Merge pull request #1106 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.8/master to 1.8/masterhdf5-1_8_21

* commit '664186b91d9198915baca4c6dca3f7b03695d316': (124 commits)
  Commit HDF5 1.8.21 release version strings.
  Update INSTALL and INSTALL_parallel files to remove references to ancient systems and add generic steps for building HDF5 on HPC clusters.
  Update various INSTALL files for 1.8.21 release.
  Add missing space and correct typo.
  Modified a section for newly supported systems and compilers (vs. 1.8.20 release); Brought edits for tools bug fixes from 1.10.2 RELEASE.txt as we agreed with Allen.
  It is my test under Larry's guidance.
  Remove build directory which was unintentionally committed.
  Updated MANIFEST
  Switch default build mode to production. Update version to 1.8.21 in anticipation of release.
  Fixed EED-319 Description:     Added an html version for the C++ function mapping table and removed     the single web page version.     Updated cpp_doc_config to use the html file.     Fixed some typos.     Running "doxygen cpp_doc_config" successfully.
  HDFFV-10473 fix HDFFV-10398 attribute location
  Add missing C++ entries to RELEASE.txt.
  pre1 release.
  Add missing RELEASE.txt entries for C++.
  Update Windows test machines
  Fix soversion naming and update cmake scripts
  Update version in RELEASE.txt. Correct merge errors from hdf5_1_8.
  Fixed typos
  Fixed typos
  Fixed typos
  ...

1 files changed, 494 insertions, 1 deletions

diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt
index a7aad02..2aa7bde 100644
--- a/release_docs/HISTORY-1_8.txt
+++ b/release_docs/HISTORY-1_8.txt
@@ -3,7 +3,8 @@ HDF5 History
 
 This file contains development history of HDF5 1.8 branch
 
-21.      Release Information for hdff5-1.8.19
+22.      Release Information for hdf5-1.8.20
+21.      Release Information for hdf5-1.8.19
 20.      Release Information for hdf5-1.8.18
 19.      Release Information for hdf5-1.8.17
 18.      Release Information for hdf5-1.8.16
@@ -27,6 +28,498 @@ This file contains development history of HDF5 1.8 branch
 
 [Search on the string '%%%%' for section breaks of each release.]
 
+%%%%1.8.20%%%%
+
+
+HDF5 version 1.8.20 released on 2017-11-28
+================================================================================
+
+INTRODUCTION
+============
+
+This document describes the differences between HDF5-1.8.19 and
+HDF5-1.8.20, and contains information on the platforms tested and
+known problems in HDF5-1.8.20.
+For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
+and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
+
+Links to the HDF5 1.8.20 source code, documentation, and additional materials
+can be found on the HDF5 web page at:
+
+     https://support.hdfgroup.org/HDF5/
+
+The HDF5 1.8.20 release can be obtained from:
+
+     https://support.hdfgroup.org/HDF5/release/obtain518.html
+
+User documentation for 1.8.20 can be accessed directly at this location:
+
+     https://support.hdfgroup.org/HDF5/doc1.8/
+
+New features in the HDF5-1.8.x release series, including brief general
+descriptions of some new and modified APIs, are described in the "What's New
+in 1.8.0?" document:
+
+     https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
+
+All new and modified APIs are listed in detail in the "HDF5 Software Changes
+from Release to Release" document, in the section "Release 1.8.20 (current
+release) versus Release 1.8.19
+
+     https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
+
+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, Languages, and Compilers
+- Bug Fixes since HDF5-1.8.20
+- Supported Platforms
+- Supported Configuration Features Summary
+- More Tested Platforms
+- Known Problems
+
+
+New Features
+============
+
+    Tools
+    -----
+    - h5diff
+
+      h5diff has new option enable-error-stack.
+
+      Updated h5diff with the --enable-error-stack argument, which
+      enables the display of the hdf5 error stack. This completes the
+      improvement to the main tools; h5copy, h5diff, h5dump, h5ls and
+      h5repack.
+
+      (ADB - 2017/08/30, HDFFV-9774)
+
+
+    C++ API
+    -------
+    - The following C++ API wrappers have been added to the C++ Library:
+
+        // Creates a binary object description of this datatype.
+        void DataType::encode() - C API H5Tencode()
+
+        // Returns the decoded type from the binary object description.
+        DataType::decode() - C API H5Tdecode()
+        ArrayType::decode() - C API H5Tdecode()
+        CompType::decode() - C API H5Tdecode()
+        DataType::decode() - C API H5Tdecode()
+        EnumType::decode() - C API H5Tdecode()
+        FloatType::decode() - C API H5Tdecode()
+        IntType::decode() - C API H5Tdecode()
+        StrType::decode() - C API H5Tdecode()
+        VarLenType::decode() - C API H5Tdecode()
+
+        // Three overloaded functions to retrieve information about an object
+        H5Location::getObjectInfo() - H5Oget_info()/H5Oget_info_by_name()
+
+      (BMR - 2017/10/17, HDFFV-10175)
+
+    - New constructors to open existing datatypes added in ArrayType,
+      CompType, DataType, EnumType, FloatType, IntType, StrType, and
+      VarLenType.
+
+      (BMR - 2017/10/17, HDFFV-10175)
+
+    - A document is added to the HDF5 C++ API Reference Manual to show the
+      mapping from a C API to C++ wrappers.  It can be found from the main
+      page of the C++ API Reference Manual.
+
+      (BMR - 2017/10/17, HDFFV-10151)
+
+
+    High-Level APIs
+    ---------------
+    - H5DOread_chunk
+
+      Users wanted to read compressed data directly from a file without any
+      processing by the HDF5 data transfer pipeline, just as they were able
+      to write it directly to a file with H5DOwrite_chunk.
+
+      New API function, corresponding to existing function H5DOwrite_chunk.
+      H5DOread_chunk reads a raw data chunk directly from a chunked dataset
+      in the file into the application buffer, bypassing the library’s internal
+      data transfer pipeline, including filters.
+
+      (VC - 2017/05/02, HDFFV-9934)
+
+
+Support for New Platforms, Languages, and Compilers
+===================================================
+
+    - Added NAG compiler
+
+
+Bug Fixes since HDF5-1.8.19
+===========================
+
+    Configuration
+    -------------
+    - cmake
+
+      The hdf5 library used shared szip and zlib, which needlessly required
+      applications to link with the same szip and zlib libraries.
+
+      Changed the target_link_libraries commands to use the static libs.
+      Removed improper link duplication of szip and zlib.
+      Adjusted the link dependencies and the link interface values of
+      the target_link_libraries commands.
+
+      (ADB - 2017/11/14, HDFFV-10329)
+
+    - cmake MPI
+
+      CMake implementation for MPI was problematic and would create incorrect
+      MPI library references in the hdf5 libraries.
+
+      Reworked the CMake MPI code to properly create CMake targets.Also merged
+      the latest CMake FindMPI.cmake changes to the local copy. This is necessary
+      until HDF changes the CMake minimum to 3.9 or greater.
+
+      (ADB - 2017/11/02, HDFFV-10321)
+
+
+    - Fixed Fortran linker flags when using the NAG Fortran compiler (autotools).
+
+      (HDFFV-10037, MSB, 2017/10/21)
+
+    - cmake
+
+      Too many commands for POST_BUILD step caused command line to be
+      too big on windows.
+
+      Changed foreach of copy command to use a custom command with the
+      use of the HDFTEST_COPY_FILE macro.
+
+      (ADB - 2017/07/12, HDFFV-10254)
+
+
+    Library
+    -------
+    - filter plugin handling in H5PL.c and H5Z.c
+
+      It was discovered that the dynamic loading process used by
+      filter plugins had issues with library dependencies.
+
+      CMake build process changed to use LINK INTERFACE keywords, which
+      allowed HDF5 C library to make dependent libraries private. The
+      filter plugin libraries no longer require dependent libraries
+      (such as szip or zlib) to be available.
+             (ADB - 2017/11/16, HDFFV-10328)
+
+    - Fix rare object header corruption bug
+
+      In certain cases, such as when converting large attributes to dense
+      storage, an error could occur which would either fail an assertion or
+      cause file corruption. Fixed and added test.
+
+      (NAF - 2017/11/14, HDFFV-10274)
+
+    - H5Zfilter_avail in H5Z.c
+
+      The public function checked for plugins, while the private
+      function did not.
+
+      Modified H5Zfilter_avail and private function, H5Z_filter_avail.
+      Moved check for plugin from public to private function. Updated
+      H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
+
+      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
+
+    - Fix H5Sencode bug when num points selected is >2^32
+
+      Modified to fail if the 32 bit limit is exceeded when encoding either
+      offsets or counts in the selection.
+
+      (HDFFV-10323, VC, 2017/09/07)
+
+    - Fix H5HL_offset_into()
+
+      (1) Fix H5HL_offset_into() to return error when offset exceeds heap data
+          block size.
+      (2) Fix other places in the library that call this routine to detect
+          error routine.
+
+      (HDFFV-10216, VC, 2017/09/05)
+
+
+    Tools
+    -----
+    - h5repack
+
+      h5repack failed to copy a dataset with existing filter.
+
+      Reworked code for h5repack and h5diff code in tools library. Added
+      improved error handling, cleanup of resources and checks of calls.
+      Modified H5Zfilter_avail and private function, H5Z_filter_avail.
+      Moved check for plugin from public to private function. Updated
+      H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
+      Note, h5repack output display has changed to clarify the individual
+      steps of the repack process. The output indicates if an operation
+      applies to all objects. Lines with notation and no information
+      have been removed.
+
+      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
+
+    - h5repack
+
+      h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.
+
+      Added another parameter to the 'UD=' option to set the flag by default
+      to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL.
+
+      (ADB - 2017/08/31, HDFFV-10269)
+
+    - h5ls
+
+      h5ls generated error on stack when it encountered a H5S_NULL
+      dataspace.
+
+      Adding checks for H5S_NULL before calling H5Sis_simple (located
+      in the h5tools_dump_mem function) fixed the issue.
+
+      (ADB - 2017/08/17, HDFFV-10188)
+
+    - h5dump
+
+      h5dump segfaulted on output of XML file.
+
+      Function that escape'd strings used the full buffer length
+      instead of just the length of the replacement string in a
+      strncpy call. Using the correct length fixed the issue.
+
+      (ADB - 2017/08/01, HDFFV-10256)
+
+    - h5diff
+
+      h5diff segfaulted on compare of a  NULL variable length string.
+
+      Improved h5diff compare of strings by adding a check for
+      NULL strings and setting the lengths to zero.
+
+      (ADB - 2017/07/25, HDFFV-10246)
+
+    - h5import
+
+      h5import crashed trying to import data from a subset of a dataset.
+
+      Improved h5import by adding the SUBSET keyword. h5import understands
+      to use the Count times the Block as the size of the dimensions.
+      Added INPUT_B_ORDER keyword to old-style configuration files.
+      The import from h5dump function expects the binary files to use native
+      types (FILE '-b' option) in the binary file.
+
+      (ADB - 2017/06/15, HDFFV-10219)
+
+
+    C++ API
+    -------
+    - Marked the following functions deprecated because they were moved to
+      class H5Object:
+        H5Location::createAttribute()
+        H5Location::openAttribute()
+        H5Location::attrExists()
+        H5Location::removeAttr()
+        H5Location::renameAttr()
+        H5Location::getNumAttrs()
+
+      (BMR - 2017/10/17)
+
+
+Supported Platforms
+===================
+The following platforms are supported and have been tested for this release.
+They are built with the configure process unless specified otherwise.
+
+    Linux 2.6.32-573.22.1.el6     GNU C (gcc), Fortran (gfortran), C++ (g++)
+    #1 SMP x86_64 GNU/Linux       compilers:
+    (platypus/mayll)              Version 4.4.7 20120313
+                                     Versions 4.9.3, 5.3.0, 6.2.0
+                                  PGI C, Fortran, C++ for 64-bit target on
+                                  x86-64;
+                                      Version 16.10-0
+                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
+                                  compilers:
+                                     Version 17.0.0.196 Build 20160721
+                                  MPICH 3.1.4 compiled with GCC 4.9.3
+                                  OpenMPI 2.0.1 compiled with GCC 4.9.3
+
+    Linux 2.6.32-573.18.1.el6     gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
+    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
+    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
+                                  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/jelly           Version 4.8.5 20150623 (Red Hat 4.8.5-4)
+                                     Versions 4.9.3, 5.3.0, 6.2.0
+                                  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
+                                  NAG Fortran Compiler Release 6.1(Tozai) Build 6116
+
+    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 2012 w/ Intel Fortran 15 (cmake)
+                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
+                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+
+    Windows 7 x64                 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
+                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
+                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+                                  Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
+                                  Visual Studio 2015 w/ MSMPI 8 (cmake)
+                                  Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
+                                      gcc and gfortran compilers (GCC 5.4.0)
+                                      (cmake and autotools)
+
+    Windows 10                    Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+                                  Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
+                                      gcc and gfortran compilers (GCC 5.4.0)
+                                      (cmake and autotools)
+
+    Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+
+    Mac OS X Mavericks 10.9.5     Apple LLVM version 6.0 (clang-600.0.57)
+    64-bit                        gfortran GNU Fortran (GCC) 4.9.2
+    (wren/quail)                  Intel icc/icpc/ifort version 15.0.3
+
+    Mac OS X Yosemite 10.10.5     Apple LLVM version 6.1 (clang-602.0.53)
+    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 LLVM version 7.3.0 (clang-703.0.29)
+    64-bit                        gfortran GNU Fortran (GCC) 5.2.0
+    (VM osx1011dev/osx1011test)   Intel icc/icpc/ifort version 16.0.2
+
+    Mac OS Sierra 10.12.6         Apple LLVM version 8.1 (clang-802.0.42)
+    64-bit                        gfortran GNU Fortran (GCC) 7.1.0
+    (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
+SunOS 5.11 32-bit                       n        y/y    n        y    y     y
+SunOS 5.11 64-bit                       n        y/y    n        y    y     y
+Windows 7                               y        y/y    n        y    y     y
+Windows 7 x64                           y        y/y    n        y    y     y
+Windows 7 Cygwin                        n        y/n    n        y    y     y
+Windows 7 x64 Cygwin                    n        y/n    n        y    y     y
+Windows 10                              y        y/y    n        y    y     y
+Windows 10 x64                          y        y/y    n        y    y     y
+Mac OS X Mavericks 10.9.5 64-bit        n        y/y    n        y    y     y
+Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     y
+Mac OS X El Capitan 10.11.6 64-bit      n        y/y    n        y    y     y
+Mac OS Sierra 10.12.6 64-bit            n        y/y    n        y    y     y
+AIX 6.1 32- and 64-bit                  n        y/n    n        y    y     y
+CentOS 6.7 Linux 2.6.32 x86_64 GNU      y        y/y    y        y    y     y
+CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU      y        y/y    y        y    y     y
+CentOS 7.1 Linux 3.10.0 x86_64 Intel    n        y/y    n        y    y     y
+Linux 2.6.32-431.11.2.el6.ppc64         n        y/n    n        y    y     y
+
+Platform                                 Shared  Shared    Shared    Thread-
+                                         C libs  F90 libs  C++ libs  safe
+SunOS 5.11 32-bit                          y       y         y         y
+SunOS 5.11 64-bit                          y       y         y         y
+Windows 7                                  y       y         y         y
+Windows 7 x64                              y       y         y         y
+Windows 7 Cygwin                           n       n         n         y
+Windows 7 x64 Cygwin                       n       n         n         y
+Windows 10                                 y       y         y         y
+Windows 10 x64                             y       y         y         y
+Mac OS X Mavericks 10.9.5 64-bit           y       n         y         y
+Mac OS X Yosemite 10.10.5 64-bit           y       n         y         y
+Mac OS X El Capitan 10.11.6 64-bit         y       n         y         y
+Mac OS Sierra 10.12.6 64-bit               y       n         y         y
+AIX 6.1 32- and 64-bit                     y       n         n         y
+CentOS 6.7 Linux 2.6.32 x86_64 GNU         y       y         y         y
+CentOS 6.7 Linux 2.6.32 x86_64 Intel       y       y         y         y
+CentOS 6.7 Linux 2.6.32 x86_64 PGI         y       y         y         y
+CentOS 7.1 Linux 3.10.0 x86_64 GNU         y       y         y         y
+CentOS 7.1 Linux 3.10.0 x86_64 Intel       y       y         y         y
+Linux 2.6.32-431.11.2.el6.ppc64            y       y         y         y
+
+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     g95 (GCC 4.0.3 (g95 0.94!)
+    #1 SMP x86_64 GNU/Linux
+    (mayll)
+
+    Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
+                                  gcc (Debian 4.9.2-10) 4.9.2
+                                  GNU Fortran (Debian 4.9.2-10) 4.9.2
+                                  (cmake and autotools)
+
+    Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
+                                  gcc (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)
+
+    CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
+                                  gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
+                                  GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
+                                  (cmake and autotools)
+
+    Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
+                                  gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
+                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
+                                  (cmake and autotools)
+
+
+Known Problems
+==============
+
+    The dynamically loaded plugin test libraries require undefined references
+    to HDF5 functions to be resolved at runtime in order to function properly.
+    With autotools on CYGWIN this results in build errors, and we have not
+    found a solution that satisfies both.  Therefore the dynamically loaded
+    plugin tests have been disabled on CYGWIN.
+
+    Mac OS X 10.13 added additional subdirectory structure in .libs for shared
+    libraries.  Consequently "make check" will fail testing java and dynamically
+    loaded plugin test libraries attempting to copy files from the previous
+    locations in .libs directories.  This will be addressed in the next release
+    when support for the Mac OS X 10.13 platform is added.
+
+    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.
+
+
 %%%%1.8.19%%%%