Replace local hdf5.m4 script with gnu's

auxdir/ax_lib_hdf5.m4

+# ===========================================================================
+#        http://www.gnu.org/software/autoconf-archive/ax_lib_hdf5.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_LIB_HDF5([serial/parallel])
+#
+# DESCRIPTION
+#
+#   This macro provides tests of the availability of HDF5 library.
+#
+#   The optional macro argument should be either 'serial' or 'parallel'. The
+#   former only looks for serial HDF5 installations via h5cc. The latter
+#   only looks for parallel HDF5 installations via h5pcc. If the optional
+#   argument is omitted, serial installations will be preferred over
+#   parallel ones.
+#
+#   The macro adds a --with-hdf5 option accepting one of three values:
+#
+#     no   - do not check for the HDF5 library.
+#     yes  - do check for HDF5 library in standard locations.
+#     path - complete path to the HDF5 helper script h5cc or h5pcc.
+#
+#   If HDF5 is successfully found, this macro calls
+#
+#     AC_SUBST(HDF5_VERSION)
+#     AC_SUBST(HDF5_CC)
+#     AC_SUBST(HDF5_CFLAGS)
+#     AC_SUBST(HDF5_CPPFLAGS)
+#     AC_SUBST(HDF5_LDFLAGS)
+#     AC_SUBST(HDF5_LIBS)
+#     AC_SUBST(HDF5_FC)
+#     AC_SUBST(HDF5_FFLAGS)
+#     AC_SUBST(HDF5_FLIBS)
+#     AC_DEFINE(HAVE_HDF5)
+#
+#   and sets with_hdf5="yes".  Additionally, the macro sets
+#   with_hdf5_fortran="yes" if a matching Fortran wrapper script is found.
+#   Note that Autconf's Fortran support is not used to perform this check.
+#   H5CC and H5FC will contain the appropriate serial or parallel HDF5
+#   wrapper script locations.
+#
+#   If HDF5 is disabled or not found, this macros sets with_hdf5="no" and
+#   with_hdf5_fortran="no".
+#
+#   Your configuration script can test $with_hdf to take any further
+#   actions. HDF5_{C,CPP,LD}FLAGS may be used when building with C or C++.
+#   HDF5_F{FLAGS,LIBS} should be used when building Fortran applications.
+#
+#   To use the macro, one would code one of the following in "configure.ac"
+#   before AC_OUTPUT:
+#
+#     1) dnl Check for HDF5 support
+#        AX_LIB_HDF5()
+#
+#     2) dnl Check for serial HDF5 support
+#        AX_LIB_HDF5([serial])
+#
+#     3) dnl Check for parallel HDF5 support
+#        AX_LIB_HDF5([parallel])
+#
+#   One could test $with_hdf5 for the outcome or display it as follows
+#
+#     echo "HDF5 support:  $with_hdf5"
+#
+#   You could also for example, override the default CC in "configure.ac" to
+#   enforce compilation with the compiler that HDF5 uses:
+#
+#     AX_LIB_HDF5([parallel])
+#     if test "$with_hdf5" = "yes"; then
+#             CC="$HDF5_CC"
+#     else
+#             AC_MSG_ERROR([Unable to find HDF5, we need parallel HDF5.])
+#     fi
+#
+# LICENSE
+#
+#   Copyright (c) 2009 Timothy Brown <tbrown@freeshell.org>
+#   Copyright (c) 2010 Rhys Ulerich <rhys.ulerich@gmail.com>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 8
+
+AC_DEFUN([AX_LIB_HDF5], [
+
+AC_REQUIRE([AC_PROG_SED])
+AC_REQUIRE([AC_PROG_AWK])
+AC_REQUIRE([AC_PROG_GREP])
+
+dnl Check first argument is one of the recognized values.
+dnl Fail eagerly if is incorrect as this simplifies case statements below.
+if   test "m4_normalize(m4_default([$1],[]))" = ""        ; then
+    : # Recognized value
+elif test "m4_normalize(m4_default([$1],[]))" = "serial"  ; then
+    : # Recognized value
+elif test "m4_normalize(m4_default([$1],[]))" = "parallel"; then
+    : # Recognized value
+else
+    AC_MSG_ERROR([
+Unrecognized value for AX[]_LIB_HDF5 within configure.ac.
+If supplied, argument 1 must be either 'serial' or 'parallel'.
+])
+fi
+
+dnl Add a default --with-hdf5 configuration option.
+AC_ARG_WITH([hdf5],
+  AS_HELP_STRING(
+    [--with-hdf5=[yes/no/PATH]],
+    m4_case(m4_normalize([$1]),
+            [serial],   [location of h5cc for serial HDF5 configuration],
+            [parallel], [location of h5pcc for parallel HDF5 configuration],
+            [location of h5cc or h5pcc for HDF5 configuration])
+  ),
+  [if test "$withval" = "no"; then
+     with_hdf5="no"
+   elif test "$withval" = "yes"; then
+     with_hdf5="yes"
+   else
+     with_hdf5="yes"
+     H5CC="$withval"
+   fi],
+   [with_hdf5="yes"]
+)
+
+dnl Set defaults to blank
+HDF5_CC=""
+HDF5_VERSION=""
+HDF5_CFLAGS=""
+HDF5_CPPFLAGS=""
+HDF5_LDFLAGS=""
+HDF5_LIBS=""
+HDF5_FC=""
+HDF5_FFLAGS=""
+HDF5_FLIBS=""
+
+dnl Try and find hdf5 compiler tools and options.
+if test "$with_hdf5" = "yes"; then
+    if test -z "$H5CC"; then
+        dnl Check to see if H5CC is in the path.
+        AC_PATH_PROGS(
+            [H5CC],
+            m4_case(m4_normalize([$1]),
+                [serial],   [h5cc],
+                [parallel], [h5pcc],
+                [h5cc h5pcc]),
+            [])
+    else
+        AC_MSG_CHECKING([Using provided HDF5 C wrapper])
+        AC_MSG_RESULT([$H5CC])
+    fi
+    AC_MSG_CHECKING([for HDF5 libraries])
+    if test ! -f "$H5CC" || test ! -x "$H5CC"; then
+        AC_MSG_RESULT([no])
+        AC_MSG_WARN(m4_case(m4_normalize([$1]),
+            [serial],  [
+Unable to locate serial HDF5 compilation helper script 'h5cc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5cc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+],            [parallel],[
+Unable to locate parallel HDF5 compilation helper script 'h5pcc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5pcc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+],            [
+Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+]))
+        with_hdf5="no"
+        with_hdf5_fortran="no"
+    else
+        dnl Get the h5cc output
+        HDF5_SHOW=$(eval $H5CC -show)
+
+        dnl Get the actual compiler used
+        HDF5_CC=$(eval $H5CC -show | $AWK '{print $[]1}')
+
+        dnl h5cc provides both AM_ and non-AM_ options
+        dnl depending on how it was compiled either one of
+        dnl these are empty. Lets roll them both into one.
+
+        dnl Look for "HDF5 Version: X.Y.Z"
+        HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
+            | $AWK '{print $[]3}')
+
+        dnl A ideal situation would be where everything we needed was
+        dnl in the AM_* variables. However most systems are not like this
+        dnl and seem to have the values in the non-AM variables.
+        dnl
+        dnl We try the following to find the flags:
+        dnl (1) Look for "NAME:" tags
+        dnl (2) Look for "H5_NAME:" tags
+        dnl (3) Look for "AM_NAME:" tags
+        dnl
+        HDF5_tmp_flags=$(eval $H5CC -showconfig \
+            | $GREP 'FLAGS\|Extra libraries:' \
+            | $AWK -F: '{printf("%s "), $[]2}' )
+
+        dnl Find the installation directory and append include/
+        HDF5_tmp_inst=$(eval $H5CC -showconfig \
+            | $GREP 'Installation point:' \
+            | $AWK -F: '{print $[]2}' )
+
+        dnl Add this to the CPPFLAGS
+        HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
+
+        dnl Now sort the flags out based upon their prefixes
+        for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
+          case "$arg" in
+            -I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+                  || HDF5_CPPFLAGS="$arg $HDF5_CPPFLAGS"
+              ;;
+            -L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+                  || HDF5_LDFLAGS="$arg $HDF5_LDFLAGS"
+              ;;
+            -l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
+                  || HDF5_LIBS="$arg $HDF5_LIBS"
+              ;;
+          esac
+        done
+
+        HDF5_LIBS="$HDF5_LIBS -lhdf5"
+        AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
+
+        dnl See if we can compile
+        ax_lib_hdf5_save_CC=$CC
+        ax_lib_hdf5_save_CPPFLAGS=$CPPFLAGS
+        ax_lib_hdf5_save_LIBS=$LIBS
+        ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
+        CC=$HDF5_CC
+        CPPFLAGS=$HDF5_CPPFLAGS
+        LIBS=$HDF5_LIBS
+        LDFLAGS=$HDF5_LDFLAGS
+        AC_CHECK_HEADER([hdf5.h], [ac_cv_hadf5_h=yes], [ac_cv_hadf5_h=no])
+        AC_CHECK_LIB([hdf5], [H5Fcreate], [ac_cv_libhdf5=yes],
+                     [ac_cv_libhdf5=no])
+        if test "$ac_cv_hadf5_h" = "no" && test "$ac_cv_libhdf5" = "no" ; then
+          AC_MSG_WARN([Unable to compile HDF5 test program])
+        fi
+        dnl Look for HDF5's high level library
+        AC_HAVE_LIBRARY([hdf5_hl], [HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"], [], [])
+
+        CC=$ax_lib_hdf5_save_CC
+        LIBS=$ax_lib_hdf5_save_LIBS
+        LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
+
+        AC_MSG_CHECKING([for matching HDF5 Fortran wrapper])
+        dnl Presume HDF5 Fortran wrapper is just a name variant from H5CC
+        H5FC=$(eval echo -n $H5CC | $SED -n 's/cc$/fc/p')
+        if test -x "$H5FC"; then
+            AC_MSG_RESULT([$H5FC])
+            with_hdf5_fortran="yes"
+            AC_SUBST([H5FC])
+
+            dnl Again, pry any remaining -Idir/-Ldir from compiler wrapper
+            for arg in `$H5FC -show`
+            do
+              case "$arg" in #(
+                -I*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
+                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
+                  ;;#(
+                -L*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
+                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
+                     dnl HDF5 installs .mod files in with libraries,
+                     dnl but some compilers need to find them with -I
+                     echo $HDF5_FFLAGS | $GREP -e "-I${arg#-L}" >/dev/null \
+                      || HDF5_FFLAGS="-I${arg#-L} $HDF5_FFLAGS"
+                  ;;
+              esac
+            done
+
+            dnl Make Fortran link line by inserting Fortran libraries
+            for arg in $HDF5_LIBS
+            do
+              case "$arg" in #(
+                -lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
+                  ;; #(
+                -lhdf5)    HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
+                  ;; #(
+                *) HDF5_FLIBS="$HDF5_FLIBS $arg"
+                  ;;
+              esac
+            done
+        else
+            AC_MSG_RESULT([no])
+            with_hdf5_fortran="no"
+        fi
+
+	AC_SUBST([HDF5_VERSION])
+	AC_SUBST([HDF5_CC])
+	AC_SUBST([HDF5_CFLAGS])
+	AC_SUBST([HDF5_CPPFLAGS])
+	AC_SUBST([HDF5_LDFLAGS])
+	AC_SUBST([HDF5_LIBS])
+	AC_SUBST([HDF5_FC])
+	AC_SUBST([HDF5_FFLAGS])
+	AC_SUBST([HDF5_FLIBS])
+	AC_DEFINE([HAVE_HDF5], [1], [Defined if you have HDF5 support])
+    fi
+fi
+])

auxdir/x_ac_hdf5.m4

-##*****************************************************************************
-#  COPIER:
-#         Rod Schultz <rod.schultz@bull.com>
-#    from example writtey by
-#         Morris Jette <jette1@llnl.gov>
-#
-#  SYNOPSIS:
-#    X_AC_HDF5
-#
-#  DESCRIPTION:
-#    Determine if the HDF5 libraries exists.
-##*****************************************************************************
-
-AC_DEFUN([X_AC_HDF5],
-[
-  _x_ac_hdf5_dirs="/usr /usr/local"
-  _x_ac_hdf5_libs="lib64 lib"
-
-  AC_ARG_WITH(
-    [hdf5],
-    AS_HELP_STRING(--with-hdf5=PATH,Specify path to hdf5 installation),
-    [_x_ac_hdf5_dirs="$withval $_x_ac_hdf5_dirs"])
-
-  AC_CACHE_CHECK(
-    [for hdf5 installation],
-    [x_ac_cv_hdf5_dir],
-    [
-      for d in $_x_ac_hdf5_dirs; do
-        test -d "$d" || continue
-        test -d "$d/include" || continue
-        test -f "$d/include/hdf5.h" || continue
-	for bit in $_x_ac_hdf5_libs; do
-          test -d "$d/$bit" || continue
-          _x_ac_hdf5_cppflags_save="$CPPFLAGS"
-          CPPFLAGS="-I$d/include $CPPFLAGS"
-	  _x_ac_hdf5_libs_save="$LIBS"
-          LIBS="-L$d/$bit -lhdf5 $LIBS"
-          AC_LINK_IFELSE(
-            [AC_LANG_CALL([], H5close)],
-            AS_VAR_SET(x_ac_cv_hdf5_dir, $d))
-          CPPFLAGS="$_x_ac_hdf5_cppflags_save"
-          LIBS="$_x_ac_hdf5_libs_save"
-          test -n "$x_ac_cv_hdf5_dir" && break
-	done
-        test -n "$x_ac_cv_hdf5_dir" && break
-      done
-    ])
-  if test -z "$x_ac_cv_hdf5_dir"; then
-    AC_MSG_WARN([unable to locate hdf5 installation])
-  else
-    # This include of mpi is here just so we get a location of mpi.h
-    # There is currently (what we consider) a bug in the way ubuntu
-    # packages the libhdf5-dev libs.  If you install one version it conflicts
-    # and thus over writes the other version (openmpi vs. mpich2 etc)
-    # This breaks the compile of our lib since we don't typically have the
-    # mpi in our path.  Ubuntu is the only version of linux we have seen this
-    # problem, others install the libhdf5-dev headers in the mpi's include
-    # dir, if it ever gets resolved in some way remove this include.
-    HDF5_CPPFLAGS="-I$x_ac_cv_hdf5_dir/include -I/usr/include/mpi"
-    HDF5_LDFLAGS="-Wl,-rpath -Wl,$x_ac_cv_hdf5_dir/$bit -L$x_ac_cv_hdf5_dir/$bit"
-    HDF5_LIBS="-lhdf5"
-  fi
-
-  AC_SUBST(HDF5_LIBS)
-  AC_SUBST(HDF5_CPPFLAGS)
-  AC_SUBST(HDF5_LDFLAGS)
-  AM_CONDITIONAL(BUILD_HDF5, test -n "$x_ac_cv_hdf5_dir")
-
-])

configure.ac

@@ -222,7 +222,9 @@ X_AC_DIMENSIONS
 
 X_AC_CFLAGS
 X_AC_OFED
-X_AC_HDF5
+
+AX_LIB_HDF5()
+AM_CONDITIONAL(BUILD_HDF5, test "$with_hdf5" = "yes")
 X_AC_HWLOC
 X_AC_FREEIPMI
 X_AC_XCPU