--- MITgcm/tools/genmake2	2006/06/07 22:33:00	1.151
+++ MITgcm/tools/genmake2	2007/10/08 07:33:28	1.165
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.151 2006/06/07 22:33:00 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.165 2007/10/08 07:33:28 mlosch Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -325,7 +325,7 @@
 
     #================================================================
     #  look for possible C compilers
-    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
     p_CC=
     for c in $tmp ; do
 	rm -f ./genmake_hello.c  ./genmake_hello
@@ -364,7 +364,7 @@
 
     #================================================================
     #  look for possible FORTRAN compilers
-    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95 gfortran"
+    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"
     p_FC=
     for c in $tmp ; do
 	rm -f ./hello.f ./hello
@@ -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
@@ -754,7 +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=$?
@@ -946,7 +950,7 @@
     RET_CPP=f
     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
     echo "$COMM" >> genmake_tnc.log
-    $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
+    eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
     if test "x$RET_CPP" = xf ; then
 	echo "  WARNING: CPP failed to pre-process the netcdf test." \
 	    >> genmake_tnc.log
@@ -954,9 +958,9 @@
 	    >> genmake_tnc.log
     fi
     echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
-    echo "  &&  $LINK -o genmake_tnc.o $LIBS" >> genmake_tnc.log
+    echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc.o $LIBS" >> genmake_tnc.log
     $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
-	&&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+	&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
     RET_COMPILE=$?
     cat genmake_tnc.log >> genmake_warnings
 
@@ -974,15 +978,30 @@
 	echo "try again with added '-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 -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> 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 -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
+	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
 	cat genmake_tnc.log >> genmake_warnings
 	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*
@@ -1018,6 +1037,7 @@
 INCLUDES="-I. $INCLUDES"
 FFLAGS=
 FOPTIM=
+FEXTRAFLAGS=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -1036,6 +1056,7 @@
 PCL=
 HPMT=
 GSL=
+DEVEL=
 HAVE_TEST_L=
 
 # DEFINES checked by test compilation or command-line
@@ -1094,10 +1115,10 @@
 
 #  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 "
+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"
@@ -1292,6 +1313,9 @@
         -gsl | --gsl)
 	    GSL=true ;;
 
+        -devel | --devel)
+	    DEVEL=true ;;
+
 	-mpi | --mpi)
 	    MPI=true ;;
 	-mpi=* | --mpi=*)
@@ -1340,19 +1364,18 @@
 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
 
 #  Find the MITgcm ${ROOTDIR}
 if test "x${ROOTDIR}" = x ; then
     tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
-    if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then
+    if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
 	ROOTDIR=".."
     else
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
@@ -1542,6 +1565,7 @@
       else
 	    DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
       fi
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPIS" = x ; then
       echo "  Turning on PAPI flop summary per timestep"
@@ -1553,6 +1577,7 @@
       fi
       INCLUDES="$INCLUDES $PAPIINC"
       LIBS="$LIBS $PAPILIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PCLS" = x ; then
       echo "  Turning on PCL counter summary per timestep"
@@ -1564,6 +1589,7 @@
       fi
       INCLUDES="$INCLUDES $PCLINC"
       LIBS="$LIBS $PCLLIB"
+      PACKAGES="$PACKAGES showflops"
 fi
 if test ! "x$PAPI" = x ; then
       if test ! "x$PAPIS" = x ; then
@@ -1818,19 +1844,21 @@
     fi
 fi
 
-#same for exch2
-if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
-    echo "  Making source files in exch2 from  templates"
-    ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-        rm -f make_exch2.errors
-    else
-        echo "Error: problem encountered while building source files in exch2:"
-        cat make_exch2.errors 1>&2
-        exit 1
+#same for pkg/exch2 and pkg/regrid
+for pdir in exch2 regrid ; do
+    if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
+	echo "  Making source files in pkg/${pdir} from templates"
+	( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
+	RETVAL=$?
+	if test "x${RETVAL}" = x0 ; then
+	    rm -f make_${pdir}.errors
+	else
+	    echo "Error: problem encountered while building source files in pkg/${pdir}:"
+	    cat make_${pdir}.errors 1>&2
+	    exit 1
+	fi
     fi
-fi
+done
 
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
@@ -1941,8 +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
@@ -1976,13 +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]}
@@ -2016,6 +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
@@ -2205,7 +2259,7 @@
 	perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
     else
 	echo " We cannot create a copy of mpif.h!"
-	exit -1
+#	exit -1
     fi
 fi
 
@@ -2408,7 +2462,7 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
@@ -2456,6 +2510,7 @@
 
 libmitgcmuv.a: \$(OBJFILES)
 	ar rcv libmitgcmuv.a \$(OBJFILES)
+	ar d   libmitgcmuv.a main.o
 
 links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
@@ -2466,7 +2521,9 @@
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.o
+	-rm -rf *.$FS
 Clean:
 	@make clean
 	@make cleanlinks
@@ -2477,7 +2534,7 @@
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) *.txt STD* *diagnostics.log datetime
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
 	-rm -rf mnc_test_*
 
 #eh3 Makefile: makefile
@@ -2536,9 +2593,7 @@
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
-.F90.$FS90:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.$FS90.o:
+.F90.o:   
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .c.o:
 	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
@@ -2585,7 +2640,7 @@
 cat >>$MAKEFILE <<EOF
 
 # ... AD ...
-adall: ad_taf
+adall: \$(EXE_AD)
 adtaf: ad_taf_output.$FS
 adtamc: ad_tamc_output.$FS
 
@@ -2605,8 +2660,8 @@
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-ad_taf: ad_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
+\${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
 ad_tamc_output.$FS: ad_input_code.$FS
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS