/[MITgcm]/MITgcm/tools/genmake2

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-revision 1.205 by jmc,
Sun May 23 03:45:58 2010 UTC
+revision 1.209 by jmc,
Mon Nov  1 00:20:28 2010 UTC
 Line 56 
 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 ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp
-Line 67 
 expand_pkg_groups() {
+Line 66 
 expand_pkg_groups() {
              if test "x$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"
-Line 110 
 EOF
+Line 109 
 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 146 
 EOF
+Line 145 
 EOF
              check_for_broken_Ff
          else
              cat <<EOF 2>&1
  ERROR: Your file system cannot distinguish between *.F and *.f files
    (fails the "make/ln" test) and this program cannot find a suitable
    replacement extension.  Please try a different build environment or
    contact the <MITgcm-support@mitgcm.org> list for help.
  EOF
-Line 194 
 look_for_makedepend()  {
+Line 193 
 look_for_makedepend()  {
          cat <<EOF >> $MAKEFILE
  #   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
  #
  #   Some "makedepend" implementations will die if they cannot
  #   find a Makefile -- so this file is here to gives them an
  #   empty one to find and parse.
  EOF
          cat <<EOF >> genmake_tc.f
-Line 212 
 EOF
+Line 211 
 EOF
              MAKEDEPEND=makedepend
          else
              echo "    a system-default makedepend was not found."
              #  Try to build the cyrus implementation
              build_cyrus_makedepend
              RETVAL=$?
-Line 269 
 build_embed_encode()
+Line 268 
 build_embed_encode()
              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 && $comm ) > /dev/null 2>&1
              RETVAL=$?
-Line 304 
 find_possible_configs()  {
+Line 303 
 find_possible_configs()  {
      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:  $PLATFORM"
      echo "test" > test
      ln -s ./test link
      RETVAL=$?
-Line 442 
 Error: No options file was found in:  $R
+Line 441 
 Error: No options file was found in:  $R
  EOF
          exit 1
      fi
  #     # look for possible MPI libraries
  #     mpi_libs=
  #     mpi_fort=`which mpif77 2>/dev/null`
-Line 461 
 EOF
+Line 460 
 EOF
  #       if test "x${RETVAL}" = x0 ; then
  #           a=`cat out`
  #           for i in $a ; do
  #               case $i in
  #                   -*)
  #                       mpi_libs="$mpi_libs $i" ;;
  #               esac
-Line 484 
 get_pdepend_list()  {
+Line 483 
 get_pdepend_list()  {
          > ./.pd_tmp
      RETVAL=$?
      if test ! "x${RETVAL}" = x0 ; then
-       echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$1\""
+       echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
        exit 1
      fi
      . ./.pd_tmp
-Line 512 
 Usage: "$0" [OPTIONS]
+Line 511 
 Usage: "$0" [OPTIONS]
        -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
+     -pgroups NAME | --pgroups NAME
-       -pdefault=NAME | --pdefault=NAME
+       -pgroups=NAME | --pgroups=NAME
-           Get the default package list from "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
-Line 542 
 Usage: "$0" [OPTIONS]
+Line 541 
 Usage: "$0" [OPTIONS]
      -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.
      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
-Line 591 
 Usage: "$0" [OPTIONS]
+Line 590 
 Usage: "$0" [OPTIONS]
      -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
-Line 628 
 Usage: "$0" [OPTIONS]
+Line 627 
 Usage: "$0" [OPTIONS]
            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]
    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'
-Line 659 
 get_fortran_c_namemangling()  {
+Line 658 
 get_fortran_c_namemangling()  {
      fi
      default_nm="#define FC_NAMEMANGLE(X) X ## _"
      cat > genmake_test.c <<EOF
  void tcall( char * string ) { tsub( string ); }
  EOF
-Line 1051 
 ENABLE=
+Line 1050 
 ENABLE=
  DISABLE=
  # MAKEFILE=
  # MAKEDEPEND=
- PDEPEND=
+ PKG_DEPEND=
+ PKG_GROUPS=
  DUMPSTATE=t
- PDEFAULT=
  OPTFILE=
  INCLUDES="-I. $INCLUDES"
  FFLAGS=
-Line 1138 
 FTL_TAF_FLAGS=
+Line 1137 
 FTL_TAF_FLAGS=
  SVD_TAMC_FLAGS=
  TAMC_EXTRA=
  #  The following state can be set directly by command-line switches
- gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
+ gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS MAKEFILE MAKEDEPEND PLATFORM ROOTDIR MODS DISABLE ENABLE"
  gm_s2="FC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
  #  The following state is not directly set by command-line switches
- gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
+ gm_s3="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
- gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
+ gm_s4="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
- gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
+ gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD THISHOST THISUSER THISDATE THISVER MACHINE"
  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
- gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
+ gm_s7="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"
  #  The following are all related to adjoint/tangent-linear stuff
  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
-Line 1169 
 quick list of options, use "genmake -h"
+Line 1167 
 quick list of options, use "genmake -h"
  EOF
+ #- clean-up previous genmake logfiles:
+ rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
  echo "===  Processing options files and arguments  ==="
  gm_local="genmake_local"
  printf "  getting local config information:  "
-Line 1194 
 for ac_option in "$@" ; do
+Line 1195 
 for ac_option in "$@" ; do
          ac_prev=
          continue
      fi
      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
      case $ac_option in
          -help | --help | -h | --h)
-Line 1215 
 for ac_option in "$@" ; do
+Line 1216 
 for ac_option in "$@" ; do
              AD_OPTFILE=$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 ;;
-Line 1372 
 for ac_option in "$@" ; do
+Line 1373 
 for ac_option in "$@" ; do
              ;;
      esac
  done
-Line 1384 
 if test -f ./.genmakerc ; then
+Line 1385 
 if test -f ./.genmakerc ; then
      echo "    http://mitgcm.org/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 1853 
 ERROR: neither of the two default script
+Line 1854 
 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 1874 
 echo " $STANDARDDIRS " | grep ' model '
+Line 1875 
 echo " $STANDARDDIRS " | grep ' model '
  ckM=$?
  echo " $STANDARDDIRS " | grep ' eesupp ' > /dev/null 2>&1
  ckE=$?
  if test $ckM = 0 -a $ckE = 1 ; then
      STANDARDDIRS="$STANDARDDIRS eesupp"
  fi
-Line 1883 
 fi
+Line 1884 
 fi
  #  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 1898 
 fi
+Line 1900 
 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_${pdir}.errors
-Line 1911 
 for pdir in exch2 regrid ; do
+Line 1914 
 for pdir in exch2 regrid ; do
  done
  printf "\n===  Determining package settings  ===\n"
- if  test "x${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."
+ else
+     if test ! -r ${PKG_DEPEND} ; then
+         echo "Error:  can't read package dependency info from PKG_DEPEND=\"$PKG_DEPEND\""
+         exit 1
      fi
+     echo "  getting package dependency info from  $PKG_DEPEND"
+ #  Strip the comments and then convert the dependency file into arrays: PNAME, DNAME
+     get_pdepend_list $PKG_DEPEND
+ fi
+ # A default package groups file "$ROOTDIR/pkg/pkg_groups" is provided
+ #  to define the "default_pkg_list" and package groups (for convenience, one
+ #  can specify a group of packages using names like "ocean" and "atmosphere").
+ if test "x${PKG_GROUPS}" = x ; then
+     tmp=$ROOTDIR"/pkg/pkg_groups"
+     if test -r $tmp ; then PKG_GROUPS=$tmp ; fi
+ fi
+ if test "x${PKG_GROUPS}" = x ; then
+         echo "Warning:  No package groups information was specified."
+         echo "  Please check that ROOTDIR/pkg/pkg_groups exists."
  else
-     if test ! -r ${PDEPEND} ; then
+     if test ! -r ${PKG_GROUPS} ; then
-         echo "Error:  can't read package dependency info from PDEPEND=\"$PDEPEND\""
+         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
- echo "  getting package dependency info from  $PDEPEND"
- #  Strip the comments and then convert the dependency file into
+ #  Search for packages to compile.
- #  two arrays: PNAME, DNAME
+ echo "  checking list of packages to compile:"
- get_pdepend_list $PDEPEND
+ PKG_LIST=
+ if test "x${PKG_LIST}" = x ; then
- #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
- #  file has been added so that, for convenience, one can specify
- #  groups of packages using names like "ocean" and "atmosphere".
- echo "  checking default package list:  "
- if test "x${PDEFAULT}" = x ; then
      for i in "." $MODS ; do
          if test -r $i"/packages.conf" ; then
-                 PDEFAULT=$i"/packages.conf"
+                 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: $PACKAGES"
+ fi
  echo "  applying DISABLE settings"
  echo "" > ./.tmp_pack
-Line 1999 
 PACKAGES="$PACKAGES $ENABLE"
+Line 2021 
 PACKAGES="$PACKAGES $ENABLE"
  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
-Line 2011 
 done
+Line 2033 
 done
  rm -f ./.tmp_pack
  echo "    packages are: $PACKAGES"
  #  Check for package MNC: if NetCDF is available, then build the MNC
  #  template files ; otherwise, delete mnc from the list of packages.
  echo " $PACKAGES " | grep ' mnc ' > /dev/null 2>&1
- RETVAL=$?
+ 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
+     # we have NetCDF, we try to build MNC template files
+     ( cd $ROOTDIR"/pkg/mnc" && $MAKE testclean && $MAKE templates ) > make_mnc.errors 2>&1
+     RETVAL=$?
+     if test "x${RETVAL}" = x0 ; then
+         rm -f make_mnc.errors
+     else
+         echo "Error: problem encountered while building source files in pkg/mnc:"
+         cat make_mnc.errors 1>&2
+         if test "x$mnc_in" = x0 ; then
+             exit 1
          else
-             echo "Error: problem encountered while building source files in pkg/mnc:"
+             DISABLE="$DISABLE mnc"
-             cat make_mnc.errors 1>&2
-             exit 1
          fi
      fi
  fi
  #  Check for package PROFILES: if NetCDF is not available,
  #  then delete profiles from the list of available packages.
- echo " $PACKAGES " | grep ' profiles ' > /dev/null 2>&1
+ if test "x$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="$DISABLE profiles"
      fi
  fi
- echo "  applying package dependency rules"
+ if  test "x${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 2136 
 while test "x$ck" != xtt ; do
+Line 2166 
 while test "x$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
-Line 2144 
 while test "x$ck" != xtt ; do
+Line 2174 
 while test "x$ck" != xtt ; do
          #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 $adr ; then
-Line 2162 
 done
+Line 2193 
 done
  # Create a list of #define and #undef to enable/disable packages
  PACKAGES_DOT_H=PACKAGES_CONFIG.h
  #  The following UGLY HACK sets multiple "#undef"s and it needs to go
  #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h
  #  file would eventually be split up so that all package-related #define
  #  statements could be separated and handled only by genmake.
  names=`ls -1 "$ROOTDIR/pkg"`
-Line 2191 
 for i in $PACKAGES ; do
+Line 2222 
 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."
-Line 2261 
 if test -f ./adSrcFiles.tmp ; then
+Line 2292 
 if test -f ./adSrcFiles.tmp ; then
      rm -f ./adSrcFiles.tmp
  fi
  echo "  Creating the list of files for the adjoint compiler."
+ touch adSrcFiles.tmp
  for i in $SOURCEDIRS ; do
      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
      for j in $list_files ; do
-Line 2293 
 if test ! "x$DIVA" = x ; then
+Line 2325 
 if test ! "x$DIVA" = x ; then
          fi
          MPIINCLUDEDIR='$MPIHOME/include'
      fi
      if test -r $MPIINCLUDEDIR/mpif.h ; then
          for i in $MPI_HEADER_FILES; do
              cp -p $MPIINCLUDEDIR/$i ./mpi_headers
-Line 2328 
 if test ! -r ".links.tmp/foo" ; then
+Line 2360 
 if test ! -r ".links.tmp/foo" ; then
  fi
  rm -f .links.tmp/foo
  if test "x$OPENAD" != x ; then
      OAD_DONT_COMPILE="/dev/null"
      OAD_DONT_TRANSFORM="/dev/null"
      OAD_KEEP_ORIGINAL="/dev/null"
-Line 2381 
 for d in $alldirs ; do
+Line 2413 
 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
-Line 2421 
 for d in $alldirs ; do
+Line 2453 
 for d in $alldirs ; do
                        F)
                          echo    " \\"  >> F77srclist.tmp
                          printf " $sf" >> F77srclist.tmp
                          if test "x$OPENAD" != x ; then
                              basename=${sf%%.F}
                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
                              if test -z "$isAD" ; then
                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
                                  if test -z "$toBeIgnored" ; then
                                      echo    " \\"  >> nonADF77srclist.tmp
                                      printf " $sf" >> nonADF77srclist.tmp
                                  else
                                      echo "    not to be compiled   :  $sf"
                                  fi
                              else # file is initially listed as an AD file we want to exclude it
                                   # or we want to retain the untransformed version
                                  notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
                                  untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
                                  if test -n "$notToBeTransformed"; then
                                      echo "    not to be transformed:  $sf"
                                  fi
                                  if test -n "$untransformedVersionToBeKept" ; then
                                      echo "    original to be kept  :  $sf"
                                  fi
                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
                                      echo    " \\"  >> nonADF77srclist.tmp
                                      printf " $sf" >> nonADF77srclist.tmp
-Line 2666 
 Clean:
+Line 2698 
 Clean:
          @make clean
          @make cleanlinks
          -rm -f \$(SPECIAL_FILES)
-         -rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
          -rm -f make.log run.log f90mkdepend.log *.bak "$MAKEFILE.old"
          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
  CLEAN:
          @make Clean
+         -rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-Line 2760 
 EOF
+Line 2792 
 EOF
  #===  Automatic Differentiation Rules  ===
  #===  for TAMC/TAF  ======================
  if test "x$OPENAD" = x ; then
  cat >>$MAKEFILE <<EOF
-Line 2820 
 adtafonly:
+Line 2852 
 adtafonly:
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
  ad_tamc_output.$FS: ad_input_code.$FS
          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
  ad_tamc: ad_tamc_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
  adonlyfwd:
          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
  adtrick:
          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
-Line 2859 
 ftltafonly:
+Line 2891 
 ftltafonly:
          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
  ftl_taf: ftl_taf_output.o \$(OBJFILES)
          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
  ftl_tamc_output.$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 ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
  # ... SVD ...
-Line 2895 
 svd_touch:
+Line 2927 
 svd_touch:
  EOF
  fi
  #===  for OpenAD  ========================
  if test "x$OPENAD" != x ; then
  # ============ begin OpenAD specific section ==============
  cat >>$MAKEFILE <<EOF
  # all the source files linked from the various locations:
  ALL_LINKED_FILES= \
  \$(F77_SRC_FILES) \
  \$(C_SRC_FILES) \
-Line 2957 
 rm -f adSrcFiles.tmp
+Line 2989 
 rm -f adSrcFiles.tmp
  cat >>$MAKEFILE <<EOF
  adAll: \$(EXE_AD)
  .PHONY: adAll
  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
-Line 2975 
 w2f__types.F90 \
+Line 3007 
 w2f__types.F90 \
  OAD_active.F90 \
  OAD_cp.F90 \
  OAD_rev.F90 \
  OAD_tape.F90
  OPENAD_SUPPORT_C_SRC_FILES = \
  iaddr.c \
-Line 2984 
 timeRatio.c
+Line 3016 
 timeRatio.c
  f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$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$FS90
          cat \$^ > \$@
  f95_test.out: f95_test_mods.f90 f95_test.f90
          f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
          f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
  # the file included below is created by the
  # postProcessor and its inclusion sets the
  # variable POSTPROCESSEDFILES
  # used below. Because the file is made during
  # make it won't be read until the second (recursive)
  # invocation in the rule below
  -include postProcess.make
-Line 3021 
 endif
+Line 3053 
 endif
  openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
  .PHONY: openad
  # create the module files
  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
  # create the header files
  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
  # change everybody else to use the new module files:
-Line 3048 
 CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS9
+Line 3080 
 CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS9
  ad_input_code.f$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 > \$@
-Line 3068 
 ad_input_code_sf.w2f.pre.f$FS90: ad_inpu
+Line 3100 
 ad_input_code_sf.w2f.pre.f$FS90: ad_inpu
          ./preProcess.py --timing --r8 -H -S \$< -o \$@
  # F -> WHIRL
  # note that the canonicalized version cuts off at col 72
  # doing this also for string constants which is ok as long
  # as we are in fixed mode and cut of exactly there.
  # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
  # characters respectively.
  ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
          ./mfef90 -r8 -z -F \$<
-Line 3091 
 ad_input_code_sf.w2f.pre.xb.x2w.B : ad_i
+Line 3123 
 ad_input_code_sf.w2f.pre.xb.x2w.B : ad_i
  # WHIRL' -> F'
  ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
          ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
  # insert template directives
  ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
-Line 3100 
 ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f
+Line 3132 
 ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f
  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
  # postprocess F'
  postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)
          # the target is a placeholder to signal execution of the rule
          touch \$@
          # this step also creates the file postProcess.make but we cannot
          # name it as the target or else make will try to remake it for
          # the include directive above for any rule, e.g. make clean
          ./postProcess.py --progress --timing --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<
-Line 3111 
 postProcess.tag: ad_input_code_sf.w2f.pr
+Line 3143 
 postProcess.tag: ad_input_code_sf.w2f.pr
  %.xsd:
          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
  mfef90:
          \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
  # link the support files:
  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
          \$(LN) ../OAD_support/\$@ .
  whirl2xaif xaif2whirl:
          \$(LN) \${OPENADFORTTK}/bin/\$@ .
  preProcess.py postProcess.py:
          \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
  whirl2f whirl2f_be:
-Line 3175 
 printf "\n\n# DO NOT DELETE\n" >> $MAKEF
+Line 3207 
 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"
  if test ! -f $PACKAGES_DOT_H ; then
      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
  else

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