/[MITgcm]/MITgcm/tools/genmake2

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-revision 1.23 by edhill,
Fri Oct 24 05:52:05 2003 UTC
+revision 1.183 by utke,
Wed Jan 14 20:08:40 2009 UTC
 Line 1
- #!/bin/bash
+ #! /usr/bin/env bash
  #
  # $Header$
  #
 Line 13
  test_for_package_in_cpp_options() {
      cpp_options=$1
      pkg=$2
-     grep -i "#define.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
-     RETVAL=$?
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
-     if test "x${RETVAL}" = x0 ; then
+     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
-         echo "Error: In $cpp_options there is an illegal line: #define ALLOW_$pkg"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
-         exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
-     fi
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
-     grep -i "#undef.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
+     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
-     RETVAL=$?
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
-     if test "x${RETVAL}" = x0 ; then
+ }
-         echo "Error: In $cpp_options there is an illegal line: #undef ALLOW_$pkg"
-         exit 99
+ # Search for particular CPP #cmds associated with MPI
-     fi
+ # usage: test_for_mpi_in_cpp_eeoptions CPP_file
-     grep -i "#define.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+ test_for_mpi_in_cpp_eeoptions() {
+     cpp_options=$1
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
+ }
+ # Search for particular string in a file. Return 1 if detected, 0 if not
+ # usage: test_for_string_in_file file string
+ test_for_string_in_file() {
+     file=$1
+     strng=$2
+     grep -i "$strng" $file > /dev/null 2>&1
      RETVAL=$?
      if test "x${RETVAL}" = x0 ; then
-         echo "Error: In $cpp_options there is an illegal line: #define DISABLE_$pkg"
+         printf "Error: In $file there is an illegal line: "
+         grep -i "$strng" $file
          exit 99
      fi
-     grep -i "#undef.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+     return 0
-     RETVAL=$?
-     if test "x${RETVAL}" = x0 ; then
-         echo "Error: In $cpp_options there is an illegal line: #undef DISABLE_$pkg"
-         exit 99
-    fi
  }
  # Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
-Line 62 
 expand_pkg_groups() {
+Line 75 
 expand_pkg_groups() {
          done
          PACKAGES=$new_packages
          rm -f ./p[1,2].tmp
+         return $matched
      else
          echo "Warning: can't read package groups definition file: $PKG_GROUPS"
      fi
  }
+ #  Check for broken environments (eg. cygwin, MacOSX w/HFS+) that
+ #  cannot distinguish [*.F/*.F90] from [*.f/*.f90] files.
+ check_for_broken_Ff()  {
+     #  Do we have defaults for $FS and/or $FS90 ?
+     tfs=f
+     tfs9=f90
+     if test "x$FS" != x ; then
+         tfs="$FS"
+     fi
+     if test "x$FS90" != x ; then
+         tfs9="$FS90"
+     fi
+     #  First check the ability to create a *.F/.f pair.
+     cat <<EOF >> genmake_hello.F
+       program hello
+       write(*,*) 'hi'
+       stop
+       end
+ EOF
+     cp genmake_hello.F "genmake_hello."$tfs > /dev/null 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" != x0 ; then
+         if test "x$FS" = x ; then
+             FS='for'
+             FS90='fr9'
+             check_for_broken_Ff
+         else
+             cat <<EOF 2>&1
+ ERROR: Your file system cannot distinguish between *.F and *.f files
+   (fails the "cp" test) and this program cannot find a suitable
+   replacement extension.  Please try a different build environment or
+   contact the <MITgcm-support@mitgcm.org> list for help.
+ EOF
+             exit -1
+         fi
+         return
+     fi
+     rm -f genmake_hello.*
+     #  Check the ability of ${MAKE} and ${LN} to use the current set
+     #  of extensions.
+     cat <<EOF >> genmake_hello.F
+       program hello
+       write(*,*) 'hi'
+       stop
+       end
+ EOF
+     test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
+     cat <<EOF >> $MAKEFILE
+ .SUFFIXES:
+ .SUFFIXES: .$tfs .F
+ .F.$tfs:
+         $LN \$< \$@
+ EOF
+     $MAKE "genmake_hello."$tfs > /dev/null 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
+         if test "x$FS" = x ; then
+             FS='for'
+             FS90='fr9'
+             check_for_broken_Ff
+         else
+             cat <<EOF 2>&1
+ ERROR: Your file system cannot distinguish between *.F and *.f files
+   (fails the "make/ln" test) and this program cannot find a suitable
+   replacement extension.  Please try a different build environment or
+   contact the <MITgcm-support@mitgcm.org> list for help.
+ EOF
+             exit -1
+             return
+         fi
+     fi
+     rm -f genmake_hello.* $MAKEFILE
+     test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
+     #  If we make it here, use the extensions
+     FS=$tfs
+     FS90=$tfs9
+     return
+ }
+ look_for_makedepend()  {
+     #  The "original" makedepend is part of the Imake system that is
+     #  most often distributed with XFree86 or with an XFree86 source
+     #  package.  As a result, many machines (eg. generic Linux) do not
+     #  have a system-default "makedepend" available.  For those
+     #  systems, we have two fall-back options:
+     #
+     #    1) a makedepend implementation shipped with the cyrus-imapd
+     #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
+     #
+     #    2) a known-buggy xmakedpend shell script
+     #
+     #  So the choices are, in order:
+     #
+     #    1) use the user-specified program
+     #    2) use a system-wide default
+     #    3) locally build and use the cyrus implementation
+     #    4) fall back to the buggy local xmakedpend script
+     #
+     if test "x${MAKEDEPEND}" = x ; then
+         which makedepend > /dev/null 2>&1
+         RV0=$?
+         test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
+         #  echo 'MAKEFILE="'$MAKEFILE'"'
+         cat <<EOF >> $MAKEFILE
+ #   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
+ #
+ #   Some "makedepend" implementations will die if they cannot
+ #   find a Makefile -- so this file is here to gives them an
+ #   empty one to find and parse.
+ EOF
+         cat <<EOF >> genmake_tc.f
+       program test
+       write(*,*) 'test'
+       stop
+       end
+ EOF
+         makedepend genmake_tc.f > /dev/null 2>&1
+         RV1=$?
+         test -f $MAKEFILE  &&  rm -f $MAKEFILE
+         test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
+         if test "x${RV0}${RV1}" = x00 ; then
+             MAKEDEPEND=makedepend
+         else
+             echo "    a system-default makedepend was not found."
+             #  Try to build the cyrus implementation
+             build_cyrus_makedepend
+             RETVAL=$?
+             if test "x$RETVAL" != x0 ; then
+                 MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+             fi
+             rm -f ./genmake_cy_md
+         fi
+     else
+         #  echo "MAKEDEPEND=${MAKEDEPEND}"
+         echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
+         RETVAL=$?
+         if test x"$RETVAL" = x0 ; then
+             build_cyrus_makedepend
+         fi
+     fi
+ }
+ build_cyrus_makedepend()  {
+     rm -f ./genmake_cy_md
+     (
+         cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
+             &&  ./configure > /dev/null 2>&1  \
+             &&  make > /dev/null 2>&1
+         if test -x ./makedepend.exe ; then
+             $LN ./makedepend.exe ./makedepend
+         fi
+         ./makedepend ifparser.c > /dev/null 2>&1  \
+             &&  echo "true"
+     ) > ./genmake_cy_md
+     grep true ./genmake_cy_md > /dev/null 2>&1
+     RETVAL=$?
+     rm -f ./genmake_cy_md
+     if test "x$RETVAL" = x0 ; then
+         MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+         return 0
+     else
+         echo "WARNING: unable to build cyrus-imapd-makedepend"
+         return 1
+     fi
+ }
+ build_embed_encode()
+ {
+     printf "  building the embed-encode utility...  "
+     if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
+         if test ! -d "$ROOTDIR/tools/embed_encode" ; then
+             echo
+             echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
+             echo
+             EMBED_SRC=f
+             return 1
+         fi
+         clist="cc gcc c89 $CC"
+         for ic in $clist ; do
+             comm="$ic -o encode_files encode_files.c"
+             ( cd $ROOTDIR/tools/embed_encode && $comm ) > /dev/null 2>&1
+             RETVAL=$?
+             if test "x$RETVAL" = x0 ; then
+                 echo "OK"
+                 DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+                 return 0
+             fi
+         done
+         echo
+         echo "    Error: unable to build $ROOTDIR/embed_encode/encode_files"
+         echo "      so it has been disabled"
+         echo
+         EMBED_SRC=f
+         return 1
+     fi
+     echo "OK"
+     DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+ }
  # Guess possible config options for this host
  find_possible_configs()  {
      tmp1=`uname`"_"`uname -m`
      tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
-     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
+     echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
      OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
      echo "  The platform appears to be:  $PLATFORM"
- #     if test "x$OFLIST" = x ; then
- #       echo "  No pre-defined options files were found matching this platform"
- #       echo "  but examples for other platforms can be found in:"
- #       echo "    $ROOTDIR/tools/build_options"
- #     else
- #       echo "  Options files (located in $ROOTDIR/tools/build_options) that"
- #       echo "  may work with this machine are:"
- #       for i in $OFLIST ; do
- #           echo "    $i"
- #       done
- #     fi
      echo "test" > test
      ln -s ./test link
-Line 103 
 find_possible_configs()  {
+Line 321 
 find_possible_configs()  {
          CPP="cpp -traditional -P"
      fi
-     # look for possible fortran compilers
+     look_for_makedepend
-     tmp="$MITGCM_FC $FC g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
+     #================================================================
+     #  look for possible C compilers
+     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
+     p_CC=
+     for c in $tmp ; do
+         rm -f ./genmake_hello.c  ./genmake_hello
+         cat >> genmake_hello.c << EOF
+ #include <stdio.h>
+ int main(int argc, char **argv) {
+   printf("Hello!\n");
+   return 0;
+ }
+ EOF
+         $c -o genmake_hello genmake_hello.c > /dev/null 2>&1
+         RETVAL=$?
+         if test "x${RETVAL}" = x0 ; then
+             p_CC="$p_CC $c"
+         fi
+     done
+     rm -f ./genmake_hello.c ./genmake_hello
+     if test "x${p_CC}" = x ; then
+         cat 1>&2 <<EOF
+ Error: No C compilers were found in your path.  Please specify one using:
+) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
+) the CC or MITGCM_CC environment variables.
+ EOF
+         exit 1
+     else
+         echo "  The possible C compilers found in your path are:"
+         echo "   "$p_CC
+         if test "x$CC" = x ; then
+             CC=`echo $p_CC | $AWK '{print $1}'`
+             echo "  Setting C compiler to: "$CC
+         fi
+     fi
+     #================================================================
+     #  look for possible FORTRAN compilers
+     tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"
      p_FC=
      for c in $tmp ; do
          rm -f ./hello.f ./hello
-Line 129 
 Error: No Fortran compilers were found i
+Line 389 
 Error: No Fortran compilers were found i
 ) an "optfile" on (eg. "-optfile=path/to/OPTFILE"),
 ) a command-line option (eg. "-fc NAME"), or
-) the MITGCM_FC environment variable.
+) the FC or MITGCM_FC environment variables.
  EOF
          exit 1
      else
          echo "  The possible FORTRAN compilers found in your path are:"
          echo "   "$p_FC
-         if test "x$FC" = x ; then
-             FC=`echo $p_FC | $AWK '{print $1}'`
-         fi
      fi
-     for i in $p_FC ; do
+     #  Use the first of the compilers found in the current PATH
-         p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+     #  that has a correctly-named optfile
-         if test -r $p_OF ; then
+     if test "x$OPTFILE" = x  -a  "x$FC" = x ; then
-             OPTFILE=$p_OF
+         for i in $p_FC ; do
-             echo "  The options file:  $p_OF"
+             OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
-             echo "    appears to match so we'll use it."
+             if test -r $OPTFILE ; then
-             break
+                 echo "  Setting OPTFILE to: "$OPTFILE
-         fi
+                 break
-     done
+             fi
+         done
+     fi
+     if test "x$OPTFILE" = x ; then
+         OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
+         if test ! -r $OPTFILE ; then
+              echo "  I looked for the file "$OPTFILE" but did not find it"
+         fi
+     fi
+ #    echo "  The options file:  $p_OF"
+ #    echo "    appears to match so we'll use it."
+ #   for i in $p_FC ; do
+ #p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+ #if test -r $p_OF ; then
+ #    OPTFILE=$p_OF
+ #    echo "  The options file:  $p_OF"
+ #    echo "    appears to match so we'll use it."
+ #    break
+ #fi
+ #   done
      if test "x$OPTFILE" = x ; then
          cat 1>&2 <<EOF
-Line 205 
 get_pdepend_list()  {
+Line 482 
 get_pdepend_list()  {
      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
+ cat <<EOF
-     echo "Usage: "$0" [OPTIONS]"
-     echo "  where [OPTIONS] can be:"
+ Usage: "$0" [OPTIONS]
-     echo
+   where [OPTIONS] can be:
-     echo "    -help | --help | -h | --h"
-     echo "    -nooptfile | --nooptfile"
+     -help | --help | -h | --h
-     echo "      -optfile NAME | --optfile NAME | -of NAME | --of NAME"
+           Print this help message and exit.
-     echo "      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME"
-     echo "    -pdepend NAME | --pdepend NAME"
+     -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
-     echo "      -pdepend=NAME | --pdepend=NAME"
+       -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
-     echo "    -pdefault NAME | --pdefault NAME"
+           Use "NAME" as the adoptfile.  By default, the file at
-     echo "      -pdefault=NAME | --pdefault=NAME"
+           "tools/adjoint_options/adjoint_default" will be used.
-     echo "    -make NAME | -m NAME"
-     echo "      --make=NAME | -m=NAME"
+     -nooptfile | --nooptfile
-     echo "    -makefile NAME | -mf NAME"
+       -optfile NAME | --optfile NAME | -of NAME | --of NAME
-     echo "      --makefile=NAME | -mf=NAME"
+       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
-     echo "    -platform NAME | --platform NAME | -pl NAME | --pl NAME"
+           Use "NAME" as the optfile.  By default, an attempt will be
-     echo "      -platform=NAME | --platform=NAME | -pl=NAME | --pl=NAME"
+           made to find an appropriate "standard" optfile in the
-     echo "    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME"
+           tools/build_options/ directory.
-     echo "      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME"
-     echo "    -mods NAME | --mods NAME | -mo NAME | --mo NAME"
+     -pdepend NAME | --pdepend NAME
-     echo "      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME"
+       -pdepend=NAME | --pdepend=NAME
-     echo "    -disable NAME | --disable NAME"
+           Get package dependency information from "NAME".
-     echo "      -disable=NAME | --disable=NAME"
-     echo "    -enable NAME | --enable NAME"
+     -pdefault NAME | --pdefault NAME
-     echo "      -enable=NAME | --enable=NAME"
+       -pdefault=NAME | --pdefault=NAME
-     echo "    -standarddirs NAME | --standarddirs NAME"
+           Get the default package list from "NAME".
-     echo "      -standarddirs=NAME | --standarddirs=NAME"
-     echo "    -noopt NAME | --noopt NAME"
+     -make NAME | -m NAME
-     echo "      -noopt=NAME | --noopt=NAME"
+       --make=NAME | -m=NAME
- #    echo "    -cpp NAME | --cpp NAME"
+           Use "NAME" for the MAKE program. The default is "make" but
- #    echo "      -cpp=NAME | --cpp=NAME"
+           many platforms, "gmake" is the preferred choice.
-     echo "    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME"
-     echo "      -fc=NAME | --fc=NAME"
+     -makefile NAME | -mf NAME
-     echo "    -[no]ieee | --[no]ieee"
+       --makefile=NAME | -mf=NAME
-     echo "    -[no]mpi | --[no]mpi"
+           Call the makefile "NAME".  The default is "Makefile".
-     echo "    -[no]jam | --[no]jam"
-     echo
+     -makedepend NAME | -md NAME
-     echo "  and NAME is a string such as:"
+       --makedepend=NAME | -md=NAME
-     echo
+           Use "NAME" for the MAKEDEPEND program.
-     echo "    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'"
-     echo "    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'"
+     -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
-     echo "    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'"
+       -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
-     echo
+           Specify the location of the MITgcm ROOTDIR as "NAME".
-     echo "  which, depending upon your shell, may need to be single-quoted"
+           By default, genamke will try to find the location by
-     echo "  if it contains spaces, dashes, or other special characters."
+           looking in parent directories (up to the 5th parent).
+     -mods NAME | --mods NAME | -mo NAME | --mo NAME
+       -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
+           Here, "NAME" specifies a list of directories that are
+           used for additional source code.  Files found in the
+           "mods list" are given preference over files of the same
+           name found elsewhere.
+     -disable NAME | --disable NAME
+       -disable=NAME | --disable=NAME
+           Here "NAME" specifies a list of packages that we don't
+           want to use.  If this violates package dependencies,
+           genamke will exit with an error message.
+     -enable NAME | --enable NAME
+       -enable=NAME | --enable=NAME
+           Here "NAME" specifies a list of packages that we wish
+           to specifically enable.  If this violates package
+           dependencies, genamke will exit with an error message.
+     -standarddirs NAME | --standarddirs NAME
+       -standarddirs=NAME | --standarddirs=NAME
+           Here, "NAME" specifies a list of directories to be
+           used as the "standard" code.
+     -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
+       -fc=NAME | --fc=NAME
+           Use "NAME" as the fortran compiler.  By default, genmake
+           will search for a working compiler by trying a list of
+           "usual suspects" such as g77, f77, etc.
+     -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
+           Use "NAME" as the C compiler.  By default, genmake
+           will search for a working compiler by trying a list of
+           "usual suspects" such as gcc, c89, cc, etc.
+     -[no]ieee | --[no]ieee
+           Do or don't use IEEE numerics.  Note that this option
+           *only* works if it is supported by the OPTFILE that
+           is being used.
+     -ignoretime | -ignore_time | --ignoretime | --ignore_time
+           Ignore all the "wall clock" routines entirely.  This will
+           not in any way hurt the model results -- it simply means
+           that the code that checks how long the model spends in
+           various routines will give junk values.
+     -ts | --ts
+           Produce timing information per timestep
+     -papis | --papis
+           Produce summary MFlop/s (and IPC) with PAPI per timestep
+     -pcls | --pcls
+           Produce summary MFlop/s etc. with PCL per timestep
+     -foolad | --foolad
+           Fool the AD code generator
+     -papi | --papi
+           Performance analysis with PAPI
+     -pcl | --pcl
+           Performance analysis with PCL
+     -hpmt | --hpmt
+           Performance analysis with the HPM Toolkit
+     -gsl | --gsl
+           Use GSL to control floating point rounding and precision
+     -devel | --devel
+           Add additional warning and debugging flags for development
+     -mpi | --mpi
+           Include MPI header files and link to MPI libraries
+     -mpi=PATH | --mpi=PATH
+           Include MPI header files and link to MPI libraries using MPI_ROOT
+           set to PATH. i.e. Include files from \$PATH/include, link to libraries
+           from \$PATH/lib and use binaries from \$PATH/bin.
+     -es | --es | -embed-source | --embed-source
+           Embed a tarball containing the full source code
+           (including the Makefile, etc.) used to build the
+           executable [off by default]
+     -bash NAME
+           Explicitly specify the Bourne or BASH shell to use
+   While it is most often a single word, the "NAME" variables specified
+   above can in many cases be a space-delimited string such as:
+     --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
+     -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
+     -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
+   which, depending upon your shell, may need to be single-quoted.
+   For more detailed genmake documentation, please see:
+     http://mitgcm.org/devel_HOWTO/
+ EOF
      exit 1
  }
- #eh3 # This is the generic configuration.
+ #  Build a CPP macro to automate calling C routines from FORTRAN
- #eh3 set LN         = ( 'ln -s' )
+ get_fortran_c_namemangling()  {
- #eh3 set CPP        = ( '/lib/cpp -P' )
- #eh3 set S64        = ( '$(TOOLSDIR)/set64bitConst.sh' )
+     #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
- #eh3 set KPP        = (  )
+     if test ! "x$FC_NAMEMANGLE" = x ; then
- #eh3 set FC         = ( 'f77' )
+         return 0
- #eh3 set LINK       = $FC
+     fi
- #eh3 set MAKEDEPEND = ( 'makedepend' )
- #eh3 set INCLUDES   = ( -I. )
+     default_nm="#define FC_NAMEMANGLE(X) X ## _"
- #eh3 set FFLAGS     = (  )
- #eh3 set FOPTIM     = (  )
+     cat > genmake_test.c <<EOF
- #eh3 set CFLAGS     = (  )
+ void tcall( char * string ) { tsub( string ); }
- #eh3 set KFLAGS1    = (  )
+ EOF
- #eh3 set KFLAGS2    = (  )
+     $MAKE genmake_test.o >> genmake_warnings 2>&1
- #eh3 set LIBS       = (  )
+     RETVAL=$?
- #eh3 set KPPFILES   = (  )
+     if test "x$RETVAL" != x0 ; then
- #eh3 if (! $?NOOPTFILES ) set NOOPTFILES = (  )
+         FC_NAMEMANGLE=$default_nm
- #eh3 if (! $?NOOPTFLAGS ) set NOOPTFLAGS = (  )
+         cat <<EOF>> genmake_errors
+ WARNING: C test compile fails
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ EOF
+         return 1
+     fi
+     c_tcall=`nm genmake_test.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+     RETVAL=$?
+     if test "x$RETVAL" != x0 ; then
+         FC_NAMEMANGLE=$default_nm
+         cat <<EOF>> genmake_warnings
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ EOF
+         return 1
+     fi
+     cat > genmake_tcomp.$FS <<EOF
+       subroutine tcall( string )
+       character*(*) string
+       call tsub( string )
+       end
+ EOF
+     $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" != x0 ; then
+         FC_NAMEMANGLE=$default_nm
+         cat <<EOF>> genmake_warnings
+ WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ EOF
+         return 1
+     fi
+     f_tcall=`nm genmake_tcomp.o 2>/dev/null | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+     RETVAL=$?
+     if test "x$RETVAL" != x0 ; then
+         FC_NAMEMANGLE=$default_nm
+         cat <<EOF>> genmake_warnings
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ EOF
+         return 1
+     fi
+     c_a=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+     f_a=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+     c_b=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+     f_b=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+     nmangle="X"
+     if test "x$c_a" != "x$f_a" ; then
+         comm="echo x$f_a | sed -e 's|x$c_a||'"
+         a=`eval $comm`
+         nmangle="$a ## $nmangle"
+     fi
+     if test "x$c_b" != "x$f_b" ; then
+         comm="echo x$f_b | sed -e 's|x$c_b||'"
+         b=`eval $comm`
+         nmangle="$nmangle ## $b"
+     fi
+     FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmangle"
+     #  cleanup the testing files
+     rm -f genmake_tcomp.* genmake_test.*
+ }
+ check_HAVE_CLOC()  {
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <assert.h>
+ #include <sys/time.h>
+ void FC_NAMEMANGLE(cloc) ( double *curtim )
+ {
+  struct timeval tv1;
+  gettimeofday(&tv1 , (void *)NULL );
+  *curtim =  (double)((tv1.tv_usec)+(tv1.tv_sec)*1.E6);
+  *curtim = *curtim/1.E6;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       REAL*8 wtime
+       external cloc
+       call cloc(wtime)
+       print *," HELLO WORLD", wtime
+       end
+ EOF
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_F=$?
+     test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_CLOC=t
+         DEFINES="$DEFINES -DHAVE_CLOC"
+     fi
+     rm -f genmake_tc*
+ }
+ check_HAVE_SIGREG()  {
+     if test ! "x$HAVE_SIGREG" = x ; then
+         return
+     fi
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include <signal.h>
+ #include <errno.h>
+ #include <ucontext.h>
+ int * ip;
+ static void killhandler(
+     unsigned int sn, siginfo_t  si, struct ucontext *sc )
+ {
+     *ip = *ip + 1;
+     return;
+ }
+ void FC_NAMEMANGLE(sigreg) (int * aip)
+ {
+     struct sigaction s;
+     ip = aip;
+     s.sa_flags = SA_SIGINFO;
+     s.sa_sigaction = (void *)killhandler;
+     if(sigaction (SIGTERM,&s,(struct sigaction *)NULL)) {
+         printf("Sigaction returned error = %d\n", errno);
+         exit(0);
+     }
+     return;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       integer anint
+       common /iv/ anint
+       external sigreg
+       call sigreg(anint)
+       end
+ EOF
+     echo >> genmake_warnings
+     echo "running: check_HAVE_SIGREG()" >> genmake_warnings
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_SIGREG=t
+         DEFINES="$DEFINES -DHAVE_SIGREG"
+     fi
+     rm -f genmake_tc*
+ }
+ check_HAVE_SETRLSTK()  {
+     if test "x$HAVE_SETRLSTK" = xt ; then
+         DEFINES="$DEFINES -DHAVE_SETRLSTK"
+         return
+     fi
+     if test ! "x$HAVE_SETRLSTK" = x ; then
+         return
+     fi
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <sys/time.h>
+ #include <sys/resource.h>
+ #include <unistd.h>
+ void FC_NAMEMANGLE(setrlstk) ()
+ {
+     struct rlimit rls;
+     rls.rlim_cur = RLIM_INFINITY;
+     rls.rlim_max = RLIM_INFINITY;
+     setrlimit(RLIMIT_STACK, &rls);
+     return;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       external setrlstk
+       call setrlstk()
+       end
+ EOF
+     echo >> genmake_warnings
+     echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_SETRLSTK=t
+         DEFINES="$DEFINES -DHAVE_SETRLSTK"
+     fi
+     rm -f genmake_tc*
+ }
+ check_HAVE_STAT()  {
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <sys/stat.h>
+ #include <sys/types.h>
+ void FC_NAMEMANGLE(tfsize) ( int *nbyte )
+ {
+     char name[512];
+     struct stat astat;
+     name[0] = 'a'; name[1] = '\0';
+     if (! stat(name, &astat))
+         *nbyte = (int)(astat.st_size);
+     else
+         *nbyte = -1;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_tc.log 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       integer nbyte
+       call tfsize(nbyte)
+       print *," HELLO WORLD", nbyte
+       end
+ EOF
+     echo >> genmake_warnings
+     echo "running: check_HAVE_STAT()" >> genmake_warnings
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_tc.log 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_STAT=t
+         DEFINES="$DEFINES -DHAVE_STAT"
+     fi
+     rm -f genmake_tc*
+ }
+ check_netcdf_libs()  {
+     if test ! "x$SKIP_NETCDF_CHECK" = x ; then
+         return
+     fi
+     echo >> genmake_warnings
+     echo "running: check_netcdf_libs()" >> genmake_warnings
+     cat <<EOF > genmake_tnc.F
+       program fgennc
+ #include "netcdf.inc"
+ EOF
+     if test ! "x$MPI" = x ; then
+         echo '#include "mpif.h"' >> genmake_tnc.F
+     fi
+     cat <<EOF >> genmake_tnc.F
+       integer iret, ncid, xid
+       iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
+       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+       iret = nf_def_dim(ncid, 'X', 11, xid)
+       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+       iret = nf_close(ncid)
+       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+       end
+ EOF
+     echo "===  genmake_tnc.F  ===" > genmake_tnc.log
+     cat genmake_tnc.F >> genmake_tnc.log
+     echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
+     RET_CPP=f
+     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
+     echo "$COMM" >> genmake_tnc.log
+     eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
+     if test "x$RET_CPP" = xf ; then
+         echo "  WARNING: CPP failed to pre-process the netcdf test." \
+             >> genmake_tnc.log
+         echo "    Please check that \$INCLUDES is properly set." \
+             >> genmake_tnc.log
+     fi
+     echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
+     echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc.o $LIBS" >> genmake_tnc.log
+     $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
+         &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+     RET_COMPILE=$?
+     cat genmake_tnc.log >> genmake_warnings
+     #EH3  Remove test program execution for machines that either disallow
+     #EH3  execution or cannot support it (eg. cross-compilers)
+     #EH3
+     #EH3 test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+     #EH3 RETVAL=$?
+     #EH3 if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+     if test "x$RET_COMPILE" = x0 ; then
+         HAVE_NETCDF=t
+     else
+         # try again with "-lnetcdf" added to the libs
+         echo "try again with added '-lnetcdf'" > genmake_tnc.log
+         echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
+         echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
+         echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+         cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
+             &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
+             &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
+         RET_COMPILE=$?
+         cat genmake_tnc.log >> genmake_warnings
+         if test "x$RET_COMPILE" = x0 ; then
+             LIBS="$LIBS -lnetcdf"
+             HAVE_NETCDF=t
+         else
+         # try again with "-lnetcdff" added to the libs
+             echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+             echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
+             echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
+             echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+             cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
+                 &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
+                 &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
+             RET_COMPILE=$?
+             cat genmake_tnc.log >> genmake_warnings
+             if test "x$RET_COMPILE" = x0 ; then
+                 LIBS="$LIBS -lnetcdff -lnetcdf"
+                 HAVE_NETCDF=t
+             fi
+         fi
+     fi
+     rm -f genmake_tnc*
+ }
+ ###############################################################################
+ #   Sequential part of script starts here
+ ###############################################################################
  #  Set defaults here
  COMMANDL="$0 $@"
-Line 289 
 PLATFORM=
+Line 1028 
 PLATFORM=
  LN=
  S64=
  KPP=
- FC=
+ #FC=
+ #CC=gcc
+ #CPP=
  LINK=
- DEFINES="-DWORDLENGTH=4"
+ DEFINES=
  PACKAGES=
  ENABLE=
  DISABLE=
- MAKEFILE=
+ # MAKEFILE=
- MAKEDEPEND=
+ # MAKEDEPEND=
  PDEPEND=
  DUMPSTATE=t
  PDEFAULT=
  OPTFILE=
- INCLUDES="-I."
+ INCLUDES="-I. $INCLUDES"
  FFLAGS=
  FOPTIM=
+ FEXTRAFLAGS=
+ USE_EXTENDED_SRC=
+ EXTENDED_SRC_FLAG=
  CFLAGS=
  KFLAGS1=
  KFLAGS2=
+ #LDADD=
  LIBS=
  KPPFILES=
  NOOPTFILES=
  NOOPTFLAGS=
+ MPI=
+ MPIPATH=
+ TS=
+ PAPIS=
+ PCLS=
+ FOOLAD=
+ PAPI=
+ PCL=
+ HPMT=
+ GSL=
+ DEVEL=
+ HAVE_TEST_L=
+ # DEFINES checked by test compilation or command-line
+ HAVE_SYSTEM=
+ HAVE_FDATE=
+ FC_NAMEMANGLE=
+ HAVE_CLOC=
+ # HAVE_SETRLSTK=
+ HAVE_STAT=
+ HAVE_NETCDF=
+ HAVE_ETIME=
+ IGNORE_TIME=
  MODS=
  TOOLSDIR=
  SOURCEDIRS=
  INCLUDEDIRS=
- STANDARDDIRS=
+ STANDARDDIRS="USE_THE_DEFAULT"
+ G2ARGS=
+ BASH=
  PWD=`pwd`
- MAKE=make
+ test "x$MAKE" = x  &&  MAKE=make
- AWK=awk
+ test "x$AWK" = x   &&  AWK=awk
- THISHOSTNAME=`hostname`
+ EMBED_SRC=
+ THISHOST=`hostname`
  THISCWD=`pwd`
  THISDATE=`date`
+ THISUSER=`echo $USER`
+ THISVER=
  MACHINE=`uname -a`
  EXECUTABLE=
  EXEHOOK=
-Line 333 
 IEEE=
+Line 1106 
 IEEE=
  if test "x$MITGCM_IEEE" != x ; then
      IEEE=$MITGCM_IEEE
  fi
+ FS=
+ FS90=
  AUTODIFF_PKG_USED=f
  AD_OPTFILE=
-Line 349 
 TAMC_EXTRA=
+Line 1124 
 TAMC_EXTRA=
  #  The following state can be set directly by command-line switches
- gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE NOOPT"
+ gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
- gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+ gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"
  #  The following state is not directly set by command-line switches
- gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
+ gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
- gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
+ gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
+ gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
  #  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_s10="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_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
- gm_s9="TAF_EXTRA TAMC_EXTRA"
+ 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
+ printf "  getting local config information:  "
-     if test -r $i/$gm_local ; then
+ if test -f $gm_local ; then
-         source $i/$gm_local
-         break
-     fi
- done
- echo -n "  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
      echo "none found"
  fi
- #  echo "$0::$1:$2:$3:$4:$5:$6:$7:"
+ #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
  #OPTIONS=
  #n=0
  #for i ; do
-Line 397 
 fi
+Line 1177 
 fi
  #done
  #parse_options
  ac_prev=
- for ac_option ; do
+ for ac_option in "$@" ; do
+     G2ARGS="$G2ARGS \"$ac_option\""
      # If the previous option needs an argument, assign it.
      if test -n "$ac_prev"; then
-Line 420 
 for ac_option ; do
+Line 1202 
 for ac_option ; do
          -optfile=* | --optfile=* | -of=* | --of=*)
              OPTFILE=$ac_optarg ;;
-         -adoptfile | --adoptfile | -ad | --ad)
+         -adoptfile | --adoptfile | -adof | --adof)
              ac_prev=AD_OPTFILE ;;
          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
              AD_OPTFILE=$ac_optarg ;;
-Line 440 
 for ac_option ; do
+Line 1222 
 for ac_option ; do
          -make=* | --make=* | -m=* | --m=*)
              MAKE=$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=$ac_optarg ;;
-         -platform | --platform | -pl | --pl)
+         -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
-             ac_prev=PLATFORM ;;
+             echo "ERROR: The platform option has been removed.  Please specify"
-         -platform=* | --platform=* | -pl=* | --pl=*)
+             echo "  the build options using the \"optfile\" mechanism."
-             PLATFORM=$ac_optarg ;;
+             echo
+             usage
+             ;;
          -rootdir | --rootdir | -rd | --rd)
              ac_prev=ROOTDIR ;;
-Line 475 
 for ac_option ; do
+Line 1269 
 for ac_option ; do
          -standarddirs=* | --standarddirs=*)
              STANDARDDIRS=$ac_optarg ;;
-         -noopt | --noopt)
-             ac_prev=NOOPT ;;
-         -noopt=* | --noopt=*)
-             NOOPT=$ac_optarg ;;
  #           -cpp | --cpp)
  #               ac_prev=cpp ;;
  #           -cpp=* | --cpp=*)
  #               CPP=$ac_optarg ;;
+         -cc | --cc)
+             ac_prev=CC ;;
+         -cc=* | --cc=*)
+             CC=$ac_optarg ;;
          -fortran | --fortran | -fc | --fc)
              ac_prev=FC ;;
          -fc=* | --fc=*)
              FC=$ac_optarg ;;
+         -fs | --fs)
+             ac_prev=FS ;;
+         -fs=* | --fs=*)
+             FS=$ac_optarg ;;
+         -fs90 | --fs90)
+             ac_prev=FS90 ;;
+         -fs90=* | --fs90=*)
+             FS90=$ac_optarg ;;
          -ieee | --ieee)
              IEEE=true ;;
          -noieee | --noieee)
              IEEE= ;;
+         -ts | --ts)
+             TS=true ;;
+         -papis | --papis)
+             PAPIS=true ;;
+         -pcls | --pcls)
+             PCLS=true ;;
+         -foolad | --foolad)
+             FOOLAD=true ;;
+         -papi | --papi)
+             PAPI=true ;;
+         -pcl | --pcl)
+             PCL=true ;;
+         -hpmt | --hpmt)
+             HPMT=true ;;
+         -gsl | --gsl)
+             GSL=true ;;
+         -devel | --devel)
+             DEVEL=true ;;
          -mpi | --mpi)
              MPI=true ;;
-         -nompi | --nompi)
+         -mpi=* | --mpi=*)
-             MPI= ;;
+             MPIPATH=$ac_optarg
+             MPI=true ;;
-         -jam | --jam)
+ #       -jam | --jam)
-             JAM=1 ;;
+ #           JAM=1 ;;
-         -nojam | --nojam)
+ #       -nojam | --nojam)
-             JAM=0 ;;
+ #           JAM=0 ;;
          -ds | --ds)
              DUMPSTATE=t ;;
-Line 517 
 for ac_option ; do
+Line 1343 
 for ac_option ; do
              ac_prev=TAMC_EXTRA ;;
          -tamc_extra=* | --tamc_extra=*)
              TAMC_EXTRA=$ac_optarg ;;
+         -ignoretime | -ignore_time | --ignoretime | --ignore_time)
+             IGNORE_TIME="-DIGNORE_TIME" ;;
+         -es | --es | -embed-source | --embed-source)
+             EMBED_SRC=t ;;
          -*)
              echo "Error: unrecognized option: "$ac_option
-Line 532 
 for ac_option ; do
+Line 1364 
 for ac_option ; do
  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 "  file.  This file format is no longer supported.  For directions on"
-     echo
+     echo "  how to setup and use the new \"genmake2\" script, please see:"
      echo "    http://mitgcm.org/devel_HOWTO/"
-     echo
+     echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
-     echo "  for directions on how to setup and use the new \"genmake2\" input"
+     echo "WARNING: ignore \"./.genmakerc\" and continue."
-     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
-     if test "${PWD##/*/}" = "bin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then
+     tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
+     if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
          ROOTDIR=".."
      else
          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
                  ROOTDIR=$d
-                 echo -n "Warning:  ROOTDIR was not specified but there appears to be"
+                 printf "Warning:  ROOTDIR was not specified but there appears to be"
                  echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
                  break
              fi
-Line 569 
 if test ! -d ${ROOTDIR} ; then
+Line 1403 
 if test ! -d ${ROOTDIR} ; then
      exit 1
  fi
+ #  Find the MITgcm ${THISVER}
+ version_file="${ROOTDIR}/doc/tag-index"
+ if test -f $version_file ; then
+     THISVER=`grep '^checkpoint' $version_file | head -1`
+ #-  remove ./BUILD_INFO.h file if older than version_file
+     if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
+         echo "  remove ./BUILD_INFO.h (older than ${version_file})"
+         rm -f ./BUILD_INFO.h
+     fi
+ fi
+ if test "x$MAKEFILE" = x ; then
+     MAKEFILE="Makefile"
+ fi
  echo "  getting OPTFILE information:  "
  if test "x${OPTFILE}" = x ; then
      if test "x$MITGCM_OF" = x ; then
-Line 582 
 fi
+Line 1431 
 fi
  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
-Line 609 
 fi
+Line 1458 
 fi
  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
-Line 625 
 if test "x${AD_OPTFILE}" != xNONE ; then
+Line 1474 
 if test "x${AD_OPTFILE}" != xNONE ; then
      fi
  fi
- #  Check that FC, LINK, CPP, and S64 are defined.  If not, complain
+ #====================================================================
- #  and abort!
+ #  Set default values if not set by the optfile
+ #
+ #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
+ #  either set defaults or complain and abort!
+ if test ! "x$BASH" = x ; then
+     # add a trailing space so that it works within the Makefile syntax (see below)
+     BASH="$BASH "
+ fi
  if test "x$FC" = x ; then
      cat <<EOF 1>&2
-Line 635 
 Error: no Fortran compiler: please speci
+Line 1491 
 Error: no Fortran compiler: please speci
 ) the "-fc=XXX" command-line option
 ) the "./genmake_local" file
  EOF
      exit 1
+ fi
+ if test "x$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:
+) within the options file ("CPP=...") as specified by "-of=OPTFILE"
+) the "./genmake_local" file
+) 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$RETVAL" != x0 ; then
+     cat <<EOF 1>&2
+ Error: The command "ln -s" failed -- please specify a working soft-link
+   command in the optfile.
+ EOF
+     exit 1
+ fi
+ test -L genmake_tlink > /dev/null 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     HAVE_TEST_L=t
+ fi
+ rm -f genmake_test_ln genmake_tlink
+ #  Check for broken *.F/*.f handling and fix if possible
+ check_for_broken_Ff
+ if test ! "x$MPI" = x ; then
+       echo "  Turning on MPI cpp macros"
+       DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
+ fi
+ if test ! "x$TS" = x ; then
+       echo "  Turning on timing per timestep"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
+       else
+             DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
+       fi
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PAPIS" = x ; then
+       echo "  Turning on PAPI flop summary per timestep"
+       echo "  Please make sure PAPIINC, PAPILIB are defined"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
+       else
+             DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
+       fi
+       INCLUDES="$INCLUDES $PAPIINC"
+       LIBS="$LIBS $PAPILIB"
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PCLS" = x ; then
+       echo "  Turning on PCL counter summary per timestep"
+       echo "  Please make sure PCLINC, PCLLIB are defined"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
+       else
+             DEFINES="$DEFINES -DUSE_PCL_FLOPS"
+       fi
+       INCLUDES="$INCLUDES $PCLINC"
+       LIBS="$LIBS $PCLLIB"
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PAPI" = x ; then
+       if test ! "x$PAPIS" = x ; then
+           echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
+           echo "  Sticking with PAPI flop summary per timestep!"
+       else
+           echo "  Turning on performance analysis with PAPI"
+           echo "  Please make sure PAPIINC, PAPILIB are defined"
+           DEFINES="$DEFINES -DUSE_PAPI"
+           INCLUDES="$INCLUDES $PAPIINC"
+           LIBS="$LIBS $PAPILIB"
+       fi
+ fi
+ if test ! "x$PCL" = x ; then
+       if test ! "x$PCLS" = x ; then
+           echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
+           echo "  Sticking with PCL flop summary per timestep!"
+       else
+           echo "  Turning on performance analysis with PCL"
+           echo "  Please make sure PCLINC, PCLLIB are defined"
+           DEFINES="$DEFINES -DUSE_PCL"
+           INCLUDES="$INCLUDES $PCLINC"
+           LIBS="$LIBS $PCLLIB"
+       fi
+ fi
+ if test ! "x$HPMT" = x ; then
+       if test ! "x$PAPI" = x ; then
+           echo "  PAPI and the HPM Toolkit cannot co-exist!"
+           echo "  Sticking with PAPI!"
+       else if test ! "x$PCL" = x ; then
+           echo "  PCL and the HPM Toolkit cannot co-exist!"
+           echo "  Sticking with PCL!"
+       else
+           echo "  Turning on performance analysis with the HPM Toolkit"
+           echo "  Please make sure HPMTINC, HPMTLIB are defined"
+           DEFINES="$DEFINES -DUSE_LIBHPM"
+           INCLUDES="$INCLUDES $HPMTINC"
+           LIBS="$LIBS $HPMTLIB"
+       fi
+       fi
+ fi
+ if test ! "x$GSL" = x ; then
+       echo "  Turning on use of GSL to control floating point calculations"
+       echo "  Please make sure GSLINC, GSLLIB are defined"
+       DEFINES="$DEFINES -DUSE_GSL_IEEE"
+       INCLUDES="$INCLUDES $GSLINC"
+       LIBS="$LIBS $GSLLIB"
+ fi
+ #- if USE_EXTENDED_SRC is set, add EXTENDED_SRC_FLAG to FFLAGS :
+ if test ! "x$USE_EXTENDED_SRC" = x ; then
+       FFLAGS="$FFLAGS $EXTENDED_SRC_FLAG"
+       F90FIXEDFORMAT="$F90FIXEDFORMAT $EXTENDED_SRC_FLAG"
+ fi
+ printf "\n===  Checking system libraries  ===\n"
+ printf "  Do we have the system() command using $FC...  "
+ cat > genmake_tcomp.$FS <<EOF
+       program hello
+       call system('echo hi')
+       end
+ EOF
+ $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$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 $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     HAVE_FDATE=t
+     DEFINES="$DEFINES -DHAVE_FDATE"
+     echo "yes"
+ else
+     HAVE_FDATE=
+     echo "no"
+ fi
+ rm -f genmake_tcomp*
+ printf "  Do we have the etime() command using $FC...  "
+ cat > genmake_tcomp.$FS <<EOF
+       program hello
+       REAL*4 ACTUAL, TARRAY(2)
+       EXTERNAL ETIME
+       REAL*4 ETIME
+       actual = etime( tarray )
+       print *, tarray
+       end
+ EOF
+ $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     HAVE_ETIME=t
+     DEFINES="$DEFINES -DHAVE_ETIME"
+     echo "yes"
+ else
+     HAVE_ETIME=
+     echo "no"
  fi
- if test "x$LINK" = x ; then
+ rm -f genmake_tcomp*
-     LINK=$FC
+ printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+ check_HAVE_CLOC
+ if test "x$HAVE_CLOC" != x ; then
+     echo "yes"
+ else
+     echo "no"
+     if test "x$EMBED_SRC" = xt ; then
+         echo "    WARNING: you requested file embedding but it has"
+         echo "      been disabled since C code cannot be called"
+         EMBED_SRC=
+     fi
  fi
- if test "x$CPP" = x ; then
+ rm -f genmake_t*
-     CPP="cpp"
+ printf "  Can we unlimit the stack size using $FC...  "
+ check_HAVE_SETRLSTK
+ if test "x$HAVE_SETRLSTK" = xt ; then
+     echo "yes"
+ else
+     echo "no"
  fi
- echo "#define A a" | $CPP > test_cpp 2>&1
+ rm -f genmake_t*
- RETVAL=$?
- if test "x$RETVAL" != x0 ; then
-     cat <<EOF 1>&2
- Error: C pre-processor "$CPP" failed the test case: please specify using:
+ printf "  Can we register a signal handler using $FC...  "
+ check_HAVE_SIGREG
+ if test "x$HAVE_SIGREG" = xt ; then
+     echo "yes"
+ else
+     echo "no"
+ fi
+ rm -f genmake_t*
-) within the options file ("CPP=...") as specified by "-of=OPTFILE"
+ printf "  Can we use stat() through C calls...  "
-) the "./genmake_local" file
+ check_HAVE_STAT
+ if test "x$HAVE_STAT" != x ; then
+     echo "yes"
+ else
+     echo "no"
+ fi
+ rm -f genmake_t*
- EOF
+ printf "  Can we create NetCDF-enabled binaries...  "
-     exit 1
+ check_netcdf_libs
+ if test "x$HAVE_NETCDF" != x ; then
+     echo "yes"
  else
-     rm -f test_cpp
+     echo "no"
  fi
- if test "x$MAKEDEPEND" = x ; then
+ DEFINES="$DEFINES $IGNORE_TIME"
-     MAKEDEPEND=makedepend
+ if test "x$EMBED_SRC" = xt ; then
+     build_embed_encode
+ fi
+ if test "x$EMBED_SRC" = xt ; then
+     ENABLE="$ENABLE embed_files"
  fi
  printf "\n===  Setting defaults  ===\n"
- echo -n "  Adding MODS directories:  "
+ printf "  Adding MODS directories:  "
  for d in $MODS ; do
      if test ! -d $d ; then
          echo
          echo "Error: MODS directory \"$d\" not found!"
          exit 1
      else
-         echo -n " $d"
+         printf " $d"
          SOURCEDIRS="$SOURCEDIRS $d"
          INCLUDEDIRS="$INCLUDEDIRS $d"
      fi
  done
  echo
- if test "x$MAKEFILE" = x ; then
-     MAKEFILE="Makefile"
- fi
  if test "x${PLATFORM}" = x ; then
      PLATFORM=$p_PLATFORM
  fi
  if test "x${EXEDIR}" = x ; then
-     if test "${PWD##/*/}" = "bin" -a -d ../exe -a $ROOTDIR = .. ; then
+     tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
+     if test "x$tmp" = "xbin" -a -d ../exe -a $ROOTDIR = .. ; then
          EXEDIR=../exe
      else
          EXEDIR=.
-Line 700 
 if test "x${TOOLSDIR}" = x ; then
+Line 1810 
 if test "x${TOOLSDIR}" = x ; then
      TOOLSDIR="$ROOTDIR/tools"
  fi
  if test ! -d ${TOOLSDIR} ; then
-     echo "Error: the specified $TOOLSDIR (\"$TOOLSDIR\") does not exist!"
+     echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
      exit 1
  fi
  if test "x$S64" = x ; then
-     S64='$(TOOLSDIR)/set64bitConst.sh'
+     echo "3.0 _d 3" | ${TOOLSDIR}/set64bitConst.sh > /dev/null 2>&1
+     RETVAL=$?
+     if test "x${RETVAL}" = x0 ; then
+         S64='$(TOOLSDIR)/set64bitConst.sh'
+     else
+         echo "3.0 _d 3" | ${TOOLSDIR}/set64bitConst.csh > /dev/null 2>&1
+         RETVAL=$?
+         if test "x${RETVAL}" = x0 ; then
+             S64='$(TOOLSDIR)/set64bitConst.csh'
+         else
+             cat <<EOF
+ ERROR: neither of the two default scripts:
+     ${TOOLSDIR}/set64bitConst.sh
+     ${TOOLSDIR}/set64bitConst.csh
+   are working so please check paths or specify (with \$S64) a
+   working version of this script.
+ EOF
+             exit 1
+         fi
+     fi
  fi
+ THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSDIR':\$(TOOLSDIR):'`
  EXECUTABLE=${EXECUTABLE:-mitgcmuv}
-Line 714 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
+Line 1848 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
  #  they appear as regular source code
  if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
      echo "  Making source files in eesupp from templates"
-     $MAKE -C $ROOTDIR"/eesupp/src/" > make_eesupp.errors 2>&1
+     ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
      RETVAL=$?
      if test "x${RETVAL}" = x0 ; then
          rm -f make_eesupp.errors
      else
          echo "Error: problem encountered while building source files in eesupp:"
-         cat make_eesupp.errors
+         cat make_eesupp.errors 1>&2
          exit 1
      fi
  fi
+ #same for pkg/exch2 and pkg/regrid
+ for pdir in exch2 regrid ; do
+     if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
+         echo "  Making source files in pkg/${pdir} from templates"
+         ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
+         RETVAL=$?
+         if test "x${RETVAL}" = x0 ; then
+             rm -f make_${pdir}.errors
+         else
+             echo "Error: problem encountered while building source files in pkg/${pdir}:"
+             cat make_${pdir}.errors 1>&2
+             exit 1
+         fi
+     fi
+ done
  printf "\n===  Determining package settings  ===\n"
  if  test "x${PDEPEND}" = x ; then
      tmp=$ROOTDIR"/pkg/pkg_depend"
-Line 751 
 if test ! "x${RETVAL}" = x0 ; then
+Line 1901 
 if test ! "x${RETVAL}" = x0 ; then
      echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$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 $i"/packages.conf" ; then
-Line 770 
 if test "x${PDEFAULT}" = x ; then
+Line 1920 
 if test "x${PDEFAULT}" = x ; then
      PDEFAULT="$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
-Line 789 
 else
+Line 1938 
 else
              PACKAGES="$PACKAGES $i"
          done
          echo "    before group expansion packages are: $PACKAGES"
-         expand_pkg_groups
+         RET=1
+         while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
          echo "    after group expansion packages are:  $PACKAGES"
      fi
  fi
  echo "  applying DISABLE settings"
+ for i in $PACKAGES ; do
+     echo $i >> ./.tmp_pack
+ done
+ for i in `grep  "-" ./.tmp_pack` ; do
+     j=`echo $i | sed 's/[-]//'`
+     DISABLE="$DISABLE $j"
+ done
  pack=
  for p in $PACKAGES ; do
      addit="t"
-Line 811 
 PACKAGES="$pack"
+Line 1968 
 PACKAGES="$pack"
  echo "  applying ENABLE settings"
  echo "" > ./.tmp_pack
  PACKAGES="$PACKAGES $ENABLE"
+ # Test if each explicitly referenced package exists
  for i in $PACKAGES ; do
-     if test ! -d "$ROOTDIR/pkg/$i" ; then
+     j=`echo $i | sed 's/[-+]//'`
+     if test ! -d "$ROOTDIR/pkg/$j" ; then
          echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""
          exit 1
      fi
      echo $i >> ./.tmp_pack
  done
- pack=`cat ./.tmp_pack | sort | uniq`
- rm -f ./.tmp_pack
  PACKAGES=
- for i in $pack ; do
+ for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do
      PACKAGES="$PACKAGES $i"
  done
+ rm -f ./.tmp_pack
  echo "    packages are:  $PACKAGES"
+ #  Check for package MNC: if NetCDF is available, then build the MNC
+ #  template files ; otherwise, delete mnc from the list of packages.
+ echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     if test "x$HAVE_NETCDF" != xt ; then
+         cat <<EOF
+ *********************************************************************
+ WARNING: the "mnc" package was enabled but tests failed to compile
+   NetCDF applications.  Please check that:
+) NetCDF is correctly installed for this compiler and
+) the LIBS variable (within the "optfile") specifies the correct
+        NetCDF library to link against.
+   Due to this failure, the "mnc" package is now DISABLED.
+ *********************************************************************
+ EOF
+         PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`
+         DISABLE="$DISABLE mnc"
+     else
+         ( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
+         RETVAL=$?
+         if test "x${RETVAL}" = x0 ; then
+             rm -f make_mnc.errors
+         else
+             echo "Error: problem encountered while building source files in pkg/mnc:"
+             cat make_mnc.errors 1>&2
+             exit 1
+         fi
+     fi
+ fi
+ #  Check for package PROFILES: if NetCDF is not available,
+ #  then delete profiles from the list of available packages.
+ echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     if test "x$HAVE_NETCDF" != xt ; then
+         cat <<EOF
+ *********************************************************************
+ WARNING: the "profiles" package was enabled but tests failed to
+   compile NetCDF applications.  Please check that:
+) NetCDF is correctly installed for this compiler and
+) the LIBS variable (within the "optfile") specifies the correct
+        NetCDF library to link against.
+   Due to this failure, the "profiles" package is now DISABLED.
+ *********************************************************************
+ EOF
+         PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
+         DISABLE="$DISABLE profiles"
+     fi
+ fi
  echo "  applying package dependency rules"
  ck=
  while test "x$ck" != xtt ; do
      i=0
      # rtot=${#PNAME[@]}
      rtot=$nname
-     while test $i -lt $rtot ; do
+     while test $i -le $rtot ; do
          #  Is $pname in the current $PACKAGES list?
          #  pname=${PNAME[$i]}
-Line 866 
 while test "x$ck" != xtt ; do
+Line 2084 
 while test "x$ck" != xtt ; do
          #  Do we need to add $dname according to the dependency rules?
          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
+             #echo "   " $pname ": need to add :" $dname
              in_dis="f"
              for dis in $DISABLE ; do
                  if test "x$dis" = "x$dname" ; then
-Line 890 
 while test "x$ck" != xtt ; do
+Line 2109 
 while test "x$ck" != xtt ; do
              echo "  the dependency rules for \"$dname\""
              exit 1
          fi
-         i=$(( $i + 1 ))
+         i=`echo "$i + 1" | bc -l`
+         #i=$(( $i + 1 ))
      done
      ck=$ck"t"
  done
-Line 909 
 for i in $PACKAGES ; do
+Line 2129 
 for i in $PACKAGES ; do
      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.
- #ifndef PACKAGES_H
- #define PACKAGES_H
- C  Packages disabled by genmake:
- EOF
  #  The following UGLY HACK sets multiple "#undef"s and it needs to go
  #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h
  #  file would eventually be split up so that all package-related #define
  #  statements could be separated and handled only by genmake.
  names=`ls -1 "$ROOTDIR/pkg"`
  all_pack=
+ DISABLED_PACKAGES=
  for n in $names ; do
      if test -d "$ROOTDIR/pkg/$n" -a "x$n" != xCVS ; then
          has_pack="f"
-Line 958 
 for n in $names ; do
+Line 2148 
 for n in $names ; do
              fi
          done
          if test "x$has_pack" = xf ; then
-             undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
+             undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
-             echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
+             DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
- #           DEFINES="$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!!!
          fi
      fi
  done
- cat <<EOF >>$PACKAGES_DOT_H".tmp"
+ ENABLED_PACKAGES=
- C  Packages enabled by genmake:
- EOF
  for i in $PACKAGES ; do
-     def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`
+     def=`echo "ALLOW_$i" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
-     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" >> $PACKAGES_DOT_H".tmp"
+             ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
-             DEFINES="$DEFINES -DALLOW_AIM"
+             echo "Warning: ALLOW_AIM is set to enable aim_v23."
-             echo "Warning: ALLOW_AIM is set to enable aim_v23. This is REALLY ugly Jean-Michel :-)"
              ;;
      esac
  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
  done
- cat <<EOF >>$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 $STANDARDDIRS ; do
+ if test "x$STANDARDDIRS" != x ; then
-     adr="$ROOTDIR/$d/src"
+     for d in $STANDARDDIRS ; do
-     if test ! -d $adr ; then
+         adr="$ROOTDIR/$d/src"
-         echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+         if test ! -d $adr ; then
-         echo "  is correct and that you correctly specified the STANDARDDIRS option"
+             echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-         exit 1
+             echo "  is correct and that you correctly specified the STANDARDDIRS option"
-     else
+             exit 1
-         SOURCEDIRS="$SOURCEDIRS $adr"
+         else
-     fi
+             SOURCEDIRS="$SOURCEDIRS $adr"
-     adr="$ROOTDIR/$d/inc"
+         fi
-     if test ! -d $adr ; then
+         adr="$ROOTDIR/$d/inc"
-         echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+         if test ! -d $adr ; then
-         echo "  is correct and that you correctly specified the STANDARDDIRS option"
+             echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-         exit 1
+             echo "  is correct and that you correctly specified the STANDARDDIRS option"
-     else
+             exit 1
-         INCLUDEDIRS="$INCLUDEDIRS $adr"
+         else
-     fi
+             INCLUDEDIRS="$INCLUDEDIRS $adr"
- done
+         fi
+     done
+ fi
- echo "  Searching for CPP_OPTIONS.h in order to warn about the presence"
+ echo "  Searching for *OPTIONS.h files in order to warn about the presence"
- echo "    of \"#define ALLOW_PKGNAME\"-type statements:"
+ 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 $try -a "x$CPP_OPTIONS" = x ; then
-     if test -f $try -a -r $try ; then
          echo "    found CPP_OPTIONS=\"$try\""
          CPP_OPTIONS="$try"
-         break
+         # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
+         for n in $names ; do
+             test_for_package_in_cpp_options $CPP_OPTIONS $n
+         done
+     fi
+     try="$i/CPP_EEOPTIONS.h"
+     if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
+         echo "    found CPP_EEOPTIONS=\"$try\""
+         # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
+ #**** not yet enabled ****
+ #        test_for_mpi_in_cpp_eeoptions $try
+ #**** not yet enabled ****
+         CPP_EEOPTIONS="$try"
      fi
  done
  if test "x$CPP_OPTIONS" = x ; then
      echo "Error: can't find \"CPP_OPTIONS.h\" in the path list: $spaths"
      exit 1
  fi
- # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
- names=`ls -1 "$ROOTDIR/pkg"`
- for n in $names ; do
-     test_for_package_in_cpp_options $CPP_OPTIONS $n
- done
  #  Here, we build the list of files to be "run through" the adjoint
  #  compiler.
- if test -f ./ad_files ; then
+ if test -f ./adSrcFiles.tmp ; then
-     rm -f ./ad_files
+     rm -f ./adSrcFiles.tmp
  fi
  echo "  Creating the list of files for the adjoint compiler."
  for i in $SOURCEDIRS ; do
      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
      for j in $list_files ; do
-         cat $i/$j >> ad_files
+         cat $i/$j >> adSrcFiles.tmp
      done
  done
+ if test ! "x"$FS = "x.f" ; then
- cat <<EOF > adjoint_sed
+     cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
- s/call adopen(/call adopen ( mythid,\\
+     mv -f adSrcFiles.tmp_f adSrcFiles.tmp
-      \&           /g
+ fi
- 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  ==="
  echo "  setting INCLUDES"
  for i in $INCLUDEDIRS ; do
-     if ! test -d $i ; then
+     if test ! -d $i ; then
- #       INCLUDES="$INCLUDES -I$i"
- #   else
          echo "Warning: can't find INCLUDEDIRS=\"$i\""
      fi
  done
+ if test ! "x$DIVA" = x ; then
+     echo "  Creating the pseudo-MPI include directory"
+     INCLUDES="-I./mpi_headers $INCLUDES"
+     rm -rf ./mpi_headers
+     mkdir -p ./mpi_headers
+     if test "x$MPIINCLUDEDIR" = x ; then
+         if test "x$MPIHOME" = x ; then
+             MPIHOME='/usr'
+         fi
+         MPIINCLUDEDIR='$MPIHOME/include'
+     fi
+     if test -r $MPIINCLUDEDIR/mpif.h ; then
+         for i in $MPI_HEADER_FILES; do
+             cp -p $MPIINCLUDEDIR/$i ./mpi_headers
+         done
+         perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
+     else
+         echo " We cannot create a copy of mpif.h!"
+ #       exit -1
+     fi
+ fi
  echo "  Determining the list of source and include files"
  rm -rf .links.tmp
  mkdir .links.tmp
+ touch .links.tmp/foo
+ if test ! -r ".links.tmp/foo" ; then
+     echo
+     echo "ERROR : something is wrong with your directory permissions or"
+     echo "   your user file-creation mask (\"umask\") since creating a"
+     echo "   sub-dir, touch-ing a file within it, and then reading it is"
+     echo "   not working.  Please try setting your umask to something"
+     echo "   sane such as:"
+     echo
+     echo "      umask 0002"
+     echo
+     echo "   and please verify that you have the proper permissions for"
+     echo "   creating sub-directories and then reading files created"
+     echo "   within them."
+     echo
+     exit 1
+ fi
+ rm -f .links.tmp/foo
+ if test "x$OPENAD" != x ; then
+     OAD_DONT_COMPILE="/dev/null"
+     OAD_DONT_TRANSFORM="/dev/null"
+     OAD_KEEP_ORIGINAL="/dev/null"
+     OAD_CB2M_FILES="/dev/null"
+     echo "  looking for dontCompile file:  "
+     for i in "." $MODS ; do
+         if test -r $i"/dontCompile" ; then
+             OAD_DONT_COMPILE=$i"/dontCompile"
+             echo "     found $OAD_DONT_COMPILE"
+             break
+         fi
+     done
+     echo "  looking for dontTransform file:  "
+     for i in "." $MODS ; do
+         if test -r $i"/dontTransform" ; then
+             OAD_DONT_TRANSFORM=$i"/dontTransform"
+             echo "     found $OAD_DONT_TRANSFORM"
+             break
+         fi
+     done
+     echo "  looking for keepOriginal file:  "
+     for i in "." $MODS ; do
+         if test -r $i"/keepOriginal" ; then
+             OAD_KEEP_ORIGINAL=$i"/keepOriginal"
+             echo "     found $OAD_KEEP_ORIGINAL"
+             break
+         fi
+     done
+     echo "  looking for cb2mFiles:  "
+     for i in "." $MODS ; do
+         if test -r $i"/cb2mFiles" ; then
+             OAD_CB2M_FILES=$i"/cb2mFiles"
+             echo "     found $OAD_CB2M_FILES"
+             break
+         fi
+     done
+     echo "   OpenAD exceptions:  "
+ fi
  echo "# This section creates symbolic links" > srclinks.tmp
  echo "" >> srclinks.tmp
- echo -n 'SRCFILES = '    > srclist.inc
+ printf 'F77_SRC_FILES = ' > F77srclist.tmp
- echo -n 'CSRCFILES = '   > csrclist.inc
+ printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
- echo -n 'F90SRCFILES = ' > f90srclist.inc
+ printf 'C_SRC_FILES = '   > csrclist.tmp
- echo -n 'HEADERFILES = ' > hlist.inc
+ printf 'F90_SRC_FILES = ' > F90srclist.tmp
- echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+ printf 'H_SRC_FILES = '   > hsrclist.tmp
+ printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
  for d in $alldirs ; do
      deplist=
      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
+     if test "x$OPENAD" != x ; then
+         sfiles=`( echo $sfiles | grep -v _cb2m\. )`
+     fi
      for sf in $sfiles ; do
          if test ! -r ".links.tmp/$sf" ; then
              if test -f "$d/$sf" ; then
-                 extn=`echo $sf | $AWK -F '.' '{print $NF}'`
+                 ignore_f=f
-                 touch .links.tmp/$sf
+                 case $d/$sf in
-                 deplist="$deplist $sf"
+                   ./$PACKAGES_DOT_H)
-                 case $extn in
+                         ignore_f=t
-                     F)
+                         ;;
-                         echo    " \\"  >> srclist.inc
+                   ./AD_CONFIG.h)
-                         echo -n " $sf" >> srclist.inc
+                         ignore_f=t
+                         ;;
+                   ./FC_NAMEMANGLE.h)
+                         ignore_f=t
+                         ;;
+                   ./BUILD_INFO.h)
+                         ignore_f=t
+                         ;;
+                   ./EMBEDDED_FILES.h)
+                         ignore_f=t
+                         ;;
+                   *)
+                         #  For the local directory *ONLY*,
+                         #  ignore all soft-links
+                         if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
+                             ignore_f=t
+                         else
+                             touch .links.tmp/$sf
+                             deplist="$deplist $sf"
+                         fi
+                         ;;
+                 esac
+                 if test "x$ignore_f" = xf ; then
+                     extn=`echo $sf | $AWK -F. '{print $NF}'`
+                     case $extn in
+                       F)
+                         echo    " \\"  >> F77srclist.tmp
+                         printf " $sf" >> F77srclist.tmp
+                         if test "x$OPENAD" != x ; then
+                             basename=${sf%%.F}
+                             isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
+                             if test -z "$isAD" ; then
+                                 toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
+                                 if test -z "$toBeIgnored" ; then
+                                     echo    " \\"  >> nonADF77srclist.tmp
+                                     printf " $sf" >> nonADF77srclist.tmp
+                                 else
+                                     echo "    not to be compiled   :  $sf"
+                                 fi
+                             else # file is initially listed as an AD file we want to exclude it
+                                  # or we want to retain the untransformed version
+                                 notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
+                                 untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
+                                 if test -n "$notToBeTransformed"; then
+                                     echo "    not to be transformed:  $sf"
+                                 fi
+                                 if test -n "$untransformedVersionToBeKept" ; then
+                                     echo "    original to be kept  :  $sf"
+                                 fi
+                                 if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
+                                     echo    " \\"  >> nonADF77srclist.tmp
+                                     printf " $sf" >> nonADF77srclist.tmp
+                                 fi
+                             fi
+                         fi
                          ;;
                      F90)
-                         echo    " \\"  >> f90srclist.inc
+                         echo    " \\"  >> F90srclist.tmp
-                         echo -n " $sf" >> f90srclist.inc
+                         printf " $sf" >> F90srclist.tmp
                          ;;
                      c)
-                         echo    " \\"  >> csrclist.inc
+                         echo    " \\"  >> csrclist.tmp
-                         echo -n " $sf" >> csrclist.inc
+                         printf " $sf" >> csrclist.tmp
                          ;;
                      h)
-                         echo    " \\"  >> hlist.inc
+                         echo    " \\"  >> hsrclist.tmp
-                         echo -n " $sf" >> hlist.inc
+                         printf " $sf" >> hsrclist.tmp
                          ;;
                      flow)
-                         echo    " \\"  >> ad_flow_files.inc
+                         echo    " \\"  >> ad_flow_files.tmp
-                         echo -n " $sf" >> ad_flow_files.inc
+                         printf " $sf" >> ad_flow_files.tmp
                          ;;
-                 esac
+                    esac
+                 fi
              fi
          fi
      done
      if test "x$deplist" != x ; then
-         echo "" >> srclinks.tmp
+       if test "$d" != "." ; then
+         echo "" >> srclinks.tmp
          echo "#  These files are linked from $d" >> srclinks.tmp
          echo "$deplist :" >> srclinks.tmp
-         printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp
+ # We need to make sure that the link isn't already there.
+ # This may happen when make thinks that a header file has to be "remade"
+ # because a module it depends on has changed.  In this case we do nothing.
+         printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
+       fi
      fi
  done
  rm -rf .links.tmp
- echo "" >> srclist.inc
+ echo "" >> F77srclist.tmp
- echo "" >> csrclist.inc
+ echo "" >> nonADF77srclist.tmp
- echo "" >> f90srclist.inc
+ echo "" >> csrclist.tmp
- echo "" >> hlist.inc
+ echo "" >> F90srclist.tmp
- echo "" >> ad_flow_files.inc
+ echo "" >> hsrclist.tmp
+ echo "" >> ad_flow_files.tmp
- if test -e $MAKEFILE ; then
+ if test -f $MAKEFILE ; then
      mv -f $MAKEFILE "$MAKEFILE.bak"
  fi
  echo "  Writing makefile: $MAKEFILE"
-Line 1170 
 echo "#    $MACHINE" >> $MAKEFILE
+Line 2471 
 echo "#    $MACHINE" >> $MAKEFILE
  echo "# This makefile was generated automatically on" >> $MAKEFILE
  echo "#    $THISDATE" >> $MAKEFILE
  echo "# by the command:" >> $MAKEFILE
- echo "#    $0 $@" >> $MAKEFILE
+ echo "#    $0 $G2ARGS" >> $MAKEFILE
  echo "# executed by:" >> $MAKEFILE
- echo "#    $USER@${THISHOSTNAME}:${THISCWD}" >> $MAKEFILE
+ echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
  EXE_AD=$EXECUTABLE"_ad"
  EXE_FTL=$EXECUTABLE"_ftl"
  EXE_SVD=$EXECUTABLE"_svd"
  cat >>$MAKEFILE <<EOF
+ #
+ # OPTFILE="$OPTFILE"
  #
  # BUILDDIR     : Directory where object files are written
  # SOURCEDIRS   : Directories containing the source (.F) files
-Line 1212 
 EXE_AD      = ${EXE_AD}
+Line 2515 
 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 = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h
  EOF
- #  Note: figure out some way to add Hyades JAM libraries here
+ if test "x$EMBED_SRC" = xt ; then
+     echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
+ else
+     echo "EMBEDDED_FILES = " >>$MAKEFILE
+ fi
+ #  Note: figure out some way to add Hyades JAM libraries here
  cat >>$MAKEFILE <<EOF
  # Unix ln (link)
  LN = ${LN}
-Line 1229 
 KPP = ${KPP}
+Line 2542 
 KPP = ${KPP}
  FC = ${FC}
  # Fortran compiler
  F90C = ${F90C}
+ # C compiler
+ CC = ${CC}
  # Link editor
- LINK = ${LINK}
+ LINK = ${LINK} ${LDADD}
  # Defines for CPP
  DEFINES = ${DEFINES}
-Line 1240 
 INCLUDES = ${INCLUDES}
+Line 2555 
 INCLUDES = ${INCLUDES}
  KFLAGS1 = ${KFLAGS1}
  KFLAGS2 = ${KFLAGS2}
  # Optim./debug for FC
- FFLAGS = ${FFLAGS}
+ FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
  FOPTIM = ${FOPTIM}
  # Optim./debug for FC
  F90FLAGS = ${F90FLAGS}
  F90OPTIM = ${F90OPTIM}
+ F90FIXEDFORMAT = ${F90FIXEDFORMAT}
  # Flags for CC
  CFLAGS = ${CFLAGS}
  # Files that should not be optimized
  NOOPTFILES = ${NOOPTFILES}
  NOOPTFLAGS = ${NOOPTFLAGS}
  # Flags and libraries needed for linking
- LIBS = ${LIBS} \$(XLIBS)
+ LIBS = ${LIBS}
  # Name of the Mekfile
  MAKEFILE=${MAKEFILE}
  EOF
- cat srclist.inc       >> $MAKEFILE
+ cat F77srclist.tmp      >> $MAKEFILE
- cat csrclist.inc      >> $MAKEFILE
+ cat nonADF77srclist.tmp >> $MAKEFILE
- cat f90srclist.inc    >> $MAKEFILE
+ cat csrclist.tmp        >> $MAKEFILE
- cat hlist.inc         >> $MAKEFILE
+ cat F90srclist.tmp      >> $MAKEFILE
- cat ad_flow_files.inc >> $MAKEFILE
+ cat hsrclist.tmp        >> $MAKEFILE
- echo               >> $MAKEFILE
+ cat ad_flow_files.tmp   >> $MAKEFILE
- echo 'F77FILES =  $(SRCFILES:.F=.f)'                                           >> $MAKEFILE
- echo 'F90FILES =  $(F90SRCFILES:.F90=.f90)'                                    >> $MAKEFILE
- echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
- rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc
+ rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
- rm -f ad_flow_files.inc
- cat >>$MAKEFILE <<EOF
+ echo >> $MAKEFILE
- .SUFFIXES:
+ # add definitions for preprocessed sources
- .SUFFIXES: .o .f .p .F .c .F90 .f90
+ # and note that not all systems allow case sensitive extensions
+ # hence the $FS and $FS90 here.
+ # for fixed format f90 files we use ff90 or FF90 resp
+ # but these are not expected to be the original source files
+ echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
+ echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
+ echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
+ echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
+ echo >> $MAKEFILE
+ echo '.SUFFIXES:' >> $MAKEFILE
+ echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
+ cat >>$MAKEFILE <<EOF
  all: \$(EXECUTABLE)
- \$(EXECUTABLE): \$(OBJFILES)
+ \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
+         @echo Creating \$@ ...
          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
  depend:
          @make links
-         \$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
+         \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
-         ${TOOLSDIR}/f90mkdepend >> \$(MAKEFILE)
+         \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+         -rm -f makedepend.out
- links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+ lib: libmitgcmuv.a
- small_f: \$(F77FILES) \$(F90FILES)
+ libmitgcmuv.a: \$(OBJFILES)
+         ar rcv libmitgcmuv.a \$(OBJFILES)
+         ar d   libmitgcmuv.a main.o
+ links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
+ small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
  output.txt: \$(EXECUTABLE)
          @printf 'running ... '
          @\$(EXECUTABLE) > \$@
  clean:
-         -cat AD_CONFIG.template > AD_CONFIG.h
+         -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
-         -rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl}
+         -rm -rf *.o
+         -rm -rf *.$FS *.flowdir
+         -rm -rf *.f$FS90 *_mod.h *_mod.F90 *.FF90 *.mod-whirl ad_input*
+         -rm -rf temp.sed
  Clean:
          @make clean
          @make cleanlinks
-         -rm -f Makefile.bak genmake_state genmake_*optfile make.log
+         -rm -f \$(SPECIAL_FILES)
+         -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log f90mkdepend.log *.bak
+         -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
  CLEAN:
          @make Clean
          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-         -rm -f \$(EXECUTABLE) output.txt
+         -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+         -rm -f *_MIT_CE_000.opt0000 costfunction*0000
+         -rm -rf mnc_test_*
  #eh3 Makefile: makefile
  makefile:
-         ${0} $@
+         $THIS_SCRIPT $G2ARGS
  cleanlinks:
          -find . -type l -exec rm {} \;
- # The normal chain of rules is (  .F - .f - .o  )
+ # Special targets (SPECIAL_FILES) which are created by make
- .F.f:
+ ${PACKAGES_DOT_H}:
+         @echo Creating \$@ ...
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+ AD_CONFIG.h:
+         @echo Creating \$@ ...
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+ FC_NAMEMANGLE.h:
+         @echo Creating \$@ ...
+         echo "$FC_NAMEMANGLE" > \$@
+ BUILD_INFO.h:
+         @echo Creating \$@ ...
+ EOF
+ test ! "x$THISVER" = x  && echo "       -echo \"#define THISVER '$THISVER'\" > \$@"   >> $MAKEFILE
+ test ! "x$THISUSER" = x && echo "       -echo \"#define THISUSER '$THISUSER'\" >> \$@" >> $MAKEFILE
+ test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
+ test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
+ if test "x$EMBED_SRC" = xt ; then
+     cat >>$MAKEFILE <<EOF
+ decode_files.o : EMBEDDED_FILES.h
+ ##  \$(F77_PP_SRC_FILES)
+ all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
+         @echo Creating \$@ ...
+         -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
+         -rm -f all_fF.tar.gz
+         -gzip all_fF.tar
+ EMBEDDED_FILES.h : all_fF.tar.gz
+         @echo Creating \$@ ...
+         -\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
+ EOF
+ fi
+ cat >>$MAKEFILE <<EOF
+ # The normal chain of rules is (  .F - .$FS - .o  )
+ ## This nullifies any default implicit rules concerning these two file types:
+ ## %.o : %.F
+ .F.$FS:
          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
- .f.o:
+ .$FS.o:
          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
- .F90.f90:
+ .F90.$FS90:
+         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+ .FF90.f$FS90:
          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
- .f90.o:
+ .$FS90.o:
          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
+ .f$FS90.o:
+         cp \$< \$(basename  \$<).f90
+         \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
  .c.o:
-         \$(CC) \$(CFLAGS) -c \$<
+         \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
+ .flow.flowdir:
+         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
- # Special exceptions that use the ( .F - .p - .f - .o ) rule-chain
+ # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
  .F.p:
          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
- .p.f:
+ .p.$FS:
          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
+ EOF
  #=========================================
  #===  Automatic Differentiation Rules  ===
+ #===  for TAMC/TAF  ======================
+ if test "x$OPENAD" == x ; then
+ cat >>$MAKEFILE <<EOF
  TAMC           = ${TAMC}
  TAF            = ${TAF}
-Line 1345 
 ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF
+Line 2744 
 ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF
  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
  for i in $ad_vars ; do
      name=$i
-     t1="t2=\$"`echo $i`
+     t1="t2=\$"`echo "$i"`
      eval $t1
      printf "%-20s = " $name >> $MAKEFILE
-     echo $t2 >> $MAKEFILE
+     echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
  done
  echo "  Add the source list for AD code generation"
  echo >> $MAKEFILE
- echo -n "AD_FILES = " >> $MAKEFILE
+ printf "AD_FILES = " >> $MAKEFILE
- AD_FILES=`cat ad_files`
+ AD_FILES=`cat adSrcFiles.tmp`
  for i in $AD_FILES ; do
      echo    " \\" >> $MAKEFILE
-     echo -n " $i" >> $MAKEFILE
+     printf " $i" >> $MAKEFILE
  done
  echo >> $MAKEFILE
- rm -f ad_files
+ rm -f adSrcFiles.tmp
  cat >>$MAKEFILE <<EOF
  # ... AD ...
- adall: ad_taf
+ adall: \$(EXE_AD)
- adtaf: ad_taf_output.f
+ adtaf: ad_taf_output.$FS
- adtamc: ad_tamc_output.f
+ adtamc: ad_tamc_output.$FS
- ad_input_code.f: \$(SRCFILES) \$(HEADERFILES)
+ ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
-         @make \$(F77FILES)
+         -rm -f ad_config.template
-         @make \$(AD_FLOW_FILES)
+         @make \$(F77_PP_SRC_FILES)
-         cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
+         @make \$(FLOFILES)
+         cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
- ad_taf_output.f: ad_input_code.f
-         \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
+ ad_taf_output.$FS: ad_input_code.$FS
-         cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+         \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
+         ls -l ad_input_code_ad.$FS
- ad_taf: ad_taf_output.o \$(OBJFILES)
+         cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
-         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
+ adtafonly:
- ad_tamc_output.f: ad_input_code.f
+         \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
-         \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f
+         ls -l ad_input_code_ad.$FS
-         cat ad_input_code_ad.f | sed -f adjoint_sed > ad_tamc_output.f
+         cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
+ \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+         \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
+ ad_tamc_output.$FS: ad_input_code.$FS
+         \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
+         cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
  ad_tamc: ad_tamc_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
+ adonlyfwd:
+         patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
+ adtrick:
+         patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
  # ... FTL ...
  ftlall: ftl_taf
- ftltaf: ftl_taf_output.f
+ ftltaf: ftl_taf_output.$FS
- ftltamc: ftl_tamc_output.f
+ ftltamc: ftl_tamc_output.$FS
- ftl_input_code.f: \$(SRCFILES)
+ ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
-         @make \$(F77FILES)
+         -rm -f ftl_config.template
+         @make \$(F77_PP_SRC_FILES)
          @make \$(AD_FLOW_FILES)
-         cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
+         cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
- ftl_taf_output.f: ftl_input_code.f
+ ftl_taf_output.$FS: ftl_input_code.$FS
-         \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
+         \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
-         cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_taf_output.f
+         ls -l ftl_input_code_ftl.$FS
+         cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+ ftltafonly:
+         \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
+         ls -l ftl_input_code_ftl.$FS
+         cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
  ftl_taf: ftl_taf_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
- ftl_tamc_output.f: ftl_input_code.f
+ ftl_tamc_output.$FS: ftl_input_code.$FS
-         \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.f
+         \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
-         cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_tamc_output.f
+         cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
  # ... SVD ...
- svd: svd_taf
+ svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
- svd_taf_f: svd_taf_output.f
+         @echo "--->>> Only ran TAF to generate SVD code!    <<<---"
+         @echo "--->>> Do make svdall afterwards to compile. <<<---"
+ svdall: svd_touch svd_taf
+ svd_taf: \$(OBJFILES)
+         \$(LINK) -o mitgcmuv_svd \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o ftl_taf_output.o \$(LIBS)
+         @echo "--->>> Only COMPILE svd code! <<<---"
+         @echo "--->>> Assumes you previously <<<---"
+         @echo "--->>> did make svdtaf        <<<---"
+ svd_touch:
+         @echo "--->>> Only COMPILE svd code! <<<---"
+         @echo "--->>> Assumes you previously <<<---"
+         @echo "--->>> did make svdtaf        <<<---"
+         touch ad_taf_output.$FS ftl_taf_output.$FS
+         \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
+         \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
+         cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+         -rm -f ftl_config.template
- svd_input_code.f: \$(SRCFILES)
+ EOF
-         cmp svd_config.template AD_CONFIG.h || cat svd_config.template > AD_CONFIG.h
-         @make \$(F77FILES)
-         @make \$(AD_FLOW_FILES)
-         cat \$(AD_FLOW_FILES) \$(AD_FILES) > svd_input_code.f
- svd_taf_output.f: svd_input_code.f
+ fi
-         \$(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)
+ #===  for OpenAD  ========================
-         \$(LINK) -o ${EXE_SVD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) svd_taf_output.o \$(LIBS)
+ if test "x$OPENAD" != x ; then
- #=========================================
+ # ============ begin OpenAD specific section ==============
+ cat >>$MAKEFILE <<EOF
+ # all the source files linked from the various locations:
+ ALL_LINKED_FILES= \
+ \$(F77_SRC_FILES) \
+ \$(C_SRC_FILES) \
+ \$(H_SRC_FILES) \
+ \$(F90_SRC_FILES) \
+ \$(SPECIAL_FILES)
+ ifndef OPENADROOT
+   \$(error "Error:  environment variable OPENADROOT not defined!")
+ endif
+ ifndef XAIFSCHEMAROOT
+   \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
+ endif
+ ifndef XAIFBOOSTERROOT
+   \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
+ endif
+ EOF
+ echo "  Add the source list for common block to module conversion "
+ echo >> $MAKEFILE
+ printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
+ for i in `cat ${OAD_CB2M_FILES}` ; do
+   echo    " \\" >> $MAKEFILE
+   printf " $i" >> $MAKEFILE
+ done
+ echo >> $MAKEFILE
+ echo "  Add the source list for AD code generation"
+ echo >> $MAKEFILE
+ printf "AD_FILES = " >> $MAKEFILE
+ for i in `cat ${OAD_CB2M_FILES}` ; do
+   echo    " \\" >> $MAKEFILE
+   printf " ${i}_mod.f$FS90" >> $MAKEFILE
+ done
+ AD_FILES=`cat adSrcFiles.tmp`
+ for i in $AD_FILES ; do
+   basename=${i%%.f}
+   toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
+   if test -z "$toBeIgnored" ; then
+     echo    " \\" >> $MAKEFILE
+     printf " $i" >> $MAKEFILE
+   fi
+ done
+ echo >> $MAKEFILE
+ rm -f adSrcFiles.tmp
+ cat >>$MAKEFILE <<EOF
+ adAll: \$(EXE_AD)
+ .PHONY: adAll
+ CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
+ .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
+ .PHONY: adDepend
+ adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
+         \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+         \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+         -rm -f makedepend.out
+ OPENAD_SUPPORT_F90_SRC_FILES = \
+ w2f__types.F90 \
+ OAD_active.F90 \
+ OAD_cp.F90 \
+ OAD_rev.F90 \
+ OAD_tape.F90
+ OPENAD_SUPPORT_C_SRC_FILES = \
+ iaddr.c \
+ timeRatio.c
+ f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
+         cat \$^ > \$@
+ f95_test.f90: all_mods.xb.x2w.w2f.pp.f$FS90 \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90) ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+         cat \$^ > \$@
+ f95_test.out: f95_test_mods.f90 f95_test.f90
+         f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
+         f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
+ AD_OBJ_FILES=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) all_mods.xb.x2w.w2f.pp.o  ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.o \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
+ \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(AD_OBJ_FILES)
+         @echo Creating \$@ ...
+         \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES) \$(LIBS)
+ # makefile debug rule
+ openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+ .PHONY: openad
+ # create the module files
+ %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
+         ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
+ # create the header files
+ %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
+         ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+ # change everybody else to use the new module files:
+ %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
+         ../OAD_support/cb2mUseModules.bash $< ${MPI}
+ # makefile debug rule
+ small_f: \$(CB2M_F90_PP_SRC_FILES)
+ .PHONY: small_f
+ ad_output.txt: \$(EXE_AD)
+         @printf 'linking data files ... '
+         \$(LN) -f ../input_ad/data* ../input_ad/eedata .
+         \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
+         @printf 'running ... '
+         @./\$(EXE_AD) > \$@
+ CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
+ ad_input_code.f$FS90: ../OAD_support/maxMinDefs.f \$(CB2M_AD_FILES)
+         cat \$^ > \$@
+ # strip all comments and blanks to reduce
+ # the file size in order to reduce perl's memory requirements
+ ad_input_code_sf.f$FS90 : ad_input_code.f$FS90
+         cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
+ # mfef90 preprocessing
+ # expand statement functions
+ # expose mfef90 specific substring handling
+ # add the w2f__types module
+ ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
+         ./mfef90 -r8 -z -F -N132 \$<
+         mv \$<.B \$(basename \$<).B
+         ./whirl2f -openad \$(basename \$<).B
+         cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
+ # canonicalizer
+ ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
+         ./preProcess.py -H -S \$< -o \$@
+ # F -> WHIRL
+ # note that the canonicalized version cuts off at col 72
+ # doing this also for string constants which is ok as long
+ # as we are in fixed mode and cut of exactly there.
+ # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
+ # characters respectively.
+ ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
+         ./mfef90 -r8 -z -F \$<
+         mv \$<.B \$@
+ # WHIRL -> XAIF
+ ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif
+         ./whirl2xaif -s -n --debug 1 -o \$@ \$<
+ # XAIF -> XAIF'
+ ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver
+         ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+ # XAIF' -> WHIRL'
+ ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
+         ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
+ # WHIRL' -> F'
+ ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
+         ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
+ # insert template directives
+ ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
+         ../OAD_support/insertTemplateDir.bash \$< \$@
+ # postprocess F'
+ ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl ../OAD_support/ad_inline.f \$(wildcard ../OAD_support/ad_template.*.f)
+         perl multi-pp.pl -inline=../OAD_support/ad_inline.f \$<
+         # the postprocessor still gets the name wrong
+         cat \$<.pp | sed 's/RETURN//' > \$@
+ # extract all transformed modules
+ all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+         cat \$< | sed -n '/MODULE /,/END MODULE/p' > \$@
+ # remove the transformed globals module from the
+ # transformed ad_input_code file
+ # and remove for now the duplicate variables
+ # and fix 2 data statements
+ ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+         cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' > \$@
+ # setup some links
+ %.xsd:
+         \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
+ mfef90:
+         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
+ # link the support files:
+ \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
+         \$(LN) ../OAD_support/\$@ .
+ whirl2xaif xaif2whirl:
+         \$(LN) \${OPENADFORTTK}/bin/\$@ .
+ %.pl:
+         \$(LN) \${OPENADFORTTK}/bin/\$@ .
+ preProcess.py:
+         \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
+ whirl2f whirl2f_be:
+         \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
+ oadDriver:
+         \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
+ # ============ end OpenAD specific section ==============
  EOF
+ fi
+ #=========================================
  if test "x$EXEHOOK" != x ; then
      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
  fi
-Line 1449 
 for i in $KPPFILES ; do
+Line 3106 
 for i in $KPPFILES ; do
      if test "x$RETVAL" != x0 ; then
          echo "Error: unable to add file \"$i\" to the exceptions list"
      fi
-     echo "$base.f: $base.p" >> $MAKEFILE
+     echo "$base.$FS: $base.p" >> $MAKEFILE
  done
  echo "  Making list of NOOPTFILES"
-Line 1459 
 for i in $NOOPTFILES ; do
+Line 3116 
 for i in $NOOPTFILES ; do
      if test "x$RETVAL" != x0 ; then
          echo "Error: unable to add file \"$i\" to the exceptions list"
      fi
-     echo "$base.o: $base.f" >> $MAKEFILE
+     echo "$base.o: $base.$FS" >> $MAKEFILE
      printf "\t\$(FC) \$(FFLAGS) \$(NOOPTFLAGS) -c \$<\n" >> $MAKEFILE
  done
-Line 1472 
 printf "\n\n# DO NOT DELETE\n" >> $MAKEF
+Line 3129 
 printf "\n\n# DO NOT DELETE\n" >> $MAKEF
  printf "\n===  Done  ===\n"
- #  Write the "template" files for the adjoint builds
+ # Create special header files
- cat >AD_CONFIG.template <<EOF
+ $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"
- C  WARNING: This file is automatically generated by genmake2 and
+ if test ! -f $PACKAGES_DOT_H ; then
- C    used by the Makefile rules.  Please DO NOT EDIT this file
+     mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
- C    unless you are CERTAIN that you know what you are doing.
+ else
+     cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H > /dev/null 2>&1
- #undef ALLOW_ADJOINT_RUN
+     RETVAL=$?
- #undef ALLOW_TANGENTLINEAR_RUN
+     if test "x$RETVAL" = x0 ; then
- #undef ALLOW_ECCO_OPTIMIZATION
+         rm -f $PACKAGES_DOT_H".tmp"
- EOF
+     else
- cat >ad_config.template <<EOF
+         mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
- C  WARNING: This file is automatically generated by genmake2 and
+         mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
- C    used by the Makefile rules.  Please DO NOT EDIT this file
+     fi
- C    unless you are CERTAIN that you know what you are doing.
+ fi
+ if test ! -f AD_CONFIG.h ; then
- #define ALLOW_ADJOINT_RUN
+     $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
- #undef ALLOW_TANGENTLINEAR_RUN
+ fi
- #undef ALLOW_ECCO_OPTIMIZATION
- EOF
- cat >ftl_config.template <<EOF
- C  WARNING: This file is automatically generated by genmake2 and
- C    used by the Makefile rules.  Please DO NOT EDIT this file
- C    unless you are CERTAIN that you know what you are doing.
- #undef ALLOW_ADJOINT_RUN
- #define ALLOW_TANGENTLINEAR_RUN
- #undef ALLOW_ECCO_OPTIMIZATION
- EOF
- cat >svd_config.template <<EOF
- C  WARNING: This file is automatically generated by genmake2 and
- C    used by the Makefile rules.  Please DO NOT EDIT this file
- C    unless you are CERTAIN that you know what you are doing.
- #undef ALLOW_ADJOINT_RUN
- #undef ALLOW_TANGENTLINEAR_RUN
- #undef ALLOW_ECCO_OPTIMIZATION
- EOF
- cp AD_CONFIG.template AD_CONFIG.h
  #  Write the "state" for future records
  if test "x$DUMPSTATE" != xf ; then
-     echo -n "" > genmake_state
+     printf "" > genmake_state
      for i in $gm_state ; do
          t1="t2=\$$i"
          eval $t1

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