Log Message:
hdf5: Update to 1.10.6

New Features
============

    Configuration:
    -------------
    - 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
      process.

      (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)

    Library:
    --------
    - 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/HDF5/Virtual+File+Drivers+-+S3+and+HDFS.

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

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

            Open a Visual Studio Command prompt
            change to the libcurl root folder
            run the "buildconf.bat" batch file
            change to the winbuild directory
            nmake /f Makefile.vc mode=dll MACHINE=x64
            copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl \ 
(installation dir)
            set ENV variable CURL_ROOT to C:\curl (installation dir)
            update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
            the aws credentials file should be in %USERPROFILE%\.aws folder
            set the ENV variable \ 
"HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3"

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

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

      (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
==================================

    Library
    -------
    - 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 \ 
"FALSE".
      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
      messages

      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 \ 
H5O__chunk_update_idx()
      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
      test/swmr.c

      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
      failure.

      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)

    Configuration
    -------------
    - Correct option for default API version

      CMake options for default API version are not mutually exclusive.
      Change the multiple BOOL options to a single STRING option with the
      strings; v16, v18, v110.

      (ADB - 2019/08/12, HDFFV-10879)

    Tools
    -----
    - 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)