--- MITgcm/tools/genmake2	2007/02/18 21:39:59	1.161
+++ 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 1.161 2007/02/18 21:39:59 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
@@ -756,7 +758,9 @@
       print *," HELLO WORLD", wtime
       end
 EOF
-    $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_F=$?
     test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
     RETVAL=$?
@@ -803,7 +807,9 @@
     return;
 }
 EOF
-    make genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -851,7 +857,9 @@
     return;
 }
 EOF
-    make genmake_tc_1.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -895,7 +903,9 @@
         *nbyte = -1;
 }
 EOF
-    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    COMM="$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
@@ -1035,6 +1045,7 @@
 INCLUDES="-I. $INCLUDES"
 FFLAGS=
 FOPTIM=
+FEXTRAFLAGS=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -1115,7 +1126,7 @@
 gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
-gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
+gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
 gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
 gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
@@ -1142,12 +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 $gm_local"
@@ -1562,6 +1567,7 @@
       else
 	    DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
       fi
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPIS" = x ; then
       echo "  Turning on PAPI flop summary per timestep"
@@ -1573,6 +1579,7 @@
       fi
       INCLUDES="$INCLUDES $PAPIINC"
       LIBS="$LIBS $PAPILIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PCLS" = x ; then
       echo "  Turning on PCL counter summary per timestep"
@@ -1584,6 +1591,7 @@
       fi
       INCLUDES="$INCLUDES $PCLINC"
       LIBS="$LIBS $PCLLIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPI" = x ; then
       if test ! "x$PAPIS" = x ; then
@@ -2029,7 +2037,7 @@
     i=0
     # rtot=${#PNAME[@]}
     rtot=$nname
-    while test $i -lt $rtot ; do
+    while test $i -le $rtot ; do
 
 	#  Is $pname in the current $PACKAGES list?
 	#  pname=${PNAME[$i]}
@@ -2063,6 +2071,7 @@
 
 	#  Do we need to add $dname according to the dependency rules?
 	if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
+            #echo "   " $pname ": need to add :" $dname
 	    in_dis="f"
 	    for dis in $DISABLE ; do
 		if test "x$dis" = "x$dname" ; then
@@ -2352,7 +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
@@ -2455,7 +2467,7 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
@@ -2481,9 +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
 
@@ -2516,18 +2529,20 @@
 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
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
 	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
 	-rm -rf mnc_test_*
 
 #eh3 Makefile: makefile
@@ -2586,10 +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 - .$FS - .o ) rule-chain
 .F.p:
@@ -2642,8 +2661,8 @@
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
 	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$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