--- MITgcm/tools/genmake2	2004/03/12 15:50:06	1.72
+++ MITgcm/tools/genmake2	2004/07/30 15:59:33	1.92
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.72 2004/03/12 15:50:06 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.92 2004/07/30 15:59:33 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -67,11 +67,176 @@
 	done
 	PACKAGES=$new_packages
 	rm -f ./p[1,2].tmp
+	return $matched
     else
 	echo "Warning: can't read package groups definition file: $PKG_GROUPS"
     fi
 }
 
+#  Check for broken environments (eg. cygwin, MacOSX w/HFS+) that
+#  cannot distinguish [*.F/*.F90] from [*.f/*.f90] files.
+check_for_broken_Ff()  {
+    #  Do we have defaults for $FS and/or $FS90 ?
+    tfs=f
+    tfs9=f90
+    if test "x$FS" != x ; then
+	tfs="$FS"
+    fi
+    if test "x$FS90" != x ; then
+	tfs9="$FS90"
+    fi
+
+    #  First check the ability to create a *.F/.f pair.
+    cat <<EOF >> genmake_hello.F
+      program hello
+      write(*,*) 'hi'
+      stop
+      end
+EOF
+    cp genmake_hello.F "genmake_hello."$tfs > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	if test "x$FS" = x ; then
+	    FS='for'
+	    FS90='fr9'
+	    check_for_broken_Ff
+	else
+	    cat <<EOF 2>&1
+ERROR: Your file system cannot distinguish between *.F and *.f files 
+  (fails the "cp" test) and this program cannot find a suitable 
+  replacement extension.  Please try a different build environment or 
+  contact the <MITgcm-support@mitgcm.org> list for help.
+
+EOF
+	    exit -1
+	fi
+	return
+    fi
+    rm -f genmake_hello.*
+
+    #  Check the ability of ${MAKE} and ${LN} to use the current set
+    #  of extensions.
+    cat <<EOF >> genmake_hello.F
+      program hello
+      write(*,*) 'hi'
+      stop
+      end
+EOF
+    test -f Makefile  &&  mv -f Makefile Makefile.bak
+    cat <<EOF >> Makefile
+%.$tfs : %.F
+.SUFFIXES:
+genmake_hello.$tfs: genmake_hello.F
+	$LN genmake_hello.F genmake_hello.$tfs
+EOF
+    $MAKE "genmake_hello."$tfs > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
+	if test "x$FS" = x ; then
+	    FS='for'
+	    FS90='fr9'
+	    check_for_broken_Ff
+	else
+	    cat <<EOF 2>&1
+ERROR: Your file system cannot distinguish between *.F and *.f files 
+  (fails the "make/ln" test) and this program cannot find a suitable 
+  replacement extension.  Please try a different build environment or 
+  contact the <MITgcm-support@mitgcm.org> list for help.
+
+EOF
+	    exit -1
+	    return
+	fi
+    fi
+    rm -f genmake_hello.* Makefile
+    test -f Makefile  &&  mv -f Makefile.bak Makefile
+
+    #  If we make it here, use the extensions
+    FS=$tfs
+    FS90=$tfs9
+    return
+}
+
+
+look_for_makedepend()  {
+
+    #  The "original" makedepend is part of the Imake system that is
+    #  most often distributed with XFree86 or with an XFree86 source
+    #  package.  As a result, many machines (eg. generic Linux) do not
+    #  have a system-default "makedepend" available.  For those
+    #  systems, we have two fall-back options:
+    #
+    #    1) a makedepend implementation shipped with the cyrus-imapd
+    #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
+    #
+    #    2) a known-buggy xmakedpend shell script
+    #
+    #  So the choices are, in order:
+    #
+    #    1) use the user-specified program
+    #    2) use a system-wide default
+    #    3) locally build and use the cyrus implementation
+    #    4) fall back to the buggy local xmakedpend script
+    #
+    if test "x${MAKEDEPEND}" = x ; then
+	which makedepend > /dev/null 2>&1
+	RV0=$?
+	cat <<EOF >> genmake_tc.f
+      program test
+      write(*,*) 'test'
+      stop
+      end
+EOF
+	makedepend genmake_tc.f > /dev/null 2>&1
+	RV1=$?
+	if test "x${RV0}${RV1}" = x00 ; then
+	    MAKEDEPEND=makedepend
+	else
+	    echo "    a system-default makedepend was not found."
+	    
+	    #  Try to build the cyrus implementation
+	    build_cyrus_makedepend
+	    RETVAL=$?
+	    if test "x$RETVAL" != x0 ; then
+		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	    fi
+	    rm -f ./genmake_cy_md
+	fi
+    else
+	#  echo "MAKEDEPEND=${MAKEDEPEND}"
+	echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
+	RETVAL=$?
+	if test x"$RETVAL" = x0 ; then
+	    build_cyrus_makedepend
+	fi
+    fi
+}
+
+
+build_cyrus_makedepend()  {
+    rm -f ./genmake_cy_md
+    (
+	cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
+	    &&  ./configure > /dev/null 2>&1  \
+	    &&  make > /dev/null 2>&1
+	if test -x ./makedepend.exe ; then
+	    $LN ./makedepend.exe ./makedepend
+	fi
+	./makedepend ifparser.c > /dev/null 2>&1  \
+	    &&  echo "true"
+    ) > ./genmake_cy_md
+    grep true ./genmake_cy_md > /dev/null 2>&1
+    RETVAL=$?
+    rm -f ./genmake_cy_md
+    if test "x$RETVAL" = x0 ; then
+	MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+	return 0
+    else
+	echo "WARNING: unable to build cyrus-imapd-makedepend"
+	return 1
+    fi
+}
+
 # Guess possible config options for this host
 find_possible_configs()  {
 
@@ -82,6 +247,7 @@
     tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
     tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
     PLATFORM=$tmp3
+    echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
     echo "  The platform appears to be:  $PLATFORM"
     
@@ -101,51 +267,49 @@
 	CPP="cpp -traditional -P"
     fi
 
-    #  The "original" makedepend is part of the Imake system that is
-    #  most often distributed with XFree86 or with an XFree86 source
-    #  package.  As a result, many machines (eg. generic Linux) do not
-    #  have a system-default "makedepend" available.  For those
-    #  systems, we have two fall-back options:
-    #
-    #    1) a makedepend implementation shipped with the cyrus-imapd
-    #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
-    #
-    #    2) a known-buggy xmakedpend shell script
-    #
-    #  So the choices are, in order:
-    #
-    #    1) use the user-specified program
-    #    2) use a system-wide default
-    #    3) locally build and use the cyrus implementation
-    #    4) fall back to the buggy local xmakedpend script
-    #
-    if test "x${MAKEDEPEND}" = x ; then
-      which makedepend > /dev/null 2>&1
-      RETVAL=$?
-      if test ! "x${RETVAL}" = x0 ; then
-         echo "    a system-default makedepend was not found."
-
-	 #  Try to build the cyrus impl
-	 rm -f ./genmake_cy_md
-	 (
-	     cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
-		 &&  ./configure > /dev/null 2>&1  \
-		 &&  make > /dev/null 2>&1  \
-		 &&  ./makedepend ifparser.c > /dev/null 2>&1  \
-		 &&  echo "true"
-	 ) > ./genmake_cy_md
-	 grep true ./genmake_cy_md > /dev/null 2>&1
-	 RETVAL=$?
-	 if test "x$RETVAL" = x0 ; then
-	     MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
-	 else
-	     MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
-	 fi
-	 rm -f ./genmake_cy_md
-      fi
+    look_for_makedepend
+
+    #================================================================
+    #  look for possible C compilers
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"
+    p_CC=
+    for c in $tmp ; do
+	rm -f ./genmake_hello.c  ./genmake_hello
+	cat >> genmake_hello.c << EOF
+#include <stdio.h>
+int main(int argc, char **argv) {
+  printf("Hello!\n");
+  return 0;
+}
+EOF
+	$c -o genmake_hello genmake_hello.c > /dev/null 2>&1
+	RETVAL=$?
+	if test "x${RETVAL}" = x0 ; then
+	    p_CC="$p_CC $c"
+	fi
+    done
+    rm -f ./genmake_hello.c ./genmake_hello
+    if test "x${p_CC}" = x ; then
+	cat 1>&2 <<EOF
+
+Error: No C compilers were found in your path.  Please specify one using:
+
+    1) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
+    2) the CC or MITGCM_CC environment variables.
+
+EOF
+	exit 1
+    else
+	echo "  The possible C compilers found in your path are:"
+	echo "   "$p_CC
+	if test "x$CC" = x ; then
+	    CC=`echo $p_CC | $AWK '{print $1}'`
+	    echo "  Setting C compiler to: "$CC
+	fi
     fi
 
-    # look for possible fortran compilers
+    #================================================================
+    #  look for possible FORTRAN compilers
     tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
     p_FC=
     for c in $tmp ; do
@@ -171,7 +335,7 @@
 
     1) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
     2) a command-line option (eg. "-fc NAME"), or
-    3) the MITGCM_FC environment variable.
+    3) the FC or MITGCM_FC environment variables.
 
 EOF
 	exit 1
@@ -273,6 +437,11 @@
     -help | --help | -h | --h
           Print this help message and exit.
 
+    -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
+      -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
+          Use "NAME" as the adoptfile.  By default, the file at
+          "tools/adjoint_options/adjoint_default" will be used.
+
     -nooptfile | --nooptfile
       -optfile NAME | --optfile NAME | -of NAME | --of NAME
       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
@@ -337,6 +506,11 @@
           will search for a working compiler by trying a list of
           "usual suspects" such as g77, f77, etc.
 
+    -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
+          Use "NAME" as the C compiler.  By default, genmake 
+          will search for a working compiler by trying a list of
+          "usual suspects" such as gcc, c89, cc, etc.
+
     -[no]ieee | --[no]ieee
           Do or don't use IEEE numerics.  Note that this option 
           *only* works if it is supported by the OPTFILE that 
@@ -372,6 +546,12 @@
 
 #  Build a CPP macro to automate calling C routines from FORTRAN
 get_fortran_c_namemangling()  {
+
+    #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
+    if test ! "x$FC_NAMEMANGLE" = x ; then
+        return 0
+    fi
+
     default_nm="#define FC_NAMEMANGLE(X) X ## _"
     
     cat > genmake_test.c <<EOF
@@ -389,7 +569,7 @@
 EOF
 	return 1
     fi
-    c_tcall=`nm genmake_test.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    c_tcall=`nm genmake_test.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -419,7 +599,7 @@
 EOF
 	return 1
     fi
-    f_tcall=`nm genmake_tcomp.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    f_tcall=`nm genmake_tcomp.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -496,7 +676,8 @@
 
 
 check_netcdf_libs()  {
-    cat <<EOF > genmake_tnc.F
+    echo "" > genmake_tnc.log
+    cat <<EOF > genmake_tnc.for
       program fgennc
 #include "netcdf.inc"
       integer iret, ncid, xid
@@ -508,7 +689,8 @@
       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
       end
 EOF
-    $CPP genmake_tnc.F > genmake_tnc.f  \
+    #echo "$CPP $DEFINES $INCLUDES"
+    $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
 	&&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f $LIBS >> genmake_tnc.log 2>&1
     RET_COMPILE=$?
     test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
@@ -517,7 +699,7 @@
 	HAVE_NETCDF=t
     else
 	# try again with "-lnetcdf" added to the libs
-	$CPP genmake_tnc.F > genmake_tnc.f  \
+	$CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
 	    &&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f \
 	    $LIBS -lnetcdf >> genmake_tnc_2.log 2>&1
 	RET_COMPILE=$?
@@ -547,6 +729,7 @@
 S64=
 KPP=
 FC=
+CC=
 CPP=
 LINK=
 DEFINES=
@@ -554,7 +737,7 @@
 ENABLE=
 DISABLE=
 MAKEFILE=
-MAKEDEPEND=
+#MAKEDEPEND=
 PDEPEND=
 DUMPSTATE=t
 PDEFAULT=
@@ -579,6 +762,7 @@
 FC_NAMEMANGLE=
 HAVE_CLOC=
 HAVE_NETCDF=
+HAVE_ETIME=
 
 MODS=
 TOOLSDIR=
@@ -586,6 +770,7 @@
 INCLUDEDIRS=
 STANDARDDIRS="USE_THE_DEFAULT"
 
+G2ARGS=
 BASH=
 PWD=`pwd`
 MAKE=make
@@ -602,6 +787,8 @@
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
 fi
+FS=
+FS90=
 
 AUTODIFF_PKG_USED=f
 AD_OPTFILE=
@@ -626,7 +813,7 @@
 gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
 gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
-gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE"
+gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
 
 #  The following are all related to adjoint/tangent-linear stuff
 gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
@@ -656,7 +843,7 @@
     fi
 done
 printf "  getting local config information:  "
-if test -e $gm_local ; then
+if test -f $gm_local ; then
     echo "using $gm_local"
     . $gm_local
     # echo "DISABLE=$DISABLE"
@@ -677,7 +864,9 @@
 #done
 #parse_options
 ac_prev=
-for ac_option ; do
+for ac_option in $@ ; do
+
+    G2ARGS="$G2ARGS \"$ac_option\""
 
     # If the previous option needs an argument, assign it.
     if test -n "$ac_prev"; then
@@ -771,12 +960,27 @@
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
 #		CPP=$ac_optarg ;;
-	    
+	
+	-cc | --cc)
+	    ac_prev=CC ;;
+	-cc=* | --cc=*)
+	    CC=$ac_optarg ;;
+	
 	-fortran | --fortran | -fc | --fc)
 	    ac_prev=FC ;;
 	-fc=* | --fc=*)
 	    FC=$ac_optarg ;;
 	
+	-fs | --fs)
+	    ac_prev=FS ;;
+	-fs=* | --fs=*)
+	    FS=$ac_optarg ;;
+	
+	-fs90 | --fs90)
+	    ac_prev=FS90 ;;
+	-fs90=* | --fs90=*)
+	    FS90=$ac_optarg ;;
+	
 	-ieee | --ieee)
 	    IEEE=true ;;
 	-noieee | --noieee)
@@ -833,7 +1037,8 @@
 fi
 
 if test "x${ROOTDIR}" = x ; then
-    if test "${PWD##/*/}" = "bin" -a -d ../model -a -d ../eesup -a -d ../pkg ; 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
 	ROOTDIR=".."
     else
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
@@ -886,6 +1091,9 @@
     fi
 fi
 
+#  Check for broken systems that cannot correctly distinguish *.F and *.f files
+# check_for_broken_Ff
+
 echo "  getting AD_OPTFILE information:  "
 if test "x${AD_OPTFILE}" = x ; then
     if test "x$MITGCM_AD_OF" = x ; then
@@ -913,7 +1121,7 @@
     fi
 fi
 
-#  Check that FC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
+#  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
 #  either set defaults or complain and abort!
 if test ! "x$BASH" = x ; then
     # add a trailing space so that it works within the Makefile syntax (see below)
@@ -929,6 +1137,16 @@
 EOF
     exit 1
 fi
+if test "x$CC" = x ; then
+    cat <<EOF 1>&2
+
+Error: no C compiler: please specify using one of the following:
+  1) within the options file ("CC=...") as specified by "-of=OPTFILE"
+  2) the "-cc=XXX" command-line option
+  3) the "./genmake_local" file
+EOF
+    exit 1
+fi
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
@@ -939,8 +1157,8 @@
     CPP=cpp
 fi
 #EH3 === UGLY ===
-#  The following an ugly little hack to check for $CPP in /lib/ and it
-#  should eventually be replaced with a more general function that
+#  The following is an ugly little hack to check for $CPP in /lib/ and
+#  it should eventually be replaced with a more general function that
 #  searches a combo of the user's path and a list of "usual suspects"
 #  to find the correct location for binaries such as $CPP.
 for i in " " "/lib/" ; do
@@ -963,9 +1181,7 @@
 else
     rm -f test_cpp
 fi
-if test "x$MAKEDEPEND" = x ; then
-    MAKEDEPEND=makedepend
-fi
+look_for_makedepend
 if test "x$LN" = x ; then
     LN="ln -s"
 fi
@@ -983,6 +1199,9 @@
 fi
 rm -f genmake_test_ln genmake_tlink
 
+#  Check for broken *.F/*.f handling and fix if possible
+check_for_broken_Ff
+
 if test ! "x$MPI" = x ; then
       echo "  Turning on MPI cpp macros"
       DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
@@ -1028,6 +1247,28 @@
 fi
 rm -f genmake_tcomp*
 
+printf "  Do we have the etime() command using $FC...  "
+cat > genmake_tcomp.f <<EOF
+      program hello
+      REAL*4 ACTUAL, TARRAY(2)
+      EXTERNAL ETIME
+      REAL*4 ETIME
+      actual = etime( tarray )
+      print *, tarray
+      end
+EOF
+$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_ETIME=t
+    DEFINES="$DEFINES -DHAVE_ETIME"
+    echo "yes"
+else
+    HAVE_ETIME=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
 printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
 check_HAVE_CLOC
 if test "x$HAVE_CLOC" != x ; then
@@ -1069,7 +1310,8 @@
 fi
 
 if test "x${EXEDIR}" = x ; then
-    if test "${PWD##/*/}" = "bin" -a -d ../exe -a $ROOTDIR = .. ; then
+    tmp=`echo $PWD | sed -e 's/\// /g' | awk '{print $NR}'`
+    if test "x$tmp" = "xbin" -a -d ../exe -a $ROOTDIR = .. ; then
 	EXEDIR=../exe
     else
 	EXEDIR=.
@@ -1187,12 +1429,20 @@
 	    PACKAGES="$PACKAGES $i"
 	done
 	echo "    before group expansion packages are: $PACKAGES"
-	expand_pkg_groups
+	RET=1
+        while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
 	echo "    after group expansion packages are:  $PACKAGES"
     fi
 fi
 
 echo "  applying DISABLE settings"
+for i in $PACKAGES ; do
+    echo $i >> ./.tmp_pack
+done
+for i in `grep  "-" ./.tmp_pack` ; do
+    j=`echo $i | sed 's/[-]//'`
+    DISABLE="$DISABLE $j"
+done
 pack=
 for p in $PACKAGES ; do
     addit="t"
@@ -1209,19 +1459,20 @@
 echo "  applying ENABLE settings"
 echo "" > ./.tmp_pack
 PACKAGES="$PACKAGES $ENABLE"
+# Test if each explicitly referenced package exists
 for i in $PACKAGES ; do
-    if test ! -d "$ROOTDIR/pkg/$i" ; then
+    j=`echo $i | sed 's/[-+]//'`
+    if test ! -d "$ROOTDIR/pkg/$j" ; then
 	echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""
-	exit 1
+ 	exit 1
     fi
     echo $i >> ./.tmp_pack
 done
-pack=`cat ./.tmp_pack | sort | uniq`
-rm -f ./.tmp_pack
 PACKAGES=
-for i in $pack ; do
+for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do
     PACKAGES="$PACKAGES $i"
 done
+rm -f ./.tmp_pack
 echo "    packages are:  $PACKAGES"
 
 echo "  applying package dependency rules"
@@ -1288,7 +1539,8 @@
 	    echo "  the dependency rules for \"$dname\""
 	    exit 1
 	fi
-	i=$(( $i + 1 ))
+        i=`echo "$i + 1" | bc -l`
+	#i=$(( $i + 1 ))
     done
     ck=$ck"t"
 done
@@ -1450,9 +1702,7 @@
 echo "===  Creating the Makefile  ==="
 echo "  setting INCLUDES"
 for i in $INCLUDEDIRS ; do
-    if ! test -d $i ; then
-#	INCLUDES="$INCLUDES -I$i"
-#   else
+    if test ! -d $i ; then
 	echo "Warning: can't find INCLUDEDIRS=\"$i\""
     fi
 done
@@ -1527,7 +1777,7 @@
 echo "" >> hlist.inc
 echo "" >> ad_flow_files.inc
 
-if test -e $MAKEFILE ; then
+if test -f $MAKEFILE ; then
     mv -f $MAKEFILE "$MAKEFILE.bak"
 fi
 echo "  Writing makefile: $MAKEFILE"
@@ -1536,7 +1786,7 @@
 echo "# This makefile was generated automatically on" >> $MAKEFILE
 echo "#    $THISDATE" >> $MAKEFILE
 echo "# by the command:" >> $MAKEFILE
-echo "#    $0 $@" >> $MAKEFILE
+echo "#    $0 $G2ARGS" >> $MAKEFILE
 echo "# executed by:" >> $MAKEFILE
 echo "#    $USER@${THISHOSTNAME}:${THISCWD}" >> $MAKEFILE
 
@@ -1600,9 +1850,11 @@
 # Special preprocessor (KAP on DECs, FPP on Crays)
 KPP = ${KPP}
 # Fortran compiler
-FC = ${FC}
+FC = ${FC} in
 # Fortran compiler
 F90C = ${F90C}
+# C compiler
+CC = ${CC}
 # Link editor
 LINK = ${LINK} ${LDADD}
 
@@ -1636,26 +1888,25 @@
 cat f90srclist.inc    >> $MAKEFILE
 cat hlist.inc         >> $MAKEFILE
 cat ad_flow_files.inc >> $MAKEFILE
-echo               >> $MAKEFILE
-echo 'F77FILES =  $(SRCFILES:.F=.f)'                                           >> $MAKEFILE
-echo 'F90FILES =  $(F90SRCFILES:.F90=.f90)'                                    >> $MAKEFILE
+echo >> $MAKEFILE
+echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE
+echo 'F90FILES =  $(F90SRCFILES:.F=.'$FS90')' >> $MAKEFILE
 echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
-
+echo >> $MAKEFILE
+echo '.SUFFIXES:' >> $MAKEFILE
+echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
 rm -f ad_flow_files.inc
 
 cat >>$MAKEFILE <<EOF
 
-.SUFFIXES:
-.SUFFIXES: .o .f .p .F .c .F90 .f90
-
 all: \$(EXECUTABLE)
 \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)
 	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 depend:
 	@make links
-	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
+	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
@@ -1668,7 +1919,7 @@
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 Clean:
 	@make clean
 	@make cleanlinks
@@ -1679,11 +1930,11 @@
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) output.txt
+	-rm -f \$(EXECUTABLE) output.txt STD*
 
 #eh3 Makefile: makefile
 makefile:
-	$THIS_SCRIPT $@
+	$THIS_SCRIPT $G2ARGS
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
@@ -1698,22 +1949,25 @@
 	@echo Creating \$@ ...
 	echo "$FC_NAMEMANGLE" > \$@
 
-# The normal chain of rules is (  .F - .f - .o  )
-.F.f:
+# The normal chain of rules is (  .F - .$FS - .o  )
+
+%.o : %.F
+
+.F.$FS:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.f.o:
+.$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
-.F90.f90:
+.F90.$FS90:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.f90.o:
+.$FS90.o:
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .c.o:
 	\$(CC) \$(CFLAGS) -c \$<
 
-# Special exceptions that use the ( .F - .p - .f - .o ) rule-chain
+# Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
 .F.p:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.p.f:
+.p.$FS:
 	\$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
 
 #=========================================
@@ -1838,7 +2092,7 @@
     if test "x$RETVAL" != x0 ; then
 	echo "Error: unable to add file \"$i\" to the exceptions list"
     fi
-    echo "$base.f: $base.p" >> $MAKEFILE
+    echo "$base.$FS: $base.p" >> $MAKEFILE
 done
 
 echo "  Making list of NOOPTFILES"
@@ -1848,7 +2102,7 @@
     if test "x$RETVAL" != x0 ; then
 	echo "Error: unable to add file \"$i\" to the exceptions list"
     fi
-    echo "$base.o: $base.f" >> $MAKEFILE
+    echo "$base.o: $base.$FS" >> $MAKEFILE
     printf "\t\$(FC) \$(FFLAGS) \$(NOOPTFLAGS) -c \$<\n" >> $MAKEFILE
 done