1060 lines
40 KiB
Plaintext
1060 lines
40 KiB
Plaintext
HDF5 version 1.10.5-snap1 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 HDF5-1.10.3
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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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- Rework CMake command files to fix MPI testing.
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Added setup fixture to remove any test generated files and added DEPENDS
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to test properties to execute tests in order expected.
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(ADB - 2019/02/14, TILABS-111)
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- Disable SZIP or ZLIB options if TGZ files are not available.
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Changed the TGZ option for SZip and ZLib to disable the options
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if the source tar.gz files are not found.
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(ADB - 2019/02/05, HDFFV-10697)
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- Rework CMake versioning for OSX platforms.
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Changed the current_version and compatibility_version flags from optional
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with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX.
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(ADB - 2019/01/22, HDFFV-10685)
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- Rework CMake command files to eliminate developer CMP005 warning
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Use variables without quotes in if () statements.
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(ADB - 2019/01/18, TILABS-105)
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- Rework CMake configure files to eliminate developer CMP0075 warning
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Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not
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required for configuration. Also moved check includes calls to top of
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files.
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(ADB - 2019/01/03, HDFFV-10546)
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- Keep stderr and stdout separate in tests
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Changed test handling of output capture. Tests now keep the stderr
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output separate from the stdout output. It is up to the test to decide
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which output to check against a reference. Also added the option
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to grep for a string in either output.
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(ADB - 2018/12/12, HDFFV-10632)
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- Add toolchain and cross-compile support
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Added info on using a toolchain file to INSTALL_CMAKE.txt. A
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toolchain file is also used in cross-compiling, which requires
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CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
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the fortran configure process, the HDF5UseFortran.cmake file macros
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were improved. Fixed a Fortran configure file issue that incorrectly
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used #cmakedefine instead of #define.
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(ADB - 2018/10/04, HDFFV-10594)
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- Add warning flags for Intel compilers
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Identified Intel compiler specific warnings flags that should be used
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instead of GNU flags.
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(ADB - 2018/10/04, TRILABS-21)
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- Add default rpath to targets
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Default rpaths should be set in shared executables and
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libraries to allow the use of loading dependent libraries
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without requiring LD_LIBRARY_PATH to be set. The default
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path should be relative using @rpath on osx and $ORIGIN
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on linux. Windows is not affected.
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(ADB - 2018/09/26, HDFFV-10594)
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- Incorrectly installed private header files were removed from
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CMake installs.
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The CMake build files incorrectly flagged the following header files
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as public and installed them. They are private and will no longer be
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installed.
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HDF5 library private package files (H5Xpkg.h)
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H5Edefin.h
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H5Einit.h
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H5Eterm.h
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H5LTparse.h
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h5diff.h
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h5tools_dump.h
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h5tools.h
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h5tools_ref.h
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h5tools_str.h
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h5tools_utils.h
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h5trav.h
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(DER - 2018/10/26, HDFFV-10614, 10609)
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- Autotools installs now install H5FDwindows.h
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This is simply to align the installed header files between the
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autotools and CMake. H5FDwindows.h has no functionality on
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non-Windows systems.
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(DER - 2018/10/26, HDFFV-10614)
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- Added a new option to enable/disable using pread/pwrite instead of
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read/write in the sec2, log, and core VFDs.
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This option is enabled by default when pread/pwrite are detected.
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Autotools: --enable-preadwrite
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CMake: HDF5_ENABLE_PREADWRITE
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(DER - 2019/02/03, HDFFV-10696)
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Library:
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--------
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- Added new chunk query functions
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The following public functions were added to discover information about
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the chunks in an HDF5 file.
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herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
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herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
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herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
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(BMR - 2018/11/07, HDFFV-10615)
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- Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
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Rather than always running H5detect and generating H5Tinit.c and
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H5make_libsettings.c, supply a location for those files.
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(ADB - 2018/09/18, HDFFV-10332)
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- Several empty public header files where removed from the distribution
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The following files were empty placeholders. They are for internal
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packages that are unlikely to ever have public functionality and have
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thus been removed.
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H5Bpublic.h
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H5B2public.h
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H5FSpublic.h
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H5HFpublic.h
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H5HGpublic.h
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H5HLpublic.h
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They were only installed in CMake builds.
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(DER - 2018/10/26, HDFFV-10614)
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- Add ability to minimze dataset object headers.
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Creation of many, very small datasets resulted in extensive file bloat
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due to extra space in the dataset object headers -- this space is
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allocated by default to allow for the insertion of a small number of
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attributes within the object header and not require a continuation
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block, an unnecessary provision in the target use case.
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Inform the library to expect no attributes on created datasets, and to
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allocate the least space possible for the object headers.
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NOTE: A continuation block is created if attributes are added to a
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'minimized' dataset, which can reduce performance.
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NOTE: Some extra space is allocated for attributes essential to the
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correct behavior of the object header (store creation times, e.g.). This
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does not violate the design principle, as the space is calculated and
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allocated as needed at the time of dataset object header creation --
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unused space is not generated.
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New API calls:
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H5Fget_dset_no_attrs_hint
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H5Fset_dset_no_attrs_hint
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H5Pget_dset_no_attrs_hint
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H5Pset_dset_no_attrs_hint
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(JOS - 2019/01/04, TRILAB-45)
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- The sec2, log, and core VFDs can now use pread/pwrite instead of
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read/write.
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pread and pwrite do not change the file offset, a feature that was
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requested by a user working with a multi-threaded application.
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The option to configure this feature is described above.
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(DER - 2019/02/03, HDFFV-10696)
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Parallel Library:
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-----------------
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- All MPI-1 API calls have been replaced with MPI-2 equivalents.
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This was done to better support OpenMPI, as default builds no longer
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include MPI-1 support (as of OpenMPI 4.0).
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(DER - 2018/12/30, HDFFV-10566)
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- Changed the default behavior in parallel when reading the same dataset in its entirely
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(i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
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The dataset mush be contiguous, less than 2GB, and of an atomic datatype.
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The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
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the disk by the root process to the remain processes in the MPI communicator associated
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with the HDF5 file.
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(MSB - 2019/01/02, HDFFV-10652)
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Fortran Library:
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----------------
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- Added wrappers for dataset object header minimization calls.
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(see the note for TRILAB-45, above)
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New API calls:
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h5fget_dset_no_attrs_hint_f
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h5fset_dset_no_attrs_hint_f
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h5pget_dset_no_attrs_hint_f
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h5pset_dset_no_attrs_hint_f
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(DER - 2019/01/09, TRILAB-45)
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- Added new Fortran derived type, c_h5o_info_t, which is interoperable with
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C's h5o_info_t. This is needed for callback functions which
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pass C's h5o_info_t data type definition.
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(MSB, 2019/01/08, HDFFV-10443)
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- Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
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to Fortran DATE AND TIME storage format.
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(MSB, 2019/01/08, HDFFV-10443)
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- Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
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h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
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(MSB, 2019/01/08, HDFFV-10443)
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C++ Library:
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------------
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-
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Java Library:
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----------------
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- Add new functions to java interface
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Added wrappers for:
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H5Fset_libver_bounds
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H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint
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H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint
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(ADB - 2019/01/07, HDFFV-10664)
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- Fix java unit tests when Time is a natural number
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Time substitution in java/test/junit.sh.in doesn't
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handle the case when Time is a natural number. Fixed
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the regular expression.
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(ADB - 2019/01/07, HDFFV-10674)
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- Duplicate the data read/write functions of Datasets for Attributes.
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Region references could not be displayed for attributes as they could
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for datasets. Datasets had overloaded read and write functions for different
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datatypes that were not available for attributes. After adding similar
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functions, attribute region references work normally.
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(ADB - 2018/12/12, HDFVIEW-4)
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Tools:
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------
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- The h5repart -family-to-sec2 argument was changed to -family-to-single
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In order to better support other single-file VFDs which could work with
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h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
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This is just a name change and the functionality of the argument has not
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changed.
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The -family-to-sec2 argument has been kept for backwards-compatibility.
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This argument should be considered deprecated.
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(DER - 2018/11/14, HDFFV-10633)
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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 HDF5-1.10.3 release
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==================================
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Library
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-------
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- Fix hangs with collective metadata reads during chunked dataset I/O
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In the parallel library, it was discovered that when a particular
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sequence of operations following a pattern of:
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"write to chunked dataset" -> "flush file" -> "read from dataset"
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occurred with collective metadata reads enabled, hangs could be
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observed due to certain MPI ranks not participating in the collective
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metadata reads.
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To fix the issue, collective metadata reads are now disabled during
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chunked dataset raw data I/O.
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(JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
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- Performance issue when closing an object
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The slow down is due to the search of the "tag_list" to find
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out the "corked" status of an object and "uncork" it if so.
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Improve porformance by skipping the search of the "tag_list"
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if there are no "corked" objects when closing an object.
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(VC - 2019/2/6)
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- Revert H5Oget_info* and H5Ovisit* functions
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In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were
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added for performance. Inadvertently, the original functions;
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H5Oget_info,
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H5Oget_info_by_name,
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H5Oget_info_by_idx,
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H5Ovisit,
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H5Ovisit_by_name
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were versioned to H5Oget_info*1 and H5Ovisit*1. This
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broke the API compatibility for a maintenance release. The
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original functions have been restored.
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(ADB - 2019/01/24, HDFFV-10686)
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- Fixed a potential invalid memory access and failure that could occur when
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decoding an unknown object header message (from a future version of the
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library).
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(NAF - 2019/01/07)
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- Deleting attributes in dense storage
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The library aborts with "infinite loop closing library" after
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attributes in dense storage are created and then deleted.
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When deleting the attribute nodes from the name index v2 B-tree,
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if an attribute is found in the intermediate B-tree nodes,
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which may be merged/redistributed in the process, we need to
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free the dynamically allocated spaces for the intermediate
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decoded attribute.
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(VC - 2018/12/26, HDFFV-10659)
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- Fixed an issue where the parallel filters tests would fail
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if zlib was not available on the system. Until support can
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be added in the tests for filters beyond gzip/zlib, the tests
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will be skipped if zlib is not available.
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(JTH - 2018/12/05)
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- A bug was discovered in the parallel library where an application
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would eventually consume all of the available MPI communicators
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when continually writing to a compressed dataset in parallel. This
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was due to internal copies of an HDF5 File Access Property List,
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which each contained a copy of the MPI communicator, not being
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closed at the end of each write operation. This problem was
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exacerbated by larger numbers of processors.
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(JTH - 2018/12/05, HDFFV-10629)
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- Allow H5detect and H5make_libsettings to take a file as an argument.
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Rather than only writing to stdout, add a command argument to name
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the file that H5detect and H5make_libsettings will use for output.
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Without an argument, stdout is still used, so backwards compatibility
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is maintained.
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(ADB - 2018/09/05, HDFFV-9059)
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- A bug was discovered in the parallel library where an application
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would hang if a collective read/write of a chunked dataset occurred
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when collective metadata reads were enabled and some of the ranks
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had no selection in the dataset's dataspace. The ranks which had no
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selection in the dataset's dataspace called H5D__chunk_addrmap() to
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retrieve the lowest chunk address in the dataset. This is because we
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require reads/writes to be performed in strictly non-decreasing order
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of chunk address in the file.
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When the chunk index used was a version 1 or 2 B-tree, these
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non-participating ranks would issue a collective MPI_Bcast() call
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that the participating ranks would not issue, causing the hang. Since
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the non-participating ranks are not actually reading/writing anything,
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the H5D__chunk_addrmap() call can be safely removed and the address used
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for the read/write can be set to an arbitrary number (0 was chosen).
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(JTH - 2018/08/25, HDFFV-10501)
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- There was missing protection against division by zero reported to
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The HDF Group as issue #CVE-2018-17233.
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Protection against division by zero was added to address the issue
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#CVE-2018-17233. In addition, several similar occurrences in the same
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file were fixed as well.
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(BMR - 2018/12/23, HDFFV-10577)
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- There was missing protection against division by zero reported to
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The HDF Group as issue #CVE-2018-17434.
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Protection against division by zero was added to address the issue
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#CVE-2018-17434.
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(BMR - 2019/01/29, HDFFV-10586)
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- The issue CVE-2018-17437 was reported to The HDF Group
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Although CVE-2018-17437 reported a memory leak, the actual issue
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was invalid read. It was found that the attribute name length
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in an attribute message was corrupted, which caused the buffer
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pointer to be advanced too far and later caused an invalid read.
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A check was added to detect when the attribute name or its length
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was corrupted and report the potential of data corruption.
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(BMR - 2019/01/29, HDFFV-10588)
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- H5Ewalk did not stop when it was supposed to
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H5Ewalk was supposed to stop when the callback function stopped
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even though the errors in the stack were not all visited, but it
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did not. This problem is now fixed.
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(BMR - 2019/01/29, HDFFV-10684)
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- Uninitialized bytes from a type conversion buffer could be written
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to disk in H5Dwrite calls where type conversion takes place
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and the type conversion buffer was created by the HDF5 library.
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When H5Dwrite is called and datatype conversion must be performed,
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the library will create a temporary buffer for type conversion if
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one is not provided by the user via H5Pset_buffer. This internal
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buffer is allocated via malloc and contains uninitialized data. In
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some datatype conversions (float to long double, possibly others),
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some of this uninitialized data could be written to disk.
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This was flagged by valgrind in the dtransform test and does not
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appear to be a common occurrence (it is flagged in one test out
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of the entire HDF5 test suite).
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Switching to calloc fixed the problem.
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(DER - 2019/02/03, HDFFV-10694)
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Java Library:
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----------------
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- JNI native library dependencies
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The build for the hdf5_java native library used the wrong
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hdf5 target library for CMake builds. Correcting the hdf5_java
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library to build with the shared hdf5 library required testing
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paths to change also.
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|
|
(ADB - 2018/08/31, HDFFV-10568)
|
|
- Java iterator callbacks
|
|
|
|
Change global callback object to a small stack structure in order
|
|
to fix a runtime crash. This crash was discovered when iterating
|
|
through a file with nested group members. The global variable
|
|
visit_callback is overwritten when recursion starts. When recursion
|
|
completes, visit_callback will be pointing to the wrong callback method.
|
|
|
|
(ADB - 2018/08/15, HDFFV-10536)
|
|
|
|
- Java HDFLibraryException class
|
|
|
|
Change parent class from Exception to RuntimeException.
|
|
|
|
(ADB - 2018/07/30, HDFFV-10534)
|
|
|
|
- JNI Read and Write
|
|
|
|
Refactored variable-length functions, H5DreadVL and H5AreadVL,
|
|
to correct dataset and attribute reads. New write functions,
|
|
H5DwriteVL and H5AwriteVL, are under construction.
|
|
|
|
(ADB - 2018/06/02, HDFFV-10519)
|
|
|
|
Fortran
|
|
--------
|
|
- 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 cmake 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 - 2019/01/04, HDFFV-10596)
|
|
|
|
- Made Fortran specific subroutines PRIVATE in generic procedures.
|
|
|
|
Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
|
|
|
|
(MSB, 2018/12/04, HDFFV-10511)
|
|
|
|
- Fixed issue with Fortran not returning h5o_info_t field values
|
|
meta_size%attr%index_size and meta_size%attr%heap_size.
|
|
|
|
(MSB, 2018/1/8, HDFFV-10443)
|
|
|
|
|
|
Tools
|
|
-----
|
|
-
|
|
|
|
High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Fortran High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Documentation
|
|
-------------
|
|
-
|
|
|
|
F90 APIs
|
|
--------
|
|
-
|
|
|
|
C++ APIs
|
|
--------
|
|
-
|
|
|
|
Testing
|
|
-------
|
|
- Fixed a test failure in testpar/t_dset.c caused by
|
|
the test trying to use the parallel filters feature
|
|
on MPI-2 implementations.
|
|
|
|
(JTH, 2019/2/7)
|
|
|
|
Bug Fixes since HDF5-1.10.2 release
|
|
==================================
|
|
|
|
Library
|
|
-------
|
|
- Java HDF5LibraryException class
|
|
|
|
The error minor and major values would be lost after the
|
|
constructor executed.
|
|
|
|
Created two local class variables to hold the values obtained during
|
|
execution of the constructor. Refactored the class functions to retrieve
|
|
the class values rather then calling the native functions.
|
|
The native functions were renamed and called only during execution
|
|
of the constructor.
|
|
Added error checking to calling class constructors in JNI classes.
|
|
|
|
(ADB - 2018/08/06, HDFFV-10544)
|
|
|
|
- Added checks of the defined MPI_VERSION to guard against usage of
|
|
MPI-3 functions in the Parallel Compression and "big Parallel I/O"
|
|
features when HDF5 is built with MPI-2. Previously, the configure
|
|
step would pass but the build itself would fail when it could not
|
|
locate the MPI-3 functions used.
|
|
|
|
As a result of these new checks, HDF5 can again be built with MPI-2,
|
|
but the Parallel Compression feature will be disabled as it relies
|
|
on the MPI-3 functions used.
|
|
|
|
(JTH - 2018/08/02, HDFFV-10512)
|
|
|
|
- User's patches: CVEs
|
|
|
|
The following patches have been applied:
|
|
|
|
CVE-2018-11202 - NULL pointer dereference was discovered in
|
|
H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476)
|
|
https://security-tracker.debian.org/tracker/CVE-2018-11202
|
|
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202
|
|
|
|
CVE-2018-11203 - A division by zero was discovered in
|
|
H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477)
|
|
https://security-tracker.debian.org/tracker/CVE-2018-11203
|
|
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203
|
|
|
|
CVE-2018-11204 - A NULL pointer dereference was discovered in
|
|
H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478)
|
|
https://security-tracker.debian.org/tracker/CVE-2018-11204
|
|
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204
|
|
|
|
CVE-2018-11206 - An out of bound read was discovered in
|
|
H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
|
|
(HDFFV-10480)
|
|
https://security-tracker.debian.org/tracker/CVE-2018-11206
|
|
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206
|
|
|
|
CVE-2018-11207 - A division by zero was discovered in
|
|
H5D__chunk_init in H5Dchunk.c (HDFFV-10481)
|
|
https://security-tracker.debian.org/tracker/CVE-2018-11207
|
|
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207
|
|
|
|
(BMR - 2018/7/22, PR#s: 1134 and 1139,
|
|
HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481)
|
|
|
|
- H5Adelete
|
|
|
|
H5Adelete failed when deleting the last "large" attribute that
|
|
is stored densely via fractal heap/v2 b-tree.
|
|
|
|
After removing the attribute, update the ainfo message. If the
|
|
number of attributes goes to zero, remove the message.
|
|
|
|
(VC - 2018/07/20, HDFFV-9277)
|
|
|
|
- A bug was discovered in the parallel library which caused partial
|
|
parallel reads of filtered datasets to return incorrect data. The
|
|
library used the incorrect dataspace for each chunk read, causing
|
|
the selection used in each chunk to be wrong.
|
|
|
|
The bug was not caught during testing because all of the current
|
|
tests which do parallel reads of filtered data read all of the data
|
|
using an H5S_ALL selection. Several tests were added which exercise
|
|
partial parallel reads.
|
|
|
|
(JTH - 2018/07/16, HDFFV-10467)
|
|
|
|
- A bug was discovered in the parallel library which caused parallel
|
|
writes of filtered datasets to trigger an assertion failure in the
|
|
file free space manager.
|
|
|
|
This occurred when the filter used caused chunks to repeatedly shrink
|
|
and grow over the course of several dataset writes. The previous chunk
|
|
information, such as the size of the chunk and the offset in the file,
|
|
was being cached and not updated after each write, causing the next write
|
|
to the chunk to retrieve the incorrect cached information and run into
|
|
issues when reallocating space in the file for the chunk.
|
|
|
|
(JTH - 2018/07/16, HDFFV-10509)
|
|
|
|
- A bug was discovered in the parallel library which caused the
|
|
H5D__mpio_array_gatherv() function to allocate too much memory.
|
|
|
|
When the function is called with the 'allgather' parameter set
|
|
to a non-true value, the function will receive data from all MPI
|
|
ranks and gather it to the single rank specied by the 'root'
|
|
parameter. However, the bug in the function caused memory for
|
|
the received data to be allocated on all MPI ranks, not just the
|
|
singular rank specified as the receiver. In some circumstances,
|
|
this would cause an application to fail due to the large amounts
|
|
of memory being allocated.
|
|
|
|
(JTH - 2018/07/16, HDFFV-10467)
|
|
|
|
- Error checks in h5stat and when decoding messages
|
|
|
|
h5stat exited with seg fault/core dumped when
|
|
errors are encountered in the internal library.
|
|
|
|
Add error checks and --enable-error-stack option to h5stat.
|
|
Add range checks when decoding messages: old fill value, old
|
|
layout and refcount.
|
|
|
|
(VC - 2018/07/11, HDFFV-10333)
|
|
|
|
- If an HDF5 file contains a malformed compound datatype with a
|
|
suitably large offset, the type conversion code can run off
|
|
the end of the type conversion buffer, causing a segmentation
|
|
fault.
|
|
|
|
This issue was reported to The HDF Group as issue #CVE-2017-17507.
|
|
|
|
NOTE: The HDF5 C library cannot produce such a file. This condition
|
|
should only occur in a corrupt (or deliberately altered) file
|
|
or a file created by third-party software.
|
|
|
|
THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
|
|
|
|
Fixing this problem would involve updating the publicly visible
|
|
H5T_conv_t function pointer typedef and versioning the API calls
|
|
which use it. We normally only modify the public API during
|
|
major releases, so this bug will not be fixed at this time.
|
|
|
|
(DER - 2018/02/26, HDFFV-10356)
|
|
|
|
Configuration
|
|
-------------
|
|
- Applied patches to address Cywin build issues
|
|
|
|
There were three issues for Cygwin builds:
|
|
- Shared libs were not built.
|
|
- The -std=c99 flag caused a SIG_SETMASK undeclared error.
|
|
- Undefined errors when buildbing test shared libraries.
|
|
|
|
Patches to address these issues were received and incorporated in this version.
|
|
|
|
(LRK - 2018/07/18, HDFFV-10475)
|
|
|
|
- Moved the location of gcc attribute.
|
|
|
|
The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN,
|
|
was located after the function name. Builds with GCC 7 did not
|
|
indicate any problem, but GCC 8 issued errors. Moved the
|
|
attribute before the function name, as required.
|
|
|
|
(ADB - 2018/05/22, HDFFV-10473)
|
|
|
|
- Reworked java test suite into individual JUnit tests.
|
|
|
|
Testing the whole suite of java unit tests in a single JUnit run
|
|
made it difficult to determine actual failures when tests would fail.
|
|
Running each file set of tests individually, allows individual failures
|
|
to be diagnosed easier. A side benefit is that tests for optional components
|
|
of the library can be disabled if not configured.
|
|
|
|
(ADB - 2018/05/16, HDFFV-9739)
|
|
|
|
- Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES
|
|
to use target_* type commands. This change modernizes the CMake usage
|
|
in the HDF5 library.
|
|
|
|
In addition, there is the intention to convert to generator expressions,
|
|
where possible. The exception is Fortran FLAGS on Windows Visual Studio.
|
|
The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have
|
|
been removed with this change in usage.
|
|
|
|
The additional language (C++ and Fortran) checks have also been localized
|
|
to only be checked when that language is enabled.
|
|
|
|
(ADB - 2018/05/08)
|
|
|
|
Performance
|
|
-------------
|
|
-
|
|
|
|
Fortran
|
|
--------
|
|
-
|
|
|
|
Tools
|
|
-----
|
|
-
|
|
|
|
High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Fortran High-Level APIs:
|
|
------
|
|
-
|
|
|
|
Documentation
|
|
-------------
|
|
-
|
|
|
|
F90 APIs
|
|
--------
|
|
-
|
|
|
|
C++ APIs
|
|
--------
|
|
- Adding default arguments to existing functions
|
|
|
|
Added the following items:
|
|
+ Two more property list arguments are added to H5Location::createDataSet:
|
|
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
|
|
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
|
|
|
|
+ One more property list argument is added to H5Location::openDataSet:
|
|
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
|
|
|
|
(BMR - 2018/07/21, PR# 1146)
|
|
|
|
- Improvement C++ documentation
|
|
|
|
Replaced the table in main page of the C++ documentation from mht to htm format
|
|
for portability.
|
|
|
|
(BMR - 2018/07/17, PR# 1141)
|
|
|
|
Testing
|
|
-------
|
|
|
|
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 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
|
|
|
|
Windows 7 x64 Visual Studio 2013
|
|
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
|
|
Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
|
|
Visual Studio 2015 w/ MSMPI 8 (cmake)
|
|
|
|
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
|
|
|
|
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
|
|
Visual Studio 2017 w/ Intel Fortran 18 (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
|
|
|
|
Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
|
|
gcc, g++ (Debian 4.9.2-10) 4.9.2
|
|
GNU Fortran (Debian 4.9.2-10) 4.9.2
|
|
(cmake and autotools)
|
|
|
|
Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc, g++ (GCC) 6.1.1 20160621
|
|
(Red Hat 6.1.1-3)
|
|
GNU Fortran (GCC) 6.1.1 20160621
|
|
(Red Hat 6.1.1-3)
|
|
(cmake and autotools)
|
|
|
|
Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
|
|
gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
|
|
5.4.0 20160609
|
|
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
|
|
5.4.0 20160609
|
|
(cmake and autotools)
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Known Problems
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==============
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At present, metadata cache images may not be generated by parallel
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applications. Parallel applications can read files with metadata cache
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images, but since this is a collective operation, a deadlock is possible
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if one or more processes do not participate.
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Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
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testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
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t_shapesame (sscontig2)
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t_pflush1/fails on exit
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The first two tests fail attempting collective writes.
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CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
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This test will pass with VS2015 with Intel compiler.
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Known problems in previous releases can be found in the HISTORY*.txt files
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in the HDF5 source. Please report any new problems found to
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help@hdfgroup.org.
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CMake vs. Autotools installations
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=================================
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While both build systems produce similar results, there are differences.
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Each system produces the same set of folders on linux (only CMake works
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on standard Windows); bin, include, lib and share. Autotools places the
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COPYING and RELEASE.txt file in the root folder, CMake places them in
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the share folder.
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The bin folder contains the tools and the build scripts. Additionally, CMake
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creates dynamic versions of the tools with the suffix "-shared". Autotools
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installs one set of tools depending on the "--enable-shared" configuration
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option.
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build scripts
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-------------
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Autotools: h5c++, h5cc, h5fc
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CMake: h5c++, h5cc, h5hlc++, h5hlcc
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The include folder holds the header files and the fortran mod files. CMake
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places the fortran mod files into separate shared and static subfolders,
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while Autotools places one set of mod files into the include folder. Because
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CMake produces a tools library, the header files for tools will appear in
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the include folder.
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The lib folder contains the library files, and CMake adds the pkgconfig
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subfolder with the hdf5*.pc files used by the bin/build scripts created by
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the CMake build. CMake separates the C interface code from the fortran code by
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creating C-stub libraries for each Fortran library. In addition, only CMake
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installs the tools library. The names of the szip libraries are different
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between the build systems.
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The share folder will have the most differences because CMake builds include
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a number of CMake specific files for support of CMake's find_package and support
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for the HDF5 Examples CMake project.
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