--- MITgcm/tools/genmake2	2007/10/29 20:47:42	1.166
+++ MITgcm/tools/genmake2	2008/06/25 18:28:06	1.172
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.166 2007/10/29 20:47:42 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.172 2008/06/25 18:28:06 dfer Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -746,7 +746,9 @@
  *curtim = *curtim/1.E6;
 }
 EOF
-    make genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -805,7 +807,9 @@
     return;
 }
 EOF
-    make genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -853,7 +857,9 @@
     return;
 }
 EOF
-    make genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -897,7 +903,9 @@
         *nbyte = -1;
 }
 EOF
-    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_tc.log 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -1145,12 +1153,6 @@
 
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
-for i in . $MODS ; do
-    if test -r $i/$gm_local ; then
-	. $i/$gm_local
-	break
-    fi
-done
 printf "  getting local config information:  "
 if test -f $gm_local ; then
     echo "using $gm_local"
@@ -2359,7 +2361,10 @@
 	echo "" >> srclinks.tmp
 	echo "#  These files are linked from $d" >> srclinks.tmp
 	echo "$deplist :" >> srclinks.tmp
-	printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp
+# We need to make sure that the link isn't already there.
+# This may happen when make thinks that a header file has to be "remade"
+# because a module it depends on has changed.  In this case we do nothing.
+	printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
     fi
 done
 rm -rf .links.tmp
@@ -2488,9 +2493,10 @@
 echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE
 echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE
 echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
+echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
 echo >> $MAKEFILE
 echo '.SUFFIXES:' >> $MAKEFILE
-echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE
+echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90 .flowdir .flow' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
 rm -f ad_flow_files.inc
 
@@ -2523,12 +2529,12 @@
 clean:
 	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 	-rm -rf *.o
-	-rm -rf *.$FS
+	-rm -rf *.$FS *.flowdir
 Clean:
 	@make clean
 	@make cleanlinks
 	-rm -f \$(SPECIAL_FILES)
-	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log f90mkdepend.log *.bak
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
 CLEAN:
 	@make Clean
@@ -2595,10 +2601,14 @@
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
+.F.o:
+	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
 .F90.o:   
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .c.o:
 	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
+.flow.flowdir:
+	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 
 # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
 .F.p:
@@ -2651,8 +2661,8 @@
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
 	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS
+	@make \$(FLOFILES)
+	cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
 
 ad_taf_output.$FS: ad_input_code.$FS
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS