--- MITgcm/tools/genmake2	2006/11/23 05:23:05	1.158
+++ MITgcm/tools/genmake2	2007/05/05 20:18:52	1.162
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.158 2006/11/23 05:23:05 heimbach Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.162 2007/05/05 20:18:52 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -601,6 +601,8 @@
 
     -gsl | --gsl
           Use GSL to control floating point rounding and precision
+    -devel | --devel
+          Add additional warning and debugging flags for development
 
     -mpi | --mpi
           Include MPI header files and link to MPI libraries
@@ -983,6 +985,21 @@
 	if test "x$RET_COMPILE" = x0 ; then
 	    LIBS="$LIBS -lnetcdf"
 	    HAVE_NETCDF=t
+	else
+	# try again with "-lnetcdff" added to the libs
+	    echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+	    echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
+	    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
+	    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+	    cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
+		&&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
+		&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
+	    RET_COMPILE=$?
+	    cat genmake_tnc.log >> genmake_warnings
+	    if test "x$RET_COMPILE" = x0 ; then
+		LIBS="$LIBS -lnetcdff -lnetcdf"
+		HAVE_NETCDF=t
+	    fi
 	fi
     fi
     rm -f genmake_tnc*
@@ -1036,6 +1053,7 @@
 PCL=
 HPMT=
 GSL=
+DEVEL=
 HAVE_TEST_L=
 
 # DEFINES checked by test compilation or command-line
@@ -1094,7 +1112,7 @@
 
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL MPI JAM DUMPSTATE STANDARDDIRS"
+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 "
@@ -1292,6 +1310,9 @@
         -gsl | --gsl)
 	    GSL=true ;;
 
+        -devel | --devel)
+	    DEVEL=true ;;
+
 	-mpi | --mpi)
 	    MPI=true ;;
 	-mpi=* | --mpi=*)
@@ -1340,12 +1361,11 @@
 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
 
@@ -1943,8 +1963,8 @@
 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
@@ -1978,13 +1998,38 @@
     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]}
@@ -2018,6 +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
@@ -2458,6 +2504,7 @@
 
 libmitgcmuv.a: \$(OBJFILES)
 	ar rcv libmitgcmuv.a \$(OBJFILES)
+	ar d   libmitgcmuv.a main.o
 
 links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
@@ -2540,9 +2587,7 @@
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
-.F90.$FS90:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.$FS90.o:
+.F90.o:   
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .c.o:
 	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<