--- MITgcm/tools/genmake2	2009/02/20 21:08:02	1.184
+++ MITgcm/tools/genmake2	2009/03/27 20:18:07	1.185
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.184 2009/02/20 21:08:02 utke Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.185 2009/03/27 20:18:07 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -1775,16 +1775,58 @@
 
 
 printf "\n===  Setting defaults  ===\n"
-printf "  Adding MODS directories:  "
+printf "  Adding MODS directories: "
+MPI_LNKF=
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	printf " $d"
+	printf "$d "
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
+	#-------------------------------------------------------
+	# Put special links so that MPI specific files are used
+	MPI_FILES=`(cd $d ; find . -name "*_mpi" -print)`
+	for i in $MPI_FILES ; do
+	  ii=`echo $i | sed 's:^\./::'`
+	  name=`echo $ii | sed 's:_mpi::' `
+	  if test "x$MPI" = x ; then
+	  # NO: We undo an _mpi symbolically linked file
+	    if test -L $name ; then
+	      cmp $name "$d/$ii" > /dev/null 2>&1
+	      RETVAL=$?
+	      if test "x$RETVAL" = x0 ; then
+		printf "Un-linking $name ; "
+		rm -f $name
+	      fi
+	    fi
+	  else
+	  # YES: We symbolically link this file (with conditions if already there)
+	    if test -L $name ; then
+	      cmp $d/$ii $name > /dev/null 2>&1
+	      RETVAL=$?
+	      xx=`echo $MPI_LNKF | grep -c $name`
+ 	      if test "x$RETVAL" != x0 -a $xx == 0 ; then
+	      # remove sym-link if different and has not just been linked
+		printf "Un-link + "
+		rm -f $name
+	      fi
+	      if test "x$RETVAL" = x0 ; then
+	      # if identical, keep sym-link and keep record of it
+		MPI_LNKF="$MPI_LNKF $name"
+	      fi
+	    fi
+	    if ! test -f $name ; then
+	      # make sym-link and keep record of it
+		printf "Linking $ii to $name ; "
+		ln -s $d/$ii $name
+		MPI_LNKF="$MPI_LNKF $name"
+	    fi
+	  fi
+	done
+	#-------------------------------------------------------
     fi
 done
 echo