Merge pull request #811 in HDFFV/hdf5 from hdf5_1_8_20 to 1.8/masterhdf5-1_8_20

* commit '60f76980aab92f0e0730170b99a2363acd3c97fa': (108 commits)
  Update version numbers and remove empty sections in RELEASE.txt.
  Restore line 1154: C2Cppfunction_map.mht to HTML_EXTRA_FILES.
  Update version for 1.8.20 release.
  Fixed documentation warnings
  HDFFV-10329 Correct LINK INTERFACE and VS20013 compile
  Switch default build mode from development to production. Increment version string to pre2.
  Add RELEASE.txt note for HDFFV-10274. (cherry picked from commit f7a7d0a00613cba997212fa8032091629a678797)
  Initialize hid_t variables in test_Attr_bug9. (cherry picked from commit 97bc393449f3fe02c5992872ab2842e12f611ef0)
  Fix HDFFV-10274.  When deleting all (or almost all) of the messages in an object header chunk, where the total amount deleted was greater than 64K, an error would occur due to an off by one error in the code that handled that case.  Fixed this and added a test case. (cherry picked from commit 1b2c2ca9a6a7d7e1fcd5c3302e203f2e2dabf0af)
  Fix linking of libs
  Changed file path to relative.
  iAdd NAG to supported compilers in RELEASE.txt.
  Add description to RELEASE.txt for HDFFV-10323
  Correct issue number
  Set version to 1.8.20-pre1
  Update supported and tested platforms in RELEASE.txt.
  HDFFV-10321 Merge from 1.8
  Incremented lib file .so numbers: revision for all except c++ for code change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  updated issues related to Fortran
  Incremented lib file .so numbers: revision for all except c++ for dcode change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  ...

1 files changed, 200 insertions, 141 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index f7a7f34..2050a1c 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -1,25 +1,25 @@
-HDF5 version 1.8.19 released on 2017-06-15
+HDF5 version 1.8.20 released on 2017-11-28
 ================================================================================
 
 INTRODUCTION
 ============
 
-This document describes the differences between HDF5-1.8.18 and
-HDF5-1.8.19, and contains information on the platforms tested and
-known problems in HDF5-1.8.19.
+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 1.8.19 source code, documentation, and additional materials
+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 1.8.19 release can be obtained from:
+The HDF5 1.8.20 release can be obtained from:
 
      https://support.hdfgroup.org/HDF5/release/obtain518.html
 
-User documentation for 1.8.19 can be accessed directly at this location:
+User documentation for 1.8.20 can be accessed directly at this location:
 
      https://support.hdfgroup.org/HDF5/doc1.8/
 
@@ -30,8 +30,8 @@ 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 1.8.19 (current
-release) versus Release 1.8.18
+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
 
@@ -45,7 +45,7 @@ CONTENTS
 
 - New Features
 - Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.19
+- Bug Fixes since HDF5-1.8.20
 - Supported Platforms
 - Supported Configuration Features Summary
 - More Tested Platforms
@@ -55,89 +55,54 @@ CONTENTS
 New Features
 ============
 
-    Configuration
-    --------------
-    - CMake in the Tools
-
-      User-defined filters on Windows require that tools be built
-      with shared libraries.
-
-      CMake command code added to build tools with
-      shared libraries as well as with static libraries.
-
-      (ADB - 2017/02/07, HDFFV-10123)
-
-
-    Library
-    -------
-    - H5PL package
-
-      Users would like to be able to set the plugin path programmatically
-      instead of through the environment variable.
-
-      H5PL package obtained new APIs for manipulating the entries of
-      the plugin path table. The new APIs are;
-        H5PLappend  - Insert a plugin path at the end of the list.
-        H5PLprepend - Insert a plugin path at the beginning of the list.
-        H5PLreplace - Replace the path at the specified index.
-        H5PLinsert  - Insert a plugin path at the specified index, moving
-                      other paths after the index.
-        H5PLremove  - Remove the plugin path at the specifed index and
-                      compacting the list.
-        H5PLget     - Query the plugin path at the specified index.
-        H5PLsize    - Query the size of the current list of plugin paths.
-
-      (ADB - 2017/04/04, HDFFV-10143)
+    Tools
+    -----
+    - h5diff
 
-    - H5Dget_chunk_storage_size
+      h5diff has new option enable-error-stack.
 
-      The storage size of a chunk in the file is needed to determine the size
-      of the buffer to be allocated for reading a chunk directly from a file.
+      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.
 
-      New API function gets the size in bytes currently allocated within a
-      file for a raw data chunk in a dataset.  This function was added to get
-      the chunk size in support of the implementation of H5DOread_chunks, but
-      may also be useful for other purposes.
+      (ADB - 2017/08/30, HDFFV-9774)
 
-      (VC - 2017/05/02, HDFFV-9934)
 
     C++ API
     -------
     - The following C++ API wrappers have been added to the C++ Library:
-        // Determines if a name exists.
-        H5Location::nameExists() - C API H5Lexists()
-
-        // Checks if an ID is valid.
-        IdComponent::isValid() - C API H5Iis_valid()
-
-        // Sets the number of soft or user-defined links that can be
-        // traversed before a failure occurs.
-        LinkAccPropList::setNumLinks() - C API H5Pset_nlinks()
-
-        // Gets the number of soft or user-defined link traversals allowed
-        LinkAccPropList::getNumLinks() - C API H5Pget_nlinks()
 
-        // Returns a copy of the creation property list of a datatype.
-        DataType::getCreatePlist() - C API H5Tget_create_plist()
+        // Creates a binary object description of this datatype.
+        void DataType::encode() - C API H5Tencode()
 
-        // Opens an object within a location, regarless its type.
-        H5Location::openObjId() - C API H5Oopen()
-        H5Location::openObjId() - C API H5Oopen()
+        // 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()
 
-        // Closes an object opened by openObjId().
-        H5Location::closeObjId() - C API H5Oclose()
+        // Three overloaded functions to retrieve information about an object
+        H5Location::getObjectInfo() - H5Oget_info()/H5Oget_info_by_name()
 
-        // Gets general information about a file.
-        H5File::getFileInfo() - C API H5Fget_info()
+      (BMR - 2017/10/17, HDFFV-10175)
 
-        // Returns the header version of an HDF5 object.
-        H5Object::objVersion() - C API H5Oget_info()
+    - New constructors to open existing datatypes added in ArrayType,
+      CompType, DataType, EnumType, FloatType, IntType, StrType, and
+      VarLenType.
 
-      (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156)
+      (BMR - 2017/10/17, HDFFV-10175)
 
-    - New class LinkAccPropList is added for link access proprety list
+    - 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, 2017/05/13, HDFFV-10156)
+      (BMR - 2017/10/17, HDFFV-10151)
 
 
     High-Level APIs
@@ -147,7 +112,7 @@ New Features
       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
@@ -159,98 +124,183 @@ New Features
 Support for New Platforms, Languages, and Compilers
 ===================================================
 
-    - Added OpenMPI 2.0.1 compiled with GCC 4.9.3
+    - Added NAG compiler
 
 
-Bug Fixes since HDF5-1.8.18
+Bug Fixes since HDF5-1.8.19
 ===========================
 
     Configuration
     -------------
-    - Support for Fortran shared libraries on OS X with autotools now
-      works. Cmake builds still disables Fortran shared libraries on OS X.
-      (MSB - 2017/04/30, HDFFV-2772)
+    - 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
     -------
-    - bitfield datatypes
+    - 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)
 
-      bitfield datatypes did not fully support endianness of the data.
+    - Fix rare object header corruption bug
 
-      Improved the endianness of bitfield datatypes by adding missing functional
-      code. This code used integer types as a template.
+      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.
 
-      (ADB - 2017/05/12, HDFFV-10186)
+      (NAF - 2017/11/14, HDFFV-10274)
 
-    - Newly created datasets with H5D_COMPACT layout failed to open after 
-      several H5Dopen/H5Dclose cycles.
+    - H5Zfilter_avail in H5Z.c
 
-      The layout "dirty" flag for a compact dataset is now properly reset 
-      before flushing the message.
+      The public function checked for plugins, while the private
+      function did not.
 
-      (VC - 2017/05/11, HDFFV-10051)
+      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.
 
-    - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file.
+      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
 
-      (DER - 2017/04/25, HDFFV-9638)
+    - 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 did not maintain the creation order flag of the root
-      group.
+      h5repack failed to copy a dataset with existing filter.
 
-      Improved h5repack by reading the creation order and applying the
-      flag to the new root group. Also added arguments to set the
-      order and index direction, which applies to the traversing of the
-      original file, on the command line.
+      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 - 2017/05/26, HDFFV-8611)
+      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
 
-    - h5diff
+    - h5repack
 
-      h5diff failed to account for strpad type and null terminators
-      of char strings. Also, h5diff failed to account for string length
-      differences and would give a different result depending on file
-      order in the command line.
+      h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.
 
-      Improved h5diff compare of strings and arrays by adding a check for
-      string lengths and if the strpad was null filled.
+      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 - 2017/05/18, HDFFV-9055, HDFFV-10128)
+      (ADB - 2017/08/31, HDFFV-10269)
 
-    - h5diff
+    - 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)
 
-      h5diff help text about epsilon comparison was confusing.
+    - h5dump
 
-      Changed h5diff help text to indicate that the 'a' refers to the
-      datapoint in file1 and 'b' refers to the datapoint value in file2.
+      h5dump segfaulted on output of XML file.
 
-      (ADB - 2017/05/16, HDFFV-9995)
+      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 did not report user-defined filter data differences correctly.
+      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)
 
-      Improved h5diff compare of user-defined filter data by reporting an
-      error if the user-defined filter plugin cannot be found.
+    - 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)
 
-      (ADB - 2017/01/18, HDFFV-9994)
 
     C++ API
     -------
-    - The class hierarchy is revised to better reflect the HDF5 model.
-      Class H5File is now derived from class Group instead of H5Location.
-      Class Attribute is now derived from H5Location instead of IdComponent.
-      Wrappers of H5A APIs in H5Location are now duplicated in H5Object,
-      the original wrappers in H5Location will be deprecated in future
-      releases.
-
-      (BMR - 2017/05/15, HDFFV-10156)
+    - 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
@@ -261,13 +311,13 @@ 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, 5.2.0, 6.2.0
+                                     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 17.0.0.098 Build 20160721
+                                     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
 
@@ -279,12 +329,13 @@ They are built with the configure process unless specified otherwise.
 
     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)
-                                    Versions 4.9.3, 5.3.0, 6.2.0
+    (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
@@ -310,10 +361,6 @@ They are built with the configure process unless specified otherwise.
 
     Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 16 (cmake)
 
-    Mac OS X Mt. Lion 10.8.5      Apple LLVM version 5.1 (clang-503.0.40)
-    64-bit                        gfortran GNU Fortran (GCC) 4.8.2
-    (swallow/kite)                Intel icc/icpc/ifort version 15.0.3
-
     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
@@ -322,10 +369,14 @@ They are built with the configure process unless specified otherwise.
     64-bit                        gfortran GNU Fortran (GCC) 4.9.2
     (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3
 
-    Mac OS X El Capitan 10.11.4   Apple LLVM version 7.3.0 (clang-703.0.29)
+    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
 =====================================
@@ -350,9 +401,10 @@ 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     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
@@ -371,9 +423,10 @@ 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
+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
@@ -418,12 +471,18 @@ The following platforms are not supported but have been tested for this release.
 Known Problems
 ==============
 
-    The dynamically loaded plugin test libraries require undefined references 
+    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 
+    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.