--- MITgcm/tools/genmake2	2004/09/07 21:28:47	1.98
+++ MITgcm/tools/genmake2	2012/08/28 21:11:22	1.238
@@ -1,6 +1,7 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.98 2004/09/07 21:28:47 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.238 2012/08/28 21:11:22 jmc Exp $
+# $Name:  $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -8,25 +9,193 @@
 #   modified by aja 01/00
 #   rewritten in bash by eh3 08/03
 
+#  Explain usage
+usage()  {
+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".
+
+    -pgroups NAME | --pgroups NAME
+      -pgroups=NAME | --pgroups=NAME
+	  Get the package groups information from "NAME".
+
+    -bash NAME
+	  Explicitly specify the Bourne or BASH shell to use
+
+    -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.
+
+    -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
+	  Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
+	  *only* works if CPP_EEOPTIONS.h allows this.
+
+    -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
+
+    -ieee | --ieee
+	  use IEEE numerics.  Note that this option *only* works
+	  if it is supported by the OPTFILE that is being used.
+    -devel | --devel
+	  Add additional warning and debugging flags for development
+	  (if supported by the OPTFILE); also switch to IEEE numerics.
+    -gsl | --gsl
+	  Use GSL to control floating point rounding and precision
+
+    -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]
+
+    -ds | --ds
+	  Report genmake internal variables status (DUMPSTATE)
+	  to file "genmake_state" (for debug purpose)
+
+  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/public/devel_HOWTO/
+
+EOF
+
+    exit 1
+}
+
 # Search for particular CPP #cmds associated with packages
 # usage: test_for_package_in_cpp_options CPP_file package_name
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+    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" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+    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
@@ -38,8 +207,8 @@
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	printf "Error: In $file there is an illegal line: "
-        grep -i "$strng" $file
-	return 1
+	grep -i "$strng" $file
+	exit 99
     fi
     return 0
 }
@@ -48,7 +217,6 @@
 # the package list.
 expand_pkg_groups() {
     new_packages=
-    PKG_GROUPS=$ROOTDIR"/pkg/pkg_groups"
     if test -r $PKG_GROUPS ; then
 	cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp
 	cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp
@@ -59,7 +227,7 @@
 	    if test "x$RETVAL" = x0 ; then
 		matched=1
 		replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`
-		echo "    replacing \"$i\" with: $replace"
+		echo "    replacing \"$i\" with:$replace"
 		new_packages="$new_packages $replace"
 	    else
 		new_packages="$new_packages $i"
@@ -102,9 +270,9 @@
 	    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 
+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
@@ -122,14 +290,14 @@
       stop
       end
 EOF
-    test -f Makefile  &&  mv -f Makefile Makefile.bak
-    cat <<EOF >> Makefile
-%.$tfs : %.F
+    test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
+    cat <<EOF >> $MAKEFILE
 .SUFFIXES:
-genmake_hello.$tfs: genmake_hello.F
-	$LN genmake_hello.F genmake_hello.$tfs
+.SUFFIXES: .$tfs .F
+.F.$tfs:
+	$LN \$< \$@
 EOF
-    $MAKE "genmake_hello."$tfs > /dev/null 2>&1
+    $MAKE -f $MAKEFILE "genmake_hello."$tfs > /dev/null 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
 	if test "x$FS" = x ; then
@@ -137,19 +305,18 @@
 	    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
+	    echo "ERROR: test: '$MAKE -f $MAKEFILE genmake_hello.$tfs' Failed"
+	    echo "       see simple makefile: '$MAKEFILE' (left here)"
+	    echo "  Please check (1) your '$MAKE' command, (2) your '$LN' command"
+	    echo "           and (3) the allowed sufix '.F' and '.$tfs' in makefile"
+	    echo "  or contact the <MITgcm-support@mitgcm.org> list for help."
+	    echo ""
 	    exit -1
 	    return
 	fi
     fi
-    rm -f genmake_hello.* Makefile
-    test -f Makefile  &&  mv -f Makefile.bak Makefile
+    rm -f genmake_hello.* $MAKEFILE
+    test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
 
     #  If we make it here, use the extensions
     FS=$tfs
@@ -157,7 +324,6 @@
     return
 }
 
-
 look_for_makedepend()  {
 
     #  The "original" makedepend is part of the Imake system that is
@@ -178,47 +344,74 @@
     #    3) locally build and use the cyrus implementation
     #    4) fall back to the buggy local xmakedpend script
     #
+    echo >> $LOGFILE
+    echo "running: look_for_makedepend()" >> $LOGFILE
+    if test "x${MAKEDEPEND}" != x ; then
+	echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
+	RETVAL=$?
+	if test x"$RETVAL" = x0 ; then
+	    build_cyrus_makedepend
+	    RETVAL=$?
+	    if test "x$RETVAL" != x0 ; then
+		echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"
+		MAKEDEPEND=
+	    fi
+	else
+	    echo "${MAKEDEPEND}" | grep 'tools.xmakedepend' > /dev/null 2>&1
+	    RETVAL=$?
+	    if test "x$RETVAL" = x0 ; then
+		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	    fi
+	    echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+	fi
+    fi
     if test "x${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
+	makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
 	RV1=$?
+	test -f $MAKEFILE  &&  rm -f $MAKEFILE
+	test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
 	if test "x${RV0}${RV1}" = x00 ; then
 	    MAKEDEPEND=makedepend
+	    echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	else
-	    echo "    a system-default makedepend was not found."
-	    
+	    echo "    system-default makedepend not found. Try to build cyrus-makedepend"
 	    #  Try to build the cyrus implementation
 	    build_cyrus_makedepend
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
+		echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"
 		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+		echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	    fi
-	    rm -f ./genmake_cy_md
-	fi
-    else
-	#  echo "MAKEDEPEND=${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()  {
+    echo >> $LOGFILE
+    echo "running: build_cyrus_makedepend()" >> $LOGFILE
     rm -f ./genmake_cy_md
     (
 	cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
 	    &&  ./configure > /dev/null 2>&1  \
-	    &&  make > /dev/null 2>&1
+	    &&  $MAKE > /dev/null 2>&1
 	if test -x ./makedepend.exe ; then
 	    $LN ./makedepend.exe ./makedepend
 	fi
@@ -230,61 +423,66 @@
     rm -f ./genmake_cy_md
     if test "x$RETVAL" = x0 ; then
 	MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+ 	echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	return 0
     else
-	echo "WARNING: unable to build cyrus-imapd-makedepend"
+	echo "WARNING: fail to build cyrus-imapd-makedepend" >> $LOGFILE
 	return 1
     fi
 }
 
-# Guess possible config options for this host
-find_possible_configs()  {
-
-    tmp1=`uname`"_"`uname -m`
-    tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
-    tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-    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:  $PLATFORM"
-    
-    echo "test" > test
-    ln -s ./test link
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	LN="ln -s"
-    else
-	echo "Error: \"ln -s\" does not appear to work on this system!"
-	echo "  For help, please contact <MITgcm-support@mitgcm.org>."
-	exit 1
-    fi
-    rm -f test link
-
-    if test "x$CPP" = x ; then
-	CPP="cpp -traditional -P"
+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"
+		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"
+}
 
-    look_for_makedepend
-
-    #================================================================
-    #  look for possible C compilers
-    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"
-    p_CC=
-    for c in $tmp ; do
-	rm -f ./genmake_hello.c  ./genmake_hello
-	cat >> genmake_hello.c << EOF
+#  look for possible C compilers
+look_for_C_compilers() {
+    echo >> $LOGFILE
+    echo "running: look_for_C_compilers()" >> $LOGFILE
+    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
-	$c -o genmake_hello genmake_hello.c > /dev/null 2>&1
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
+    p_CC=
+    for c in $tmp ; do
+	COMM="$c $CFLAGS -o genmake_hello genmake_hello.c"
+	echo $COMM >> $LOGFILE
+	$COMM >> $LOGFILE 2>&1
 	RETVAL=$?
 	if test "x${RETVAL}" = x0 ; then
+	    echo " $c test successful" >> $LOGFILE
 	    p_CC="$p_CC $c"
 	fi
     done
@@ -300,34 +498,55 @@
 EOF
 	exit 1
     else
-	echo "  The possible C compilers found in your path are:"
-	echo "   "$p_CC
+	echo "  The possible C compilers found in your path are: $p_CC" | tee -a $LOGFILE
 	if test "x$CC" = x ; then
 	    CC=`echo $p_CC | $AWK '{print $1}'`
 	    echo "  Setting C compiler to: "$CC
 	fi
     fi
+    echo " --> set CC='$CC'" >> $LOGFILE
+}
+
+# Guess possible config options for this host
+find_possible_optfile()  {
+
+    echo >> $LOGFILE
+    echo "running: find_possible_optfile()" >> $LOGFILE
+    tmp1=`uname`"_"`uname -m`
+    tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
+    tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
+    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" | tee -a $LOGFILE
 
     #================================================================
     #  look for possible FORTRAN compilers
-    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
+    echo "  look for possible FORTRAN compilers" >> $LOGFILE
+    tmp="$MITGCM_FC $FC efc gfortran g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 g95"
     p_FC=
-    for c in $tmp ; do
-	rm -f ./hello.f ./hello
-	cat >> hello.f <<EOF
+    rm -f ./genmake_hello.f
+    cat >> genmake_hello.f <<EOF
       program hello
       do i=1,3
         print *, 'hello world : ', i
       enddo
       end
 EOF
-	$c -o hello hello.f > /dev/null 2>&1
+    for f in $tmp ; do
+	COMM="$f -o genmake_hello genmake_hello.f"
+	echo $COMM >> $LOGFILE
+	$COMM >> $LOGFILE 2>&1
 	RETVAL=$?
 	if test "x${RETVAL}" = x0 ; then
-	    p_FC="$p_FC $c"
+	    echo " $f test successful" >> $LOGFILE
+	    p_FC="$p_FC $f"
 	fi
     done
-    rm -f ./hello.f ./hello
+    rm -f ./genmake_hello.f ./genmake_hello
     if test "x${p_FC}" = x ; then
 	cat 1>&2 <<EOF
 
@@ -340,31 +559,28 @@
 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 $1}'`
-	    echo "  Setting FORTRAN compiler to: "$FC
-	fi
+	echo "  The possible FORTRAN compilers found in your path are: $p_FC" | tee -a $LOGFILE
+    fi
+
+    #  Use the first of the compilers found in the current PATH
+    #  that has a correctly-named optfile
+    if test "x$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 | tee -a $LOGFILE
+		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
+	     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
 
@@ -380,36 +596,6 @@
 EOF
 	exit 1
     fi
-    
-#     # look for possible MPI libraries
-#     mpi_libs=
-#     mpi_fort=`which mpif77 2>/dev/null`
-#     RETVAL=$?
-#     if test "x${RETVAL}" = x0 ; then
-# 	cat >>test.f <<EOF
-#       PROGRAM HELLO
-#       DO 10, I=1,10
-#       PRINT *,'Hello World'
-#    10 CONTINUE
-#       STOP
-#       END
-# EOF
-# 	eval "$mpi_fort -showme test.f > out"
-# 	RETVAL=$?
-# 	if test "x${RETVAL}" = x0 ; then
-# 	    a=`cat out`
-# 	    for i in $a ; do
-# 		case $i in 
-# 		    -*)
-# 			mpi_libs="$mpi_libs $i" ;;
-# 		esac
-# 	    done
-# 	    echo "The MPI libs appear to be:"
-# 	    echo "  "$mpi_libs
-# 	fi
-# 	rm -f test.f out
-#     fi
-
 }
 
 #  Parse the package dependency information
@@ -418,130 +604,15 @@
     #  strip the comments and then convert the dependency file into
     #  two arrays: PNAME, DNAME
     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} }' \
+	| $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \
 	> ./.pd_tmp
+    RETVAL=$?
+    if test ! "x${RETVAL}" = x0 ; then
+      echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
+      exit 1
+    fi
     . ./.pd_tmp
     rm -f ./.pd_tmp
-
-    printf "PNAME = "${}
-}
-
-
-#  Explain usage
-usage()  {
-cat <<EOF
-
-Usage: "$0" [OPTIONS]
-  where [OPTIONS] can be:
-
-    -help | --help | -h | --h
-          Print this help message and exit.
-
-    -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
-      -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
-          Use "NAME" as the adoptfile.  By default, the file at
-          "tools/adjoint_options/adjoint_default" will be used.
-
-    -nooptfile | --nooptfile
-      -optfile NAME | --optfile NAME | -of NAME | --of NAME
-      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
-          Use "NAME" as the optfile.  By default, an attempt will be
-          made to find an appropriate "standard" optfile in the 
-          tools/build_options/ directory.
-
-    -pdepend NAME | --pdepend NAME
-      -pdepend=NAME | --pdepend=NAME
-          Get package dependency information from "NAME".
-
-    -pdefault NAME | --pdefault NAME
-      -pdefault=NAME | --pdefault=NAME
-          Get the default package list from "NAME".
-
-    -make NAME | -m NAME
-      --make=NAME | -m=NAME
-          Use "NAME" for the MAKE program. The default is "make" but 
-          many platforms, "gmake" is the preferred choice.
-
-    -makefile NAME | -mf NAME
-      --makefile=NAME | -mf=NAME
-          Call the makefile "NAME".  The default is "Makefile".
-
-    -makedepend NAME | -md NAME
-      --makedepend=NAME | -md=NAME
-          Use "NAME" for the MAKEDEPEND program.
-
-    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
-      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
-          Specify the location of the MITgcm ROOTDIR as "NAME".
-          By default, genamke will try to find the location by 
-          looking in parent directories (up to the 5th parent).
-
-    -mods NAME | --mods NAME | -mo NAME | --mo NAME
-      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
-          Here, "NAME" specifies a list of directories that are 
-          used for additional source code.  Files found in the 
-          "mods list" are given preference over files of the same 
-          name found elsewhere.
-
-    -disable NAME | --disable NAME
-      -disable=NAME | --disable=NAME
-          Here "NAME" specifies a list of packages that we don't 
-          want to use.  If this violates package dependencies, 
-          genamke will exit with an error message.
-
-    -enable NAME | --enable NAME
-      -enable=NAME | --enable=NAME
-          Here "NAME" specifies a list of packages that we wish 
-          to specifically enable.  If this violates package 
-          dependencies, genamke will exit with an error message.
-
-    -standarddirs NAME | --standarddirs NAME
-      -standarddirs=NAME | --standarddirs=NAME
-          Here, "NAME" specifies a list of directories to be 
-          used as the "standard" code.
-
-    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
-      -fc=NAME | --fc=NAME
-          Use "NAME" as the fortran compiler.  By default, genmake 
-          will search for a working compiler by trying a list of
-          "usual suspects" such as g77, f77, etc.
-
-    -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
-          Use "NAME" as the C compiler.  By default, genmake 
-          will search for a working compiler by trying a list of
-          "usual suspects" such as gcc, c89, cc, etc.
-
-    -[no]ieee | --[no]ieee
-          Do or don't use IEEE numerics.  Note that this option 
-          *only* works if it is supported by the OPTFILE that 
-          is being used.
-
-    -mpi | --mpi
-          Include MPI header files and link to MPI libraries
-    -mpi=PATH | --mpi=PATH
-          Include MPI header files and link to MPI libraries using MPI_ROOT
-          set to PATH. i.e. Include files from \$PATH/include, link to libraries
-          from \$PATH/lib and use binaries from \$PATH/bin.
-
-    -bash NAME
-          Explicitly specify the Bourne or BASH shell to use
-
-  While it is most often a single word, the "NAME" variables specified 
-  above can in many cases be a space-delimited string such as:
-
-    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
-    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
-    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
-
-  which, depending upon your shell, may need to be single-quoted.
-
-  For more detailed genmake documentation, please see:
-
-    http://mitgcm.org/devel_HOWTO/
-
-EOF
-
-    exit 1
 }
 
 #  Build a CPP macro to automate calling C routines from FORTRAN
@@ -549,23 +620,26 @@
 
     #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
     if test ! "x$FC_NAMEMANGLE" = x ; then
-        return 0
+	return 0
     fi
+    echo " running: get_fortran_c_namemangling()" >> $LOGFILE
 
     default_nm="#define FC_NAMEMANGLE(X) X ## _"
-    
+
     cat > genmake_test.c <<EOF
 void tcall( char * string ) { tsub( string ); }
 EOF
-    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_test.c"
+    echo ' '$COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_errors
+	cat <<EOF>> $LOGFILE
 
-WARNING: C test compile fails
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ WARNING: C test compile fails
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
 EOF
 	return 1
     fi
@@ -573,29 +647,31 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: The "nm" command failed.
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
 EOF
 	return 1
     fi
-    cat > genmake_tcomp.f <<EOF
+    cat > genmake_tcomp.$FS <<EOF
       subroutine tcall( string )
       character*(*) string
       call tsub( string )
       end
 EOF
-    $FC $FFLAGS $DEFINES -c genmake_tcomp.f >> genmake_warnings 2>&1
+    COMM="$FC $FFLAGS -c genmake_tcomp.$FS"
+    echo ' '$COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: FORTRAN test compile fails -- please see "genmake_errors"
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ WARNING: FORTRAN test compile fails -- please see '$LOGFILE'
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
 EOF
 	return 1
     fi
@@ -603,11 +679,11 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: The "nm" command failed.
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
 EOF
 	return 1
     fi
@@ -633,10 +709,13 @@
 
     #  cleanup the testing files
     rm -f genmake_tcomp.* genmake_test.*
-}
 
+    echo " --> set FC_NAMEMANGLE='$FC_NAMEMANGLE'" >> $LOGFILE
+}
 
 check_HAVE_CLOC()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_CLOC()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -653,33 +732,195 @@
  *curtim = *curtim/1.E6;
 }
 EOF
-    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    COMM="$CC $CFLAGS -c genmake_tc_1.c"
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
-    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 >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_F=$?
-    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1
+    test -x ./genmake_tc  &&  ./genmake_tc >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_CLOC=t
-	DEFINES="$DEFINES -DHAVE_CLOC"
     fi
     rm -f genmake_tc*
+    echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
 }
 
+check_HAVE_SIGREG()  {
+    if test ! "x$HAVE_SIGREG" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SIGREG()" >> $LOGFILE
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$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 >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      integer anint
+      common /iv/ anint
+      external sigreg
+      call sigreg(anint)
+      end
+EOF
+    cat genmake_tc_2.$FS >> $LOGFILE
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_SIGREG=t
+    fi
+    rm -f genmake_tc*
+    echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
+}
+
+check_HAVE_SETRLSTK()  {
+    if test ! "x$HAVE_SETRLSTK" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SETRLSTK()" >> $LOGFILE
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$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 >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      external setrlstk
+      call setrlstk()
+      end
+EOF
+    cat genmake_tc_2.$FS >> $LOGFILE
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_SETRLSTK=t
+    fi
+    rm -f genmake_tc*
+    echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
+}
+
+check_HAVE_STAT()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_STAT()" >> $LOGFILE
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$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 >> $LOGFILE
+    $COMM >> genmake_tc.log 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.$FS
+      program hello
+      integer nbyte
+      call tfsize(nbyte)
+      print *," HELLO WORLD", nbyte
+      end
+EOF
+    cat genmake_tc_2.$FS >> $LOGFILE
+    COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+    echo $COMM >> $LOGFILE
+    $COMM >> genmake_tc.log 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_STAT=t
+    fi
+    rm -f genmake_tc*
+    echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
+}
 
 check_netcdf_libs()  {
-    echo "" > genmake_tnc.log
-    cat <<EOF > genmake_tnc.for
+    if test ! "x$SKIP_NETCDF_CHECK" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_netcdf_libs()" >> $LOGFILE
+    cat <<EOF > genmake_tnc.F
       program fgennc
 #include "netcdf.inc"
+EOF
+    if test ! "x$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)
@@ -689,35 +930,177 @@
       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
       end
 EOF
-    #echo "$CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f"
-    #echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.f"
-    #echo "$LINK -o genmake_tnc.o $LIBS"
-    $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
-	&&  $FC $FFLAGS $FOPTIM -c genmake_tnc.f  \
-	&&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+    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 $LIBS >> genmake_tnc.log 2>&1
     RET_COMPILE=$?
-    test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
-    RETVAL=$?
-    if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+    cat genmake_tnc.log >> $LOGFILE
+
+    #EH3  Remove test program execution for machines that either disallow
+    #EH3  execution or cannot support it (eg. cross-compilers)
+    #EH3
+    #EH3 test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    #EH3 RETVAL=$?
+    #EH3 if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+
+    if test "x$RET_COMPILE" = x0 ; then
 	HAVE_NETCDF=t
+	echo "check_netcdf: successful" >> $LOGFILE
     else
 	# try again with "-lnetcdf" added to the libs
-	$CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \
-	    &&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f \
-	    $LIBS -lnetcdf >> genmake_tnc_2.log 2>&1
+	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 $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
-	test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
-	RETVAL=$?
-	if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	echo >> $LOGFILE
+	cat genmake_tnc.log >> $LOGFILE
+	if test "x$RET_COMPILE" = x0 ; then
 	    LIBS="$LIBS -lnetcdf"
 	    HAVE_NETCDF=t
+	    echo "check_netcdf: successful" >> $LOGFILE
 	else
-	    cat genmake_tnc.log >> genmake_warnings
+	# 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 $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
+	    RET_COMPILE=$?
+	    echo >> $LOGFILE
+	    cat genmake_tnc.log >> $LOGFILE
+	    if test "x$RET_COMPILE" = x0 ; then
+		LIBS="$LIBS -lnetcdff -lnetcdf"
+		HAVE_NETCDF=t
+		echo "check_netcdf: successful" >> $LOGFILE
+	    fi
 	fi
     fi
     rm -f genmake_tnc*
+    echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
 }
 
+check_lapack_libs()  {
+    if test ! "x$SKIP_LAPACK_CHECK" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_lapack_libs()" >> $LOGFILE
+    cat <<EOF > genmake_tla.F
+      program fgenla
+      integer info
+      integer ipiv( 2 )
+      double precision ab( 4, 2 ), b( 2 )
+      data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
+      data b / 1., 1. /
+      call dgbsv( 2, 1, 1, 1, ab, 4, ipiv, b, 2, info )
+      IF (info .NE. 0) write(*,*) 'Error:', info
+      write(*,*) b
+      end
+EOF
+    echo "===  genmake_tla.F  >>>" > genmake_tla.log
+    cat genmake_tla.F >> genmake_tla.log
+    echo "<<<  genmake_tla.F  ===" >> genmake_tla.log
+    RET_CPP=f
+    COMM="cat genmake_tla.F | $CPP $DEFINES $INCLUDES"
+    echo "$COMM" >> genmake_tla.log
+    eval $COMM > genmake_tla.$FS 2>/dev/null  &&  RET_CPP=t
+    if test "x$RET_CPP" = xf ; then
+	echo "  WARNING: CPP failed to pre-process the lapack test." \
+	    >> genmake_tla.log
+	echo "    Please check that \$INCLUDES is properly set." \
+	    >> genmake_tla.log
+    fi
+    echo "$FC $FFLAGS $FOPTIM -c genmake_tla.$FS  \ " >> genmake_tla.log
+    echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tla.o $LIBS" >> genmake_tla.log
+    $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+	&&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS >> genmake_tla.log 2>&1
+    RET_COMPILE=$?
+    cat genmake_tla.log >> $LOGFILE
+
+    # test program execution not always possible (see check_netcdf_libs)
+    #
+    #test -x ./genmake_tla  &&  ./genmake_tla >> genmake_tla.log 2>&1
+    #RETVAL=$?
+    #if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+
+    if test "x$RET_COMPILE" = x0 ; then
+	HAVE_LAPACK=t
+	echo "check_lapack: successful" >> $LOGFILE
+    else
+	# try again with "-llapack" added to the libs
+	echo "==> try again with added '-llapack'" > genmake_tla.log
+	echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+	echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+	echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack" >> genmake_tla.log
+	cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+	    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack >> genmake_tla.log 2>&1
+	RET_COMPILE=$?
+	echo >> $LOGFILE
+	cat genmake_tla.log >> $LOGFILE
+	if test "x$RET_COMPILE" = x0 ; then
+	    LIBS="$LIBS -llapack"
+	    HAVE_LAPACK=t
+	    echo "check_lapack: successful" >> $LOGFILE
+	else
+	# try again with "-lf77blas -lcblas" added to the libs
+	    echo "==> try again with added '-llapack -lf77blas -lcblas'" > genmake_tla.log
+	    echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+	    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+	    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas" >> genmake_tla.log
+	    cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+		&&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+		&&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas >> genmake_tla.log 2>&1
+	    RET_COMPILE=$?
+	    echo >> $LOGFILE
+	    cat genmake_tla.log >> $LOGFILE
+	    if test "x$RET_COMPILE" = x0 ; then
+		LIBS="$LIBS -llapack -lf77blas -lcblas"
+		HAVE_LAPACK=t
+		echo "check_lapack: successful" >> $LOGFILE
+	    else
+	    # try again with "-latlas" added to the libs
+		echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
+		echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+		echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+		echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
+		cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+		    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+		    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
+		RET_COMPILE=$?
+		echo >> $LOGFILE
+		cat genmake_tla.log >> $LOGFILE
+		if test "x$RET_COMPILE" = x0 ; then
+		    LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
+		    HAVE_LAPACK=t
+		    echo "check_lapack: successful" >> $LOGFILE
+		fi
+	    fi
+	fi
+    fi
+    rm -f genmake_tla*
+    echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
+}
 
 
 ###############################################################################
@@ -731,23 +1114,27 @@
 LN=
 S64=
 KPP=
-FC=
+#FC=
 #CC=gcc
-CPP=
+#CPP=
 LINK=
 DEFINES=
 PACKAGES=
 ENABLE=
 DISABLE=
-MAKEFILE=
-#MAKEDEPEND=
-PDEPEND=
-DUMPSTATE=t
-PDEFAULT=
+# MAKEFILE=
+# MAKEDEPEND=
+PKG_DEPEND=
+PKG_GROUPS=
+DUMPSTATE=f
 OPTFILE=
-INCLUDES="-I."
+INCLUDES="-I. $INCLUDES"
 FFLAGS=
 FOPTIM=
+FEXTRAFLAGS=
+USE_EXTENDED_SRC=
+EXTENDED_SRC_FLAG=
+GET_FC_VERSION=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -758,14 +1145,31 @@
 NOOPTFLAGS=
 MPI=
 MPIPATH=
+OMP=
+OMPFLAG=
+USE_R4=
+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=
+HAVE_LAPACK=
 
 MODS=
 TOOLSDIR=
@@ -773,11 +1177,15 @@
 INCLUDEDIRS=
 STANDARDDIRS="USE_THE_DEFAULT"
 
+#- local config file
+gm_local="genmake_local"
+
 G2ARGS=
 BASH=
 PWD=`pwd`
-MAKE=make
-AWK=awk
+test "x$MAKE" = x  &&  MAKE=make
+test "x$AWK" = x   &&  AWK=awk
+EMBED_SRC=
 THISHOST=`hostname`
 THISCWD=`pwd`
 THISDATE=`date`
@@ -787,7 +1195,6 @@
 EXECUTABLE=
 EXEHOOK=
 EXEDIR=
-PACKAGES_CONF=
 IEEE=
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
@@ -808,68 +1215,47 @@
 SVD_TAMC_FLAGS=
 TAMC_EXTRA=
 
-
 #  The following state can be set directly by command-line switches
-gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC CPP IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
+gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
+gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
 
 #  The following state is not directly set by command-line switches
-gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
-gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
-gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
-gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
+gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
+gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
+gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
+gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"
+gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK"
 
 #  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"
 gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
 gm_s12="TAF_EXTRA TAMC_EXTRA"
 
-gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
+gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
 gm_state="$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/
+A program for GENerating MAKEfiles for the MITgcm project.
+   For a quick list of options, use "genmake2 -h"
+or for more detail see the Developer's HOWTO manual at:
+   http://mitgcm.org/public/docs.html
 
 EOF
 
+LOGFILE="genmake.log"
+#- clean-up previous genmake logfiles:
+rm -f genmake_state genmake_*optfile $LOGFILE
+
 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
-printf "  getting local config information:  "
-if test -f $gm_local ; then
-    echo "using $gm_local"
-    . $gm_local
-    # echo "DISABLE=$DISABLE"
-    # echo "ENABLE=$ENABLE"
-else
-    echo "none found"
-fi
 
-#  echo "$0::$1:$2:$3:$4:$5:$6:$7:"
-#OPTIONS=
-#n=0
-#for i ; do 
-#   echo "$i  $n"
-#   setvar="OPTIONS[$n]='$i'"
-#   #  echo "  $setvar"
-#   eval "$setvar"
-#   n=$(( $n + 1 ))
-#done
+#echo "$0::$1:$2:$3:$4:$5:$6:$7:"
 #parse_options
 ac_prev=
-for ac_option in $@ ; do
+for ac_option in "$@" ; do
 
     G2ARGS="$G2ARGS \"$ac_option\""
 
@@ -879,83 +1265,83 @@
 	ac_prev=
 	continue
     fi
-    
+
     ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
-    
+
     case $ac_option in
-	
+
 	-help | --help | -h | --h)
 	    usage ;;
-	
+
 	-nooptfile | --nooptfile)
 	    OPTFILE="NONE" ;;
 	-optfile | --optfile | -of | --of)
 	    ac_prev=OPTFILE ;;
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
-	
+
 	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
-	
+
 	-pdepend | --pdepend)
-	    ac_prev=PDEPEND ;;
+	    ac_prev=PKG_DEPEND ;;
 	-pdepend=* | --pdepend=*)
-	    PDEPEND=$ac_optarg ;;
-	
-	-pdefault | --pdefault)
-	    ac_prev=PDEFAULT ;;
-	-pdefault=* | --pdefault=*)
-	    PDEFAULT=$ac_optarg ;;
-	
+	    PKG_DEPEND=$ac_optarg ;;
+
+	-pgroups | --pgroups)
+	    ac_prev=PKG_GROUPS ;;
+	-pgroups=* | --pgroups=*)
+	    PKG_GROUPS=$ac_optarg ;;
+
 	-make | --make | -m | --m)
 	    ac_prev=MAKE ;;
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$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)
+
+	-makefile | --makefile | -mf | --mf)
 	    ac_prev=MAKEFILE ;;
-	-makefile=* | --makefile=* | -ma=* | --ma=*)
+	-makefile=* | --makefile=* | -mf=* | --mf=*)
 	    MAKEFILE=$ac_optarg ;;
-	
+
 	-platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
 	    echo "ERROR: The platform option has been removed.  Please specify"
 	    echo "  the build options using the \"optfile\" mechanism."
 	    echo
 	    usage
 	    ;;
-	
+
 	-rootdir | --rootdir | -rd | --rd)
 	    ac_prev=ROOTDIR ;;
 	-rootdir=* | --rootdir=* | -rd=* | --rd=*)
 	    ROOTDIR=$ac_optarg ;;
-	
+
 	-mods | --mods | -mo | --mo)
 	    ac_prev=MODS ;;
 	-mods=* | --mods=* | -mo=* | --mo=*)
 	    MODS=$ac_optarg ;;
-	
+
 	-disable | --disable)
 	    ac_prev=DISABLE ;;
 	-disable=* | --disable=*)
 	    DISABLE=$ac_optarg ;;
-	
+
 	-enable | --enable)
 	    ac_prev=ENABLE ;;
 	-enable=* | --enable=*)
 	    ENABLE=$ac_optarg ;;
-	
+
 	-standarddirs | --standarddirs)
 	    ac_prev=STANDARDDIRS ;;
 	-standarddirs=* | --standarddirs=*)
@@ -965,46 +1351,74 @@
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
 #		CPP=$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 ;;
-	
+
+	-use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
+	    USE_R4=true ;;
+
 	-ieee | --ieee)
 	    IEEE=true ;;
 	-noieee | --noieee)
-	    IEEE= ;;
+	    echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
+	-devel | --devel)
+	    IEEE=true ; DEVEL=true ;;
+	-gsl | --gsl)
+	    GSL=true ;;
+
+	-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 ;;
 
 	-mpi | --mpi)
 	    MPI=true ;;
 	-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 ;;
-	
+
+	-extra_flag | --extra_flag)
+	    ac_prev=FEXTRAFLAGS ;;
+	-extra_flag=* | --extra_flag=*)
+	    FEXTRAFLAGS=$ac_optarg ;;
+
 	-taf_extra | --taf_extra)
 	    ac_prev=TAF_EXTRA ;;
 	-taf_extra=* | --taf_extra=*)
@@ -1015,43 +1429,56 @@
 	-tamc_extra=* | --tamc_extra=*)
 	    TAMC_EXTRA=$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: "$ac_option
 	    usage
 	    ;;
-	
+
 	*)
 	    echo "Error: unrecognized argument: "$ac_option
 	    usage
 	    ;;
-	
+
     esac
-    
+
 done
 
+printf "  getting local config information:  "
+if test -f $gm_local ; then
+    echo "using $gm_local"
+    . $gm_local
+else
+    echo "none found"
+fi
+
 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 "    http://mitgcm.org/devel_HOWTO/"
+    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/public/devel_HOWTO/"
+    echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
+    echo "WARNING: ignore \"./.genmakerc\" and continue."
     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 
 fi
 
 #  Find the MITgcm ${ROOTDIR}
 if test "x${ROOTDIR}" = x ; then
-    tmp=`echo $PWD | sed -e 's/\// /g' | awk '{print $NR}'`
-    if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then
+    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
-		printf "Warning:  ROOTDIR was not specified but there appears to be"
-		echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
+		printf "Warning: ROOTDIR was not specified ;"
+		echo " try using a local copy of MITgcm found at \"$ROOTDIR\""
 		break
 	    fi
 	done
@@ -1069,16 +1496,26 @@
 fi
 
 #  Find the MITgcm ${THISVER}
-if test -f "${ROOTDIR}/doc/tag-index" ; then
-    THISVER=`grep checkpoint ${ROOTDIR}/doc/tag-index | head -1`
+version_file="${ROOTDIR}/doc/tag-index"
+if test -f $version_file ; then
+    THISVER=`$AWK '/^checkpoint/{print $1; exit}' $version_file`
+#-  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
 
-echo "  getting OPTFILE information:  "
+if test "x$MAKEFILE" = x ; then
+    MAKEFILE="Makefile"
+fi
+
+echo "  getting OPTFILE information:"
 if test "x${OPTFILE}" = x ; then
     if test "x$MITGCM_OF" = x ; then
 	echo "Warning: no OPTFILE specified so we'll look for possible settings"
 	printf "\n===  Searching for possible settings for OPTFILE  ===\n"
-	find_possible_configs
+	find_possible_optfile
     else
 	OPTFILE=$MITGCM_OF
     fi
@@ -1093,7 +1530,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $OPTFILE "genmake_optfile"
 	fi
     else
@@ -1102,10 +1539,7 @@
     fi
 fi
 
-#  Check for broken systems that cannot correctly distinguish *.F and *.f files
-# check_for_broken_Ff
-
-echo "  getting AD_OPTFILE information:  "
+echo "  getting AD_OPTFILE information:"
 if test "x${AD_OPTFILE}" = x ; then
     if test "x$MITGCM_AD_OF" = x ; then
 	AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
@@ -1123,7 +1557,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $AD_OPTFILE "genmake_ad_optfile"
 	fi
     else
@@ -1132,6 +1566,9 @@
     fi
 fi
 
+#====================================================================
+#  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$BASH" = x ; then
@@ -1148,16 +1585,24 @@
 EOF
     exit 1
 fi
+if test "x$GET_FC_VERSION" != x ; then
+  echo "Get compiler version using: $FC $GET_FC_VERSION" >> $LOGFILE
+  ff=`echo $FC | sed 's/ .*//'` ; xx=`echo $ff | sed 's/^./& /' | sed 's/ .*//'`
+  if test $xx != '/' ; then which $ff >> $LOGFILE ; fi
+  $FC $GET_FC_VERSION > genmake_fc_vers1 2> genmake_fc_vers2
+  if test -s genmake_fc_vers1 ; then
+    cat genmake_fc_vers1 >> $LOGFILE
+  else
+    cat genmake_fc_vers2 >> $LOGFILE
+  fi
+  echo "<-- compiler version ----" >> $LOGFILE
+  rm -f genmake_fc_vers1 genmake_fc_vers2
+fi
+
 if test "x$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
+    look_for_C_compilers
 fi
+
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
@@ -1165,7 +1610,7 @@
     MAKE="make"
 fi
 if test "x$CPP" = x ; then
-    CPP=cpp
+    CPP="cpp -traditional -P"
 fi
 #EH3 === UGLY ===
 #  The following is an ugly little hack to check for $CPP in /lib/ and
@@ -1192,7 +1637,10 @@
 else
     rm -f test_cpp
 fi
+
 look_for_makedepend
+
+#  Check that soft-link command is set and usable
 if test "x$LN" = x ; then
     LN="ln -s"
 fi
@@ -1202,12 +1650,17 @@
 if test "x$RETVAL" != x0 ; then
     cat <<EOF 1>&2
 
-Error: The command "ln -s" failed -- please specify a working soft-link
+Error: The command "$LN" 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
@@ -1217,15 +1670,113 @@
       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$USE_R4" = x ; then
+      echo "  Turning on LET_RS_BE_REAL4 cpp flag"
+      DEFINES="$DEFINES -DLET_RS_BE_REAL4"
+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"
 printf "  Do we have the system() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
+cat > genmake_tcomp.$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
@@ -1238,15 +1789,15 @@
 rm -f genmake_tcomp*
 
 printf "  Do we have the fdate() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
+cat > genmake_tcomp.$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
@@ -1259,7 +1810,7 @@
 rm -f genmake_tcomp*
 
 printf "  Do we have the etime() command using $FC...  "
-cat > genmake_tcomp.f <<EOF
+cat > genmake_tcomp.$FS <<EOF
       program hello
       REAL*4 ACTUAL, TARRAY(2)
       EXTERNAL ETIME
@@ -1268,7 +1819,7 @@
       print *, tarray
       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_ETIME=t
@@ -1283,6 +1834,42 @@
 printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
 check_HAVE_CLOC
 if test "x$HAVE_CLOC" != x ; then
+    DEFINES="$DEFINES -DHAVE_CLOC"
+    echo "yes"
+else
+    echo "no"
+    if test "x$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
+    DEFINES="$DEFINES -DHAVE_SETRLSTK"
+    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
+    DEFINES="$DEFINES -DHAVE_SIGREG"
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
+
+printf "  Can we use stat() through C calls...  "
+check_HAVE_STAT
+if test "x$HAVE_STAT" != x ; then
+    DEFINES="$DEFINES -DHAVE_STAT"
     echo "yes"
 else
     echo "no"
@@ -1292,36 +1879,51 @@
 printf "  Can we create NetCDF-enabled binaries...  "
 check_netcdf_libs
 if test "x$HAVE_NETCDF" != x ; then
+    DEFINES="$DEFINES -DHAVE_NETCDF"
+    echo "yes"
+else
+    echo "no"
+fi
+
+printf "  Can we create LAPACK-enabled binaries...  "
+check_lapack_libs
+if test "x$HAVE_LAPACK" != x ; then
+    DEFINES="$DEFINES -DHAVE_LAPACK"
     echo "yes"
 else
     echo "no"
 fi
+DEFINES="$DEFINES $IGNORE_TIME"
 
+if test "x$EMBED_SRC" = xt ; then
+    build_embed_encode
+fi
+if test "x$EMBED_SRC" = xt ; then
+    ENABLE="$ENABLE embed_files"
+#   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+fi
 
 printf "\n===  Setting defaults  ===\n"
-printf "  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
-	printf " $d"
+	printf "$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=$p_PLATFORM
-fi
+#if test "x${PLATFORM}" = x ; then
+#    PLATFORM=$p_PLATFORM
+#fi
 
 if test "x${EXEDIR}" = x ; then
-    tmp=`echo $PWD | sed -e 's/\// /g' | awk '{print $NR}'`
+    tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
     if test "x$tmp" = "xbin" -a -d ../exe -a $ROOTDIR = .. ; then
 	EXEDIR=../exe
     else
@@ -1341,18 +1943,55 @@
     exit 1
 fi
 if test "x$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}
 
+#  Set Standard Code Directories:
+if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
+    STANDARDDIRS="eesupp model"
+fi
+#  if model in Standard-Code-Dir, add eesupp (needed to compile model)
+echo " $STANDARDDIRS " | grep ' model ' > /dev/null 2>&1
+ckM=$?
+echo " $STANDARDDIRS " | grep ' eesupp ' > /dev/null 2>&1
+ckE=$?
+if test $ckM = 0 -a $ckE = 1 ; then
+    STANDARDDIRS="$STANDARDDIRS eesupp"
+fi
+
 #  We have a special set of source files in eesupp/src which are
 #  generated from some template source files. We'll make them first so
 #  they appear as regular source code
 if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
     echo "  Making source files in eesupp from templates"
-    ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
+    ( cd $ROOTDIR"/eesupp/src/" && $MAKE clean_old && $MAKE \
+    ) > make_eesupp.errors 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	rm -f make_eesupp.errors
@@ -1363,90 +2002,104 @@
     fi
 fi
 
-#same for exch2
-if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
-    echo "  Making source files in exch2 from  templates"
-    ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-        rm -f make_exch2.errors
-    else
-        echo "Error: problem encountered while building source files in exch2:"
-        cat make_exch2.errors 1>&2
-        exit 1
+#same for pkg/exch2 and pkg/regrid
+for pdir in exch2 regrid ; do
+    if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
+	echo "  Making source files in pkg/${pdir} from templates"
+	( cd $ROOTDIR"/pkg/"${pdir} && $MAKE clean_old && $MAKE \
+	) > make_${pdir}.errors 2>&1
+	RETVAL=$?
+	if test "x${RETVAL}" = x0 ; then
+	    rm -f make_${pdir}.errors
+	else
+	    echo "Error: problem encountered while building source files in pkg/${pdir}:"
+	    cat make_${pdir}.errors 1>&2
+	    exit 1
+	fi
     fi
-fi
+done
 
 printf "\n===  Determining package settings  ===\n"
-if  test "x${PDEPEND}" = x ; then
+if  test "x${PKG_DEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
-    if test -r $tmp ; then
-	PDEPEND=$tmp
-    else
+    if test -r $tmp ; then PKG_DEPEND=$tmp ; fi
+fi
+if  test "x${PKG_DEPEND}" = x ; then
 	echo "Warning:  No package dependency information was specified."
 	echo "  Please check that ROOTDIR/pkg/pkg_depend exists."
-    fi
 else
-    if test ! -r ${PDEPEND} ; then
-	echo "Error:  can't read package dependency info from PDEPEND=\"$PDEPEND\""
+    if test ! -r ${PKG_DEPEND} ; then
+	echo "Error:  can't read package dependency info from PKG_DEPEND=\"$PKG_DEPEND\""
 	exit 1
     fi
+    echo "  getting package dependency info from  $PKG_DEPEND"
+#  Strip the comments and then convert the dependency file into arrays: PNAME, DNAME
+    get_pdepend_list $PKG_DEPEND
 fi
-echo "  getting package dependency info from  $PDEPEND"
-#  Strip the comments and then convert the dependency file into
-#  two arrays: PNAME, DNAME
-cat $PDEPEND | sed -e 's/#.*$//g' \
-    | $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \
-    > ./.pd_tmp
-RETVAL=$?
-if test ! "x${RETVAL}" = x0 ; then
-    echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""
-    exit 1
+
+# A default package groups file "$ROOTDIR/pkg/pkg_groups" is provided
+#  to define the "default_pkg_list" and package groups (for convenience, one
+#  can specify a group of packages using names like "ocean" and "atmosphere").
+if test "x${PKG_GROUPS}" = x ; then
+    tmp=$ROOTDIR"/pkg/pkg_groups"
+    if test -r $tmp ; then PKG_GROUPS=$tmp ; fi
+fi
+if test "x${PKG_GROUPS}" = x ; then
+	echo "Warning:  No package groups information was specified."
+	echo "  Please check that ROOTDIR/pkg/pkg_groups exists."
+else
+    if test ! -r ${PKG_GROUPS} ; then
+	echo "Error:  can't read package groups info from PKG_GROUPS=\"$PKG_GROUPS\""
+	exit 1
+    fi
+    echo "  getting package groups info from      $PKG_GROUPS"
 fi
-. ./.pd_tmp
-rm -f ./.pd_tmp
 
-#  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
-#  file should eventually be added so that, for convenience, one can 
-#  specify groups of packages using names like "ocean" and "atmosphere".
-echo "  checking default package list:  "
-if test "x${PDEFAULT}" = x ; then
+#  Search for packages to compile.
+echo "  checking list of packages to compile:"
+PKG_LIST=
+if test "x${PKG_LIST}" = x ; then
     for i in "." $MODS ; do
 	if test -r $i"/packages.conf" ; then
-		PDEFAULT=$i"/packages.conf"
+		PKG_LIST=$i"/packages.conf"
 		break
 	fi
     done
 fi
-if test "x${PDEFAULT}" = x ; then
-    PDEFAULT="$ROOTDIR/pkg/pkg_default"
-fi
-if test "x${PDEFAULT}" = xNONE ; then
-    echo "    default packages file disabled"
+if test "x${PKG_LIST}" = x ; then
+    pkg_list='default_pkg_list'
+    if test "x${PKG_GROUPS}" = x ; then
+	echo "Error:  need package groups info to expand pkg_list=\"$pkg_list\""
+	exit 1
+    fi
 else
-    if test ! -r $PDEFAULT ; then
-	echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
+    if test ! -r $PKG_LIST ; then
+	echo "Error:  can't read package list from PKG_LIST=\"$PKG_LIST\""
+	exit 1
     else
-	echo "    using PDEFAULT=\"$PDEFAULT\""
-        #  Strip the comments and add all the names
-	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
+	echo "    using PKG_LIST=\"$PKG_LIST\""
+	#  Strip the comments and add all the names
+	pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
 	if test "x${RETVAL}" != x0 ; then
-	    printf "Error: can't parse default package list "
-	    echo "-- please check PDEFAULT=\"$PDEFAULT\""
+	    printf "Error: can't parse package list "
+	    echo "-- please check PKG_LIST=\"$PKG_LIST\""
 	    exit 1
 	fi
-	for i in $def ; do
-	    PACKAGES="$PACKAGES $i"
-	done
-	echo "    before group expansion packages are: $PACKAGES"
-	RET=1
-        while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
-	echo "    after group expansion packages are:  $PACKAGES"
     fi
 fi
+for i in $pkg_list ; do
+    PACKAGES="$PACKAGES $i"
+done
+echo     "    before group expansion packages are:$PACKAGES"
+if test "x${PKG_GROUPS}" != x ; then
+    RET=1
+    while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
+    echo "    after group expansion packages are: $PACKAGES"
+fi
 
 echo "  applying DISABLE settings"
+echo "" > ./.tmp_pack
 for i in $PACKAGES ; do
     echo $i >> ./.tmp_pack
 done
@@ -1474,8 +2127,8 @@
 for i in $PACKAGES ; do
     j=`echo $i | sed 's/[-+]//'`
     if test ! -d "$ROOTDIR/pkg/$j" ; then
-	echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""
- 	exit 1
+	echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
+	exit 1
     fi
     echo $i >> ./.tmp_pack
 done
@@ -1484,15 +2137,104 @@
     PACKAGES="$PACKAGES $i"
 done
 rm -f ./.tmp_pack
-echo "    packages are:  $PACKAGES"
+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 " $PACKAGES " | grep ' mnc ' > /dev/null 2>&1
+mnc_in=$?
+if test "x$HAVE_NETCDF" != xt ; then
+    if test "x$mnc_in" = x0 ; 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
+    #  this prevent to add mnc (due to pdepend rules) if not available
+	DISABLE="$DISABLE mnc"
+    fi
+else
+    # we have NetCDF, we try to build MNC template files
+    ( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+	rm -f make_mnc.errors
+    else
+	echo "Error: problem encountered while building source files in pkg/mnc:"
+	cat make_mnc.errors 1>&2
+	if test "x$mnc_in" = x0 ; then
+	    exit 1
+	else
+	    DISABLE="$DISABLE mnc"
+	fi
+    fi
+fi
+
+#  Check for package PROFILES: if NetCDF is not available,
+#  then delete profiles from the list of available packages.
+if test "x$HAVE_NETCDF" != xt ; then
+    echo " $PACKAGES " | grep ' profiles ' > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; 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"
+    else
+    #  this prevent to add profiles (due to pdepend rules) if not available
+	DISABLE="$DISABLE profiles"
+    fi
+fi
+
+#  Check for package RADTRANS: if LAPACK is not available,
+#  then issue a warning that the direct radtrans solver is not available.
+if test "x$HAVE_LAPACK" != xt ; then
+    echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	cat <<EOF
+*********************************************************************
+WARNING: the "radtrans" package was enabled but tests failed to
+  compile LAPACK applications.  This means that the direct radtrans
+  solver is not available and compilation will fail if it is enabled.
+  If you want to use the direct solver, please check that:
+
+  1) LAPACK is correctly installed for this compiler and
+  2) the LIBS variable (within the "optfile") specifies the correct
+     LAPACK library to link against.
+*********************************************************************
+EOF
+    fi
+fi
 
-echo "  applying package dependency rules"
-ck=
-while test "x$ck" != xtt ; do
+if  test "x${PKG_DEPEND}" != x ; then
+  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]}
@@ -1504,6 +2246,10 @@
 		pin="t"
 	    fi
 	done
+	#  or in the current $STANDARDDIRS list?
+	for p in $STANDARDDIRS ; do
+	    if test "x$p" = "x$pname" ; then pin="t" ; fi
+	done
 
 	#  Is the DNAME entry a (+) or (-) rule ?
 	tmp="dname=\"\$DNAME_$i\""
@@ -1526,6 +2272,7 @@
 
 	#  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
@@ -1546,16 +2293,17 @@
 	#  Do we need to get rid of $dname according to the dependency rules?
 	if test "x$pin" = xt -a "x$plus" = "x-" -a "x$din" = xt; then
 	    echo "Error: can't satisfy package dependencies:"
-	    echo "  \"$pname\" was requested but is disallowed by" 
+	    echo "  \"$pname\" was requested but is disallowed by"
 	    echo "  the dependency rules for \"$dname\""
 	    exit 1
 	fi
-        i=`echo "$i + 1" | bc -l`
+	i=`echo "$i + 1" | bc -l`
 	#i=$(( $i + 1 ))
     done
     ck=$ck"t"
-done
-echo "    packages are:  $PACKAGES"
+  done
+  echo "    packages are: $PACKAGES"
+fi
 for i in $PACKAGES ; do
     adr="$ROOTDIR/pkg/$i"
     if test -d $adr ; then
@@ -1570,37 +2318,10 @@
     fi
 done
 
-#  Build MNC templates and check for ability to build and use NetCDF
-echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
-RETVAL=$?
-if test "x$RETVAL" = x0 ; then
-    ( cd $ROOTDIR"/pkg/mnc" && $MAKE templates ) > make_mnc.errors 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	rm -f make_mnc.errors
-    else
-	echo "Error: problem encountered while building source files in pkg/mnc:"
-	cat make_mnc.errors 1>&2
-	exit 1
-    fi
-    if test "x$HAVE_NETCDF" != xt ; then
-	cat <<EOF
-
-WARNING: the "mnc" package has been enabled but tests failed to 
-  compile and/or execute NetCDF applications.  Please check that:
-
-  1) NetCDF is installed for your compiler and
-  2) the LIBS variable (within the 'optfile") specifies the correct 
-       NetCDF library to link against.
-  
-EOF
-    fi
-fi
-
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
-#  The following UGLY HACK sets multiple "#undef"s and it needs to go 
-#  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h 
+#  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 "$ROOTDIR/pkg"`
@@ -1616,21 +2337,21 @@
 	    fi
 	done
 	if test "x$has_pack" = xf ; then
-	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
-            DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
+	    undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
+	    DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
 	fi
     fi
 done
 ENABLED_PACKAGES=
 for i in $PACKAGES ; do
-    def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`
+    def=`echo "ALLOW_$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 
+    case $i in
 	aim_v23)
-            ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
+	    ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
 	    echo "Warning: ALLOW_AIM is set to enable aim_v23."
 	    ;;
     esac
@@ -1638,11 +2359,8 @@
 
 done
 
-echo "  Adding STANDARDDIRS"
+echo "  Adding STANDARDDIRS='$STANDARDDIRS'"
 BUILDDIR=${BUILDDIR:-.}
-if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
-    STANDARDDIRS="eesupp model"
-fi
 if test "x$STANDARDDIRS" != x ; then
     for d in $STANDARDDIRS ; do
 	adr="$ROOTDIR/$d/src"
@@ -1675,15 +2393,15 @@
     if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
-        # 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
+	# 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
+	# 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 ****
@@ -1697,17 +2415,21 @@
 
 #  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."
+touch adSrcFiles.tmp
 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
-
+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  ==="
@@ -1718,80 +2440,223 @@
     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 $OAD_CB2M_FILES"
+	    break
+	fi
+    done
+    echo "   OpenAD exceptions:  "
+fi
+
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-printf 'SRCFILES = '    > srclist.inc
-printf 'CSRCFILES = '   > csrclist.inc
-printf 'F90SRCFILES = ' > f90srclist.inc
-printf 'HEADERFILES = ' > hlist.inc
-printf 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'F77_SRC_FILES = ' > F77srclist.tmp
+printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
+printf 'C_SRC_FILES = '   > csrclist.tmp
+printf 'F90_SRC_FILES = ' > F90srclist.tmp
+printf 'H_SRC_FILES = '   > hsrclist.tmp
+printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
 alldirs="$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
-                case $d/$sf in
-                  ./$PACKAGES_DOT_H)
+		ignore_f=f
+		case $d/$sf in
+		  ./$PACKAGES_DOT_H)
+			ignore_f=t
+			;;
+		  ./AD_CONFIG.h)
+			ignore_f=t
 			;;
-                  ./AD_CONFIG.h)
+		  ./FC_NAMEMANGLE.h)
+			ignore_f=t
 			;;
-                  ./FC_NAMEMANGLE.h)
+		  ./BUILD_INFO.h)
+			ignore_f=t
 			;;
-                  ./BUILD_INFO.h)
+		  ./EMBEDDED_FILES.h)
+			ignore_f=t
 			;;
-                  *)
-		  	touch .links.tmp/$sf
-		  	deplist="$deplist $sf"
+		  *)
+			#  For the local directory *ONLY*,
+			#  ignore all soft-links
+			if test "x$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
-		extn=`echo $sf | $AWK -F '.' '{print $NF}'`
-		case $extn in
-		    F)
-			echo    " \\"  >> srclist.inc
-			printf " $sf" >> srclist.inc
+		esac
+		if test "x$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
-			printf " $sf" >> f90srclist.inc
+			echo    " \\"  >> F90srclist.tmp
+			printf " $sf" >> F90srclist.tmp
 			;;
 		    c)
-			echo    " \\"  >> csrclist.inc
-			printf " $sf" >> csrclist.inc
+			echo    " \\"  >> csrclist.tmp
+			printf " $sf" >> csrclist.tmp
 			;;
 		    h)
-			echo    " \\"  >> hlist.inc
-			printf " $sf" >> hlist.inc
+			echo    " \\"  >> hsrclist.tmp
+			printf " $sf" >> hsrclist.tmp
 			;;
 		    flow)
-			echo    " \\"  >> ad_flow_files.inc
-			printf " $sf" >> ad_flow_files.inc
+			echo    " \\"  >> ad_flow_files.tmp
+			printf " $sf" >> ad_flow_files.tmp
 			;;
-		esac
+		   esac
+	        fi
 	    fi
 	fi
     done
     if test "x$deplist" != x ; then
+      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
+
+CMDLINE=$0
+for xx in "$@" ; do nw=`echo $xx | wc -w`
+    if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
+			else CMDLINE="$CMDLINE '$xx'" ; fi
+done
 
 if test -f $MAKEFILE ; then
-    mv -f $MAKEFILE "$MAKEFILE.bak"
+    mv -f $MAKEFILE "$MAKEFILE.old"
 fi
 echo "  Writing makefile: $MAKEFILE"
 echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE
@@ -1799,7 +2664,7 @@
 echo "# This makefile was generated automatically on" >> $MAKEFILE
 echo "#    $THISDATE" >> $MAKEFILE
 echo "# by the command:" >> $MAKEFILE
-echo "#    $0 $G2ARGS" >> $MAKEFILE
+echo "#    $CMDLINE"  >> $MAKEFILE
 echo "# executed by:" >> $MAKEFILE
 echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
 
@@ -1810,7 +2675,7 @@
 cat >>$MAKEFILE <<EOF
 #
 # OPTFILE="$OPTFILE"
-# 
+#
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
 # INCLUDEDIRS  : Directories containing the header-source (.h) files
@@ -1821,8 +2686,6 @@
 # INCLUDES     : Directories searched for header files
 # DEFINES      : Macro definitions for CPP
 # MAKEDEPEND   : Dependency generator
-# KPP          : Special preprocessor command (specific to platform)
-# KFLAGS       : Flags for KPP
 # FC           : Fortran compiler command
 # FFLAGS       : Configuration/debugging options for FC
 # FOPTIM       : Optimization options for FC
@@ -1830,7 +2693,7 @@
 # LIBS         : Library flags /or/ additional optimization/debugging flags
 
 ROOTDIR     = ${ROOTDIR}
-BUILDDIR    = ${BUILDDIR}  
+BUILDDIR    = ${BUILDDIR}
 SOURCEDIRS  = ${SOURCEDIRS}
 INCLUDEDIRS = ${INCLUDEDIRS}
 EXEDIR      = ${EXEDIR}
@@ -1848,11 +2711,14 @@
 
 # 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}
@@ -1879,85 +2745,128 @@
 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 = ${LIBS} \$(XLIBS)
-# Name of the Mekfile
-MAKEFILE=${MAKEFILE}
+LIBS = ${LIBS}
+# Name of the makefile
+MAKEFILE = ${MAKEFILE}
+# Name of the make program
+MAKE = ${MAKE}
 
 EOF
 
-cat srclist.inc       >> $MAKEFILE
-cat csrclist.inc      >> $MAKEFILE
-cat f90srclist.inc    >> $MAKEFILE
-cat hlist.inc         >> $MAKEFILE
-cat ad_flow_files.inc >> $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 F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
+
 echo >> $MAKEFILE
-echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE
-echo 'F90FILES =  $(F90SRCFILES:.F=.'$FS90')' >> $MAKEFILE
-echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
+
+# 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 'FLOWFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
 echo >> $MAKEFILE
 echo '.SUFFIXES:' >> $MAKEFILE
-echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE
-rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
-rm -f ad_flow_files.inc
+echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
 
 cat >>$MAKEFILE <<EOF
 
-all: \$(EXECUTABLE)
-\$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)
+all: fwd_exe_target
+fwd_exe_target:
+	@echo Update AD_CONFIG.h and make \$(EXECUTABLE)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+	@cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
+	\$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
+
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
 	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
+
 depend:
-	@make links
-	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
+	@\$(MAKE) -f \$(MAKEFILE) links
+	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
+lib: libmitgcmuv.a
+
+libmitgcmuv.a: \$(OBJFILES)
+	ar rcv libmitgcmuv.a \$(OBJFILES)
+	ar d   libmitgcmuv.a main.o
+
+obj: \$(OBJFILES)
+
+links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
 
-small_f: \$(F77FILES) \$(F90FILES)
+small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
 
 output.txt: \$(EXECUTABLE)
 	@printf 'running ... '
 	@\$(EXECUTABLE) > \$@
 
+# remove most of the files that "make" generates
 clean:
-	-rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
+	-rm -rf *.o
+	-rm -rf *.$FS *.flowdir
+	-rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
+
+# remove most of the files that "make" and "make depend" generate
 Clean:
-	@make clean
-	@make cleanlinks
-	-rm -f \$(SPECIAL_FILES)
-	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
+	@\$(MAKE) -f \$(MAKEFILE) clean
+	@\$(MAKE) -f \$(MAKEFILE) cleanlinks
+	-rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
+	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log
+	-rm -f genmake_warnings genmake_errors make.log
+
+# remove also the executable, files that "genmake2" generates (except Makefile)
+#         and output from a run (plus log files from testreport)
 CLEAN:
-	@make Clean
+	@\$(MAKE) -f \$(MAKEFILE) Clean
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
+	-rm -f $LOGFILE genmake_state genmake_*optfile
+	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) output.txt STD*
+	-rm -f *.txt STD* *diagnostics.log datetime
+	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
+	-rm -rf mnc_test_*
 
-#eh3 Makefile: makefile
 makefile:
 	$THIS_SCRIPT $G2ARGS
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
-# Special targets (SPECIAL_FILES) which are create by make
+# 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) > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
 AD_CONFIG.h:
 	@echo Creating \$@ ...
-	@$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 > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
 FC_NAMEMANGLE.h:
 	@echo Creating \$@ ...
 	echo "$FC_NAMEMANGLE" > \$@
@@ -1971,22 +2880,51 @@
 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  )
 
-%.o : %.F
+## This nullifies any default implicit rules concerning these two file types:
+## %.o : %.F
 
 .F.$FS:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
+.F.o:
+	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
 .F90.$FS90:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+.FF90.f$FS90:
+	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS90.o:
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
+.f$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 - .$FS - .o ) rule-chain
 .F.p:
@@ -1994,8 +2932,15 @@
 .p.$FS:
 	\$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
 
+EOF
+
 #=========================================
 #===  Automatic Differentiation Rules  ===
+#===  for TAMC/TAF  ======================
+
+if test "x$OPENAD" = x ; then
+
+cat >>$MAKEFILE <<EOF
 
 TAMC           = ${TAMC}
 TAF            = ${TAF}
@@ -2010,101 +2955,329 @@
 ad_vars="$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
 printf "AD_FILES = " >> $MAKEFILE
-AD_FILES=`cat ad_files`
+AD_FILES=`cat adSrcFiles.tmp`
 for i in $AD_FILES ; do
     echo    " \\" >> $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: ad_exe_target
+adtaf: ad_taf_output.$FS
+adtamc: ad_tamc_output.$FS
+
+ad_exe_target:
+	@echo Update AD_CONFIG.h and make \$(EXE_AD)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+	@cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
+	\$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
 
-ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
+ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
-	-rm -f ad_config.template
-	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
-
-ad_taf_output.f: ad_input_code.f
-	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
+	@-rm -f ad_config.template
+	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
+	cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$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.f
-	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
+	\$(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_taf: ad_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
+ad_tamc: ad_tamc_output.o \$(OBJFILES)
+	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_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 \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.f
+adonlyfwd:
+	patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
 
-ad_tamc: ad_tamc_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS) 
+adtrick:
+	patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
 
+adobj: ad_taf_output.o \$(OBJFILES)
 
 # ... FTL ...
-ftlall: ftl_taf
-ftltaf: ftl_taf_output.f
-ftltamc: ftl_tamc_output.f
-
-ftl_input_code.f: \$(AD_FILES) \$(HEADERFILES)
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
-	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
-	-rm -f ftl_config.template
-	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
-
-ftl_taf_output.f: ftl_input_code.f
-	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
-
-ftltafonly:
-	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
+ftlall: ftl_exe_target
+ftltaf: ftl_taf_output.$FS
+ftltamc: ftl_tamc_output.$FS
+
+ftl_exe_target:
+	@echo Update AD_CONFIG.h and make \$(EXE_FTL)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+	@cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
+	\$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
 
-ftl_taf: ftl_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS) 
+ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
+	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
+	cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
+
+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
 
-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 \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.f
+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
+
+\${EXE_FTL}: ftl_taf_output.o \$(OBJFILES)
+	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
+
+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) 
-
+	\$(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 "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
 
-#=========================================
+EOF
+
+fi
+
+#===  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) -f \$(MAKEFILE) -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$FS90
+	cat \$^ > \$@
+
+f95_test.out: f95_test_mods.f90 f95_test.f90
+	f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
+	f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
+
+CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
+
+AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o)  OAD_intrinsics_oad.o \$(CB2M_AD_FILES:.f$FS90=_oad.o)
+
+AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(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)) postProcess.tag \$(AD_OBJ_FILES_S2)
+	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
+
+# create sources files modules from header files containing common blocks
+%_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
+	../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
+
+# create new header files with USE statements for the new modules made above
+%_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
+	../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+
+# change the include directives of everybody to refer to  the new header files with the USE statements
+%_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
+	../OAD_support/cb2mUseModules.bash $< ${MPI}
+
+# makefile debug rule
+small_f: \$(CB2M_F90_PP_SRC_FILES)
+.PHONY: small_f
+
+ad_output.txt: \$(EXE_AD)
+	@printf 'linking data files ... '
+	\$(LN) -f ../input_ad/data* ../input_ad/eedata .
+	\$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
+	@printf 'running ... '
+	@./\$(EXE_AD) > \$@
+
+ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
+	cat \$^ > \$@
+
+# canonicalizer
+ad_input_code_sf.pre.f90 : \$(CB2M_AD_FILES)
+	\${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
+
+# replace stop statements (to avoid the implied unstructured control flow)  with print statements
+ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
+	cat \$< | sed -f ../OAD_support/stop2print.sed > ad_input_code_sf.pre.s2p.f90
+
+# F -> WHIRL
+ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
+	\${OPEN64ROOT}/crayf90/sgi/mfef90 -r8 -z -F ad_input_code_sf.pre.s2p.f90
+
+# WHIRL -> XAIF
+ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
+	\${OPENADFORTTK}/bin/whirl2xaif -s -n --debug 1 -o \$@ \$<
+
+# XAIF -> XAIF'
+ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
+	\${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+
+# XAIF' -> WHIRL'
+ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
+	\${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
+
+# WHIRL' -> F'
+ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
+	\${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
+
+# insert template directives
+ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
+	../OAD_support/insertTemplateDir.bash \$< \$@
+
+PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
+# postprocess F'
+postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
+	\${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ../OAD_support/ad_inline.f \$<
+	# the target is a placeholder to trigger a single execution of the rule
+	touch \$@
+# put this so make knows about the postprocessing output
+OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$FS90=_oad.f): postProcess.tag
+
+# link the XAIF schema files
+%.xsd:
+	\$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
+
+# link the support files:
+\$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
+	\$(LN) ../OAD_support/\$@ .
+
+AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag \$(PPEXTRAS:.F=.f)
+
+# ============ end OpenAD specific section ==============
 
 EOF
 
+fi
+
+#=========================================
+
 if test "x$EXEHOOK" != x ; then
     printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
 fi
@@ -2140,7 +3313,7 @@
 printf "\n===  Done  ===\n"
 
 # 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 > $PACKAGES_DOT_H".tmp" 
+$BASH $TOOLSDIR/convert_cpp_cmd2defines -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
@@ -2154,16 +3327,15 @@
     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
+    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
 fi
 
-
 #  Write the "state" for future records
-if test "x$DUMPSTATE" != xf ; then
+if test "x$DUMPSTATE" = xt ; then
     printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"
 	eval $t1
-	echo "$i='$t2'" >> genmake_state
+	echo "$i='$t2'" | sed -e 's/  */ /g' >> genmake_state
     done
 fi