--- trunk/OOPSE-3.0/configure	2004/09/29 17:57:47	1509
+++ trunk/OOPSE-3.0/configure	2005/04/14 21:41:56	2199
@@ -312,7 +312,7 @@ ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKA
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROGNAME debug build build_cpu build_vendor build_os host host_cpu host_vendor host_os CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX OOPSE_TEMPLATE_FLAGS EXTRA_CC_FLAG F90 F90FLAGS ac_ct_F90 PREPFLAG PREPDEFFLAG F90LIBS F90_FUNC F90_FUNC_ MOD F90_WORK_FILES_ARG MODDIRFLAG F90MODINCSPEC CPP EGREP LIBOBJS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA LN_S SET_MAKE RANLIB ac_ct_RANLIB YACC LEX LEXLIB LEX_OUTPUT_ROOT AR MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI SPRNG_LIB_DIR SPRNG_INC_DIR SPRNG_LIB USE_SPRNG MKL_LIBDIR MKL_LIB MKL_INC HAVE_MKL BATEXT MKINSTALLDIRS OOPSE OOPSE_HOME SUBDIRS FFLAGS LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROGNAME debug build build_cpu build_vendor build_os host host_cpu host_vendor host_os CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX OOPSE_TEMPLATE_FLAGS EXTRA_CC_FLAG F90 F90FLAGS ac_ct_F90 PREPFLAG PREPDEFFLAG F90LIBS F90_FUNC F90_FUNC_ MOD F90_WORK_FILES_ARG MODDIRFLAG F90MODINCSPEC F90_MODULE_NAMES CPP EGREP LIBOBJS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA LN_S SET_MAKE RANLIB ac_ct_RANLIB YACC LEX LEXLIB LEX_OUTPUT_ROOT PERLINTERP PERL_SHEBANG AR PS MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI CXXCPP USE_CGAL CGAL_INC_DIR CGAL_LIB_DIR CGAL_RLIB_DIR CGAL_DEFINES CGAL_CXXFLAGS CGAL_LIBS DOXYGEN DOT DOC enable_dot enable_html_docs enable_latex_docs BATEXT MKINSTALLDIRS OOPSE OOPSE_HOME SUBDIRS FFLAGS LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
@@ -789,6 +789,10 @@ ac_cv_env_CPP_value=$CPP
 ac_env_CPP_value=$CPP
 ac_cv_env_CPP_set=${CPP+set}
 ac_cv_env_CPP_value=$CPP
+ac_env_CXXCPP_set=${CXXCPP+set}
+ac_env_CXXCPP_value=$CXXCPP
+ac_cv_env_CXXCPP_set=${CXXCPP+set}
+ac_cv_env_CXXCPP_value=$CXXCPP
 
 #
 # Report the --help message.
@@ -866,15 +870,19 @@ Optional Features:
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
   --enable-debug          Compile OOPSE in debug mode
+  --enable-doxygen        enable documentation generation with doxygen (auto)
+  --enable-dot            use 'dot' to generate graphs in doxygen (auto)
+  --enable-html-docs      enable HTML generation with doxygen (yes)
+  --enable-latex-docs     enable LaTeX documentation generation with doxygen (no)
   --enable-oopse-home=DIR      define oopse home dir PREFIX/oopse
 
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
+  --with-perl-shebang     override what perl thinks is the way for the kernel
+                          to start it (seldom needed)
   --with-mpi=<prefix>     compile with MPI installed in <prefix> [default=no]
-  --with-sprng=<prefix>   compile with SPRNG installed in <prefix>
-                          [default=/usr/local]
-  --with-mkl              Do we want MKL will check /usr/local/intel/mkl61 /opt/intel/mkl61
+  --with-cgal-makefile=FILE  CGAL makefile that should be used
 
 Some influential environment variables:
   CC          C compiler command
@@ -888,6 +896,7 @@ Some influential environment variables:
   F90         Fortran 90 compiler command
   F90FLAGS    Fortran 90 compiler flags
   CPP         C preprocessor
+  CXXCPP      C++ preprocessor
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -1814,6 +1823,12 @@ ac_configure="$SHELL $ac_aux_dir/configure" # This sho
 # argument is not supplied, it defaults to NAME.
 # AC_F95_FUNC
 
+# AC_F90_MODULE_NAMES
+# -------------------
+#
+# Figure out how the Fortran 90 compiler constructs module file names
+#
+ # AC_F90_MODULE_NAMES
 
 
 
@@ -1867,7 +1882,15 @@ ac_configure="$SHELL $ac_aux_dir/configure" # This sho
 
 
 
+#
+#
+#
 
+
+
+
+
+
 # set program name
 PROGNAME="oopse"
 
@@ -3527,7 +3550,7 @@ F90FLAGS="$F90FLAGS $ac_verb"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_verb"
 
-(eval echo $as_me:3530: \"$ac_link\") >&5
+(eval echo $as_me:3553: \"$ac_link\") >&5
 ac_f90_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f90_v_output" >&5
 F90FLAGS=$ac_save_F90FLAGS
@@ -3604,7 +3627,7 @@ F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 
-(eval echo $as_me:3607: \"$ac_link\") >&5
+(eval echo $as_me:3630: \"$ac_link\") >&5
 ac_f90_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f90_v_output" >&5
 F90FLAGS=$ac_save_F90FLAGS
@@ -4202,6 +4225,233 @@ ac_ext=c
 fi
 
 
+echo "$as_me:$LINENO: checking for Fortran 90 module file names" >&5
+echo $ECHO_N "checking for Fortran 90 module file names... $ECHO_C" >&6
+if test "${ac_cv_f90_module_names+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_ext=f90
+ac_compile='$F90 -c $F90FLAGS conftest.$ac_ext >&5'
+ac_link='$F90 -o conftest$ac_exeext $F90FLAGS $LD90FLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f90_compiler_gnu
+
+# carry out the test in a new directory, so that we don't miss anything
+mkdir conftest
+cd conftest
+cat >conftest.$ac_ext <<_ACEOF
+MODULE Bar
+END MODULE Bar
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_f90_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest.$ac_objext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_f90_module_names=
+ac_file_list=*
+for ac_file in $ac_file_list; do
+   case $ac_file in
+      # don't care for original source and object files
+      conftest.$ac_ext | conftest.$ac_objext | conftest.err )
+          :
+          ;;
+      # look for new files derived from the file name
+      *conftest*)
+          ac_pat=`echo $ac_file | sed s/conftest/%FILE%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      # look for new files derived from the module name,
+      # with different case translation schemes
+      *Bar*)
+          ac_pat=`echo $ac_file | sed s/Bar/%Module%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      *bar*)
+          ac_pat=`echo $ac_file | sed s/bar/%module%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      *BAR*)
+          ac_pat=`echo $ac_file | sed s/BAR/%MODULE%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+       # Other files - we have no idea how they are generated
+       *)
+          { echo "$as_me:$LINENO: WARNING: Bogus file found: $ac_file" >&5
+echo "$as_me: WARNING: Bogus file found: $ac_file" >&2;}
+          ;;
+   esac
+done
+if test "x$ac_cv_f90_module_names" = "x"; then
+  { echo "$as_me:$LINENO: WARNING: Couldn't determine module file names" >&5
+echo "$as_me: WARNING: Couldn't determine module file names" >&2;}
+fi
+
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_f90_module_names=
+{ echo "$as_me:$LINENO: WARNING: Couldn't determine module file names" >&5
+echo "$as_me: WARNING: Couldn't determine module file names" >&2;}
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+cd ..
+# cleanup
+rm -rf conftest
+ac_ext=f90
+ac_compile='$F90 -c $F90FLAGS conftest.$ac_ext >&5'
+ac_link='$F90 -o conftest$ac_exeext $F90FLAGS $LD90FLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f90_compiler_gnu
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_f90_module_names" >&5
+echo "${ECHO_T}$ac_cv_f90_module_names" >&6 # AC_CACHE_CHECK
+
+# We now generate a shell script that will help us to figure out the correct
+# module file names, using the value of ac_cv_f90_module_names
+
+echo "Generating shell script modnam"
+
+cat > scripts/modnam << EOF
+#! /bin/sh
+# This script is auto-generated by configure
+#
+usage="\\
+Usage: \$0 [FILES]
+
+[FILES] are Fortran 90 source files.
+The output is a list of module file names that the Fortran 90 compiler
+generates when compiling [FILES]."
+
+list=
+empty=
+
+if test \$# -eq 0; then
+   echo "\$usage"; exit 0
+fi
+
+while test \$# != 0; do
+
+  file=\$1
+  shift
+
+# strip suffix
+  base=\`echo \$file | sed 's/[.][^.]*$//'\`
+
+  test ! -f \$file && continue
+
+# Look for module definitions and transform them to upper / lower case
+  mods=\`cat \$file | sed '/^ *[mM][oO][dD][uU][lL][eE]/!d;s/^ *[mM][oO][dD][uU][lL][eE] *\([A-Za-z_][A-Za-z0-9_]*\).*\$/\1/'\`
+  upper=\`echo \$mods | tr a-z A-Z\`
+  lower=\`echo \$mods | tr A-Z a-z\`
+
+# Here, the patterns for generating module file names were inserted by configure
+  for trans in $ac_cv_f90_module_names; do
+
+    pat=\`echo \$trans | sed 's/.*\(%.*%\).*/\1/'\`
+    var=empty
+    case \$pat in
+       %MODULE%)
+          var=upper ;;
+       %Module%)
+          var=mods ;;
+       %module%)
+          var=lower ;;
+       %FILE%)
+          test -n "\$mods" && var=base ;;
+    esac
+    new=\`eval '(for i in \$'\$var '; do echo \$trans | sed s/\$pat/\$i/; done)'\`
+    list="\$list \$new"
+  done
+done
+
+echo \$list
+# end of configure-generated script
+EOF
+chmod 755 scripts/modnam
+
+pat=`echo $ac_cv_f90_module_names | sed 's/.*\(%.*%\).*/\1/'`
+F90_MODULE_NAMES=empty
+case $pat in
+       %MODULE%)
+          F90_MODULE_NAMES=UPPER ;;
+       %Module%)
+          F90_MODULE_NAMES=Mixed ;;
+       %module%)
+          F90_MODULE_NAMES=lower ;;
+       *)
+          F90_MODULE_NAMES=unknown ;;
+esac
+
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -4703,8 +4953,329 @@ done
 done
 
 
+
+
+
+
+
+
+
+
+
+for ac_header in unistd.h sys/pstat.h sys/sysmp.h sys/sysinfo.h sys/table.h sys/param.h sys/sysctl.h sys/sytemcfg.h machine/hal_sysinfo.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+  echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6
+else
+  # Is the header compilable?
+echo "$as_me:$LINENO: checking $ac_header usability" >&5
+echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_c_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest.$ac_objext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_header_compiler=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6
+
+# Is the header present?
+echo "$as_me:$LINENO: checking $ac_header presence" >&5
+echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <$ac_header>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_c_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+rm -f conftest.err conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: $ac_header:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+    (
+      cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to gezelter@nd.edu ##
+## ------------------------------ ##
+_ASBOX
+    ) |
+      sed "s/^/$as_me: WARNING:     /" >&2
+    ;;
+esac
+echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  eval "$as_ac_Header=\$ac_header_preproc"
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6
+
+fi
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+
+
+
+
+for ac_func in pstat_getstatic sysmp getsysinfo sysctl table
+do
+as_ac_var=`echo "ac_cv_func_$ac_func" | $as_tr_sh`
+echo "$as_me:$LINENO: checking for $ac_func" >&5
+echo $ECHO_N "checking for $ac_func... $ECHO_C" >&6
+if eval "test \"\${$as_ac_var+set}\" = set"; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char $ac_func (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any gcc2 internal prototype to avoid an error.  */
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+/* We use char because int might match the return type of a gcc2
+   builtin and then its argument prototype would still apply.  */
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined (__stub_$ac_func) || defined (__stub___$ac_func)
+choke me
+#else
+char (*f) () = $ac_func;
+#endif
+#ifdef __cplusplus
+}
+#endif
+
+int
+main ()
+{
+return f != $ac_func;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_c_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest$ac_exeext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  eval "$as_ac_var=yes"
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+eval "$as_ac_var=no"
+fi
+rm -f conftest.err conftest.$ac_objext \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_var'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_var'}'`" >&6
+if test `eval echo '${'$as_ac_var'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+# special check for _system_configuration because AIX <4.3.2 do not
+# contain the `physmem' member.
+echo "$as_me:$LINENO: checking for external symbol _system_configuration" >&5
+echo $ECHO_N "checking for external symbol _system_configuration... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/systemcfg.h>
+int
+main ()
+{
+double x = _system_configuration.physmem;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_c_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest.$ac_objext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE__SYSTEM_CONFIGURATION 1
+_ACEOF
+
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+
   # clean out junk possibly left behind by a previous configuration
-  rm -f utils/getopt.h
+  rm -f src/getopt.h
   # Check for getopt_long support
 
 for ac_header in getopt.h
@@ -5044,7 +5615,7 @@ esac
   *) LIBOBJS="$LIBOBJS getopt1.$ac_objext" ;;
 esac
 
-                ac_config_links="$ac_config_links utils/getopt.h:utils/gnugetopt.h"
+                ac_config_links="$ac_config_links src/getopt.h:src/utils/gnugetopt.h"
 
 fi
 
@@ -5138,7 +5709,7 @@ if test "$ac_test_CFLAGS" != "set"; then
         fi;;
    *darwin*)
 	if test "$CC" = xlc -o "$CC" = cc; then
-        	CFLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
+        	CFLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
         fi;;
   esac
 
@@ -5589,8 +6160,8 @@ if test "$ac_test_CXXFLAGS" != "set"; then
 		echo "*******************************************************"
         fi;;
    *darwin*)
-	if test "$CXX" = xlc++; then
-        	CXXFLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
+	if test "$CXX" = xlc++ -o "$CXX" = xlC ; then
+        	CXXFLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
         fi;;
   esac
 
@@ -6002,7 +6573,7 @@ if test x"$F90FLAGS" = x ; then
         fi;;
    *darwin*)
 	if test "$F90" = f90 -o "$F90" = xlf90 -o "$F90" = xlf95; then
-        	F90FLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto"
+        	F90FLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto"
         fi;;
   esac
 
@@ -6595,6 +7166,125 @@ fi
 fi
 
 fi
+
+   # Extract the first word of "perl", so it can be a program name with args.
+set dummy perl; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_PERLINTERP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $PERLINTERP in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_PERLINTERP="$PERLINTERP" # 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_PERLINTERP="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+
+  test -z "$ac_cv_path_PERLINTERP" && ac_cv_path_PERLINTERP="perl"
+  ;;
+esac
+fi
+PERLINTERP=$ac_cv_path_PERLINTERP
+
+if test -n "$PERLINTERP"; then
+  echo "$as_me:$LINENO: result: $PERLINTERP" >&5
+echo "${ECHO_T}$PERLINTERP" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+   ac_cv_path_perlinterp="$PERLINTERP"
+   _sHpB='#!'
+
+
+# Check whether --with-perl-shebang or --without-perl-shebang was given.
+if test "${with_perl_shebang+set}" = set; then
+  withval="$with_perl_shebang"
+  opt_perl_shebang="$withval"
+else
+  		opt_perl_shebang="not_set"
+fi;
+   echo "$as_me:$LINENO: checking whether explicit instead of detected sharpbang is to be used" >&5
+echo $ECHO_N "checking whether explicit instead of detected sharpbang is to be used... $ECHO_C" >&6
+if test "${ax_cv_opt_perl_shebang+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+   case "$opt_perl_shebang" in
+		      not_set  ) ax_cv_opt_perl_shebang=''
+		               ;;
+		         *     )
+	ax_cv_opt_perl_shebang=`echo "$opt_perl_shebang" | sed -e's|^#!\s*\(.*\)$|\1|'`
+		    esac
+
+fi
+echo "$as_me:$LINENO: result: $ax_cv_opt_perl_shebang" >&5
+echo "${ECHO_T}$ax_cv_opt_perl_shebang" >&6
+   if test "A$ax_cv_opt_perl_shebang" != "A"
+     then
+       ac_cv_sys_kernshrpbang_perl="$ax_cv_opt_perl_shebang"
+       PERL_SHEBANG="$ac_cv_sys_kernshrpbang_perl"
+              { echo "$as_me:$LINENO: OK - PERL_SHEBANG is $_sHpB$PERL_SHEBANG." >&5
+echo "$as_me: OK - PERL_SHEBANG is $_sHpB$PERL_SHEBANG." >&6;}
+
+# Automatic detection of sharpbang formula starts here
+     else
+   _somian_shbangperl=`$PERLINTERP -V:startperl`
+   negclass="[^']"; # must leave this comment:  m4 will remove the outer brackets for us, heheh
+   echo "$as_me:$LINENO: checking for kernel sharpbang invocation to start perl" >&5
+echo $ECHO_N "checking for kernel sharpbang invocation to start perl... $ECHO_C" >&6
+if test "${ac_cv_sys_kernshrpbang_perl+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  _somian_kspb_perl=`echo "$_somian_shbangperl" | sed -ne"s|.*='\($negclass*\)';$|\1|p"`
+	if test "x$_somian_kspb_perl" == x
+	  then _somian_ksbp_warn_empty='durnit'
+	  else
+	  case "A$_somian_kspb_perl" in
+	         A#!*perl* )
+           ac_cv_sys_kernshrpbang_perl=`echo "$_somian_kspb_perl" | sed -e's|#!\(.*\)$|\1|'`
+			;;
+	             A*    )  _somian_ksbp_warn_defau='trouble'
+		              ac_cv_sys_kernshrpbang_perl="$PERLINTERP"
+	  esac
+	fi
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_sys_kernshrpbang_perl" >&5
+echo "${ECHO_T}$ac_cv_sys_kernshrpbang_perl" >&6
+# The above prints Checking ... result message to user.
+   PERL_SHEBANG="$ac_cv_sys_kernshrpbang_perl"
+
+    if test A${_somian_ksbp_warn_empty+set} == Aset
+      then   { echo "$as_me:$LINENO: WARNING: In last check, doing $PERLINTERP -V:startperl yielded empty result! That should not happen." >&5
+echo "$as_me: WARNING: In last check, doing $PERLINTERP -V:startperl yielded empty result! That should not happen." >&2;}
+    fi
+# Inform user after printing result value
+    if test A${_somian_ksbp_warn_defau+set} == Aset
+      then { echo "$as_me:$LINENO: Maybe Not good -" >&5
+echo "$as_me: Maybe Not good -" >&6;}
+	   { echo "$as_me:$LINENO: WARNING: In last check perl's Config query did not work so we bunted: $_sHpB$PERLINTERP" >&5
+echo "$as_me: WARNING: In last check perl's Config query did not work so we bunted: $_sHpB$PERLINTERP" >&2;}
+      else { echo "$as_me:$LINENO: OK Good result - " >&5
+echo "$as_me: OK Good result - " >&6;}
+	   { echo "$as_me:$LINENO: In last check we got a proper-looking answer from perl's Config: $_somian_shbangperl" >&5
+echo "$as_me: In last check we got a proper-looking answer from perl's Config: $_somian_shbangperl" >&6;}
+    fi
+  fi
+
 # Extract the first word of "ar", so it can be a program name with args.
 set dummy ar; ac_word=$2
 echo "$as_me:$LINENO: checking for $ac_word" >&5
@@ -6692,8 +7382,102 @@ fi
   exit 1
 fi
 
+# Extract the first word of "ps", so it can be a program name with args.
+set dummy ps; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_PS+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $PS in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_PS="$PS" # 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_PS="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
 
+  ;;
+esac
+fi
+PS=$ac_cv_path_PS
 
+if test -n "$PS"; then
+  echo "$as_me:$LINENO: result: $PS" >&5
+echo "${ECHO_T}$PS" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+echo "$as_me:$LINENO: checking for POSIX or BSD ps syntax" >&5
+echo $ECHO_N "checking for POSIX or BSD ps syntax... $ECHO_C" >&6
+if test "${ac_cv_prog_ps_syntax+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+	if $PS ax -o rss > /dev/null 2>&1; then
+		ac_cv_prog_ps_ax=yes
+	else
+		ac_cv_prog_ps_ax=no
+	fi
+	if $PS -ef -o rss > /dev/null 2>&1; then
+		ac_cv_prog_ps_ef=yes
+	else
+		ac_cv_prog_ps_ef=no
+	fi
+	if test "$ac_cv_prog_ps_ax" = yes; then
+		ac_cv_prog_ps_syntax=BSD
+        else
+		if test "$ac_cv_prog_ps_ef" = yes; then
+			ac_cv_prog_ps_syntax=POSIX
+		else
+			{ { echo "$as_me:$LINENO: error: Could not determine ps syntax" >&5
+echo "$as_me: error: Could not determine ps syntax" >&2;}
+   { (exit 1); exit 1; }; }
+		fi
+	fi
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_prog_ps_syntax" >&5
+echo "${ECHO_T}$ac_cv_prog_ps_syntax" >&6
+
+
+cat >>confdefs.h <<_ACEOF
+#define PSCOMMAND $PS
+_ACEOF
+
+
+if test "$ac_cv_prog_ps_syntax" = BSD; then
+  cat >>confdefs.h <<\_ACEOF
+#define PSTYPE_IS_BSD 1
+_ACEOF
+
+else
+   if test "$ac_cv_prog_ps_syntax" = POSIX; then
+       cat >>confdefs.h <<\_ACEOF
+#define PSTYPE_IS_POSIX 1
+_ACEOF
+
+   else
+       { { echo "$as_me:$LINENO: error: Unknown ps syntax type!" >&5
+echo "$as_me: error: Unknown ps syntax type!" >&2;}
+   { (exit 1); exit 1; }; }
+   fi
+fi
+
+
 # Check whether --with-mpi or --without-mpi was given.
 if test "${with_mpi+set}" = set; then
   withval="$with_mpi"
@@ -6993,7 +7777,78 @@ fi
 fi
 
 fi
+$as_unset ac_cv_lib_mpich_MPI_Init
+if test x = x"$MPI_LIB"; then
+        echo "$as_me:$LINENO: checking for MPI_Init in -lmpich" >&5
+echo $ECHO_N "checking for MPI_Init in -lmpich... $ECHO_C" >&6
+if test "${ac_cv_lib_mpich_MPI_Init+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lmpich "-lpmpich" $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
 
+/* Override any gcc2 internal prototype to avoid an error.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+/* We use char because int might match the return type of a gcc2
+   builtin and then its argument prototype would still apply.  */
+char MPI_Init ();
+int
+main ()
+{
+MPI_Init ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_c_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest$ac_exeext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_lib_mpich_MPI_Init=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_lib_mpich_MPI_Init=no
+fi
+rm -f conftest.err conftest.$ac_objext \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+echo "$as_me:$LINENO: result: $ac_cv_lib_mpich_MPI_Init" >&5
+echo "${ECHO_T}$ac_cv_lib_mpich_MPI_Init" >&6
+if test $ac_cv_lib_mpich_MPI_Init = yes; then
+  MPI_LIB="-lmpich -lpmpich"
+fi
+
+fi
+
 $as_unset ac_cv_lib_mpi_MPI_Init
 if test x = x"$MPI_LIB"; then
 echo "$as_me:$LINENO: checking for MPI_Init in -lmpi" >&5
@@ -7093,196 +7948,346 @@ fi
 
 
 
-# Check whether --with-sprng or --without-sprng was given.
-if test "${with_sprng+set}" = set; then
-  withval="$with_sprng"
-  with_sprng=$withval
-else
-  with_sprng="/usr/local"
-fi;
 
-case "x$with_sprng" in
-        xyes | "x")  USE_SPRNG=yes;;
-        xno) USE_SPRNG=no ;;
-        *) SPRNG="$with_sprng"; USE_SPRNG=yes ;;
-esac
-if test "$USE_SPRNG" = "yes" -a -z "$with_sprng"; then
-        SPRNG="/usr/local"
-fi
-if test "$USE_SPRNG" = "yes"; then
+USE_CGAL=no
+cgal_makefile=auto
 
+# Check whether --with-cgal-makefile or --without-cgal-makefile was given.
+if test "${with_cgal_makefile+set}" = set; then
+  withval="$with_cgal_makefile"
+  cgal_makefile="$withval"
+fi;
 
-# Set variables...
-SPRNG_LIB_DIR="$SPRNG/lib"
-SPRNG_INC_DIR="$SPRNG/include"
+if test "x$cgal_makefile" != xno; then
 
+  if test "x$cgal_makefile" = xauto -a "x$CGAL_MAKEFILE" != x; then
+    cgal_makefile="$CGAL_MAKEFILE"
+  fi
 
+  echo "cgal_makefile      $cgal_makefile"
 
-echo "$as_me:$LINENO: checking for sprng.h" >&5
-echo $ECHO_N "checking for sprng.h... $ECHO_C" >&6
-have_sprng_h=0
-echo '#include <sprng.h>' > conftest.cc
-if test -z "`${CXX} -I${SPRNG_INC_DIR} -c conftest.cc 2>&1`"; then
-        echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
-        have_sprng_h=1
-else
-        echo "$as_me:$LINENO: result: no! Check SPRNG include path!" >&5
-echo "${ECHO_T}no! Check SPRNG include path!" >&6
-        USE_SPRNG="no"
-fi
-rm -f conftest*
-if test "$have_sprng_h" = 1; then
+  if test -f "$cgal_makefile"; then
 
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SPRNG_H 1
-_ACEOF
+    cat >config.tmp.Makefile <<EOF
+include $cgal_makefile
+default:
+	@echo CGAL_OS_COMPILER=\"\${CGAL_OS_COMPILER}\" >config.tmp.cgalvariables
+	@echo CGAL_INCLDIR=\"\${CGAL_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo CGAL_INCLCONFDIR=\"\${CGAL_INCL_CONF_DIR}\" >>config.tmp.cgalvariables
+	@echo CGAL_LIBDIR=\"\${CGAL_LIB_DIR}/\${CGAL_OS_COMPILER}\" >>config.tmp.cgalvariables
+	@echo CGAL_RLIBDIR=\"\${CGAL_LIB_DIR}/\${CGAL_OS_COMPILER}\" >>config.tmp.cgalvariables
+	@echo CGAL_CXXFLAGS=\"\${CGAL_CXXFLAGS}\" >>config.tmp.cgalvariables
+	@echo GMP_INCLDIR=\"\${GMP_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo GMP_LIBDIR=\"\${GMP_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo GMP_RLIBDIR=\"\${GMP_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_INCLDIR=\"\${LEDA_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_LIBDIR=\"\${LEDA_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_RLIBDIR=\"\${LEDA_LIB_DIR}\" >>config.tmp.cgalvariables
+EOF
 
-fi
+    make -s -f config.tmp.Makefile
+    . config.tmp.cgalvariables
 
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+    rm -f config.tmp.Makefile config.tmp.cgalvariables
 
-ac_save_LDFLAGS=$LDFLAGS
-LDFLAGS="${LDFLAGS} -L${SPRNG_LIB_DIR} "
+    if test "x$CGAL_INCLDIR" = "x"; then
+      CGAL_INCLDIR=""
+    fi
 
-echo "$as_me:$LINENO: checking for init_rng in -lsprng" >&5
-echo $ECHO_N "checking for init_rng in -lsprng... $ECHO_C" >&6
-if test "${ac_cv_lib_sprng_init_rng+set}" = set; then
+    if test "x$CGAL_LIBDIR" = "x"; then
+      CGAL_LIBDIR=""
+    fi
+
+    if test "x$CGAL_RLIBDIR" = "x"; then
+      CGAL_RLIBDIR=""
+    fi
+
+    if test "x$LEDA_INCLDIR" = "x"; then
+      LEDA_INCLDIR=""
+    fi
+
+    if test "x$LEDA_LIBDIR" = "x"; then
+      LEDA_LIBDIR=""
+    fi
+
+    if test "x$LEDA_RLIBDIR" = "x"; then
+      LEDA_RLIBDIR=""
+    fi
+
+    if test "x$GMP_INCLDIR" = "x"; then
+      GMP_INCLDIR=""
+    fi
+
+    if test "x$GMP_LIBDIR" = "x"; then
+      GMP_LIBDIR=""
+    fi
+
+    if test "x$GMP_RLIBDIR" = "x"; then
+      GMP_RLIBDIR=""
+    fi
+
+    echo "CGAL_OS_COMPILER   $CGAL_OS_COMPILER"
+    echo "CGAL_INCLDIR       $CGAL_INCLDIR"
+    echo "CGAL_INCLCONFDIR   $CGAL_INCLCONFDIR"
+    echo "CGAL_LIBDIR        $CGAL_LIBDIR"
+    echo "CGAL_CXXFLAGS      $CGAL_CXXFLAGS"
+    echo "LEDA_INCLDIR       $LEDA_INCLDIR"
+    echo "LEDA_LIBDIR        $LEDA_LIBDIR"
+    echo "GMP_INCLDIR        $GMP_INCLDIR"
+    echo "GMP_LIBDIR         $GMP_LIBDIR"
+
+    ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+    save_CXXFLAGS="$CXXFLAGS"
+    CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6
+if test -z "$CXXCPP"; then
+  if test "${ac_cv_prog_CXXCPP+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
-  ac_check_lib_save_LIBS=$LIBS
-LIBS="-lsprng  $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
+      # Double quotes because CXXCPP needs to be expanded
+    for CXXCPP in "$CXX -E" "/lib/cpp"
+    do
+      ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
 /* confdefs.h.  */
 _ACEOF
 cat confdefs.h >>conftest.$ac_ext
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
-
-/* Override any gcc2 internal prototype to avoid an error.  */
-#ifdef __cplusplus
-extern "C"
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
 #endif
-/* We use char because int might match the return type of a gcc2
-   builtin and then its argument prototype would still apply.  */
-char init_rng ();
-int
-main ()
-{
-init_rng ();
-  ;
-  return 0;
-}
+		     Syntax error
 _ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
-  (eval $ac_link) 2>conftest.er1
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
   ac_status=$?
   grep -v '^ *+' conftest.er1 >conftest.err
   rm -f conftest.er1
   cat conftest.err >&5
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
-  (exit $ac_status); } &&
-	 { ac_try='test -z "$ac_c_werror_flag"
-			 || test ! -s conftest.err'
-  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
-  (eval $ac_try) 2>&5
-  ac_status=$?
-  echo "$as_me:$LINENO: \$? = $ac_status" >&5
-  (exit $ac_status); }; } &&
-	 { ac_try='test -s conftest$ac_exeext'
-  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
-  (eval $ac_try) 2>&5
-  ac_status=$?
-  echo "$as_me:$LINENO: \$? = $ac_status" >&5
-  (exit $ac_status); }; }; then
-  ac_cv_lib_sprng_init_rng=yes
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
 else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  :
+else
   echo "$as_me: failed program was:" >&5
 sed 's/^/| /' conftest.$ac_ext >&5
 
-ac_cv_lib_sprng_init_rng=no
+  # Broken: fails on valid input.
+continue
 fi
-rm -f conftest.err conftest.$ac_objext \
-      conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-echo "$as_me:$LINENO: result: $ac_cv_lib_sprng_init_rng" >&5
-echo "${ECHO_T}$ac_cv_lib_sprng_init_rng" >&6
-if test $ac_cv_lib_sprng_init_rng = yes; then
-  SPRNG_LIB="-lsprng"
-else
+rm -f conftest.err conftest.$ac_ext
 
-             { { echo "$as_me:$LINENO: error: Didn't find libsprng; check path for SPRNG package first..." >&5
-echo "$as_me: error: Didn't find libsprng; check path for SPRNG package first..." >&2;}
-   { (exit 1); exit 1; }; }
-             USE_SPRNG="no"
-
-fi
-
-
-if test "$USE_SPRNG" = "no"; then
-  { { echo "$as_me:$LINENO: error: No working SPRNG library found" >&5
-echo "$as_me: error: No working SPRNG library found" >&2;}
-   { (exit 1); exit 1; }; }
+  # OK, works on sane cases.  Now check whether non-existent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
 fi
+if test -z "$ac_cpp_err"; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.$ac_ext
 
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  break
 fi
 
+    done
+    ac_cv_prog_CXXCPP=$CXXCPP
 
+fi
+  CXXCPP=$ac_cv_prog_CXXCPP
+else
+  ac_cv_prog_CXXCPP=$CXXCPP
+fi
+echo "$as_me:$LINENO: result: $CXXCPP" >&5
+echo "${ECHO_T}$CXXCPP" >&6
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
-echo "$as_me:$LINENO: checking if MKL is wanted" >&5
-echo $ECHO_N "checking if MKL is wanted... $ECHO_C" >&6
+  # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.$ac_ext
 
-# Check whether --with-mkl or --without-mkl was given.
-if test "${with_mkl+set}" = set; then
-  withval="$with_mkl"
-     echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
-    for dir in $withval /usr/local/intel/mkl61 /opt/intel/mkl61; do
-        mkldir="$dir"
-        if test -f "$dir/include/mkl.h"; then
-            found_mkl="yes";
-            break;
-        fi
-    done
-    if test x_$found_mkl != x_yes; then
-        { { echo "$as_me:$LINENO: error: Cannot find MKL includes" >&5
-echo "$as_me: error: Cannot find MKL includes" >&2;}
-   { (exit 1); exit 1; }; }
-    else
-        printf "MKL includes found in $mkldir/include\n";
-    fi
+  # OK, works on sane cases.  Now check whether non-existent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.$ac_ext
 
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  :
+else
+  { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&5
+echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
 
-  ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
-  ac_save_CPPFLAGS=$CPPFLAGS
-  CPPFLAGS="${CPPFLAGS} -I${mkldir}/include"
-  ac_save_LDFLAGS=$LDFLAGS
-  LDFLAGS="${LDFLAGS} -L${mkldir}/lib/32 -lmkl -lvml -lguide"
-  if test "${ac_cv_header_mkl_h+set}" = set; then
-  echo "$as_me:$LINENO: checking for mkl.h" >&5
-echo $ECHO_N "checking for mkl.h... $ECHO_C" >&6
-if test "${ac_cv_header_mkl_h+set}" = set; then
+
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
+  echo "$as_me:$LINENO: checking for CGAL/Cartesian.h" >&5
+echo $ECHO_N "checking for CGAL/Cartesian.h... $ECHO_C" >&6
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 fi
-echo "$as_me:$LINENO: result: $ac_cv_header_mkl_h" >&5
-echo "${ECHO_T}$ac_cv_header_mkl_h" >&6
+echo "$as_me:$LINENO: result: $ac_cv_header_CGAL_Cartesian_h" >&5
+echo "${ECHO_T}$ac_cv_header_CGAL_Cartesian_h" >&6
 else
   # Is the header compilable?
-echo "$as_me:$LINENO: checking mkl.h usability" >&5
-echo $ECHO_N "checking mkl.h usability... $ECHO_C" >&6
+echo "$as_me:$LINENO: checking CGAL/Cartesian.h usability" >&5
+echo $ECHO_N "checking CGAL/Cartesian.h usability... $ECHO_C" >&6
 cat >conftest.$ac_ext <<_ACEOF
 /* confdefs.h.  */
 _ACEOF
@@ -7290,7 +8295,7 @@ $ac_includes_default
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 $ac_includes_default
-#include <mkl.h>
+#include <CGAL/Cartesian.h>
 _ACEOF
 rm -f conftest.$ac_objext
 if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
@@ -7301,7 +8306,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   cat conftest.err >&5
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
   (exit $ac_status); } &&
-	 { ac_try='test -z "$ac_c_werror_flag"
+	 { ac_try='test -z "$ac_cxx_werror_flag"
 			 || test ! -s conftest.err'
   { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
@@ -7326,15 +8331,15 @@ echo "$as_me:$LINENO: checking mkl.h presence" >&5
 echo "${ECHO_T}$ac_header_compiler" >&6
 
 # Is the header present?
-echo "$as_me:$LINENO: checking mkl.h presence" >&5
-echo $ECHO_N "checking mkl.h presence... $ECHO_C" >&6
+echo "$as_me:$LINENO: checking CGAL/Cartesian.h presence" >&5
+echo $ECHO_N "checking CGAL/Cartesian.h presence... $ECHO_C" >&6
 cat >conftest.$ac_ext <<_ACEOF
 /* confdefs.h.  */
 _ACEOF
 cat confdefs.h >>conftest.$ac_ext
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
-#include <mkl.h>
+#include <CGAL/Cartesian.h>
 _ACEOF
 if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
   (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
@@ -7345,8 +8350,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$a
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
   (exit $ac_status); } >/dev/null; then
   if test -s conftest.err; then
-    ac_cpp_err=$ac_c_preproc_warn_flag
-    ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
   else
     ac_cpp_err=
   fi
@@ -7366,27 +8371,27 @@ case $ac_header_compiler:$ac_header_preproc:$ac_c_prep
 echo "${ECHO_T}$ac_header_preproc" >&6
 
 # So?  What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
   yes:no: )
-    { echo "$as_me:$LINENO: WARNING: mkl.h: accepted by the compiler, rejected by the preprocessor!" >&5
-echo "$as_me: WARNING: mkl.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h: proceeding with the compiler's result" >&5
-echo "$as_me: WARNING: mkl.h: proceeding with the compiler's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: proceeding with the compiler's result" >&2;}
     ac_header_preproc=yes
     ;;
   no:yes:* )
-    { echo "$as_me:$LINENO: WARNING: mkl.h: present but cannot be compiled" >&5
-echo "$as_me: WARNING: mkl.h: present but cannot be compiled" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h:     check for missing prerequisite headers?" >&5
-echo "$as_me: WARNING: mkl.h:     check for missing prerequisite headers?" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h: see the Autoconf documentation" >&5
-echo "$as_me: WARNING: mkl.h: see the Autoconf documentation" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h:     section \"Present But Cannot Be Compiled\"" >&5
-echo "$as_me: WARNING: mkl.h:     section \"Present But Cannot Be Compiled\"" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h: proceeding with the preprocessor's result" >&5
-echo "$as_me: WARNING: mkl.h: proceeding with the preprocessor's result" >&2;}
-    { echo "$as_me:$LINENO: WARNING: mkl.h: in the future, the compiler will take precedence" >&5
-echo "$as_me: WARNING: mkl.h: in the future, the compiler will take precedence" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: present but cannot be compiled" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: in the future, the compiler will take precedence" >&2;}
     (
       cat <<\_ASBOX
 ## ------------------------------ ##
@@ -7397,44 +8402,113 @@ echo "$as_me:$LINENO: checking for mkl.h" >&5
       sed "s/^/$as_me: WARNING:     /" >&2
     ;;
 esac
-echo "$as_me:$LINENO: checking for mkl.h" >&5
-echo $ECHO_N "checking for mkl.h... $ECHO_C" >&6
-if test "${ac_cv_header_mkl_h+set}" = set; then
+echo "$as_me:$LINENO: checking for CGAL/Cartesian.h" >&5
+echo $ECHO_N "checking for CGAL/Cartesian.h... $ECHO_C" >&6
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
-  ac_cv_header_mkl_h=$ac_header_preproc
+  ac_cv_header_CGAL_Cartesian_h=$ac_header_preproc
 fi
-echo "$as_me:$LINENO: result: $ac_cv_header_mkl_h" >&5
-echo "${ECHO_T}$ac_cv_header_mkl_h" >&6
+echo "$as_me:$LINENO: result: $ac_cv_header_CGAL_Cartesian_h" >&5
+echo "${ECHO_T}$ac_cv_header_CGAL_Cartesian_h" >&6
 
 fi
-if test $ac_cv_header_mkl_h = yes; then
-
-    echo "$as_me:$LINENO: checking for vslNewStream in -lmkl" >&5
-echo $ECHO_N "checking for vslNewStream in -lmkl... $ECHO_C" >&6
-if test "${ac_cv_lib_mkl_vslNewStream+set}" = set; then
-  echo $ECHO_N "(cached) $ECHO_C" >&6
+if test $ac_cv_header_CGAL_Cartesian_h = yes; then
+  cgal=yes
 else
-  ac_check_lib_save_LIBS=$LIBS
-LIBS="-lmkl  $LIBS"
+  cgal=no
+fi
+
+
+    CXXFLAGS="$save_CXXFLAGS"
+
+    if test "x$cgal" = xyes; then
+      echo "$as_me:$LINENO: checking for CGAL version" >&5
+echo $ECHO_N "checking for CGAL version... $ECHO_C" >&6
+      LOCATION=${CGAL_INCLDIR}
+      LOCATION=${LOCATION:-/usr/include}
+      if test -f $LOCATION/CGAL/version.h; then
+        CGAL_VERSION=`grep '#define.*\<CGAL_VERSION\>.*' $LOCATION/CGAL/version.h | sed 's/[^0-9\.]*//g'`
+      else
+        CGAL_VERSION=`grep '#define.*\<CGAL_VERSION\>.*' $LOCATION/CGAL/config.h | sed 's/[^0-9\.]*//g'`
+      fi
+      if echo $CGAL_VERSION | grep -q "^[3456789]"; then
+        echo "$as_me:$LINENO: result: ($CGAL_VERSION) yes" >&5
+echo "${ECHO_T}($CGAL_VERSION) yes" >&6
+      else
+        echo "$as_me:$LINENO: result: ($CGAL_VERSION) no" >&5
+echo "${ECHO_T}($CGAL_VERSION) no" >&6
+        cgal=no
+      fi
+    fi
+
+    if test "x$cgal" = xyes; then
+      CGAL_LIBS="-lCGAL"
+      echo "$as_me:$LINENO: checking whether CGAL uses LEDA" >&5
+echo $ECHO_N "checking whether CGAL uses LEDA... $ECHO_C" >&6
+      if echo $CGAL_CXXFLAGS | grep -q -- -DCGAL_USE_LEDA; then
+        CGAL_USES_LEDA=yes
+        echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+        CGAL_DEFINES="-DCGAL_USE_LEDA -DLEDA_PREFIX"
+      else
+        echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+        CGAL_USES_LEDA=no
+      fi
+
+      echo "$as_me:$LINENO: checking whether CGAL uses GMP" >&5
+echo $ECHO_N "checking whether CGAL uses GMP... $ECHO_C" >&6
+      if echo $CGAL_CXXFLAGS | grep -q -- -DCGAL_USE_GMP; then
+        CGAL_USES_GMP=yes
+        echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+        CGAL_DEFINES="-DCGAL_USE_GMP $CGAL_DEFINES"
+      else
+        echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+        CGAL_USES_GMP=no
+      fi
+
+      CGAL_LIBS="$CGAL_LIBS -lm"
+
+      CGAL_CXXFLAGS="-ftemplate-depth-50"
+
+      echo "CGAL_USES_LEDA     $CGAL_USES_LEDA"
+      echo "CGAL_USES_GMP      $CGAL_USES_GMP"
+      echo "CGAL_INCLDIR       $CGAL_INCLDIR"
+      echo "CGAL_LIBDIR        $CGAL_LIBDIR"
+      echo "CGAL_DEFINES       $CGAL_DEFINES"
+      echo "CGAL_CXXFLAGS      $CGAL_CXXFLAGS"
+      echo "CGAL_LIBS          $CGAL_LIBS"
+    fi
+
+    if test "x$cgal" = xyes; then
+      save_LIBS="$LIBS"
+      LIBS="$LIBS -L$CGAL_LIBDIR"
+      if test "x$CGAL_USES_LEDA" = xyes; then
+        LIBS="-lL $LIBS -L$LEDA_LIBDIR"
+      fi
+      # if test "x$CGAL_USES_GMP" = xyes; then
+      #   LIBS="-lgmp $LIBS $GMP_LIBDIR"
+      # fi
+      echo "$as_me:$LINENO: checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL" >&5
+echo $ECHO_N "checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL... $ECHO_C" >&6
+save_CXXFLAGS_CHECK_CXX_LIB="$CXXFLAGS"
+CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+save_LIBS_CHECK_CXX_LIB="$LIBS"
+LIBS="-lCGAL  $LIBS"
 cat >conftest.$ac_ext <<_ACEOF
 /* confdefs.h.  */
 _ACEOF
 cat confdefs.h >>conftest.$ac_ext
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
-
-/* Override any gcc2 internal prototype to avoid an error.  */
-#ifdef __cplusplus
-extern "C"
-#endif
-/* We use char because int might match the return type of a gcc2
-   builtin and then its argument prototype would still apply.  */
-char vslNewStream ();
+#include <CGAL/Cartesian.h>
 int
 main ()
 {
-vslNewStream ();
+::CGAL::Cartesian<int>::Point_2 P
   ;
   return 0;
 }
@@ -7448,7 +8522,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
   cat conftest.err >&5
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
   (exit $ac_status); } &&
-	 { ac_try='test -z "$ac_c_werror_flag"
+	 { ac_try='test -z "$ac_cxx_werror_flag"
 			 || test ! -s conftest.err'
   { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
@@ -7461,33 +8535,25 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
   ac_status=$?
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
-  ac_cv_lib_mkl_vslNewStream=yes
+  echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+cgal=yes
 else
   echo "$as_me: failed program was:" >&5
 sed 's/^/| /' conftest.$ac_ext >&5
 
-ac_cv_lib_mkl_vslNewStream=no
+echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+cgal=no
 fi
 rm -f conftest.err conftest.$ac_objext \
       conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-echo "$as_me:$LINENO: result: $ac_cv_lib_mkl_vslNewStream" >&5
-echo "${ECHO_T}$ac_cv_lib_mkl_vslNewStream" >&6
-if test $ac_cv_lib_mkl_vslNewStream = yes; then
-  MKL_LIBDIR="${mkldir}/lib/32",
-                     MKL_LIB="-lmkl -lvml -lguide",
-                     HAVE_MKL="yes"
-fi
+CXXFLAGS="$save_CXXFLAGS_CHECK_CXX_LIB"
+LIBS="$save_LIBS_CHECK_CXX_LIB"
+      LIBS="$save_LIBS"
+    fi
 
-
-else
-  MKL_INC="-I${mkldir}/include"
-fi
-
-
-  CPPFLAGS=$ac_save_CPPFLAGS
-  LDFLAGS=$ac_save_LDFLAGS
+  fi
   ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -7495,27 +8561,205 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-  if test x_$HAVE_MKL != x_yes; then
-        { { echo "$as_me:$LINENO: error: Can't build with MKL" >&5
-echo "$as_me: error: Can't build with MKL" >&2;}
-   { (exit 1); exit 1; }; }
+fi
+
+if test "x$cgal" = xyes; then
+  USE_CGAL=yes
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_CGAL 1
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define CGAL_VERSION $CGAL_VERSION
+_ACEOF
+
+  if ! echo $CGAL_VERSION | grep -q "^3.0"; then
+    { echo "$as_me:$LINENO: WARNING: *****************************************************" >&5
+echo "$as_me: WARNING: *****************************************************" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Warning: Your CGAL version is newer than the  ***" >&5
+echo "$as_me: WARNING: *** Warning: Your CGAL version is newer than the  ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** supported versions. It may still work though. ***" >&5
+echo "$as_me: WARNING: *** supported versions. It may still work though. ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *****************************************************" >&5
+echo "$as_me: WARNING: *****************************************************" >&2;}
   fi
+else
+   if test "x$cgal_makefile" != xno; then
+    { echo "$as_me:$LINENO: WARNING: *********************************************************" >&5
+echo "$as_me: WARNING: *********************************************************" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Warning: CGAL was not found.                      ***" >&5
+echo "$as_me: WARNING: *** Warning: CGAL was not found.                      ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Run \"configure\" with the appropriate options.     ***" >&5
+echo "$as_me: WARNING: *** Run \"configure\" with the appropriate options.     ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** CGAL support will be disabled.                    ***" >&5
+echo "$as_me: WARNING: *** CGAL support will be disabled.                    ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *********************************************************" >&5
+echo "$as_me: WARNING: *********************************************************" >&2;}
+  fi
+  CGAL_INCLDIR=
+  CGAL_LIBDIR=
+  CGAL_RLIBDIR=
+  CGAL_DEFINES=
+  CGAL_CXXFLAGS=
+  CGAL_LIBS=
+fi
 
 
+CGAL_INC_DIR="${CGAL_INCLDIR} ${CGAL_INCLCONFDIR}"
 
+CGAL_LIB_DIR=${CGAL_LIBDIR}
 
+CGAL_RLIB_DIR=${CGAL_RLIBDIR}
 
+
+
+
+
+
+
+# Check whether --enable-doxygen or --disable-doxygen was given.
+if test "${enable_doxygen+set}" = set; then
+  enableval="$enable_doxygen"
+
+fi;
+# Check whether --enable-dot or --disable-dot was given.
+if test "${enable_dot+set}" = set; then
+  enableval="$enable_dot"
+
+fi;
+# Check whether --enable-html-docs or --disable-html-docs was given.
+if test "${enable_html_docs+set}" = set; then
+  enableval="$enable_html_docs"
+
 else
+   enable_html_docs=yes
+fi;
+# Check whether --enable-latex-docs or --disable-latex-docs was given.
+if test "${enable_latex_docs+set}" = set; then
+  enableval="$enable_latex_docs"
 
-    echo "$as_me:$LINENO: result: no" >&5
+else
+   enable_latex_docs=no
+fi;
+if test "x$enable_doxygen" = xno; then
+        enable_doc=no
+else
+        # Extract the first word of "doxygen", so it can be a program name with args.
+set dummy doxygen; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_DOXYGEN+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $DOXYGEN in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_DOXYGEN="$DOXYGEN" # 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_DOXYGEN="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+
+  ;;
+esac
+fi
+DOXYGEN=$ac_cv_path_DOXYGEN
+
+if test -n "$DOXYGEN"; then
+  echo "$as_me:$LINENO: result: $DOXYGEN" >&5
+echo "${ECHO_T}$DOXYGEN" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
 echo "${ECHO_T}no" >&6
+fi
 
-fi;
+        if test "x$DOXYGEN" = x; then
+                if test "x$enable_doxygen" = xyes; then
+                        { { echo "$as_me:$LINENO: error: could not find doxygen" >&5
+echo "$as_me: error: could not find doxygen" >&2;}
+   { (exit 1); exit 1; }; }
+                fi
+                enable_doc=no
+        else
+                enable_doc=yes
+                # Extract the first word of "dot", so it can be a program name with args.
+set dummy dot; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_DOT+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $DOT in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_DOT="$DOT" # 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_DOT="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+
+  ;;
+esac
+fi
+DOT=$ac_cv_path_DOT
+
+if test -n "$DOT"; then
+  echo "$as_me:$LINENO: result: $DOT" >&5
+echo "${ECHO_T}$DOT" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+        fi
+fi
+
+if test "x$enable_doc" = xyes; then
+  DOC=1
+else
+  DOC=0
+fi
+
+
+if test x$DOT = x; then
+        if test "x$enable_dot" = xyes; then
+                { { echo "$as_me:$LINENO: error: could not find dot" >&5
+echo "$as_me: error: could not find dot" >&2;}
+   { (exit 1); exit 1; }; }
+        fi
+        enable_dot=no
+else
+        enable_dot=yes
+fi
 
 
 
 
 
+
+
 OBJEXT=".$OBJEXT"
 
 OOPSE=oopse
@@ -7572,9 +8816,10 @@ esac
 
 
 
+
           ac_config_headers="$ac_config_headers src/config.h"
 
-          ac_config_files="$ac_config_files make/Makefile"
+                                        ac_config_files="$ac_config_files make/Makefile src/utils/Makefile src/applications/nanoRodBuilder/Makefile scripts/filepp"
 
 
 cat >confcache <<\_ACEOF
@@ -8106,7 +9351,10 @@ do
   case "$ac_config_target" in
   # Handling of arguments.
   "make/Makefile" ) CONFIG_FILES="$CONFIG_FILES make/Makefile" ;;
-  "utils/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS utils/getopt.h:utils/gnugetopt.h" ;;
+  "src/utils/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/utils/Makefile" ;;
+  "src/applications/nanoRodBuilder/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/applications/nanoRodBuilder/Makefile" ;;
+  "scripts/filepp" ) CONFIG_FILES="$CONFIG_FILES scripts/filepp" ;;
+  "src/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS src/getopt.h:src/utils/gnugetopt.h" ;;
   "src/config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
 echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
@@ -8227,6 +9475,7 @@ s,@CPP@,$CPP,;t t
 s,@F90_WORK_FILES_ARG@,$F90_WORK_FILES_ARG,;t t
 s,@MODDIRFLAG@,$MODDIRFLAG,;t t
 s,@F90MODINCSPEC@,$F90MODINCSPEC,;t t
+s,@F90_MODULE_NAMES@,$F90_MODULE_NAMES,;t t
 s,@CPP@,$CPP,;t t
 s,@EGREP@,$EGREP,;t t
 s,@LIBOBJS@,$LIBOBJS,;t t
@@ -8241,21 +9490,30 @@ s,@AR@,$AR,;t t
 s,@LEX@,$LEX,;t t
 s,@LEXLIB@,$LEXLIB,;t t
 s,@LEX_OUTPUT_ROOT@,$LEX_OUTPUT_ROOT,;t t
+s,@PERLINTERP@,$PERLINTERP,;t t
+s,@PERL_SHEBANG@,$PERL_SHEBANG,;t t
 s,@AR@,$AR,;t t
+s,@PS@,$PS,;t t
 s,@MPI_LIB_DIR@,$MPI_LIB_DIR,;t t
 s,@MPI_INC_DIR@,$MPI_INC_DIR,;t t
 s,@MPI_F90_INC@,$MPI_F90_INC,;t t
 s,@MPI_LIB@,$MPI_LIB,;t t
 s,@MPI_F90_LIB@,$MPI_F90_LIB,;t t
 s,@USE_MPI@,$USE_MPI,;t t
-s,@SPRNG_LIB_DIR@,$SPRNG_LIB_DIR,;t t
-s,@SPRNG_INC_DIR@,$SPRNG_INC_DIR,;t t
-s,@SPRNG_LIB@,$SPRNG_LIB,;t t
-s,@USE_SPRNG@,$USE_SPRNG,;t t
-s,@MKL_LIBDIR@,$MKL_LIBDIR,;t t
-s,@MKL_LIB@,$MKL_LIB,;t t
-s,@MKL_INC@,$MKL_INC,;t t
-s,@HAVE_MKL@,$HAVE_MKL,;t t
+s,@CXXCPP@,$CXXCPP,;t t
+s,@USE_CGAL@,$USE_CGAL,;t t
+s,@CGAL_INC_DIR@,$CGAL_INC_DIR,;t t
+s,@CGAL_LIB_DIR@,$CGAL_LIB_DIR,;t t
+s,@CGAL_RLIB_DIR@,$CGAL_RLIB_DIR,;t t
+s,@CGAL_DEFINES@,$CGAL_DEFINES,;t t
+s,@CGAL_CXXFLAGS@,$CGAL_CXXFLAGS,;t t
+s,@CGAL_LIBS@,$CGAL_LIBS,;t t
+s,@DOXYGEN@,$DOXYGEN,;t t
+s,@DOT@,$DOT,;t t
+s,@DOC@,$DOC,;t t
+s,@enable_dot@,$enable_dot,;t t
+s,@enable_html_docs@,$enable_html_docs,;t t
+s,@enable_latex_docs@,$enable_latex_docs,;t t
 s,@BATEXT@,$BATEXT,;t t
 s,@MKINSTALLDIRS@,$MKINSTALLDIRS,;t t
 s,@OOPSE@,$OOPSE,;t t
@@ -8499,6 +9757,13 @@ done
     rm -f $tmp/out
   fi
 
+  # Run the commands associated with the file.
+  case $ac_file in
+    make/Makefile ) chmod 0755 scripts/* ;;
+    src/utils/Makefile ) chmod 0755 scripts/* ;;
+    src/applications/nanoRodBuilder/Makefile ) chmod 0755 scripts/* ;;
+    scripts/filepp ) chmod 0755 scripts/* ;;
+  esac
 done
 _ACEOF
 cat >>$CONFIG_STATUS <<\_ACEOF