--- MITgcm/tools/genmake2	2003/11/20 00:25:43	1.41
+++ MITgcm/tools/genmake2	2007/11/26 21:39:58	1.167
@@ -1,6 +1,6 @@
-#!/bin/sh
+#! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.41 2003/11/20 00:25:43 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.167 2007/11/26 21:39:58 jmc 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 $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -62,18 +75,233 @@
 	done
 	PACKAGES=$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"
     
@@ -93,18 +321,50 @@
 	CPP="cpp -traditional -P"
     fi
 
-    # makedepend is not always available
-    if test "x${MAKEDEPEND}" = x ; then
-      which makedepend >& /dev/null
-      RETVAL=$?
-      if test "x${RETVAL}" = x1 ; then
-         echo "    makedepend was not found. Using xmakedpend instead."
-         MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
-      fi
+    look_for_makedepend
+
+    #================================================================
+    #  look for possible C compilers
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc 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 $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
+    #================================================================
+    #  look for possible FORTRAN compilers
+    tmp="$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
@@ -129,27 +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
 
@@ -208,7 +485,7 @@
     . ./.pd_tmp
     rm -f ./.pd_tmp
 
-    echo -n "PNAME = "${}
+    printf "PNAME = "${}
 }
 
 
@@ -222,6 +499,11 @@
     -help | --help | -h | --h
           Print this help message and exit.
 
+    -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
+      -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
+          Use "NAME" as the adoptfile.  By default, the file at
+          "tools/adjoint_options/adjoint_default" will be used.
+
     -nooptfile | --nooptfile
       -optfile NAME | --optfile NAME | -of NAME | --of NAME
       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
@@ -246,6 +528,10 @@
       --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".
@@ -282,11 +568,57 @@
           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.
+
+    -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:
 
@@ -307,6 +639,12 @@
 
 #  Build a CPP macro to automate calling C routines from FORTRAN
 get_fortran_c_namemangling()  {
+
+    #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
+    if test ! "x$FC_NAMEMANGLE" = x ; then
+        return 0
+    fi
+
     default_nm="#define FC_NAMEMANGLE(X) X ## _"
     
     cat > genmake_test.c <<EOF
@@ -324,7 +662,7 @@
 EOF
 	return 1
     fi
-    c_tcall=`nm genmake_test.o | grep tcall | cut -d ' ' -f 3`
+    c_tcall=`nm genmake_test.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -336,13 +674,13 @@
 EOF
 	return 1
     fi
-    cat > genmake_tcomp.f <<EOF
+    cat > genmake_tcomp.$FS <<EOF
       subroutine tcall( string )
       character*(*) string
       call tsub( string )
       end
 EOF
-    $FC $FFLAGS $DEFINES -c genmake_tcomp.f >> genmake_warnings 2>&1
+    $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -354,7 +692,7 @@
 EOF
 	return 1
     fi
-    f_tcall=`nm genmake_tcomp.o | grep tcall | cut -d ' ' -f 3`
+    f_tcall=`nm genmake_tcomp.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -408,19 +746,21 @@
  *curtim = *curtim/1.E6;
 }
 EOF
-    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    make genmake_tc_1.o >> genmake_warnings 2>&1
     RET_C=$?
-    cat <<EOF > genmake_tc_2.f
+    cat <<EOF > genmake_tc_2.$FS
       program hello
-      Real*8 wtime
+      REAL*8 wtime
       external cloc
       call cloc(wtime)
       print *," HELLO WORLD", wtime
-      end program hello
+      end
 EOF
-    $FC $FFLAGS -o genmake_tc genmake_tc_2.f genmake_tc_1.o >> genmake_tc.log 2>&1
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> genmake_warnings
+    $COMM >> genmake_warnings 2>&1
     RET_F=$?
-    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1
+    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_CLOC=t
@@ -430,6 +770,249 @@
 }
 
 
+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
+    make genmake_tc_1.o >> 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
+    make genmake_tc_1.o >> 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
+$FC_NAMEMANGLE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+void FC_NAMEMANGLE(tfsize) ( int *nbyte )
+{
+    char name[512];
+    struct stat astat;
+
+    name[0] = 'a'; name[1] = '\0';
+    if (! stat(name, &astat))
+        *nbyte = (int)(astat.st_size);
+    else
+        *nbyte = -1;
+}
+EOF
+    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    RET_C=$?
+    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 $@"
 
@@ -437,48 +1020,73 @@
 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=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
+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 $USER`
+THISVER=
 MACHINE=`uname -a`
 EXECUTABLE=
 EXEHOOK=
@@ -488,6 +1096,8 @@
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
 fi
+FS=
+FS90=
 
 AUTODIFF_PKG_USED=f
 AD_OPTFILE=
@@ -505,14 +1115,14 @@
 
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
-gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
+gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
 gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE 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"
@@ -535,14 +1145,8 @@
 
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
-for i in . $MODS ; do
-    if test -r $i/$gm_local ; then
-	. $i/$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"
     . $gm_local
     # echo "DISABLE=$DISABLE"
@@ -551,7 +1155,7 @@
     echo "none found"
 fi
 
-#  echo "$0::$1:$2:$3:$4:$5:$6:$7:"
+#echo "$0::$1:$2:$3:$4:$5:$6:$7:"
 #OPTIONS=
 #n=0
 #for i ; do 
@@ -563,7 +1167,9 @@
 #done
 #parse_options
 ac_prev=
-for ac_option ; do
+for ac_option in "$@" ; do
+
+    G2ARGS="$G2ARGS \"$ac_option\""
 
     # If the previous option needs an argument, assign it.
     if test -n "$ac_prev"; then
@@ -586,7 +1192,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -606,6 +1212,16 @@
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$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=*)
@@ -647,16 +1263,58 @@
 #		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 ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
 #	-jam | --jam)
 #	    JAM=1 ;;
@@ -675,6 +1333,12 @@
 	    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
@@ -690,26 +1354,28 @@
     
 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
@@ -727,6 +1393,15 @@
     exit 1
 fi
 
+#  Find the MITgcm ${THISVER}
+if test -f "${ROOTDIR}/doc/tag-index" ; then
+    THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`
+fi
+
+if test "x$MAKEFILE" = x ; then
+    MAKEFILE="Makefile"
+fi
+
 echo "  getting OPTFILE information:  "
 if test "x${OPTFILE}" = x ; then
     if test "x$MITGCM_OF" = x ; then
@@ -743,7 +1418,7 @@
 	. "$OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source OPTFILE \"$OPTFILE\""
+	    printf "Error: failed to source OPTFILE \"$OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -770,7 +1445,7 @@
 	. "$AD_OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
+	    printf "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -783,8 +1458,15 @@
     fi
 fi
 
-#  Check that FC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
+#====================================================================
+#  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
 
@@ -795,15 +1477,34 @@
 EOF
     exit 1
 fi
+if test "x$CC" = x ; then
+    CC=cc
+#     cat <<EOF 1>&2
+# Error: no C compiler: please specify using one of the following:
+#   1) within the options file ("CC=...") as specified by "-of=OPTFILE"
+#   2) the "-cc=XXX" command-line option
+#   3) the "./genmake_local" file
+# EOF
+#     exit 1
+fi
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
-if test "x$CPP" = x ; then
-    CPP="cpp"
-fi
 if test "x$MAKE" = x ; then
     MAKE="make"
 fi
+if test "x$CPP" = x ; then
+    CPP=cpp
+fi
+#EH3 === UGLY ===
+#  The following is an ugly little hack to check for $CPP in /lib/ and
+#  it should eventually be replaced with a more general function that
+#  searches a combo of the user's path and a list of "usual suspects"
+#  to find the correct location for binaries such as $CPP.
+for i in " " "/lib/" ; do
+    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
+done
+#EH3 === UGLY ===
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -820,9 +1521,7 @@
 else
     rm -f test_cpp
 fi
-if test "x$MAKEDEPEND" = x ; then
-    MAKEDEPEND=makedepend
-fi
+look_for_makedepend
 if test "x$LN" = x ; then
     LN="ln -s"
 fi
@@ -838,17 +1537,110 @@
 EOF
     exit 1
 fi
+test -L genmake_tlink > /dev/null 2>&1
+RETVAL=$?
+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$TS" = x ; then
+      echo "  Turning on timing per timestep"
+      if test ! "x$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
 
 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
@@ -860,16 +1652,16 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Do we have the fdate() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
+printf "  Do we have the fdate() command using $FC...  "
+cat > genmake_tcomp.$FS <<EOF
       program hello
-      CHARACTER(128) string
+      CHARACTER*(128) string
       string = ' '
       call fdate( string )
       print *, string
       end
 EOF
-$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+$FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
 RETVAL=$?
 if test "x$RETVAL" = x0 ; then
     HAVE_FDATE=t
@@ -881,46 +1673,108 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+printf "  Do we have the etime() command using $FC...  "
+cat > genmake_tcomp.$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$EMBED_SRC" = xt ; then
+	echo "    WARNING: you requested file embedding but it has"
+	echo "      been disabled since C code cannot be called"
+	EMBED_SRC=
+    fi
 fi
-echo "$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
+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$HAVE_STAT" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
+
+printf "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+DEFINES="$DEFINES $IGNORE_TIME"
+
+if test "x$EMBED_SRC" = xt ; then
+    build_embed_encode
+fi
+if test "x$EMBED_SRC" = xt ; then
+    ENABLE="$ENABLE embed_files"
+fi
+
 
 printf "\n===  Setting defaults  ===\n"
-echo -n "  Adding MODS directories:  "
+printf "  Adding MODS directories:  "
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	echo -n " $d"
+	printf " $d"
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
     fi
 done
 echo
 
-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 $ROOTDIR = .. ; then
 	EXEDIR=../exe
     else
 	EXEDIR=.
@@ -935,12 +1789,36 @@
     TOOLSDIR="$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}
 
@@ -955,11 +1833,27 @@
 	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"
@@ -1015,7 +1909,7 @@
 	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
@@ -1023,12 +1917,20 @@
 	    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 $PACKAGES ; do
     addit="t"
@@ -1045,28 +1947,89 @@
 echo "  applying ENABLE settings"
 echo "" > ./.tmp_pack
 PACKAGES="$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]}
@@ -1100,6 +2063,7 @@
 
 	#  Do we need to add $dname according to the dependency rules?
 	if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
+            #echo "   " $pname ": need to add :" $dname
 	    in_dis="f"
 	    for dis in $DISABLE ; do
 		if test "x$dis" = "x$dname" ; then
@@ -1124,7 +2088,8 @@
 	    echo "  the dependency rules for \"$dname\""
 	    exit 1
 	fi
-	i=$(( $i + 1 ))
+        i=`echo "$i + 1" | bc -l`
+	#i=$(( $i + 1 ))
     done
     ck=$ck"t"
 done
@@ -1143,27 +2108,15 @@
     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"
@@ -1174,96 +2127,84 @@
 	    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.
@@ -1277,40 +2218,73 @@
 	cat $i/$j >> ad_files
     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"$FS = "x.f" ; then
+    cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f
+    mv -f ad_files_f ad_files
+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
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-echo -n 'SRCFILES = '    > srclist.inc
-echo -n 'CSRCFILES = '   > csrclist.inc
-echo -n 'F90SRCFILES = ' > f90srclist.inc
-echo -n 'HEADERFILES = ' > hlist.inc
-echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'SRCFILES = '    > srclist.inc
+printf 'CSRCFILES = '   > csrclist.inc
+printf 'F90SRCFILES = ' > f90srclist.inc
+printf 'HEADERFILES = ' > hlist.inc
+printf 'AD_FLOW_FILES = ' > ad_flow_files.inc
 alldirs="$SOURCEDIRS $INCLUDEDIRS ."
 for d in $alldirs ; do
     deplist=
@@ -1319,31 +2293,59 @@
     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
 			;;
-		    F90)
-			echo    " \\"  >> f90srclist.inc
-			echo -n " $sf" >> f90srclist.inc
+                  ./AD_CONFIG.h)
+			ignore_f=t
 			;;
-		    c)
-			echo    " \\"  >> csrclist.inc
-			echo -n " $sf" >> csrclist.inc
+                  ./FC_NAMEMANGLE.h)
+			ignore_f=t
 			;;
-		    h)
-			echo    " \\"  >> hlist.inc
-			echo -n " $sf" >> hlist.inc
+                  ./BUILD_INFO.h)
+			ignore_f=t
 			;;
-		    flow)
-			echo    " \\"  >> ad_flow_files.inc
-			echo -n " $sf" >> ad_flow_files.inc
+                  ./EMBEDDED_FILES.h)
+			ignore_f=t
 			;;
-		esac
+                  *)
+			#  For the local directory *ONLY*,
+			#  ignore all soft-links
+			if test "x$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    " \\"  >> srclist.inc
+			    printf " $sf" >> srclist.inc
+			    ;;
+			F90)
+			    echo    " \\"  >> f90srclist.inc
+			    printf " $sf" >> f90srclist.inc
+			    ;;
+			c)
+			    echo    " \\"  >> csrclist.inc
+			    printf " $sf" >> csrclist.inc
+			    ;;
+			h)
+			    echo    " \\"  >> hlist.inc
+			    printf " $sf" >> hlist.inc
+			    ;;
+			flow)
+			    echo    " \\"  >> ad_flow_files.inc
+			    printf " $sf" >> ad_flow_files.inc
+			    ;;
+		    esac
+		fi
 	    fi
 	fi
     done
@@ -1361,7 +2363,7 @@
 echo "" >> hlist.inc
 echo "" >> ad_flow_files.inc
 
-if test -e $MAKEFILE ; then
+if test -f $MAKEFILE ; then
     mv -f $MAKEFILE "$MAKEFILE.bak"
 fi
 echo "  Writing makefile: $MAKEFILE"
@@ -1370,15 +2372,17 @@
 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
@@ -1412,10 +2416,20 @@
 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 = " >>$MAKEFILE
+fi
+
+#  Note: figure out some way to add Hyades JAM libraries here 
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
@@ -1429,8 +2443,10 @@
 FC = ${FC}
 # Fortran compiler
 F90C = ${F90C}
+# C compiler
+CC = ${CC}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1440,7 +2456,7 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS}
+FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
 FOPTIM = ${FOPTIM}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
@@ -1451,7 +2467,7 @@
 NOOPTFILES = ${NOOPTFILES}
 NOOPTFLAGS = ${NOOPTFLAGS}
 # Flags and libraries needed for linking
-LIBS = ${LIBS} \$(XLIBS)
+LIBS = ${LIBS}
 # Name of the Mekfile
 MAKEFILE=${MAKEFILE}
 
@@ -1462,28 +2478,35 @@
 cat f90srclist.inc    >> $MAKEFILE
 cat hlist.inc         >> $MAKEFILE
 cat ad_flow_files.inc >> $MAKEFILE
-echo               >> $MAKEFILE
-echo 'F77FILES =  $(SRCFILES:.F=.f)'                                           >> $MAKEFILE
-echo 'F90FILES =  $(F90SRCFILES:.F90=.f90)'                                    >> $MAKEFILE
+echo >> $MAKEFILE
+echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE
+echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE
 echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
-
+echo >> $MAKEFILE
+echo '.SUFFIXES:' >> $MAKEFILE
+echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
 rm -f ad_flow_files.inc
 
 cat >>$MAKEFILE <<EOF
 
-.SUFFIXES:
-.SUFFIXES: .o .f .p .F .c .F90 .f90
-
 all: \$(EXECUTABLE)
-\$(EXECUTABLE): \$(OBJFILES)
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES) \$(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) \$(SRCFILES)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
+
+lib: libmitgcmuv.a
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+libmitgcmuv.a: \$(OBJFILES)
+	ar rcv libmitgcmuv.a \$(OBJFILES)
+	ar d   libmitgcmuv.a main.o
+
+links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77FILES) \$(F90FILES)
 
@@ -1492,41 +2515,89 @@
 	@\$(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
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f Makefile.bak genmake_state genmake_*optfile make.log
+	-rm -f \$(SPECIAL_FILES)
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
+	-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 create by make
+${PACKAGES_DOT_H}:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+AD_CONFIG.h:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+FC_NAMEMANGLE.h:
+	@echo Creating \$@ ...
+	echo "$FC_NAMEMANGLE" > \$@
+
+BUILD_INFO.h:
+	@echo Creating \$@ ...
+EOF
+
+test ! "x$THISVER" = x  && echo "	-echo \"#define THISVER '$THISVER'\" > \$@"   >> $MAKEFILE
+test ! "x$THISUSER" = x && echo "	-echo \"#define THISUSER '$THISUSER'\" >> \$@" >> $MAKEFILE
+test ! "x$THISDATE" = x && echo "	-echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
+test ! "x$THISHOST" = x && echo "	-echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
+
+if test "x$EMBED_SRC" = xt ; then
+    cat >>$MAKEFILE <<EOF
+
+decode_files.o : EMBEDDED_FILES.h
+
+##  \$(F77FILES) 
+all_fF.tar.gz : \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile
+	@echo Creating \$@ ...
+	-tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile
+	-rm -f all_fF.tar.gz
+	-gzip all_fF.tar
+
+EMBEDDED_FILES.h : all_fF.tar.gz
+	@echo Creating \$@ ...
+	-\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
+
+EOF
+fi
+
+cat >>$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:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.f90.o:
+.F90.o:   
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .c.o:
-	\$(CC) \$(CFLAGS) -c \$<
+	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
 
-# Special exceptions that use the ( .F - .p - .f - .o ) rule-chain
+# Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
 .F.p:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
-.p.f:
+.p.$FS:
 	\$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
 
 #=========================================
@@ -1545,19 +2616,19 @@
 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
+printf "AD_FILES = " >> $MAKEFILE
 AD_FILES=`cat ad_files`
 for i in $AD_FILES ; do
     echo    " \\" >> $MAKEFILE
-    echo -n " $i" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
 done
 echo >> $MAKEFILE
 rm -f ad_files
@@ -1565,72 +2636,97 @@
 cat >>$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.$FS: \$(AD_FILES) \$(HEADERFILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	-rm -f ad_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
+	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS
 
-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_output.$FS: ad_input_code.$FS
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
 adtafonly:
-	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-ad_taf: ad_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
+\${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
-ad_tamc_output.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
+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.$FS: \$(AD_FILES) \$(HEADERFILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+	-rm -f ftl_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
+	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.$FS
+	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
 ftltafonly:
-	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_taf_output.f
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+	cat ftl_input_code_ftl.$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 ...
-svdtaf: ad_taf_output.f ftl_taf_output.f
-svdall: svd_taf
+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: ad_taf_output.o ftl_taf_output.o \$(OBJFILES)
+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
 
 #=========================================
 
@@ -1647,7 +2743,7 @@
     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"
@@ -1657,7 +2753,7 @@
     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
 
@@ -1670,49 +2766,28 @@
 
 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