--- MITgcm/tools/genmake2	2007/02/18 21:39:59	1.161
+++ MITgcm/tools/genmake2	2007/11/26 21:39:58	1.167
@@ -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 1.167 2007/11/26 21:39:58 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -756,7 +756,9 @@
       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=$?
@@ -1035,6 +1037,7 @@
 INCLUDES="-I. $INCLUDES"
 FFLAGS=
 FOPTIM=
+FEXTRAFLAGS=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -1115,7 +1118,7 @@
 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 +1145,6 @@
 
 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 $gm_local"
@@ -1562,6 +1559,7 @@
       else
 	    DEFINES="$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 +1571,7 @@
       fi
       INCLUDES="$INCLUDES $PAPIINC"
       LIBS="$LIBS $PAPILIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PCLS" = x ; then
       echo "  Turning on PCL counter summary per timestep"
@@ -1584,6 +1583,7 @@
       fi
       INCLUDES="$INCLUDES $PCLINC"
       LIBS="$LIBS $PCLLIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPI" = x ; then
       if test ! "x$PAPIS" = x ; then
@@ -2029,7 +2029,7 @@
     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 +2063,7 @@
 
 	#  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
@@ -2455,7 +2456,7 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
@@ -2522,12 +2523,14 @@
 	@make cleanlinks
 	-rm -f \$(SPECIAL_FILES)
 	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.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