Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits)
  Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting
  More minor whitespace cleanup
  Fixed a minor comment typo in H5R.c
  * Reverted removal of H5I_REFERENCE to avoid breaking binary   compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19()   in tmisc.c.
  Added missing free() call to test_misc19().
  Purged the unused H5I_REFERENCE from the library.
  Added a test for VFD IDs to testhdf5.
  Revert "Partial removal of NDEBUG ifdefs from the library."
  Partial removal of NDEBUG ifdefs from the library.
  Removed compiler flag cleanup since Solaris chokes on it.
  Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file.
  Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true.
  Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely).
  Added awk processing to remove extraneous whitespace from H5_ flags in configure.
  Fixed a comment in configure.ac
  HDFFV-10219 another mode change
  HDFFV-10219 change subset to use BINARY mode for h5dump
  HDFFV-10219 default input binary to NATIVE
  Set default of var to NATIVE
  HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed
  ...

1 files changed, 33 insertions, 35 deletions

diff --git a/configure.ac b/configure.ac
index ca4d4b6..163f6d3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -6,12 +6,10 @@
 ##
 ## This file is part of HDF5.  The full HDF5 copyright notice, including
 ## terms governing use, modification, and redistribution, is contained in
-## the files COPYING and Copyright.html.  COPYING can be found at the root
-## of the source code distribution tree; Copyright.html can be found at the
-## root level of an installed copy of the electronic HDF5 document set and
-## is linked from the top-level documents page.  It can also be found at
-## http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-## access to either file, you may request a copy from help@hdfgroup.org.
+## the COPYING file, which can be found at the root of the source code
+## distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+## If you do not have access to either file, you may request a copy from
+## help@hdfgroup.org.
 
 ## ----------------------------------------------------------------------
 ## Initialize configure.
@@ -587,11 +585,11 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
     AC_DEFINE([FORTRAN_HAVE_STORAGE_SIZE], [1], [Define if we have Fortran intrinsic STORAGE_SIZE])
   fi
 
-  if  test "X$HAVE_C_SIZEOF_FORTRAN" = "Xyes"; then
+  if test "X$HAVE_C_SIZEOF_FORTRAN" = "Xyes"; then
     AC_DEFINE([FORTRAN_HAVE_C_SIZEOF], [1], [Define if we have Fortran intrinsic C_SIZEOF])
   fi
 
-  if  test "X$HAVE_SIZEOF_FORTRAN" = "Xyes"; then
+  if test "X$HAVE_SIZEOF_FORTRAN" = "Xyes"; then
     AC_DEFINE([FORTRAN_HAVE_SIZEOF], [1], [Define if we have Fortran intrinsic SIZEOF])
   fi
 
@@ -606,7 +604,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
 
   ## Is C_LONG_DOUBLE different from C_DOUBLE
   FORTRAN_C_LONG_DOUBLE_IS_UNIQUE="0"
-  if test "X$FORTRAN_HAVE_C_LONG_DOUBLE"; then
+  if test "$FORTRAN_HAVE_C_LONG_DOUBLE" = "1"; then
     PAC_PROG_FC_C_LONG_DOUBLE_EQ_C_DOUBLE
     if test "X$C_LONG_DOUBLE_IS_UNIQUE_FORTRAN" = "Xyes"; then
       FORTRAN_C_LONG_DOUBLE_IS_UNIQUE="1"
@@ -920,14 +918,13 @@ H5_FORTRAN_SHARED="no"
 if test "X${HDF_FORTRAN}" = "Xyes" && test "X${enable_shared}" != "Xno"; then
   AC_MSG_CHECKING([if shared Fortran libraries are supported])
   H5_FORTRAN_SHARED="yes"
-
-  ## Disable fortran shared libraries on Mac. (MAM - 03/30/11)
-
+  ## tell libtool to do the right thing with COMMON symbols, this fixes 
+  ## corrupt values with COMMON and EQUIVALENCE when building shared 
+  ## Fortran libraries on OSX with gnu and Intel compilers (HDFFV-2772).
   case "`uname`" in
     Darwin*)
-    H5_FORTRAN_SHARED="no"
-    CHECK_WARN="Shared Fortran libraries not currently supported on Mac."
-      ;;
+    H5_LDFLAGS="$H5_LDFLAGS -Wl,-commons,use_dylibs"
+    ;;
   esac
 
   ## Report results of check(s)
@@ -1254,10 +1251,11 @@ AC_ARG_WITH([fnord],
   ])
 
 ## ----------------------------------------------------------------------
-## Is the dmalloc present? It has a header file `dmalloc.h' and a library
-## `-ldmalloc' and their locations might be specified with the `--with-dmalloc'
-## command-line switch. The value is an include path and/or a library path.
-## If the library path is specified then it must be preceded by a comma.
+## Is dmalloc (debug malloc library) requested? It has a header file 
+## `dmalloc.h' and a library `-ldmalloc' and their locations might be
+## specified with the `--with-dmalloc' command-line switch. The value 
+## is an include path and/or a library path. If the library path is
+## specified then it must be preceded by a comma.
 ##
 AC_SUBST([HAVE_DMALLOC])
 
@@ -1943,26 +1941,17 @@ AC_DEFINE_UNQUOTED([PRINTF_LL_WIDTH], ["$hdf5_cv_printf_ll"],
                    [Width for printf() for type `long long' or `__int64', use `ll'])
 
 ## ----------------------------------------------------------------------
-## Deprecate old ways of determining debug/production build
-## These can probably be removed in the future (1.10.1?)
+## Remove old ways of determining debug/production build.
+## These were used in 1.8.x and earlier. We should probably keep these checks
+## around to help people migrate to 1.10.x and newer versions.
 ##
 AC_ARG_ENABLE([debug],
-              [AS_HELP_STRING([--enable-debug],
-               [DEPRECATED: use --enable-build-mode=debug])],
-              [DEPRECATED_DEBUG=$enableval])
-
-if test "X-$DEPRECATED_DEBUG" != "X-" ; then
-    AC_MSG_ERROR([--enable-debug is deprecated, use --enable-build-mode=debug instead.])
-fi
+              [AS_HELP_STRING([--enable-debug], [DEPRECATED: use --enable-build-mode=debug])],
+              [AC_MSG_ERROR([--enable-debug is deprecated, use --enable-build-mode=debug instead.])])
 
 AC_ARG_ENABLE([production],
-              [AS_HELP_STRING([--enable-production],
-               [DEPRECATED: use --enable-build-mode=production])],
-              [DEPRECATED_PRODUCTION=$enableval])
-
-if test "X-$DEPRECATED_PRODUCTION" != "X-" ; then
-    AC_MSG_ERROR([--enable-production is deprecated, use --enable-build-mode=production instead.])
-fi
+              [AS_HELP_STRING([--enable-production], [DEPRECATED: use --enable-build-mode=production])],
+              [AC_MSG_ERROR([--enable-production is deprecated, use --enable-build-mode=production instead.])])
 
 
 ## ----------------------------------------------------------------------
@@ -3364,6 +3353,7 @@ AC_CONFIG_FILES([src/libhdf5.settings
                  test/H5srcdir_str.h
                  test/testlibinfo.sh
                  test/testlinks_env.sh
+                 test/test_filenotclosed.sh
                  test/testswmr.sh
                  test/test_plugin.sh
                  test/test_usecases.sh
@@ -3486,6 +3476,14 @@ chmod 755 tools/src/misc/h5cc
 
 if test "X$HDF_FORTRAN" = "Xyes"; then
   chmod 755 fortran/src/h5fc
+  ## libtool does not pass the correct argument linker (wl=) for the Intel Fortran compiler 
+  ## on OS X, which is needed when building shared libraries on OS X.  This script 
+  ## replaces the 3rd occurrence, which is for Fortran, of wl="" with wl="-Wl," (HDFFV-2772)
+  case "`uname`" in
+    Darwin*)
+      cat libtool | awk '/wl=\"/{c++;if(c==3){sub("wl=\"\"","wl=\"-Wl,\"");c=0}}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool
+      ;;
+  esac
 fi
 
 if test "X$HDF_CXX" = "Xyes"; then