CXXFLAGS="${OLD_CXXFLAGS}"
])
+dnl ===========================================================================
+dnl http://www.gnu.org/software/autoconf-archive/ax_lib_hdf5.html
+dnl ===========================================================================
+dnl
+dnl SYNOPSIS
+dnl
+dnl AX_LIB_HDF5([serial/parallel])
+dnl
+dnl DESCRIPTION
+dnl
+dnl This macro provides tests of the availability of HDF5 library.
+dnl
+dnl The optional macro argument should be either 'serial' or 'parallel'. The
+dnl former only looks for serial HDF5 installations via h5cc. The latter
+dnl only looks for parallel HDF5 installations via h5pcc. If the optional
+dnl argument is omitted, serial installations will be preferred over
+dnl parallel ones.
+dnl
+dnl The macro adds a --with-hdf5 option accepting one of three values:
+dnl
+dnl no - do not check for the HDF5 library.
+dnl yes - do check for HDF5 library in standard locations.
+dnl path - complete path to where lib/libhdf5* libraries and
+dnl include/H5* include files reside.
+dnl
+dnl If HDF5 is successfully found, this macro calls
+dnl
+dnl AC_SUBST(DEAL_II_HDF5_VERSION)
+dnl AC_SUBST(DEAL_II_HDF5_CFLAGS)
+dnl AC_SUBST(DEAL_II_HDF5_CPPFLAGS)
+dnl AC_SUBST(DEAL_II_HDF5_LDFLAGS)
+dnl AC_SUBST(DEAL_II_HDF5_INCDIR)
+dnl AC_DEFINE(DEAL_II_HAVE_HDF5)
+dnl
+dnl and sets with_hdf5="yes".
+dnl
+dnl If HDF5 is disabled or not found, this macros sets with_hdf5="no".
+dnl
+dnl Your configuration script can test $with_hdf to take any further
+dnl actions. HDF5_{C,CPP,LD}FLAGS may be used when building with C or C++.
+dnl
+dnl LICENSE
+dnl
+dnl Copyright (c) 2009 Timothy Brown <tbrown@freeshell.org>
+dnl Copyright (c) 2010 Rhys Ulerich <rhys.ulerich@gmail.com>
+dnl
+dnl Copying and distribution of this file, with or without modification, are
+dnl permitted in any medium without royalty provided the copyright notice
+dnl and this notice are preserved. This file is offered as-is, without any
+dnl warranty.
+
+AC_DEFUN(DEAL_II_CONFIGURE_HDF5, dnl
+[
+
+AC_REQUIRE([AC_PROG_SED])
+AC_REQUIRE([AC_PROG_AWK])
+AC_REQUIRE([AC_PROG_GREP])
+
+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
+USE_CONTRIB_HDF5=no
+DEAL_II_HDF5_VERSION=""
+DEAL_II_HDF5_CFLAGS=""
+DEAL_II_HDF5_CPPFLAGS=""
+DEAL_II_HDF5_LDFLAGS=""
+DEAL_II_HDF5_INCDIR=""
+
+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 ! -x "$H5CC"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN(m4_case(m4_normalize([$1]),
+ [serial], [
+Unable to locate serial HDF5 compilation helper script 'h5cc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5cc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+], [parallel],[
+Unable to locate parallel HDF5 compilation helper script 'h5pcc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5pcc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+], [
+Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
+Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
+HDF5 support is being disabled (equivalent to --with-hdf5=no).
+]))
+ with_hdf5="no"
+ else
+ dnl h5cc provides both AM_ and non-AM_ options
+ dnl depending on how it was compiled either one of
+ dnl these are empty. Lets roll them both into one.
+
+ dnl Look for "HDF5 Version: X.Y.Z"
+ DEAL_II_HDF5_VERSION=$(eval $H5CC -showconfig | grep 'HDF5 Version:' \
+ | $AWK '{print $[]3}')
+
+dnl A ideal situation would be where everything we needed was
+dnl in the AM_* variables. However most systems are not like this
+dnl and seem to have the values in the non-AM variables.
+dnl
+dnl We try the following to find the flags:
+dnl (1) Look for "NAME:" tags
+dnl (2) Look for "NAME/H5_NAME:" tags
+dnl (3) Look for "AM_NAME:" tags
+dnl
+ dnl (1)
+ dnl Look for "CFLAGS: "
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig | grep '\bCFLAGS:' \
+ | $AWK -F: '{print $[]2}')
+ dnl Look for "CPPFLAGS"
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig | grep '\bCPPFLAGS:' \
+ | $AWK -F: '{print $[]2}')
+ dnl Look for "LD_FLAGS"
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig | grep '\bLDFLAGS:' \
+ | $AWK -F: '{print $[]2}')
+
+ dnl (2)
+ dnl CFLAGS/H5_CFLAGS: .../....
+ dnl We could use $SED with something like the following
+ dnl 's/CFLAGS.*\/H5_CFLAGS.*[:]\(.*\)\/\(.*\)/\1/p'
+ if test -z "$DEAL_II_HDF5_CFLAGS"; then
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/CFLAGS.*[:]\(.*\)\/\(.*\)/\1/p')
+ fi
+ dnl Look for "CPPFLAGS"
+ if test -z "$DEAL_II_HDF5_CPPFLAGS"; then
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/CPPFLAGS.*[:]\(.*\)\/\(.*\)/\1/p')
+ fi
+ dnl Look for "LD_FLAGS"
+ if test -z "$DEAL_II_HDF5_LDFLAGS"; then
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/LDFLAGS.*[:]\(.*\)\/\(.*\)/\1/p')
+ fi
+
+ dnl (3)
+ dnl Check to see if these are not empty strings. If so
+ dnl find the AM_ versions and use them.
+ if test -z "$DEAL_II_HDF5_CFLAGS"; then
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_CFLAGS:' | $AWK -F: '{print $[]2}')
+ fi
+ if test -z "$DEAL_II_HDF5_CPPFLAGS"; then
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_CPPFLAGS:' | $AWK -F: '{print $[]2}')
+ fi
+ if test -z "$DEAL_II_HDF5_LDFLAGS"; then
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_LDFLAGS:' | $AWK -F: '{print $[]2}')
+ fi
+
+ dnl Frustratingly, the necessary -Idir,-Ldir still may not be found!
+ dnl Attempt to pry any more required include directories from wrapper.
+ for arg in `$H5CC -c -show`
+ do
+ case "$arg" in #(
+ -I*) echo $DEAL_II_HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+ || DEAL_II_HDF5_CPPFLAGS="$arg $DEAL_II_HDF5_CPPFLAGS"
+ ;;
+ esac
+ done
+ for arg in `$H5CC -show`
+ do
+ case "$arg" in #(
+ -L*) echo $DEAL_II_HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+ || DEAL_II_HDF5_LDFLAGS="$arg $DEAL_II_HDF5_LDFLAGS"
+ ;;
+ esac
+ done
+
+ AC_MSG_RESULT([yes (version $[DEAL_II_HDF5_VERSION])])
+
+ dnl Look for any extra libraries also needed to link properly
+ EXTRA_LIBS=$(eval $H5CC -showconfig | grep 'Extra libraries:'\
+ | $AWK -F: '{print $[]2}')
+
+ dnl Look for HDF5's high level library
+ ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
+ ax_lib_hdf5_save_LIBS=$LIBS
+ LDFLAGS=$DEAL_II_HDF5_LDFLAGS
+ AC_HAVE_LIBRARY([hdf5_hl],
+ [DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS -lhdf5_hl"],
+ [],
+ [-lhdf5 $EXTRA_LIBS])
+ LIBS=$ax_lib_hdf5_save_LIBS
+ LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
+
+ dnl Add the HDF5 library itself
+ DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS -lhdf5"
+
+ dnl Add any EXTRA_LIBS afterwards
+ if test "$EXTRA_LIBS"; then
+ DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS $EXTRA_LIBS"
+ fi
+
+ dnl remove "-I" from cpp flags to get include path
+ DEAL_II_HDF5_INCDIR=$(eval echo $DEAL_II_HDF5_CPPFLAGS | cut -c 3-)
+
+ LDFLAGS="$LDFLAGS $DEAL_II_HDF5_LDFLAGS"
+ USE_CONTRIB_HDF5=yes
+ AC_DEFINE([DEAL_II_HAVE_HDF5], [1], [Defined if you have HDF5 support])
+ fi
+fi
+])
+
+
+
dnl ------------------------------------------------------------
DEAL_II_ARPACK_ARCH
DEAL_II_ARPACK_DIR
USE_CONTRIB_ARPACK
+DEAL_II_HDF5_INCDIR
+DEAL_II_HDF5_LDFLAGS
+DEAL_II_HDF5_CPPFLAGS
+DEAL_II_HDF5_CFLAGS
+DEAL_II_HDF5_VERSION
+USE_CONTRIB_HDF5
+H5CC
+AWK
+SED
DEAL_II_TRILINOS_STATIC
DEAL_II_TRILINOS_SHARED
DEAL_II_TRILINOS_LIBDIR
with_trilinos
with_trilinos_include
with_trilinos_libs
+with_hdf5
with_arpack
with_mumps
with_scalapack
Specify the path to the Trilinos libraries; use this
if you want to override the TRILINOS_LIBDIR
environment variable.
+ --with-hdf5=yes/no/PATH location of h5cc or h5pcc for HDF5 configuration
--with-arpack=path/to/arpack
Specify the path to the ARPACK installation, for
which the include directory and lib directory are
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5
+$as_echo_n "checking for a sed that does not truncate output... " >&6; }
+if ${ac_cv_path_SED+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/
+ for ac_i in 1 2 3 4 5 6 7; do
+ ac_script="$ac_script$as_nl$ac_script"
+ done
+ echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed
+ { ac_script=; unset ac_script;}
+ if test -z "$SED"; then
+ ac_path_SED_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+# Check for GNU ac_path_SED and select it if it is found.
+ # Check for GNU $ac_path_SED
+case `"$ac_path_SED" --version 2>&1` in
+*GNU*)
+ ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo '' >> "conftest.nl"
+ "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_SED_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_SED="$ac_path_SED"
+ ac_path_SED_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_SED_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_SED"; then
+ as_fn_error $? "no acceptable sed could be found in \$PATH" "$LINENO" 5
+ fi
+else
+ ac_cv_path_SED=$SED
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_SED" >&5
+$as_echo "$ac_cv_path_SED" >&6; }
+ SED="$ac_cv_path_SED"
+ rm -f conftest.sed
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+
+
+
+
+
+
+
+# Check whether --with-hdf5 was given.
+if test "${with_hdf5+set}" = set; then :
+ withval=$with_hdf5; if test "$withval" = "no"; then
+ with_hdf5="no"
+ elif test "$withval" = "yes"; then
+ with_hdf5="yes"
+ else
+ with_hdf5="yes"
+ H5CC="$withval"
+ fi
+else
+ with_hdf5="yes"
+
+fi
+
+
+USE_CONTRIB_HDF5=no
+DEAL_II_HDF5_VERSION=""
+DEAL_II_HDF5_CFLAGS=""
+DEAL_II_HDF5_CPPFLAGS=""
+DEAL_II_HDF5_LDFLAGS=""
+DEAL_II_HDF5_INCDIR=""
+
+if test "$with_hdf5" = "yes"; then
+ if test -z "$H5CC"; then
+ for ac_prog in h5cc h5pcc
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_path_H5CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $H5CC in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_H5CC="$H5CC" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_H5CC="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+H5CC=$ac_cv_path_H5CC
+if test -n "$H5CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $H5CC" >&5
+$as_echo "$H5CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$H5CC" && break
+done
+
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking Using provided HDF5 C wrapper" >&5
+$as_echo_n "checking Using provided HDF5 C wrapper... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $H5CC" >&5
+$as_echo "$H5CC" >&6; }
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for HDF5 libraries" >&5
+$as_echo_n "checking for HDF5 libraries... " >&6; }
+ if test ! -x "$H5CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING:
+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).
+" >&5
+$as_echo "$as_me: WARNING:
+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).
+" >&2;}
+ with_hdf5="no"
+ else
+
+ DEAL_II_HDF5_VERSION=$(eval $H5CC -showconfig | grep 'HDF5 Version:' \
+ | $AWK '{print $3}')
+
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig | grep '\bCFLAGS:' \
+ | $AWK -F: '{print $2}')
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig | grep '\bCPPFLAGS:' \
+ | $AWK -F: '{print $2}')
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig | grep '\bLDFLAGS:' \
+ | $AWK -F: '{print $2}')
+
+ if test -z "$DEAL_II_HDF5_CFLAGS"; then
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/CFLAGS.*:\(.*\)\/\(.*\)/\1/p')
+ fi
+ if test -z "$DEAL_II_HDF5_CPPFLAGS"; then
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/CPPFLAGS.*:\(.*\)\/\(.*\)/\1/p')
+ fi
+ if test -z "$DEAL_II_HDF5_LDFLAGS"; then
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig \
+ | $SED -n 's/LDFLAGS.*:\(.*\)\/\(.*\)/\1/p')
+ fi
+
+ if test -z "$DEAL_II_HDF5_CFLAGS"; then
+ DEAL_II_HDF5_CFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_CFLAGS:' | $AWK -F: '{print $2}')
+ fi
+ if test -z "$DEAL_II_HDF5_CPPFLAGS"; then
+ DEAL_II_HDF5_CPPFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_CPPFLAGS:' | $AWK -F: '{print $2}')
+ fi
+ if test -z "$DEAL_II_HDF5_LDFLAGS"; then
+ DEAL_II_HDF5_LDFLAGS=$(eval $H5CC -showconfig \
+ | grep '\bAM_LDFLAGS:' | $AWK -F: '{print $2}')
+ fi
+
+ for arg in `$H5CC -c -show`
+ do
+ case "$arg" in #(
+ -I*) echo $DEAL_II_HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+ || DEAL_II_HDF5_CPPFLAGS="$arg $DEAL_II_HDF5_CPPFLAGS"
+ ;;
+ esac
+ done
+ for arg in `$H5CC -show`
+ do
+ case "$arg" in #(
+ -L*) echo $DEAL_II_HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+ || DEAL_II_HDF5_LDFLAGS="$arg $DEAL_II_HDF5_LDFLAGS"
+ ;;
+ esac
+ done
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes (version $DEAL_II_HDF5_VERSION)" >&5
+$as_echo "yes (version $DEAL_II_HDF5_VERSION)" >&6; }
+
+ EXTRA_LIBS=$(eval $H5CC -showconfig | grep 'Extra libraries:'\
+ | $AWK -F: '{print $2}')
+
+ ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
+ ax_lib_hdf5_save_LIBS=$LIBS
+ LDFLAGS=$DEAL_II_HDF5_LDFLAGS
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lhdf5_hl" >&5
+$as_echo_n "checking for main in -lhdf5_hl... " >&6; }
+if ${ac_cv_lib_hdf5_hl_main+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lhdf5_hl -lhdf5 $EXTRA_LIBS $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+
+int
+main ()
+{
+return main ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_hdf5_hl_main=yes
+else
+ ac_cv_lib_hdf5_hl_main=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_hdf5_hl_main" >&5
+$as_echo "$ac_cv_lib_hdf5_hl_main" >&6; }
+if test "x$ac_cv_lib_hdf5_hl_main" = xyes; then :
+ DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS -lhdf5_hl"
+fi
+ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+
+ LIBS=$ax_lib_hdf5_save_LIBS
+ LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
+
+ DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS -lhdf5"
+
+ if test "$EXTRA_LIBS"; then
+ DEAL_II_HDF5_LDFLAGS="$DEAL_II_HDF5_LDFLAGS $EXTRA_LIBS"
+ fi
+
+ DEAL_II_HDF5_INCDIR=$(eval echo $DEAL_II_HDF5_CPPFLAGS | cut -c 3-)
+
+ LDFLAGS="$LDFLAGS $DEAL_II_HDF5_LDFLAGS"
+ USE_CONTRIB_HDF5=yes
+
+$as_echo "#define DEAL_II_HAVE_HDF5 1" >>confdefs.h
+
+ fi
+fi
+
+
+
+
+
+
+
+
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ARPACK library directory" >&5
$as_echo_n "checking for ARPACK library directory... " >&6; }
ac_pwd='$ac_pwd'
srcdir='$srcdir'
+AWK='$AWK'
test -n "\$AWK" || AWK=awk
_ACEOF
# include <zlib.h>
#endif
+#ifdef DEAL_II_HAVE_HDF5
+#include <hdf5.h>
+#endif
DEAL_II_NAMESPACE_OPEN
std::vector<double> vertices;
std::vector<int32_t> cells;
};
+
+
+ class HDF5MemStream
+ {
+ public:
+ /**
+ * Constructor, storing
+ * persistent values for
+ * later use.
+ */
+ HDF5MemStream (const unsigned int local_points_cell_count[2], const unsigned int global_points_cell_offsets[2], const unsigned int dim);
+
+ /**
+ * Output operator for points.
+ */
+ template <int dim>
+ void write_point (const unsigned int index,
+ const Point<dim>&);
+
+ /**
+ * Do whatever is necessary to
+ * terminate the list of points.
+ * In this case, nothing.
+ */
+ void flush_points () {};
+
+ /**
+ * Write dim-dimensional cell
+ * with first vertex at
+ * number start and further
+ * vertices offset by the
+ * specified values. Values
+ * not needed are ignored.
+ *
+ * The order of vertices for
+ * these cells in different
+ * dimensions is
+ * <ol>
+ * <li> [0,1]
+ * <li> []
+ * <li> []
+ * </ol>
+ */
+ template <int dim>
+ void write_cell(const unsigned int index,
+ const unsigned int start,
+ const unsigned int x_offset,
+ const unsigned int y_offset,
+ const unsigned int z_offset);
+
+ /**
+ * Do whatever is necessary to
+ * terminate the list of cells.
+ * In this case, nothing.
+ */
+ void flush_cells () {};
+
+ const double *node_data(void) const { return &vertices[0]; };
+ const unsigned int *cell_data(void) const { return &cells[0]; };
+
+ private:
+ /**
+ * A list of vertices and
+ * cells, used to write HDF5 data.
+ */
+ std::vector<double> vertices;
+ std::vector<unsigned int> cells;
+ unsigned int cell_offset;
+ };
//----------------------------------------------------------------------//
return stream;
}
-
+ HDF5MemStream::HDF5MemStream(const unsigned int local_points_cell_count[2], const unsigned int global_points_cell_offsets[2], const unsigned int dim) {
+ unsigned int entries_per_cell = (2 << (dim-1));
+
+ vertices.resize(local_points_cell_count[0]*dim);
+ cells.resize(local_points_cell_count[1]*entries_per_cell);
+ cell_offset = global_points_cell_offsets[1]*entries_per_cell;
+ }
+
+ template<int dim>
+ void
+ HDF5MemStream::write_point (const unsigned int index,
+ const Point<dim>& p)
+ {
+ for (int i=0;i<dim;++i) vertices[index*dim+i] = p(i);
+ }
+
+ template<int dim>
+ void
+ HDF5MemStream::write_cell(
+ unsigned int index,
+ unsigned int start,
+ unsigned int d1,
+ unsigned int d2,
+ unsigned int d3)
+ {
+ unsigned int base_entry = index * GeometryInfo<dim>::vertices_per_cell;
+ cells[base_entry+0] = cell_offset+start;
+ cells[base_entry+1] = cell_offset+start+d1;
+ if (dim>=2)
+ {
+ cells[base_entry+2] = cell_offset+start+d2+d1;
+ cells[base_entry+3] = cell_offset+start+d2;
+ if (dim>=3)
+ {
+ cells[base_entry+4] = cell_offset+start+d3;
+ cells[base_entry+5] = cell_offset+start+d3+d1;
+ cells[base_entry+6] = cell_offset+start+d3+d2+d1;
+ cells[base_entry+7] = cell_offset+start+d3+d2;
+ }
+ }
+ }
+
template <typename T>
std::ostream&
DXStream::operator<< (const T& t)
if (format_name == "deal.II intermediate")
return deal_II_intermediate;
+
+ if (format_name == "hdf5")
+ return hdf5;
AssertThrow (false,
ExcMessage ("The given file format name is not recognized: <"
std::string
DataOutBase::get_output_format_names ()
{
- return "none|dx|ucd|gnuplot|povray|eps|gmv|tecplot|tecplot_binary|vtk|vtu|deal.II intermediate";
+ return "none|dx|ucd|gnuplot|povray|eps|gmv|tecplot|tecplot_binary|vtk|vtu|hdf5|deal.II intermediate";
}
return ".vtu";
case deal_II_intermediate:
return ".d2";
+ case hdf5:
+ return ".h5";
default:
Assert (false, ExcNotImplemented());
return "";
}
+template <int dim, int spacedim>
+XDMFEntry DataOutInterface<dim,spacedim>::
+create_xdmf_entry (const char *h5_filename, const double cur_time, MPI_Comm comm) const
+{
+ return DataOutBase::create_xdmf_entry(get_patches(), get_dataset_names(), get_vector_data_ranges(),
+ h5_filename, cur_time, comm);
+}
+
+template <int dim, int spacedim>
+XDMFEntry DataOutBase::create_xdmf_entry (const std::vector<Patch<dim,spacedim> > &patches,
+ const std::vector<std::string> &data_names,
+ const std::vector<std_cxx1x::tuple<unsigned int, unsigned int, std::string> > &vector_data_ranges,
+ const char* h5_filename,
+ const double cur_time,
+ MPI_Comm comm)
+{
+ unsigned int local_node_cell_count[2], global_node_cell_count[2];
+ const unsigned int n_data_sets = data_names.size();
+ int myrank;
+
+#ifndef DEAL_II_HAVE_HDF5
+ AssertThrow(false, ExcMessage ("XDMF support requires HDF5 to be turned on."));
+#endif
+ AssertThrow(dim == 2 || dim == 3, ExcMessage ("XDMF only supports 2 or 3 dimensions."));
+
+ compute_sizes<dim,spacedim>(patches, local_node_cell_count[0], local_node_cell_count[1]);
+
+ // And compute the global total
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+ MPI_Comm_rank(comm, &myrank);
+ MPI_Allreduce(local_node_cell_count, global_node_cell_count, 2, MPI_UNSIGNED, MPI_SUM, comm);
+#else
+ myrank = 0;
+ global_node_cell_count[0] = local_node_cell_count[0];
+ global_node_cell_count[1] = local_node_cell_count[1];
+#endif
+
+ // Output the XDMF file only on the root process
+ if (myrank == 0) {
+ XDMFEntry entry(h5_filename, cur_time, global_node_cell_count[0], global_node_cell_count[1], dim);
+
+ // The vector names generated here must match those generated in the HDF5 file
+ unsigned int i, n_th_vector, data_set, pt_data_vector_dim;
+ std::string vector_name;
+ for (n_th_vector=0,data_set=0;data_set<n_data_sets;) {
+ // Advance n_th_vector to at least the current data set we are on
+ while (n_th_vector < vector_data_ranges.size() && std_cxx1x::get<0>(vector_data_ranges[n_th_vector]) < data_set) n_th_vector++;
+
+ // Determine whether the data is multiple dimensions or one
+ if (std_cxx1x::get<0>(vector_data_ranges[n_th_vector]) == data_set) {
+ // Multiple dimensions
+ pt_data_vector_dim = std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) - std_cxx1x::get<0>(vector_data_ranges[n_th_vector])+1;
+
+ // Ensure the dimensionality of the data is correct
+ AssertThrow (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) >= std_cxx1x::get<0>(vector_data_ranges[n_th_vector]),
+ ExcLowerRange (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]), std_cxx1x::get<0>(vector_data_ranges[n_th_vector])));
+ AssertThrow (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) < n_data_sets,
+ ExcIndexRange (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]), 0, n_data_sets));
+
+ // Determine the vector name
+ // Concatenate all the
+ // component names with double
+ // underscores unless a vector
+ // name has been specified
+ if (std_cxx1x::get<2>(vector_data_ranges[n_th_vector]) != "") {
+ vector_name = std_cxx1x::get<2>(vector_data_ranges[n_th_vector]);
+ } else {
+ vector_name = "";
+ for (i=std_cxx1x::get<0>(vector_data_ranges[n_th_vector]);i<std_cxx1x::get<1>(vector_data_ranges[n_th_vector]);++i)
+ vector_name += data_names[i] + "__";
+ vector_name += data_names[std_cxx1x::get<1>(vector_data_ranges[n_th_vector])];
+ }
+ } else {
+ // One dimension
+ pt_data_vector_dim = 1;
+ vector_name = data_names[data_set];
+ }
+
+ entry.add_attribute(vector_name, pt_data_vector_dim);
+
+ // Advance the current data set
+ data_set += pt_data_vector_dim;
+ }
+
+ return entry;
+ } else {
+ return XDMFEntry();
+ }
+}
+
+template <int dim, int spacedim>
+void DataOutInterface<dim,spacedim>::
+write_xdmf_file (const std::vector<XDMFEntry> &entries, const char *filename, MPI_Comm comm) const
+{
+ DataOutBase::write_xdmf_file(get_patches(), entries, filename, comm);
+}
+
+template <int dim, int spacedim>
+void DataOutBase::write_xdmf_file (const std::vector<Patch<dim,spacedim> > &patches,
+ const std::vector<XDMFEntry> &entries,
+ const char *filename,
+ MPI_Comm comm)
+{
+ int myrank;
+
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+ MPI_Comm_rank(comm, &myrank);
+#else
+ myrank = 0;
+#endif
+
+ // Only rank 0 process writes the XDMF file
+ if (myrank == 0) {
+ std::ofstream xdmf_file(filename);
+ std::vector<XDMFEntry>::const_iterator it;
+
+ xdmf_file << "<?xml version=\"1.0\" ?>\n";
+ xdmf_file << "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []>\n";
+ xdmf_file << "<Xdmf Version=\"2.0\">\n";
+ xdmf_file << " <Domain>\n";
+ xdmf_file << " <Grid Name=\"CellTime\" GridType=\"Collection\" CollectionType=\"Temporal\">\n";
+
+ // Write out all the entries indented
+ for (it=entries.begin();it!=entries.end();++it)
+ xdmf_file << it->get_xdmf_content(3);
+
+ xdmf_file << " </Grid>\n";
+ xdmf_file << " </Domain>\n";
+ xdmf_file << "</Xdmf>\n";
+
+ xdmf_file.close();
+ }
+}
+
+// Get the XDMF content associated with this entry
+// If the entry is not valid, this returns false
+std::string XDMFEntry::get_xdmf_content(const unsigned int indent_level) const {
+ std::stringstream ss;
+ unsigned int i;
+ std::map<std::string, unsigned int>::const_iterator it;
+
+ if (!valid) return "";
+
+ ss << indent(indent_level+0) << "<Grid Name=\"mesh\" GridType=\"Uniform\">\n";
+ ss << indent(indent_level+1) << "<Time Value=\"" << entry_time << "\"/>\n";
+ ss << indent(indent_level+1) << "<Geometry GeometryType=\"" << (dimension == 2 ? "XY" : "XYZ" ) << "\">\n";
+ ss << indent(indent_level+2) << "<DataItem Dimensions=\"" << num_nodes << " " << dimension << "\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n";
+ ss << indent(indent_level+3) << h5_filename << ":/nodes\n";
+ ss << indent(indent_level+2) << "</DataItem>\n";
+ ss << indent(indent_level+1) << "</Geometry>\n";
+ // If we have cells defined, use a quadrilateral (2D) or hexahedron (3D) topology
+ if (num_cells > 0) {
+ ss << indent(indent_level+1) << "<Topology TopologyType=\"" << (dimension == 2 ? "Quadrilateral" : "Hexahedron") << "\" NumberOfElements=\"" << num_cells << "\">\n";
+ ss << indent(indent_level+2) << "<DataItem Dimensions=\"" << num_cells << " " << (2 << (dimension-1)) << "\" NumberType=\"UInt\" Format=\"HDF\">\n";
+ ss << indent(indent_level+3) << h5_filename << ":/cells\n";
+ ss << indent(indent_level+2) << "</DataItem>\n";
+ ss << indent(indent_level+1) << "</Topology>\n";
+ } else {
+ // Otherwise, we assume the points are isolated in space and use a Polyvertex topology
+ ss << indent(indent_level+1) << "<Topology TopologyType=\"Polyvertex\" NumberOfElements=\"" << num_nodes << "\">\n";
+ ss << indent(indent_level+1) << "</Topology>\n";
+ }
+
+ for (it=attribute_dims.begin();it!=attribute_dims.end();++it) {
+ ss << indent(indent_level+1) << "<Attribute Name=\"" << it->first << "\" AttributeType=\"" << (it->second > 1 ? "Vector" : "Scalar") << "\" Center=\"Node\">\n";
+ // Vectors must have 3 elements even for 2D models
+ ss << indent(indent_level+2) << "<DataItem Dimensions=\"" << num_nodes << " " << (it->second > 1 ? 3 : 1) << "\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n";
+ ss << indent(indent_level+3) << h5_filename << ":/" << it->first << "\n";
+ ss << indent(indent_level+2) << "</DataItem>\n";
+ ss << indent(indent_level+1) << "</Attribute>\n";
+ }
+
+ ss << indent(indent_level+0) << "</Grid>\n";
+
+ return ss.str();
+}
+
+template <int dim, int spacedim>
+void DataOutInterface<dim,spacedim>::
+write_hdf5_parallel (const char* filename, MPI_Comm comm) const
+{
+#ifndef DEAL_II_HAVE_HDF5
+ AssertThrow(false, ExcMessage ("HDF5 support is disabled."));
+#endif
+ DataOutBase::write_hdf5_parallel(get_patches(), get_dataset_names(),
+ get_vector_data_ranges(),
+ filename, comm);
+}
+
+template <int dim, int spacedim>
+void DataOutBase::write_hdf5_parallel (const std::vector<Patch<dim,spacedim> > &patches,
+ const std::vector<std::string> &data_names,
+ const std::vector<std_cxx1x::tuple<unsigned int, unsigned int, std::string> > &vector_data_ranges,
+ const char* filename,
+ MPI_Comm comm)
+{
+#ifndef DEAL_II_HAVE_HDF5
+ AssertThrow(false, ExcMessage ("HDF5 support is disabled."));
+#else
+ int world_size;
+ hid_t h5_file_id, plist_id;
+ hid_t node_dataspace, node_dataset, node_file_dataspace, node_memory_dataspace;
+ hid_t cell_dataspace, cell_dataset, cell_file_dataspace, cell_memory_dataspace;
+ hid_t pt_data_dataspace, pt_data_dataset, pt_data_file_dataspace, pt_data_memory_dataspace;
+ herr_t status;
+ unsigned int local_node_cell_count[2], global_node_cell_count[2], global_node_cell_offsets[2];
+ hsize_t count[2], offset[2], node_ds_dim[2], cell_ds_dim[2];
+ const unsigned int n_data_sets = data_names.size();
+
+ // If HDF5 is not parallel and we're using multiple processes, abort
+#ifndef H5_HAVE_PARALLEL
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+ MPI_Comm_size(comm, &world_size);
+ AssertThrow (world_size <= 1,
+ ExcMessage ("Serial HDF5 output on multiple processes is not yet supported."));
+#endif
+#endif
+
+ compute_sizes<dim,spacedim>(patches, local_node_cell_count[0], local_node_cell_count[1]);
+
+ Table<2,double> data_vectors (n_data_sets, local_node_cell_count[0]);
+ void (*fun_ptr) (const std::vector<Patch<dim,spacedim> > &, Table<2,double> &) = &DataOutBase::template write_gmv_reorder_data_vectors<dim,spacedim>;
+ Threads::Task<> reorder_task = Threads::new_task (fun_ptr, patches, data_vectors);
+
+ // Create file access properties
+ plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ AssertThrow(plist_id != -1, ExcIO());
+ // If MPI is enabled *and* HDF5 is parallel, we can do parallel output
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+#ifdef H5_HAVE_PARALLEL
+ // Set the access to use the specified MPI_Comm object
+ status = H5Pset_fapl_mpio(plist_id, comm, MPI_INFO_NULL);
+ AssertThrow(status >= 0, ExcIO());
+#endif
+#endif
+
+ // Overwrite any existing files (change this to an option?) and close the property list
+ h5_file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ AssertThrow(h5_file_id >= 0, ExcIO());
+ status = H5Pclose(plist_id);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Compute the global total number of nodes/cells
+ // And determine the offset of the data for this process
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+ MPI_Allreduce(local_node_cell_count, global_node_cell_count, 2, MPI_UNSIGNED, MPI_SUM, comm);
+ MPI_Scan(local_node_cell_count, global_node_cell_offsets, 2, MPI_UNSIGNED, MPI_SUM, comm);
+ global_node_cell_offsets[0] -= local_node_cell_count[0];
+ global_node_cell_offsets[1] -= local_node_cell_count[1];
+#else
+ global_node_cell_offsets[0] = global_node_cell_offsets[1] = 0;
+#endif
+
+ // Write the nodes/cells to the HDF5 "stream" object. Record the process offset
+ // so that node reference indices are correctly calculated
+ HDF5MemStream hdf5_data(local_node_cell_count, global_node_cell_offsets, dim);
+ write_nodes(patches, hdf5_data);
+ write_cells(patches, hdf5_data);
+
+ // Create the dataspace for the nodes and cells
+ node_ds_dim[0] = global_node_cell_count[0];
+ node_ds_dim[1] = dim;
+ node_dataspace = H5Screate_simple(2, node_ds_dim, NULL);
+ AssertThrow(node_dataspace >= 0, ExcIO());
+
+ cell_ds_dim[0] = global_node_cell_count[1];
+ cell_ds_dim[1] = GeometryInfo<dim>::vertices_per_cell;
+ cell_dataspace = H5Screate_simple(2, cell_ds_dim, NULL);
+ AssertThrow(cell_dataspace >= 0, ExcIO());
+
+ // Create the dataset for the nodes and cells
+ node_dataset = H5Dcreate(h5_file_id, "nodes", H5T_NATIVE_DOUBLE, node_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ AssertThrow(node_dataset >= 0, ExcIO());
+ cell_dataset = H5Dcreate(h5_file_id, "cells", H5T_NATIVE_UINT, cell_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ AssertThrow(cell_dataset >= 0, ExcIO());
+
+ // Close the node and cell dataspaces since we're done with them
+ status = H5Sclose(node_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Create the data subset we'll use to read from memory
+ count[0] = local_node_cell_count[0];
+ count[1] = dim;
+ offset[0] = global_node_cell_offsets[0];
+ offset[1] = 0;
+ node_memory_dataspace = H5Screate_simple(2, count, NULL);
+ AssertThrow(node_memory_dataspace >= 0, ExcIO());
+
+ // Select the hyperslab in the file
+ node_file_dataspace = H5Dget_space(node_dataset);
+ AssertThrow(node_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(node_file_dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
+ AssertThrow(status >= 0, ExcIO());
+
+ // And repeat for cells
+ count[0] = local_node_cell_count[1];
+ count[1] = GeometryInfo<dim>::vertices_per_cell;
+ offset[0] = global_node_cell_offsets[1];
+ offset[1] = 0;
+ cell_memory_dataspace = H5Screate_simple(2, count, NULL);
+ AssertThrow(cell_memory_dataspace >= 0, ExcIO());
+
+ cell_file_dataspace = H5Dget_space(cell_dataset);
+ AssertThrow(cell_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(cell_file_dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Create the property list for a collective write
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ AssertThrow(plist_id >= 0, ExcIO());
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+#ifdef H5_HAVE_PARALLEL
+ status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ AssertThrow(status >= 0, ExcIO());
+#endif
+#endif
+
+ // And finally, write the node data
+ status = H5Dwrite(node_dataset, H5T_NATIVE_DOUBLE, node_memory_dataspace, node_file_dataspace, plist_id, hdf5_data.node_data());
+ AssertThrow(status >= 0, ExcIO());
+
+ // And the cell data
+ status = H5Dwrite(cell_dataset, H5T_NATIVE_UINT, cell_memory_dataspace, cell_file_dataspace, plist_id, hdf5_data.cell_data());
+ AssertThrow(status >= 0, ExcIO());
+
+ reorder_task.join ();
+
+ // when writing, first write out
+ // all vector data, then handle the
+ // scalar data sets that have been
+ // left over
+ unsigned int i, n, q, r, n_th_vector, data_set, pt_data_vector_dim, mem_vector_dim;
+ double *pt_data;
+ std::string vector_name;
+ for (n_th_vector=0,data_set=0;data_set<n_data_sets;) {
+ // Advance n_th_vector to at least the current data set we are on
+ while (n_th_vector < vector_data_ranges.size() && std_cxx1x::get<0>(vector_data_ranges[n_th_vector]) < data_set) n_th_vector++;
+
+ // Determine the dimension of this data
+ if (std_cxx1x::get<0>(vector_data_ranges[n_th_vector]) == data_set) {
+ // Multiple dimensions
+ pt_data_vector_dim = std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) - std_cxx1x::get<0>(vector_data_ranges[n_th_vector])+1;
+
+ // Ensure the dimensionality of the data is correct
+ AssertThrow (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) >= std_cxx1x::get<0>(vector_data_ranges[n_th_vector]),
+ ExcLowerRange (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]), std_cxx1x::get<0>(vector_data_ranges[n_th_vector])));
+ AssertThrow (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]) < n_data_sets,
+ ExcIndexRange (std_cxx1x::get<1>(vector_data_ranges[n_th_vector]), 0, n_data_sets));
+
+ // Determine the vector name
+ // Concatenate all the
+ // component names with double
+ // underscores unless a vector
+ // name has been specified
+ if (std_cxx1x::get<2>(vector_data_ranges[n_th_vector]) != "") {
+ vector_name = std_cxx1x::get<2>(vector_data_ranges[n_th_vector]);
+ } else {
+ vector_name = "";
+ for (i=std_cxx1x::get<0>(vector_data_ranges[n_th_vector]);i<std_cxx1x::get<1>(vector_data_ranges[n_th_vector]);++i)
+ vector_name += data_names[i] + "__";
+ vector_name += data_names[std_cxx1x::get<1>(vector_data_ranges[n_th_vector])];
+ }
+ } else {
+ // One dimension
+ pt_data_vector_dim = 1;
+ vector_name = data_names[data_set];
+ }
+
+ // Allocate space for the point data
+ // Must be either 1D or 3D
+ mem_vector_dim = (pt_data_vector_dim>1?3:1);
+ pt_data = new double[local_node_cell_count[0]*mem_vector_dim];
+
+ // Create the dataspace for the point data
+ node_ds_dim[0] = global_node_cell_count[0];
+ node_ds_dim[1] = mem_vector_dim;
+ pt_data_dataspace = H5Screate_simple(2, node_ds_dim, NULL);
+ AssertThrow(pt_data_dataspace >= 0, ExcIO());
+
+ pt_data_dataset = H5Dcreate(h5_file_id, vector_name.c_str(), H5T_NATIVE_DOUBLE, pt_data_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ AssertThrow(pt_data_dataset >= 0, ExcIO());
+
+ // Create the data subset we'll use to read from memory
+ count[0] = local_node_cell_count[0];
+ count[1] = mem_vector_dim;
+ offset[0] = global_node_cell_offsets[0];
+ offset[1] = 0;
+ pt_data_memory_dataspace = H5Screate_simple(2, count, NULL);
+ AssertThrow(pt_data_memory_dataspace >= 0, ExcIO());
+
+ // Select the hyperslab in the file
+ pt_data_file_dataspace = H5Dget_space(pt_data_dataset);
+ AssertThrow(pt_data_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(pt_data_file_dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Write point data to the memory array
+ r = 0;
+ for (i=0;i<local_node_cell_count[0];++i) {
+ // Get the offset to the vector
+ q = data_set;
+ // Write the data vector
+ for (n=0;n<pt_data_vector_dim;++n) pt_data[r++] = data_vectors(q+n, i);
+ // Write 0 for the remainder of entries in 2D
+ for (;n<mem_vector_dim;++n) pt_data[r++] = 0;
+ }
+
+ // And finally, write the data
+ status = H5Dwrite(pt_data_dataset, H5T_NATIVE_DOUBLE, pt_data_memory_dataspace, pt_data_file_dataspace, plist_id, pt_data);
+ AssertThrow(status >= 0, ExcIO());
+
+ delete pt_data;
+
+ // Close the dataspaces
+ status = H5Sclose(pt_data_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(pt_data_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(pt_data_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ // Close the dataset
+ status = H5Dclose(pt_data_dataset);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Advance the current data set
+ data_set += pt_data_vector_dim;
+ }
+
+ // Close the file dataspaces
+ status = H5Sclose(node_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the memory dataspaces
+ status = H5Sclose(node_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the datasets
+ status = H5Dclose(node_dataset);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Dclose(cell_dataset);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the parallel access
+ status = H5Pclose(plist_id);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the file
+ status = H5Fclose(h5_file_id);
+ AssertThrow(status >= 0, ExcIO());
+#endif
+}
+
+
template <int dim, int spacedim>
void
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