--- MITgcm/tools/genmake2	2007/01/31 21:28:10	1.160
+++ MITgcm/tools/genmake2	2007/10/29 20:47:42	1.166
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.160 2007/01/31 21:28:10 ce107 Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.166 2007/10/29 20:47:42 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"
@@ -1361,12 +1364,11 @@
 if test -f ./.genmakerc ; then
     echo
     echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
-    echo "  file.  This file format is no longer supported.  Please see:"
-    echo 
+    echo "  file.  This file format is no longer supported.  For directions on"
+    echo "  how to setup and use the new \"genmake2\" script, please see:"
     echo "    http://mitgcm.org/devel_HOWTO/"
-    echo
-    echo "  for directions on how to setup and use the new \"genmake2\" input"
-    echo "  files and send an email to MITgcm-support@mitgcm.org if you want help."
+    echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
+    echo "WARNING: ignore \"./.genmakerc\" and continue."
     echo 
 fi
 
@@ -1563,6 +1565,7 @@
       else
 	    DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
       fi
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPIS" = x ; then
       echo "  Turning on PAPI flop summary per timestep"
@@ -1574,6 +1577,7 @@
       fi
       INCLUDES="$INCLUDES $PAPIINC"
       LIBS="$LIBS $PAPILIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PCLS" = x ; then
       echo "  Turning on PCL counter summary per timestep"
@@ -1585,6 +1589,7 @@
       fi
       INCLUDES="$INCLUDES $PCLINC"
       LIBS="$LIBS $PCLLIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPI" = x ; then
       if test ! "x$PAPIS" = x ; then
@@ -1964,8 +1969,8 @@
 rm -f ./.tmp_pack
 echo "    packages are:  $PACKAGES"
 
-#  Check availability of NetCDF and then either build the MNC template
-#  files or delete mnc from the list of available packages.
+#  Check for package MNC: if NetCDF is available, then build the MNC 
+#  template files ; otherwise, delete mnc from the list of packages.
 echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
 RETVAL=$?
 if test "x$RETVAL" = x0 ; then
@@ -1999,13 +2004,38 @@
     fi
 fi
 
+#  Check for package PROFILES: if NetCDF is not available,
+#  then delete profiles from the list of available packages.
+echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    if test "x$HAVE_NETCDF" != xt ; then
+	cat <<EOF
+
+*********************************************************************
+WARNING: the "profiles" package was enabled but tests failed to
+  compile NetCDF applications.  Please check that:
+
+  1) NetCDF is correctly installed for this compiler and
+  2) the LIBS variable (within the "optfile") specifies the correct 
+       NetCDF library to link against.
+
+  Due to this failure, the "profiles" package is now DISABLED.
+*********************************************************************
+
+EOF
+	PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
+	DISABLE="$DISABLE profiles"
+    fi
+fi
+
 echo "  applying package dependency rules"
 ck=
 while test "x$ck" != xtt ; do
     i=0
     # rtot=${#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]}
@@ -2039,6 +2069,7 @@
 
 	#  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
@@ -2431,7 +2462,7 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
@@ -2498,12 +2529,14 @@
 	@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