--- MITgcm/tools/genmake2	2008/02/13 07:39:34	1.168
+++ MITgcm/tools/genmake2	2008/07/20 18:01:05	1.173
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.168 2008/02/13 07:39:34 mlosch Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.173 2008/07/20 18:01:05 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -2361,7 +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
@@ -2490,9 +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
 
@@ -2525,12 +2529,12 @@
 clean:
 	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 	-rm -rf *.o
-	-rm -rf *.$FS
+	-rm -rf *.$FS *.flowdir
 Clean:
 	@make clean
 	@make cleanlinks
 	-rm -f \$(SPECIAL_FILES)
-	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log f90mkdepend.log *.bak
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
 CLEAN:
 	@make Clean
@@ -2597,10 +2601,14 @@
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$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 - .$FS - .o ) rule-chain
 .F.p:
@@ -2653,15 +2661,17 @@
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
 	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$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.$FS
+	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
 adtafonly:
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
 \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
@@ -2695,10 +2705,12 @@
 
 ftl_taf_output.$FS: ftl_input_code.$FS
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+	ls -l ftl_input_code_ftl.$FS
 	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
 ftltafonly:
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+	ls -l ftl_input_code_ftl.$FS
 	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
 ftl_taf: ftl_taf_output.o \$(OBJFILES)