--- MITgcm/tools/genmake2	2003/11/11 20:38:27	1.29
+++ MITgcm/tools/genmake2	2009/04/22 18:35:00	1.190
@@ -1,6 +1,6 @@
-#!/bin/bash
+#! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.29 2003/11/11 20:38:27 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.190 2009/04/22 18:35:00 utke Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,30 +13,43 @@
 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[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
+}
+
+# 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[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
+}
+
+# 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"
+	printf "Error: In $file there is an illegal line: "
+        grep -i "$strng" $file
 	exit 99
     fi
-    grep -i "#undef.*DISABLE_$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 $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -62,31 +75,235 @@
 	done
 	PACKAGES=$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".tst"
+    cat <<EOF >> $MAKEFILE
+.SUFFIXES:
+.SUFFIXES: .$tfs .F
+.F.$tfs:
+	$LN \$< \$@
+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".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
+
+    #  If we make it here, use the extensions
+    FS=$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=$?
+	test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
+	#  echo 'MAKEFILE="'$MAKEFILE'"'
+	cat <<EOF >> $MAKEFILE
+#   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
+#
+#   Some "makedepend" implementations will die if they cannot 
+#   find a Makefile -- so this file is here to gives them an 
+#   empty one to find and parse.
+EOF
+	cat <<EOF >> genmake_tc.f
+      program test
+      write(*,*) 'test'
+      stop
+      end
+EOF
+	makedepend genmake_tc.f > /dev/null 2>&1
+	RV1=$?
+	test -f $MAKEFILE  &&  rm -f $MAKEFILE
+	test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
+	if test "x${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
+}
+
+
+build_embed_encode()
+{
+    printf "  building the embed-encode utility...  "
+    if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
+        if test ! -d "$ROOTDIR/tools/embed_encode" ; then
+            echo
+            echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
+            echo
+            EMBED_SRC=f
+	    return 1
+        fi
+	clist="cc gcc c89 $CC"
+	for ic in $clist ; do 
+	    comm="$ic -o encode_files encode_files.c"
+	    ( cd $ROOTDIR/tools/embed_encode && $comm ) > /dev/null 2>&1
+	    RETVAL=$?
+	    if test "x$RETVAL" = x0 ; then
+		echo "OK"
+		DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+		return 0
+	    fi
+	done
+	echo
+	echo "    Error: unable to build $ROOTDIR/embed_encode/encode_files"
+	echo "      so it has been disabled"
+	echo
+	EMBED_SRC=f
+	return 1
+    fi
+    echo "OK"
+    DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+}
+
+
 # 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
@@ -104,8 +321,50 @@
 	CPP="cpp -traditional -P"
     fi
 
-    # look for possible fortran compilers
-    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
+    look_for_makedepend
+
+    #================================================================
+    #  look for possible C compilers
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
+    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
+    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
@@ -130,27 +389,44 @@
 
     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
     else
 	echo "  The possible FORTRAN compilers found in your path are:"
 	echo "   "$p_FC
-	if test "x$FC" = x ; then
-	    FC=`echo $p_FC | $AWK '{print $1}'`
-	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:  $p_OF"
-	    echo "    appears to match so we'll use it."
-	    break
-	fi
-    done
+    #  Use the first of the compilers found in the current PATH
+    #  that has a correctly-named optfile
+    if test "x$OPTFILE" = x  -a  "x$FC" = x ; then
+	for i in $p_FC ; do
+	    OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+	    if test -r $OPTFILE ; then
+		echo "  Setting OPTFILE to: "$OPTFILE
+		break
+	    fi
+	done
+    fi
+
+    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
 
@@ -206,82 +482,549 @@
     cat $1 | sed -e 's/#.*$//g' \
 	| $AWK 'BEGIN{nn=0;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME["nn"]="$1"\nDNAME["nn"]="$i} }' \
 	> ./.pd_tmp
-    source ./.pd_tmp
+    . ./.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.
+
+    -ignoretime | -ignore_time | --ignoretime | --ignore_time
+          Ignore all the "wall clock" routines entirely.  This will
+          not in any way hurt the model results -- it simply means 
+          that the code that checks how long the model spends in 
+          various routines will give junk values.
+
+    -ts | --ts
+          Produce timing information per timestep
+    -papis | --papis
+          Produce summary MFlop/s (and IPC) with PAPI per timestep
+    -pcls | --pcls
+          Produce summary MFlop/s etc. with PCL per timestep
+    -foolad | --foolad
+          Fool the AD code generator
+    -papi | --papi
+          Performance analysis with PAPI
+    -pcl | --pcl
+          Performance analysis with PCL
+    -hpmt | --hpmt
+          Performance analysis with the HPM Toolkit
+
+    -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
+    -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.
+
+    -omp | --omp
+          Activate OpenMP code + use Compiler option OMPFLAG
+    -omp=OMPFLAG | --omp=OMPFLAG
+          Activate OpenMP code + use Compiler option OMPFLAG
+
+    -es | --es | -embed-source | --embed-source
+          Embed a tarball containing the full source code 
+          (including the Makefile, etc.) used to build the 
+          executable [off by default]
+
+    -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
 }
 
-#eh3 # This is the generic configuration.
-#eh3 set LN         = ( 'ln -s' )
-#eh3 set CPP        = ( '/lib/cpp -P' )
-#eh3 set S64        = ( '$(TOOLSDIR)/set64bitConst.sh' )
-#eh3 set KPP        = (  )
-#eh3 set FC         = ( 'f77' )
-#eh3 set LINK       = $FC
-#eh3 set MAKEDEPEND = ( 'makedepend' )
-#eh3 set INCLUDES   = ( -I. )
-#eh3 set FFLAGS     = (  )
-#eh3 set FOPTIM     = (  )
-#eh3 set CFLAGS     = (  )
-#eh3 set KFLAGS1    = (  )
-#eh3 set KFLAGS2    = (  )
-#eh3 set LIBS       = (  )
-#eh3 set KPPFILES   = (  )
-#eh3 if (! $?NOOPTFILES ) set NOOPTFILES = (  )
-#eh3 if (! $?NOOPTFLAGS ) set NOOPTFLAGS = (  )
+#  Build a CPP macro to automate calling C routines from FORTRAN
+get_fortran_c_namemangling()  {
+
+    #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
+    if test ! "x$FC_NAMEMANGLE" = x ; then
+        return 0
+    fi
+
+    default_nm="#define FC_NAMEMANGLE(X) X ## _"
+    
+    cat > genmake_test.c <<EOF
+void tcall( char * string ) { tsub( string ); }
+EOF
+    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_errors
+
+WARNING: C test compile fails
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    c_tcall=`nm genmake_test.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    cat > genmake_tcomp.$FS <<EOF
+      subroutine tcall( string )
+      character*(*) string
+      call tsub( string )
+      end
+EOF
+    $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+    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=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+
+    c_a=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    f_a=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    c_b=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+    f_b=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+
+    nmangle="X"
+    if test "x$c_a" != "x$f_a" ; then
+	comm="echo x$f_a | sed -e 's|x$c_a||'"
+	a=`eval $comm`
+	nmangle="$a ## $nmangle"
+    fi
+    if test "x$c_b" != "x$f_b" ; then
+	comm="echo x$f_b | sed -e 's|x$c_b||'"
+	b=`eval $comm`
+	nmangle="$nmangle ## $b"
+    fi
+
+    FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmangle"
+
+    #  cleanup the testing files
+    rm -f genmake_tcomp.* genmake_test.*
+}
+
+
+check_HAVE_CLOC()  {
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <assert.h>
+#include <sys/time.h>
+void FC_NAMEMANGLE(cloc) ( double *curtim )
+{
+ struct timeval tv1;
+ gettimeofday(&tv1 , (void *)NULL );
+ *curtim =  (double)((tv1.tv_usec)+(tv1.tv_sec)*1.E6);
+ *curtim = *curtim/1.E6;
+}
+EOF
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      REAL*8 wtime
+      external cloc
+      call cloc(wtime)
+      print *," HELLO WORLD", wtime
+      end
+EOF
+    COMM="$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=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_CLOC=t
+	DEFINES="$DEFINES -DHAVE_CLOC"
+    fi
+    rm -f genmake_tc*
+}
+
+
+check_HAVE_SIGREG()  {
+    if test ! "x$HAVE_SIGREG" = x ; then
+	return
+    fi
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <stdlib.h>
+#include <stdio.h>
+#include <signal.h>
+#include <errno.h>
+#include <ucontext.h>
+
+int * ip;
+
+static void killhandler(
+    unsigned int sn, siginfo_t  si, struct ucontext *sc )
+{
+    *ip = *ip + 1;
+    return;
+}
+
+void FC_NAMEMANGLE(sigreg) (int * aip)
+{
+    struct sigaction s;
+    ip = aip;
+    s.sa_flags = SA_SIGINFO;
+    s.sa_sigaction = (void *)killhandler;
+    if(sigaction (SIGTERM,&s,(struct sigaction *)NULL)) {
+	printf("Sigaction returned error = %d\n", errno);
+	exit(0);
+    }
+    return;
+}
+EOF
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      integer anint
+      common /iv/ anint
+      external sigreg
+      call sigreg(anint)
+      end
+EOF
+    echo >> genmake_warnings
+    echo "running: check_HAVE_SIGREG()" >> genmake_warnings
+    cat genmake_tc_2.$FS >> genmake_warnings
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_SIGREG=t
+	DEFINES="$DEFINES -DHAVE_SIGREG"
+    fi
+    rm -f genmake_tc*
+}
+
+
+check_HAVE_SETRLSTK()  {
+    if test "x$HAVE_SETRLSTK" = xt ; then
+	DEFINES="$DEFINES -DHAVE_SETRLSTK"
+	return
+    fi	
+    if test ! "x$HAVE_SETRLSTK" = x ; then
+	return
+    fi
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <sys/time.h>
+#include <sys/resource.h>
+#include <unistd.h>
+void FC_NAMEMANGLE(setrlstk) ()
+{
+    struct rlimit rls;
+    rls.rlim_cur = RLIM_INFINITY;
+    rls.rlim_max = RLIM_INFINITY;
+    setrlimit(RLIMIT_STACK, &rls);
+    return;
+}
+EOF
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      external setrlstk
+      call setrlstk()
+      end
+EOF
+    echo >> genmake_warnings
+    echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
+    cat genmake_tc_2.$FS >> genmake_warnings
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_SETRLSTK=t
+	DEFINES="$DEFINES -DHAVE_SETRLSTK"
+    fi
+    rm -f genmake_tc*
+}
+
+
+check_HAVE_STAT()  {
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+void FC_NAMEMANGLE(tfsize) ( int *nbyte )
+{
+    char name[512];
+    struct stat astat;
+
+    name[0] = 'a'; name[1] = '\0';
+    if (! stat(name, &astat))
+        *nbyte = (int)(astat.st_size);
+    else
+        *nbyte = -1;
+}
+EOF
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_tc.log 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      integer nbyte
+      call tfsize(nbyte)
+      print *," HELLO WORLD", nbyte
+      end
+EOF
+    echo >> genmake_warnings
+    echo "running: check_HAVE_STAT()" >> genmake_warnings
+    cat genmake_tc_2.$FS >> genmake_warnings
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_tc.log 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_STAT=t
+	DEFINES="$DEFINES -DHAVE_STAT"
+    fi
+    rm -f genmake_tc*
+}
+
+
+check_netcdf_libs()  {
+    if test ! "x$SKIP_NETCDF_CHECK" = x ; then
+	return
+    fi
+    echo >> genmake_warnings
+    echo "running: check_netcdf_libs()" >> genmake_warnings
+    cat <<EOF > genmake_tnc.F
+      program fgennc
+#include "netcdf.inc"
+EOF
+    if test ! "x$MPI" = x ; then
+	echo '#include "mpif.h"' >> genmake_tnc.F
+    fi
+    cat <<EOF >> genmake_tnc.F
+      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 "===  genmake_tnc.F  ===" > genmake_tnc.log
+    cat genmake_tnc.F >> genmake_tnc.log
+    echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
+    RET_CPP=f
+    COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
+    echo "$COMM" >> genmake_tnc.log
+    eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
+    if test "x$RET_CPP" = xf ; then
+	echo "  WARNING: CPP failed to pre-process the netcdf test." \
+	    >> genmake_tnc.log
+	echo "    Please check that \$INCLUDES is properly set." \
+	    >> genmake_tnc.log
+    fi
+    echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> 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 $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+    RET_COMPILE=$?
+    cat genmake_tnc.log >> genmake_warnings
+
+    #EH3  Remove test program execution for machines that either disallow
+    #EH3  execution or cannot support it (eg. cross-compilers)
+    #EH3
+    #EH3 test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    #EH3 RETVAL=$?
+    #EH3 if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+
+    if test "x$RET_COMPILE" = x0 ; then
+	HAVE_NETCDF=t
+    else
+	# try again with "-lnetcdf" added to the libs
+	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 $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 $LIBS -lnetcdf >> genmake_tnc.log 2>&1
+	RET_COMPILE=$?
+	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*
+}
+
+
+
+###############################################################################
+#   Sequential part of script starts here
+###############################################################################
 
 #  Set defaults here
 COMMANDL="$0 $@"
@@ -290,46 +1033,77 @@
 LN=
 S64=
 KPP=
-FC=
+#FC=
+#CC=gcc
+#CPP=
 LINK=
-DEFINES="-DWORDLENGTH=4"
+DEFINES=
 PACKAGES=
 ENABLE=
 DISABLE=
-MAKEFILE=
-MAKEDEPEND=
+# MAKEFILE=
+# MAKEDEPEND=
 PDEPEND=
 DUMPSTATE=t
 PDEFAULT=
 OPTFILE=
-INCLUDES="-I."
+INCLUDES="-I. $INCLUDES"
 FFLAGS=
 FOPTIM=
+FEXTRAFLAGS=
+USE_EXTENDED_SRC=
+EXTENDED_SRC_FLAG=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
+OMP=
+OMPFLAG=
+TS=
+PAPIS=
+PCLS=
+FOOLAD=
+PAPI=
+PCL=
+HPMT=
+GSL=
+DEVEL=
+HAVE_TEST_L=
 
-# DEFINES checked by test compilation
+# DEFINES checked by test compilation or command-line
 HAVE_SYSTEM=
 HAVE_FDATE=
 FC_NAMEMANGLE=
+HAVE_CLOC=
+# HAVE_SETRLSTK=
+HAVE_STAT=
+HAVE_NETCDF=
+HAVE_ETIME=
+IGNORE_TIME=
 
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
 INCLUDEDIRS=
-STANDARDDIRS=
+STANDARDDIRS="USE_THE_DEFAULT"
 
+G2ARGS=
+BASH=
 PWD=`pwd`
-MAKE=make
-AWK=awk
-THISHOSTNAME=`hostname`
+test "x$MAKE" = x  &&  MAKE=make
+test "x$AWK" = x   &&  AWK=awk
+EMBED_SRC=
+THISHOST=`hostname`
 THISCWD=`pwd`
 THISDATE=`date`
+THISUSER=`echo $USER`
+THISVER=
 MACHINE=`uname -a`
 EXECUTABLE=
 EXEHOOK=
@@ -339,6 +1113,8 @@
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
 fi
+FS=
+FS90=
 
 AUTODIFF_PKG_USED=f
 AD_OPTFILE=
@@ -355,15 +1131,15 @@
 
 
 #  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 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP 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 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"
@@ -373,27 +1149,30 @@
 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
-    if test -r $i/$gm_local ; then
-	source $i/$gm_local
-	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"
-    source $gm_local
+    . $gm_local
     # echo "DISABLE=$DISABLE"
     # echo "ENABLE=$ENABLE"
 else
     echo "none found"
 fi
 
-#  echo "$0::$1:$2:$3:$4:$5:$6:$7:"
+#echo "$0::$1:$2:$3:$4:$5:$6:$7:"
 #OPTIONS=
 #n=0
 #for i ; do 
@@ -405,7 +1184,9 @@
 #done
 #parse_options
 ac_prev=
-for ac_option ; do
+for ac_option in "$@" ; do
+
+    G2ARGS="$G2ARGS \"$ac_option\""
 
     # If the previous option needs an argument, assign it.
     if test -n "$ac_prev"; then
@@ -428,7 +1209,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -448,15 +1229,27 @@
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$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 ;;
@@ -483,35 +1276,68 @@
 	-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= ;;
-	
+
+	-ts | --ts)
+	    TS=true ;;
+	-papis | --papis)
+	    PAPIS=true ;;
+	-pcls | --pcls)
+	    PCLS=true ;;
+	-foolad | --foolad)
+	    FOOLAD=true ;;
+	-papi | --papi)
+	    PAPI=true ;;
+	-pcl | --pcl)
+	    PCL=true ;;
+	-hpmt | --hpmt)
+	    HPMT=true ;;
+
+        -gsl | --gsl)
+	    GSL=true ;;
+
+        -devel | --devel)
+	    DEVEL=true ;;
+
 	-mpi | --mpi)
 	    MPI=true ;;
-	-nompi | --nompi)
-	    MPI= ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
-	-jam | --jam)
-	    JAM=1 ;;
-	-nojam | --nojam)
-	    JAM=0 ;;
+ 	-omp | --omp)
+ 	    OMP=true ;;
+	-omp=* | --omp=*)
+	    OMPFLAG=$ac_optarg
+	    OMP=true ;;
 	
 	-ds | --ds)
 	    DUMPSTATE=t ;;
@@ -525,6 +1351,12 @@
 	    ac_prev=TAMC_EXTRA ;;
 	-tamc_extra=* | --tamc_extra=*)
 	    TAMC_EXTRA=$ac_optarg ;;
+	
+	-ignoretime | -ignore_time | --ignoretime | --ignore_time)
+	    IGNORE_TIME="-DIGNORE_TIME" ;;
+
+	-es | --es | -embed-source | --embed-source)
+	    EMBED_SRC=t ;;
 
 	-*)
 	    echo "Error: unrecognized option: "$ac_option
@@ -540,26 +1372,28 @@
     
 done
 
+
 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
-    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 ../eesupp -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
@@ -577,6 +1411,21 @@
     exit 1
 fi
 
+#  Find the MITgcm ${THISVER}
+version_file="${ROOTDIR}/doc/tag-index"
+if test -f $version_file ; then
+    THISVER=`grep '^checkpoint' $version_file | head -1`
+#-  remove ./BUILD_INFO.h file if older than version_file
+    if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
+	echo "  remove ./BUILD_INFO.h (older than ${version_file})"
+	rm -f ./BUILD_INFO.h
+    fi
+fi
+
+if test "x$MAKEFILE" = x ; then
+    MAKEFILE="Makefile"
+fi
+
 echo "  getting OPTFILE information:  "
 if test "x${OPTFILE}" = x ; then
     if test "x$MITGCM_OF" = x ; then
@@ -590,10 +1439,10 @@
 if test "x$OPTFILE" != xNONE ; then
     if test -f "$OPTFILE" -a -r "$OPTFILE" ; then
 	echo "    using OPTFILE=\"$OPTFILE\""
-	source "$OPTFILE"
+	. "$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
@@ -617,10 +1466,10 @@
 if test "x${AD_OPTFILE}" != xNONE ; then
     if test -f "$AD_OPTFILE" -a -r "$AD_OPTFILE" ; then
 	echo "    using AD_OPTFILE=\"$AD_OPTFILE\""
-	source "$AD_OPTFILE"
+	. "$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
@@ -633,8 +1482,15 @@
     fi
 fi
 
-#  Check that FC, LINK, CPP, and S64 are defined.  If not, complain 
-#  and abort!
+#====================================================================
+#  Set default values if not set by the optfile
+#
+#  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
 
@@ -645,12 +1501,34 @@
 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=$FC
 fi
+if test "x$MAKE" = x ; then
+    MAKE="make"
+fi
 if test "x$CPP" = x ; then
-    CPP="cpp"
+    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
@@ -660,25 +1538,144 @@
 
   1) within the options file ("CPP=...") as specified by "-of=OPTFILE"
   2) the "./genmake_local" file
+  3) with the CPP environment variable
 
 EOF
     exit 1
 else
     rm -f test_cpp
 fi
-if test "x$MAKEDEPEND" = x ; then
-    MAKEDEPEND=makedepend
+look_for_makedepend
+if test "x$LN" = x ; then
+    LN="ln -s"
 fi
+echo "test" > genmake_test_ln
+$LN genmake_test_ln genmake_tlink
+RETVAL=$?
+if test "x$RETVAL" != x0 ; then
+    cat <<EOF 1>&2
 
+Error: The command "ln -s" failed -- please specify a working soft-link
+  command in the optfile.
+
+EOF
+    exit 1
+fi
+test -L genmake_tlink > /dev/null 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_TEST_L=t
+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
+if test ! "x$OMP" = x ; then
+      echo "  Add OMPFLAG and turn on OpenMP cpp macros"
+      FFLAGS="$FFLAGS $OMPFLAG"
+      F90FLAGS="$F90FLAGS $OMPFLAG"
+      DEFINES="$DEFINES -DUSE_OMP_THREADING"
+fi
+
+if test ! "x$TS" = x ; then
+      echo "  Turning on timing per timestep"
+      if test ! "x$FOOLAD" = x ; then
+            DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
+      else
+	    DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
+      fi
+      PACKAGES="$PACKAGES showflops"
+fi
+if test ! "x$PAPIS" = x ; then
+      echo "  Turning on PAPI flop summary per timestep"
+      echo "  Please make sure PAPIINC, PAPILIB are defined"
+      if test ! "x$FOOLAD" = x ; then
+	    DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
+      else
+	    DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
+      fi
+      INCLUDES="$INCLUDES $PAPIINC"
+      LIBS="$LIBS $PAPILIB"
+      PACKAGES="$PACKAGES showflops"
+fi
+if test ! "x$PCLS" = x ; then
+      echo "  Turning on PCL counter summary per timestep"
+      echo "  Please make sure PCLINC, PCLLIB are defined"
+      if test ! "x$FOOLAD" = x ; then
+	    DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
+      else
+	    DEFINES="$DEFINES -DUSE_PCL_FLOPS"
+      fi
+      INCLUDES="$INCLUDES $PCLINC"
+      LIBS="$LIBS $PCLLIB"
+      PACKAGES="$PACKAGES showflops"
+fi
+if test ! "x$PAPI" = x ; then
+      if test ! "x$PAPIS" = x ; then
+	  echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
+	  echo "  Sticking with PAPI flop summary per timestep!"
+      else
+	  echo "  Turning on performance analysis with PAPI"
+          echo "  Please make sure PAPIINC, PAPILIB are defined"
+	  DEFINES="$DEFINES -DUSE_PAPI"
+	  INCLUDES="$INCLUDES $PAPIINC"
+	  LIBS="$LIBS $PAPILIB"
+      fi
+fi
+if test ! "x$PCL" = x ; then
+      if test ! "x$PCLS" = x ; then
+	  echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
+	  echo "  Sticking with PCL flop summary per timestep!"
+      else
+	  echo "  Turning on performance analysis with PCL"
+          echo "  Please make sure PCLINC, PCLLIB are defined"
+	  DEFINES="$DEFINES -DUSE_PCL"
+	  INCLUDES="$INCLUDES $PCLINC"
+	  LIBS="$LIBS $PCLLIB"
+      fi
+fi
+if test ! "x$HPMT" = x ; then
+      if test ! "x$PAPI" = x ; then
+	  echo "  PAPI and the HPM Toolkit cannot co-exist!"
+	  echo "  Sticking with PAPI!"
+      else if test ! "x$PCL" = x ; then
+	  echo "  PCL and the HPM Toolkit cannot co-exist!"
+	  echo "  Sticking with PCL!"
+      else
+	  echo "  Turning on performance analysis with the HPM Toolkit"
+          echo "  Please make sure HPMTINC, HPMTLIB are defined"
+	  DEFINES="$DEFINES -DUSE_LIBHPM"
+          INCLUDES="$INCLUDES $HPMTINC"
+	  LIBS="$LIBS $HPMTLIB"
+      fi
+      fi
+fi
+if test ! "x$GSL" = x ; then
+      echo "  Turning on use of GSL to control floating point calculations"
+      echo "  Please make sure GSLINC, GSLLIB are defined"
+      DEFINES="$DEFINES -DUSE_GSL_IEEE"
+      INCLUDES="$INCLUDES $GSLINC"
+      LIBS="$LIBS $GSLLIB"
+fi
+#- if USE_EXTENDED_SRC is set, add EXTENDED_SRC_FLAG to FFLAGS :
+if test ! "x$USE_EXTENDED_SRC" = x ; then
+      FFLAGS="$FFLAGS $EXTENDED_SRC_FLAG"
+      F90FIXEDFORMAT="$F90FIXEDFORMAT $EXTENDED_SRC_FLAG"
+fi
 
 printf "\n===  Checking system libraries  ===\n"
-echo -n "  Do we have the system() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
+printf "  Do we have the system() command using $FC...  "
+cat > genmake_tcomp.$FS <<EOF
       program hello
       call system('echo hi')
       end
 EOF
-$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+$FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
 RETVAL=$?
 if test "x$RETVAL" = x0 ; then
     HAVE_SYSTEM=t
@@ -688,95 +1685,175 @@
     HAVE_SYSTEM=
     echo "no"
 fi
-rm -f genmake_tcomp*
+rm -f genmake_tcomp*
+
+printf "  Do we have the fdate() command using $FC...  "
+cat > genmake_tcomp.$FS <<EOF
+      program hello
+      CHARACTER*(128) string
+      string = ' '
+      call fdate( string )
+      print *, string
+      end
+EOF
+$FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_FDATE=t
+    DEFINES="$DEFINES -DHAVE_FDATE"
+    echo "yes"
+else
+    HAVE_FDATE=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
+printf "  Do we have the etime() command using $FC...  "
+cat > genmake_tcomp.$FS <<EOF
+      program hello
+      REAL*4 ACTUAL, TARRAY(2)
+      EXTERNAL ETIME
+      REAL*4 ETIME
+      actual = etime( tarray )
+      print *, tarray
+      end
+EOF
+$FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > 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"
+    if test "x$EMBED_SRC" = xt ; then
+	echo "    WARNING: you requested file embedding but it has"
+	echo "      been disabled since C code cannot be called"
+	EMBED_SRC=
+    fi
+fi
+rm -f genmake_t*
+
+printf "  Can we unlimit the stack size using $FC...  "
+check_HAVE_SETRLSTK
+if test "x$HAVE_SETRLSTK" = xt ; then
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
+
+printf "  Can we register a signal handler using $FC...  "
+check_HAVE_SIGREG
+if test "x$HAVE_SIGREG" = xt ; then
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
+
+printf "  Can we use stat() through C calls...  "
+check_HAVE_STAT
+if test "x$HAVE_STAT" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
 
-echo -n "  Do we have the fdate() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
-      program hello
-      CHARACTER(128) string
-      string = ' '
-      call fdate( string )
-      print *, string
-      end
-EOF
-$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
-RETVAL=$?
-if test "x$RETVAL" = x0 ; then
-    HAVE_FDATE=t
-    DEFINES="$DEFINES -DHAVE_FDATE"
+printf "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
     echo "yes"
 else
-    HAVE_FDATE=
     echo "no"
 fi
-rm -f genmake_tcomp*
+DEFINES="$DEFINES $IGNORE_TIME"
 
-echo -n "  The name mangling convention for $FC is...  "
-if test "x$FC_NAMEMANGLE" = x ; then
-    FC_NAMEMANGLE="#define FC_NAMEMANGLE(X) X ## _" 
-fi
-cat > genmake_tcomp.f <<EOF
-      subroutine tcall( string )
-      character*(*) string
-      call tsub( string )
-      end
-EOF
-$FC $FFLAGS $DEFINES -c genmake_tcomp.f > genmake_tcomp.log 2>&1
-RETVAL=$?
-if test "x$RETVAL" != x0 ; then
-    cat genmake_tcomp.log >> genmake_errors
-    echo
-    echo "WARNING: test compile fails -- please see \"genmake_errors\""
-    echo "WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'"
-    echo "WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here."
-else
-    tcall=`nm genmake_tcomp.o | grep tcall | cut -d ' ' -f 3`
-    RETVAL=$?
-    if test "x$RETVAL" != x0 ; then
-	echo
-	echo "WARNING: The \"nm\" command failed."
-	echo "WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'"
-	echo "WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here."
-    else
-	t0=`echo $tcall | sed -e 's|_tcall|_ ## X|g'`
-	nmres=`echo $t0 | sed -e 's|tcall_|X ## _|g'`
-	FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmres"
-	echo "'$FC_NAMEMANGLE'"
-    fi
+if test "x$EMBED_SRC" = xt ; then
+    build_embed_encode
 fi
-echo "$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
+if test "x$EMBED_SRC" = xt ; then
+    ENABLE="$ENABLE embed_files"
 fi
-rm -f genmake_tcomp*
 
 
 printf "\n===  Setting defaults  ===\n"
-echo -n "  Adding MODS directories:  "
+printf "  Adding MODS directories: "
+MPI_LNKF=
 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"
+	#-------------------------------------------------------
+	# Put special links so that MPI specific files are used
+	MPI_FILES=`(cd $d ; find . -name "*_mpi" -print)`
+	for i in $MPI_FILES ; do
+	  ii=`echo $i | sed 's:^\./::'`
+	  name=`echo $ii | sed 's:_mpi::' `
+	  if test "x$MPI" = x ; then
+	  # NO: We undo an _mpi symbolically linked file
+	    if test -L $name ; then
+	      cmp $name "$d/$ii" > /dev/null 2>&1
+	      RETVAL=$?
+	      if test "x$RETVAL" = x0 ; then
+		printf "Un-linking $name ; "
+		rm -f $name
+	      fi
+	    fi
+	  else
+	  # YES: We symbolically link this file (with conditions if already there)
+	    if test -L $name ; then
+	      cmp $d/$ii $name > /dev/null 2>&1
+	      RETVAL=$?
+	      yy=0 ; 
+	      for xx in $MPI_LNKF ; do if test $xx = $name ; then yy=1 ; fi ; done
+ 	      if test "x$RETVAL" != x0 -a $yy = 0 ; then
+	      # remove sym-link if different and has not just been linked
+		printf "Un-link + "
+		rm -f $name
+	      fi
+	      if test "x$RETVAL" = x0 ; then
+	      # if identical, keep sym-link and keep record of it
+		MPI_LNKF="$MPI_LNKF $name"
+	      fi
+	    fi
+	    if ! test -f $name ; then
+	      # make sym-link and keep record of it
+		printf "Linking $ii to $name ; "
+		ln -sf $d/$ii $name
+		MPI_LNKF="$MPI_LNKF $name"
+	    fi
+	  fi
+	done
+	#-------------------------------------------------------
     fi
 done
 echo
+#echo "MPI_LNKF='$MPI_LNKF'"
 
-if test "x$MAKEFILE" = x ; then
-    MAKEFILE="Makefile"
-fi
 if test "x${PLATFORM}" = x ; then
     PLATFORM=$p_PLATFORM
 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 $ROOTDIR = .. ; then
 	EXEDIR=../exe
     else
 	EXEDIR=.
@@ -791,12 +1868,36 @@
     TOOLSDIR="$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'
+    echo "3.0 _d 3" | ${TOOLSDIR}/set64bitConst.sh > /dev/null 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+	S64='$(TOOLSDIR)/set64bitConst.sh'
+    else
+	echo "3.0 _d 3" | ${TOOLSDIR}/set64bitConst.csh > /dev/null 2>&1
+	RETVAL=$?
+	if test "x${RETVAL}" = x0 ; then
+	    S64='$(TOOLSDIR)/set64bitConst.csh'
+	else
+	    cat <<EOF
+
+ERROR: neither of the two default scripts:
+
+    ${TOOLSDIR}/set64bitConst.sh
+    ${TOOLSDIR}/set64bitConst.csh
+
+  are working so please check paths or specify (with \$S64) a 
+  working version of this script.
+
+EOF
+	    exit 1
+	fi
+    fi
 fi
+THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSDIR':\$(TOOLSDIR):'`
 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
 
@@ -805,17 +1906,33 @@
 #  they appear as regular source code
 if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
     echo "  Making source files in eesupp from templates"
-    $MAKE -C $ROOTDIR"/eesupp/src/" > make_eesupp.errors 2>&1
+    ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	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 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_${pdir}.errors 1>&2
+	    exit 1
+	fi
+    fi
+done
+
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
@@ -842,13 +1959,13 @@
     echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""
     exit 1
 fi
-source ./.pd_tmp
+. ./.pd_tmp
 rm -f ./.pd_tmp
 
 #  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 $i"/packages.conf" ; then
@@ -861,18 +1978,17 @@
     PDEFAULT="$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
@@ -880,12 +1996,20 @@
 	    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 $PACKAGES ; do
     addit="t"
@@ -902,28 +2026,89 @@
 echo "  applying ENABLE settings"
 echo "" > ./.tmp_pack
 PACKAGES="$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"
 
+#  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$RETVAL" = x0 ; then
+    if test "x$HAVE_NETCDF" != xt ; then
+	cat <<EOF
+
+*********************************************************************
+WARNING: the "mnc" 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 "mnc" package is now DISABLED.
+*********************************************************************
+
+EOF
+	PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`
+	DISABLE="$DISABLE mnc"
+    else
+	( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
+	RETVAL=$?
+	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
+    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]}
@@ -957,6 +2142,7 @@
 
 	#  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$dname" ; then
@@ -981,7 +2167,8 @@
 	    echo "  the dependency rules for \"$dname\""
 	    exit 1
 	fi
-	i=$(( $i + 1 ))
+        i=`echo "$i + 1" | bc -l`
+	#i=$(( $i + 1 ))
     done
     ck=$ck"t"
 done
@@ -1000,27 +2187,15 @@
     fi
 done
 
-
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
-cat <<EOF >$PACKAGES_DOT_H".tmp"
-C=== GENMAKE v2 ===
-C  The following defines have been set by GENMAKE, so please do not
-C  edit anything below these comments.  In general, you should
-C  add or remove packages by re-running genmake with different 
-C  "-enable" and/or "-disable" options.
-
-#ifndef PACKAGES_H
-#define PACKAGES_H
-
-C  Packages disabled by genmake:
-EOF
 #  The following UGLY HACK sets multiple "#undef"s and it needs to go 
 #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h 
 #  file would eventually be split up so that all package-related #define
 #  statements could be separated and handled only by genmake.
 names=`ls -1 "$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"
@@ -1031,194 +2206,321 @@
 	    fi
 	done
 	if test "x$has_pack" = xf ; then
-	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
-	    echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
+	    undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
+            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" >> $PACKAGES_DOT_H".tmp"
+    def=`echo "ALLOW_$i" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
+    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.
-if test -f ./ad_files ; then
-    rm -f ./ad_files
+if test -f ./adSrcFiles.tmp ; then
+    rm -f ./adSrcFiles.tmp
 fi
 echo "  Creating the list of files for the adjoint compiler."
 for i in $SOURCEDIRS ; do
     list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
     for j in $list_files ; do
-	cat $i/$j >> ad_files
+	cat $i/$j >> adSrcFiles.tmp
     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
+if test ! "x"$FS = "x.f" ; then
+    cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
+    mv -f adSrcFiles.tmp_f adSrcFiles.tmp
+fi
 
 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
 
+if test ! "x$DIVA" = x ; then
+    echo "  Creating the pseudo-MPI include directory"
+    INCLUDES="-I./mpi_headers $INCLUDES"
+    rm -rf ./mpi_headers
+    mkdir -p ./mpi_headers
+
+    if test "x$MPIINCLUDEDIR" = x ; then
+	if test "x$MPIHOME" = x ; then
+	    MPIHOME='/usr'
+	fi
+	MPIINCLUDEDIR='$MPIHOME/include'
+    fi
+    
+    if test -r $MPIINCLUDEDIR/mpif.h ; then
+	for i in $MPI_HEADER_FILES; do
+	    cp -p $MPIINCLUDEDIR/$i ./mpi_headers
+	done
+
+	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
+    fi
+fi
+
 echo "  Determining the list of source and include files"
 rm -rf .links.tmp
 mkdir .links.tmp
+touch .links.tmp/foo
+if test ! -r ".links.tmp/foo" ; then
+    echo
+    echo "ERROR : something is wrong with your directory permissions or"
+    echo "   your user file-creation mask (\"umask\") since creating a"
+    echo "   sub-dir, touch-ing a file within it, and then reading it is"
+    echo "   not working.  Please try setting your umask to something"
+    echo "   sane such as:"
+    echo
+    echo "      umask 0002"
+    echo
+    echo "   and please verify that you have the proper permissions for"
+    echo "   creating sub-directories and then reading files created"
+    echo "   within them."
+    echo
+    exit 1
+fi
+rm -f .links.tmp/foo
+
+if test "x$OPENAD" != x ; then 
+    OAD_DONT_COMPILE="/dev/null"
+    OAD_DONT_TRANSFORM="/dev/null"
+    OAD_KEEP_ORIGINAL="/dev/null"
+    OAD_CB2M_FILES="/dev/null"
+    echo "  looking for dontCompile file:  "
+    for i in "." $MODS ; do
+	if test -r $i"/dontCompile" ; then
+	    OAD_DONT_COMPILE=$i"/dontCompile"
+	    echo "     found $OAD_DONT_COMPILE"
+	    break
+	fi
+    done
+    echo "  looking for dontTransform file:  "
+    for i in "." $MODS ; do
+	if test -r $i"/dontTransform" ; then
+	    OAD_DONT_TRANSFORM=$i"/dontTransform"
+	    echo "     found $OAD_DONT_TRANSFORM"
+	    break
+	fi
+    done
+    echo "  looking for keepOriginal file:  "
+    for i in "." $MODS ; do
+	if test -r $i"/keepOriginal" ; then
+	    OAD_KEEP_ORIGINAL=$i"/keepOriginal"
+	    echo "     found $OAD_KEEP_ORIGINAL"
+	    break
+	fi
+    done
+    echo "  looking for cb2mFiles:  "
+    for i in "." $MODS ; do
+	if test -r $i"/cb2mFiles" ; then
+	    OAD_CB2M_FILES=$i"/cb2mFiles"
+	    echo "     found $OAD_CB2M_FILES"
+	    break
+	fi
+    done
+    echo "   OpenAD exceptions:  "
+fi
+
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-echo -n 'SRCFILES = '    > srclist.inc
-echo -n 'CSRCFILES = '   > csrclist.inc
-echo -n 'F90SRCFILES = ' > f90srclist.inc
-echo -n 'HEADERFILES = ' > hlist.inc
-echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'F77_SRC_FILES = ' > F77srclist.tmp
+printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
+printf 'C_SRC_FILES = '   > csrclist.tmp
+printf 'F90_SRC_FILES = ' > F90srclist.tmp
+printf 'H_SRC_FILES = '   > hsrclist.tmp
+printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
 alldirs="$SOURCEDIRS $INCLUDEDIRS ."
 for d in $alldirs ; do
     deplist=
     sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
     sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
+    if test "x$OPENAD" != x ; then 
+	sfiles=`( echo $sfiles | grep -v _cb2m\. )`
+    fi
     for sf in $sfiles ; do
 	if test ! -r ".links.tmp/$sf" ; then
 	    if test -f "$d/$sf" ; then
-		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
+		ignore_f=f
+                case $d/$sf in
+                  ./$PACKAGES_DOT_H)
+			ignore_f=t
+			;;
+                  ./AD_CONFIG.h)
+			ignore_f=t
+			;;
+                  ./FC_NAMEMANGLE.h)
+			ignore_f=t
+			;;
+                  ./BUILD_INFO.h)
+			ignore_f=t
+			;;
+                  ./EMBEDDED_FILES.h)
+			ignore_f=t
+			;;
+                  *)
+			#  For the local directory *ONLY*,
+			#  ignore all soft-links
+			if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
+			    ignore_f=t
+			else
+			    touch .links.tmp/$sf
+			    deplist="$deplist $sf"
+			fi
+			;;
+                esac
+		if test "x$ignore_f" = xf ; then
+		    extn=`echo $sf | $AWK -F. '{print $NF}'`
+		    case $extn in
+		      F)
+			echo    " \\"  >> F77srclist.tmp
+			printf " $sf" >> F77srclist.tmp
+			if test "x$OPENAD" != x ; then 
+			    basename=${sf%%.F}
+			    isAD=`egrep ^$basename.f'[ 	]*' adSrcFiles.tmp`
+			    if test -z "$isAD" ; then 
+				toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
+				if test -z "$toBeIgnored" ; then 
+				    echo    " \\"  >> nonADF77srclist.tmp
+				    printf " $sf" >> nonADF77srclist.tmp
+				else 
+				    echo "    not to be compiled   :  $sf"
+				fi
+			    else # file is initially listed as an AD file we want to exclude it 
+				 # or we want to retain the untransformed version
+				notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
+				untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
+				if test -n "$notToBeTransformed"; then 
+				    echo "    not to be transformed:  $sf"
+				fi
+				if test -n "$untransformedVersionToBeKept" ; then
+				    echo "    original to be kept  :  $sf"
+				fi    
+				if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
+				    echo    " \\"  >> nonADF77srclist.tmp
+				    printf " $sf" >> nonADF77srclist.tmp
+				fi
+			    fi
+			fi
 			;;
 		    F90)
-			echo    " \\"  >> f90srclist.inc
-			echo -n " $sf" >> f90srclist.inc
+			echo    " \\"  >> F90srclist.tmp
+			printf " $sf" >> F90srclist.tmp
 			;;
 		    c)
-			echo    " \\"  >> csrclist.inc
-			echo -n " $sf" >> csrclist.inc
+			echo    " \\"  >> csrclist.tmp
+			printf " $sf" >> csrclist.tmp
 			;;
 		    h)
-			echo    " \\"  >> hlist.inc
-			echo -n " $sf" >> hlist.inc
+			echo    " \\"  >> hsrclist.tmp
+			printf " $sf" >> hsrclist.tmp
 			;;
-		    flow)
-			echo    " \\"  >> ad_flow_files.inc
-			echo -n " $sf" >> ad_flow_files.inc
+  		    flow)
+			echo    " \\"  >> ad_flow_files.tmp
+			printf " $sf" >> ad_flow_files.tmp
 			;;
-		esac
+		   esac
+	        fi
 	    fi
 	fi
     done
     if test "x$deplist" != x ; then
-	echo "" >> srclinks.tmp
+      if test "$d" != "." ; then
+  	echo "" >> srclinks.tmp
 	echo "#  These files are linked from $d" >> srclinks.tmp
 	echo "$deplist :" >> srclinks.tmp
-	printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp
+# We need to make sure that the link isn't already there.
+# This may happen when make thinks that a header file has to be "remade"
+# because a module it depends on has changed.  In this case we do nothing.
+	printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
+      fi
     fi
 done
 rm -rf .links.tmp
-echo "" >> srclist.inc
-echo "" >> csrclist.inc
-echo "" >> f90srclist.inc
-echo "" >> hlist.inc
-echo "" >> ad_flow_files.inc
+echo "" >> F77srclist.tmp
+echo "" >> nonADF77srclist.tmp
+echo "" >> csrclist.tmp
+echo "" >> F90srclist.tmp
+echo "" >> hsrclist.tmp
+echo "" >> ad_flow_files.tmp
 
-if test -e $MAKEFILE ; then
+if test -f $MAKEFILE ; then
     mv -f $MAKEFILE "$MAKEFILE.bak"
 fi
 echo "  Writing makefile: $MAKEFILE"
@@ -1227,15 +2529,17 @@
 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
@@ -1269,10 +2573,19 @@
 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
- 
+if test "x$EMBED_SRC" = xt ; then
+    echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
+else
+    echo "EMBEDDED_FILES = " >>$MAKEFILE
+fi
+
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
@@ -1286,8 +2599,10 @@
 FC = ${FC}
 # Fortran compiler
 F90C = ${F90C}
+# C compiler
+CC = ${CC}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1297,97 +2612,181 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
 F90OPTIM = ${F90OPTIM}
+F90FIXEDFORMAT = ${F90FIXEDFORMAT}
 # Flags for CC
 CFLAGS = ${CFLAGS}
 # Files that should not be optimized
 NOOPTFILES = ${NOOPTFILES}
 NOOPTFLAGS = ${NOOPTFLAGS}
 # Flags and libraries needed for linking
-LIBS = ${LIBS} \$(XLIBS)
+LIBS = ${LIBS}
 # Name of the Mekfile
 MAKEFILE=${MAKEFILE}
 
 EOF
 
-cat srclist.inc       >> $MAKEFILE
-cat csrclist.inc      >> $MAKEFILE
-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 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
+cat F77srclist.tmp      >> $MAKEFILE
+cat nonADF77srclist.tmp >> $MAKEFILE
+cat csrclist.tmp        >> $MAKEFILE
+cat F90srclist.tmp      >> $MAKEFILE
+cat hsrclist.tmp        >> $MAKEFILE
+cat ad_flow_files.tmp   >> $MAKEFILE
 
-rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
-rm -f ad_flow_files.inc
+rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
 
-cat >>$MAKEFILE <<EOF
+echo >> $MAKEFILE
 
-.SUFFIXES:
-.SUFFIXES: .o .f .p .F .c .F90 .f90
+# add definitions for preprocessed sources 
+# and note that not all systems allow case sensitive extensions 
+# hence the $FS and $FS90 here. 
+# for fixed format f90 files we use ff90 or FF90 resp 
+# but these are not expected to be the original source files
+
+echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
+echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
+echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
+echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
+echo >> $MAKEFILE
+echo '.SUFFIXES:' >> $MAKEFILE
+echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
+
+cat >>$MAKEFILE <<EOF
 
 all: \$(EXECUTABLE)
-\$(EXECUTABLE): \$(OBJFILES)
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
+	@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) \$(F77_SRC_FILES)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+lib: libmitgcmuv.a
 
-small_f: \$(F77FILES) \$(F90FILES)
+libmitgcmuv.a: \$(OBJFILES)
+	ar rcv libmitgcmuv.a \$(OBJFILES)
+	ar d   libmitgcmuv.a main.o
+
+links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
+
+small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
 
 output.txt: \$(EXECUTABLE)
 	@printf 'running ... '
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-cat AD_CONFIG.template > AD_CONFIG.h
-	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl}
+	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.o
+	-rm -rf *.$FS *.flowdir
+	-rm -rf *.f$FS90 *_mod.h *_mod.F90 *.FF90 *.mod-whirl ad_input*
+	-rm -rf temp.sed
 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 f90mkdepend.log *.bak
+	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
 CLEAN:
 	@make Clean
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) output.txt
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
+	-rm -rf mnc_test_*
 
 #eh3 Makefile: makefile
 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 created 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'\" >> \$@" >> $MAKEFILE
+
+if test "x$EMBED_SRC" = xt ; then
+    cat >>$MAKEFILE <<EOF
+
+decode_files.o : EMBEDDED_FILES.h
+
+##  \$(F77_PP_SRC_FILES) 
+all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
+	@echo Creating \$@ ...
+	-tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
+	-rm -f all_fF.tar.gz
+	-gzip all_fF.tar
+
+EMBEDDED_FILES.h : all_fF.tar.gz
+	@echo Creating \$@ ...
+	-\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
+
+EOF
+fi
+
+cat >>$MAKEFILE <<EOF
+
+# The normal chain of rules is (  .F - .$FS - .o  )
+
+## This nullifies any default implicit rules concerning these two file types:
+## %.o : %.F
+
+.F.$FS:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.f.o:
+.$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
-.F90.f90:
+.F90.$FS90:
+	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+.FF90.f$FS90:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.f90.o:
+.$FS90.o:
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
+.f$FS90.o:
+	cp \$< \$(basename  \$<).f90
+	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
 .c.o:
-	\$(CC) \$(CFLAGS) -c \$<
+	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
+.flow.flowdir:
+	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 
-# 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) \$<
 
+EOF
+
 #=========================================
 #===  Automatic Differentiation Rules  ===
+#===  for TAMC/TAF  ======================
+
+if test "x$OPENAD" = x ; then 
+
+cat >>$MAKEFILE <<EOF
 
 TAMC           = ${TAMC}
 TAF            = ${TAF}
@@ -1402,99 +2801,353 @@
 ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
 for i in $ad_vars ; do
     name=$i
-    t1="t2=\$"`echo $i`
+    t1="t2=\$"`echo "$i"`
     eval $t1
     printf "%-20s = " $name >> $MAKEFILE
-    echo $t2 >> $MAKEFILE
+    echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
 done
 
 echo "  Add the source list for AD code generation"
 echo >> $MAKEFILE
-echo -n "AD_FILES = " >> $MAKEFILE
-AD_FILES=`cat ad_files`
+printf "AD_FILES = " >> $MAKEFILE
+AD_FILES=`cat adSrcFiles.tmp`
 for i in $AD_FILES ; do
     echo    " \\" >> $MAKEFILE
-    echo -n " $i" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
 done
 echo >> $MAKEFILE
-rm -f ad_files
+rm -f adSrcFiles.tmp
 
 cat >>$MAKEFILE <<EOF
 
 # ... AD ...
-adall: ad_taf
-adtaf: ad_taf_output.f
-adtamc: ad_tamc_output.f
+adall: \$(EXE_AD)
+adtaf: ad_taf_output.$FS
+adtamc: ad_tamc_output.$FS
 
-ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)
+ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
+	@$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
-	@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
-
-ad_taf: ad_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
-
-ad_tamc_output.f: ad_input_code.f
-	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_tamc_output.f
+	-rm -f ad_config.template
+	@make \$(F77_PP_SRC_FILES)
+	@make \$(FLOFILES)
+	cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
+
+ad_taf_output.$FS: ad_input_code.$FS
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+	ls -l ad_input_code_ad.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
+
+adtafonly:
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+	ls -l ad_input_code_ad.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
+
+\${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.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
 
 ad_tamc: ad_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS) 
 
+adonlyfwd:
+	patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
+ 
+adtrick:
+	patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
 
 # ... FTL ...
 ftlall: ftl_taf
-ftltaf: ftl_taf_output.f
-ftltamc: ftl_tamc_output.f
+ftltaf: ftl_taf_output.$FS
+ftltamc: ftl_tamc_output.$FS
 
-ftl_input_code.f: \$(AD_FILES) \$(HEADERFILES)
+ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+	@$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
-	@make \$(F77FILES)
+	-rm -f ftl_config.template
+	@make \$(F77_PP_SRC_FILES)
 	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
+	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
 
-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
+ftl_taf_output.$FS: ftl_input_code.$FS
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+	ls -l ftl_input_code_ftl.$FS
+	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+
+ftltafonly:
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+	ls -l ftl_input_code_ftl.$FS
+	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
 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
+ftl_tamc_output.$FS: ftl_input_code.$FS
+	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
+	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
 
 ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS) 
 
 
 # ... SVD ...
-svd: svd_taf
-svd_taf_f: svd_taf_output.f
+svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
+	@echo "--->>> Only ran TAF to generate SVD code!    <<<---"
+	@echo "--->>> Do make svdall afterwards to compile. <<<---"
+svdall: svd_touch svd_taf
+
+svd_taf: \$(OBJFILES)
+	\$(LINK) -o mitgcmuv_svd \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o ftl_taf_output.o \$(LIBS)
+
+	@echo "--->>> Only COMPILE svd code! <<<---"
+	@echo "--->>> Assumes you previously <<<---"
+	@echo "--->>> did make svdtaf        <<<---"
+
+svd_touch:
+	@echo "--->>> Only COMPILE svd code! <<<---"
+	@echo "--->>> Assumes you previously <<<---"
+	@echo "--->>> did make svdtaf        <<<---"
+	touch ad_taf_output.$FS ftl_taf_output.$FS
+	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
+	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
+	@$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
 
-svd_input_code.f: \$(SRCFILES)
-	cmp svd_config.template AD_CONFIG.h || cat svd_config.template > AD_CONFIG.h
-	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > svd_input_code.f
+EOF
 
-svd_taf_output.f: svd_input_code.f
-	\$(TAF) \$(SVD_TAF_FLAGS) \$(TAF_EXTRA) svd_input_code.f
-	cat svd_input_code_ad.f | sed -f adjoint_sed > svd_taf_output.f
+fi 
 
-svd_taf: svd_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_SVD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) svd_taf_output.o \$(LIBS) 
+#===  for OpenAD  ========================
 
+if test "x$OPENAD" != x ; then 
 
-#=========================================
+# ============ begin OpenAD specific section ==============
+
+cat >>$MAKEFILE <<EOF
+
+# all the source files linked from the various locations: 
+ALL_LINKED_FILES= \
+\$(F77_SRC_FILES) \
+\$(C_SRC_FILES) \
+\$(H_SRC_FILES) \
+\$(F90_SRC_FILES) \
+\$(SPECIAL_FILES)
+
+ifndef OPENADROOT
+  \$(error "Error:  environment variable OPENADROOT not defined!")
+endif
+
+ifndef XAIFSCHEMAROOT
+  \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
+endif
+
+ifndef XAIFBOOSTERROOT
+  \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
+endif
+
+EOF
+
+echo "  Add the source list for common block to module conversion "
+echo >> $MAKEFILE
+printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
+for i in `cat ${OAD_CB2M_FILES}` ; do
+  echo    " \\" >> $MAKEFILE
+  printf " $i" >> $MAKEFILE
+done
+echo >> $MAKEFILE
+
+echo "  Add the source list for AD code generation"
+echo >> $MAKEFILE
+printf "AD_FILES = " >> $MAKEFILE
+for i in `cat ${OAD_CB2M_FILES}` ; do
+  echo    " \\" >> $MAKEFILE
+  printf " ${i}_mod.f$FS90" >> $MAKEFILE
+done
+AD_FILES=`cat adSrcFiles.tmp`
+for i in $AD_FILES ; do
+  basename=${i%%.f}
+  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
+  if test -z "$toBeIgnored" ; then
+    echo    " \\" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
+  fi
+done
+echo >> $MAKEFILE
+rm -f adSrcFiles.tmp
+
+cat >>$MAKEFILE <<EOF
+
+adAll: \$(EXE_AD) 
+.PHONY: adAll
+
+CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
+
+.PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
+
+.PHONY: adDepend
+adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
+	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
+
+OPENAD_SUPPORT_F90_SRC_FILES = \
+w2f__types.F90 \
+OAD_active.F90 \
+OAD_cp.F90 \
+OAD_rev.F90 \
+OAD_tape.F90         
+
+OPENAD_SUPPORT_C_SRC_FILES = \
+iaddr.c \
+timeRatio.c
+
+f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
+	cat \$^ > \$@
+
+f95_test.f90: all_mods.xb.x2w.w2f.pp.f$FS90 \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90) ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90 
+	cat \$^ > \$@
+
+f95_test.out: f95_test_mods.f90 f95_test.f90
+	f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
+	f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
+
+AD_OBJ_FILES=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) all_mods.xb.x2w.w2f.pp.o  ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.o \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
+
+\$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(AD_OBJ_FILES)
+	@echo Creating \$@ ...
+	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES) \$(LIBS)
+
+# makefile debug rule
+openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+.PHONY: openad
+
+# create the module files 
+%_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk 
+	../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
+
+# create the header files 
+%_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk 
+	../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+
+# change everybody else to use the new module files:
+%_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
+	../OAD_support/cb2mUseModules.bash $< ${MPI}
+
+# makefile debug rule
+small_f: \$(CB2M_F90_PP_SRC_FILES)
+.PHONY: small_f
+
+ad_output.txt: \$(EXE_AD)
+	@printf 'linking data files ... '
+	\$(LN) -f ../input_ad/data* ../input_ad/eedata .
+	\$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
+	@printf 'running ... '
+	@./\$(EXE_AD) > \$@
+
+CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
+ad_input_code.f$FS90: ../OAD_support/maxMinDefs.f \$(CB2M_AD_FILES) 
+	cat \$^ > \$@
+
+# strip all comments and blanks to reduce 
+# the file size in order to reduce perl's memory requirements 
+ad_input_code_sf.f$FS90 : ad_input_code.f$FS90 
+	cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
+
+# mfef90 preprocessing
+# expand statement functions 
+# expose mfef90 specific substring handling 
+# add the w2f__types module
+ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
+	./mfef90 -r8 -z -F -N132 \$< 
+	mv \$<.B \$(basename \$<).B 
+	./whirl2f -openad \$(basename \$<).B
+	cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
+
+# canonicalizer
+ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
+	./preProcess.py -H -S \$< -o \$@
+
+# F -> WHIRL
+# note that the canonicalized version cuts off at col 72 
+# doing this also for string constants which is ok as long 
+# as we are in fixed mode and cut of exactly there. 
+# Otherwise mfef90 patches in spaces to fill up to 72 (or 132) 
+# characters respectively.
+ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
+	./mfef90 -r8 -z -F \$<
+	mv \$<.B \$@
+
+# WHIRL -> XAIF
+ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif
+	./whirl2xaif -s -n --debug 1 -o \$@ \$<
+
+# XAIF -> XAIF'
+ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver
+	./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+
+# XAIF' -> WHIRL'
+ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
+	./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
+
+# WHIRL' -> F'
+ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
+	./whirl2f -FLIST:ftn_file=\$@ -openad \$< 
+
+# insert template directives
+ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
+	../OAD_support/insertTemplateDir.bash \$< \$@
+
+PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
+# postprocess F'
+ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)
+	./postProcess.py -m r -i ../OAD_support/ad_inline.f -o \$@ \$<
+
+# extract all transformed modules 
+all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+	cat \$< | sed -n '/MODULE /,/END MODULE/p' > \$@
+
+# remove the transformed globals module from the 
+# transformed ad_input_code file
+# and remove for now the duplicate variables
+# and fix 2 data statements
+ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90 
+	cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' > \$@
+
+# setup some links
+%.xsd:
+	\$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
+
+mfef90: 
+	\$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
+
+# link the support files:
+\$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES): 
+	\$(LN) ../OAD_support/\$@ .
+
+whirl2xaif xaif2whirl: 
+	\$(LN) \${OPENADFORTTK}/bin/\$@ .
+
+preProcess.py postProcess.py: 
+	\$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
+
+whirl2f whirl2f_be:
+	\$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
+
+oadDriver:
+	\$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
+
+# ============ end OpenAD specific section ==============
 
 EOF
 
+fi
+
+#=========================================
+
 if test "x$EXEHOOK" != x ; then
     printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
 fi
@@ -1506,7 +3159,7 @@
     if test "x$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"
@@ -1516,7 +3169,7 @@
     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
 
@@ -1529,49 +3182,28 @@
 
 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