./devel/hdf5, Hierarchical Data Format (new generation)

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Branch: CURRENT, Version: 1.10.7, Package name: hdf5-1.10.7, Maintainer: pkgsrc-users

HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes, and
is designed for flexible and efficient I/O and for high volume and
complex data. HDF5 is portable and is extensible, allowing applications
to evolve in their use of HDF5. The HDF5 Technology suite includes
tools and applications for managing, manipulating, viewing, and
analyzing data in the HDF5 format.

Required to run:

Required to build:

Package options: szip

Master sites:

SHA1: 125b2dacb4fdac33f7bfbc7dfdeeb000ff68466b
RMD160: 6da25b3aee83ad2aba421ac7b7026aa1f8c1d38f
Filesize: 8747.895 KB

Version history: (Expand)

CVS history: (Expand)

   2021-06-07 13:52:48 by Adam Ciarcinski | Files touched by this commit (16) | Package removed
Log message:
hdf5: updated to 1.10.7

HDF5 version 1.10.7 released on 2020-09-11


This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.

Note that documentation in the links below will be updated at the time of each
final release.

Links to HDF5 documentation can be found on The HDF5 web page:


The official HDF5 releases can be obtained from:


     HDF5 binaries provided are fully tested with ZLIB and the free
     Open Source SZIP successor Libaec (with BSD license).
     The official ZLIB and SZIP/Libaec pages are at:

        ZLIB: http://www.zlib.net/
        SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec
            https://gitlab.dkrz.de/k202009/libaec/- … yright.txt

Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:

     https://portal.hdfgroup.org/display/HDF … %27s+Guide

If you have any questions or comments, please send them to the HDF Help Desk:



- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.6
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations

New Features

    - Disable memory sanity checks in the Autotools in release branches

      The library can be configured to use internal memory sanity checking,
      which replaces C API calls like malloc(3) and free(3) with our own calls
      which add things like heap canaries. These canaries can cause problems
      when external filter plugins reallocate canary-marked buffers.

      For this reason, the default will be to not use the memory allocation
      sanity check feature in release branches (e.g., hdf5_1_10_7).
      Debug builds in development branches (e.g., develop, hdf5_1_10) will
      still use them by default.

      This change only affects Autotools debug builds. Non-debug autotools
      builds and all CMake builds do not enable this feature by default.

      (DER - 2020/08/19)

    - Add file locking configure and CMake options

      HDF5 1.10.0 introduced a file locking scheme, primarily to help
      enforce SWMR setup. Formerly, the only user-level control of the scheme
      was via the HDF5_USE_FILE_LOCKING environment variable.

      This change introduces configure-time options that control whether
      or not file locking will be used and whether or not the library
      ignores errors when locking has been disabled on the file system
      (useful on some HPC Lustre installations).

      In both the Autotools and CMake, the settings have the effect of changing
      the default property list settings (see the H5Pset/get_file_locking()
      entry, below).

      The yes/no/best-effort file locking configure setting has also been
      added to the libhdf5.settings file.


        An --enable-file-locking=(yes|no|best-effort) option has been added.

        yes:          Use file locking.
        no:           Do not use file locking.
        best-effort:  Use file locking and ignore "disabled" errors.


        Two self-explanatory options have been added:


        Setting both of these to ON is the equivalent to the Autotools'
        best-effort setting.

      The precedence order of the various file locking control mechanisms is:

        1) HDF5_USE_FILE_LOCKING environment variable (highest)

        2) H5Pset_file_locking()

        3) configure/CMake options (which set the property list defaults)

        4) library defaults (currently best-effort)

      (DER - 2020/07/30, HDFFV-11092)

    - CMake option to link the generated Fortran MOD files into the include

      The Fortran generation of MOD files by a Fortran compile can produce
      different binary files between SHARED and STATIC compiles with different
      compilers and/or different platforms. Note that it has been found that
      different versions of Fortran compilers will produce incompatible MOD
      files. Currently, CMake will locate these MOD files in subfolders of
      the include directory and add that path to the Fortran library target
      in the CMake config file, which can be used by the CMake find library
      process. For other build systems using the binary from a CMake install,
      a new CMake configuration can be used to copy the pre-chosen version
      of the Fortran MOD files into the install include directory.

      The default will depend on the configuration of
            YES                   YES         Default to SHARED
            YES                   NO          Default to STATIC
            NO                    YES         Default to SHARED
            NO                    NO          Default to SHARED
      The defaults can be overriden by setting the config option

      (ADB - 2020/07/09, HDFFV-11116)

    - CMake option to use AEC (open source SZip) library instead of SZip

      The open source AEC library is a replacement library for SZip. In
      order to use it for hdf5, the libaec CMake source was changed to add
      "-fPIC" and exclude test files. A new option USE_LIBAEC is required
      to compensate for the different files produced by AEC build.

      Autotools does not build the compression libraries within hdf5 builds,
      but will use an installed libaec when configured as before with the
      option --with-libsz=<path to libaec directory>.

      (ADB - 2020/04/22, OESS-65)

    - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER

      Some handcrafted tests in HDFTests.c have been removed and the CMake
      CHECK_STRUCT_HAS_MEMBER module has been used.

      (ADB - 2020/03/24, TRILAB-24)

    - Both build systems use same set of warnings flags

      GNU C, C++ and gfortran warnings flags were moved to files in a config
      sub-folder named gnu-warnings. Flags that only are available for a specific
      version of the compiler are in files named with that version.
      Clang C warnings flags were moved to files in a config sub-folder
      named clang-warnings.
      Intel C, Fortran warnings flags were moved to files in a config sub-folder
      named intel-warnings.

      There are flags in named "error-xxx" files with warnings that may
      be promoted to errors. Some source files may still need fixes.

      There are also pairs of files named "developer-xxx" and \ 
      that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
      configure option:--enable-developer-warnings.

      In addition, CMake no longer applies these warnings for examples.

      (ADB - 2020/03/24, TRILAB-192)

    - Update CMake minimum version to 3.12

      Updated CMake minimum version to 3.12 and added version checks
      for Windows features.

      (ADB - 2020/02/05, TRILABS-142)

    - Fixed CMake include properties for Fortran libraries

      Corrected the library properties for Fortran to use the
      correct path for the Fortran module files.

      (ADB - 2020/02/04, HDFFV-11012)

    - Added common warnings files for gnu and intel

      Added warnings files to use one common set of flags
      during configure for both autotools and CMake build
      systems. The initial implementation only affects a
      general set of flags for gnu and intel compilers.

      (ADB - 2020/01/17)

    - Added new options to CMake for control of testing

      Added CMake options (default ON);
          combined with:

      (ADB - 2020/01/15, HDFFV-11001)

    - Added Clang sanitizers to CMake for analyzer support if compiler is clang.

      Added CMake code and files to execute the Clang sanitizers if
      HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
      is set to one of the following:

      (ADB - 2019/12/12, TRILAB-135)

    - Add metadata cache optimization to reduce skip list usage

      On file flush or close, the metadata cache attempts to write out
      all dirty entries in increasing address order.  To do this, it needs
      an address sorted list of metadata entries.  Further, since flushing
      one metadata cache entry can dirty another, this list must support
      efficient insertion and deletion.

      The metadata cache uses a skip list of all dirty entries for this
      purpose.  Before this release, this skip list was maintained at all
      times.  However, since profiling indicates that this imposes a
      significant cost, we now construct and maintain the skip list only
      when needed.  Specifically, we enable the skip list and load it with
      a list of all dirty entries in the metadata cache just before a flush,
      and disable it after the flush.

      (JRM - 2020/08/17, HDFFV-11034)

    - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable

      This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that
      were previously accepted. This option turns on file locking but
      ignores locking errors when the library detects that file locking
      has been disabled on a file system (useful on some HPC Lustre

      The capitalization of BEST_EFFORT is mandatory.

      See the configure option discussion for HDFFV-11092 (above) for more
      information on the file locking feature and how it's controlled.

      (DER - 2020/07/30, HDFFV-11092)

    - Add H5Pset/get_file_locking() API calls

      This change adds new API calls which can be used to set or get the
      file locking parameters. The single API call sets both the "use file
      locking" flag and the "ignore disabled file locking" flag.

      When opening a file multiple times without closing, the file MUST be
      opened with the same file locking settings. Opening a file with different
      file locking settings will fail (this is similar to the behavior of

      See the configure option discussion for HDFFV-11092 (above) for more
      information on the file locking feature and how it's controlled.

      (DER - 2020/07/30, HDFFV-11092)

    - Add Mirror VFD

      Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
      machine. Must be used in conjunction with the Splitter VFD.

      (JOS - 2020/03/13, TBD)

    - Add Splitter VFD

      Maintain separate R/W and W/O channels for "concurrent" file writes
      to two files using a single HDF5 file handle.

      (JOS - 2020/03/13, TBD)

    - Fixed an assertion failure in the parallel library when collectively
      filling chunks. As it is required that chunks be written in
      monotonically non-decreasing order of offset in the file, this assertion
      was being triggered when the list of chunk file space allocations being
      passed to the collective chunk filling routine was not sorted according
      to this particular requirement.

      The addition of a sort of the out of order chunks trades a bit of
      performance for the elimination of this assertion and of any complaints
      from MPI implementations about the file offsets used being out of order.

      (JTH - 2019/10/07)

    Fortran Library:
    - Add wrappers for H5Pset/get_file_locking() API calls


      See the configure option discussion for HDFFV-11092 (above) for more
      information on the file locking feature and how it's controlled.

      (DER - 2020/07/30, HDFFV-11092)

    - Added new Fortran parameters:


    - Added new Fortran API: h5pget_libver_bounds_f

      (MSB - 2020/02/11, HDFFV-11018)

    C++ Library:
    - Add wrappers for H5Pset/get_file_locking() API calls


      See the configure option discussion for HDFFV-11092 (above) for more
      information on the file locking feature and how it's controlled.

      (DER - 2020/07/30, HDFFV-11092)

    Java Library:
    - Add wrappers for H5Pset/get_file_locking() API calls


      Unlike the C++ and Fortran wrappers, there are separate getters for the
      two file locking settings, each of which returns a boolean value.

      See the configure option discussion for HDFFV-11092 (above) for more
      information on the file locking feature and how it's controlled.

      (DER - 2020/07/30, HDFFV-11092)

    - h5repack added options to control how external links are handled.

      Currently h5repack preserves external links and cannot copy and merge
      data from the external files. Two options, merge and prune, were added to
      control how to merge data from an external link into the resulting file.
       --merge             Follow external soft link recursively and merge data.
       --prune             Do not follow external soft links and remove link.
       --merge --prune     Follow external link, merge data and remove dangling link.

      (ADB - 2020/08/05, HDFFV-9984)

    High-Level APIs:
    - None

    C Packet Table API
    - None

    Internal header file
    - None

    - None

Support for new platforms, languages and compilers.
    - None

Bug Fixes since HDF5-1.10.6 release

    - Fix bug and simplify collective metadata write operation when some ranks
        have no entries to contribute.  This fixes parallel regression test
        failures with IBM SpectrumScale MPI on the Summit system at ORNL.

      (QAK - 2020/09/02)

    - Avoid setting up complex MPI types with 0-length vectors, which some
        MPI implementations don't handle well.  (In particular, IBM
        SpectrumScale MPI on the Summit system at ORNL)

      (QAK - 2020/08/21)

    - Fixed use-of-uninitialized-value error

      Appropriate initialization of local structs was added to remove the
      use-of-uninitialized-value errors reported by MemorySanitizer.

      (BMR - 2020/8/13, HDFFV-11101)

    - Creation of dataset with optional filter

      When the combination of type, space, etc doesn't work for filter
      and the filter is optional, it was supposed to be skipped but it was
      not skipped and the creation failed.

      A fix is applied to allow the creation of a dataset in such
      situation, as specified in the user documentation.

      (BMR - 2020/8/13, HDFFV-10933)

    - Explicitly declared dlopen to use RTLD_LOCAL

      dlopen documentation states that if neither RTLD_GLOBAL nor
      RTLD_LOCAL are specified, then the default behavior is unspecified.
      The default on linux is usually RTLD_LOCAL while macos will default
      to RTLD_GLOBAL.

      (ADB - 2020/08/12, HDFFV-11127)

    - Fixed issues CVE-2018-13870 and CVE-2018-13869

      When a buffer overflow occurred because a name length was corrupted
      and became very large, h5dump crashed on memory access violation.

      A check for reading past the end of the buffer was added to multiple
      locations to prevent the crashes and h5dump now simply fails with an
      error message when this error condition occurs.

      (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)

    - 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)

    - Fixed the segmentation fault when reading attributes with multiple threads

      It was reported that the reading of attributes with variable length string
      datatype will crash with segmentation fault particularly when the number
      of threads is high (>16 threads).  The problem was due to the file pointer
      that was set in the variable length string datatype for the attribute.
      That file pointer was already closed when the attribute was accessed.

      The problem was fixed by setting the file pointer to the current opened
      file pointer when the attribute was accessed.  Similar patch up was done
      before when reading dataset with variable length string datatype.

      (VC - 2020/07/13, HDFFV-11080)

    -  Fixed issue CVE-2018-17438

      A division by zero was discovered in H5D__select_io() of H5Dselect.c.
        https://security-tracker.debian.org/tra … 2018-17438

      A check was added to protect against division by zero.  When such
      situation occurs again, the normal HDF5 error handling will be invoked,
      instead of segmentation fault.

      (BMR, DER - 2020/07/09, HDFFV-10587)

    - Fixed CVE-2018-17435

      The tool h52gif produced a segfault when the size of an attribute message
      was corrupted and caused a buffer overflow.

      The problem was fixed by verifying the attribute message's size against the
      buffer size before accessing the buffer.  h52gif was also fixed to display
      the failure instead of silently exiting after the segfault was eliminated.

      (BMR - 2020/6/19, HDFFV-10591)

    - Don't allocate an empty (0-dimensioned) chunked dataset's chunk
      index, until the dataset's dimensions are increased.

      (QAK - 2020/05/07)

    - Stopped addition of szip header and include directory path for
      incompatible libsz

      szlib.h is the same for both 32-bit and 64-bit szip, and the header file
      and its path were added to the HDF5 binary even though the configure
      check of a function in libsz later failed and szip compression was not
      enabled.  The header file and include path are now added only when the
      libsz function passes the configure check.

      (LRK - 2020/08/17, HDFFV-10830)

    - Added -fsanitize=address autotools configure option for Clang compiler

      Clang sanitizer options were also added for Clang compilers with CMake.

      (LRK, 2020/08/05, HDFFV-10836)

    - Updated testh5cc.sh.in for functions versioned in HDF5 1.10.

      testh5cc.sh previously tested that the correct version of a function
      versioned in HDF5 1.6 or 1.8 was compiled when one of
      H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined.  This
      test was extended for additional testing with H5_USE_18_API_DEFAULT.

      (LRK, 2020/06/22, HDFFV-11000)

    - 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)

    - None

    Java Library:
    - None

    - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in \ 

      (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)

    - The tools library was updated by standardizing the error stack process.

      General sequence is:
          ... process the command-line (check for error-stack enable) ...
          ... (do work) ...

      (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 \ 
      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)

    High-Level APIs:
    - The H5DSis_scale function was updated to return "not a dimension \ 
scale" (0)
      instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
      not written according to Dimension Scales Specification.

     (EIP - 2020/08/12, HDFFV-10436)

    Fortran High-Level APIs:
    - None

    - None

    F90 APIs
    - None

    C++ APIs
    - None

    - 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)
   2020-03-17 23:29:34 by Roland Illig | Files touched by this commit (1)
Log message:
devel/hdf5: skip some files for the portability check
   2020-01-08 13:30:51 by Nia Alarie | Files touched by this commit (1)
Log message:
hdf5: Missing patch
   2020-01-08 13:30:34 by Nia Alarie | Files touched by this commit (5) | Package updated
Log message:
hdf5: Update to 1.10.6

New Features

    - Update CMake for VS2019 support

      CMake added support for VS2019 in version 3.15. Changes to the CMake
      generator setting required changes to scripts. Also updated version
      references in CMake files as necessary.

      (ADB - 2019/11/18, HDFFV-10962)

    - Update CMake options to match new autotools options

      Add configure options (autotools - CMake):
            enable-asserts       HDF5_ENABLE_ASSERTS
            enable-symbols       HDF5_ENABLE_SYMBOLS
            enable-profiling     HDF5_ENABLE_PROFILING
            enable-optimization  HDF5_ENABLE_OPTIMIZATION
      In addition NDEBUG is no longer forced defined and relies on the CMake

      (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)

    - Update CMake tests to use FIXTURES

      CMake test fixtures allow setup/cleanup tests and other dependency
      requirements as properties for tests. This is more flexible for
      modern CMake code.

      (ADB - 2019/07/23, HDFFV-10529)

    - Windows PDB files are always installed

      There are build configuration or flag settings for Windows that may not
      generate PDB files. If those files are not generated then the install
      utility will fail because those PDB files are not found. An optional
      variable, DISABLE_PDB_FILES, was added to not install PDB files.

      (ADB - 2019/07/17, HDFFV-10424)

    - Add mingw CMake support with a toolchain file

      There have been a number of mingw issues that have been linked under
      HDFFV-10845. It has been decided to implement the CMake cross-compiling
      technique of toolchain files. We will use a linux platform with the mingw
      compiler stack for testing. Only the C language is fully supported, and
      the error tests are skipped. The C++ language works for static but shared
      builds have a shared library issue with the mingw Standard Exception Handling
      library, which is not available on Windows. Fortran has a common cross-compile
      problem with the fortran configure tests.

      (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)

    - Windows PDB files are installed incorrectly

      For static builds, the PDB files for windows should be installed next
      to the static libraries in the lib folder. Also the debug versions of
      libraries and PDB files are now correctly built using the default
      CMAKE_DEBUG_POSTFIX setting.

      (ADB - 2019/07/09, HDFFV-10581)

    - Add option to build only shared libs

      A request was made to prevent building static libraries and only build
      shared.  A new option was added to CMake, ONLY_SHARED_LIBS, which will
      skip building static libraries. Certain utility functions will build with
      static libs but are not published. Tests are adjusted to use the correct
      libraries depending on SHARED/STATIC settings.

      (ADB - 2019/06/12, HDFFV-10805)

    - Add options to enable or disable building tools and tests

      Configure options --enable-tests and --enable-tools were added for
      autotools configure.  These options are enabled by default, and can be
      disabled with either --disable-tests (or tools) or --enable-tests=no
      (or --enable-tools=no).  Build time is reduced ~20% when tools are
      disabled, 35% when tests are disabled, 45% when both are disabled.
      Re-enabling them after the initial build requires running configure
      again with the option(s) enabled.

      (LRK - 2019/06/12, HDFFV-9976)

    - Change tools tests to search the error stack

      There are some use cases which can cause the error stack of tools to be
      different then the expected output. These tests now use grepTest.cmake;
      this was changed to allow the error file to be searched for an expected string.

      (ADB - 2019/04/15, HDFFV-10741)

    - Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5

      These new VFDs have been introduced in HDF5-1.10.6.  Instructions to
      enable them when configuring HDF5 on Linux and Mac may be found at
      https://portal.hdfgroup.org/display/HDF … +and+HDFS.

      Installing on Windows requires CMake 3.13 and the following additional setup.
            Install openssl library (with dev files);
            from "Shining Light Productions". msi package preferred.

            PATH should have been updated with the installation dir.
            set ENV variable OPENSSL_ROOT_DIR to the installation dir.
            set ENV variable OPENSSL_CONF to the cfg file, likely \ 
            Install libcurl library (with dev files);
            download the latest released version using git: \ 

            Open a Visual Studio Command prompt
            change to the libcurl root folder
            run the "buildconf.bat" batch file
            change to the winbuild directory
            nmake /f Makefile.vc mode=dll MACHINE=x64
            copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl \ 
(installation dir)
            set ENV variable CURL_ROOT to C:\curl (installation dir)
            update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
            the aws credentials file should be in %USERPROFILE%\.aws folder
            set the ENV variable \ 

      (ADB - 2019/09/12, HDFFV-10854)

    C++ Library:
    - Added new wrappers for H5Pset/get_create_intermediate_group()

      (BMR - 2019/04/22, HDFFV-10622)

    Java Library:
    - Fixed a failure in JUnit-TestH5P on 32-bit architectures

      (JTH - 2019/04/30)

Support for new platforms, languages and compilers.
    - CMake added support for VS2019 in version 3.15. Updated scripts.

    - macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0

    - macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1

Bug Fixes since HDF5-1.10.5 release

    - Improved performance when creating a large number of small datasets by
      retrieving default property values from the API context instead of doing
      skip list searches. More work is required to achieve parity with HDF5 1.8.

      (CJH - 2019/12/10, HDFFV-10658)

    - Fixed user-created data access properties not existing in the property list
      returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
      reproducer and a patch.

      (CJH - 2019/12/9, HDFFV-10934)

    - 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)

    - fcntl(2)-based file locking incorrectly passed the lock argument struct
      instead of a pointer to the struct, causing errors on systems where
      flock(2) is not available.

      File locking is used when files are opened to enforce SWMR semantics. A
      lock operation takes place on all file opens unless the
      HDF5_USE_FILE_LOCKING environment variable is set to the string \ 
      flock(2) is preferentially used, with fcntl(2) locks as a backup if
      flock(2) is unavailable on a system (if neither is available, the lock
      operation fails). On these systems, the file lock will often fail, which
      causes HDF5 to not open the file and report an error.

      This bug only affects POSIX systems. Win32 builds on Windows use a no-op
      locking call which always succeeds. Systems which exhibit this bug will
      have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.

      This bug affects HDF5 1.10.0 through 1.10.5.

      fcntl(2)-based file locking now correctly passes the struct pointer.

      (DER - 2019/08/27, HDFFV-10892)

    - Fixed a bug caused by a bad tag value when condensing object header

      There was an assertion failure when moving messages from running a
      user test program with library release HDF5 1.10.4. It was because
      the tag value (object header's address) was not set up when entering
      the library routine H5O__chunk_update_idx(), which eventually
      verifies the metadata tag value when protecting the object header.

      The problem was fixed by replacing FUNC_ENTER_PACKAGE in \ 
      with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.

      (VC - 2019/08/23, HDFFV-10873)

    - Fixed the test failure from test_metadata_read_retry_info() in

      The test failure is due to an incorrect number of bins returned for
      retry info (info.nbins).  The # of bins expected for 101 read attempts
      is 3 instead of 2.  The routine H5F_set_retries() in src/H5Fint.c
      calculates the # of bins by first obtaining the log10 value for
      (read attempts - 1).  For PGI/19, the log10 value for 100 read attempts
      is 1.9999999999999998 instead of 2.00000.  When casting the log10 value
      to unsigned later on, the decimal part is chopped off causing the test

      This was fixed by obtaining the rounded integer value (HDceil) for the
      log10 value of read attempts first before casting the result to unsigned.

      (VC - 2019/8/14, HDFFV-10813)

    - Fixed an issue when creating a file with non-default file space info
      together with library high bound setting to H5F_LIBVER_V18.

      When setting non-default file space info in fcpl via
      H5Pset_file_space_strategy() and then creating a file with both high and
      low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in
      creating the file.  File creation should fail because the feature of
      setting non-default file space info does not exist in library release 1.8
      or earlier.

      This was fixed by setting and checking the proper version in the file
      space info message based on the library low and high bounds when creating
      and opening the HDF5 file.

      (VC - 2019/6/25, HDFFV-10808)

    - Fixed an issue where copying a version 1.8 dataset between files using
      H5Ocopy fails due to an incompatible fill version

      When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
      dataset to a file created with both high and low library bounds set to
      H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
      that the fill value version is out of bounds.

      This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
      (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.

      (VC - 2019/6/14, HDFFV-10800)

    - Fixed a bug that would cause an error or cause fill values to be
      incorrectly read from a chunked dataset using the "single chunk" \ 
index if
      the data was held in cache and there was no data on disk.

      (NAF - 2019/03/06)

    - Fixed a bug that could cause an error or cause fill values to be
      incorrectly read from a dataset that was written to using H5Dwrite_chunk
      if the dataset was not closed after writing.

      (NAF - 2019/03/06, HDFFV-10716)

    - Fixed memory leak in scale offset filter

      In a special case where the MinBits is the same as the number of bits in
      the datatype's precision, the filter's data buffer was not freed, causing
      the memory usage to grow. In general the buffer was freed correctly.  The
      Minbits are the minimal number of bits to store the data values.  Please
      see the reference manual for H5Pset_scaleoffset for the details.

      (RL - 2019/3/4, HDFFV-10705)

    - 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)

    - 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)
   2019-11-03 11:39:32 by Roland Illig | Files touched by this commit (274)
Log message:
devel: align variable assignments

pkglint -Wall -F --only aligned --only indent -r

No manual corrections.
   2019-10-06 14:05:34 by Nia Alarie | Files touched by this commit (4) | Package updated
Log message:
hdf5: Update to 1.10.5

No changelog...
   2019-05-02 00:39:29 by Jason Bacon | Files touched by this commit (3)
Log message:
devel/hdf5: Enable szip support by default

Support was off by default due to non-distributable archivers/szip dependency.
Replaced with BSD-licensed archivers/libaec, containing drop-in replacement
szip library.
   2018-11-08 03:56:06 by Mark Davies | Files touched by this commit (2) | Package updated
Log message:
hdf5: update to 1.10.4

changes unknown other than builds with gcc8.