HDF5  HISTORY
=============


INTRODUCTION

This document describes the differences between the HDF5-1.10.0 and
HDF5 1.12.0 releases. For more details check the HISTORY*.txt files in the
HDF5 source.

Information about supported and tested platforms is provided for historical
reasons only and may not be accurate.


For more information, see the HDF5 home page:

    http://www.hdfgroup.org/HDF5/

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

    help@hdfgroup.org


CONTENTS

- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.3
- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations


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

    Configuration:
    -------------
    - Update CMake tests to use FIXTURES

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

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

    - Windows PDB files are always installed

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

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

    - Add mingw CMake support with a toolchain file

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

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

    - Windows PDB files are installed incorrectly

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

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

    - Add option to build only shared libs

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

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

    - Add options to enable or disable building tools and tests

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

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

    - Change tools test that test 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)

    - Keep stderr and stdout separate in tests

      Changed test handling of output capture. Tests now keep the stderr
      output separate from the stdout output. It is up to the test to decide
      which output to check against a reference. Also added the option
      to grep for a string in either output.

      (ADB - 2018/12/12, HDFFV-10632)

    - Add toolchain and cross-compile support

      Added info on using a toolchain file to INSTALL_CMAKE.txt. A
      toolchain file is also used in cross-compiling, which requires
      CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
      the fortran configure process, the HDF5UseFortran.cmake file macros
      were improved. Fixed a Fortran configure file issue that incorrectly
      used #cmakedefine instead of #define.

      (ADB - 2018/10/04, HDFFV-10594)

    - Add warning flags for Intel compilers

      Identified Intel compiler specific warnings flags that should be used
      instead of GNU flags.

      (ADB - 2018/10/04, TRILABS-21)

    - Add default rpath to targets

      Default rpaths should be set in shared executables and
      libraries to allow the use of loading dependent libraries
      without requiring LD_LIBRARY_PATH to be set. The default
      path should be relative using @rpath on osx and $ORIGIN
      on linux. Windows is not affected.

      (ADB - 2018/09/26, HDFFV-10594)

    - Add missing USE_110_API_DEFAULT option.

      Option USE_110_API_DEFAULT sets the default version of
      versioned APIs. The bin/makevers perl script did not set
      the maxidx variable correctly when the 1.10 branch was
      created. This caused the versioning process to always use
      the latest version of any API.

      (ADB - 2018/08/17, HDFFV-10552)

    - Added configuration checks for the following MPI functions:

      MPI_Mprobe - Used for the Parallel Compression feature
      MPI_Imrecv - Used for the Parallel Compression feature

      MPI_Get_elements_x - Used for the "big Parallel I/O" feature
      MPI_Type_size_x - Used for the "big Parallel I/O" feature

      (JTH - 2018/08/02, HDFFV-10512)

    - Added section to the libhdf5.settings file to indicate
      the status of the Parallel Compression and "big Parallel I/O"
      features.

      (JTH - 2018/08/02, HDFFV-10512)

    - Add option to execute swmr shell scripts from CMake.

      Option TEST_SHELL_SCRIPTS redirects processing into a
      separate ShellTests.cmake file for UNIX types. The tests
      execute the shell scripts if a SH program is found.

      (ADB - 2018/07/16)


    Library:
    --------
    - Add new H5R_ref_t type for object, dataset region and _attribute_
      references. This new type will deprecate the current hobj_ref_t
      and hdset_reg_ref_t types for references. Added H5T_REF datatype
      to read and write new reference types. As opposed to previous
      reference types, reference creation no longer modifies existing
      files. New reference types also now support references to external
      files.

      (JS - 2019/10/08)

    - Add S3 and HDFS VFDs to HDF5 maintenance

      Fix windows requirements and java tests. Windows requires CMake 3.13.
            Install openssl library (with dev files);
            from "Shining Light Productions". msi package preferred.

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

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

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

    - Added new chunk query functions

      The following public functions were added to discover information about
      the chunks in an HDF5 file.
        herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
        herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
        herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)

      (BMR - 2019/06/11, HDFFV-10677)

    - Improved the performance of virtual dataset I/O

      Refactored the internal dataspace routines used by the virtual dataset
      code to improve performance, especially when one of the selections
      involved is very long and non-contiguous.

      (NAF - 2019/05/31, HDFFV-10693)

    - Added the ability to open files with UTF-8 file names on Windows.

      The POSIX open(2) API call on Windows is limited to ASCII
      file names. The library has been updated to convert incoming file
      names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use
      _wopen() instead.

     (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691)

    - Add new API H5M for map objects.  Currently not supported by native
      library, can be supported by VOL connectors.

      (NAF - 2019/03/01)

    - Remove H5I_REFERENCE from the library

      This ID class was never used by the library and has been removed.

      (DER - 2018/12/08, HDFFV-10252)

    - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.

      Rather than always running H5detect and generating H5Tinit.c and
      H5make_libsettings.c, supply a location for those files.

      (ADB - 2018/09/18, HDFFV-10332)


    Parallel Library:
    -----------------
    - Changed the default behavior in parallel when reading the same dataset in its entirely
      (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
      The dataset mush be contiguous, less than 2GB, and of an atomic datatype.
      The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
      the disk by the root process to the remain processes in the MPI communicator associated
      with the HDF5 file.

      (MSB - 2019/01/02, HDFFV-10652)

    Fortran Library:
    ----------------
    - Added new Fortran derived type, c_h5o_info_t, which is interoperable with
      C's h5o_info_t. This is needed for callback functions which
      pass C's h5o_info_t data type definition.

      (MSB, 2019/01/08, HDFFV-10443)

    - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
      to Fortran DATE AND TIME storage format.

      (MSB, 2019/01/08, HDFFV-10443)

    - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
      h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.

      (MSB, 2019/01/08, HDFFV-10443)

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

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

    - Added new wrapper for H5Ovisit2()
          H5Object::visit()

      (BMR - 2019/02/14, HDFFV-10532)


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

      (JTH - 2019/04/30)

    - Duplicate the data read/write functions of Datasets for Attributes.

      Region references could not be displayed for attributes as they could
      for datasets. Datasets had overloaded read and write functions for different
      datatypes that were not available for attributes. After adding similar
      functions, attribute region references work normally.

      (ADB - 2018/12/12, HDFVIEW-4)

    - Removed H5I_REFERENCE from the Java wrappers

      This ID class was never used by the library and has been removed
      from the Java wrappers.

      (DER - 2018/12/08, HDFFV-10252)


    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)

    - h5dump was fixed for 128-bit floats, but was missing a test.

      New test greps for the first 15 numbers of the 128-bit value.

      (ADB - 2019/06/23, HDFFV-9407)


    High-Level APIs:
    ---------------
    -

    C Packet Table API
    ------------------
    -

    Internal header file
    --------------------
    -

    Documentation
    -------------
    -

Support for new platforms, languages and compilers.
=======================================
    -

Bug Fixes since HDF5-1.10.3 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.

      (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)

    - Fixed the iteration error in test_versionbounds() in test/dtypes.c

      The test was supposed to loop through all valid combinations of
      low and high bounds in the array versions[], but they were set to
      H5F_LIBVER_EARLIEST always without changing.

      The problem was fixed by indexing low and high into the array versions[].

      (VC - 2019/09/30)

    - Fixed the slowness of regular hyperslab selection in a chunked dataset

      It was reported that the selection of every 10th element from a 20G
      chunked dataset was extremely slow and sometimes could hang the system.
      The problem was due to the iteration and the building of the span tree
      for all the selected elements in file space.

      As the selected elements are going to a 1-d contiguous single block
      memory space, the problem was fixed by building regular hyperslab selections
      in memory space for the selected elements in file space.

      (VC - 2019/09/26, HDFFV-10585)

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

      There was an assertion failure when moving meessages 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 will 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 the 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 where 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)

    - When iterating over an old-style group (i.e., when not using the latest
      file format) of size 0, a NULL pointer representing the empty links
      table would be sent to qsort(3) for sorting, which is undefined behavior.

      Iterating over an empty group is explicitly tested in the links test.
      This has not caused any failures to date and was flagged by gcc's
      -fsanitize=undefined.

      The library no longer attempts to sort an empty array.

      (DER - 2019/06/18, HDFFV-10829)

    - 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)

    - Some oversights in the index iterating area of the library caused
      a callback function to continue iterating even though it's supposed
      to stop.

      Added the returned value check to the for loop's conditions in
      H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate().  The
      iteration now stops when it should.

      (BMR - 2019/06/11, HDFFV-10661)

    - 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 detail.

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

    - Fix hangs with collective metadata reads during chunked dataset I/O

      In the parallel library, it was discovered that when a particular
      sequence of operations following a pattern of:

      "write to chunked dataset" -> "flush file" -> "read from dataset"

      occurred with collective metadata reads enabled, hangs could be
      observed due to certain MPI ranks not participating in the collective
      metadata reads.

      To fix the issue, collective metadata reads are now disabled during
      chunked dataset raw data I/O.

      (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)

    - Performance issue when closing an object

      The slow down is due to the search of the "tag_list" to find
      out the "corked" status of an object and "uncork" it if so.

      Improve porformance by skipping the search of the "tag_list"
      if there are no "corked" objects when closing an object.

      (VC - 2019/2/6)

    - Fixed a potential invalid memory access and failure that could occur when
      decoding an unknown object header message (from a future version of the
      library).

      (NAF - 2019/01/07)

    - Deleting attributes in dense storage

      The library aborts with "infinite loop closing library" after
      attributes in dense storage are created and then deleted.

      When deleting the attribute nodes from the name index v2 B-tree,
      if an attribute is found in the intermediate B-tree nodes,
      which may be merged/redistributed in the process, we need to
      free the dynamically allocated spaces for the intermediate
      decoded attribute.

      (VC - 2018/12/26, HDFFV-10659)

    - Allow H5detect and H5make_libsettings to take a file as an argument.

      Rather than only writing to stdout, add a command argument to name
      the file that H5detect and H5make_libsettings will use for output.
      Without an argument, stdout is still used, so backwards compatibility
      is maintained.

      (ADB - 2018/09/05, HDFFV-9059)

    - A bug was discovered in the parallel library where an application
      would hang if a collective read/write of a chunked dataset occurred
      when collective metadata reads were enabled and some of the ranks
      had no selection in the dataset's dataspace. The ranks which had no
      selection in the dataset's dataspace called H5D__chunk_addrmap() to
      retrieve the lowest chunk address in the dataset. This is because we
      require reads/writes to be performed in strictly non-decreasing order
      of chunk address in the file.

      When the chunk index used was a version 1 or 2 B-tree, these
      non-participating ranks would issue a collective MPI_Bcast() call
      that the participating ranks would not issue, causing the hang. Since
      the non-participating ranks are not actually reading/writing anything,
      the H5D__chunk_addrmap() call can be safely removed and the address used
      for the read/write can be set to an arbitrary number (0 was chosen).

      (JTH - 2018/08/25, HDFFV-10501)

    - 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)


    Java Library:
    ----------------
    - JNI native library dependencies

      The build for the hdf5_java native library used the wrong
      hdf5 target library for CMake builds. Correcting the hdf5_java
      library to build with the shared hdf5 library required testing
      paths to change also.

      (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)


    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, v112.

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


    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.

      Effected 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)

    - 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)



    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
    -------
    - The dt_arith test failed on IBM Power8 and Power9 machines when testing
      conversions from or to long double types, especially when special values
      such as infinity or NAN were involved.  In some cases the results differed
      by extremely small amounts from those on other machines, while some other
      tests resulted in segmentation faults.  These conversion tests with long
      double types have been disabled for ppc64 machines until the problems are
      better understood and can be properly addressed.

      (SRL - 2019/01/07, TRILAB-98)

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 Mountain Lion 10.8.5 64-bit    n        y/y    n        y    y     y
Mac OS X Mavericks 10.9.5 64-bit        n        y/y    n        y    y     ?
Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     ?
Mac OS X El Capitan 10.11.6 64-bit      n        y/y    n        y    y     ?
CentOS 6.7 Linux 2.6.18 x86_64 GNU      n        y/y    n        y    y     y
CentOS 6.7 Linux 2.6.18 x86_64 Intel    n        y/y    n        y    y     y
CentOS 6.7 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/n    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 Mountain Lion 10.8.5 64-bit       y       n         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
CentOS 6.7 Linux 2.6.18 x86_64 GNU         y       y         y         y
CentOS 6.7 Linux 2.6.18 x86_64 Intel       y       y         y         n
CentOS 6.7 Linux 2.6.32 x86_64 PGI         y       y         y         n
CentOS 7.2 Linux 2.6.32 x86_64 GNU         y       y         y         n
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
                                  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)


Known Problems
==============
    CMake files do not behave correctly with paths containing spaces.
    Do not use spaces in paths because the required escaping for handling spaces
    results in very complex and fragile build files.
    ADB - 2019/05/07

    At present, metadata cache images may not be generated by parallel
    applications.  Parallel applications can read files with metadata cache
    images, but since this is a collective operation, a deadlock is possible
    if one or more processes do not participate.

    Known problems in previous releases can be found in the HISTORY*.txt files
    in the HDF5 source. Please report any new problems found to
    help@hdfgroup.org.


CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.

The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
  build scripts
  -------------
  Autotools: h5c++, h5cc, h5fc
  CMake: h5c++, h5cc, h5hlc++, h5hlcc

The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.

The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.

The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.

