/[MITgcm]/MITgcm/tools/genmake2

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-revision 1.195 by utke,
Wed Jun 17 22:47:49 2009 UTC
+revision 1.266 by jmc,
Wed May  7 19:36:22 2014 UTC
 Line 1
  #! /usr/bin/env bash
  #
  # $Header$
+ # $Name$
  #
  # Makefile generator for MITgcm UV codes
  #   created  by cnh 03/98
-Line 8
+Line 9
  #   modified by aja 01/00
  #   rewritten in bash by eh3 08/03
+ #  Explain usage
+ usage()  {
+ cat <<EOF
+ Usage: "$0" [OPTIONS]
+   where [OPTIONS] can be:
+     -help | --help | -h | --h
+           Print this help message and exit.
+     -oad | --oad
+           Generate a Makefile for an OpenAD built
+     -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
+       -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
+           Use "NAME" as the adoptfile.  By default, the file at
+           "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
+           "tools/adjoint_options/adjoint_default" will be used.
+     -nooptfile | --nooptfile
+       -optfile NAME | --optfile NAME | -of NAME | --of NAME
+       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
+           Use "NAME" as the optfile.  By default, an attempt will be
+           made to find an appropriate "standard" optfile in the
+           tools/build_options/ directory.
+     -pdepend NAME | --pdepend NAME
+       -pdepend=NAME | --pdepend=NAME
+           Get package dependency information from "NAME".
+     -pgroups NAME | --pgroups NAME
+       -pgroups=NAME | --pgroups=NAME
+           Get the package groups information from "NAME".
+     -bash NAME
+           Explicitly specify the Bourne or BASH shell to use
+     -make NAME | -m NAME
+       --make=NAME | -m=NAME
+           Use "NAME" for the MAKE program. The default is "make" but
+           many platforms, "gmake" is the preferred choice.
+     -makefile NAME | -mf NAME
+       --makefile=NAME | -mf=NAME
+           Call the makefile "NAME".  The default is "Makefile".
+     -makedepend NAME | -md NAME
+       --makedepend=NAME | -md=NAME
+           Use "NAME" for the MAKEDEPEND program.
+     -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
+       -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
+           Specify the location of the MITgcm ROOTDIR as "NAME".
+           By default, genamke will try to find the location by
+           looking in parent directories (up to the 5th parent).
+     -mods NAME | --mods NAME | -mo NAME | --mo NAME
+       -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
+           Here, "NAME" specifies a list of directories that are
+           used for additional source code.  Files found in the
+           "mods list" are given preference over files of the same
+           name found elsewhere.
+     -disable NAME | --disable NAME
+       -disable=NAME | --disable=NAME
+           Here "NAME" specifies a list of packages that we don't
+           want to use.  If this violates package dependencies,
+           genamke will exit with an error message.
+     -enable NAME | --enable NAME
+       -enable=NAME | --enable=NAME
+           Here "NAME" specifies a list of packages that we wish
+           to specifically enable.  If this violates package
+           dependencies, genamke will exit with an error message.
+     -standarddirs NAME | --standarddirs NAME
+       -standarddirs=NAME | --standarddirs=NAME
+           Here, "NAME" specifies a list of directories to be
+           used as the "standard" code.
+     -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
+       -fc=NAME | --fc=NAME
+           Use "NAME" as the fortran compiler.  By default, genmake
+           will search for a working compiler by trying a list of
+           "usual suspects" such as g77, f77, etc.
+     -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
+           Use "NAME" as the C compiler.  By default, genmake
+           will search for a working compiler by trying a list of
+           "usual suspects" such as gcc, c89, cc, etc.
+     -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
+           Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
+           *only* works if CPP_EEOPTIONS.h allows this.
+     -ignoretime | -ignore_time | --ignoretime | --ignore_time
+           Ignore all the "wall clock" routines entirely.  This will
+           not in any way hurt the model results -- it simply means
+           that the code that checks how long the model spends in
+           various routines will give junk values.
+     -ts | --ts
+           Produce timing information per timestep
+     -papis | --papis
+           Produce summary MFlop/s (and IPC) with PAPI per timestep
+     -pcls | --pcls
+           Produce summary MFlop/s etc. with PCL per timestep
+     -foolad | --foolad
+           Fool the AD code generator
+     -papi | --papi
+           Performance analysis with PAPI
+     -pcl | --pcl
+           Performance analysis with PCL
+     -hpmt | --hpmt
+           Performance analysis with the HPM Toolkit
+     -ieee | --ieee
+           use IEEE numerics.  Note that this option *only* works
+           if it is supported by the OPTFILE that is being used.
+     -devel | --devel
+           Add additional warning and debugging flags for development
+           (if supported by the OPTFILE); also switch to IEEE numerics.
+     -gsl | --gsl
+           Use GSL to control floating point rounding and precision
+     -mpi | --mpi
+           Include MPI header files and link to MPI libraries
+     -mpi=PATH | --mpi=PATH
+           Include MPI header files and link to MPI libraries using MPI_ROOT
+           set to PATH. i.e. Include files from \$PATH/include, link to libraries
+           from \$PATH/lib and use binaries from \$PATH/bin.
+     -omp | --omp
+           Activate OpenMP code + use Compiler option OMPFLAG
+     -omp=OMPFLAG | --omp=OMPFLAG
+           Activate OpenMP code + use Compiler option OMPFLAG
+     -es | --es | -embed-source | --embed-source
+           Embed a tarball containing the full source code
+           (including the Makefile, etc.) used to build the
+           executable [off by default]
+     -ds | --ds
+           Report genmake internal variables status (DUMPSTATE)
+           to file "genmake_state" (for debug purpose)
+   While it is most often a single word, the "NAME" variables specified
+   above can in many cases be a space-delimited string such as:
+     --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
+     -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
+     -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
+   which, depending upon your shell, may need to be single-quoted.
+   For more detailed genmake documentation, please see:
+     http://mitgcm.org/public/devel_HOWTO/
+ EOF
+     exit 1
+ }
  # Search for particular CPP #cmds associated with packages
  # usage: test_for_package_in_cpp_options CPP_file package_name
  test_for_package_in_cpp_options() {
      cpp_options=$1
      pkg=$2
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
+     test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
+     test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
-     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
+     test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
+     test_for_string_in_file $cpp_options "^ *# *undef *\<DISABLE_$pkg\>"
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
-     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
  }
  # Search for particular CPP #cmds associated with MPI
  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
  test_for_mpi_in_cpp_eeoptions() {
      cpp_options=$1
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*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
-Line 42 
 test_for_mpi_in_cpp_eeoptions() {
+Line 197 
 test_for_mpi_in_cpp_eeoptions() {
  test_for_string_in_file() {
      file=$1
      strng=$2
-     grep -i "$strng" $file > /dev/null 2>&1
+     grep "$strng" $file > /dev/null 2>&1
      RETVAL=$?
      if test "x${RETVAL}" = x0 ; then
          printf "Error: In $file there is an illegal line: "
          grep -i "$strng" $file
          exit 99
      fi
      return 0
-Line 56 
 test_for_string_in_file() {
+Line 211 
 test_for_string_in_file() {
  # the package list.
  expand_pkg_groups() {
      new_packages=
-     PKG_GROUPS=$ROOTDIR"/pkg/pkg_groups"
      if test -r $PKG_GROUPS ; then
-         cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp
+         cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > $TMP.p1
-         cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp
+         cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
          matched=0
          for i in $PACKAGES ; do
-             line=`grep "^ *$i" ./p2.tmp`
+             line=`grep "^ *$i" $TMP.p2`
              RETVAL=$?
              if test "x$RETVAL" = x0 ; then
                  matched=1
                  replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`
-                 echo "    replacing \"$i\" with: $replace"
+                 echo "    replacing \"$i\" with:$replace"
                  new_packages="$new_packages $replace"
              else
                  new_packages="$new_packages $i"
              fi
          done
          PACKAGES=$new_packages
-         rm -f ./p[1,2].tmp
+         rm -f $TMP.p[1,2]
          return $matched
      else
          echo "Warning: can't read package groups definition file: $PKG_GROUPS"
-Line 110 
 EOF
+Line 264 
 EOF
              check_for_broken_Ff
          else
              cat <<EOF 2>&1
  ERROR: Your file system cannot distinguish between *.F and *.f files
    (fails the "cp" test) and this program cannot find a suitable
    replacement extension.  Please try a different build environment or
    contact the <MITgcm-support@mitgcm.org> list for help.
  EOF
-Line 137 
 EOF
+Line 291 
 EOF
  .F.$tfs:
          $LN \$< \$@
  EOF
-     $MAKE "genmake_hello."$tfs > /dev/null 2>&1
+     $MAKE -f $MAKEFILE "genmake_hello."$tfs > /dev/null 2>&1
      RETVAL=$?
      if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
          if test "x$FS" = x ; then
-Line 145 
 EOF
+Line 299 
 EOF
              FS90='fr9'
              check_for_broken_Ff
          else
-             cat <<EOF 2>&1
+             echo "ERROR: test: '$MAKE -f $MAKEFILE genmake_hello.$tfs' Failed"
- ERROR: Your file system cannot distinguish between *.F and *.f files
+             echo "       see simple makefile: '$MAKEFILE' (left here)"
-   (fails the "make/ln" test) and this program cannot find a suitable
+             echo "  Please check (1) your '$MAKE' command, (2) your '$LN' command"
-   replacement extension.  Please try a different build environment or
+             echo "           and (3) the allowed sufix '.F' and '.$tfs' in makefile"
-   contact the <MITgcm-support@mitgcm.org> list for help.
+             echo "  or contact the <MITgcm-support@mitgcm.org> list for help."
+             echo ""
- EOF
              exit -1
              return
          fi
-Line 165 
 EOF
+Line 318 
 EOF
      return
  }
  look_for_makedepend()  {
      #  The "original" makedepend is part of the Imake system that is
-Line 176 
 look_for_makedepend()  {
+Line 328 
 look_for_makedepend()  {
      #
      #    1) a makedepend implementation shipped with the cyrus-imapd
      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
-     #
+     #    2) a local tools/xmakedepend shell script
-     #    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
+     #    2) use the local xmakedepend script (get all dependencies, but slower)
-     #    3) locally build and use the cyrus implementation
+     #    3) use a system-wide default
-     #    4) fall back to the buggy local xmakedpend script
+     #    4) locally build and use the cyrus makedepend
+     #             (faster, but can miss some dependencies)
      #
+     echo >> $LOGFILE
+     echo "running: look_for_makedepend()" >> $LOGFILE
+     if test "x${MAKEDEPEND}" != x ; then
+         echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
+         RETVAL=$?
+         if test x"$RETVAL" = x0 ; then
+             build_cyrus_makedepend
+             RETVAL=$?
+             if test "x$RETVAL" != x0 ; then
+                 echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
+                 MAKEDEPEND=
+             fi
+         else
+             echo "${MAKEDEPEND}" | grep 'tools.xmakedepend' > /dev/null 2>&1
+             RETVAL=$?
+             if test "x$RETVAL" = x0 ; then
+                 MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+             fi
+             echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+         fi
+     fi
      if test "x${MAKEDEPEND}" = x ; then
-         which makedepend > /dev/null 2>&1
-         RV0=$?
          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
          #  echo 'MAKEFILE="'$MAKEFILE'"'
          cat <<EOF >> $MAKEFILE
  #   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
  #
  #   Some "makedepend" implementations will die if they cannot
  #   find a Makefile -- so this file is here to gives them an
  #   empty one to find and parse.
  EOF
          cat <<EOF >> genmake_tc.f
-Line 204 
 EOF
+Line 374 
 EOF
        stop
        end
  EOF
-         makedepend genmake_tc.f > /dev/null 2>&1
+         $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
          RV1=$?
+         which makedepend > /dev/null 2>&1
+         RV2=$?
+         if test "x${RV2}" = x0 ; then
+             makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
+             RV3=$? ; loc_msg='not working.'
+         else RV3=$RV2 ; loc_msg='not found.'
+         fi
          test -f $MAKEFILE  &&  rm -f $MAKEFILE
          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
-         if test "x${RV0}${RV1}" = x00 ; then
+         echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
+         if test "x${RV1}" = x0 ; then
+             MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+             echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+         elif test "x${RV3}" = x0 ; then
+             echo "    local tools/xmakedepend not working. Use system-default makedepend"
              MAKEDEPEND=makedepend
+             echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
          else
-             echo "    a system-default makedepend was not found."
+             echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
+             echo -n "    Try to build cyrus-makedepend ..."
              #  Try to build the cyrus implementation
              build_cyrus_makedepend
              RETVAL=$?
-             if test "x$RETVAL" != x0 ; then
+             if test "x$RETVAL" = x0 ; then
-                 MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+                 echo "  Works"
+             else
+                 echo "  Fails" ; echo "" >> $LOGFILE
+                 echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
+                 echo ""
+                 exit -1
+                 return
              fi
-             rm -f ./genmake_cy_md
-         fi
-     else
-         #  echo "MAKEDEPEND=${MAKEDEPEND}"
-         echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
-         RETVAL=$?
-         if test x"$RETVAL" = x0 ; then
-             build_cyrus_makedepend
          fi
      fi
  }
  build_cyrus_makedepend()  {
+     echo >> $LOGFILE
+     echo "running: build_cyrus_makedepend()" >> $LOGFILE
      rm -f ./genmake_cy_md
      (
          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
              &&  ./configure > /dev/null 2>&1  \
-             &&  make > /dev/null 2>&1
+             &&  $MAKE > /dev/null 2>&1
          if test -x ./makedepend.exe ; then
              $LN ./makedepend.exe ./makedepend
          fi
-Line 249 
 build_cyrus_makedepend()  {
+Line 431 
 build_cyrus_makedepend()  {
      rm -f ./genmake_cy_md
      if test "x$RETVAL" = x0 ; then
          MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+         echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
          return 0
      else
-         echo "WARNING: unable to build cyrus-imapd-makedepend"
+         echo "WARNING: fail to build cyrus-imapd-makedepend" >> $LOGFILE
          return 1
      fi
  }
  build_embed_encode()
  {
      printf "  building the embed-encode utility...  "
      if test ! -e "$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
-Line 287 
 build_embed_encode()
+Line 468 
 build_embed_encode()
          return 1
      fi
      echo "OK"
-     DEFINES="$DEFINES -DHAVE_EMBED_SRC"
  }
+ #  look for possible C compilers
- # Guess possible config options for this host
+ look_for_C_compilers() {
- find_possible_configs()  {
+     echo >> $LOGFILE
+     echo "running: look_for_C_compilers()" >> $LOGFILE
-     tmp1=`uname`"_"`uname -m`
+     rm -f ./genmake_hello.c  ./genmake_hello
-     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
+     cat >> genmake_hello.c << EOF
-     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-     tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
-     tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
-     tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
-     PLATFORM=$tmp3
-     echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
-     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
-     echo "  The platform appears to be:  $PLATFORM"
-     echo "test" > test
-     ln -s ./test link
-     RETVAL=$?
-     if test "x${RETVAL}" = x0 ; then
-         LN="ln -s"
-     else
-         echo "Error: \"ln -s\" does not appear to work on this system!"
-         echo "  For help, please contact <MITgcm-support@mitgcm.org>."
-         exit 1
-     fi
-     rm -f test link
-     if test "x$CPP" = x ; then
-         CPP="cpp -traditional -P"
-     fi
-     look_for_makedepend
-     #================================================================
-     #  look for possible C compilers
-     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc 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
-         $c -o genmake_hello genmake_hello.c > /dev/null 2>&1
+     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
+     p_CC=
+     for c in $tmp ; do
+         COMM="$c $CFLAGS -o genmake_hello genmake_hello.c"
+         echo $COMM >> $LOGFILE
+         $COMM >> $LOGFILE 2>&1
          RETVAL=$?
          if test "x${RETVAL}" = x0 ; then
+             echo " $c test successful" >> $LOGFILE
              p_CC="$p_CC $c"
          fi
      done
-Line 354 
 Error: No C compilers were found in your
+Line 506 
 Error: No C compilers were found in your
  EOF
          exit 1
      else
-         echo "  The possible C compilers found in your path are:"
+         echo "  The possible C compilers found in your path are: $p_CC" | tee -a $LOGFILE
-         echo "   "$p_CC
          if test "x$CC" = x ; then
              CC=`echo $p_CC | $AWK '{print $1}'`
              echo "  Setting C compiler to: "$CC
          fi
      fi
+     echo " --> set CC='$CC'" >> $LOGFILE
+ }
+ # Guess possible config options for this host
+ find_possible_optfile()  {
+     echo >> $LOGFILE
+     echo "running: find_possible_optfile()" >> $LOGFILE
+     tmp1=`uname`"_"`uname -m`
+     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
+     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
+     tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
+     tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+     tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
+     PLATFORM=$tmp3
+     echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
+     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
+     echo "  The platform appears to be:  $PLATFORM" | tee -a $LOGFILE
      #================================================================
      #  look for possible FORTRAN compilers
-     tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"
+     echo "  look for possible FORTRAN compilers" >> $LOGFILE
+     tmp="$MITGCM_FC $FC efc gfortran g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 g95"
      p_FC=
-     for c in $tmp ; do
+     rm -f ./genmake_hello.f
-         rm -f ./hello.f ./hello
+     cat >> genmake_hello.f <<EOF
-         cat >> hello.f <<EOF
        program hello
        do i=1,3
          print *, 'hello world : ', i
        enddo
        end
  EOF
-         $c -o hello hello.f > /dev/null 2>&1
+     for f in $tmp ; do
+         COMM="$f -o genmake_hello genmake_hello.f"
+         echo $COMM >> $LOGFILE
+         $COMM >> $LOGFILE 2>&1
          RETVAL=$?
          if test "x${RETVAL}" = x0 ; then
-             p_FC="$p_FC $c"
+             echo " $f test successful" >> $LOGFILE
+             p_FC="$p_FC $f"
          fi
      done
-     rm -f ./hello.f ./hello
+     rm -f ./genmake_hello.f ./genmake_hello
      if test "x${p_FC}" = x ; then
          cat 1>&2 <<EOF
-Line 394 
 Error: No Fortran compilers were found i
+Line 567 
 Error: No Fortran compilers were found i
  EOF
          exit 1
      else
-         echo "  The possible FORTRAN compilers found in your path are:"
+         echo "  The possible FORTRAN compilers found in your path are: $p_FC" | tee -a $LOGFILE
-         echo "   "$p_FC
      fi
      #  Use the first of the compilers found in the current PATH
-Line 404 
 EOF
+Line 576 
 EOF
          for i in $p_FC ; do
              OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
              if test -r $OPTFILE ; then
-                 echo "  Setting OPTFILE to: "$OPTFILE
+                 echo "  Setting OPTFILE to: "$OPTFILE | tee -a $LOGFILE
                  break
              fi
          done
-Line 413 
 EOF
+Line 585 
 EOF
      if test "x$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 442 
 Error: No options file was found in:  $R
+Line 604 
 Error: No options file was found in:  $R
  EOF
          exit 1
      fi
- #     # look for possible MPI libraries
- #     mpi_libs=
- #     mpi_fort=`which mpif77 2>/dev/null`
- #     RETVAL=$?
- #     if test "x${RETVAL}" = x0 ; then
- #       cat >>test.f <<EOF
- #       PROGRAM HELLO
- #       DO 10, I=1,10
- #       PRINT *,'Hello World'
- #    10 CONTINUE
- #       STOP
- #       END
- # EOF
- #       eval "$mpi_fort -showme test.f > out"
- #       RETVAL=$?
- #       if test "x${RETVAL}" = x0 ; then
- #           a=`cat out`
- #           for i in $a ; do
- #               case $i in
- #                   -*)
- #                       mpi_libs="$mpi_libs $i" ;;
- #               esac
- #           done
- #           echo "The MPI libs appear to be:"
- #           echo "  "$mpi_libs
- #       fi
- #       rm -f test.f out
- #     fi
  }
- #  Parse the package dependency information
+ #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
- get_pdepend_list()  {
+ #  checking for additional included headers (in case of chain of included header)
+ mpi_headers_do_local_copy() {
-     #  strip the comments and then convert the dependency file into
-     #  two arrays: PNAME, DNAME
-     cat $1 | sed -e 's/#.*$//g' \
-         | $AWK 'BEGIN{nn=0;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME["nn"]="$1"\nDNAME["nn"]="$i} }' \
-         > ./.pd_tmp
-     . ./.pd_tmp
-     rm -f ./.pd_tmp
-     printf "PNAME = "${}
- }
- #  Explain usage
- usage()  {
- cat <<EOF
- Usage: "$0" [OPTIONS]
-   where [OPTIONS] can be:
-     -help | --help | -h | --h
-           Print this help message and exit.
-     -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
-       -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
-           Use "NAME" as the adoptfile.  By default, the file at
-           "tools/adjoint_options/adjoint_default" will be used.
-     -nooptfile | --nooptfile
-       -optfile NAME | --optfile NAME | -of NAME | --of NAME
-       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
-           Use "NAME" as the optfile.  By default, an attempt will be
-           made to find an appropriate "standard" optfile in the
-           tools/build_options/ directory.
-     -pdepend NAME | --pdepend NAME
-       -pdepend=NAME | --pdepend=NAME
-           Get package dependency information from "NAME".
-     -pdefault NAME | --pdefault NAME
-       -pdefault=NAME | --pdefault=NAME
-           Get the default package list from "NAME".
-     -make NAME | -m NAME
-       --make=NAME | -m=NAME
-           Use "NAME" for the MAKE program. The default is "make" but
-           many platforms, "gmake" is the preferred choice.
-     -makefile NAME | -mf NAME
-       --makefile=NAME | -mf=NAME
-           Call the makefile "NAME".  The default is "Makefile".
-     -makedepend NAME | -md NAME
+     dBug=0
-       --makedepend=NAME | -md=NAME
+     rm -rf ./mpi_headers
-           Use "NAME" for the MAKEDEPEND program.
+     if test -d $MPIINCLUDEDIR ; then
-     -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
-       -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
-           Specify the location of the MITgcm ROOTDIR as "NAME".
-           By default, genamke will try to find the location by
-           looking in parent directories (up to the 5th parent).
-     -mods NAME | --mods NAME | -mo NAME | --mo NAME
-       -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
-           Here, "NAME" specifies a list of directories that are
-           used for additional source code.  Files found in the
-           "mods list" are given preference over files of the same
-           name found elsewhere.
-     -disable NAME | --disable NAME
-       -disable=NAME | --disable=NAME
-           Here "NAME" specifies a list of packages that we don't
-           want to use.  If this violates package dependencies,
-           genamke will exit with an error message.
-     -enable NAME | --enable NAME
-       -enable=NAME | --enable=NAME
-           Here "NAME" specifies a list of packages that we wish
-           to specifically enable.  If this violates package
-           dependencies, genamke will exit with an error message.
-     -standarddirs NAME | --standarddirs NAME
-       -standarddirs=NAME | --standarddirs=NAME
-           Here, "NAME" specifies a list of directories to be
-           used as the "standard" code.
-     -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
-       -fc=NAME | --fc=NAME
-           Use "NAME" as the fortran compiler.  By default, genmake
-           will search for a working compiler by trying a list of
-           "usual suspects" such as g77, f77, etc.
-     -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
-           Use "NAME" as the C compiler.  By default, genmake
-           will search for a working compiler by trying a list of
-           "usual suspects" such as gcc, c89, cc, etc.
-     -[no]ieee | --[no]ieee
-           Do or don't use IEEE numerics.  Note that this option
-           *only* works if it is supported by the OPTFILE that
-           is being used.
-     -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.
-     -omp | --omp
-           Activate OpenMP code + use Compiler option OMPFLAG
-     -omp=OMPFLAG | --omp=OMPFLAG
-           Activate OpenMP code + use Compiler option OMPFLAG
-     -es | --es | -embed-source | --embed-source
-           Embed a tarball containing the full source code
-           (including the Makefile, etc.) used to build the
-           executable [off by default]
-     -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:
+         #----- check for additional headers (chain of included headers)
+         echo -n '  Check MPI headers ... '
+         listIni=$MPI_HEADER_FILES
+         echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
+         outp=$?
+         #- always check mpif.h (the only mpi-header included in standard MITgcm code)
+         if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
+         if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
+         doCheck=1 ; list2copy='' ; list2check=$listIni
+         while test $doCheck = 1 ; do
+           newList=''
+           for i in $list2check ; do
+             if test -f $MPIINCLUDEDIR/$i ; then
+               newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
+                 sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
+               if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
+               for j in $newInc ; do
+                 echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
+                 outp=$?
+                 if test $outp != 0 ; then
+                   if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
+                   newList="$newList $j"
+                 fi
+               done
+               if test $dBug = 1 ; then echo "" ; fi
+             fi
+           done
+           if test "x$newList" = x ; then doCheck=0
+           else list2check=$newList ; list2copy="$list2copy $newList"
+           fi
+         done
+         list2copy="$MPI_HEADER_FILES $list2copy"
+         if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
-     http://mitgcm.org/devel_HOWTO/
+         #----- create local mpi_headers dir if we have files to copy
+         mkListInc=`echo $list2copy | wc -w`
+         if test $mkListInc != 0 ; then
+           echo 'create local "./mpi_headers" dir'
+           mkdir -p ./mpi_headers
+           INCLUDES="-I./mpi_headers $INCLUDES"
+           mkListInc=1
+         fi
+         if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
+         #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
+         for i in $list2copy ; do
+           if test -f $MPIINCLUDEDIR/$i ; then
+             cp -p $MPIINCLUDEDIR/$i ./mpi_headers
+             if test $i = 'mpif.h' ; then
+                 perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
+             fi
+             if test $mkListInc = 2 ; then
+                 LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
+             fi
+             if test $mkListInc = 1 ; then
+                 LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
+             fi
+           fi
+         done
+     else
+         echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
+         echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
+ #       exit -1
+     fi
+ }
- EOF
+ #  Parse the package dependency information
+ get_pdepend_list()  {
-     exit 1
+     #  strip the comments and then convert the dependency file into
+     #  two arrays: PNAME, DNAME
+     cat $1 | sed -e 's/#.*$//g' \
+         | $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \
+         > ./.pd_tmp
+     RETVAL=$?
+     if test ! "x${RETVAL}" = x0 ; then
+       echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
+       exit 1
+     fi
+     . ./.pd_tmp
+     rm -f ./.pd_tmp
  }
  #  Build a CPP macro to automate calling C routines from FORTRAN
-Line 647 
 get_fortran_c_namemangling()  {
+Line 703 
 get_fortran_c_namemangling()  {
      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
      if test ! "x$FC_NAMEMANGLE" = x ; then
          return 0
      fi
+     echo " running: get_fortran_c_namemangling()" >> $LOGFILE
      default_nm="#define FC_NAMEMANGLE(X) X ## _"
      cat > genmake_test.c <<EOF
  void tcall( char * string ) { tsub( string ); }
  EOF
-     $MAKE genmake_test.o >> genmake_warnings 2>&1
+     COMM="$CC $CFLAGS -c genmake_test.c"
+     echo ' '$COMM >> $LOGFILE
+     $COMM >> $LOGFILE 2>&1
      RETVAL=$?
      if test "x$RETVAL" != x0 ; then
          FC_NAMEMANGLE=$default_nm
-         cat <<EOF>> genmake_errors
+         cat <<EOF>> $LOGFILE
- WARNING: C test compile fails
+  WARNING: C test compile fails
- WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
- WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
  EOF
          return 1
      fi
-Line 671 
 EOF
+Line 730 
 EOF
      RETVAL=$?
      if test "x$RETVAL" != x0 ; then
          FC_NAMEMANGLE=$default_nm
-         cat <<EOF>> genmake_warnings
+         cat <<EOF>> $LOGFILE
- WARNING: The "nm" command failed.
+  WARNING: The "nm" command failed.
- WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
- WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
  EOF
          return 1
      fi
-Line 685 
 EOF
+Line 744 
 EOF
        call tsub( string )
        end
  EOF
-     $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+     COMM="$FC $FFLAGS -c genmake_tcomp.$FS"
+     echo ' '$COMM >> $LOGFILE
+     $COMM >> $LOGFILE 2>&1
      RETVAL=$?
      if test "x$RETVAL" != x0 ; then
          FC_NAMEMANGLE=$default_nm
-         cat <<EOF>> genmake_warnings
+         cat <<EOF>> $LOGFILE
- WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+  WARNING: FORTRAN test compile fails -- please see '$LOGFILE'
- WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
- WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
  EOF
          return 1
      fi
-Line 701 
 EOF
+Line 762 
 EOF
      RETVAL=$?
      if test "x$RETVAL" != x0 ; then
          FC_NAMEMANGLE=$default_nm
-         cat <<EOF>> genmake_warnings
+         cat <<EOF>> $LOGFILE
- WARNING: The "nm" command failed.
+  WARNING: The "nm" command failed.
- WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
- WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
  EOF
          return 1
      fi
-Line 731 
 EOF
+Line 792 
 EOF
      #  cleanup the testing files
      rm -f genmake_tcomp.* genmake_test.*
- }
+     echo " --> set FC_NAMEMANGLE='$FC_NAMEMANGLE'" >> $LOGFILE
+ }
  check_HAVE_CLOC()  {
+     echo >> $LOGFILE
+     echo "running: check_HAVE_CLOC()" >> $LOGFILE
      get_fortran_c_namemangling
      cat <<EOF > genmake_tc_1.c
  $FC_NAMEMANGLE
-Line 752 
 void FC_NAMEMANGLE(cloc) ( double *curti
+Line 816 
 void FC_NAMEMANGLE(cloc) ( double *curti
  }
  EOF
      COMM="$CC $CFLAGS -c genmake_tc_1.c"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
        program hello
-Line 764 
 EOF
+Line 828 
 EOF
        end
  EOF
      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RET_F=$?
-     test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
+     test -x ./genmake_tc  &&  ./genmake_tc >> $LOGFILE 2>&1
      RETVAL=$?
      if test "x$RETVAL" = x0 ; then
          HAVE_CLOC=t
-         DEFINES="$DEFINES -DHAVE_CLOC"
      fi
      rm -f genmake_tc*
+     echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
  }
  check_HAVE_SIGREG()  {
      if test ! "x$HAVE_SIGREG" = x ; then
          return
      fi
+     echo >> $LOGFILE
+     echo "running: check_HAVE_SIGREG()" >> $LOGFILE
      get_fortran_c_namemangling
      cat <<EOF > genmake_tc_1.c
  $FC_NAMEMANGLE
-Line 813 
 void FC_NAMEMANGLE(sigreg) (int * aip)
+Line 878 
 void FC_NAMEMANGLE(sigreg) (int * aip)
  }
  EOF
      COMM="$CC $CFLAGS -c genmake_tc_1.c"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
        program hello
-Line 824 
 EOF
+Line 889 
 EOF
        call sigreg(anint)
        end
  EOF
-     echo >> genmake_warnings
+     cat genmake_tc_2.$FS >> $LOGFILE
-     echo "running: check_HAVE_SIGREG()" >> genmake_warnings
-     cat genmake_tc_2.$FS >> genmake_warnings
      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RETVAL=$?
      if test "x$RETVAL" = x0 ; then
          HAVE_SIGREG=t
-         DEFINES="$DEFINES -DHAVE_SIGREG"
      fi
      rm -f genmake_tc*
+     echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
  }
  check_HAVE_SETRLSTK()  {
-     if test "x$HAVE_SETRLSTK" = xt ; then
-         DEFINES="$DEFINES -DHAVE_SETRLSTK"
-         return
-     fi
      if test ! "x$HAVE_SETRLSTK" = x ; then
          return
      fi
+     echo >> $LOGFILE
+     echo "running: check_HAVE_SETRLSTK()" >> $LOGFILE
      get_fortran_c_namemangling
      cat <<EOF > genmake_tc_1.c
  $FC_NAMEMANGLE
-Line 863 
 void FC_NAMEMANGLE(setrlstk) ()
+Line 923 
 void FC_NAMEMANGLE(setrlstk) ()
  }
  EOF
      COMM="$CC $CFLAGS -c genmake_tc_1.c"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
        program hello
-Line 872 
 EOF
+Line 932 
 EOF
        call setrlstk()
        end
  EOF
-     echo >> genmake_warnings
+     cat genmake_tc_2.$FS >> $LOGFILE
-     echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
-     cat genmake_tc_2.$FS >> genmake_warnings
      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
-     $COMM >> genmake_warnings 2>&1
+     $COMM >> $LOGFILE 2>&1
      RETVAL=$?
      if test "x$RETVAL" = x0 ; then
          HAVE_SETRLSTK=t
-         DEFINES="$DEFINES -DHAVE_SETRLSTK"
      fi
      rm -f genmake_tc*
+     echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
  }
  check_HAVE_STAT()  {
+     echo >> $LOGFILE
+     echo "running: check_HAVE_STAT()" >> $LOGFILE
      get_fortran_c_namemangling
      cat <<EOF > genmake_tc_1.c
  $FC_NAMEMANGLE
-Line 909 
 void FC_NAMEMANGLE(tfsize) ( int *nbyte
+Line 968 
 void FC_NAMEMANGLE(tfsize) ( int *nbyte
  }
  EOF
      COMM="$CC $CFLAGS -c genmake_tc_1.c"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
      $COMM >> genmake_tc.log 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
-Line 919 
 EOF
+Line 978 
 EOF
        print *," HELLO WORLD", nbyte
        end
  EOF
-     echo >> genmake_warnings
+     cat genmake_tc_2.$FS >> $LOGFILE
-     echo "running: check_HAVE_STAT()" >> genmake_warnings
-     cat genmake_tc_2.$FS >> genmake_warnings
      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-     echo $COMM >> genmake_warnings
+     echo $COMM >> $LOGFILE
      $COMM >> genmake_tc.log 2>&1
      RETVAL=$?
      if test "x$RETVAL" = x0 ; then
          HAVE_STAT=t
-         DEFINES="$DEFINES -DHAVE_STAT"
      fi
      rm -f genmake_tc*
+     echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
  }
  check_netcdf_libs()  {
      if test ! "x$SKIP_NETCDF_CHECK" = x ; then
          return
      fi
-     echo >> genmake_warnings
+     echo >> $LOGFILE
-     echo "running: check_netcdf_libs()" >> genmake_warnings
+     echo "running: check_netcdf_libs()" >> $LOGFILE
      cat <<EOF > genmake_tnc.F
        program fgennc
  #include "netcdf.inc"
  EOF
-     if test ! "x$MPI" = x ; then
+    #if test ! "x$MPI" = x ; then
-         echo '#include "mpif.h"' >> genmake_tnc.F
+    #    echo '#include "mpif.h"' >> genmake_tnc.F
-     fi
+    #fi
      cat <<EOF >> genmake_tnc.F
        integer iret, ncid, xid
        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
-Line 957 
 EOF
+Line 1013 
 EOF
        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
        end
  EOF
-     echo "===  genmake_tnc.F  ===" > genmake_tnc.log
+     echo "===  genmake_tnc.F  >>>" > genmake_tnc.log
      cat genmake_tnc.F >> genmake_tnc.log
-     echo "===  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
-Line 975 
 EOF
+Line 1031 
 EOF
      $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
+     cat genmake_tnc.log >> $LOGFILE
      #EH3  Remove test program execution for machines that either disallow
      #EH3  execution or cannot support it (eg. cross-compilers)
-Line 986 
 EOF
+Line 1042 
 EOF
      if test "x$RET_COMPILE" = x0 ; then
          HAVE_NETCDF=t
+         echo "check_netcdf: successful" >> $LOGFILE
      else
          # try again with "-lnetcdf" added to the libs
-         echo "try again with added '-lnetcdf'" > genmake_tnc.log
+         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
-Line 996 
 EOF
+Line 1053 
 EOF
              &&  $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
+         echo >> $LOGFILE
+         cat genmake_tnc.log >> $LOGFILE
          if test "x$RET_COMPILE" = x0 ; then
              LIBS="$LIBS -lnetcdf"
              HAVE_NETCDF=t
+             echo "check_netcdf: successful" >> $LOGFILE
          else
          # try again with "-lnetcdff" added to the libs
-             echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+             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
-Line 1010 
 EOF
+Line 1069 
 EOF
                  &&  $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
+             echo >> $LOGFILE
+             cat genmake_tnc.log >> $LOGFILE
              if test "x$RET_COMPILE" = x0 ; then
                  LIBS="$LIBS -lnetcdff -lnetcdf"
                  HAVE_NETCDF=t
+                 echo "check_netcdf: successful" >> $LOGFILE
              fi
          fi
      fi
      rm -f genmake_tnc*
+     echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
+ }
+ check_lapack_libs()  {
+     if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
+     echo >> $LOGFILE
+     echo "running: check_lapack_libs()" >> $LOGFILE
+     cat <<EOF > genmake_tla.F
+       program fgenla
+       integer info
+       integer ipiv( 2 )
+       double precision ab( 4, 2 ), b( 2 )
+       data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
+       data b / 1., 1. /
+       call dgbsv( 2, 1, 1, 1, ab, 4, ipiv, b, 2, info )
+       IF (info .NE. 0) write(*,*) 'Error:', info
+       write(*,*) b
+       end
+ EOF
+     echo "===  genmake_tla.F  >>>" > genmake_tla.log
+     cat genmake_tla.F >> genmake_tla.log
+     echo "<<<  genmake_tla.F  ===" >> genmake_tla.log
+     RET_CPP=f
+     COMM="cat genmake_tla.F | $CPP $DEFINES $INCLUDES"
+     echo "$COMM" >> genmake_tla.log
+     eval $COMM > genmake_tla.$FS 2>/dev/null  &&  RET_CPP=t
+     if test "x$RET_CPP" = xf ; then
+         echo "  WARNING: CPP failed to pre-process the lapack test." \
+             >> genmake_tla.log
+         echo "    Please check that \$INCLUDES is properly set." \
+             >> genmake_tla.log
+     fi
+     echo "$FC $FFLAGS $FOPTIM -c genmake_tla.$FS  \ " >> genmake_tla.log
+     echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tla.o $LIBS" >> genmake_tla.log
+     $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+         &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS >> genmake_tla.log 2>&1
+     RET_COMPILE=$?
+     cat genmake_tla.log >> $LOGFILE
+     # test program execution not always possible (see check_netcdf_libs)
+     #
+     #test -x ./genmake_tla  &&  ./genmake_tla >> genmake_tla.log 2>&1
+     #RETVAL=$?
+     #if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+     if test "x$RET_COMPILE" = x0 ; then
+         HAVE_LAPACK=t
+         echo "check_lapack: successful" >> $LOGFILE
+     else
+         # try again with "-llapack" added to the libs
+         echo "==> try again with added '-llapack'" > genmake_tla.log
+         echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+         echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+         echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack" >> genmake_tla.log
+         cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+             &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+             &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack >> genmake_tla.log 2>&1
+         RET_COMPILE=$?
+         echo >> $LOGFILE
+         cat genmake_tla.log >> $LOGFILE
+         if test "x$RET_COMPILE" = x0 ; then
+             LIBS="$LIBS -llapack"
+             HAVE_LAPACK=t
+             echo "check_lapack: successful" >> $LOGFILE
+         else
+         # try again with "-lf77blas -lcblas" added to the libs
+             echo "==> try again with added '-llapack -lf77blas -lcblas'" > genmake_tla.log
+             echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+             echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+             echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas" >> genmake_tla.log
+             cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+                 &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+                 &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas >> genmake_tla.log 2>&1
+             RET_COMPILE=$?
+             echo >> $LOGFILE
+             cat genmake_tla.log >> $LOGFILE
+             if test "x$RET_COMPILE" = x0 ; then
+                 LIBS="$LIBS -llapack -lf77blas -lcblas"
+                 HAVE_LAPACK=t
+                 echo "check_lapack: successful" >> $LOGFILE
+             else
+             # try again with "-latlas" added to the libs
+                 echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
+                 echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+                 echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+                 echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
+                 cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+                     &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+                     &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
+                 RET_COMPILE=$?
+                 echo >> $LOGFILE
+                 cat genmake_tla.log >> $LOGFILE
+                 if test "x$RET_COMPILE" = x0 ; then
+                     LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
+                     HAVE_LAPACK=t
+                     echo "check_lapack: successful" >> $LOGFILE
+                 fi
+             fi
+         fi
+     fi
+     rm -f genmake_tla*
+     echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
  }
+ check_HAVE_FLUSH()  {
+     if test ! "x$SKIP_CHECK_FLUSH" = x ; then
+         return
+     fi
+     echo >> $LOGFILE
+     echo "running: check_HAVE_FLUSH()" >> $LOGFILE
+     cat <<EOF > genmake_tflsh.$FS
+       program fgenflsh
+       integer iounit
+       character*9 fname
+       iounit = 26
+       fname = 'tmp.tflsh'
+       open(iounit,FILE=fname,STATUS='unknown')
+       write(iounit,*) 'genmake_tflsh: hello'
+       call flush(iounit)
+       close(iounit)
+       end
+ EOF
+     echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
+     cat genmake_tflsh.$FS >> genmake_tflsh.log
+     echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
+     echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
+     echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
+     $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
+         &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
+     RET_COMPILE=$?
+     if test "x$RET_COMPILE" = x0 ; then
+         HAVE_FLUSH=t
+         #cat genmake_tflsh.log >> $LOGFILE
+         echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
+     else
+         HAVE_FLUSH=f
+         cat genmake_tflsh.log >> $LOGFILE
+     fi
+     rm -f genmake_tflsh*
+     echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
+ }
  ###############################################################################
  #   Sequential part of script starts here
-Line 1043 
 ENABLE=
+Line 1244 
 ENABLE=
  DISABLE=
  # MAKEFILE=
  # MAKEDEPEND=
- PDEPEND=
+ PKG_DEPEND=
- DUMPSTATE=t
+ PKG_GROUPS=
- PDEFAULT=
+ DUMPSTATE=f
  OPTFILE=
  INCLUDES="-I. $INCLUDES"
  FFLAGS=
-Line 1053 
 FOPTIM=
+Line 1254 
 FOPTIM=
  FEXTRAFLAGS=
  USE_EXTENDED_SRC=
  EXTENDED_SRC_FLAG=
+ GET_FC_VERSION=
  CFLAGS=
  KFLAGS1=
  KFLAGS2=
-Line 1065 
 MPI=
+Line 1267 
 MPI=
  MPIPATH=
  OMP=
  OMPFLAG=
+ USE_R4=
  TS=
  PAPIS=
  PCLS=
-Line 1076 
 GSL=
+Line 1279 
 GSL=
  DEVEL=
  HAVE_TEST_L=
+ # set this to "t" to enable lapack test
+ CHECK_FOR_LAPACK=f
  # DEFINES checked by test compilation or command-line
  HAVE_SYSTEM=
  HAVE_FDATE=
-Line 1086 
 HAVE_STAT=
+Line 1292 
 HAVE_STAT=
  HAVE_NETCDF=
  HAVE_ETIME=
  IGNORE_TIME=
+ HAVE_LAPACK=
+ HAVE_FLUSH=
  MODS=
  TOOLSDIR=
-Line 1093 
 SOURCEDIRS=
+Line 1301 
 SOURCEDIRS=
  INCLUDEDIRS=
  STANDARDDIRS="USE_THE_DEFAULT"
+ #- local config file
+ gm_local="genmake_local"
  G2ARGS=
  BASH=
  PWD=`pwd`
-Line 1108 
 MACHINE=`uname -a`
+Line 1319 
 MACHINE=`uname -a`
  EXECUTABLE=
  EXEHOOK=
  EXEDIR=
- PACKAGES_CONF=
  IEEE=
  if test "x$MITGCM_IEEE" != x ; then
      IEEE=$MITGCM_IEEE
-Line 1117 
 FS=
+Line 1327 
 FS=
  FS90=
  AUTODIFF_PKG_USED=f
+ OPENAD=
  AD_OPTFILE=
  TAF=
  AD_TAF_FLAGS=
-Line 1129 
 FTL_TAF_FLAGS=
+Line 1340 
 FTL_TAF_FLAGS=
  SVD_TAMC_FLAGS=
  TAMC_EXTRA=
+ DIVA=
+ MPIINCLUDEDIR=
+ MPI_HEADER_FILES=
+ LOCAL_MPI_HEADERS=
  #  The following state can be set directly by command-line switches
- gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
+ gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
- gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
+ gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
+ gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
  #  The following state is not directly set by command-line switches
- gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
+ gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
- gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
+ gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
- gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
+ gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
- gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
+ gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
- gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
+ gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
  #  The following are all related to adjoint/tangent-linear stuff
- gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
+ gm_s10="AUTODIFF_PKG_USED AD_OPTFILE OPENAD TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
- gm_s12="TAF_EXTRA TAMC_EXTRA"
+ gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
- gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
+ gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
  cat <<EOF
  GENMAKE :
- A program for GENerating MAKEfiles for the MITgcm project.  For a
+ A program for GENerating MAKEfiles for the MITgcm project.
- quick list of options, use "genmake -h" or for more detail see:
+    For a quick list of options, use "genmake2 -h"
+ or for more detail see the Developer's HOWTO manual at:
-   http://mitgcm.org/devel_HOWTO/
+    http://mitgcm.org/public/docs.html
  EOF
+ LOGFILE="genmake.log"
+ #- clean-up previous genmake logfiles:
+ rm -f genmake_state genmake_*optfile $LOGFILE
  echo "===  Processing options files and arguments  ==="
- gm_local="genmake_local"
- printf "  getting local config information:  "
- if test -f $gm_local ; then
-     echo "using $gm_local"
-     . $gm_local
-     # echo "DISABLE=$DISABLE"
-     # echo "ENABLE=$ENABLE"
- else
-     echo "none found"
- fi
  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
  #parse_options
-Line 1185 
 for ac_option in "$@" ; do
+Line 1395 
 for ac_option in "$@" ; do
          ac_prev=
          continue
      fi
      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
      case $ac_option in
          -help | --help | -h | --h)
              usage ;;
          -nooptfile | --nooptfile)
              OPTFILE="NONE" ;;
          -optfile | --optfile | -of | --of)
              ac_prev=OPTFILE ;;
          -optfile=* | --optfile=* | -of=* | --of=*)
              OPTFILE=$ac_optarg ;;
+         -oad | --oad)
+             OPENAD="true" ;;
          -adoptfile | --adoptfile | -adof | --adof)
              ac_prev=AD_OPTFILE ;;
          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
              AD_OPTFILE=$ac_optarg ;;
          -pdepend | --pdepend)
-             ac_prev=PDEPEND ;;
+             ac_prev=PKG_DEPEND ;;
          -pdepend=* | --pdepend=*)
-             PDEPEND=$ac_optarg ;;
+             PKG_DEPEND=$ac_optarg ;;
-         -pdefault | --pdefault)
+         -pgroups | --pgroups)
-             ac_prev=PDEFAULT ;;
+             ac_prev=PKG_GROUPS ;;
-         -pdefault=* | --pdefault=*)
+         -pgroups=* | --pgroups=*)
-             PDEFAULT=$ac_optarg ;;
+             PKG_GROUPS=$ac_optarg ;;
          -make | --make | -m | --m)
              ac_prev=MAKE ;;
          -make=* | --make=* | -m=* | --m=*)
              MAKE=$ac_optarg ;;
          -bash | --bash)
              ac_prev=BASH ;;
          -bash=* | --bash=*)
              BASH=$ac_optarg ;;
          -makedepend | --makedepend | -md | --md)
              ac_prev=MAKEDEPEND ;;
          -makedepend=* | --makedepend=* | -md=* | --md=*)
              MAKEDEPEND=$ac_optarg ;;
-         -makefile | --makefile | -ma | --ma)
+         -makefile | --makefile | -mf | --mf)
              ac_prev=MAKEFILE ;;
-         -makefile=* | --makefile=* | -ma=* | --ma=*)
+         -makefile=* | --makefile=* | -mf=* | --mf=*)
              MAKEFILE=$ac_optarg ;;
          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
              echo "ERROR: The platform option has been removed.  Please specify"
              echo "  the build options using the \"optfile\" mechanism."
              echo
              usage
              ;;
          -rootdir | --rootdir | -rd | --rd)
              ac_prev=ROOTDIR ;;
          -rootdir=* | --rootdir=* | -rd=* | --rd=*)
              ROOTDIR=$ac_optarg ;;
          -mods | --mods | -mo | --mo)
              ac_prev=MODS ;;
          -mods=* | --mods=* | -mo=* | --mo=*)
              MODS=$ac_optarg ;;
          -disable | --disable)
              ac_prev=DISABLE ;;
          -disable=* | --disable=*)
              DISABLE=$ac_optarg ;;
          -enable | --enable)
              ac_prev=ENABLE ;;
          -enable=* | --enable=*)
              ENABLE=$ac_optarg ;;
          -standarddirs | --standarddirs)
              ac_prev=STANDARDDIRS ;;
          -standarddirs=* | --standarddirs=*)
-Line 1271 
 for ac_option in "$@" ; do
+Line 1483 
 for ac_option in "$@" ; do
  #               ac_prev=cpp ;;
  #           -cpp=* | --cpp=*)
  #               CPP=$ac_optarg ;;
          -cc | --cc)
              ac_prev=CC ;;
          -cc=* | --cc=*)
              CC=$ac_optarg ;;
          -fortran | --fortran | -fc | --fc)
              ac_prev=FC ;;
          -fc=* | --fc=*)
              FC=$ac_optarg ;;
          -fs | --fs)
              ac_prev=FS ;;
          -fs=* | --fs=*)
              FS=$ac_optarg ;;
          -fs90 | --fs90)
              ac_prev=FS90 ;;
          -fs90=* | --fs90=*)
              FS90=$ac_optarg ;;
+         -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
+             USE_R4=true ;;
          -ieee | --ieee)
              IEEE=true ;;
          -noieee | --noieee)
-             IEEE= ;;
+             echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
+         -devel | --devel)
+             IEEE=true ; DEVEL=true ;;
+         -gsl | --gsl)
+             GSL=true ;;
          -ts | --ts)
              TS=true ;;
-Line 1312 
 for ac_option in "$@" ; do
+Line 1531 
 for ac_option in "$@" ; do
          -hpmt | --hpmt)
              HPMT=true ;;
-         -gsl | --gsl)
-             GSL=true ;;
-         -devel | --devel)
-             DEVEL=true ;;
          -mpi | --mpi)
              MPI=true ;;
          -mpi=* | --mpi=*)
              MPIPATH=$ac_optarg
              MPI=true ;;
          -omp | --omp)
              OMP=true ;;
          -omp=* | --omp=*)
              OMPFLAG=$ac_optarg
              OMP=true ;;
          -ds | --ds)
              DUMPSTATE=t ;;
+         -extra_flag | --extra_flag)
+             ac_prev=FEXTRAFLAGS ;;
+         -extra_flag=* | --extra_flag=*)
+             FEXTRAFLAGS=$ac_optarg ;;
          -taf_extra | --taf_extra)
              ac_prev=TAF_EXTRA ;;
          -taf_extra=* | --taf_extra=*)
-Line 1342 
 for ac_option in "$@" ; do
+Line 1560 
 for ac_option in "$@" ; do
              ac_prev=TAMC_EXTRA ;;
          -tamc_extra=* | --tamc_extra=*)
              TAMC_EXTRA=$ac_optarg ;;
          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
              IGNORE_TIME="-DIGNORE_TIME" ;;
-Line 1353 
 for ac_option in "$@" ; do
+Line 1571 
 for ac_option in "$@" ; do
              echo "Error: unrecognized option: "$ac_option
              usage
              ;;
          *)
              echo "Error: unrecognized argument: "$ac_option
              usage
              ;;
      esac
  done
+ #TMP=./genmk_$$
+ #- try to put temporary files in system-local /tmp dir
+ TMP=/tmp/genmk_$$
+ touch $TMP ; retVal=$?
+ if [ $retVal -eq 0 ] ; then
+   if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
+ else
+   TMP=./genmk_$$
+ fi
+ rm -f $TMP
+ #echo "  temp files: $TMP.*"
+ printf "  getting local config information:  "
+ if test -f $gm_local ; then
+     echo "using $gm_local"
+     . $gm_local
+ else
+     echo "none found"
+ fi
  if test -f ./.genmakerc ; then
      echo
      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
      echo "  file.  This file format is no longer supported.  For directions on"
      echo "  how to setup and use the new \"genmake2\" script, please see:"
-     echo "    http://mitgcm.org/devel_HOWTO/"
+     echo "    http://mitgcm.org/public/devel_HOWTO/"
      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
      echo "WARNING: ignore \"./.genmakerc\" and continue."
      echo
  fi
  #  Find the MITgcm ${ROOTDIR}
-Line 1384 
 if test "x${ROOTDIR}" = x ; then
+Line 1621 
 if test "x${ROOTDIR}" = x ; then
          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
                  ROOTDIR=$d
-                 printf "Warning:  ROOTDIR was not specified but there appears to be"
+                 printf "Warning: ROOTDIR was not specified ;"
-                 echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
+                 echo " try using a local copy of MITgcm found at \"$ROOTDIR\""
                  break
              fi
          done
-Line 1405 
 fi
+Line 1642 
 fi
  #  Find the MITgcm ${THISVER}
  version_file="${ROOTDIR}/doc/tag-index"
  if test -f $version_file ; then
-     THISVER=`grep '^checkpoint' $version_file | head -1`
+     THISVER=`$AWK '/^checkpoint/{print $1; exit}' $version_file`
  #-  remove ./BUILD_INFO.h file if older than version_file
      if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
          echo "  remove ./BUILD_INFO.h (older than ${version_file})"
-Line 1417 
 if test "x$MAKEFILE" = x ; then
+Line 1654 
 if test "x$MAKEFILE" = x ; then
      MAKEFILE="Makefile"
  fi
- echo "  getting OPTFILE information:  "
+ echo "  getting OPTFILE information:"
  if test "x${OPTFILE}" = x ; then
      if test "x$MITGCM_OF" = x ; then
          echo "Warning: no OPTFILE specified so we'll look for possible settings"
          printf "\n===  Searching for possible settings for OPTFILE  ===\n"
-         find_possible_configs
+         find_possible_optfile
      else
          OPTFILE=$MITGCM_OF
      fi
-Line 1437 
 if test "x$OPTFILE" != xNONE ; then
+Line 1674 
 if test "x$OPTFILE" != xNONE ; then
              echo "--please check that variable syntax is bash-compatible"
              exit 1
          fi
-         if test "x$DUMPSTATE" != xf ; then
+         if test "x$DUMPSTATE" = xt ; then
              cp -f $OPTFILE "genmake_optfile"
          fi
      else
-Line 1446 
 if test "x$OPTFILE" != xNONE ; then
+Line 1683 
 if test "x$OPTFILE" != xNONE ; then
      fi
  fi
- echo "  getting AD_OPTFILE information:  "
+ echo "  getting AD_OPTFILE information:"
  if test "x${AD_OPTFILE}" = x ; then
-     if test "x$MITGCM_AD_OF" = x ; then
+     if test "x$MITGCM_AD_OF" != x ; then
+         AD_OPTFILE=$MITGCM_AD_OF
+     elif test "x$OPENAD" = x ; then
          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
      else
-         AD_OPTFILE=$MITGCM_AD_OF
+         AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
      fi
  fi
  if test "x${AD_OPTFILE}" != xNONE ; then
-Line 1464 
 if test "x${AD_OPTFILE}" != xNONE ; then
+Line 1703 
 if test "x${AD_OPTFILE}" != xNONE ; then
              echo "--please check that variable syntax is bash-compatible"
              exit 1
          fi
-         if test "x$DUMPSTATE" != xf ; then
+         if test "x$DUMPSTATE" = xt ; then
              cp -f $AD_OPTFILE "genmake_ad_optfile"
          fi
      else
-Line 1492 
 Error: no Fortran compiler: please speci
+Line 1731 
 Error: no Fortran compiler: please speci
  EOF
      exit 1
  fi
+ if test "x$GET_FC_VERSION" != x ; then
+   echo "Get compiler version using: $FC $GET_FC_VERSION" >> $LOGFILE
+   ff=`echo $FC | sed 's/ .*//'` ; xx=`echo $ff | sed 's/^./& /' | sed 's/ .*//'`
+   if test $xx != '/' ; then which $ff >> $LOGFILE ; fi
+   $FC $GET_FC_VERSION > genmake_fc_vers1 2> genmake_fc_vers2
+   if test -s genmake_fc_vers1 ; then
+     cat genmake_fc_vers1 >> $LOGFILE
+   else
+     cat genmake_fc_vers2 >> $LOGFILE
+   fi
+   echo "<-- compiler version ----" >> $LOGFILE
+   rm -f genmake_fc_vers1 genmake_fc_vers2
+ fi
  if test "x$CC" = x ; then
-     CC=cc
+     look_for_C_compilers
- #     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
-Line 1509 
 if test "x$MAKE" = x ; then
+Line 1756 
 if test "x$MAKE" = x ; then
      MAKE="make"
  fi
  if test "x$CPP" = x ; then
-     CPP=cpp
+     CPP="cpp -traditional -P"
  fi
  #EH3 === UGLY ===
  #  The following is an ugly little hack to check for $CPP in /lib/ and
-Line 1536 
 EOF
+Line 1783 
 EOF
  else
      rm -f test_cpp
  fi
  look_for_makedepend
+ #  Check that soft-link command is set and usable
  if test "x$LN" = x ; then
      LN="ln -s"
  fi
-Line 1546 
 RETVAL=$?
+Line 1796 
 RETVAL=$?
  if test "x$RETVAL" != x0 ; then
      cat <<EOF 1>&2
- Error: The command "ln -s" failed -- please specify a working soft-link
+ Error: The command "$LN" failed -- please specify a working soft-link
    command in the optfile.
  EOF
-Line 1564 
 check_for_broken_Ff
+Line 1814 
 check_for_broken_Ff
  if test ! "x$MPI" = x ; then
        echo "  Turning on MPI cpp macros"
-       DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
+       DEFINES="$DEFINES -DALLOW_USE_MPI"
+ #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
+ #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
  fi
  if test ! "x$OMP" = x ; then
        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
-Line 1573 
 if test ! "x$OMP" = x ; then
+Line 1825 
 if test ! "x$OMP" = x ; then
        DEFINES="$DEFINES -DUSE_OMP_THREADING"
  fi
+ if test ! "x$USE_R4" = x ; then
+       echo "  Turning on LET_RS_BE_REAL4 cpp flag"
+       DEFINES="$DEFINES -DLET_RS_BE_REAL4"
+ fi
  if test ! "x$TS" = x ; then
        echo "  Turning on timing per timestep"
        if test ! "x$FOOLAD" = x ; then
              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
        else
              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
        fi
-Line 1612 
 if test ! "x$PAPI" = x ; then
+Line 1869 
 if test ! "x$PAPI" = x ; then
            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 $PAPILIB"
-Line 1624 
 if test ! "x$PCL" = x ; then
+Line 1881 
 if test ! "x$PCL" = x ; then
            echo "  Sticking with PCL flop summary per timestep!"
        else
            echo "  Turning on performance analysis with PCL"
            echo "  Please make sure PCLINC, PCLLIB are defined"
            DEFINES="$DEFINES -DUSE_PCL"
            INCLUDES="$INCLUDES $PCLINC"
            LIBS="$LIBS $PCLLIB"
-Line 1634 
 if test ! "x$HPMT" = x ; then
+Line 1891 
 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$PCL" = x ; then
+       else
+         if test ! "x$PCL" = x ; then
            echo "  PCL and the HPM Toolkit cannot co-exist!"
            echo "  Sticking with PCL!"
-       else
+         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 $HPMTLIB"
-       fi
+         fi
        fi
  fi
  if test ! "x$GSL" = x ; then
-Line 1724 
 rm -f genmake_tcomp*
+Line 1982 
 rm -f genmake_tcomp*
  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
  check_HAVE_CLOC
  if test "x$HAVE_CLOC" != x ; then
+     DEFINES="$DEFINES -DHAVE_CLOC"
      echo "yes"
  else
      echo "no"
-Line 1738 
 rm -f genmake_t*
+Line 1997 
 rm -f genmake_t*
  printf "  Can we unlimit the stack size using $FC...  "
  check_HAVE_SETRLSTK
  if test "x$HAVE_SETRLSTK" = xt ; then
+     DEFINES="$DEFINES -DHAVE_SETRLSTK"
      echo "yes"
  else
      echo "no"
-Line 1747 
 rm -f genmake_t*
+Line 2007 
 rm -f genmake_t*
  printf "  Can we register a signal handler using $FC...  "
  check_HAVE_SIGREG
  if test "x$HAVE_SIGREG" = xt ; then
+     DEFINES="$DEFINES -DHAVE_SIGREG"
      echo "yes"
  else
      echo "no"
-Line 1756 
 rm -f genmake_t*
+Line 2017 
 rm -f genmake_t*
  printf "  Can we use stat() through C calls...  "
  check_HAVE_STAT
  if test "x$HAVE_STAT" != x ; then
+     DEFINES="$DEFINES -DHAVE_STAT"
      echo "yes"
  else
      echo "no"
-Line 1765 
 rm -f genmake_t*
+Line 2027 
 rm -f genmake_t*
  printf "  Can we create NetCDF-enabled binaries...  "
  check_netcdf_libs
  if test "x$HAVE_NETCDF" != x ; then
+     DEFINES="$DEFINES -DHAVE_NETCDF"
      echo "yes"
  else
      echo "no"
  fi
- DEFINES="$DEFINES $IGNORE_TIME"
+ printf "  Can we create LAPACK-enabled binaries...  "
+ check_lapack_libs
+ if test "x$HAVE_LAPACK" != x ; then
+     DEFINES="$DEFINES -DHAVE_LAPACK"
+     echo "yes"
+ else
+     echo "no"
+ fi
+ printf "  Can we call FLUSH intrinsic subroutine...  "
+ check_HAVE_FLUSH
+ if test "x$HAVE_FLUSH" = xt ; then
+     DEFINES="$DEFINES -DHAVE_FLUSH"
+     echo "yes"
+ else
+     echo "no"
+ fi
+ DEFINES="$DEFINES $IGNORE_TIME"
  if test "x$EMBED_SRC" = xt ; then
      build_embed_encode
  fi
  if test "x$EMBED_SRC" = xt ; then
      ENABLE="$ENABLE embed_files"
+ #   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
  fi
  printf "\n===  Setting defaults  ===\n"
  printf "  Adding MODS directories: "
  for d in $MODS ; do
-Line 1794 
 for d in $MODS ; do
+Line 2075 
 for d in $MODS ; do
  done
  echo
- if test "x${PLATFORM}" = x ; then
+ #if test "x${PLATFORM}" = x ; then
-     PLATFORM=$p_PLATFORM
+ #    PLATFORM=$p_PLATFORM
- fi
+ #fi
  if test "x${EXEDIR}" = x ; then
      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
-Line 1836 
 ERROR: neither of the two default script
+Line 2117 
 ERROR: neither of the two default script
      ${TOOLSDIR}/set64bitConst.sh
      ${TOOLSDIR}/set64bitConst.csh
    are working so please check paths or specify (with \$S64) a
    working version of this script.
  EOF
-Line 1848 
 THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSD
+Line 2129 
 THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSD
  EXECUTABLE=${EXECUTABLE:-mitgcmuv}
+ #  Set Standard Code Directories:
+ if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
+     STANDARDDIRS="eesupp model"
+ fi
+ #  if model in Standard-Code-Dir, add eesupp (needed to compile model)
+ echo " $STANDARDDIRS " | grep ' model ' > /dev/null 2>&1
+ ckM=$?
+ echo " $STANDARDDIRS " | grep ' eesupp ' > /dev/null 2>&1
+ ckE=$?
+ if test $ckM = 0 -a $ckE = 1 ; then
+     STANDARDDIRS="$STANDARDDIRS eesupp"
+ fi
  #  We have a special set of source files in eesupp/src which are
  #  generated from some template source files. We'll make them first so
  #  they appear as regular source code
  if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
      echo "  Making source files in eesupp from templates"
-     ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
+     ( cd $ROOTDIR"/eesupp/src/" && $MAKE clean_old && $MAKE \
+     ) > make_eesupp.errors 2>&1
      RETVAL=$?
      if test "x${RETVAL}" = x0 ; then
          rm -f make_eesupp.errors
-Line 1868 
 fi
+Line 2163 
 fi
  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
+         ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE clean_old && $MAKE \
+         ) > make_${pdir}.errors 2>&1
          RETVAL=$?
          if test "x${RETVAL}" = x0 ; then
              rm -f make_${pdir}.errors
-Line 1881 
 for pdir in exch2 regrid ; do
+Line 2177 
 for pdir in exch2 regrid ; do
  done
  printf "\n===  Determining package settings  ===\n"
- if  test "x${PDEPEND}" = x ; then
+ if  test "x${PKG_DEPEND}" = x ; then
      tmp=$ROOTDIR"/pkg/pkg_depend"
-     if test -r $tmp ; then
+     if test -r $tmp ; then PKG_DEPEND=$tmp ; fi
-         PDEPEND=$tmp
+ fi
-     else
+ if  test "x${PKG_DEPEND}" = x ; then
          echo "Warning:  No package dependency information was specified."
          echo "  Please check that ROOTDIR/pkg/pkg_depend exists."
-     fi
  else
-     if test ! -r ${PDEPEND} ; then
+     if test ! -r ${PKG_DEPEND} ; then
-         echo "Error:  can't read package dependency info from PDEPEND=\"$PDEPEND\""
+         echo "Error:  can't read package dependency info from PKG_DEPEND=\"$PKG_DEPEND\""
          exit 1
      fi
+     echo "  getting package dependency info from  $PKG_DEPEND"
+ #  Strip the comments and then convert the dependency file into arrays: PNAME, DNAME
+     get_pdepend_list $PKG_DEPEND
  fi
- echo "  getting package dependency info from  $PDEPEND"
- #  Strip the comments and then convert the dependency file into
+ # A default package groups file "$ROOTDIR/pkg/pkg_groups" is provided
- #  two arrays: PNAME, DNAME
+ #  to define the "default_pkg_list" and package groups (for convenience, one
- cat $PDEPEND | sed -e 's/#.*$//g' \
+ #  can specify a group of packages using names like "ocean" and "atmosphere").
-     | $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \
+ if test "x${PKG_GROUPS}" = x ; then
-     > ./.pd_tmp
+     tmp=$ROOTDIR"/pkg/pkg_groups"
- RETVAL=$?
+     if test -r $tmp ; then PKG_GROUPS=$tmp ; fi
- if test ! "x${RETVAL}" = x0 ; then
+ fi
-     echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""
+ if test "x${PKG_GROUPS}" = x ; then
-     exit 1
+         echo "Warning:  No package groups information was specified."
+         echo "  Please check that ROOTDIR/pkg/pkg_groups exists."
+ else
+     if test ! -r ${PKG_GROUPS} ; then
+         echo "Error:  can't read package groups info from PKG_GROUPS=\"$PKG_GROUPS\""
+         exit 1
+     fi
+     echo "  getting package groups info from      $PKG_GROUPS"
  fi
- . ./.pd_tmp
- rm -f ./.pd_tmp
- #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
+ #  Search for packages to compile.
- #  file should eventually be added so that, for convenience, one can
+ echo "  checking list of packages to compile:"
- #  specify groups of packages using names like "ocean" and "atmosphere".
+ PKG_LIST=
- echo "  checking default package list:  "
+ if test "x${PKG_LIST}" = x ; then
- if test "x${PDEFAULT}" = x ; then
      for i in "." $MODS ; do
          if test -r $i"/packages.conf" ; then
-                 PDEFAULT=$i"/packages.conf"
+                 PKG_LIST=$i"/packages.conf"
                  break
          fi
      done
  fi
- if test "x${PDEFAULT}" = x ; then
+ if test "x${PKG_LIST}" = x ; then
-     PDEFAULT="$ROOTDIR/pkg/pkg_default"
+     pkg_list='default_pkg_list'
- fi
+     if test "x${PKG_GROUPS}" = x ; then
- if test "x${PDEFAULT}" = xNONE ; then
+         echo "Error:  need package groups info to expand pkg_list=\"$pkg_list\""
-     echo "    default packages file disabled"
+         exit 1
+     fi
  else
-     if test ! -r $PDEFAULT ; then
+     if test ! -r $PKG_LIST ; then
-         echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
+         echo "Error:  can't read package list from PKG_LIST=\"$PKG_LIST\""
+         exit 1
      else
-         echo "    using PDEFAULT=\"$PDEFAULT\""
+         echo "    using PKG_LIST=\"$PKG_LIST\""
          #  Strip the comments and add all the names
-         def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
+         pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
          RETVAL=$?
          if test "x${RETVAL}" != x0 ; then
-             printf "Error: can't parse default package list "
+             printf "Error: can't parse package list "
-             echo "-- please check PDEFAULT=\"$PDEFAULT\""
+             echo "-- please check PKG_LIST=\"$PKG_LIST\""
              exit 1
          fi
-         for i in $def ; do
-             PACKAGES="$PACKAGES $i"
-         done
-         echo "    before group expansion packages are: $PACKAGES"
-         RET=1
-         while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
-         echo "    after group expansion packages are:  $PACKAGES"
      fi
  fi
+ for i in $pkg_list ; do
+     PACKAGES="$PACKAGES $i"
+ done
+ echo     "    before group expansion packages are:$PACKAGES"
+ if test "x${PKG_GROUPS}" != x ; then
+     RET=1
+     while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
+     echo "    after group expansion packages are: $PACKAGES"
+ fi
  echo "  applying DISABLE settings"
+ echo "" > $TMP.pack
  for i in $PACKAGES ; do
-     echo $i >> ./.tmp_pack
+     echo $i >> $TMP.pack
  done
- for i in `grep  "-" ./.tmp_pack` ; do
+ for i in `grep  "-" $TMP.pack` ; do
      j=`echo $i | sed 's/[-]//'`
      DISABLE="$DISABLE $j"
  done
-Line 1971 
 for p in $PACKAGES ; do
+Line 2278 
 for p in $PACKAGES ; do
  done
  PACKAGES="$pack"
  echo "  applying ENABLE settings"
- echo "" > ./.tmp_pack
+ echo "" > $TMP.pack
  PACKAGES="$PACKAGES $ENABLE"
  # Test if each explicitly referenced package exists
  for i in $PACKAGES ; do
      j=`echo $i | sed 's/[-+]//'`
      if test ! -d "$ROOTDIR/pkg/$j" ; then
-         echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""
+         echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
          exit 1
      fi
-     echo $i >> ./.tmp_pack
+     echo $i >> $TMP.pack
  done
  PACKAGES=
- for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do
+ for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
      PACKAGES="$PACKAGES $i"
  done
- rm -f ./.tmp_pack
+ rm -f $TMP.pack
- echo "    packages are:  $PACKAGES"
+ echo "    packages are: $PACKAGES"
  #  Check for package MNC: if NetCDF is available, then build the MNC
  #  template files ; otherwise, delete mnc from the list of packages.
- echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
+ echo " $PACKAGES " | grep ' mnc ' > /dev/null 2>&1
- RETVAL=$?
+ mnc_in=$?
- if test "x$RETVAL" = x0 ; then
+ if test "x$HAVE_NETCDF" != xt ; then
-     if test "x$HAVE_NETCDF" != xt ; then
+     if test "x$mnc_in" = x0 ; then
          cat <<EOF
  *********************************************************************
  WARNING: the "mnc" package was enabled but tests failed to compile
    NetCDF applications.  Please check that:
 ) 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 && $MAKE templates ) > make_mnc.errors 2>&1
+     #  this prevent to add mnc (due to pdepend rules) if not available
-         RETVAL=$?
+         DISABLE="$DISABLE mnc"
-         if test "x${RETVAL}" = x0 ; then
+     fi
-             rm -f make_mnc.errors
+ else
-         else
+     # we have NetCDF, we try to build MNC template files
-             echo "Error: problem encountered while building source files in pkg/mnc:"
+     ( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
-             cat make_mnc.errors 1>&2
+     RETVAL=$?
+     if test "x${RETVAL}" = x0 ; then
+         rm -f make_mnc.errors
+     else
+         echo "Error: problem encountered while building source files in pkg/mnc:"
+         cat make_mnc.errors 1>&2
+         if test "x$mnc_in" = x0 ; then
              exit 1
+         else
+             DISABLE="$DISABLE mnc"
          fi
      fi
  fi
  #  Check for package PROFILES: if NetCDF is not available,
  #  then delete profiles from the list of available packages.
- echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
+ if test "x$HAVE_NETCDF" != xt ; then
- RETVAL=$?
+     echo " $PACKAGES " | grep ' profiles ' > /dev/null 2>&1
- if test "x$RETVAL" = x0 ; then
+     RETVAL=$?
-     if test "x$HAVE_NETCDF" != xt ; then
+     if test "x$RETVAL" = x0 ; 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"
+     else
+     #  this prevent to add profiles (due to pdepend rules) if not available
+         DISABLE="$DISABLE profiles"
+     fi
+ fi
+ #  Make sure the openad package is enabled if using OpenAD
+ if test "x$OPENAD" != x ; then
+     echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" != x0 ; then
+         cat <<EOF
+ *********************************************************************
+ ERROR: when generating an adjoint with OpenAD, the openad package
+   must be enabled.  Please add it to packages.conf.
+ *********************************************************************
+ EOF
+         exit 1
      fi
  fi
- echo "  applying package dependency rules"
+ if  test "x${PKG_DEPEND}" != x ; then
- ck=
+   echo "  applying package dependency rules"
- while test "x$ck" != xtt ; do
+   ck=
+   while test "x$ck" != xtt ; do
      i=0
      # rtot=${#PNAME[@]}
      rtot=$nname
-Line 2067 
 while test "x$ck" != xtt ; do
+Line 2399 
 while test "x$ck" != xtt ; do
                  pin="t"
              fi
          done
+         #  or in the current $STANDARDDIRS list?
+         for p in $STANDARDDIRS ; do
+             if test "x$p" = "x$pname" ; then pin="t" ; fi
+         done
          #  Is the DNAME entry a (+) or (-) rule ?
          tmp="dname=\"\$DNAME_$i\""
-Line 2089 
 while test "x$ck" != xtt ; do
+Line 2425 
 while test "x$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$dname" ; then
-Line 2110 
 while test "x$ck" != xtt ; do
+Line 2446 
 while test "x$ck" != xtt ; do
          #  Do we need to get rid of $dname according to the dependency rules?
          if test "x$pin" = xt -a "x$plus" = "x-" -a "x$din" = xt; then
              echo "Error: can't satisfy package dependencies:"
              echo "  \"$pname\" was requested but is disallowed by"
              echo "  the dependency rules for \"$dname\""
              exit 1
          fi
          i=`echo "$i + 1" | bc -l`
          #i=$(( $i + 1 ))
      done
      ck=$ck"t"
- done
+   done
- echo "    packages are:  $PACKAGES"
+   echo "    packages are: $PACKAGES"
+ fi
  for i in $PACKAGES ; do
      adr="$ROOTDIR/pkg/$i"
      if test -d $adr ; then
-Line 2136 
 done
+Line 2473 
 done
  # Create a list of #define and #undef to enable/disable packages
  PACKAGES_DOT_H=PACKAGES_CONFIG.h
  #  The following UGLY HACK sets multiple "#undef"s and it needs to go
  #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h
  #  file would eventually be split up so that all package-related #define
  #  statements could be separated and handled only by genmake.
  names=`ls -1 "$ROOTDIR/pkg"`
-Line 2154 
 for n in $names ; do
+Line 2491 
 for n in $names ; do
          done
          if test "x$has_pack" = xf ; then
              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
          fi
      fi
  done
-Line 2165 
 for i in $PACKAGES ; do
+Line 2502 
 for i in $PACKAGES ; do
  #eh3 DEFINES="$DEFINES -D$def"
  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
      case $i in
          aim_v23)
              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
              echo "Warning: ALLOW_AIM is set to enable aim_v23."
              ;;
      esac
-Line 2175 
 for i in $PACKAGES ; do
+Line 2512 
 for i in $PACKAGES ; do
  done
- echo "  Adding STANDARDDIRS"
+ echo "  Adding STANDARDDIRS='$STANDARDDIRS'"
  BUILDDIR=${BUILDDIR:-.}
- if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
-     STANDARDDIRS="eesupp model"
- fi
  if test "x$STANDARDDIRS" != x ; then
      for d in $STANDARDDIRS ; do
          adr="$ROOTDIR/$d/src"
-Line 2212 
 for i in $spaths ; do
+Line 2546 
 for i in $spaths ; do
      if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
          echo "    found CPP_OPTIONS=\"$try\""
          CPP_OPTIONS="$try"
          # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
          for n in $names ; do
              test_for_package_in_cpp_options $CPP_OPTIONS $n
          done
      fi
      try="$i/CPP_EEOPTIONS.h"
      if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
          echo "    found CPP_EEOPTIONS=\"$try\""
          # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
  #**** not yet enabled ****
  #        test_for_mpi_in_cpp_eeoptions $try
  #**** not yet enabled ****
-Line 2234 
 fi
+Line 2568 
 fi
  #  Here, we build the list of files to be "run through" the adjoint
  #  compiler.
- if test -f ./adSrcFiles.tmp ; then
+ if test -f $TMP.adSrcFiles ; then
-     rm -f ./adSrcFiles.tmp
+     rm -f $TMP.adSrcFiles
  fi
  echo "  Creating the list of files for the adjoint compiler."
+ touch $TMP.adSrcFiles
  for i in $SOURCEDIRS ; do
      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
      for j in $list_files ; do
-         cat $i/$j >> adSrcFiles.tmp
+         cat $i/$j >> $TMP.adSrcFiles
      done
  done
  if test ! "x"$FS = "x.f" ; then
-     cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
+     cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
-     mv -f adSrcFiles.tmp_f adSrcFiles.tmp
+     mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
  fi
  echo
-Line 2258 
 for i in $INCLUDEDIRS ; do
+Line 2593 
 for i in $INCLUDEDIRS ; do
      fi
  done
- if test ! "x$DIVA" = x ; then
+ if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
-     echo "  Creating the pseudo-MPI include directory"
+     if test ! "x$MPIINCLUDEDIR" = x ; then
-     INCLUDES="-I./mpi_headers $INCLUDES"
+         #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
-     rm -rf ./mpi_headers
+         #   checking for additional included headers (in case of chain of included
-     mkdir -p ./mpi_headers
+         #   header); also set LOCAL_MPI_HEADERS (if not already set)
+         mpi_headers_do_local_copy
-     if test "x$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
+ rm -rf $TMP.links
- mkdir .links.tmp
+ mkdir $TMP.links
- touch .links.tmp/foo
+ touch $TMP.links/foo
- if test ! -r ".links.tmp/foo" ; then
+ if test ! -r "$TMP.links/foo" ; then
      echo
      echo "ERROR : something is wrong with your directory permissions or"
      echo "   your user file-creation mask (\"umask\") since creating a"
-Line 2303 
 if test ! -r ".links.tmp/foo" ; then
+Line 2622 
 if test ! -r ".links.tmp/foo" ; then
      echo
      exit 1
  fi
- rm -f .links.tmp/foo
+ rm -f $TMP.links/foo
  if test "x$OPENAD" != x ; then
      OAD_DONT_COMPILE="/dev/null"
      OAD_DONT_TRANSFORM="/dev/null"
      OAD_KEEP_ORIGINAL="/dev/null"
      OAD_CB2M_FILES="/dev/null"
+     OADTOOLS="$TOOLSDIR/OAD_support"
      echo "  looking for dontCompile file:  "
      for i in "." $MODS ; do
          if test -r $i"/dontCompile" ; then
-Line 2345 
 if test "x$OPENAD" != x ; then
+Line 2665 
 if test "x$OPENAD" != x ; then
      echo "   OpenAD exceptions:  "
  fi
- echo "# This section creates symbolic links" > srclinks.tmp
+ echo "# This section creates symbolic links" > $TMP.srclinks
- echo "" >> srclinks.tmp
+ echo "" >> $TMP.srclinks
- printf 'F77_SRC_FILES = ' > F77srclist.tmp
+ printf 'F77_SRC_FILES = ' > $TMP.F77srclist
- printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
+ printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
- printf 'C_SRC_FILES = '   > csrclist.tmp
+ printf 'C_SRC_FILES = '   > $TMP.csrclist
- printf 'F90_SRC_FILES = ' > F90srclist.tmp
+ printf 'F90_SRC_FILES = ' > $TMP.F90srclist
- printf 'H_SRC_FILES = '   > hsrclist.tmp
+ printf 'H_SRC_FILES = '   > $TMP.hsrclist
- printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
+ printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
  alldirs="$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 ! -r "$TMP.links/$sf" ; then
              if test -f "$d/$sf" ; then
                  ignore_f=f
                  case $d/$sf in
                    ./$PACKAGES_DOT_H)
                          ignore_f=t
                          ;;
                    ./AD_CONFIG.h)
                          ignore_f=t
                          ;;
                    ./FC_NAMEMANGLE.h)
                          ignore_f=t
                          ;;
                    ./BUILD_INFO.h)
                          ignore_f=t
                          ;;
                    ./EMBEDDED_FILES.h)
                          ignore_f=t
                          ;;
                    *)
                          #  For the local directory *ONLY*,
                          #  ignore all soft-links
                          if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
                              ignore_f=t
                          else
-                             touch .links.tmp/$sf
+                             touch $TMP.links/$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
+                         echo    " \\"  >> $TMP.F77srclist
-                         printf " $sf" >> F77srclist.tmp
+                         printf " $sf" >> $TMP.F77srclist
-                         if test "x$OPENAD" != x ; then
+                         if test "x$OPENAD" = x ; then
+                             basename=${sf%%.F}
+                             isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
+                             if test -z "$isAD" ; then
+                                 echo    " \\"  >> $TMP.nonADF77srclist
+                                 printf " $sf" >> $TMP.nonADF77srclist
+                             fi
+                         else #- OpenAD case:
                              basename=${sf%%.F}
-                             isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
+                             isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
                              if test -z "$isAD" ; then
                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
                                  if test -z "$toBeIgnored" ; then
-                                     echo    " \\"  >> nonADF77srclist.tmp
+                                     echo    " \\"  >> $TMP.nonADF77srclist
-                                     printf " $sf" >> nonADF77srclist.tmp
+                                     printf " $sf" >> $TMP.nonADF77srclist
                                  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
+                                     echo    " \\"  >> $TMP.nonADF77srclist
-                                     printf " $sf" >> nonADF77srclist.tmp
+                                     printf " $sf" >> $TMP.nonADF77srclist
                                  fi
                              fi
                          fi
                          ;;
                      F90)
-                         echo    " \\"  >> F90srclist.tmp
+                         echo    " \\"  >> $TMP.F90srclist
-                         printf " $sf" >> F90srclist.tmp
+                         printf " $sf" >> $TMP.F90srclist
                          ;;
                      c)
-                         echo    " \\"  >> csrclist.tmp
+                         echo    " \\"  >> $TMP.csrclist
-                         printf " $sf" >> csrclist.tmp
+                         printf " $sf" >> $TMP.csrclist
                          ;;
                      h)
-                         echo    " \\"  >> hsrclist.tmp
+                         echo    " \\"  >> $TMP.hsrclist
-                         printf " $sf" >> hsrclist.tmp
+                         printf " $sf" >> $TMP.hsrclist
                          ;;
                      flow)
-                         echo    " \\"  >> ad_flow_files.tmp
+                         echo    " \\"  >> $TMP.ad_flow_files
-                         printf " $sf" >> ad_flow_files.tmp
+                         printf " $sf" >> $TMP.ad_flow_files
                          ;;
                     esac
                  fi
-Line 2449 
 for d in $alldirs ; do
+Line 2776 
 for d in $alldirs ; do
      done
      if test "x$deplist" != x ; then
        if test "$d" != "." ; then
-         echo "" >> srclinks.tmp
+         echo "" >> $TMP.srclinks
-         echo "#  These files are linked from $d" >> srclinks.tmp
+         echo "#  These files are linked from $d" >> $TMP.srclinks
-         echo "$deplist :" >> srclinks.tmp
+         echo "$deplist :" >> $TMP.srclinks
  # 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
+         printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
        fi
      fi
  done
- rm -rf .links.tmp
+ rm -rf $TMP.links
- echo "" >> F77srclist.tmp
+ echo "" >> $TMP.F77srclist
- echo "" >> nonADF77srclist.tmp
+ echo "" >> $TMP.nonADF77srclist
- echo "" >> csrclist.tmp
+ echo "" >> $TMP.csrclist
- echo "" >> F90srclist.tmp
+ echo "" >> $TMP.F90srclist
- echo "" >> hsrclist.tmp
+ echo "" >> $TMP.hsrclist
- echo "" >> ad_flow_files.tmp
+ echo "" >> $TMP.ad_flow_files
  CMDLINE=$0
  for xx in "$@" ; do nw=`echo $xx | wc -w`
      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
                          else CMDLINE="$CMDLINE '$xx'" ; fi
  done
  if test -f $MAKEFILE ; then
-     mv -f $MAKEFILE "$MAKEFILE.bak"
+     mv -f $MAKEFILE "$MAKEFILE.old"
  fi
  echo "  Writing makefile: $MAKEFILE"
  echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE
-Line 2493 
 EXE_SVD=$EXECUTABLE"_svd"
+Line 2820 
 EXE_SVD=$EXECUTABLE"_svd"
  cat >>$MAKEFILE <<EOF
  #
  # OPTFILE="$OPTFILE"
  #
  # BUILDDIR     : Directory where object files are written
  # SOURCEDIRS   : Directories containing the source (.F) files
  # INCLUDEDIRS  : Directories containing the header-source (.h) files
-Line 2504 
 cat >>$MAKEFILE <<EOF
+Line 2831 
 cat >>$MAKEFILE <<EOF
  # INCLUDES     : Directories searched for header files
  # DEFINES      : Macro definitions for CPP
  # MAKEDEPEND   : Dependency generator
- # KPP          : Special preprocessor command (specific to platform)
- # KFLAGS       : Flags for KPP
  # FC           : Fortran compiler command
  # FFLAGS       : Configuration/debugging options for FC
  # FOPTIM       : Optimization options for FC
-Line 2513 
 cat >>$MAKEFILE <<EOF
+Line 2838 
 cat >>$MAKEFILE <<EOF
  # LIBS         : Library flags /or/ additional optimization/debugging flags
  ROOTDIR     = ${ROOTDIR}
  BUILDDIR    = ${BUILDDIR}
  SOURCEDIRS  = ${SOURCEDIRS}
  INCLUDEDIRS = ${INCLUDEDIRS}
  EXEDIR      = ${EXEDIR}
  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
  TOOLSDIR    = ${TOOLSDIR}
+ OADTOOLS    = ${OADTOOLS}
  #eh3  new defines for the adjoint work
  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
-Line 2539 
 else
+Line 2865 
 else
      echo "EMBEDDED_FILES = " >>$MAKEFILE
  fi
+ # extract default cpp search path so we can pass it to makedepend
+ CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
  cat >>$MAKEFILE <<EOF
  # Unix ln (link)
  LN = ${LN}
- # C preprocessor
- CPP = cat \$< | ${S64} | ${CPP}
  # Dependency generator
  MAKEDEPEND = ${MAKEDEPEND}
  # Special preprocessor (KAP on DECs, FPP on Crays)
-Line 2561 
 LINK = ${LINK} ${LDADD}
+Line 2888 
 LINK = ${LINK} ${LDADD}
  DEFINES = ${DEFINES}
  # Includes for CPP
  INCLUDES = ${INCLUDES}
+ # default CPP includes for makedepend
+ CPPINCLUDES = ${CPPINCLUDES}
  # Flags for KPP
  KFLAGS1 = ${KFLAGS1}
  KFLAGS2 = ${KFLAGS2}
-Line 2578 
 NOOPTFILES = ${NOOPTFILES}
+Line 2907 
 NOOPTFILES = ${NOOPTFILES}
  NOOPTFLAGS = ${NOOPTFLAGS}
  # Flags and libraries needed for linking
  LIBS = ${LIBS}
- # Name of the Mekfile
+ # Name of the makefile
- MAKEFILE=${MAKEFILE}
+ MAKEFILE = ${MAKEFILE}
+ # Name of the make program
+ MAKE = ${MAKE}
  EOF
- cat F77srclist.tmp      >> $MAKEFILE
+ cat $TMP.F77srclist      >> $MAKEFILE
- cat nonADF77srclist.tmp >> $MAKEFILE
+ cat $TMP.nonADF77srclist >> $MAKEFILE
- cat csrclist.tmp        >> $MAKEFILE
+ cat $TMP.csrclist        >> $MAKEFILE
- cat F90srclist.tmp      >> $MAKEFILE
+ cat $TMP.F90srclist      >> $MAKEFILE
- cat hsrclist.tmp        >> $MAKEFILE
+ cat $TMP.hsrclist        >> $MAKEFILE
- cat ad_flow_files.tmp   >> $MAKEFILE
+ cat $TMP.ad_flow_files   >> $MAKEFILE
- rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
+ rm -f $TMP.F77srclist $TMP.nonADF77srclist $TMP.csrclist $TMP.F90srclist $TMP.hsrclist $TMP.ad_flow_files
  echo >> $MAKEFILE
  # add definitions for preprocessed sources
  # and note that not all systems allow case sensitive extensions
  # hence the $FS and $FS90 here.
  # for fixed format f90 files we use ff90 or FF90 resp
  # but these are not expected to be the original source files
  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
  echo '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 'FLOWFILES =  $(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)
+ all: fwd_exe_target
+ fwd_exe_target:
+         @echo Update AD_CONFIG.h and make \$(EXECUTABLE)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+         @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         \$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
          @echo Creating \$@ ...
          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
  depend:
-         @make links
+         @\$(MAKE) -f \$(MAKEFILE) links
-         \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+         \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
          -rm -f makedepend.out
-Line 2626 
 libmitgcmuv.a: \$(OBJFILES)
+Line 2965 
 libmitgcmuv.a: \$(OBJFILES)
          ar rcv libmitgcmuv.a \$(OBJFILES)
          ar d   libmitgcmuv.a main.o
+ obj: \$(OBJFILES)
  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
- output.txt: \$(EXECUTABLE)
+ # remove most of the files that "make" generates
-         @printf 'running ... '
-         @\$(EXECUTABLE) > \$@
  clean:
          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
          -rm -rf *.o
          -rm -rf *.$FS *.flowdir
          -rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
+ # remove most of the files that "make" and "make depend" generate
  Clean:
-         @make clean
+         @\$(MAKE) -f \$(MAKEFILE) clean
-         @make cleanlinks
+         @\$(MAKE) -f \$(MAKEFILE) cleanlinks
-         -rm -f \$(SPECIAL_FILES)
+         -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
-         -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 taf_ftl.log
-         -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
+ # remove also the executable, files that "genmake2" generates (except Makefile)
+ #         and output from a run (plus log files from testreport)
  CLEAN:
-         @make Clean
+         @\$(MAKE) -f \$(MAKEFILE) Clean
+         -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
+         -rm -f $LOGFILE genmake_state genmake_*optfile
+         -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
+         -rm -rf mpi_headers mnc_test_*
          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-         -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+         -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
+         -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
-         -rm -rf mnc_test_*
+         -rm -f oad_cp.[0-9][0-9][0-9].?????
- #eh3 Makefile: makefile
  makefile:
          $THIS_SCRIPT $G2ARGS
  cleanlinks:
-Line 2663 
 cleanlinks:
+Line 3009 
 cleanlinks:
  # Special targets (SPECIAL_FILES) which are created by make
  ${PACKAGES_DOT_H}:
          @echo Creating \$@ ...
-         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
  AD_CONFIG.h:
          @echo Creating \$@ ...
-         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
  FC_NAMEMANGLE.h:
          @echo Creating \$@ ...
          echo "$FC_NAMEMANGLE" > \$@
-Line 2685 
 if test "x$EMBED_SRC" = xt ; then
+Line 3031 
 if test "x$EMBED_SRC" = xt ; then
  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
-Line 2706 
 cat >>$MAKEFILE <<EOF
+Line 3052 
 cat >>$MAKEFILE <<EOF
  ## This nullifies any default implicit rules concerning these two file types:
  ## %.o : %.F
+ # C preprocessing and replacing the _d in constants:
+ CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
  .F.$FS:
-         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+         \$(CPPCMD)  > \$@
  .$FS.o:
          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
+ .F.o:
+         \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
  .F90.$FS90:
-         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+         \$(CPPCMD)  > \$@
  .FF90.f$FS90:
-         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+         \$(CPPCMD)  > \$@
  .$FS90.o:
          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
  .f$FS90.o:
-Line 2722 
 cat >>$MAKEFILE <<EOF
+Line 3073 
 cat >>$MAKEFILE <<EOF
  .c.o:
          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
  .flow.flowdir:
-         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+         \$(CPPCMD) > \$@
  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
  .F.p:
-         \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+         \$(CPPCMD) > \$@
  .p.$FS:
          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
-Line 2736 
 EOF
+Line 3087 
 EOF
  #===  Automatic Differentiation Rules  ===
  #===  for TAMC/TAF  ======================
  if test "x$OPENAD" = x ; then
  cat >>$MAKEFILE <<EOF
-Line 2745 
 TAF            = ${TAF}
+Line 3096 
 TAF            = ${TAF}
  TAF_EXTRA      = ${TAF_EXTRA}
  TAMC_EXTRA     = ${TAMC_EXTRA}
+ LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
  EOF
-Line 2762 
 done
+Line 3114 
 done
  echo "  Add the source list for AD code generation"
  echo >> $MAKEFILE
  printf "AD_FILES = " >> $MAKEFILE
- AD_FILES=`cat adSrcFiles.tmp`
+ AD_FILES=`cat $TMP.adSrcFiles`
  for i in $AD_FILES ; do
      echo    " \\" >> $MAKEFILE
      printf " $i" >> $MAKEFILE
  done
  echo >> $MAKEFILE
- rm -f adSrcFiles.tmp
+ rm -f $TMP.adSrcFiles
  cat >>$MAKEFILE <<EOF
  # ... AD ...
- adall: \$(EXE_AD)
+ adall: ad_exe_target
  adtaf: ad_taf_output.$FS
  adtamc: ad_tamc_output.$FS
- ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
+ ad_exe_target:
-         @$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
+         @echo Update AD_CONFIG.h and make \$(EXE_AD)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+         @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
+ ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
-         -rm -f ad_config.template
+         @-rm -f ad_config.template
-         @make \$(F77_PP_SRC_FILES)
+         @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
-         @make \$(FLOFILES)
+         @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
-         cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
+         cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
  ad_taf_output.$FS: ad_input_code.$FS
+         @-rm -f ad_input_code_ad.$FS ; echo ''
          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
          ls -l ad_input_code_ad.$FS
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
-Line 2795 
 adtafonly:
+Line 3155 
 adtafonly:
          ls -l ad_input_code_ad.$FS
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
- \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+ \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
-         \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
+         \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
  ad_tamc_output.$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 ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
  adonlyfwd:
          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
  adtrick:
          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
+ adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
  # ... FTL ...
- ftlall: ftl_taf
+ ftlall: ftl_exe_target
  ftltaf: ftl_taf_output.$FS
  ftltamc: ftl_tamc_output.$FS
- ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+ ftl_exe_target:
-         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
+         @echo Update AD_CONFIG.h and make \$(EXE_FTL)
-         cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
-         -rm -f ftl_config.template
+         @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
-         @make \$(F77_PP_SRC_FILES)
+         @-rm -f ad_config.template
-         @make \$(AD_FLOW_FILES)
+         \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
-         cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
+ ftl_input_code.$FS: \$(AD_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+         cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+         @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
+         cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
  ftl_taf_output.$FS: ftl_input_code.$FS
+         @-rm -f ftl_input_code_tl.$FS ; echo ''
          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
-         ls -l ftl_input_code_ftl.$FS
+         ls -l ftl_input_code_tl.$FS
-         cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+         cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
  ftltafonly:
          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
-         ls -l ftl_input_code_ftl.$FS
+         ls -l ftl_input_code_tl.$FS
-         cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+         cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
- ftl_taf: ftl_taf_output.o \$(OBJFILES)
+ \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
-         \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
+         \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
  ftl_tamc_output.$FS: ftl_input_code.$FS
          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
  # ... SVD ...
  svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
-Line 2865 
 svd_touch:
+Line 3234 
 svd_touch:
          touch ad_taf_output.$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
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
-         cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+         cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
-         -rm -f ftl_config.template
+         @-rm -f ad_config.template
  EOF
  fi
  #===  for OpenAD  ========================
  if test "x$OPENAD" != x ; then
  # ============ begin OpenAD specific section ==============
  cat >>$MAKEFILE <<EOF
+ # ... OpenAD ...
  # all the source files linked from the various locations:
  ALL_LINKED_FILES= \
  \$(F77_SRC_FILES) \
  \$(C_SRC_FILES) \
-Line 2919 
 for i in `cat ${OAD_CB2M_FILES}` ; do
+Line 3289 
 for i in `cat ${OAD_CB2M_FILES}` ; do
    echo    " \\" >> $MAKEFILE
    printf " ${i}_mod.f$FS90" >> $MAKEFILE
  done
- AD_FILES=`cat adSrcFiles.tmp`
+ AD_FILES=`cat $TMP.adSrcFiles`
  for i in $AD_FILES ; do
    basename=${i%%.f}
    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
-Line 2929 
 for i in $AD_FILES ; do
+Line 3299 
 for i in $AD_FILES ; do
    fi
  done
  echo >> $MAKEFILE
- rm -f adSrcFiles.tmp
+ rm -f $TMP.adSrcFiles
  cat >>$MAKEFILE <<EOF
- adAll: \$(EXE_AD)
+ adAll: ad_exe_target
  .PHONY: adAll
+ ad_exe_target:
+         @echo Update AD_CONFIG.h and make \$(EXE_AD)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+         @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$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)
+         \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
          -rm -f makedepend.out
-Line 2951 
 w2f__types.F90 \
+Line 3328 
 w2f__types.F90 \
  OAD_active.F90 \
  OAD_cp.F90 \
  OAD_rev.F90 \
- OAD_tape.F90
+ OAD_tape.F90 \
+ revolve.F90
  OPENAD_SUPPORT_C_SRC_FILES = \
  iaddr.c \
-Line 2960 
 timeRatio.c
+Line 3338 
 timeRatio.c
  f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$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$FS90
          cat \$^ > \$@
  f95_test.out: f95_test_mods.f90 f95_test.f90
          f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
          f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
- # the file included below is created by the
+ CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
- # postProcessor and its inclusion sets the
- # variable POSTPROCESSEDFILES
- # used below. Because the file is made during
- # make it won't be read until the second (recursive)
- # invocation in the rule below
- -include postProcess.make
- AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$FS90=.o)
+ AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o)  OAD_intrinsics_oad.o \$(CB2M_AD_FILES:.f$FS90=_oad.o)
  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
- postProcess.comp: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S1)
+ \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S2)
- ifeq (\$(MAKELEVEL),0)
-         \$(MAKE) adAll
- else
-         touch \$@
- endif
- \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.comp \$(AD_OBJ_FILES_S2)
- ifeq (\$(MAKELEVEL),1)
          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
- else
-         touch \$@
- endif
- # makefile debug rule
+ # create sources files modules from header files containing common blocks
- openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
+ %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
- .PHONY: openad
+         \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
- # create the module files
+ # create new header files with USE statements for the new modules made above
- %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
+ %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
-         ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
+         \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
- # create the header files
+ # change the include directives of everybody to refer to  the new header files with the USE statements
- %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
+ %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
-         ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+         \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
- # 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$FS90:  \$(CB2M_AD_FILES)
          cat \$^ > \$@
- # strip all comments and blanks to reduce
- # the file size in order to reduce perl's memory requirements
- ad_input_code_sf.f$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$FS90 preProcess.py
+ ad_input_code_sf.pre.f90 : \$(CB2M_AD_FILES)
-         ./preProcess.py --timing -H -S \$< -o \$@
+         \${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
+ # replace stop statements (to avoid the implied unstructured control flow)  with print statements
+ ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
+         cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
  # F -> WHIRL
- # note that the canonicalized version cuts off at col 72
+ ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
- # doing this also for string constants which is ok as long
+         \${OPEN64ROOT}/crayf90/sgi/mfef90 -r8 -z -F ad_input_code_sf.pre.s2p.f90
- # as we are in fixed mode and cut of exactly there.
- # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
- # characters respectively.
- ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$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
+ ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
-         ./whirl2xaif -s -n --debug 1 -o \$@ \$<
+         \${OPENADFORTTK}/bin/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
+ ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
-         ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+         \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
  # XAIF' -> WHIRL'
- ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
+ ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
-         ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
+         \${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
  # WHIRL' -> F'
- ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
+ ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
-         ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
+         \${OPEN64ROOT}/whirl2f/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
+ ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \${OADTOOLS}/insertTemplateDir.bash
-         ../OAD_support/insertTemplateDir.bash \$< \$@
+         \${OADTOOLS}/insertTemplateDir.bash \$< \$@
- PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
+ PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
  # postprocess F'
- postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)
+ postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
-         # the target is a placeholder to signal execution of the rule
+         \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
+         # the target is a placeholder to trigger a single execution of the rule
          touch \$@
-         # this step also creates the file postProcess.make but we cannot
+ # put this so make knows about the postprocessing output
-         # name it as the target or else make will try to remake it for
+ OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$FS90=_oad.f): postProcess.tag
-         # the include directive above for any rule, e.g. make clean
-         ./postProcess.py --progress --timing -m r -i ../OAD_support/ad_inline.f --width 4 \$<
- # setup some links
+ # link the XAIF schema files
  %.xsd:
          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
- mfef90:
-         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
  # link the support files:
- \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
+ \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
-         \$(LN) ../OAD_support/\$@ .
+         \$(LN) \${OADTOOLS}/\$@ .
- whirl2xaif xaif2whirl:
-         \$(LN) \${OPENADFORTTK}/bin/\$@ .
- preProcess.py postProcess.py:
+ AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag
-         \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
- whirl2f whirl2f_be:
-         \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
- oadDriver:
-         \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
- AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.make postProcess.tag postProcess.comp
  # ============ end OpenAD specific section ==============
-Line 3142 
 for i in $NOOPTFILES ; do
+Line 3458 
 for i in $NOOPTFILES ; do
  done
  echo "  Add rules for links"
- cat srclinks.tmp >> $MAKEFILE
+ cat $TMP.srclinks >> $MAKEFILE
- rm -f srclinks.tmp
+ rm -f $TMP.srclinks
  echo "  Adding makedepend marker"
  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE
-Line 3151 
 printf "\n\n# DO NOT DELETE\n" >> $MAKEF
+Line 3467 
 printf "\n\n# DO NOT DELETE\n" >> $MAKEF
  printf "\n===  Done  ===\n"
  # Create special header files
- $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp"
+ $BASH $TOOLSDIR/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp"
  if test ! -f $PACKAGES_DOT_H ; then
      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
  else
-Line 3165 
 else
+Line 3481 
 else
      fi
  fi
  if test ! -f AD_CONFIG.h ; then
-     $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
+     $BASH $TOOLSDIR/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
  fi
  #  Write the "state" for future records
- if test "x$DUMPSTATE" != xf ; then
+ if test "x$DUMPSTATE" = xt ; then
      printf "" > genmake_state
      for i in $gm_state ; do
          t1="t2=\$$i"
          eval $t1
-         echo "$i='$t2'" >> genmake_state
+         echo "$i='$t2'" | sed -e 's/  */ /g' >> genmake_state
      done
  fi

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