Annotation of /MITgcm_contrib/heimbach/OpenAD/code_shallow_openad3/genmake2


#! /usr/bin/env bash
#
# $Header: /u/gcmpack/MITgcm_contrib/heimbach/OpenAD/code_shallow_openad3/genmake2,v 1.5 2007/01/11 19:58:43 utke Exp $
#
# Makefile generator for MITgcm UV codes
#   created  by cnh 03/98
#   adapted  by aja 06/98
#   modified by aja 01/00
#   rewritten in bash by eh3 08/03

# 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
}

# 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
        printf "Error: In $file there is an illegal line: "
        grep -i "$strng" $file
        return 1
    fi
    return 0
}

# Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
# the package list.
expand_pkg_groups() {
    new_packages=
    PKG_GROUPS=$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
        matched=0
        for i in $PACKAGES ; do
            line=`grep "^ *$i" ./p2.tmp`
            RETVAL=$?
            if test "x$RETVAL" = x0 ; then
                matched=1
                replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`
                echo "    replacing \"$i\" with: $replace"
                new_packages="$new_packages $replace"
            else
                new_packages="$new_packages $i"
            fi
        done
        PACKAGES=$new_packages
        rm -f ./p[1,2].tmp
        return $matched
    else
        echo "Warning: can't read package groups definition file: $PKG_GROUPS"
    fi
}

#  Check for broken environments (eg. cygwin, MacOSX w/HFS+) that
#  cannot distinguish [*.F/*.F90] from [*.f/*.f90] files.
check_for_broken_Ff()  {
    #  Do we have defaults for $FS and/or $FS90 ?
    tfs=f
    tfs9=f90
    if test "x$FS" != x ; then
        tfs="$FS"
    fi
    if test "x$FS90" != x ; then
        tfs9="$FS90"
    fi

    #  First check the ability to create a *.F/.f pair.
    cat <<EOF >> genmake_hello.F
      program hello
      write(*,*) 'hi'
      stop
      end
EOF
    cp genmake_hello.F "genmake_hello."$tfs > /dev/null 2>&1
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        if test "x$FS" = x ; then
            FS='for'
            FS90='fr9'
            check_for_broken_Ff
        else
            cat <<EOF 2>&1
ERROR: Your file system cannot distinguish between *.F and *.f files 
  (fails the "cp" test) and this program cannot find a suitable 
  replacement extension.  Please try a different build environment or 
  contact the <MITgcm-support@mitgcm.org> list for help.

EOF
            exit -1
        fi
        return
    fi
    rm -f genmake_hello.*

    #  Check the ability of ${MAKE} and ${LN} to use the current set
    #  of extensions.
    cat <<EOF >> genmake_hello.F
      program hello
      write(*,*) 'hi'
      stop
      end
EOF
    test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
    cat <<EOF >> $MAKEFILE
.SUFFIXES:
.SUFFIXES: .$tfs .F
.F.$tfs:
        $LN \$< \$@
EOF
    $MAKE "genmake_hello."$tfs > /dev/null 2>&1
    RETVAL=$?
    if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
        if test "x$FS" = x ; then
            FS='for'
            FS90='fr9'
            check_for_broken_Ff
        else
            cat <<EOF 2>&1
ERROR: Your file system cannot distinguish between *.F and *.f files 
  (fails the "make/ln" test) and this program cannot find a suitable 
  replacement extension.  Please try a different build environment or 
  contact the <MITgcm-support@mitgcm.org> list for help.

EOF
            exit -1
            return
        fi
    fi
    rm -f genmake_hello.* $MAKEFILE
    test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE

    #  If we make it here, use the extensions
    FS=$tfs
    FS90=$tfs9
    return
}


look_for_makedepend()  {

    #  The "original" makedepend is part of the Imake system that is
    #  most often distributed with XFree86 or with an XFree86 source
    #  package.  As a result, many machines (eg. generic Linux) do not
    #  have a system-default "makedepend" available.  For those
    #  systems, we have two fall-back options:
    #
    #    1) a makedepend implementation shipped with the cyrus-imapd
    #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
    #
    #    2) a known-buggy xmakedpend shell script
    #
    #  So the choices are, in order:
    #
    #    1) use the user-specified program
    #    2) use a system-wide default
    #    3) locally build and use the cyrus implementation
    #    4) fall back to the buggy local xmakedpend script
    #
    if test "x${MAKEDEPEND}" = x ; then
        which makedepend > /dev/null 2>&1
        RV0=$?
        test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
        #  echo 'MAKEFILE="'$MAKEFILE'"'
        cat <<EOF >> $MAKEFILE
#   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
#
#   Some "makedepend" implementations will die if they cannot 
#   find a Makefile -- so this file is here to gives them an 
#   empty one to find and parse.
EOF
        cat <<EOF >> genmake_tc.f
      program test
      write(*,*) 'test'
      stop
      end
EOF
        makedepend genmake_tc.f > /dev/null 2>&1
        RV1=$?
        test -f $MAKEFILE  &&  rm -f $MAKEFILE
        test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
        if test "x${RV0}${RV1}" = x00 ; then
            MAKEDEPEND=makedepend
        else
            echo "    a system-default makedepend was not found."
            
            #  Try to build the cyrus implementation
            build_cyrus_makedepend
            RETVAL=$?
            if test "x$RETVAL" != x0 ; then
                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
            fi
            rm -f ./genmake_cy_md
        fi
    else
        #  echo "MAKEDEPEND=${MAKEDEPEND}"
        echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
        RETVAL=$?
        if test x"$RETVAL" = x0 ; then
            build_cyrus_makedepend
        fi
    fi
}


build_cyrus_makedepend()  {
    rm -f ./genmake_cy_md
    (
        cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
            &&  ./configure > /dev/null 2>&1  \
            &&  make > /dev/null 2>&1
        if test -x ./makedepend.exe ; then
            $LN ./makedepend.exe ./makedepend
        fi
        ./makedepend ifparser.c > /dev/null 2>&1  \
            &&  echo "true"
    ) > ./genmake_cy_md
    grep true ./genmake_cy_md > /dev/null 2>&1
    RETVAL=$?
    rm -f ./genmake_cy_md
    if test "x$RETVAL" = x0 ; then
        MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
        return 0
    else
        echo "WARNING: unable to build cyrus-imapd-makedepend"
        return 1
    fi
}

# 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"
    fi

    look_for_makedepend

    #================================================================
    #  look for possible C compilers
    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"
    p_CC=
    for c in $tmp ; do
        rm -f ./genmake_hello.c  ./genmake_hello
        cat >> genmake_hello.c << EOF
#include <stdio.h>
int main(int argc, char **argv) {
  printf("Hello!\n");
  return 0;
}
EOF
        $c -o genmake_hello genmake_hello.c > /dev/null 2>&1
        RETVAL=$?
        if test "x${RETVAL}" = x0 ; then
            p_CC="$p_CC $c"
        fi
    done
    rm -f ./genmake_hello.c ./genmake_hello
    if test "x${p_CC}" = x ; then
        cat 1>&2 <<EOF

Error: No C compilers were found in your path.  Please specify one using:

    1) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
    2) the CC or MITGCM_CC environment variables.

EOF
        exit 1
    else
        echo "  The possible C compilers found in your path are:"
        echo "   "$p_CC
        if test "x$CC" = x ; then
            CC=`echo $p_CC | $AWK '{print $1}'`
            echo "  Setting C compiler to: "$CC
        fi
    fi

    #================================================================
    #  look for possible FORTRAN compilers
    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95 gfortran"
    p_FC=
    for c in $tmp ; do
        rm -f ./hello.f ./hello
        cat >> hello.f <<EOF
      program hello
      do i=1,3
        print *, 'hello world : ', i
      enddo
      end
EOF
        $c -o hello hello.f > /dev/null 2>&1
        RETVAL=$?
        if test "x${RETVAL}" = x0 ; then
            p_FC="$p_FC $c"
        fi
    done
    rm -f ./hello.f ./hello
    if test "x${p_FC}" = x ; then
        cat 1>&2 <<EOF

Error: No Fortran compilers were found in your path.  Please specify one using:

    1) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
    2) a command-line option (eg. "-fc NAME"), or
    3) the FC or MITGCM_FC environment variables.

EOF
        exit 1
    else
        echo "  The possible FORTRAN compilers found in your path are:"
        echo "   "$p_FC
        if test "x$FC" = x ; then
            FC=`echo $p_FC | $AWK '{print $1}'`
            echo "  Setting FORTRAN compiler to: "$FC
        fi
    fi

    if test "x$OPTFILE" = x ; then
        OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
        if test ! -r $OPTFILE ; then
             echo "  I looked for the file "$OPTFILE" but did not find it"
        fi
    fi
#    echo "  The options file:  $p_OF"
#    echo "    appears to match so we'll use it."
#   for i in $p_FC ; do
#p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
#if test -r $p_OF ; then
#    OPTFILE=$p_OF
#    echo "  The options file:  $p_OF"
#    echo "    appears to match so we'll use it."
#    break
#fi
#   done
    if test "x$OPTFILE" = x ; then
        cat 1>&2 <<EOF

Error: No options file was found in:  $ROOTDIR/tools/build_options/
  that matches this platform ("$PLATFORM") and the compilers found in
  your path.  Please specify an "optfile" using:

    1) the command line (eg. "-optfile=path/to/OPTFILE"), or
    2) the MITGCM_OF environment variable.

  If you need help, please contact the developers at <MITgcm-support@mitgcm.org>.

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
get_pdepend_list()  {

    #  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} }' \
        > ./.pd_tmp
    . ./.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.

    -ts | --ts
          Produce timing information per timestep

    -mpi | --mpi
          Include MPI header files and link to MPI libraries
    -mpi=PATH | --mpi=PATH
          Include MPI header files and link to MPI libraries using MPI_ROOT
          set to PATH. i.e. Include files from \$PATH/include, link to libraries
          from \$PATH/lib and use binaries from \$PATH/bin.

    -bash NAME
          Explicitly specify the Bourne or BASH shell to use

  While it is most often a single word, the "NAME" variables specified 
  above can in many cases be a space-delimited string such as:

    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'

  which, depending upon your shell, may need to be single-quoted.

  For more detailed genmake documentation, please see:

    http://mitgcm.org/devel_HOWTO/

EOF

    exit 1
}

#  Build a CPP macro to automate calling C routines from FORTRAN
get_fortran_c_namemangling()  {

    #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
    if test ! "x$FC_NAMEMANGLE" = x ; then
        return 0
    fi

    default_nm="#define FC_NAMEMANGLE(X) X ## _"
    
    cat > genmake_test.c <<EOF
void tcall( char * string ) { tsub( string ); }
EOF
    $MAKE genmake_test.o >> genmake_warnings 2>&1
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        FC_NAMEMANGLE=$default_nm
        cat <<EOF>> genmake_errors

WARNING: C test compile fails
WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
EOF
        return 1
    fi
    c_tcall=`nm genmake_test.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        FC_NAMEMANGLE=$default_nm
        cat <<EOF>> genmake_warnings

WARNING: The "nm" command failed.
WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
EOF
        return 1
    fi
    cat > genmake_tcomp.$FS <<EOF
      subroutine tcall( string )
      character*(*) string
      call tsub( string )
      end
EOF
    $FC $FFLAGS $DEFINES -c genmake_tcomp.$FS >> genmake_warnings 2>&1
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        FC_NAMEMANGLE=$default_nm
        cat <<EOF>> genmake_warnings

WARNING: FORTRAN test compile fails -- please see "genmake_errors"
WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
EOF
        return 1
    fi
    f_tcall=`nm genmake_tcomp.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        FC_NAMEMANGLE=$default_nm
        cat <<EOF>> genmake_warnings

WARNING: The "nm" command failed.
WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
EOF
        return 1
    fi

    c_a=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
    f_a=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
    c_b=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
    f_b=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`

    nmangle="X"
    if test "x$c_a" != "x$f_a" ; then
        comm="echo x$f_a | sed -e 's|x$c_a||'"
        a=`eval $comm`
        nmangle="$a ## $nmangle"
    fi
    if test "x$c_b" != "x$f_b" ; then
        comm="echo x$f_b | sed -e 's|x$c_b||'"
        b=`eval $comm`
        nmangle="$nmangle ## $b"
    fi

    FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmangle"

    #  cleanup the testing files
    rm -f genmake_tcomp.* genmake_test.*
}


check_HAVE_CLOC()  {
    get_fortran_c_namemangling
    cat <<EOF > genmake_tc_1.c
$FC_NAMEMANGLE
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <assert.h>
#include <sys/time.h>
void FC_NAMEMANGLE(cloc) ( double *curtim )
{
 struct timeval tv1;
 gettimeofday(&tv1 , (void *)NULL );
 *curtim =  (double)((tv1.tv_usec)+(tv1.tv_sec)*1.E6);
 *curtim = *curtim/1.E6;
}
EOF
    make genmake_tc_1.o >> genmake_warnings 2>&1
    RET_C=$?
    cat <<EOF > genmake_tc_2.$FS
      program hello
      Real*8 wtime
      external cloc
      call cloc(wtime)
      print *," HELLO WORLD", wtime
      end program hello
EOF
    $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_warnings 2>&1
    RET_F=$?
    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
    RETVAL=$?
    if test "x$RETVAL" = x0 ; then
        HAVE_CLOC=t
        DEFINES="$DEFINES -DHAVE_CLOC"
    fi
    rm -f genmake_tc*
}


check_HAVE_STAT()  {
    get_fortran_c_namemangling
    cat <<EOF > genmake_tc_1.c
$FC_NAMEMANGLE
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <sys/stat.h>
#include <sys/types.h>
void FC_NAMEMANGLE(tfsize) ( int *nbyte )
{
    char name[512];
    struct stat astat;

    name[0] = 'a'; name[1] = '\0';
    if (! stat(name, &astat))
        *nbyte = (int)(astat.st_size);
    else
        *nbyte = -1;
}
EOF
    make genmake_tc_1.o >> genmake_tc.log 2>&1
    RET_C=$?
    cat <<EOF > genmake_tc_2.$FS
      program hello
      integer nbyte
      call tfsize(nbyte)
      print *," HELLO WORLD", nbyte
      end program hello
EOF
    $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS 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$RETVAL" = x0 ; then
        HAVE_STAT=t
        DEFINES="$DEFINES -DHAVE_STAT"
    fi
    rm -f genmake_tc*
}


check_netcdf_libs()  {
    if test ! "x$SKIP_NETCDF_CHECK" = x ; then
        return
    fi
    echo "" > genmake_tnc.log
    cat <<EOF > genmake_tnc.F
      program fgennc
#include "netcdf.inc"
EOF
    if test ! "x$MPI" = x ; then
        echo '#include "mpif.h"' >> genmake_tnc.F
    fi
    cat <<EOF >> genmake_tnc.F
      integer iret, ncid, xid
      iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
      iret = nf_def_dim(ncid, 'X', 11, xid)
      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
      iret = nf_close(ncid)
      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
      end
EOF
    echo "Executing:" > genmake_tnc.log
    echo "  $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS" \
        > genmake_tnc.log
    RET_CPP=f
    $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$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 "Executing:" > genmake_tnc.log
    echo "  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS" > genmake_tnc.log
    echo "  $LINK -o genmake_tnc.o $LIBS" > genmake_tnc.log
    $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
        &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
    RET_COMPILE=$?

    #EH3  Remove test program execution for machines that either disallow
    #EH3  execution or cannot support it (eg. cross-compilers)
    #EH3
    #EH3 test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
    #EH3 RETVAL=$?
    #EH3 if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then

    if test "x$RET_COMPILE" = x0 ; then
        HAVE_NETCDF=t
    else
        # try again with "-lnetcdf" added to the libs
        $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS 2>/dev/null  \
            &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
            &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
        RET_COMPILE=$?
        if test "x$RET_COMPILE" = x0 ; then
            LIBS="$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 $@"

PLATFORM=
LN=
S64=
KPP=
#FC=
#CC=gcc
#CPP=
LINK=
DEFINES=
PACKAGES=
ENABLE=
DISABLE=
# MAKEFILE=
# MAKEDEPEND=
PDEPEND=
DUMPSTATE=t
PDEFAULT=
OPTFILE=
INCLUDES="-I. $INCLUDES"
FFLAGS=
FOPTIM=
CFLAGS=
KFLAGS1=
KFLAGS2=
#LDADD=
LIBS=
KPPFILES=
NOOPTFILES=
NOOPTFLAGS=
MPI=
MPIPATH=
TS=

# DEFINES checked by test compilation or command-line
HAVE_SYSTEM=
HAVE_FDATE=
FC_NAMEMANGLE=
HAVE_CLOC=
HAVE_STAT=
HAVE_NETCDF=
HAVE_ETIME=
IGNORE_TIME=

MODS=
TOOLSDIR=
SOURCEDIRS=
INCLUDEDIRS=
STANDARDDIRS="USE_THE_DEFAULT"

G2ARGS=
BASH=
PWD=`pwd`
test "x$MAKE" = x  &&  MAKE=make
test "x$AWK" = x   &&  AWK=awk
THISHOST=`hostname`
THISCWD=`pwd`
THISDATE=`date`
THISUSER=`echo $USER`
THISVER=
MACHINE=`uname -a`
EXECUTABLE=
EXEHOOK=
EXEDIR=
PACKAGES_CONF=
IEEE=
if test "x$MITGCM_IEEE" != x ; then
    IEEE=$MITGCM_IEEE
fi
FS=
FS90=

AUTODIFF_PKG_USED=f
AD_OPTFILE=
TAF=
AD_TAF_FLAGS=
FTL_TAF_FLAGS=
SVD_TAF_FLAGS=
TAF_EXTRA=
TAMC=
AD_TAMC_FLAGS=
FTL_TAF_FLAGS=
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 TS 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 THISHOST THISUSER THISDATE THISVER MACHINE"
gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"

#  The following are all related to adjoint/tangent-linear stuff
gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
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 $gm_s7"
gm_state="$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 "===  Processing options files and arguments  ==="
gm_local="genmake_local"
modsCount=0
for i in . $MODS ; do
    if test -r $i/$gm_local ; then
        . $i/$gm_local
        break
    fi
    let modsCount=modsCount+1
done
if test $modsCount -gt 1 ; then 
  echo "ERROR: some uses of MODS break with more than one directory specified"
  exit -1;
fi
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=$(( $n + 1 ))
#done
#parse_options
ac_prev=
for ac_option in "$@" ; do

    G2ARGS="$G2ARGS \"$ac_option\""

    # If the previous option needs an argument, assign it.
    if test -n "$ac_prev"; then
        eval "$ac_prev=\$ac_option"
        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 ;;
        -pdepend=* | --pdepend=*)
            PDEPEND=$ac_optarg ;;
        
        -pdefault | --pdefault)
            ac_prev=PDEFAULT ;;
        -pdefault=* | --pdefault=*)
            PDEFAULT=$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)
            ac_prev=MAKEFILE ;;
        -makefile=* | --makefile=* | -ma=* | --ma=*)
            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=*)
            STANDARDDIRS=$ac_optarg ;;

#           -cpp | --cpp)
#               ac_prev=cpp ;;
#           -cpp=* | --cpp=*)
#               CPP=$ac_optarg ;;
        
        -cc | --cc)
            ac_prev=CC ;;
        -cc=* | --cc=*)
            CC=$ac_optarg ;;
        
        -fortran | --fortran | -fc | --fc)
            ac_prev=FC ;;
        -fc=* | --fc=*)
            FC=$ac_optarg ;;
        
        -fs | --fs)
            ac_prev=FS ;;
        -fs=* | --fs=*)
            FS=$ac_optarg ;;
        
        -fs90 | --fs90)
            ac_prev=FS90 ;;
        -fs90=* | --fs90=*)
            FS90=$ac_optarg ;;
        
        -ieee | --ieee)
            IEEE=true ;;
        -noieee | --noieee)
            IEEE= ;;

        -ts | --ts)
            TS=true ;;

        -mpi | --mpi)
            MPI=true ;;
        -mpi=* | --mpi=*)
            MPIPATH=$ac_optarg
            MPI=true ;;
        
#       -jam | --jam)
#           JAM=1 ;;
#       -nojam | --nojam)
#           JAM=0 ;;
        
        -ds | --ds)
            DUMPSTATE=t ;;
        
        -taf_extra | --taf_extra)
            ac_prev=TAF_EXTRA ;;
        -taf_extra=* | --taf_extra=*)
            TAF_EXTRA=$ac_optarg ;;

        -tamc_extra | --tamc_extra)
            ac_prev=TAMC_EXTRA ;;
        -tamc_extra=* | --tamc_extra=*)
            TAMC_EXTRA=$ac_optarg ;;
        
        -ignoretime | -ignore_time | --ignoretime | --ignore_time)
            IGNORE_TIME="-DIGNORE_TIME" ;;

        -*)
            echo "Error: unrecognized option: "$ac_option
            usage
            ;;
        
        *)
            echo "Error: unrecognized argument: "$ac_option
            usage
            ;;
        
    esac
    
done


if test -f ./.genmakerc ; then
    echo
    echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
    echo "  file.  This file format is no longer supported.  Please see:"
    echo 
    echo "    http://mitgcm.org/devel_HOWTO/"
    echo
    echo "  for directions on how to setup and use the new \"genmake2\" input"
    echo "  files and send an email to MITgcm-support@mitgcm.org if you want help."
    echo 
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
        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 \"$ROOTDIR\" so we'll try it."
                break
            fi
        done
    fi
fi
if test "x${ROOTDIR}" = x ; then
    echo "Error: Cannot determine ROOTDIR for MITgcm code."
    echo "  Please specify a ROOTDIR using either an options "
    echo "  file or a command-line option."
    exit 1
fi
if test ! -d ${ROOTDIR} ; then
    echo "Error: the specified ROOTDIR (\"$ROOTDIR\") does not exist!"
    exit 1
fi

#  Find the MITgcm ${THISVER}
if test -f "${ROOTDIR}/doc/tag-index" ; then
    THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`
fi

if test "x$MAKEFILE" = x ; then
    MAKEFILE="Makefile"
fi

echo "  getting OPTFILE information:  "
if test "x${OPTFILE}" = x ; then
    if test "x$MITGCM_OF" = x ; then
        echo "Warning: no OPTFILE specified so we'll look for possible settings"
        printf "\n===  Searching for possible settings for OPTFILE  ===\n"
        find_possible_configs
    else
        OPTFILE=$MITGCM_OF
    fi
fi
if test "x$OPTFILE" != xNONE ; then
    if test -f "$OPTFILE" -a -r "$OPTFILE" ; then
        echo "    using OPTFILE=\"$OPTFILE\""
        . "$OPTFILE"
        RETVAL=$?
        if test "x$RETVAL" != x0 ; then
            printf "Error: failed to source OPTFILE \"$OPTFILE\""
            echo "--please check that variable syntax is bash-compatible"
            exit 1
        fi
        if test "x$DUMPSTATE" != xf ; then
            cp -f $OPTFILE "genmake_optfile"
        fi
    else
        echo "Error: can't read OPTFILE=\"$OPTFILE\""
        exit 1
    fi
fi

echo "  getting AD_OPTFILE information:  "
if test "x${AD_OPTFILE}" = x ; then
    if test "x$MITGCM_AD_OF" = x ; then
        AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
    else
        AD_OPTFILE=$MITGCM_AD_OF
    fi
fi
if test "x${AD_OPTFILE}" != xNONE ; then
    if test -f "$AD_OPTFILE" -a -r "$AD_OPTFILE" ; then
        echo "    using AD_OPTFILE=\"$AD_OPTFILE\""
        . "$AD_OPTFILE"
        RETVAL=$?
        if test "x$RETVAL" != x0 ; then
            printf "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
            echo "--please check that variable syntax is bash-compatible"
            exit 1
        fi
        if test "x$DUMPSTATE" != xf ; then
            cp -f $AD_OPTFILE "genmake_ad_optfile"
        fi
    else
        echo "Error: can't read AD_OPTFILE=\"$AD_OPTFILE\""
        exit 1
    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$BASH" = x ; then
    # add a trailing space so that it works within the Makefile syntax (see below)
    BASH="$BASH "
fi
if test "x$FC" = x ; then
    cat <<EOF 1>&2

Error: no Fortran compiler: please specify using one of the following:
  1) within the options file ("FC=...") as specified by "-of=OPTFILE"
  2) the "-fc=XXX" command-line option
  3) the "./genmake_local" file
EOF
    exit 1
fi
if test "x$CC" = x ; then
    CC=cc
#     cat <<EOF 1>&2
# Error: no C compiler: please specify using one of the following:
#   1) within the options file ("CC=...") as specified by "-of=OPTFILE"
#   2) the "-cc=XXX" command-line option
#   3) the "./genmake_local" file
# EOF
#     exit 1
fi
if test "x$LINK" = x ; then
    LINK=$FC
fi
if test "x$MAKE" = x ; then
    MAKE="make"
fi
if test "x$CPP" = x ; then
    CPP=cpp
fi
#EH3 === UGLY ===
#  The following is an ugly little hack to check for $CPP in /lib/ and
#  it should eventually be replaced with a more general function that
#  searches a combo of the user's path and a list of "usual suspects"
#  to find the correct location for binaries such as $CPP.
for i in " " "/lib/" ; do
    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
done
#EH3 === UGLY ===
echo "#define A a" | $CPP > test_cpp 2>&1
RETVAL=$?
if test "x$RETVAL" != x0 ; then
    cat <<EOF 1>&2

Error: C pre-processor "$CPP" failed the test case: please specify using:

  1) within the options file ("CPP=...") as specified by "-of=OPTFILE"
  2) the "./genmake_local" file
  3) with the CPP environment variable

EOF
    exit 1
else
    rm -f test_cpp
fi
look_for_makedepend
if test "x$LN" = x ; then
    LN="ln -s"
fi
echo "test" > genmake_test_ln
$LN genmake_test_ln genmake_tlink
RETVAL=$?
if test "x$RETVAL" != x0 ; then
    cat <<EOF 1>&2

Error: The command "ln -s" failed -- please specify a working soft-link
  command in the optfile.

EOF
    exit 1
fi
rm -f genmake_test_ln genmake_tlink

#  Check for broken *.F/*.f handling and fix if possible
check_for_broken_Ff

if test ! "x$MPI" = x ; then
      echo "  Turning on MPI cpp macros"
      DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
fi

if test ! "x$TS" = x ; then
      echo "  Turning on timing per timestep"
      DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
fi

printf "\n===  Checking system libraries  ===\n"
printf "  Do we have the system() command using $FC...  "
cat > genmake_tcomp.$FS <<EOF
      program hello
      call system('echo hi')
      end
EOF
$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > 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 $FC...  "
cat > genmake_tcomp.$FS <<EOF
      program hello
      CHARACTER(128) string
      string = ' '
      call fdate( string )
      print *, string
      end
EOF
$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
RETVAL=$?
if test "x$RETVAL" = x0 ; then
    HAVE_FDATE=t
    DEFINES="$DEFINES -DHAVE_FDATE"
    echo "yes"
else
    HAVE_FDATE=
    echo "no"
fi
rm -f genmake_tcomp*

printf "  Do we have the etime() command using $FC...  "
cat > genmake_tcomp.$FS <<EOF
      program hello
      REAL*4 ACTUAL, TARRAY(2)
      EXTERNAL ETIME
      REAL*4 ETIME
      actual = etime( tarray )
      print *, tarray
      end
EOF
$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
RETVAL=$?
if test "x$RETVAL" = x0 ; then
    HAVE_ETIME=t
    DEFINES="$DEFINES -DHAVE_ETIME"
    echo "yes"
else
    HAVE_ETIME=
    echo "no"
fi
rm -f genmake_tcomp*

printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
check_HAVE_CLOC
if test "x$HAVE_CLOC" != x ; then
    echo "yes"
else
    echo "no"
fi
rm -f genmake_t*

printf "  Can we use stat() through C calls...  "
check_HAVE_STAT
if test "x$HAVE_STAT" != x ; then
    echo "yes"
else
    echo "no"
fi
rm -f genmake_t*

printf "  Can we create NetCDF-enabled binaries...  "
check_netcdf_libs
if test "x$HAVE_NETCDF" != x ; then
    echo "yes"
else
    echo "no"
fi
DEFINES="$DEFINES $IGNORE_TIME"

printf "\n===  Setting defaults  ===\n"
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 " $d"
        SOURCEDIRS="$SOURCEDIRS $d"
        INCLUDEDIRS="$INCLUDEDIRS $d"
    fi
done
echo

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 $NR}'`
    if test "x$tmp" = "xbin" -a -d ../exe -a $ROOTDIR = .. ; then
        EXEDIR=../exe
    else
        EXEDIR=.
    fi
fi
if test ! -d ${EXEDIR} ; then
    echo "Error:  the specified EXEDIR (\"$EXEDIR\") does not exist!"
    exit 1
fi

if test "x${TOOLSDIR}" = x ; then
    TOOLSDIR="$ROOTDIR/tools"
fi
if test ! -d ${TOOLSDIR} ; then
    echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
    exit 1
fi
if test "x$S64" = x ; then
    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}

#  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/" && $MAKE ) > make_eesupp.errors 2>&1
    RETVAL=$?
    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 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"
    if test -r $tmp ; then
        PDEPEND=$tmp
    else
        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\""
        exit 1
    fi
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
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
    for i in "." $MODS ; do
        if test -r $i"/packages.conf" ; then
                PDEFAULT=$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"
else
    if test ! -r $PDEFAULT ; then
        echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
    else
        echo "    using PDEFAULT=\"$PDEFAULT\""
        #  Strip the comments and add all the names
        def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
        RETVAL=$?
        if test "x${RETVAL}" != x0 ; then
            printf "Error: can't parse default package list "
            echo "-- please check PDEFAULT=\"$PDEFAULT\""
            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

echo "  applying DISABLE settings"
for i in $PACKAGES ; do
    echo $i >> ./.tmp_pack
done
for i in `grep  "-" ./.tmp_pack` ; do
    j=`echo $i | sed 's/[-]//'`
    DISABLE="$DISABLE $j"
done
pack=
for p in $PACKAGES ; do
    addit="t"
    for d in $DISABLE ; do
        if test "x$p" = "x$d" ; then
            addit="f"
        fi
    done
    if test "x$addit" = xt ; then
        pack="$pack $p"
    fi
done
PACKAGES="$pack"
echo "  applying ENABLE settings"
echo "" > ./.tmp_pack
PACKAGES="$PACKAGES $ENABLE"
# Test if each explicitly referenced package exists
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
    fi
    echo $i >> ./.tmp_pack
done
PACKAGES=
for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do
    PACKAGES="$PACKAGES $i"
done
rm -f ./.tmp_pack
echo "    packages are:  $PACKAGES"

#  Check availability of NetCDF and then either build the MNC template
#  files or delete mnc from the list of available packages.
echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
RETVAL=$?
if test "x$RETVAL" = x0 ; then
    if test "x$HAVE_NETCDF" != xt ; then
        cat <<EOF

*********************************************************************
WARNING: the "mnc" package was enabled but tests failed to compile
  NetCDF applications.  Please check that:

  1) NetCDF is correctly installed for this compiler and
  2) the LIBS variable (within the "optfile") specifies the correct 
       NetCDF library to link against.

  Due to this failure, the "mnc" package is now DISABLED.
*********************************************************************

EOF
        PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`
        DISABLE="$DISABLE mnc"
    else
        ( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
        RETVAL=$?
        if test "x${RETVAL}" = x0 ; then
            rm -f make_mnc.errors
        else
            echo "Error: problem encountered while building source files in pkg/mnc:"
            cat make_mnc.errors 1>&2
            exit 1
        fi
    fi
fi

echo "  applying package dependency rules"
ck=
while test "x$ck" != xtt ; do
    i=0
    # rtot=${#PNAME[@]}
    rtot=$nname
    while test $i -lt $rtot ; do

        #  Is $pname in the current $PACKAGES list?
        #  pname=${PNAME[$i]}
        tmp="pname=\"\$PNAME_$i\""
        eval $tmp
        pin="f"
        for p in $PACKAGES ; do
            if test "x$p" = "x$pname" ; then
                pin="t"
            fi
        done

        #  Is the DNAME entry a (+) or (-) rule ?
        tmp="dname=\"\$DNAME_$i\""
        eval $tmp
        plus="-"
        echo $dname | grep '^+' > /dev/null 2>&1
        RETVAL=$?
        if test "x$RETVAL" = x0 ; then
            plus="+"
        fi

        #  Is $dname in the current $PACKAGES list?
        dname=`echo $dname | sed -e 's/^[+-]//'`
        din="f"
        for p in $PACKAGES ; do
            if test "x$p" = "x$dname" ; then
                din="t"
            fi
        done

        #  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
            in_dis="f"
            for dis in $DISABLE ; do
                if test "x$dis" = "x$dname" ; then
                    in_dis="t"
                fi
            done
            if test "x$in_dis" = xt ; then
                echo "Error: can't satisfy package dependencies:"
                echo "  \"$dname\" is required by the dependency rules"
                echo "  but is disallowed by the DISABLE settings"
                exit 1
            else
                PACKAGES="$PACKAGES $dname"
                ck=
            fi
        fi

        #  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 "  \"$pname\" was requested but is disallowed by" 
            echo "  the dependency rules for \"$dname\""
            exit 1
        fi
        i=`echo "$i + 1" | bc -l`
        #i=$(( $i + 1 ))
    done
    ck=$ck"t"
done
echo "    packages are:  $PACKAGES"
for i in $PACKAGES ; do
    adr="$ROOTDIR/pkg/$i"
    if test -d $adr ; then
        SOURCEDIRS="$SOURCEDIRS $adr"
        INCLUDEDIRS="$INCLUDEDIRS $adr"
        if test "x$i" = xautodiff ; then
            AUTODIFF_PKG_USED=t
        fi
    else
        echo "Error: the directory \"$adr\" for package $i doesn't exist"
        exit 1
    fi
done

# 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"
        for pack in $PACKAGES ; do
            if test "x$pack" = "x$n" ; then
                has_pack="t"
                break
            fi
        done
        if test "x$has_pack" = xf ; then
            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" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
    ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"
#eh3 DEFINES="$DEFINES -D$def"

#EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
    case $i in 
        aim_v23)
            ENABLED_PACKAGES="$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

echo "  Adding 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"
        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 *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"
    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 $n
        done
    fi
    try="$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

#  Here, we build the list of files to be "run through" the adjoint
#  compiler.
if test -f ./adSrcFiles.tmp ; then
    rm -f ./adSrcFiles.tmp
fi
echo "  Creating the list of files for the adjoint compiler."
for i in $SOURCEDIRS ; do
    list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
    for j in $list_files ; do
        cat $i/$j >> 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  ==="
echo "  setting INCLUDES"
for i in $INCLUDEDIRS ; do
    if test ! -d $i ; then
        echo "Warning: can't find INCLUDEDIRS=\"$i\""
    fi
done

echo "  Determining the list of source and include files"
rm -rf .links.tmp
mkdir .links.tmp
echo "# This section creates symbolic links" > srclinks.tmp
echo "" >> srclinks.tmp
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
alldirs="$SOURCEDIRS $INCLUDEDIRS ."
for d in $alldirs ; do
    deplist=
    sfiles=`( cd $d; echo *.[h,c,F] | grep -v _cb2m)`
    sfiles=`( echo $sfiles; cd $d; echo *.F90 | grep -v _cb2m)`
    for sf in $sfiles ; do
        if test ! -r ".links.tmp/$sf" ; then
            if test -f "$d/$sf" ; then
                case $d/$sf in
                  ./$PACKAGES_DOT_H)
                        ;;
                  ./AD_CONFIG.h)
                        ;;
                  ./FC_NAMEMANGLE.h)
                        ;;
                  ./BUILD_INFO.h)
                        ;;
                  *)
                        touch .links.tmp/$sf
                        deplist="$deplist $sf"
                        ;;
                esac
                extn=`echo $sf | $AWK -F. '{print $NF}'`
                case $extn in
                    F)
                        echo    " \\"  >> F77srclist.tmp
                        printf " $sf" >> F77srclist.tmp
                        basename=${sf%%.F}
                        isAD=`egrep ^$basename.f'[      ]*' adSrcFiles.tmp`
                        if test -z "$isAD" ; then 
                          toBeIgnored=`egrep ^$basename'[      ]*' ${MODS}/dontCompile`
                          if test -z "$toBeIgnored" ; then 
                            echo    " \\"  >> nonADF77srclist.tmp
                            printf " $sf" >> nonADF77srclist.tmp
                          else 
                            echo "Ignoring $sf"
                          fi
                        fi
                        ;;
                    F90)
                        echo    " \\"  >> F90srclist.tmp
                        printf " $sf" >> F90srclist.tmp
                        ;;
                    c)
                        echo    " \\"  >> csrclist.tmp
                        printf " $sf" >> csrclist.tmp
                        ;;
                    h)
                        echo    " \\"  >> hsrclist.tmp
                        printf " $sf" >> hsrclist.tmp
                        ;;
                esac
            fi
        fi
    done
    if test "x$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
      fi
    fi
done
rm -rf .links.tmp
echo "" >> F77srclist.tmp
for i in `cat ${MODS}/keepOriginal`
do
  echo   " \\" >> nonADF77srclist.tmp
  printf " $i" >> nonADF77srclist.tmp
done  
echo "" >> nonADF77srclist.tmp
echo "" >> csrclist.tmp
echo "" >> F90srclist.tmp
echo "" >> hsrclist.tmp

if test -f $MAKEFILE ; then
    mv -f $MAKEFILE "$MAKEFILE.bak"
fi

echo "  Writing makefile: $MAKEFILE"

echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE
echo "#    $MACHINE" >> $MAKEFILE
echo "# This makefile was generated automatically on" >> $MAKEFILE
echo "#    $THISDATE" >> $MAKEFILE
echo "# by the command:" >> $MAKEFILE
echo "#    $0 $G2ARGS" >> $MAKEFILE
echo "# executed by:" >> $MAKEFILE
echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE

EXE_AD=$EXECUTABLE"_ad"
EXE_FTL=$EXECUTABLE"_ftl"
EXE_SVD=$EXECUTABLE"_svd"

cat >>$MAKEFILE <<EOF
#
# OPTFILE="$OPTFILE"
# 
# BUILDDIR     : Directory where object files are written
# SOURCEDIRS   : Directories containing the source (.F) files
# INCLUDEDIRS  : Directories containing the header-source (.h) files
# EXEDIR       : Directory where executable that is generated is written
# EXECUTABLE   : Full path of executable binary
#
# CPP          : C-preprocessor command
# 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
# LINK         : Command for link editor program
# LIBS         : Library flags /or/ additional optimization/debugging flags

ROOTDIR     = ${ROOTDIR}
BUILDDIR    = ${BUILDDIR}  
SOURCEDIRS  = ${SOURCEDIRS}
INCLUDEDIRS = ${INCLUDEDIRS}
EXEDIR      = ${EXEDIR}
EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
TOOLSDIR    = ${TOOLSDIR}

#eh3  new defines for the adjoint work
AUTODIFF    = ${ROOTDIR}/pkg/autodiff
EXE_AD      = ${EXE_AD}
EXE_FTL     = ${EXE_FTL}
EXE_SVD     = ${EXE_SVD}

ENABLED_PACKAGES  = ${ENABLED_PACKAGES}
DISABLED_PACKAGES = ${DISABLED_PACKAGES}

# These files are created by Makefile
SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h

EOF

#  Note: figure out some way to add Hyades JAM libraries here
 
cat >>$MAKEFILE <<EOF
# Unix ln (link)
LN = ${LN}
# C preprocessor
CPP = cat \$< | ${S64} | ${CPP}
# Dependency generator
MAKEDEPEND = ${MAKEDEPEND}
# Special preprocessor (KAP on DECs, FPP on Crays)
KPP = ${KPP}
# Fortran compiler
FC = ${FC}
# Fortran compiler
F90C = ${F90C}
# C compiler
CC = ${CC}
# Link editor
LINK = ${LINK} ${LDADD}

# Defines for CPP
DEFINES = ${DEFINES}
# Includes for CPP
INCLUDES = ${INCLUDES}
# Flags for KPP
KFLAGS1 = ${KFLAGS1}
KFLAGS2 = ${KFLAGS2}
# Optim./debug for FC
FFLAGS = ${FFLAGS}
FOPTIM = ${FOPTIM}
# Optim./debug/format 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 = ${LIBS}
# Name of the Mekfile
MAKEFILE=${MAKEFILE}

EOF

cat F77srclist.tmp      >> $MAKEFILE
cat nonADF77srclist.tmp >> $MAKEFILE
cat csrclist.tmp        >> $MAKEFILE
cat F90srclist.tmp      >> $MAKEFILE
cat hsrclist.tmp        >> $MAKEFILE

rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp hsrclist.tmp flist.tmp clist.tmp F90srclist.tmp

echo >> $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 >> $MAKEFILE
echo '.SUFFIXES:' >> $MAKEFILE
echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90' >> $MAKEFILE

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)

all: depend \$(EXECUTABLE)

depend: \$(ALL_LINKED_FILES) 
        \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
        \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
        -rm -f makedepend.out

.PHONY: depend

OBJFILES= \$(F77_SRC_FILES:.F=.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o) 

\$(EXECUTABLE): \$(OBJFILES)
        @echo Creating \$@ ...
        \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)

output.txt: \$(EXECUTABLE)
        @printf 'running ... '
        @\$(EXECUTABLE) > \$@

# Special targets (SPECIAL_FILES) which are created by make
${PACKAGES_DOT_H}:
        @echo Creating \$@ ...
        @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
AD_CONFIG.h:
        @echo Creating \$@ ...
        @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
FC_NAMEMANGLE.h:
        @echo Creating \$@ ...
        echo "$FC_NAMEMANGLE" > \$@

BUILD_INFO.h:
        @echo Creating \$@ ...
EOF

test ! "x$THISVER" = x  && echo "       -echo \"#define THISVER '$THISVER'\" > \$@"   >> $MAKEFILE
test ! "x$THISUSER" = x && echo "       -echo \"#define THISUSER '$THISUSER'\" >> \$@" >> $MAKEFILE
test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE

cat >>$MAKEFILE <<EOF

# The normal chain of rules is (  .F - .$FS - .o  )

## This nullifies any default implicit rules concerning these two file types:
%.o : %.F

.F.$FS:
        \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
.$FS.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:
        \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$<
.c.o:
        \$(CC) \$(CFLAGS) -c \$<

# Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
.F.p:
        \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
.p.$FS:
        \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<

#=========================================
#===  Cleanup Rules  ===

CLEAN: Clean
        -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
        -find \$(EXEDIR) -name "*.data" -exec rm {} \;
        -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
        -rm -f \$(EXECUTABLE) output.txt ad_output.txt STD*

Clean: clean cleanlinks
        -rm -f *.F
        -rm -f \$(SPECIAL_FILES)
        -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak

clean:
        -rm -rf *.o *.$FS *.p *.f$FS90 *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template *_mod.h *_mod.F90 *.FF90 *.mod-whirl ad_input*
        -rm -rf temp.sed reslice.dat 

cleanlinks:
        -find . -type l -exec rm {} \;

.PHONY: clean Clean CLEAN


#=========================================
#===  self regeneration  ===
# can't call this target  "Makefile"
# because unfortunately the genmake script 
# invoked here uses
# make itself for checking things and we 
# end up in a recursion.  

makefile:
        $THIS_SCRIPT $G2ARGS

# because the file is called Makefile
.PHONY: makefile

#====================================
#===  Automatic Differentiation   ===

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 AD code generation"
echo >> $MAKEFILE
printf "AD_FILES = " >> $MAKEFILE
AD_FILES=`cat adSrcFiles.tmp`
for i in $AD_FILES ; do
    echo    " \\" >> $MAKEFILE
    printf " $i" >> $MAKEFILE
done
echo >> $MAKEFILE
rm -f adSrcFiles.tmp

cat >>$MAKEFILE <<EOF


# files to be converted: 
# right now there is no quick hack 
# to pick these out automatically 
# but we will be using the 
# canonicalizer anyway
CB2M_F90_SRC_NAMES = \
SIZE \
EEPARAMS \
PARAMS \
BAR2 \
BARRIER \
CD_CODE_VARS \
CG2D \
CG3D \
DFILE \
DYNVARS \
EEIO \
EESUPPORT \
EOS \
EXCH_JAM \
EXCH \
FC_NAMEMANGLE \
FFIELDS \
GAD \
GLOBAL_MAX \
GLOBAL_SUM \
GMREDI \
GMREDI_TAVE \
GRID \
MPI_INFO \
SOLVE_FOR_PRESSURE3D \
SOLVE_FOR_PRESSURE \
SURFACE \
tamc \
tamc_keys \
cost \
g_cost \
ctrl \
ctrl_dummy \
ctrl_weights \
optim \
grdchk 

.PHONY: adAll
adAll: \$(EXE_AD) ncheckLev.conf

# these are all fixed format:
CB2M_F77_TO_FF90_SRC_FILES=\$(F77_SRC_FILES:.F=_cb2m.FF90)
CB2M_F90_SRC_FILES=\$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES))
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.ff90)

.PHONY: adDepend
#this file is included at the bottom
adDepend: \$(ALL_LINKED_FILES) \$(CB2M_F90_SRC_FILES) \$(CB2M_F77_TO_FF90_SRC_FILES) 
        \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
        \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
        -rm -f makedepend.out


OPENAD_SUPPORT_F90_SRC_FILES = \
w2f__types.f90 \
active_module.f90 \
OpenAD_checkpoints.f90 \
OpenAD_dct.f90 \
OpenAD_rev.f90 \
OpenAD_tape.f90         

OPENAD_SUPPORT_C_SRC_FILES = \
iaddr.c \
timeRatio.c

f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES)
        cat \$^ > \$@

f95_test.f90: all_mods.xb.x2w.w2f.pp.f \$(NON_AD_F77_SRC_FILES:.F=_cb2m.ff90) ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f 
        cat \$^ > \$@

f95_test.out: f95_test_mods.f90 f95_test.f90
        f95 -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
        f95 -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1

AD_OBJ_FILES=\$(OPENAD_SUPPORT_F90_SRC_FILES:.f90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) all_mods.xb.x2w.w2f.pp.o ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.o \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)

\$(EXE_AD): \$(AD_OBJ_FILES)
        @echo Creating \$@ ...
        \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$^ \$(LIBS)

# makefile debug rule
openad: ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f
.PHONY: openad

CB2MFILES= cb2m1.csh cb2m1.awk cb2m2.bash 
# create the module files and change the header files
\$(CB2M_F90_SRC_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) : \$(ALL_LINKED_FILES) \$(CB2MFILES) 
        ./cb2m1.csh \$(CB2M_F90_SRC_NAMES)

# change everybody else to use the module files:
\$(CB2M_F77_TO_FF90_SRC_FILES): \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(CB2M_F90_SRC_FILES) 
        ./cb2m2.bash

# makefile debug rule
small_f: \$(CB2M_F77_PP_SRC_FILES) \$(CB2M_F90_PP_SRC_FILES)
.PHONY: small_f

ad_output.txt: \$(EXE_AD)
        @printf 'linking data files ... '
        \$(LN) -f ../input_ad/data* ../input_ad/eedata .
        \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
        @printf 'running ... '
        @./\$(EXE_AD) > \$@

CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.ff90)
ad_input_code.$FS: ${MODS}/maxMinDefs.f \$(CB2M_AD_FILES) 
        cat \$^ > \$@

\$(CB2MFILES):
        \$(LN) \$(addprefix ${MODS}/, \$(CB2MFILES)) .

# strip all comments and blanks to reduce 
# the file size in order to reduce perl's memory requirements 
ad_input_code_sf.f : ad_input_code.f 
        cat \$^ | sed -f ${MODS}/strip.sed | sed -f ${MODS}/stop2print.sed > \$@

# mfef90 preprocessing
# expand statement functions 
# expose mfef90 specific substring handling 
# add the w2f__types module
ad_input_code_sf.w2f.f: ad_input_code_sf.f mfef90 whirl2f whirl2f_be w2f__types.f90
        ./mfef90 -F -N132 \$< 
        ./whirl2f \$<
        cat w2f__types.f90 \$@ > \$@.1
        mv \$@.1 \$@  

# canonicalizer
ad_input_code_sf.w2f.canon.f: ad_input_code_sf.w2f.f canon.v1.py
        python canon.v1.py \$< > \$@

# F -> WHIRL
# note that the canonicalized version cuts off at col 72 
# doing this also for string constants which is ok as long 
# as we are in fixed mode and cut of exactly there. 
# Otherwise mfef90 patches in spaces to fill up to 72 (or 132) 
# characters respectively.
ad_input_code_sf.w2f.canon.B: ad_input_code_sf.w2f.canon.f mfef90
        ./mfef90 -F \$<

# WHIRL -> XAIF
ad_input_code_sf.w2f.canon.xaif : ad_input_code_sf.w2f.canon.B whirl2xaif
        ./whirl2xaif -s -n --debug 1 -o \$@ \$<

# XAIF -> XAIF'
ad_input_code_sf.w2f.canon.xb.xaif : ad_input_code_sf.w2f.canon.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd openad_adm
        ./openad_adm -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r -p "recip_hFacC recip_rA GM_Kmin_horiz"

# XAIF' -> WHIRL'
ad_input_code_sf.w2f.canon.xb.x2w.B : ad_input_code_sf.w2f.canon.xb.xaif xaif2whirl
        ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.canon.B \$<

# WHIRL' -> F'
ad_input_code_sf.w2f.canon.xb.x2w.w2f.f: ad_input_code_sf.w2f.canon.xb.x2w.B whirl2f whirl2f_be
        ./whirl2f -openad \$<

# undo slice hiding 
# insert template directives
ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.f: ad_input_code_sf.w2f.canon.xb.x2w.w2f.f reslicer.py ${MODS}/insertTemplateDir.bash
        python reslicer.py \$< > \$<.1
        ${MODS}/insertTemplateDir.bash \$<.1  \$@
        rm \$<.1

# postprocess F'
ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.f multi-pp.pl ${MODS}/ad_inline.f ${MODS}/ad_template.checkpoint.f ${MODS}/ad_template.plain.f ${MODS}/ad_template.split.f ${MODS}/ad_template.sa_cg2d.f
        perl multi-pp.pl -inline=${MODS}/ad_inline.f \$<
        cat \$@ | sed 's/RETURN//' > \$@.1
        mv \$@.1 \$@

# extract all transformed modules 
all_mods.xb.x2w.w2f.pp.f: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f
        cat \$< | sed -n '/MODULE /,/END MODULE/p' > \$@

# remove the transformed globals module from the 
# transformed ad_input_code file
# and remove for now the duplicate variables
# and fix 2 data statements
ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f ${MODS}/fixData.sed
#       cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' | sed -f ${MODS}/fixData.sed > \$@
        cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' > \$@

# setup some links
%.xsd:
        \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .

mfef90: 
        \$(LN) \${OPENADROOT}/Open64/osprey1.0/targ_ia32_ia64_linux/crayf90/sgi/mfef90 .

# link the support files:
\$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) ncheckLev.conf : 
        \$(LN) ${MODS}/\$@ .

whirl2xaif xaif2whirl: 
        \$(LN) \${OPENADROOT}/OpenADFortTk/OpenADFortTk-x86-Linux/bin/\$@ .

%.pl: 
        \$(LN) \${OPENADROOT}/OpenADFortTk/OpenADFortTk-x86-Linux/bin/\$@ .

%.py: 
        \$(LN) \${OPENADROOT}/OpenADFortTk/tools/canonicalize/\$@ .

whirl2f whirl2f_be:
        \$(LN) \${OPENADROOT}/Open64/osprey1.0/targ_ia32_ia64_linux/whirl2f/\$@ .

openad_adm:
        \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/test/t \$@

EOF

if test "x$EXEHOOK" != x ; then
    printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
fi

echo "  Making list of \"exceptions\" that need \".p\" files"
for i in $KPPFILES ; do
    base=`echo $i | sed -e 's/\/.*\///g' | sed -e 's/\..*$//g'`
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        echo "Error: unable to add file \"$i\" to the exceptions list"
    fi
    echo "$base.$FS: $base.p" >> $MAKEFILE
done

echo "  Making list of NOOPTFILES"
for i in $NOOPTFILES ; do
    base=`echo $i | sed -e 's/\/.*\///g' | sed -e 's/\..*$//g'`
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then
        echo "Error: unable to add file \"$i\" to the exceptions list"
    fi
    echo "$base.o: $base.$FS" >> $MAKEFILE
    printf "\t\$(FC) \$(FFLAGS) \$(NOOPTFLAGS) -c \$<\n" >> $MAKEFILE
done

echo "  Add rules for links"
cat srclinks.tmp >> $MAKEFILE
rm -f srclinks.tmp

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" 
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
    printf "" > genmake_state
    for i in $gm_state ; do
        t1="t2=\$$i"
        eval $t1
        echo "$i='$t2'" >> genmake_state
    done
fi