--- MITgcm/tools/genmake2	2003/10/23 04:41:41	1.22
+++ MITgcm/tools/genmake2	2004/03/12 15:50:06	1.72
@@ -1,6 +1,6 @@
-#!/bin/bash
+#! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.22 2003/10/23 04:41:41 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.72 2004/03/12 15:50:06 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,30 +13,35 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    grep -i "#define.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#undef.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#define.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+}
+
+# Search for particular CPP #cmds associated with MPI
+# usage: test_for_mpi_in_cpp_eeoptions CPP_file
+test_for_mpi_in_cpp_eeoptions() {
+    cpp_options=$1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+}
+
+# Search for particular string in a file. Return 1 if detected, 0 if not
+# usage: test_for_string_in_file file string
+test_for_string_in_file() {
+    file=$1
+    strng=$2
+    grep -i "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define DISABLE_$pkg"
-	exit 99
+	printf "Error: In $file there is an illegal line: "
+        grep -i "$strng" $file
+	return 1
     fi
-    grep -i "#undef.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef DISABLE_$pkg"
-	exit 99
-   fi
+    return 0
 }
 
 # Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -72,20 +77,13 @@
 
     tmp1=`uname`"_"`uname -m`
     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
-    PLATFORM=`echo $tmp2 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    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
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
     echo "  The platform appears to be:  $PLATFORM"
-#     if test "x$OFLIST" = x ; then
-# 	echo "  No pre-defined options files were found matching this platform"
-# 	echo "  but examples for other platforms can be found in:"
-# 	echo "    $ROOTDIR/tools/build_options"
-#     else
-# 	echo "  Options files (located in $ROOTDIR/tools/build_options) that"
-# 	echo "  may work with this machine are:"
-# 	for i in $OFLIST ; do
-# 	    echo "    $i"
-# 	done
-#     fi
     
     echo "test" > test
     ln -s ./test link
@@ -103,8 +101,52 @@
 	CPP="cpp -traditional -P"
     fi
 
+    #  The "original" makedepend is part of the Imake system that is
+    #  most often distributed with XFree86 or with an XFree86 source
+    #  package.  As a result, many machines (eg. generic Linux) do not
+    #  have a system-default "makedepend" available.  For those
+    #  systems, we have two fall-back options:
+    #
+    #    1) a makedepend implementation shipped with the cyrus-imapd
+    #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
+    #
+    #    2) a known-buggy xmakedpend shell script
+    #
+    #  So the choices are, in order:
+    #
+    #    1) use the user-specified program
+    #    2) use a system-wide default
+    #    3) locally build and use the cyrus implementation
+    #    4) fall back to the buggy local xmakedpend script
+    #
+    if test "x${MAKEDEPEND}" = x ; then
+      which makedepend > /dev/null 2>&1
+      RETVAL=$?
+      if test ! "x${RETVAL}" = x0 ; then
+         echo "    a system-default makedepend was not found."
+
+	 #  Try to build the cyrus impl
+	 rm -f ./genmake_cy_md
+	 (
+	     cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
+		 &&  ./configure > /dev/null 2>&1  \
+		 &&  make > /dev/null 2>&1  \
+		 &&  ./makedepend ifparser.c > /dev/null 2>&1  \
+		 &&  echo "true"
+	 ) > ./genmake_cy_md
+	 grep true ./genmake_cy_md > /dev/null 2>&1
+	 RETVAL=$?
+	 if test "x$RETVAL" = x0 ; then
+	     MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+	 else
+	     MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	 fi
+	 rm -f ./genmake_cy_md
+      fi
+    fi
+
     # look for possible fortran compilers
-    tmp="$MITGCM_FC $FC g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
+    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
     p_FC=
     for c in $tmp ; do
 	rm -f ./hello.f ./hello
@@ -138,18 +180,27 @@
 	echo "   "$p_FC
 	if test "x$FC" = x ; then
 	    FC=`echo $p_FC | $AWK '{print $1}'`
+	    echo "  Setting FORTRAN compiler to: "$FC
 	fi
     fi
 
-    for i in $p_FC ; do
-	p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
-	if test -r $p_OF ; then
-	    OPTFILE=$p_OF
-	    echo "  The options file:  $p_OF"
-	    echo "    appears to match so we'll use it."
-	    break
-	fi
-    done
+    if test "x$OPTFILE" = x ; then
+	OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
+	if test ! -r $OPTFILE ; then
+             echo "  I looked for the file "$OPTFILE" but did not find it"
+        fi
+    fi
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#   for i in $p_FC ; do
+#p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+#if test -r $p_OF ; then
+#    OPTFILE=$p_OF
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#    break
+#fi
+#   done
     if test "x$OPTFILE" = x ; then
 	cat 1>&2 <<EOF
 
@@ -205,82 +256,288 @@
     cat $1 | sed -e 's/#.*$//g' \
 	| $AWK 'BEGIN{nn=0;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME["nn"]="$1"\nDNAME["nn"]="$i} }' \
 	> ./.pd_tmp
-    source ./.pd_tmp
+    . ./.pd_tmp
     rm -f ./.pd_tmp
 
-    echo -n "PNAME = "${}
+    printf "PNAME = "${}
 }
 
 
 #  Explain usage
 usage()  {
-    echo
-    echo "Usage: "$0" [OPTIONS]"
-    echo "  where [OPTIONS] can be:"
-    echo
-    echo "    -help | --help | -h | --h"
-    echo "    -nooptfile | --nooptfile"
-    echo "      -optfile NAME | --optfile NAME | -of NAME | --of NAME"
-    echo "      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME"
-    echo "    -pdepend NAME | --pdepend NAME"
-    echo "      -pdepend=NAME | --pdepend=NAME"
-    echo "    -pdefault NAME | --pdefault NAME"
-    echo "      -pdefault=NAME | --pdefault=NAME"
-    echo "    -make NAME | -m NAME"
-    echo "      --make=NAME | -m=NAME"
-    echo "    -makefile NAME | -mf NAME"
-    echo "      --makefile=NAME | -mf=NAME"
-    echo "    -platform NAME | --platform NAME | -pl NAME | --pl NAME"
-    echo "      -platform=NAME | --platform=NAME | -pl=NAME | --pl=NAME"
-    echo "    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME"
-    echo "      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME"
-    echo "    -mods NAME | --mods NAME | -mo NAME | --mo NAME"
-    echo "      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME"
-    echo "    -disable NAME | --disable NAME"
-    echo "      -disable=NAME | --disable=NAME"
-    echo "    -enable NAME | --enable NAME"
-    echo "      -enable=NAME | --enable=NAME"
-    echo "    -standarddirs NAME | --standarddirs NAME"
-    echo "      -standarddirs=NAME | --standarddirs=NAME"
-    echo "    -noopt NAME | --noopt NAME"
-    echo "      -noopt=NAME | --noopt=NAME"
-#    echo "    -cpp NAME | --cpp NAME"
-#    echo "      -cpp=NAME | --cpp=NAME"
-    echo "    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME"
-    echo "      -fc=NAME | --fc=NAME"
-    echo "    -[no]ieee | --[no]ieee"
-    echo "    -[no]mpi | --[no]mpi"
-    echo "    -[no]jam | --[no]jam"
-    echo
-    echo "  and NAME is a string such as:"
-    echo
-    echo "    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'"
-    echo "    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'"
-    echo "    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'"
-    echo
-    echo "  which, depending upon your shell, may need to be single-quoted"
-    echo "  if it contains spaces, dashes, or other special characters."
+cat <<EOF
+
+Usage: "$0" [OPTIONS]
+  where [OPTIONS] can be:
+
+    -help | --help | -h | --h
+          Print this help message and exit.
+
+    -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.
+
+    -[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
 }
 
-#eh3 # This is the generic configuration.
-#eh3 set LN         = ( 'ln -s' )
-#eh3 set CPP        = ( '/lib/cpp -P' )
-#eh3 set S64        = ( '$(TOOLSDIR)/set64bitConst.sh' )
-#eh3 set KPP        = (  )
-#eh3 set FC         = ( 'f77' )
-#eh3 set LINK       = $FC
-#eh3 set MAKEDEPEND = ( 'makedepend' )
-#eh3 set INCLUDES   = ( -I. )
-#eh3 set FFLAGS     = (  )
-#eh3 set FOPTIM     = (  )
-#eh3 set CFLAGS     = (  )
-#eh3 set KFLAGS1    = (  )
-#eh3 set KFLAGS2    = (  )
-#eh3 set LIBS       = (  )
-#eh3 set KPPFILES   = (  )
-#eh3 if (! $?NOOPTFILES ) set NOOPTFILES = (  )
-#eh3 if (! $?NOOPTFLAGS ) set NOOPTFLAGS = (  )
+#  Build a CPP macro to automate calling C routines from FORTRAN
+get_fortran_c_namemangling()  {
+    default_nm="#define FC_NAMEMANGLE(X) X ## _"
+    
+    cat > genmake_test.c <<EOF
+void tcall( char * string ) { tsub( string ); }
+EOF
+    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_errors
+
+WARNING: C test compile fails
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    c_tcall=`nm genmake_test.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    cat > genmake_tcomp.f <<EOF
+      subroutine tcall( string )
+      character*(*) string
+      call tsub( string )
+      end
+EOF
+    $FC $FFLAGS $DEFINES -c genmake_tcomp.f >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+    f_tcall=`nm genmake_tcomp.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+
+    c_a=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    f_a=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    c_b=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+    f_b=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+
+    nmangle="X"
+    if test "x$c_a" != "x$f_a" ; then
+	comm="echo x$f_a | sed -e 's|x$c_a||'"
+	a=`eval $comm`
+	nmangle="$a ## $nmangle"
+    fi
+    if test "x$c_b" != "x$f_b" ; then
+	comm="echo x$f_b | sed -e 's|x$c_b||'"
+	b=`eval $comm`
+	nmangle="$nmangle ## $b"
+    fi
+
+    FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmangle"
+
+    #  cleanup the testing files
+    rm -f genmake_tcomp.* genmake_test.*
+}
+
+
+check_HAVE_CLOC()  {
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <assert.h>
+#include <sys/time.h>
+void FC_NAMEMANGLE(cloc) ( double *curtim )
+{
+ struct timeval tv1;
+ gettimeofday(&tv1 , (void *)NULL );
+ *curtim =  (double)((tv1.tv_usec)+(tv1.tv_sec)*1.E6);
+ *curtim = *curtim/1.E6;
+}
+EOF
+    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.f
+      program hello
+      Real*8 wtime
+      external cloc
+      call cloc(wtime)
+      print *," HELLO WORLD", wtime
+      end program hello
+EOF
+    $FC $FFLAGS -o genmake_tc genmake_tc_2.f genmake_tc_1.o >> genmake_tc.log 2>&1
+    RET_F=$?
+    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_CLOC=t
+	DEFINES="$DEFINES -DHAVE_CLOC"
+    fi
+    rm -f genmake_tc*
+}
+
+
+check_netcdf_libs()  {
+    cat <<EOF > genmake_tnc.F
+      program fgennc
+#include "netcdf.inc"
+      integer iret, ncid, xid
+      iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_def_dim(ncid, 'X', 11, xid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_close(ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      end
+EOF
+    $CPP genmake_tnc.F > genmake_tnc.f  \
+	&&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f $LIBS >> genmake_tnc.log 2>&1
+    RET_COMPILE=$?
+    test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    RETVAL=$?
+    if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	HAVE_NETCDF=t
+    else
+	# try again with "-lnetcdf" added to the libs
+	$CPP genmake_tnc.F > genmake_tnc.f  \
+	    &&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f \
+	    $LIBS -lnetcdf >> genmake_tnc_2.log 2>&1
+	RET_COMPILE=$?
+	test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+	RETVAL=$?
+	if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	    LIBS="$LIBS -lnetcdf"
+	    HAVE_NETCDF=t
+	else
+	    cat genmake_tnc.log >> genmake_warnings
+	fi
+    fi
+    rm -f genmake_tnc*
+}
+
+
+
+###############################################################################
+#   Sequential part of script starts here
+###############################################################################
 
 #  Set defaults here
 COMMANDL="$0 $@"
@@ -290,8 +547,9 @@
 S64=
 KPP=
 FC=
+CPP=
 LINK=
-DEFINES="-DWORDLENGTH=4"
+DEFINES=
 PACKAGES=
 ENABLE=
 DISABLE=
@@ -307,17 +565,28 @@
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
+
+# DEFINES checked by test compilation
+HAVE_SYSTEM=
+HAVE_FDATE=
+FC_NAMEMANGLE=
+HAVE_CLOC=
+HAVE_NETCDF=
 
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
 INCLUDEDIRS=
-STANDARDDIRS=
+STANDARDDIRS="USE_THE_DEFAULT"
 
+BASH=
 PWD=`pwd`
 MAKE=make
 AWK=awk
@@ -349,36 +618,47 @@
 
 
 #  The following state can be set directly by command-line switches
-gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE NOOPT"
-gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
+gm_s2="FC CPP IEEE MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
 gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
 gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
 gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
+gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE"
 
 #  The following are all related to adjoint/tangent-linear stuff
-gm_s7="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
-gm_s8="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
-gm_s9="TAF_EXTRA TAMC_EXTRA"
+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_s8 $gm_s9"
+gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
+gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
 
+cat <<EOF
+
+GENMAKE :
+
+A program for GENerating MAKEfiles for the MITgcm project.  For a
+quick list of options, use "genmake -h" or for more detail see:
+
+  http://mitgcm.org/devel_HOWTO/
+
+EOF
 
-echo
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
 for i in . $MODS ; do
     if test -r $i/$gm_local ; then
-	source $i/$gm_local
+	. $i/$gm_local
 	break
     fi
 done
-echo -n "  getting local config information:  "
+printf "  getting local config information:  "
 if test -e $gm_local ; then
     echo "using $gm_local"
-    source $gm_local
+    . $gm_local
     # echo "DISABLE=$DISABLE"
     # echo "ENABLE=$ENABLE"
 else
@@ -420,7 +700,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -440,15 +720,27 @@
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$ac_optarg ;;
 	
+	-bash | --bash)
+	    ac_prev=BASH ;;
+	-bash=* | --bash=*)
+	    BASH=$ac_optarg ;;
+	
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MAKEDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MAKEDEPEND=$ac_optarg ;;
+	
 	-makefile | --makefile | -ma | --ma)
 	    ac_prev=MAKEFILE ;;
 	-makefile=* | --makefile=* | -ma=* | --ma=*)
 	    MAKEFILE=$ac_optarg ;;
 	
-	-platform | --platform | -pl | --pl)
-	    ac_prev=PLATFORM ;;
-	-platform=* | --platform=* | -pl=* | --pl=*)
-	    PLATFORM=$ac_optarg ;;
+	-platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
+	    echo "ERROR: The platform option has been removed.  Please specify"
+	    echo "  the build options using the \"optfile\" mechanism."
+	    echo
+	    usage
+	    ;;
 	
 	-rootdir | --rootdir | -rd | --rd)
 	    ac_prev=ROOTDIR ;;
@@ -475,11 +767,6 @@
 	-standarddirs=* | --standarddirs=*)
 	    STANDARDDIRS=$ac_optarg ;;
 
-	-noopt | --noopt)
-	    ac_prev=NOOPT ;;
-	-noopt=* | --noopt=*)
-	    NOOPT=$ac_optarg ;;
-	
 #	    -cpp | --cpp)
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
@@ -494,16 +781,17 @@
 	    IEEE=true ;;
 	-noieee | --noieee)
 	    IEEE= ;;
-	
+
 	-mpi | --mpi)
 	    MPI=true ;;
-	-nompi | --nompi)
-	    MPI= ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
-	-jam | --jam)
-	    JAM=1 ;;
-	-nojam | --nojam)
-	    JAM=0 ;;
+#	-jam | --jam)
+#	    JAM=1 ;;
+#	-nojam | --nojam)
+#	    JAM=0 ;;
 	
 	-ds | --ds)
 	    DUMPSTATE=t ;;
@@ -551,7 +839,7 @@
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
 	    if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
 		ROOTDIR=$d
-		echo -n "Warning:  ROOTDIR was not specified but there appears to be"
+		printf "Warning:  ROOTDIR was not specified but there appears to be"
 		echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
 		break
 	    fi
@@ -582,10 +870,10 @@
 if test "x$OPTFILE" != xNONE ; then
     if test -f "$OPTFILE" -a -r "$OPTFILE" ; then
 	echo "    using OPTFILE=\"$OPTFILE\""
-	source "$OPTFILE"
+	. "$OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source OPTFILE \"$OPTFILE\""
+	    printf "Error: failed to source OPTFILE \"$OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -609,10 +897,10 @@
 if test "x${AD_OPTFILE}" != xNONE ; then
     if test -f "$AD_OPTFILE" -a -r "$AD_OPTFILE" ; then
 	echo "    using AD_OPTFILE=\"$AD_OPTFILE\""
-	source "$AD_OPTFILE"
+	. "$AD_OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
+	    printf "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -625,8 +913,12 @@
     fi
 fi
 
-#  Check that FC, LINK, CPP, and S64 are defined.  If not, complain 
-#  and abort!
+#  Check that FC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
+#  either set defaults or complain and abort!
+if test ! "x$BASH" = x ; then
+    # add a trailing space so that it works within the Makefile syntax (see below)
+    BASH="$BASH "
+fi
 if test "x$FC" = x ; then
     cat <<EOF 1>&2
 
@@ -640,9 +932,21 @@
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
+if test "x$MAKE" = x ; then
+    MAKE="make"
+fi
 if test "x$CPP" = x ; then
-    CPP="cpp"
+    CPP=cpp
 fi
+#EH3 === UGLY ===
+#  The following an ugly little hack to check for $CPP in /lib/ and it
+#  should eventually be replaced with a more general function that
+#  searches a combo of the user's path and a list of "usual suspects"
+#  to find the correct location for binaries such as $CPP.
+for i in " " "/lib/" ; do
+    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
+done
+#EH3 === UGLY ===
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -652,6 +956,7 @@
 
   1) within the options file ("CPP=...") as specified by "-of=OPTFILE"
   2) the "./genmake_local" file
+  3) with the CPP environment variable
 
 EOF
     exit 1
@@ -661,16 +966,95 @@
 if test "x$MAKEDEPEND" = x ; then
     MAKEDEPEND=makedepend
 fi
+if test "x$LN" = x ; then
+    LN="ln -s"
+fi
+echo "test" > genmake_test_ln
+$LN genmake_test_ln genmake_tlink
+RETVAL=$?
+if test "x$RETVAL" != x0 ; then
+    cat <<EOF 1>&2
+
+Error: The command "ln -s" failed -- please specify a working soft-link
+  command in the optfile.
+
+EOF
+    exit 1
+fi
+rm -f genmake_test_ln genmake_tlink
+
+if test ! "x$MPI" = x ; then
+      echo "  Turning on MPI cpp macros"
+      DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
+fi
+
+printf "\n===  Checking system libraries  ===\n"
+printf "  Do we have the system() command using $FC...  "
+cat > genmake_tcomp.f <<EOF
+      program hello
+      call system('echo hi')
+      end
+EOF
+$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_SYSTEM=t
+    DEFINES="$DEFINES -DHAVE_SYSTEM"
+    echo "yes"
+else
+    HAVE_SYSTEM=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
+printf "  Do we have the fdate() command using $FC...  "
+cat > genmake_tcomp.f <<EOF
+      program hello
+      CHARACTER(128) string
+      string = ' '
+      call fdate( string )
+      print *, string
+      end
+EOF
+$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_FDATE=t
+    DEFINES="$DEFINES -DHAVE_FDATE"
+    echo "yes"
+else
+    HAVE_FDATE=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
+printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+check_HAVE_CLOC
+if test "x$HAVE_CLOC" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+rm -f genmake_t*
+
+printf "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+
 
 printf "\n===  Setting defaults  ===\n"
-echo -n "  Adding MODS directories:  "
+printf "  Adding MODS directories:  "
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	echo -n " $d"
+	printf " $d"
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
     fi
@@ -700,12 +1084,13 @@
     TOOLSDIR="$ROOTDIR/tools"
 fi
 if test ! -d ${TOOLSDIR} ; then
-    echo "Error: the specified $TOOLSDIR (\"$TOOLSDIR\") does not exist!"
+    echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
     exit 1
 fi
 if test "x$S64" = x ; then
     S64='$(TOOLSDIR)/set64bitConst.sh'
 fi
+THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSDIR':\$(TOOLSDIR):'`
 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
 
@@ -714,17 +1099,31 @@
 #  they appear as regular source code
 if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
     echo "  Making source files in eesupp from templates"
-    $MAKE -C $ROOTDIR"/eesupp/src/" > make_eesupp.errors 2>&1
+    ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	rm -f make_eesupp.errors
     else
 	echo "Error: problem encountered while building source files in eesupp:"
-	cat make_eesupp.errors
+	cat make_eesupp.errors 1>&2
 	exit 1
     fi
 fi
 
+#same for exch2
+if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
+    echo "  Making source files in exch2 from  templates"
+    ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+        rm -f make_exch2.errors
+    else
+        echo "Error: problem encountered while building source files in exch2:"
+        cat make_exch2.errors 1>&2
+        exit 1
+    fi
+fi
+
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
@@ -751,13 +1150,13 @@
     echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""
     exit 1
 fi
-source ./.pd_tmp
+. ./.pd_tmp
 rm -f ./.pd_tmp
 
 #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
 #  file should eventually be added so that, for convenience, one can 
 #  specify groups of packages using names like "ocean" and "atmosphere".
-echo  -n "  checking default package list:  "
+echo "  checking default package list:  "
 if test "x${PDEFAULT}" = x ; then
     for i in "." $MODS ; do
 	if test -r $i"/packages.conf" ; then
@@ -770,18 +1169,17 @@
     PDEFAULT="$ROOTDIR/pkg/pkg_default"
 fi
 if test "x${PDEFAULT}" = xNONE ; then
-    echo "default packages file disabled"
+    echo "    default packages file disabled"
 else
     if test ! -r $PDEFAULT ; then
-	echo ""
 	echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
     else
-	echo "  using PDEFAULT=\"$PDEFAULT\""
+	echo "    using PDEFAULT=\"$PDEFAULT\""
         #  Strip the comments and add all the names
 	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
 	if test "x${RETVAL}" != x0 ; then
-	    echo -n "Error: can't parse default package list "
+	    printf "Error: can't parse default package list "
 	    echo "-- please check PDEFAULT=\"$PDEFAULT\""
 	    exit 1
 	fi
@@ -909,45 +1307,42 @@
     fi
 done
 
-#  This is compatible with the old genmake.  The "DISABLE_*" flags
-#  need to be replaced by the "ALLOW_*" flags set below.
-#
-# echo -n "  Setting package-specific CPP flags:  "
-# pkrm=( mom_fluxform mom_vecinv generic_advdiff )
-# pkrmdef=( -DDISABLE_MOM_FLUXFORM -DDISABLE_MOM_VECINV -DDISABLE_GENERIC_ADVDIFF -DDISABLE_DEBUGMODE )
-# echo -n "  "
-# i=0
-# while test $i -lt "${#pkrm[@]}" ; do
-#     echo "$PACKAGES" | grep "${pk[$i]}" > /dev/null 2>&1
-#     RETVAL=$?
-#     if test "x$RETVAL" = x1 ; then
-# 	DEFINES="$DEFINES ${pkdef[$i]}"
-# 	echo -n " ${pkdef[$i]}"
-#     fi
-#     i=$(( $i + 1 ))
-# done
-# echo
-
-# Create a list of #define and #undef to enable/disable packages
-PACKAGES_DOT_H=PACKAGES_CONFIG.h
-cat <<EOF >$PACKAGES_DOT_H".tmp"
-C=== GENMAKE v2 ===
-C  The following defines have been set by GENMAKE, so please do not
-C  edit anything below these comments.  In general, you should
-C  add or remove packages by re-running genmake with different 
-C  "-enable" and/or "-disable" options.
+#  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
 
-#ifndef PACKAGES_H
-#define PACKAGES_H
+WARNING: the "mnc" package has been enabled but tests failed to 
+  compile and/or execute NetCDF applications.  Please check that:
 
-C  Packages disabled by genmake:
+  1) NetCDF is installed for your compiler and
+  2) the LIBS variable (within the 'optfile") specifies the correct 
+       NetCDF library to link against.
+  
 EOF
+    fi
+fi
+
+# Create a list of #define and #undef to enable/disable packages
+PACKAGES_DOT_H=PACKAGES_CONFIG.h
 #  The following UGLY HACK sets multiple "#undef"s and it needs to go 
 #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h 
 #  file would eventually be split up so that all package-related #define
 #  statements could be separated and handled only by genmake.
 names=`ls -1 "$ROOTDIR/pkg"`
 all_pack=
+DISABLED_PACKAGES=
 for n in $names ; do
     if test -d "$ROOTDIR/pkg/$n" -a "x$n" != xCVS ; then
 	has_pack="f"
@@ -959,111 +1354,83 @@
 	done
 	if test "x$has_pack" = xf ; then
 	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
-	    echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
-#           DEFINES="$DEFINES -U$undef"
-
-#EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
-	    case $n in 
-		mom_fluxform)
-		    DEFINES="$DEFINES -DDISABLE_MOM_FLUXFORM"
-		    ;;
-		mom_vecinv)
-		    DEFINES="$DEFINES -DDISABLE_MOM_VECINV"
-		    ;;
-		debug)
-		    DEFINES="$DEFINES -DDISABLE_DEBUGMODE"
-		    ;;
-	    esac
-#EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
-
+            DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
 	fi
     fi
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-C  Packages enabled by genmake:
-EOF
+ENABLED_PACKAGES=
 for i in $PACKAGES ; do
     def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`
-    echo "#define $def" >> $PACKAGES_DOT_H".tmp"
+    ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"
 #eh3 DEFINES="$DEFINES -D$def"
 
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
     case $i in 
 	aim_v23)
-	    echo "#define   ALLOW_AIM" >> $PACKAGES_DOT_H".tmp"
-	    DEFINES="$DEFINES -DALLOW_AIM"
-	    echo "Warning: ALLOW_AIM is set to enable aim_v23. This is REALLY ugly Jean-Michel :-)"
+            ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
+	    echo "Warning: ALLOW_AIM is set to enable aim_v23."
 	    ;;
     esac
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
 
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-#endif /* PACKAGES_H */
-EOF
-
-if test ! -f $PACKAGES_DOT_H ; then
-    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-else
-    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    RETVAL=$?
-    if test "x$RETVAL" = x0 ; then
-	rm -f $PACKAGES_DOT_H".tmp"
-    else
-	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
-	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    fi
-fi
 
 echo "  Adding STANDARDDIRS"
 BUILDDIR=${BUILDDIR:-.}
-if test "x$STANDARDDIRS" = x ; then
+if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
     STANDARDDIRS="eesupp model"
 fi
-for d in $STANDARDDIRS ; do
-    adr="$ROOTDIR/$d/src"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	SOURCEDIRS="$SOURCEDIRS $adr"
-    fi
-    adr="$ROOTDIR/$d/inc"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	INCLUDEDIRS="$INCLUDEDIRS $adr"
-    fi
-done
+if test "x$STANDARDDIRS" != x ; then
+    for d in $STANDARDDIRS ; do
+	adr="$ROOTDIR/$d/src"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    SOURCEDIRS="$SOURCEDIRS $adr"
+	fi
+	adr="$ROOTDIR/$d/inc"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    INCLUDEDIRS="$INCLUDEDIRS $adr"
+	fi
+    done
+fi
 
-echo "  Searching for CPP_OPTIONS.h in order to warn about the presence"
-echo "    of \"#define ALLOW_PKGNAME\"-type statements:"
+echo "  Searching for *OPTIONS.h files in order to warn about the presence"
+echo "    of \"#define \"-type statements that are no longer allowed:"
 CPP_OPTIONS=
+CPP_EEOPTIONS=
 spaths=". $INCLUDEDIRS"
+names=`ls -1 "$ROOTDIR/pkg"`
 for i in $spaths ; do
     try="$i/CPP_OPTIONS.h"
-    #  echo -n "    trying $try : "
-    if test -f $try -a -r $try ; then
+    if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
-	break
+        # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
+        for n in $names ; do
+            test_for_package_in_cpp_options $CPP_OPTIONS $n
+        done
+    fi
+    try="$i/CPP_EEOPTIONS.h"
+    if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
+	echo "    found CPP_EEOPTIONS=\"$try\""
+        # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
+#**** not yet enabled ****
+#        test_for_mpi_in_cpp_eeoptions $try
+#**** not yet enabled ****
+	CPP_EEOPTIONS="$try"
     fi
 done
 if test "x$CPP_OPTIONS" = x ; then
     echo "Error: can't find \"CPP_OPTIONS.h\" in the path list: $spaths"
     exit 1
 fi
-# New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
-names=`ls -1 "$ROOTDIR/pkg"`
-for n in $names ; do
-    test_for_package_in_cpp_options $CPP_OPTIONS $n
-done
-
 
 #  Here, we build the list of files to be "run through" the adjoint
 #  compiler.
@@ -1078,17 +1445,6 @@
     done
 done
 
-cat <<EOF > adjoint_sed
-s/call adopen(/call adopen ( mythid,\\
-     \&           /g
-s/call adclose(/call adclose( mythid,\\
-     \&           /g
-s/call adread(/call adread ( mythid,\\
-     \&           /g
-s/call adwrite(/call adwrite( mythid,\\
-     \&           /g
-
-EOF
 
 echo
 echo "===  Creating the Makefile  ==="
@@ -1106,11 +1462,11 @@
 mkdir .links.tmp
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-echo -n 'SRCFILES = '    > srclist.inc
-echo -n 'CSRCFILES = '   > csrclist.inc
-echo -n 'F90SRCFILES = ' > f90srclist.inc
-echo -n 'HEADERFILES = ' > hlist.inc
-echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'SRCFILES = '    > srclist.inc
+printf 'CSRCFILES = '   > csrclist.inc
+printf 'F90SRCFILES = ' > f90srclist.inc
+printf 'HEADERFILES = ' > hlist.inc
+printf 'AD_FLOW_FILES = ' > ad_flow_files.inc
 alldirs="$SOURCEDIRS $INCLUDEDIRS ."
 for d in $alldirs ; do
     deplist=
@@ -1119,29 +1475,39 @@
     for sf in $sfiles ; do
 	if test ! -r ".links.tmp/$sf" ; then
 	    if test -f "$d/$sf" ; then
+                case $d/$sf in
+                  ./$PACKAGES_DOT_H)
+			;;
+                  ./AD_CONFIG.h)
+			;;
+                  ./FC_NAMEMANGLE.h)
+			;;
+                  *)
+		  	touch .links.tmp/$sf
+		  	deplist="$deplist $sf"
+			;;
+                esac
 		extn=`echo $sf | $AWK -F '.' '{print $NF}'`
-		touch .links.tmp/$sf
-		deplist="$deplist $sf"
 		case $extn in
 		    F)
 			echo    " \\"  >> srclist.inc
-			echo -n " $sf" >> srclist.inc
+			printf " $sf" >> srclist.inc
 			;;
 		    F90)
 			echo    " \\"  >> f90srclist.inc
-			echo -n " $sf" >> f90srclist.inc
+			printf " $sf" >> f90srclist.inc
 			;;
 		    c)
 			echo    " \\"  >> csrclist.inc
-			echo -n " $sf" >> csrclist.inc
+			printf " $sf" >> csrclist.inc
 			;;
 		    h)
 			echo    " \\"  >> hlist.inc
-			echo -n " $sf" >> hlist.inc
+			printf " $sf" >> hlist.inc
 			;;
 		    flow)
 			echo    " \\"  >> ad_flow_files.inc
-			echo -n " $sf" >> ad_flow_files.inc
+			printf " $sf" >> ad_flow_files.inc
 			;;
 		esac
 	    fi
@@ -1179,6 +1545,8 @@
 EXE_SVD=$EXECUTABLE"_svd"
 
 cat >>$MAKEFILE <<EOF
+#
+# OPTFILE="$OPTFILE"
 # 
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
@@ -1212,6 +1580,12 @@
 EXE_FTL     = ${EXE_FTL}
 EXE_SVD     = ${EXE_SVD}
 
+ENABLED_PACKAGES = ${ENABLED_PACKAGES}
+DISABLED_PACKAGES = ${DISABLED_PACKAGES}
+
+# These files are created by Makefile
+SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h
+
 EOF
 
 #  Note: figure out some way to add Hyades JAM libraries here
@@ -1230,7 +1604,7 @@
 # Fortran compiler
 F90C = ${F90C}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1276,14 +1650,16 @@
 .SUFFIXES: .o .f .p .F .c .F90 .f90
 
 all: \$(EXECUTABLE)
-\$(EXECUTABLE): \$(OBJFILES)
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)
+	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 depend:
 	@make links
 	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
-	${TOOLSDIR}/f90mkdepend >> \$(MAKEFILE)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77FILES) \$(F90FILES)
 
@@ -1292,12 +1668,12 @@
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-cat AD_CONFIG.template > AD_CONFIG.h
-	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl}
+	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl} *.template
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f Makefile.bak genmake_state genmake_*optfile make.log
+	-rm -f \$(SPECIAL_FILES)
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
 CLEAN:
 	@make Clean
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
@@ -1307,10 +1683,21 @@
 
 #eh3 Makefile: makefile
 makefile:
-	${0} $@
+	$THIS_SCRIPT $@
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
+# Special targets ($SPECIAL_FILES) which are create by make
+${PACKAGES_DOT_H}:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+AD_CONFIG.h:
+	@echo Creating \$@ ...
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+FC_NAMEMANGLE.h:
+	@echo Creating \$@ ...
+	echo "$FC_NAMEMANGLE" > \$@
+
 # The normal chain of rules is (  .F - .f - .o  )
 .F.f:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
@@ -1353,86 +1740,87 @@
 
 echo "  Add the source list for AD code generation"
 echo >> $MAKEFILE
-echo -n "AD_FILES = " >> $MAKEFILE
+printf "AD_FILES = " >> $MAKEFILE
 AD_FILES=`cat ad_files`
 for i in $AD_FILES ; do
     echo    " \\" >> $MAKEFILE
-    echo -n " $i" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
 done
 echo >> $MAKEFILE
 rm -f ad_files
 
 cat >>$MAKEFILE <<EOF
 
-AD_CONFIG.h:
-	cat AD_CONFIG.template > AD_CONFIG.h
-
 # ... AD ...
-ad: ad_taf
-ad_taf_f: ad_taf_output.f
-ad_tamc_f: ad_tamc_output.f
-
-ad_input_code.f: \$(SRCFILES)
-	cat ad_config.template > AD_CONFIG.h
+adall: ad_taf
+adtaf: ad_taf_output.f
+adtamc: ad_tamc_output.f
+
+ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
+	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	-rm -f ad_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
 
 ad_taf_output.f: ad_input_code.f
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
+
+adtafonly:
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
 
 ad_taf: ad_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
 ad_tamc_output.f: ad_input_code.f
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_tamc_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.f
 
 ad_tamc: ad_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS) 
 
 
 # ... FTL ...
-ftl: ftl_taf
-ftl_taf_f: ftl_taf_output.f
-ftl_tamc_f: ftl_tamc_output.f
-
-ftl_input_code.f: \$(SRCFILES)
-	cat ftl_config.template > AD_CONFIG.h
+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 adjoint_sed > ftl_taf_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
+
+ftltafonly:
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
 
 ftl_taf: ftl_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS) 
 
 ftl_tamc_output.f: ftl_input_code.f
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_tamc_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.f
 
 ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS) 
 
 
 # ... SVD ...
-svd: svd_taf
-svd_taf_f: svd_taf_output.f
-
-svd_input_code.f: \$(SRCFILES)
-	cat svd_config.template > AD_CONFIG.h
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > svd_input_code.f
+svdtaf: ad_taf_output.f ftl_taf_output.f
+svdall: svd_taf
 
-svd_taf_output.f: svd_input_code.f
-	\$(TAF) \$(SVD_TAF_FLAGS) \$(TAF_EXTRA) svd_input_code.f
-	cat svd_input_code_ad.f | sed -f adjoint_sed > svd_taf_output.f
-
-svd_taf: svd_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_SVD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) svd_taf_output.o \$(LIBS) 
+svd_taf: ad_taf_output.o ftl_taf_output.o \$(OBJFILES)
+	\$(LINK) -o mitgcmuv_svd \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o ftl_taf_output.o \$(LIBS)
 
 
 #=========================================
@@ -1473,49 +1861,28 @@
 
 printf "\n===  Done  ===\n"
 
-#  Write the "template" files for the adjoint builds
-cat >>AD_CONFIG.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you're doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >>ad_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you're doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >>ftl_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you're doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >>svd_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you're doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cp AD_CONFIG.template AD_CONFIG.h
+# Create special header files
+$BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp" 
+if test ! -f $PACKAGES_DOT_H ; then
+    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+else
+    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	rm -f $PACKAGES_DOT_H".tmp"
+    else
+	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
+	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    fi
+fi
+if test ! -f AD_CONFIG.h ; then
+    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
+fi
 
 
 #  Write the "state" for future records
 if test "x$DUMPSTATE" != xf ; then
-    echo -n "" > genmake_state
+    printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"
 	eval $t1