Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf5_1_12

9 files changed, 58 insertions, 19 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 58874cf..1ce8dbc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -237,7 +237,7 @@ string (REGEX REPLACE ".*#define[ \t]+H5_VERS_MINOR[ \t]+([0-9]*).*$"
     "\\1" H5_VERS_MINOR ${_h5public_h_contents})
 string (REGEX REPLACE ".*#define[ \t]+H5_VERS_RELEASE[ \t]+([0-9]*).*$"
     "\\1" H5_VERS_RELEASE ${_h5public_h_contents})
-string (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._\-]*)\".*$"
+string (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._-]*)\".*$"
     "\\1" H5_VERS_SUBRELEASE ${_h5public_h_contents})
 if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
   message (TRACE "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}")
diff --git a/bin/genparser b/bin/genparser
index d333c6d..462c2c2 100755
--- a/bin/genparser
+++ b/bin/genparser
@@ -219,13 +219,15 @@ perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5
 #
 # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
 # will simply ignore them, but we want to avoid those warnings.
+#
+# Note also that although clang defines __GNUC__, it doesn't support every
+# warning that GCC does.
 for f in ${path_to_hl_src}/H5LTparse.c ${path_to_hl_src}/H5LTanalyze.c
 do
     echo '#if defined (__GNUC__)                                            ' >> tmp.out
     echo '#if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 402                    ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wconversion"                     ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  ' >> tmp.out
-    echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wmissing-prototypes"             ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wnested-externs"                 ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wold-style-definition"           ' >> tmp.out
@@ -234,8 +236,11 @@ do
     echo '#pragma GCC diagnostic ignored "-Wsign-conversion"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-overflow"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-prototypes"              ' >> tmp.out
+    echo '#if !defined (__clang__)                                          ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=pure"         ' >> tmp.out
+    echo '#endif                                                            ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wswitch-default"                 ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wunused-function"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wunused-macros"                  ' >> tmp.out
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index fa21077..69c2d4a 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -605,6 +605,7 @@
 #cmakedefine H5_SIZEOF_INT_LEAST8_T @H5_SIZEOF_INT_LEAST8_T@
 
 #if !defined(__APPLE__)
+
 /* The size of `size_t', as computed by sizeof. */
 #cmakedefine H5_SIZEOF_SIZE_T @H5_SIZEOF_SIZE_T@
 
@@ -614,8 +615,17 @@
 /* The size of `long', as computed by sizeof. */
 #cmakedefine H5_SIZEOF_LONG @H5_SIZEOF_LONG@
 
+/* The size of `long double', as computed by sizeof. */
+#cmakedefine H5_SIZEOF_LONG_DOUBLE @H5_SIZEOF_LONG_DOUBLE@
+
 #else
-   # if defined(__LP64__) && __LP64__
+
+  /* On Apple, to support Universal Binaries (where multiple CPU
+     architectures exist in one library/executable), we can't assume
+     the machine doing the compiling has the same endianness or type
+     sizes as all the various architectures (PowerPC, Intel, ARM). */
+
+  # if defined(__LP64__) && __LP64__
   #define H5_SIZEOF_LONG 8
   #define H5_SIZEOF_SIZE_T 8
   #define H5_SIZEOF_SSIZE_T 8
@@ -625,10 +635,15 @@
   #define H5_SIZEOF_SSIZE_T 4
   # endif
 
-#endif
+  # if defined(__i386__) || defined(__x86_64__)
+  #define H5_SIZEOF_LONG_DOUBLE 16
+  # elif defined(__aarch64__)
+  #define H5_SIZEOF_LONG_DOUBLE 8
+  # else
+  #cmakedefine H5_SIZEOF_LONG_DOUBLE @H5_SIZEOF_LONG_DOUBLE@
+  # endif
 
-/* The size of `long double', as computed by sizeof. */
-#cmakedefine H5_SIZEOF_LONG_DOUBLE @H5_SIZEOF_LONG_DOUBLE@
+#endif
 
 /* Define size of long long and/or __int64 bit integer type only if the type
    exists.  */
diff --git a/hl/examples/ex_ds1.c b/hl/examples/ex_ds1.c
index 73578f1..d6890fa 100644
--- a/hl/examples/ex_ds1.c
+++ b/hl/examples/ex_ds1.c
@@ -91,9 +91,11 @@ main(void)
     if (H5DSattach_scale(did, dsid, DIM1) < 0)
         goto out;
 
-    /* close DS id */
+    /* close DS ids */
     if (H5Dclose(dsid) < 0)
         goto out;
+    if (H5Dclose(did) < 0)
+        goto out;
 
     /* close file */
     H5Fclose(fid);
diff --git a/hl/fortran/examples/ex_ds1.f90 b/hl/fortran/examples/ex_ds1.f90
index 7040950..d1ff678 100644
--- a/hl/fortran/examples/ex_ds1.f90
+++ b/hl/fortran/examples/ex_ds1.f90
@@ -180,8 +180,9 @@ PROGRAM example_ds
 
   WRITE(*,'(/,5X,A,I0,2A,/)') 'Dimension Scale Label for dimension ', DIM2, ' is ... ', label(1:label_len)
 
- ! close DS id
+ ! close DS ids
   CALL H5Dclose_f(dsid, err)
+  CALL H5Dclose_f(did, err)
 
  ! close file
   CALL H5Fclose_f(fid, err)
diff --git a/hl/src/H5LTanalyze.c b/hl/src/H5LTanalyze.c
index e35f20b..6673f5f 100644
--- a/hl/src/H5LTanalyze.c
+++ b/hl/src/H5LTanalyze.c
@@ -2,7 +2,6 @@
 #if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 402                    
 #pragma GCC diagnostic ignored "-Wconversion"                     
 #pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  
-#pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wmissing-prototypes"             
 #pragma GCC diagnostic ignored "-Wnested-externs"                 
 #pragma GCC diagnostic ignored "-Wold-style-definition"           
@@ -11,8 +10,11 @@
 #pragma GCC diagnostic ignored "-Wsign-conversion"                
 #pragma GCC diagnostic ignored "-Wstrict-overflow"                
 #pragma GCC diagnostic ignored "-Wstrict-prototypes"              
+#if !defined (__clang__)
+#pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=pure"         
+#endif
 #pragma GCC diagnostic ignored "-Wswitch-default"                 
 #pragma GCC diagnostic ignored "-Wunused-function"                
 #pragma GCC diagnostic ignored "-Wunused-macros"                  
diff --git a/hl/src/H5LTparse.c b/hl/src/H5LTparse.c
index 80de0a2..2ef133f 100644
--- a/hl/src/H5LTparse.c
+++ b/hl/src/H5LTparse.c
@@ -2,7 +2,6 @@
 #if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 402                    
 #pragma GCC diagnostic ignored "-Wconversion"                     
 #pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  
-#pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wmissing-prototypes"             
 #pragma GCC diagnostic ignored "-Wnested-externs"                 
 #pragma GCC diagnostic ignored "-Wold-style-definition"           
@@ -11,8 +10,11 @@
 #pragma GCC diagnostic ignored "-Wsign-conversion"                
 #pragma GCC diagnostic ignored "-Wstrict-overflow"                
 #pragma GCC diagnostic ignored "-Wstrict-prototypes"              
+#if !defined (__clang__)
+#pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=pure"         
+#endif
 #pragma GCC diagnostic ignored "-Wswitch-default"                 
 #pragma GCC diagnostic ignored "-Wunused-function"                
 #pragma GCC diagnostic ignored "-Wunused-macros"                  
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 2f5cd86..313d564 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -3,6 +3,7 @@ HDF5 version 1.12.1-4 currently under development
 
 
 INTRODUCTION
+============
 
 This document describes the new features introduced in the HDF5 1.12.0 release.
 It contains information on the platforms tested and known problems in this
@@ -276,7 +277,7 @@ New Features
         (QAK - 2020/03/25)
 
     Java Library:
-    ----------------
+    -------------
     - Added new H5S functions.
 
         H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
@@ -309,12 +310,12 @@ New Features
         (ADB - 2020/08/05, HDFFV-9984)
 
 
-Support for new platforms, languages and compilers.
-=======================================
+Support for new platforms, languages and compilers
+==================================================
     -
 
 Bug Fixes since HDF5-1.12.0 release
-==================================
+===================================
     Library
     -------
     - Fixed problems with vlens and refs inside compound using
@@ -408,8 +409,16 @@ Bug Fixes since HDF5-1.12.0 release
         (QAK - 2020/05/07)
 
 
-    Java Library:
-    ----------------
+    Java Library
+    ------------
+    - JNI utility function does not handle new references.
+
+        The JNI utility function for converting reference data to string did
+        not use the new APIs. In addition to fixing that function, added new
+        java tests for using the new APIs.
+
+        (ADB - 2021/02/16, HDFFV-11212)
+
     - The H5FArray.java class, in which virtually the entire execution time
         is spent using the HDFNativeData method that converts from an array
         of bytes to an array of the destination Java type.
@@ -477,8 +486,8 @@ Bug Fixes since HDF5-1.12.0 release
         (QAK - 2020/06/05)
 
 
-    Fortran High-Level APIs:
-    ------
+    Fortran High-Level APIs
+    -----------------------
     -
 
 
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index 9edaba6..4546178 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -329,7 +329,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, h5tools_cont
  * Purpose: Print some values from an attribute referenced by object reference.
  *
  * Description:
- *      This is a special case subfunction to dump aa attribute references.
+ *      This is a special case subfunction to dump an attribute reference.
  *
  * Return:
  *      The function returns False if the last dimension has been reached, otherwise True
@@ -448,6 +448,9 @@ done:
     if (H5Tclose(atype) < 0)
         H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
 
+    if (H5Sclose(region_space) < 0)
+        H5TOOLS_ERROR(dimension_break, "H5Sclose failed");
+
     ctx->indent_level--;
     ctx->need_prefix = TRUE;