[svn-r17896] Description:

	Bring r17546:17895 from trunk to revise_chunks branch.  Changes to
fixed and extensible array dataset chunk indexing code to accommodate changes
to private APIs in those interfaces.  Also, other adjustments to source code
and expected output in response to changes on the trunk.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
        Mac OS X/32 10.6.2 (amazon) in debug mode
        Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
                in production mode

1 files changed, 140 insertions, 287 deletions

diff --git a/configure.in b/configure.in
index 48bb854..09483fc 100644
--- a/configure.in
+++ b/configure.in
@@ -26,7 +26,7 @@ dnl
 dnl NOTE: Don't forget to change the version number here when we do a
 dnl release!!!
 dnl
-AC_INIT([HDF5], [1.9.47-FA_a4], [help@hdfgroup.org])
+AC_INIT([HDF5], [1.9.51-FA_a4], [help@hdfgroup.org])
 AC_CONFIG_SRCDIR([src/H5.c])
 AM_CONFIG_HEADER([src/H5config.h])
 
@@ -94,11 +94,34 @@ AC_SUBST([H5_CPPFLAGS])
 AC_SUBST([H5_FCFLAGS])
 AC_SUBST([H5_CXXFLAGS])
 
+dnl AM_CFLAGS (and company) are for CFLAGS that should be used on HDF5,
+dnl and WILL be exported to h5cc (or h5fc, etc) if set by configure.
+AC_SUBST([AM_CFLAGS])
+AC_SUBST([AM_FCFLAGS])
+AC_SUBST([AM_CXXFLAGS])
+AC_SUBST([AM_CPPFLAGS])
+AC_SUBST([AM_LDFLAGS])
+
 dnl Make sure flags are set to something (otherwise macros may set them later).
+AM_CFLAGS="${AM_CFLAGS}"
+AM_CXXFLAGS="${AM_CXXFLAGS}"
+AM_FCFLAGS="${AM_FCFLAGS}"
+AM_CPPFLAGS="${AM_CPPFLAGS}"
+AM_LDFLAGS="${AM_LDFLAGS}"
 CFLAGS="${CFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
 CXXFLAGS="${CXXFLAGS}"
 FCFLAGS="${FCFLAGS}"
+CPPFLAGS="${CPPFLAGS}"
+LDFLAGS="${LDFLAGS}"
+
+dnl Configure may need to alter any of the *FLAGS variables in order for
+dnl various checks to work correctly. Save the user's value here so it
+dnl can be restored once all configure checks are complete.
+saved_user_CFLAGS="$CFLAGS"
+saved_user_CXXFLAGS="$CXXFLAGS"
+saved_user_FCFLAGS="$FCFLAGS"
+saved_user_LDFLAGS="$LDFLAGS"
+saved_user_CPPFLAGS="$CPPFLAGS"
 
 dnl Different compilers may need default libraries. They are specified in
 dnl the config/* files, so we put this statement here so that it'll be
@@ -294,6 +317,16 @@ while test -n "$hname"; do
 done
 
 dnl ----------------------------------------------------------------------
+dnl Some built-in configure checks can only see CFLAGS (not AM_CFLAGS), so
+dnl we need to add this in so configure works as intended. We will need to
+dnl reset this value at the end of configure, to preserve the user's settings.
+CFLAGS="${AM_CFLAGS} ${CFLAGS}"
+FCFLAGS="${AM_FCFLAGS} ${FCFLAGS}"
+CXXFLAGS="${AM_CXXFLAGS} ${CXXFLAGS}"
+CPPFLAGS="${AM_CPPFLAGS} ${CPPFLAGS}"
+LDFLAGS="${AM_LDFLAGS} ${LDFLAGS}"
+
+dnl ----------------------------------------------------------------------
 dnl Enable dependency tracking unless the configure options or a
 dnl site-specific file told us not to.  This prevents configure from
 dnl silently disabling dependencies for some compilers.
@@ -342,6 +375,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   dnl --------------------------------------------------------------------
   dnl General Fortran flags
   dnl
+  AM_FCFLAGS="${AM_FCFLAGS} ${FFLAGS}"
   FCFLAGS="${FCFLAGS} ${FFLAGS}"
 
   dnl --------------------------------------------------------------------
@@ -374,8 +408,8 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   dnl --------------------------------------------------------------------
   dnl See if the compiler will support the "-I." option
   dnl
-dnl  FCFLAGS_saved=$FCFLAGS
-dnl  FCFLAGS="${FCFLAGS} -I."
+dnl  AM_FCFLAGS_saved=$AM_FCFLAGS
+dnl  AM_FCFLAGS="${AM_FCFLAGS} -I."
 
 dnl  AC_MSG_CHECKING(if compiler supports -I. option)
 dnl  AC_TRY_FCOMPILE([
@@ -383,7 +417,7 @@ dnl      program conftest
 dnl      end
 dnl  ], AC_MSG_RESULT(yes),
 dnl     AC_MSG_RESULT(no)
-dnl     FCFLAGS="$FCFLAGS_saved")
+dnl     AM_FCFLAGS="$AM_FCFLAGS_saved")
 
 dnl --------------------------------------------------------------------
 dnl See if the fortran compiler supports the intrinsic function "SIZEOF"
@@ -433,6 +467,7 @@ dnl compile the DOUBLE PRECISION interfaces.
   AC_LANG_POP(Fortran)
 else
   echo "no"
+  FC="no"
 fi
 
 AM_CONDITIONAL([FORTRAN_HAVE_SIZEOF], [test "X$HAVE_SIZEOF" = "Xyes"])
@@ -471,6 +506,7 @@ int main(void) { return 0; }
   ], [
     echo yes
     CXXFLAGS="${CXXFLAGS} -DOLD_HEADER_FILENAME"
+    AM_CXXFLAGS="${AM_CXXFLAGS} -DOLD_HEADER_FILENAME"
   ])
 
   AC_MSG_CHECKING([if $CXX can handle namespaces])
@@ -489,6 +525,7 @@ int main(void) {
   ], [
      echo no
      CXXFLAGS="${CXXFLAGS} -DH5_NO_NAMESPACE"
+     AM_CXXFLAGS="${AM_CXXFLAGS} -DH5_NO_NAMESPACE"
   ])
 
   AC_MSG_CHECKING([if $CXX supports std])
@@ -506,6 +543,7 @@ int main(void) {
   ], [
      echo no
      CXXFLAGS="${CXXFLAGS} -DH5_NO_STD"
+     AM_CXXFLAGS="${AM_CXXFLAGS} -DH5_NO_STD"
   ])
 
   AC_MSG_CHECKING([if $CXX supports bool types])
@@ -519,6 +557,7 @@ int main(void) {
   ], [
      echo no
      CXXFLAGS="${CXXFLAGS} -DBOOL_NOTDEFINED"
+     AM_CXXFLAGS="${AM_CXXFLAGS} -DBOOL_NOTDEFINED"
   ])
 
   AC_MSG_CHECKING([if $CXX has offsetof extension])
@@ -556,9 +595,11 @@ int main(void) {
   ], [
     echo no
     CXXFLAGS="${CXXFLAGS} -DNO_STATIC_CAST"
+    AM_CXXFLAGS="${AM_CXXFLAGS} -DNO_STATIC_CAST"
   ])
 else
   echo "no"
+  CXX="no"
 fi
 
 dnl Change back to the C language
@@ -839,18 +880,6 @@ elif test "X${enable_shared}" = "Xyes" -a "X${PARALLEL}" != "X"; then
 fi
 
 dnl ----------------------------------------------------------------------
-dnl As of Libtool 1.5.14, libtool officially doesn't know how to create
-dnl shared libraries with pgcc.  In fact, it is able to do so on some
-dnl platforms, but not all (e.g., pgcc 5.2-4 on mir).
-dnl Disable shared libraries when using pgcc.  -JL 09/2005
-if test "X${enable_shared}" != "Xno" && \
-      (${CC-cc} -V 2>&1 | grep '^pgcc') > /dev/null; then
-  echo '    warning: shared libraries are not supported for pgcc!'
-  echo '    disabling shared libraries'
-  enable_shared="no"
-fi
-
-dnl ----------------------------------------------------------------------
 dnl Many Fortran compilers don't support shared libraries.  Some of these
 dnl compilers include:
 dnl pgf90 version 6.0-4
@@ -873,6 +902,7 @@ if test "X${HDF_FORTRAN}" = "Xyes"; then
     else
 dnl echo 'adding fortran compiler flag needed for building shared libraries'
       FCFLAGS="${FCFLAGS} -fPIC"
+      AM_FCFLAGS="${AM_FCFLAGS} -fPIC"
     fi
   fi
   if (${FC} +version 2>&1 | grep '^HP F90') > /dev/null; then
@@ -894,24 +924,13 @@ fi
 
 AM_CONDITIONAL([FORTRAN_SHARED_CONDITIONAL], [test "X$H5_FORTRAN_SHARED" = "Xyes"])
 
-dnl ----------------------------------------------------------------------
-dnl Shared C++ libraries seem not to work on some platforms (modi4, shanti)
-dnl when the -xarch=v9 flag is used to enable 64-bit mode.
-dnl Try to detect the -xarch=v9 flag and disable C++ shared libraries if it's
-dnl being used.
-dnl Also disable C++ shared libraries if shared libraries are disabled.
-dnl this prevents Automake from trying to link against shared libraries,
+dnl Disable C++ shared libraries if shared libraries are disabled.
+dnl This prevents Automake from trying to link against shared libraries,
 dnl which caused problems on tg-login
 H5_CXX_SHARED="no"
 if test "X${HDF_CXX}" = "Xyes" && test "X${enable_shared}" != "Xno"; then
   H5_CXX_SHARED="yes"
 
-  if (echo dummy ${CXX} ${CXXLD} ${CFLAGS} ${CXXFLAGS} ${LDFLAGS} | grep 'xarch') > /dev/null; then
-    echo "    warning: -xarch flag detected"
-    echo "    disabling shared C++ libraries"
-    H5_CXX_SHARED="no"
-  fi
-
 dnl Try to detect the +DD64 flag for HPUX aCC compiler and disable C++ shared libraries if it's
 dnl being used.
 
@@ -1274,7 +1293,7 @@ case "$host_cpu-$host_vendor-$host_os" in
     AC_MSG_CHECKING([for large file support mode on Linux])
     if test "X$LINUX_LFS" = "Xyes"; then
       AC_MSG_RESULT([enabled])
-      CPPFLAGS="-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE $CPPFLAGS"
+      AM_CPPFLAGS="-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE $AM_CPPFLAGS"
     else
       AC_MSG_RESULT([disabled])
     fi
@@ -1282,16 +1301,20 @@ case "$host_cpu-$host_vendor-$host_os" in
     dnl Add POSIX support on Linux systems, so <features.h> defines
     dnl __USE_POSIX, which is required to get the prototype for fdopen
     dnl defined correctly in <stdio.h>
-    CPPFLAGS="-D_POSIX_SOURCE $CPPFLAGS"
+    H5_CPPFLAGS="-D_POSIX_SOURCE $H5_CPPFLAGS"
 
     dnl Also add BSD support on Linux systems, so <features.h> defines
     dnl __USE_BSD, which is required to get the prototype for strdup
     dnl defined correctly in <string.h> and snprintf & vsnprintf defined
     dnl correctly in <stdio.h>
-    CPPFLAGS="-D_BSD_SOURCE $CPPFLAGS"
+    AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
     ;;
 esac
 
+dnl Need to add AM_CPPFLAGS into CPPFLAGS to make them visible for configure checks.
+dnl Note: CPPFLAGS will be restored by the end of configure.
+CPPFLAGS="$AM_CPPFLAGS $CPPFLAGS"
+
 AC_TRY_COMPILE([#include <sys/types.h>],
                [off64_t n = 0;],
                [AC_CHECK_FUNCS([lseek64 fseek64 ftruncate64])],
@@ -1459,19 +1482,23 @@ case $withval in
     fi
 
     saved_CPPFLAGS="$CPPFLAGS"
+    saved_AM_CPPFLAGS="$AM_CPPFLAGS"
     saved_LDFLAGS="$LDFLAGS"
+    saved_AM_LDFLAGS="$AM_LDFLAGS"
 
     if test -n "$dmalloc_inc"; then
       CPPFLAGS="$CPPFLAGS -I$dmalloc_inc"
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$dmalloc_inc"
     fi
 
-    AC_CHECK_HEADERS(dmalloc.h,, CPPFLAGS="$saved_CPPFLAGS")
+    AC_CHECK_HEADERS(dmalloc.h,,CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS")
 
     if test -n "$dmalloc_lib"; then
       LDFLAGS="$LDFLAGS -L$dmalloc_lib"
+      AM_LDFLAGS="$AM_LDFLAGS -L$dmalloc_lib"
     fi
 
-    AC_CHECK_LIB(dmalloc, dmalloc_shutdown,, LDFLAGS="$saved_LDFLAGS"; unset HAVE_DMALLOC)
+    AC_CHECK_LIB(dmalloc, dmalloc_shutdown,, LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset HAVE_DMALLOC)
 
     if test -z "$HAVE_DMALLOC" -a -n "$HDF5_CONFIG_ABORT"; then
       AC_MSG_ERROR(couldn't find dmalloc library)
@@ -1533,22 +1560,26 @@ case $withval in
     fi
 
     saved_CPPFLAGS="$CPPFLAGS"
+    saved_AM_CPPFLAGS="$AM_CPPFLAGS"
     saved_LDFLAGS="$LDFLAGS"
+    saved_AM_LDFLAGS="$AM_LDFLAGS"
 
     if test -n "$zlib_inc"; then
       CPPFLAGS="$CPPFLAGS -I$zlib_inc"
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$zlib_inc"
     fi
 
     AC_CHECK_HEADERS([zlib.h],
                      [HAVE_ZLIB_H="yes"],
-                     [CPPFLAGS="$saved_CPPFLAGS"])
+                     [CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"])
 
     if test -n "$zlib_lib"; then
       LDFLAGS="$LDFLAGS -L$zlib_lib"
+      AM_LDFLAGS="$AM_LDFLAGS -L$zlib_lib"
     fi
 
     AC_CHECK_LIB([z], [compress2],,
-                 [LDFLAGS="$saved_LDFLAGS"; unset HAVE_ZLIB])
+                 [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset HAVE_ZLIB])
     AC_CHECK_FUNC([compress2], [HAVE_COMPRESS2="yes"])
 
     if test -z "$HAVE_ZLIB" -a -n "$HDF5_CONFIG_ABORT"; then
@@ -1622,23 +1653,27 @@ case $withval in
     fi
     
     saved_CPPFLAGS="$CPPFLAGS"
+    saved_AM_CPPFLAGS="$AM_CPPFLAGS"
     saved_LDFLAGS="$LDFLAGS"
+    saved_AM_LDFLAGS="$AM_LDFLAGS"
     
     if test -n "$szlib_inc"; then
       CPPFLAGS="$CPPFLAGS -I$szlib_inc"
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$szlib_inc"
     fi
     
     AC_CHECK_HEADERS([szlib.h],
                      [HAVE_SZLIB_H="yes"],
-                     [CPPFLAGS="$saved_CPPFLAGS"])
-    
+                     [CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"])
+
     if test -n "$szlib_lib"; then
       LDFLAGS="$LDFLAGS -L$szlib_lib"
+      AM_LDFLAGS="$AM_LDFLAGS -L$szlib_lib"
     fi
     
     AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress],,
-                 [LDFLAGS="$saved_LDFLAGS"; unset HAVE_SZLIB])
-    
+                 [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset HAVE_SZLIB])
+
     if test -z "$HAVE_SZLIB" -a -n "$HDF5_CONFIG_ABORT"; then
       AC_MSG_ERROR([couldn't find szlib library])
     fi
@@ -1754,17 +1789,22 @@ case "$withval" in
 
     if test -n "$pthread_inc"; then
       saved_CPPFLAGS="$CPPFLAGS"
+      saved_AM_CPPFLAGS="$AM_CPPFLAGS"
       CPPFLAGS="$CPPFLAGS -I$pthread_inc"
-      AC_CHECK_HEADERS([pthread.h],, [CPPFLAGS="$saved_CPPFLAGS"; unset PTHREAD])
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$pthread_inc"
+      AC_CHECK_HEADERS([pthread.h],, [CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"; unset PTHREAD])
     else
       AC_CHECK_HEADERS([pthread.h],, [unset PTHREAD])
     fi
 
     if test -n "$pthread_lib"; then
       saved_LDFLAGS="$LDFLAGS"
+      saved_AM_LDFLAGS="$AM_LDFLAGS"
       LDFLAGS="$LDFLAGS -L$pthread_lib"
+      AM_LDFLAGS="$AM_LDFLAGS -L$pthread_lib"
       AC_CHECK_LIB([pthread], [pthread_create],,
-                   [LDFLAGS="$saved_LDFLAGS"; unset PTHREAD])
+                   [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset PTHREAD])
+
     else
       AC_CHECK_LIB([pthread], [pthread_create],, [unset PTHREAD])
     fi
@@ -2070,7 +2110,7 @@ dnl LD_LIBRARY_PATH along with LDFLAGS or do it with the AC_TRY_RUN macro.
 dnl
 AC_MSG_CHECKING([how to print long long])
 AC_CACHE_VAL([hdf5_cv_printf_ll],
-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
+LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
 export LD_LIBRARY_PATH
 
 for hdf5_cv_printf_ll in l ll L q unknown; do
@@ -2610,19 +2650,24 @@ if test -n "$PARALLEL"; then
   
       if test -n "$mpe_inc"; then
         saved_CPPFLAGS="$CPPFLAGS"
+        saved_AM_CPPFLAGS="$AM_CPPFLAGS"
         CPPFLAGS="$CPPFLAGS -I$mpe_inc"
-        AC_CHECK_HEADERS([mpe.h],, [CPPFLAGS="$saved_CPPFLAGS"; unset MPE])
+        AM_CPPFLAGS="$AM_CPPFLAGS -I$mpe_inc"
+        AC_CHECK_HEADERS([mpe.h],, [CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"; unset MPE])
       else
         AC_CHECK_HEADERS([mpe.h],, [unset MPE])
       fi
   
       if test -n "$mpe_lib"; then
         saved_LDFLAGS="$LDFLAGS"
+        saved_AM_LDFLAGS="$AM_LDFLAGS"
         LDFLAGS="$LDFLAGS -L$mpe_lib"
+        AM_LDFLAGS="$AM_LDFLAGS -L$mpe_lib"
         AC_CHECK_LIB([mpe], [MPE_Init_log],,
-                     [LDFLAGS="$saved_LDFLAGS"; unset MPE])
+                     [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset MPE])
         AC_CHECK_LIB([lmpe], [CLOG_Init],,
-                     [LDFLAGS="$saved_LDFLAGS"; unset MPE])
+                     [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset MPE])
+
       else
         AC_CHECK_LIB([mpe], [MPE_Init_log],, [unset MPE])
         AC_CHECK_LIB([lmpe], [CLOG_Init],, [unset MPE])
@@ -2693,9 +2738,9 @@ dnl bug also occurs at SGI IRIX 6.5 C with compiler version lower than or equal
 dnl In case people still use the old compiler, we keep this flag.
 AC_MSG_CHECKING([if irregular hyperslab optimization code works inside MPI-IO])
 
-AC_CACHE_VAL([hdf5_cv_mpi_complex_derived_datatype_works],[hdf5_mpi_complex_derived_datatype_works=yes])
+AC_CACHE_VAL([hdf5_cv_mpi_complex_derived_datatype_works],[hdf5_cv_mpi_complex_derived_datatype_works=yes])
 
-if test ${hdf5_mpi_complex_derived_datatype_works} = "yes"; then
+if test ${hdf5_cv_mpi_complex_derived_datatype_works} = "yes"; then
   AC_DEFINE([MPI_COMPLEX_DERIVED_DATATYPE_WORKS], [1],
             [Define if your system can handle complicated MPI derived datatype correctly.])
   AC_MSG_RESULT([yes])
@@ -2712,9 +2757,9 @@ dnl and SGI altix. For those systems, we have to turn off this feature and use i
 dnl
 AC_MSG_CHECKING([if MPI-IO can do collective IO when one or more processes don't do IOs])
 
-AC_CACHE_VAL([hdf5_cv_mpi_special_collective_io_works],[hdf5_mpi_special_collective_io_works=yes])
+AC_CACHE_VAL([hdf5_cv_mpi_special_collective_io_works],[hdf5_cv_mpi_special_collective_io_works=yes])
 
-if test ${hdf5_mpi_special_collective_io_works} = "yes"; then
+if test ${hdf5_cv_mpi_special_collective_io_works} = "yes"; then
   AC_DEFINE([MPI_SPECIAL_COLLECTIVE_IO_WORKS], [1],
             [Define if your system can handle special collective IO properly.])
   AC_MSG_RESULT([yes])
@@ -2854,9 +2899,9 @@ if test "$DIRECT_VFD" = "yes"; then
              close(fid);  
              remove("tst_file"); 
              exit (0);
-          }], AC_TRY_LINK(, [posix_memalign()], [hdf5_direct_io=yes], [hdf5_direct_io=no]), [hdf5_direct_io=no],)])
+          }], AC_TRY_LINK(, [posix_memalign()], [hdf5_cv_direct_io=yes], [hdf5_cv_direct_io=no]), [hdf5_cv_direct_io=no],)])
 
-   if test ${hdf5_direct_io} = "yes"; then
+   if test ${hdf5_cv_direct_io} = "yes"; then
       AC_MSG_RESULT([yes])
       AC_DEFINE([HAVE_DIRECT], [1],
                 [Define if the direct I/O virtual file driver should be compiled])
@@ -2975,7 +3020,7 @@ dnl
 AC_MSG_CHECKING([if converting from long double to integers is accurate])
 
 if test ${ac_cv_sizeof_long_double} = 0; then
-   hdf5_ldouble_to_integer_accurate=${hdf5_ldouble_to_integer_accurate=no}
+   hdf5_cv_ldouble_to_integer_accurate=${hdf5_cv_ldouble_to_integer_accurate=no}
 else
    AC_CACHE_VAL([hdf5_cv_ldouble_to_integer_accurate], [hdf5_cv_ldouble_to_integer_accurate=yes])
 fi
@@ -2999,7 +3044,7 @@ dnl yet. (1/8/05 - SLU)
 AC_MSG_CHECKING([if converting from long double to integers works])
 
 if test ${ac_cv_sizeof_long_double} = 0; then
-   hdf5_ldouble_to_integer_works=${hdf5_ldouble_to_integer_works=no}
+   hdf5_cv_ldouble_to_integer_works=${hdf5_cv_ldouble_to_integer_works=no}
 else
    AC_CACHE_VAL([hdf5_cv_ldouble_to_integer_works],
         [AC_TRY_RUN([
@@ -3024,10 +3069,10 @@ else
     done:
             exit(ret);
         }
-        ], [hdf5_ldouble_to_integer_works=yes], [hdf5_ldouble_to_integer_works=no],)])
+        ], [hdf5_cv_ldouble_to_integer_works=yes], [hdf5_cv_ldouble_to_integer_works=no],)])
 fi
 
-if test ${hdf5_ldouble_to_integer_works} = "yes"; then
+if test ${hdf5_cv_ldouble_to_integer_works} = "yes"; then
   AC_DEFINE([LDOUBLE_TO_INTEGER_WORKS], [1],
             [Define if your system can convert from long double to integer values.])
   AC_MSG_RESULT([yes])
@@ -3097,9 +3142,9 @@ AC_CACHE_VAL([hdf5_cv_ulong_to_float_accurate],
 done:
         exit(ret);
     }
-    ], [hdf5_ulong_to_float_accurate=yes], [hdf5_ulong_to_float_accurate=no],)])
+    ], [hdf5_cv_ulong_to_float_accurate=yes], [hdf5_cv_ulong_to_float_accurate=no],)])
 
-if test ${hdf5_ulong_to_float_accurate} = "yes"; then
+if test ${hdf5_cv_ulong_to_float_accurate} = "yes"; then
   AC_DEFINE([ULONG_TO_FLOAT_ACCURATE], [1],
             [Define if your system accurately converting unsigned long to float values.])
   AC_MSG_RESULT([yes])
@@ -3219,9 +3264,9 @@ AC_CACHE_VAL([hdf5_cv_fp_to_ullong_accurate],
 done:
         exit(ret);
     }
-    ], [hdf5_fp_to_ullong_accurate=yes], [hdf5_fp_to_ullong_accurate=no],)])
+    ], [hdf5_cv_fp_to_ullong_accurate=yes], [hdf5_cv_fp_to_ullong_accurate=no],)])
 
-if test ${hdf5_fp_to_ullong_accurate} = "yes"; then
+if test ${hdf5_cv_fp_to_ullong_accurate} = "yes"; then
   AC_DEFINE([FP_TO_ULLONG_ACCURATE], [1],
             [Define if your system roundup accurately converting floating-point to unsigned long long values.])
   AC_MSG_RESULT([yes])
@@ -3263,9 +3308,9 @@ AC_CACHE_VAL([hdf5_cv_fp_to_ullong_right_maximum],
 done:
         exit(ret);
     }
-    ], [hdf5_fp_to_ullong_right_maximum=yes], [hdf5_fp_to_ullong_right_maximum=no],)])
+    ], [hdf5_cv_fp_to_ullong_right_maximum=yes], [hdf5_cv_fp_to_ullong_right_maximum=no],)])
 
-if test ${hdf5_fp_to_ullong_right_maximum} = "yes"; then
+if test ${hdf5_cv_fp_to_ullong_right_maximum} = "yes"; then
   AC_DEFINE([FP_TO_ULLONG_RIGHT_MAXIMUM], [1],
             [Define if your system has right maximum convert floating-point to unsigned long long values.])
   AC_MSG_RESULT([yes])
@@ -3281,7 +3326,7 @@ dnl
 AC_MSG_CHECKING([if correctly converting long double to unsigned int values])
 
 if test ${ac_cv_sizeof_long_double} = 0; then
-   hdf5_ldouble_to_uint_accurate=${hdf5_ldouble_to_uint_accurate=no}
+   hdf5_cv_ldouble_to_uint_accurate=${hdf5_cv_ldouble_to_uint_accurate=no}
 else
    AC_CACHE_VAL([hdf5_cv_ldouble_to_uint_accurate],
         [AC_TRY_RUN([
@@ -3298,10 +3343,10 @@ else
     done:
             exit(ret);
         }
-        ], [hdf5_ldouble_to_uint_accurate=yes], [hdf5_ldouble_to_uint_accurate=no],)])
+        ], [hdf5_cv_ldouble_to_uint_accurate=yes], [hdf5_cv_ldouble_to_uint_accurate=no],)])
 fi
 
-if test ${hdf5_ldouble_to_uint_accurate} = "yes"; then
+if test ${hdf5_cv_ldouble_to_uint_accurate} = "yes"; then
   AC_DEFINE([LDOUBLE_TO_UINT_ACCURATE], [1],
             [Define if your system can convert long double to unsigned int values correctly.])
   AC_MSG_RESULT([yes])
@@ -3483,7 +3528,7 @@ dnl
 AC_MSG_CHECKING([if correctly converting long double to (unsigned) long long values])
 
 if test ${ac_cv_sizeof_long_double} = 0; then
-   hdf5_ldouble_to_llong_accurate=${hdf5_ldouble_to_llong_accurate=no}
+   hdf5_cv_ldouble_to_llong_accurate=${hdf5_cv_ldouble_to_llong_accurate=no}
 else
    AC_CACHE_VAL([hdf5_cv_ldouble_to_llong_accurate],
         [AC_TRY_RUN([
@@ -3523,10 +3568,10 @@ else
     done:
             exit(ret);
         }
-        ], [hdf5_ldouble_to_llong_accurate=yes], [hdf5_ldouble_to_llong_accurate=no],)])
+        ], [hdf5_cv_ldouble_to_llong_accurate=yes], [hdf5_cv_ldouble_to_llong_accurate=no],)])
 fi
 
-if test ${hdf5_ldouble_to_llong_accurate} = "yes"; then
+if test ${hdf5_cv_ldouble_to_llong_accurate} = "yes"; then
   AC_DEFINE([LDOUBLE_TO_LLONG_ACCURATE], [1],
             [Define if your system can convert long double to (unsigned) long long values correctly.])
   AC_MSG_RESULT([yes])
@@ -3544,7 +3589,7 @@ dnl
 AC_MSG_CHECKING([if correctly converting (unsigned) long long to long double values])
 
 if test ${ac_cv_sizeof_long_double} = 0; then
-   hdf5_llong_to_ldouble_correct=${hdf5_llong_to_ldouble_correct=no}
+   hdf5_cv_llong_to_ldouble_correct=${hdf5_cv_llong_to_ldouble_correct=no}
 else
    AC_CACHE_VAL([hdf5_cv_llong_to_ldouble_correct],
         [AC_TRY_RUN([
@@ -3588,10 +3633,10 @@ else
     done:
             exit(ret);
         }
-        ], [hdf5_llong_to_ldouble_correct=yes], [hdf5_llong_to_ldouble_correct=no],)])
+        ], [hdf5_cv_llong_to_ldouble_correct=yes], [hdf5_cv_llong_to_ldouble_correct=no],)])
 fi
 
-if test ${hdf5_llong_to_ldouble_correct} = "yes"; then
+if test ${hdf5_cv_llong_to_ldouble_correct} = "yes"; then
   AC_DEFINE([LLONG_TO_LDOUBLE_CORRECT], [1],
             [Define if your system can convert (unsigned) long long to long double values correctly.])
   AC_MSG_RESULT([yes])
@@ -3702,8 +3747,8 @@ dnl libraries.
 dnl 
 AC_SUBST([DYNAMIC_DIRS]) DYNAMIC_DIRS=""
 
-if test -n "$LDFLAGS"; then
-  for d in $LDFLAGS ; do
+if test -n "$AM_LDFLAGS $LDFLAGS"; then
+  for d in $AM_LDFLAGS $LDFLAGS ; do
     case "$d" in
       -L*)
         d="`echo $d | sed -e 's/-L//g'`"
@@ -3720,9 +3765,9 @@ if test -n "$LDFLAGS"; then
   done
 fi
 
-if test -n "$CPPFLAGS"; then
+if test -n "$AM_CPPFLAGS"; then
   TEMP_CPPFLAGS=""
-  for d in $CPPFLAGS ; do
+  for d in $AM_CPPFLAGS ; do
     case "$d" in
       -I.*)
         dnl If the path isn't absolute, make it so by prepending
@@ -3733,7 +3778,7 @@ if test -n "$CPPFLAGS"; then
     esac
     TEMP_CPPFLAGS="$d $TEMP_CPPFLAGS"
   done
-  CPPFLAGS=$TEMP_CPPFLAGS
+  AM_CPPFLAGS=$TEMP_CPPFLAGS
 fi
 
 dnl ----------------------------------------------------------------------
@@ -3809,10 +3854,10 @@ dnl
 AC_SUBST([DEFAULT_API_VERSION])
 AC_MSG_CHECKING([which version of public symbols to use by default])
 AC_ARG_WITH([default-api-version],
-            [AC_HELP_STRING([--with-default-api-version=(v16|v18)],
+            [AC_HELP_STRING([--with-default-api-version=(v16|v18|v110)],
                             [Specify default release version of public symbols
-                             [default=v18]])],,
-            withval=v18)
+                             [default=v110]])],,
+            withval=v110)
 
 if test "X$withval" = "Xv16"; then
     AC_MSG_RESULT([v16])
@@ -3822,13 +3867,16 @@ if test "X$withval" = "Xv16"; then
 elif test "X$withval" = "Xv18"; then
     AC_MSG_RESULT([v18])
     DEFAULT_API_VERSION=v18
+elif test "X$withval" = "Xv110"; then
+    AC_MSG_RESULT([v110])
+    DEFAULT_API_VERSION=v110
 else
     AC_MSG_ERROR([invalid version of public symbols given])
 fi
 
 dnl It's an error to try to disable deprecated public API symbols while
 dnl choosing an older version of the public API as the default.
-if test "X${DEFAULT_API_VERSION}" != "Xv18" -a "X${DEPRECATED_SYMBOLS}" = "Xno" ; then
+if test "X${DEFAULT_API_VERSION}" != "Xv110" -a "X${DEPRECATED_SYMBOLS}" = "Xno" ; then
   AC_MSG_ERROR([Removing old public API symbols not allowed when using them as default public API symbols])
 fi
 
@@ -3933,6 +3981,16 @@ AC_RUN_IFELSE([
     AC_MSG_RESULT([unknown, assuming yes])
     ])
 
+
+dnl ----------------------------------------------------------------------
+dnl Restore user's CFLAGS.
+CFLAGS="$saved_user_CFLAGS"
+FCFLAGS="$saved_user_FCFLAGS"
+CXXFLAGS="$saved_user_CXXFLAGS"
+CPPFLAGS="$saved_user_CPPFLAGS"
+LDFLAGS="$saved_user_LDFLAGS"
+
+
 dnl ----------------------------------------------------------------------
 dnl Create automake conditionals to tell automake makefiles which directories
 dnl need to be compiled
@@ -3962,7 +4020,7 @@ else
 fi
 
 dnl Some cleanup stuff
-rm -f conftest conftest.o conftest.c dummy.o
+rm -f conftest conftest.o conftest.c dummy.o *.mod
 
 dnl Build config.status, touch the stamp files, and build all the Makefiles.
 dnl The order is such that the first `make' does not need to update any
@@ -4106,208 +4164,3 @@ EOF
 
 dnl show the configure settings
 cat src/libhdf5.settings
-
-if false; then
-dnl ============ old code to be removed ================
-dnl ----------------------------------------------------------------------
-dnl Print out a summary of what we are going to build.
-dnl
-if test -z "$ECHO_N" -o -z "$ECHO_C"; then
-  if (echo "testing\c"; echo 1,2,3) | grep c >/dev/null; then
-    if (echo -n testing; echo 1,2,3) | sed s/-n/xn/ | grep xn >/dev/null; then
-      ECHO_N=''
-      ECHO_C='
-'
-    else
-      ECHO_N=-n
-      ECHO_C=''
-    fi
-  else
-    ECHO_N=''
-    ECHO_C='\c'
-  fi
-fi
-
-PRINT_PLAIN() {
-  echo $ECHO_N "$1$ECHO_C"
-  echo $ECHO_N "$1$ECHO_C" 1>>src/libhdf5.settings
-}
-
-PRINT_N() {
-  echo $ECHO_N "$1:  $ECHO_C"
-  echo $ECHO_N "$1:  $ECHO_C" 1>>src/libhdf5.settings
-}
-
-PRINT() {
-  echo "$1"
-  echo "$1" 1>>src/libhdf5.settings
-}
-
-dnl ----------------------------------------------------------------------
-dnl Print "Yes" if all arguments are "yes", otherwise "No"
-dnl
-IF_YES_NO() {
-  if test $# -lt 1; then
-    PRINT "No"
-    return
-  else
-    while test $# -gt 0; do
-      if test "$1" != "yes"; then
-        PRINT "No"
-        return
-      fi
-      shift
-    done
-  fi
-  PRINT "Yes"
-}
-
-IF_ENABLED_DISABLED() {
-  if test "$1" = "yes"; then
-    PRINT "Enabled"
-  else
-    PRINT "Disabled"
-  fi
-}
-
-PRINT ""
-PRINT "                       Configure Summary"
-PRINT "                       ================="
-PRINT ""
-PRINT "Compiling Options:"
-PRINT "------------------"
-
-PRINT_N "               Compilation Mode"
-case "X-$enable_production" in
-  X-yes)        PRINT "Production" ;;
-  X-no)         PRINT "Development" ;;
-  X-profile)    PRINT "Profile" ;;
-  *)            PRINT "$enable_production" ;;
-esac
-
-PRINT_N "                     C Compiler"
-PRINT "$CC"
-
-PRINT_N "                         CFLAGS / H5_CFLAGS"
-PRINT "$CFLAGS"
-PRINT "                         $H5_CFLAGS"
-
-PRINT_N "                       CPPFLAGS / H5_CPPFLAGS"
-PRINT "$CPPFLAGS"
-PRINT "                         $H5_CPPFLAGS"
-
-PRINT_N "                        LDFLAGS"
-PRINT "$LDFLAGS"
-
-PRINT_N "                     Debug Mode"
-
-if test "X$DEBUG_PKG" = "X$all_packages"; then
-  PRINT "All"
-elif test "X$DEBUG_PKG" = "X"; then
-  PRINT "None"
-else
-  PRINT $DEBUG_PKG
-fi
-
-PRINT_N "               Shared Libraries"
-IF_YES_NO "$enable_shared"
-
-PRINT_N "               Static Libraries"
-IF_YES_NO "$enable_static"
-
-PRINT_N "  Statically Linked Executables"
-IF_YES_NO "$STATIC_EXEC"
-
-PRINT_N "Default Version of Public Symbols"
-PRINT $DEFAULT_API_VERSION
-
-PRINT_N " With Deprecated Public Symbols"
-IF_YES_NO "$DEPRECATED_SYMBOLS"
-
-PRINT_N "                        Tracing"
-IF_YES_NO "$TRACE_API"
-
-PRINT_N "Clear file buffers before write"
-IF_YES_NO "$CLEARFILEBUF"
-
-PRINT_N "           Using memory checker"
-IF_YES_NO "$USINGMEMCHECKER"
-
-PRINT_N "   Optimization Instrumentation"
-IF_YES_NO "$INSTRUMENT"
-
-PRINT ""
-PRINT "Languages:"
-PRINT "----------"
-
-PRINT_N "                            C++"
-IF_YES_NO "$HDF_CXX"
-if test X$HDF_CXX = Xyes; then
-    PRINT_N "                   C++ Compiler"
-    PRINT "$CXX"
-
-    PRINT_N "                       CXXFLAGS / H5_CXXFLAGS"
-    PRINT "$CXXFLAGS"
-    PRINT "                       $H5_CXXFLAGS"
-fi
-
-PRINT_N "                        Fortran"
-IF_YES_NO "$HDF_FORTRAN"
-if test X$HDF_FORTRAN = Xyes; then
-    PRINT_N "               Fortran Compiler"
-    PRINT "$FC"
-
-    PRINT_N "                         FCFLAGS / H5_FCFLAGS"
-    PRINT "$FCFLAGS"
-    PRINT "                         $H5_FCFLAGS"
-fi
-
-PRINT ""
-PRINT "Features:"
-PRINT "---------"
-
-PRINT_N "                        dmalloc"
-IF_YES_NO "$HAVE_DMALLOC"
-
-PRINT_N "         Function Stack Tracing"
-IF_ENABLED_DISABLED "$CODESTACK"
-
-PRINT_N "                           GPFS"
-IF_YES_NO "$GPFS"
-
-PRINT_N "      Strict File Format Checks"
-IF_ENABLED_DISABLED "$STRICT_FORMAT_CHECKS"
-
-PRINT_N "            Default API Mapping"
-PRINT "$DEFAULT_API_VERSION"
-
-PRINT_N "         I/O filters (external)"
-PRINT "$EXTERNAL_FILTERS"
-
-PRINT_N "         I/O filters (internal)"
-PRINT "$FILTERS"
-
-PRINT_N " Linux Large File Support (LFS)"
-IF_ENABLED_DISABLED "$LINUX_LFS"
-
-PRINT_N "                            MPE"
-IF_YES_NO "$MPE"
-
-
-PRINT_N "                  Parallel HDF5"
-if test "$PARALLEL" != "no"; then
-  PRINT "Yes"
-else
-  PRINT "No"
-fi
-
-
-PRINT_N "                     Direct VFD"
-IF_ENABLED_DISABLED "$DIRECT_VFD"
-
-PRINT_N "                   Threadsafety"
-IF_ENABLED_DISABLED "$THREADSAFE"
-
-PRINT_N "             High Level library"
-IF_ENABLED_DISABLED "$HDF5_HL"
-fi