--- MITgcm/tools/genmake2	2009/04/15 22:21:03	1.187
+++ MITgcm/tools/genmake2	2009/04/22 21:03:52	1.192
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.187 2009/04/15 22:21:03 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.192 2009/04/22 21:03:52 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -1173,15 +1173,6 @@
 fi
 
 #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
-#OPTIONS=
-#n=0
-#for i ; do 
-#   echo "$i  $n"
-#   setvar="OPTIONS[$n]='$i'"
-#   #  echo "  $setvar"
-#   eval "$setvar"
-#   n=$(( $n + 1 ))
-#done
 #parse_options
 ac_prev=
 for ac_option in "$@" ; do
@@ -1790,7 +1781,6 @@
 
 printf "\n===  Setting defaults  ===\n"
 printf "  Adding MODS directories: "
-MPI_LNKF=
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
@@ -1800,52 +1790,9 @@
 	printf "$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
@@ -2520,6 +2467,12 @@
 echo "" >> hsrclist.tmp
 echo "" >> ad_flow_files.tmp
 
+CMDLINE=$0
+for xx in "$@" ; do nw=`echo $xx | wc -w`
+    if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
+                        else CMDLINE="$CMDLINE '$xx'" ; fi
+done
+
 if test -f $MAKEFILE ; then
     mv -f $MAKEFILE "$MAKEFILE.bak"
 fi
@@ -2529,7 +2482,7 @@
 echo "# This makefile was generated automatically on" >> $MAKEFILE
 echo "#    $THISDATE" >> $MAKEFILE
 echo "# by the command:" >> $MAKEFILE
-echo "#    $0 $G2ARGS" >> $MAKEFILE
+echo "#    $CMDLINE"  >> $MAKEFILE
 echo "# executed by:" >> $MAKEFILE
 echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
 
@@ -2825,7 +2778,7 @@
 adtaf: ad_taf_output.$FS
 adtamc: ad_tamc_output.$FS
 
-ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
@@ -3103,10 +3056,8 @@
 
 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 \$(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//' > \$@
+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 postProcess.py \$(PPEXTRAS:.F=.f)
+	./postProcess.py -m r -i ../OAD_support/ad_inline.f -o \$@ \$<
 
 # extract all transformed modules 
 all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
@@ -3133,10 +3084,7 @@
 whirl2xaif xaif2whirl: 
 	\$(LN) \${OPENADFORTTK}/bin/\$@ .
 
-%.pl: 
-	\$(LN) \${OPENADFORTTK}/bin/\$@ .
-
-preProcess.py: 
+preProcess.py postProcess.py: 
 	\$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
 
 whirl2f whirl2f_be: