--- MITgcm/tools/genmake2	2003/11/14 21:20:35	1.40
+++ MITgcm/tools/genmake2	2004/09/07 21:28:47	1.98
@@ -1,6 +1,6 @@
-#!/bin/sh
+#! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.40 2003/11/14 21:20:35 heimbach Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.98 2004/09/07 21:28:47 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,30 +13,35 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    grep -i "#define.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#undef.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#define.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+}
+
+# Search for particular CPP #cmds associated with MPI
+# usage: test_for_mpi_in_cpp_eeoptions CPP_file
+test_for_mpi_in_cpp_eeoptions() {
+    cpp_options=$1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+}
+
+# Search for particular string in a file. Return 1 if detected, 0 if not
+# usage: test_for_string_in_file file string
+test_for_string_in_file() {
+    file=$1
+    strng=$2
+    grep -i "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define DISABLE_$pkg"
-	exit 99
+	printf "Error: In $file there is an illegal line: "
+        grep -i "$strng" $file
+	return 1
     fi
-    grep -i "#undef.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef DISABLE_$pkg"
-	exit 99
-   fi
+    return 0
 }
 
 # Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -62,31 +67,189 @@
 	done
 	PACKAGES=$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()  {
 
     tmp1=`uname`"_"`uname -m`
     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-    PLATFORM=`echo $tmp3 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
+    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:  $PLATFORM"
-#     if test "x$OFLIST" = x ; then
-# 	echo "  No pre-defined options files were found matching this platform"
-# 	echo "  but examples for other platforms can be found in:"
-# 	echo "    $ROOTDIR/tools/build_options"
-#     else
-# 	echo "  Options files (located in $ROOTDIR/tools/build_options) that"
-# 	echo "  may work with this machine are:"
-# 	for i in $OFLIST ; do
-# 	    echo "    $i"
-# 	done
-#     fi
     
     echo "test" > test
     ln -s ./test link
@@ -104,17 +267,49 @@
 	CPP="cpp -traditional -P"
     fi
 
-    # makedepend is not always available
-    if test "x${MAKEDEPEND}" = x ; then
-      which makedepend >& /dev/null
-      RETVAL=$?
-      if test "x${RETVAL}" = x1 ; then
-         echo "    makedepend was not found. Using xmakedpend instead."
-         MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
-      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
@@ -140,7 +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
@@ -149,18 +344,27 @@
 	echo "   "$p_FC
 	if test "x$FC" = x ; then
 	    FC=`echo $p_FC | $AWK '{print $1}'`
+	    echo "  Setting FORTRAN compiler to: "$FC
 	fi
     fi
 
-    for i in $p_FC ; do
-	p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
-	if test -r $p_OF ; then
-	    OPTFILE=$p_OF
-	    echo "  The options file:  $p_OF"
-	    echo "    appears to match so we'll use it."
-	    break
-	fi
-    done
+    if test "x$OPTFILE" = x ; then
+	OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
+	if test ! -r $OPTFILE ; then
+             echo "  I looked for the file "$OPTFILE" but did not find it"
+        fi
+    fi
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#   for i in $p_FC ; do
+#p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+#if test -r $p_OF ; then
+#    OPTFILE=$p_OF
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#    break
+#fi
+#   done
     if test "x$OPTFILE" = x ; then
 	cat 1>&2 <<EOF
 
@@ -219,63 +423,135 @@
     . ./.pd_tmp
     rm -f ./.pd_tmp
 
-    echo -n "PNAME = "${}
+    printf "PNAME = "${}
 }
 
 
 #  Explain usage
 usage()  {
-    echo
-    echo "Usage: "$0" [OPTIONS]"
-    echo "  where [OPTIONS] can be:"
-    echo
-    echo "    -help | --help | -h | --h"
-    echo "    -nooptfile | --nooptfile"
-    echo "      -optfile NAME | --optfile NAME | -of NAME | --of NAME"
-    echo "      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME"
-    echo "    -pdepend NAME | --pdepend NAME"
-    echo "      -pdepend=NAME | --pdepend=NAME"
-    echo "    -pdefault NAME | --pdefault NAME"
-    echo "      -pdefault=NAME | --pdefault=NAME"
-    echo "    -make NAME | -m NAME"
-    echo "      --make=NAME | -m=NAME"
-    echo "    -makefile NAME | -mf NAME"
-    echo "      --makefile=NAME | -mf=NAME"
-    echo "    -platform NAME | --platform NAME | -pl NAME | --pl NAME"
-    echo "      -platform=NAME | --platform=NAME | -pl=NAME | --pl=NAME"
-    echo "    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME"
-    echo "      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME"
-    echo "    -mods NAME | --mods NAME | -mo NAME | --mo NAME"
-    echo "      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME"
-    echo "    -disable NAME | --disable NAME"
-    echo "      -disable=NAME | --disable=NAME"
-    echo "    -enable NAME | --enable NAME"
-    echo "      -enable=NAME | --enable=NAME"
-    echo "    -standarddirs NAME | --standarddirs NAME"
-    echo "      -standarddirs=NAME | --standarddirs=NAME"
-    echo "    -noopt NAME | --noopt NAME"
-    echo "      -noopt=NAME | --noopt=NAME"
-#    echo "    -cpp NAME | --cpp NAME"
-#    echo "      -cpp=NAME | --cpp=NAME"
-    echo "    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME"
-    echo "      -fc=NAME | --fc=NAME"
-    echo "    -[no]ieee | --[no]ieee"
-    echo "    -[no]mpi | --[no]mpi"
-    echo "    -[no]jam | --[no]jam"
-    echo
-    echo "  and NAME is a string such as:"
-    echo
-    echo "    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'"
-    echo "    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'"
-    echo "    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'"
-    echo
-    echo "  which, depending upon your shell, may need to be single-quoted"
-    echo "  if it contains spaces, dashes, or other special characters."
+cat <<EOF
+
+Usage: "$0" [OPTIONS]
+  where [OPTIONS] can be:
+
+    -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
+          Use "NAME" as the optfile.  By default, an attempt will be
+          made to find an appropriate "standard" optfile in the 
+          tools/build_options/ directory.
+
+    -pdepend NAME | --pdepend NAME
+      -pdepend=NAME | --pdepend=NAME
+          Get package dependency information from "NAME".
+
+    -pdefault NAME | --pdefault NAME
+      -pdefault=NAME | --pdefault=NAME
+          Get the default package list from "NAME".
+
+    -make NAME | -m NAME
+      --make=NAME | -m=NAME
+          Use "NAME" for the MAKE program. The default is "make" but 
+          many platforms, "gmake" is the preferred choice.
+
+    -makefile NAME | -mf NAME
+      --makefile=NAME | -mf=NAME
+          Call the makefile "NAME".  The default is "Makefile".
+
+    -makedepend NAME | -md NAME
+      --makedepend=NAME | -md=NAME
+          Use "NAME" for the MAKEDEPEND program.
+
+    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
+      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
+          Specify the location of the MITgcm ROOTDIR as "NAME".
+          By default, genamke will try to find the location by 
+          looking in parent directories (up to the 5th parent).
+
+    -mods NAME | --mods NAME | -mo NAME | --mo NAME
+      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
+          Here, "NAME" specifies a list of directories that are 
+          used for additional source code.  Files found in the 
+          "mods list" are given preference over files of the same 
+          name found elsewhere.
+
+    -disable NAME | --disable NAME
+      -disable=NAME | --disable=NAME
+          Here "NAME" specifies a list of packages that we don't 
+          want to use.  If this violates package dependencies, 
+          genamke will exit with an error message.
+
+    -enable NAME | --enable NAME
+      -enable=NAME | --enable=NAME
+          Here "NAME" specifies a list of packages that we wish 
+          to specifically enable.  If this violates package 
+          dependencies, genamke will exit with an error message.
+
+    -standarddirs NAME | --standarddirs NAME
+      -standarddirs=NAME | --standarddirs=NAME
+          Here, "NAME" specifies a list of directories to be 
+          used as the "standard" code.
+
+    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
+      -fc=NAME | --fc=NAME
+          Use "NAME" as the fortran compiler.  By default, genmake 
+          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 
+          is being used.
+
+    -mpi | --mpi
+          Include MPI header files and link to MPI libraries
+    -mpi=PATH | --mpi=PATH
+          Include MPI header files and link to MPI libraries using MPI_ROOT
+          set to PATH. i.e. Include files from \$PATH/include, link to libraries
+          from \$PATH/lib and use binaries from \$PATH/bin.
+
+    -bash NAME
+          Explicitly specify the Bourne or BASH shell to use
+
+  While it is most often a single word, the "NAME" variables specified 
+  above can in many cases be a space-delimited string such as:
+
+    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
+    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
+    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
+
+  which, depending upon your shell, may need to be single-quoted.
+
+  For more detailed genmake documentation, please see:
+
+    http://mitgcm.org/devel_HOWTO/
+
+EOF
+
     exit 1
 }
 
 #  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
@@ -293,7 +569,7 @@
 EOF
 	return 1
     fi
-    c_tcall=`nm genmake_test.o | 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=$default_nm
@@ -323,7 +599,7 @@
 EOF
 	return 1
     fi
-    f_tcall=`nm genmake_tcomp.o | grep tcall | cut -d ' ' -f 3`
+    f_tcall=`nm genmake_tcomp.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -399,6 +675,55 @@
 }
 
 
+check_netcdf_libs()  {
+    echo "" > genmake_tnc.log
+    cat <<EOF > genmake_tnc.for
+      program fgennc
+#include "netcdf.inc"
+      integer iret, ncid, xid
+      iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_def_dim(ncid, 'X', 11, xid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_close(ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      end
+EOF
+    #echo "$CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f"
+    #echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.f"
+    #echo "$LINK -o genmake_tnc.o $LIBS"
+    $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
+	&&  $FC $FFLAGS $FOPTIM -c genmake_tnc.f  \
+	&&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+    RET_COMPILE=$?
+    test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    RETVAL=$?
+    if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	HAVE_NETCDF=t
+    else
+	# try again with "-lnetcdf" added to the libs
+	$CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
+	    &&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f \
+	    $LIBS -lnetcdf >> genmake_tnc_2.log 2>&1
+	RET_COMPILE=$?
+	test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+	RETVAL=$?
+	if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	    LIBS="$LIBS -lnetcdf"
+	    HAVE_NETCDF=t
+	else
+	    cat genmake_tnc.log >> genmake_warnings
+	fi
+    fi
+    rm -f genmake_tnc*
+}
+
+
+
+###############################################################################
+#   Sequential part of script starts here
+###############################################################################
+
 #  Set defaults here
 COMMANDL="$0 $@"
 
@@ -407,14 +732,15 @@
 S64=
 KPP=
 FC=
+#CC=gcc
+CPP=
 LINK=
-# DEFINES="-DWORDLENGTH=4"
 DEFINES=
 PACKAGES=
 ENABLE=
 DISABLE=
 MAKEFILE=
-MAKEDEPEND=
+#MAKEDEPEND=
 PDEPEND=
 DUMPSTATE=t
 PDEFAULT=
@@ -425,29 +751,38 @@
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
 
 # DEFINES checked by test compilation
 HAVE_SYSTEM=
 HAVE_FDATE=
 FC_NAMEMANGLE=
 HAVE_CLOC=
+HAVE_NETCDF=
+HAVE_ETIME=
 
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
 INCLUDEDIRS=
-STANDARDDIRS=
+STANDARDDIRS="USE_THE_DEFAULT"
 
+G2ARGS=
+BASH=
 PWD=`pwd`
 MAKE=make
 AWK=awk
-THISHOSTNAME=`hostname`
+THISHOST=`hostname`
 THISCWD=`pwd`
 THISDATE=`date`
+THISUSER=`echo $USER`
+THISVER=
 MACHINE=`uname -a`
 EXECUTABLE=
 EXEHOOK=
@@ -457,6 +792,8 @@
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
 fi
+FS=
+FS90=
 
 AUTODIFF_PKG_USED=f
 AD_OPTFILE=
@@ -473,15 +810,15 @@
 
 
 #  The following state can be set directly by command-line switches
-gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE NOOPT"
-gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
+gm_s2="FC CPP IEEE 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_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
+gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER 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"
@@ -491,8 +828,17 @@
 gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
 gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
 
+cat <<EOF
+
+GENMAKE :
+
+A program for GENerating MAKEfiles for the MITgcm project.  For a
+quick list of options, use "genmake -h" or for more detail see:
+
+  http://mitgcm.org/devel_HOWTO/
+
+EOF
 
-echo
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
 for i in . $MODS ; do
@@ -501,8 +847,8 @@
 	break
     fi
 done
-echo -n "  getting local config information:  "
-if test -e $gm_local ; then
+printf "  getting local config information:  "
+if test -f $gm_local ; then
     echo "using $gm_local"
     . $gm_local
     # echo "DISABLE=$DISABLE"
@@ -523,7 +869,9 @@
 #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 "$ac_prev"; then
@@ -546,7 +894,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -566,15 +914,27 @@
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$ac_optarg ;;
 	
+	-bash | --bash)
+	    ac_prev=BASH ;;
+	-bash=* | --bash=*)
+	    BASH=$ac_optarg ;;
+	
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MAKEDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MAKEDEPEND=$ac_optarg ;;
+	
 	-makefile | --makefile | -ma | --ma)
 	    ac_prev=MAKEFILE ;;
 	-makefile=* | --makefile=* | -ma=* | --ma=*)
 	    MAKEFILE=$ac_optarg ;;
 	
-	-platform | --platform | -pl | --pl)
-	    ac_prev=PLATFORM ;;
-	-platform=* | --platform=* | -pl=* | --pl=*)
-	    PLATFORM=$ac_optarg ;;
+	-platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
+	    echo "ERROR: The platform option has been removed.  Please specify"
+	    echo "  the build options using the \"optfile\" mechanism."
+	    echo
+	    usage
+	    ;;
 	
 	-rootdir | --rootdir | -rd | --rd)
 	    ac_prev=ROOTDIR ;;
@@ -601,35 +961,46 @@
 	-standarddirs=* | --standarddirs=*)
 	    STANDARDDIRS=$ac_optarg ;;
 
-	-noopt | --noopt)
-	    ac_prev=NOOPT ;;
-	-noopt=* | --noopt=*)
-	    NOOPT=$ac_optarg ;;
-	
 #	    -cpp | --cpp)
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
 #		CPP=$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)
 	    IEEE= ;;
-	
+
 	-mpi | --mpi)
 	    MPI=true ;;
-	-nompi | --nompi)
-	    MPI= ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
-	-jam | --jam)
-	    JAM=1 ;;
-	-nojam | --nojam)
-	    JAM=0 ;;
+#	-jam | --jam)
+#	    JAM=1 ;;
+#	-nojam | --nojam)
+#	    JAM=0 ;;
 	
 	-ds | --ds)
 	    DUMPSTATE=t ;;
@@ -670,14 +1041,16 @@
     echo 
 fi
 
+#  Find the MITgcm ${ROOTDIR}
 if test "x${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
 	    if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
 		ROOTDIR=$d
-		echo -n "Warning:  ROOTDIR was not specified but there appears to be"
+		printf "Warning:  ROOTDIR was not specified but there appears to be"
 		echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
 		break
 	    fi
@@ -695,6 +1068,11 @@
     exit 1
 fi
 
+#  Find the MITgcm ${THISVER}
+if test -f "${ROOTDIR}/doc/tag-index" ; then
+    THISVER=`grep checkpoint ${ROOTDIR}/doc/tag-index | head -1`
+fi
+
 echo "  getting OPTFILE information:  "
 if test "x${OPTFILE}" = x ; then
     if test "x$MITGCM_OF" = x ; then
@@ -711,7 +1089,7 @@
 	. "$OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source OPTFILE \"$OPTFILE\""
+	    printf "Error: failed to source OPTFILE \"$OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -724,6 +1102,9 @@
     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
@@ -738,7 +1119,7 @@
 	. "$AD_OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
+	    printf "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -751,8 +1132,12 @@
     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$BASH" = x ; then
+    # add a trailing space so that it works within the Makefile syntax (see below)
+    BASH="$BASH "
+fi
 if test "x$FC" = x ; then
     cat <<EOF 1>&2
 
@@ -763,15 +1148,34 @@
 EOF
     exit 1
 fi
+if test "x$CC" = x ; then
+    CC=cc
+#     cat <<EOF 1>&2
+# Error: no C compiler: please specify using one of the following:
+#   1) within the options file ("CC=...") as specified by "-of=OPTFILE"
+#   2) the "-cc=XXX" command-line option
+#   3) the "./genmake_local" file
+# EOF
+#     exit 1
+fi
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
-if test "x$CPP" = x ; then
-    CPP="cpp"
-fi
 if test "x$MAKE" = x ; then
     MAKE="make"
 fi
+if test "x$CPP" = x ; then
+    CPP=cpp
+fi
+#EH3 === UGLY ===
+#  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
+    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
+done
+#EH3 === UGLY ===
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -788,9 +1192,7 @@
 else
     rm -f test_cpp
 fi
-if test "x$MAKEDEPEND" = x ; then
-    MAKEDEPEND=makedepend
-fi
+look_for_makedepend
 if test "x$LN" = x ; then
     LN="ln -s"
 fi
@@ -808,9 +1210,16 @@
 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"
+fi
 
 printf "\n===  Checking system libraries  ===\n"
-echo -n "  Do we have the system() command using $FC...  "
+printf "  Do we have the system() command using $FC...  "
 cat > genmake_tcomp.f <<EOF
       program hello
       call system('echo hi')
@@ -828,7 +1237,7 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Do we have the fdate() command using $FC...  "
+printf "  Do we have the fdate() command using $FC...  "
 cat > genmake_tcomp.f <<EOF
       program hello
       CHARACTER(128) string
@@ -849,31 +1258,55 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+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
     echo "yes"
 else
     echo "no"
 fi
-echo "$FC_NAMEMANGLE" > FC_NAMEMANGLE.h.template
-cmp FC_NAMEMANGLE.h FC_NAMEMANGLE.h.template > /dev/null 2>&1
-RETVAL=$?
-if test "x$RETVAL" != x0 ; then
-    mv -f FC_NAMEMANGLE.h.template FC_NAMEMANGLE.h
-fi
 rm -f genmake_t*
 
+printf "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+
 
 printf "\n===  Setting defaults  ===\n"
-echo -n "  Adding MODS directories:  "
+printf "  Adding MODS directories:  "
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	echo -n " $d"
+	printf " $d"
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
     fi
@@ -888,7 +1321,8 @@
 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 $ROOTDIR = .. ; then
 	EXEDIR=../exe
     else
 	EXEDIR=.
@@ -903,12 +1337,13 @@
     TOOLSDIR="$ROOTDIR/tools"
 fi
 if test ! -d ${TOOLSDIR} ; then
-    echo "Error: the specified $TOOLSDIR (\"$TOOLSDIR\") does not exist!"
+    echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
     exit 1
 fi
 if test "x$S64" = x ; then
     S64='$(TOOLSDIR)/set64bitConst.sh'
 fi
+THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSDIR':\$(TOOLSDIR):'`
 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
 
@@ -923,11 +1358,25 @@
 	rm -f make_eesupp.errors
     else
 	echo "Error: problem encountered while building source files in eesupp:"
-	cat make_eesupp.errors
+	cat make_eesupp.errors 1>&2
 	exit 1
     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${RETVAL}" = x0 ; then
+        rm -f make_exch2.errors
+    else
+        echo "Error: problem encountered while building source files in exch2:"
+        cat make_exch2.errors 1>&2
+        exit 1
+    fi
+fi
+
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
@@ -960,7 +1409,7 @@
 #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
 #  file should eventually be added so that, for convenience, one can 
 #  specify groups of packages using names like "ocean" and "atmosphere".
-echo  -n "  checking default package list:  "
+echo "  checking default package list:  "
 if test "x${PDEFAULT}" = x ; then
     for i in "." $MODS ; do
 	if test -r $i"/packages.conf" ; then
@@ -973,18 +1422,17 @@
     PDEFAULT="$ROOTDIR/pkg/pkg_default"
 fi
 if test "x${PDEFAULT}" = xNONE ; then
-    echo "default packages file disabled"
+    echo "    default packages file disabled"
 else
     if test ! -r $PDEFAULT ; then
-	echo ""
 	echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
     else
-	echo "  using PDEFAULT=\"$PDEFAULT\""
+	echo "    using PDEFAULT=\"$PDEFAULT\""
         #  Strip the comments and add all the names
 	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
 	if test "x${RETVAL}" != x0 ; then
-	    echo -n "Error: can't parse default package list "
+	    printf "Error: can't parse default package list "
 	    echo "-- please check PDEFAULT=\"$PDEFAULT\""
 	    exit 1
 	fi
@@ -992,12 +1440,20 @@
 	    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 $PACKAGES ; do
     addit="t"
@@ -1014,19 +1470,20 @@
 echo "  applying ENABLE settings"
 echo "" > ./.tmp_pack
 PACKAGES="$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"
@@ -1093,7 +1550,8 @@
 	    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
@@ -1112,27 +1570,42 @@
     fi
 done
 
+#  Build MNC templates and check for ability to build and use NetCDF
+echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    ( cd $ROOTDIR"/pkg/mnc" && $MAKE templates ) > make_mnc.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+	rm -f make_mnc.errors
+    else
+	echo "Error: problem encountered while building source files in pkg/mnc:"
+	cat make_mnc.errors 1>&2
+	exit 1
+    fi
+    if test "x$HAVE_NETCDF" != xt ; then
+	cat <<EOF
 
-# Create a list of #define and #undef to enable/disable packages
-PACKAGES_DOT_H=PACKAGES_CONFIG.h
-cat <<EOF >$PACKAGES_DOT_H".tmp"
-C=== GENMAKE v2 ===
-C  The following defines have been set by GENMAKE, so please do not
-C  edit anything below these comments.  In general, you should
-C  add or remove packages by re-running genmake with different 
-C  "-enable" and/or "-disable" options.
-
-#ifndef PACKAGES_H
-#define PACKAGES_H
+WARNING: the "mnc" package has been enabled but tests failed to 
+  compile and/or execute NetCDF applications.  Please check that:
 
-C  Packages disabled by genmake:
+  1) NetCDF is installed for your compiler and
+  2) the LIBS variable (within the 'optfile") specifies the correct 
+       NetCDF library to link against.
+  
 EOF
+    fi
+fi
+
+# Create a list of #define and #undef to enable/disable packages
+PACKAGES_DOT_H=PACKAGES_CONFIG.h
 #  The following UGLY HACK sets multiple "#undef"s and it needs to go 
 #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h 
 #  file would eventually be split up so that all package-related #define
 #  statements could be separated and handled only by genmake.
 names=`ls -1 "$ROOTDIR/pkg"`
 all_pack=
+DISABLED_PACKAGES=
 for n in $names ; do
     if test -d "$ROOTDIR/pkg/$n" -a "x$n" != xCVS ; then
 	has_pack="f"
@@ -1144,95 +1617,83 @@
 	done
 	if test "x$has_pack" = xf ; then
 	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
-	    echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
+            DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
 	fi
     fi
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-C  Packages enabled by genmake:
-EOF
+ENABLED_PACKAGES=
 for i in $PACKAGES ; do
     def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`
-    echo "#define $def" >> $PACKAGES_DOT_H".tmp"
+    ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"
 #eh3 DEFINES="$DEFINES -D$def"
 
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
     case $i in 
 	aim_v23)
-	    echo "#define   ALLOW_AIM" >> $PACKAGES_DOT_H".tmp"
-	    DEFINES="$DEFINES -DALLOW_AIM"
-	    echo "Warning: ALLOW_AIM is set to enable aim_v23. This is REALLY ugly Jean-Michel :-)"
+            ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
+	    echo "Warning: ALLOW_AIM is set to enable aim_v23."
 	    ;;
     esac
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
 
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-#endif /* PACKAGES_H */
-EOF
-
-if test ! -f $PACKAGES_DOT_H ; then
-    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-else
-    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    RETVAL=$?
-    if test "x$RETVAL" = x0 ; then
-	rm -f $PACKAGES_DOT_H".tmp"
-    else
-	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
-	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    fi
-fi
 
 echo "  Adding STANDARDDIRS"
 BUILDDIR=${BUILDDIR:-.}
-if test "x$STANDARDDIRS" = x ; then
+if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
     STANDARDDIRS="eesupp model"
 fi
-for d in $STANDARDDIRS ; do
-    adr="$ROOTDIR/$d/src"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	SOURCEDIRS="$SOURCEDIRS $adr"
-    fi
-    adr="$ROOTDIR/$d/inc"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	INCLUDEDIRS="$INCLUDEDIRS $adr"
-    fi
-done
+if test "x$STANDARDDIRS" != x ; then
+    for d in $STANDARDDIRS ; do
+	adr="$ROOTDIR/$d/src"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    SOURCEDIRS="$SOURCEDIRS $adr"
+	fi
+	adr="$ROOTDIR/$d/inc"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    INCLUDEDIRS="$INCLUDEDIRS $adr"
+	fi
+    done
+fi
 
-echo "  Searching for CPP_OPTIONS.h in order to warn about the presence"
-echo "    of \"#define ALLOW_PKGNAME\"-type statements:"
+echo "  Searching for *OPTIONS.h files in order to warn about the presence"
+echo "    of \"#define \"-type statements that are no longer allowed:"
 CPP_OPTIONS=
+CPP_EEOPTIONS=
 spaths=". $INCLUDEDIRS"
+names=`ls -1 "$ROOTDIR/pkg"`
 for i in $spaths ; do
     try="$i/CPP_OPTIONS.h"
-    #  echo -n "    trying $try : "
-    if test -f $try -a -r $try ; then
+    if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
-	break
+        # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
+        for n in $names ; do
+            test_for_package_in_cpp_options $CPP_OPTIONS $n
+        done
+    fi
+    try="$i/CPP_EEOPTIONS.h"
+    if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
+	echo "    found CPP_EEOPTIONS=\"$try\""
+        # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
+#**** not yet enabled ****
+#        test_for_mpi_in_cpp_eeoptions $try
+#**** not yet enabled ****
+	CPP_EEOPTIONS="$try"
     fi
 done
 if test "x$CPP_OPTIONS" = x ; then
     echo "Error: can't find \"CPP_OPTIONS.h\" in the path list: $spaths"
     exit 1
 fi
-# New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
-names=`ls -1 "$ROOTDIR/pkg"`
-for n in $names ; do
-    test_for_package_in_cpp_options $CPP_OPTIONS $n
-done
-
 
 #  Here, we build the list of files to be "run through" the adjoint
 #  compiler.
@@ -1247,25 +1708,12 @@
     done
 done
 
-cat <<EOF > adjoint_sed
-s/call adopen(/call adopen ( mythid,\\
-     \&           /g
-s/call adclose(/call adclose( mythid,\\
-     \&           /g
-s/call adread(/call adread ( mythid,\\
-     \&           /g
-s/call adwrite(/call adwrite( mythid,\\
-     \&           /g
-
-EOF
 
 echo
 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
@@ -1275,11 +1723,11 @@
 mkdir .links.tmp
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-echo -n 'SRCFILES = '    > srclist.inc
-echo -n 'CSRCFILES = '   > csrclist.inc
-echo -n 'F90SRCFILES = ' > f90srclist.inc
-echo -n 'HEADERFILES = ' > hlist.inc
-echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'SRCFILES = '    > srclist.inc
+printf 'CSRCFILES = '   > csrclist.inc
+printf 'F90SRCFILES = ' > f90srclist.inc
+printf 'HEADERFILES = ' > hlist.inc
+printf 'AD_FLOW_FILES = ' > ad_flow_files.inc
 alldirs="$SOURCEDIRS $INCLUDEDIRS ."
 for d in $alldirs ; do
     deplist=
@@ -1288,29 +1736,41 @@
     for sf in $sfiles ; do
 	if test ! -r ".links.tmp/$sf" ; then
 	    if test -f "$d/$sf" ; then
+                case $d/$sf in
+                  ./$PACKAGES_DOT_H)
+			;;
+                  ./AD_CONFIG.h)
+			;;
+                  ./FC_NAMEMANGLE.h)
+			;;
+                  ./BUILD_INFO.h)
+			;;
+                  *)
+		  	touch .links.tmp/$sf
+		  	deplist="$deplist $sf"
+			;;
+                esac
 		extn=`echo $sf | $AWK -F '.' '{print $NF}'`
-		touch .links.tmp/$sf
-		deplist="$deplist $sf"
 		case $extn in
 		    F)
 			echo    " \\"  >> srclist.inc
-			echo -n " $sf" >> srclist.inc
+			printf " $sf" >> srclist.inc
 			;;
 		    F90)
 			echo    " \\"  >> f90srclist.inc
-			echo -n " $sf" >> f90srclist.inc
+			printf " $sf" >> f90srclist.inc
 			;;
 		    c)
 			echo    " \\"  >> csrclist.inc
-			echo -n " $sf" >> csrclist.inc
+			printf " $sf" >> csrclist.inc
 			;;
 		    h)
 			echo    " \\"  >> hlist.inc
-			echo -n " $sf" >> hlist.inc
+			printf " $sf" >> hlist.inc
 			;;
 		    flow)
 			echo    " \\"  >> ad_flow_files.inc
-			echo -n " $sf" >> ad_flow_files.inc
+			printf " $sf" >> ad_flow_files.inc
 			;;
 		esac
 	    fi
@@ -1330,7 +1790,7 @@
 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"
@@ -1339,15 +1799,17 @@
 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
+echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
 
 EXE_AD=$EXECUTABLE"_ad"
 EXE_FTL=$EXECUTABLE"_ftl"
 EXE_SVD=$EXECUTABLE"_svd"
 
 cat >>$MAKEFILE <<EOF
+#
+# OPTFILE="$OPTFILE"
 # 
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
@@ -1381,6 +1843,12 @@
 EXE_FTL     = ${EXE_FTL}
 EXE_SVD     = ${EXE_SVD}
 
+ENABLED_PACKAGES = ${ENABLED_PACKAGES}
+DISABLED_PACKAGES = ${DISABLED_PACKAGES}
+
+# These files are created by Makefile
+SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h
+
 EOF
 
 #  Note: figure out some way to add Hyades JAM libraries here
@@ -1398,8 +1866,10 @@
 FC = ${FC}
 # Fortran compiler
 F90C = ${F90C}
+# C compiler
+CC = ${CC}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1431,28 +1901,29 @@
 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): \$(OBJFILES)
+\$(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)
-	${TOOLSDIR}/f90mkdepend >> \$(MAKEFILE)
+	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77FILES) \$(F90FILES)
 
@@ -1461,41 +1932,66 @@
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-cat AD_CONFIG.template > AD_CONFIG.h
-	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl}
+	-rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f Makefile.bak genmake_state genmake_*optfile make.log
+	-rm -f \$(SPECIAL_FILES)
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
 CLEAN:
 	@make Clean
 	-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:
-	${0} $@
+	$THIS_SCRIPT $G2ARGS
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
-# The normal chain of rules is (  .F - .f - .o  )
-.F.f:
+# Special targets (SPECIAL_FILES) which are create by make
+${PACKAGES_DOT_H}:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+AD_CONFIG.h:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+FC_NAMEMANGLE.h:
+	@echo Creating \$@ ...
+	echo "$FC_NAMEMANGLE" > \$@
+
+BUILD_INFO.h:
+	@echo Creating \$@ ...
+EOF
+
+test ! "x$THISVER" = x  && echo "	-echo \"#define THISVER '$THISVER'\" > \$@"   >> $MAKEFILE
+test ! "x$THISUSER" = x && echo "	-echo \"#define THISUSER '$THISUSER'\" >> \$@" >> $MAKEFILE
+test ! "x$THISDATE" = x && echo "	-echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
+test ! "x$THISHOST" = x && echo "	-echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
+
+cat >>$MAKEFILE <<EOF
+
+# 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) \$<
 
 #=========================================
@@ -1522,11 +2018,11 @@
 
 echo "  Add the source list for AD code generation"
 echo >> $MAKEFILE
-echo -n "AD_FILES = " >> $MAKEFILE
+printf "AD_FILES = " >> $MAKEFILE
 AD_FILES=`cat ad_files`
 for i in $AD_FILES ; do
     echo    " \\" >> $MAKEFILE
-    echo -n " $i" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
 done
 echo >> $MAKEFILE
 rm -f ad_files
@@ -1539,25 +2035,27 @@
 adtamc: ad_tamc_output.f
 
 ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	-rm -f ad_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
 
 ad_taf_output.f: ad_input_code.f
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
 
 adtafonly:
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
 
 ad_taf: ad_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
 ad_tamc_output.f: ad_input_code.f
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_tamc_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.f
 
 ad_tamc: ad_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS) 
@@ -1569,25 +2067,27 @@
 ftltamc: ftl_tamc_output.f
 
 ftl_input_code.f: \$(AD_FILES) \$(HEADERFILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+	-rm -f ftl_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
 
 ftl_taf_output.f: ftl_input_code.f
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_taf_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
 
 ftltafonly:
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_taf_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
 
 ftl_taf: ftl_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS) 
 
 ftl_tamc_output.f: ftl_input_code.f
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_tamc_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.f
 
 ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS) 
@@ -1616,7 +2116,7 @@
     if test "x$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"
@@ -1626,7 +2126,7 @@
     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
 
@@ -1639,49 +2139,28 @@
 
 printf "\n===  Done  ===\n"
 
-#  Write the "template" files for the adjoint builds
-cat >AD_CONFIG.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >ad_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#define ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >ftl_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#define ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >svd_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cp AD_CONFIG.template AD_CONFIG.h
+# Create special header files
+$BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp" 
+if test ! -f $PACKAGES_DOT_H ; then
+    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+else
+    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	rm -f $PACKAGES_DOT_H".tmp"
+    else
+	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
+	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    fi
+fi
+if test ! -f AD_CONFIG.h ; then
+    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
+fi
 
 
 #  Write the "state" for future records
 if test "x$DUMPSTATE" != xf ; then
-    echo -n "" > genmake_state
+    printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"
 	eval $t1