0
|
|
(swallow/kite) Intel icc/icpc/ifort version 17.0.2
|
|
|
|
|
|
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
|
|
<blank> = testing incomplete on this feature or platform
|
|
|
|
Platform C F90/ F90 C++ zlib SZIP
|
|
parallel F2003 parallel
|
|
Solaris2.11 32-bit n y/y n y y y
|
|
Solaris2.11 64-bit n y/n n y y y
|
|
Windows 7 y y/y n y y y
|
|
Windows 7 x64 y y/y y y y y
|
|
Windows 7 Cygwin n y/n n y y y
|
|
Windows 7 x64 Cygwin n y/n 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 Mavericks 10.9.5 64-bit n y/y n y y y
|
|
Mac OS X Yosemite 10.10.5 64-bit n 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
|
|
CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
|
|
Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
|
|
|
|
|
|
Platform Shared Shared Shared Thread-
|
|
C libs F90 libs C++ libs safe
|
|
Solaris2.11 32-bit y y y y
|
|
Solaris2.11 64-bit y y y y
|
|
Windows 7 y y y y
|
|
Windows 7 x64 y y y y
|
|
Windows 7 Cygwin n n n y
|
|
Windows 7 x64 Cygwin n n n y
|
|
Windows 10 y y y y
|
|
Windows 10 x64 y y y y
|
|
Mac OS X Mavericks 10.9.5 64-bit y n y y
|
|
Mac OS X Yosemite 10.10.5 64-bit y n 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
|
|
CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
|
|
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
|
|
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
|
|
|
|
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:
|
|
(mayll/platypus) Version 4.4.7 20120313
|
|
Version 4.9.3, 5.3.0, 6.2.0
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
x86-64;
|
|
Version 17.10-0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 17.0.4.196 Build 20170411
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
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 3.0.0-GCC-7.2.0-2.29,
|
|
3.1.0-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 3.2 compiled with GCC 5.3.0
|
|
#1 SMP x86_64 GNU/Linux
|
|
(moohan)
|
|
|
|
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
|
|
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
|
|
(ostrich) and IBM XL Fortran for Linux, V15.1
|
|
|
|
Fedora30 5.3.11-200.fc30.x86_64
|
|
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
|
|
GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
|
|
(cmake and autotools)
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
CMake files do not behave correctly with paths containing spaces.
|
|
Do not use spaces in paths because the required escaping for handling spaces
|
|
results in very complex and fragile build files.
|
|
ADB - 2019/05/07
|
|
|
|
At present, metadata cache images may not be generated by parallel
|
|
applications. Parallel applications can read files with metadata cache
|
|
images, but since this is a collective operation, a deadlock is possible
|
|
if one or more processes do not participate.
|
|
|
|
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
|
|
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
|
|
t_shapesame (sscontig2)
|
|
t_pflush1/fails on exit
|
|
The first two tests fail attempting collective writes.
|
|
|
|
CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
|
|
This test will pass with VS2015 with Intel compiler.
|
|
|
|
Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
|
|
while attempting to resolve the Jira issue: HDFFV-10540.
|
|
The known problems of reading or writing > 2GBs when using MPI-2 was
|
|
partially resolved with the MPICH library. The proposed support recognizes
|
|
IO operations > 2GB and if the datatype is not a derived type, the library
|
|
breaks the IO into chunks which can be input or output with the existing
|
|
MPI 2 limitations, i.e. size reporting and function API size/count
|
|
arguments are restricted to be 32 bit integers. For derived types larger
|
|
than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
|
|
OpenMPI in contrast, implements MPI-3 APIs even in the older releases
|
|
and thus does not suffer from the 32 bit size limitation described here.
|
|
OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
|
|
e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
|
|
report data verfication errors before eventually aborting.
|
|
The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
|
|
resolved these isses and parallel HDF5 testing does not currently report
|
|
errors though occasional hangs have been observed.
|
|
|
|
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.
|
|
|