--- MITgcm/tools/genmake2	2008/12/11 17:50:56	1.180
+++ MITgcm/tools/genmake2	2009/03/29 19:09:24	1.186
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.180 2008/12/11 17:50:56 utke Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.186 2009/03/29 19:09:24 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -1046,6 +1046,8 @@
 FFLAGS=
 FOPTIM=
 FEXTRAFLAGS=
+USE_EXTENDED_SRC=
+EXTENDED_SRC_FLAG=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -1646,6 +1648,11 @@
       INCLUDES="$INCLUDES $GSLINC"
       LIBS="$LIBS $GSLLIB"
 fi
+#- if USE_EXTENDED_SRC is set, add EXTENDED_SRC_FLAG to FFLAGS :
+if test ! "x$USE_EXTENDED_SRC" = x ; then
+      FFLAGS="$FFLAGS $EXTENDED_SRC_FLAG"
+      F90FIXEDFORMAT="$F90FIXEDFORMAT $EXTENDED_SRC_FLAG"
+fi
 
 printf "\n===  Checking system libraries  ===\n"
 printf "  Do we have the system() command using $FC...  "
@@ -1768,19 +1775,63 @@
 
 
 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 $name > /dev/null 2>&1
+	      RETVAL=$?
+	      yy=0 ; 
+	      for xx in $MPI_LNKF ; do if test $xx = $name ; then yy=1 ; fi ; done
+ 	      if test "x$RETVAL" != x0 -a $yy = 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 -sf $d/$ii $name
+		MPI_LNKF="$MPI_LNKF $name"
+	    fi
+	  fi
+	done
+	#-------------------------------------------------------
     fi
 done
 echo
+#echo "MPI_LNKF='$MPI_LNKF'"
 
 if test "x${PLATFORM}" = x ; then
     PLATFORM=$p_PLATFORM
@@ -2720,7 +2771,7 @@
 #===  Automatic Differentiation Rules  ===
 #===  for TAMC/TAF  ======================
 
-if test "x$OPENAD" == x ; then 
+if test "x$OPENAD" = x ; then 
 
 cat >>$MAKEFILE <<EOF
 
@@ -3005,7 +3056,7 @@
 
 # canonicalizer
 ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
-	./preProcess.py --mode=reverse \$< -o \$@
+	./preProcess.py -H -S \$< -o \$@
 
 # F -> WHIRL
 # note that the canonicalized version cuts off at col 72 
@@ -3022,8 +3073,8 @@
 	./whirl2xaif -s -n --debug 1 -o \$@ \$<
 
 # XAIF -> XAIF'
-ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd openad_adm
-	./openad_adm -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver
+	./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
 
 # XAIF' -> WHIRL'
 ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
@@ -3037,8 +3088,9 @@
 ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
 	../OAD_support/insertTemplateDir.bash \$< \$@
 
+PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
 # postprocess F'
-ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl ../OAD_support/ad_inline.f \$(wildcard ../OAD_support/ad_template.*.f)
+ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl \$(PPEXTRAS:.F=.f)
 	perl multi-pp.pl -inline=../OAD_support/ad_inline.f \$<
 	# the postprocessor still gets the name wrong
 	cat \$<.pp | sed 's/RETURN//' > \$@
@@ -3077,8 +3129,8 @@
 whirl2f whirl2f_be:
 	\$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
 
-openad_adm:
-	\$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/test/t \$@
+oadDriver:
+	\$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
 
 # ============ end OpenAD specific section ==============