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revision 1.158 by heimbach, Thu Nov 23 05:23:05 2006 UTC revision 1.193 by utke, Tue Apr 28 18:46:06 2009 UTC
# Line 601  Usage: "$0" [OPTIONS] Line 601  Usage: "$0" [OPTIONS]
601    
602      -gsl | --gsl      -gsl | --gsl
603            Use GSL to control floating point rounding and precision            Use GSL to control floating point rounding and precision
604        -devel | --devel
605              Add additional warning and debugging flags for development
606    
607      -mpi | --mpi      -mpi | --mpi
608            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
# Line 609  Usage: "$0" [OPTIONS] Line 611  Usage: "$0" [OPTIONS]
611            set to PATH. i.e. Include files from \$PATH/include, link to libraries            set to PATH. i.e. Include files from \$PATH/include, link to libraries
612            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
613    
614        -omp | --omp
615              Activate OpenMP code + use Compiler option OMPFLAG
616        -omp=OMPFLAG | --omp=OMPFLAG
617              Activate OpenMP code + use Compiler option OMPFLAG
618    
619      -es | --es | -embed-source | --embed-source      -es | --es | -embed-source | --embed-source
620            Embed a tarball containing the full source code            Embed a tarball containing the full source code
621            (including the Makefile, etc.) used to build the            (including the Makefile, etc.) used to build the
# Line 744  void FC_NAMEMANGLE(cloc) ( double *curti Line 751  void FC_NAMEMANGLE(cloc) ( double *curti
751   *curtim = *curtim/1.E6;   *curtim = *curtim/1.E6;
752  }  }
753  EOF  EOF
754      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
755        echo $COMM >> genmake_warnings
756        $COMM >> genmake_warnings 2>&1
757      RET_C=$?      RET_C=$?
758      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
759        program hello        program hello
# Line 754  EOF Line 763  EOF
763        print *," HELLO WORLD", wtime        print *," HELLO WORLD", wtime
764        end        end
765  EOF  EOF
766      $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
767        echo $COMM >> genmake_warnings
768        $COMM >> genmake_warnings 2>&1
769      RET_F=$?      RET_F=$?
770      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
771      RETVAL=$?      RETVAL=$?
# Line 801  void FC_NAMEMANGLE(sigreg) (int * aip) Line 812  void FC_NAMEMANGLE(sigreg) (int * aip)
812      return;      return;
813  }  }
814  EOF  EOF
815      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
816        echo $COMM >> genmake_warnings
817        $COMM >> genmake_warnings 2>&1
818      RET_C=$?      RET_C=$?
819      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
820        program hello        program hello
# Line 849  void FC_NAMEMANGLE(setrlstk) () Line 862  void FC_NAMEMANGLE(setrlstk) ()
862      return;      return;
863  }  }
864  EOF  EOF
865      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
866        echo $COMM >> genmake_warnings
867        $COMM >> genmake_warnings 2>&1
868      RET_C=$?      RET_C=$?
869      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
870        program hello        program hello
# Line 893  void FC_NAMEMANGLE(tfsize) ( int *nbyte Line 908  void FC_NAMEMANGLE(tfsize) ( int *nbyte
908          *nbyte = -1;          *nbyte = -1;
909  }  }
910  EOF  EOF
911      make genmake_tc_1.o >> genmake_tc.log 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
912        echo $COMM >> genmake_warnings
913        $COMM >> genmake_tc.log 2>&1
914      RET_C=$?      RET_C=$?
915      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
916        program hello        program hello
# Line 983  EOF Line 1000  EOF
1000          if test "x$RET_COMPILE" = x0 ; then          if test "x$RET_COMPILE" = x0 ; then
1001              LIBS="$LIBS -lnetcdf"              LIBS="$LIBS -lnetcdf"
1002              HAVE_NETCDF=t              HAVE_NETCDF=t
1003            else
1004            # try again with "-lnetcdff" added to the libs
1005                echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
1006                echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
1007                echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
1008                echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
1009                cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
1010                    &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
1011                    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
1012                RET_COMPILE=$?
1013                cat genmake_tnc.log >> genmake_warnings
1014                if test "x$RET_COMPILE" = x0 ; then
1015                    LIBS="$LIBS -lnetcdff -lnetcdf"
1016                    HAVE_NETCDF=t
1017                fi
1018          fi          fi
1019      fi      fi
1020      rm -f genmake_tnc*      rm -f genmake_tnc*
# Line 1018  OPTFILE= Line 1050  OPTFILE=
1050  INCLUDES="-I. $INCLUDES"  INCLUDES="-I. $INCLUDES"
1051  FFLAGS=  FFLAGS=
1052  FOPTIM=  FOPTIM=
1053    FEXTRAFLAGS=
1054    USE_EXTENDED_SRC=
1055    EXTENDED_SRC_FLAG=
1056  CFLAGS=  CFLAGS=
1057  KFLAGS1=  KFLAGS1=
1058  KFLAGS2=  KFLAGS2=
# Line 1028  NOOPTFILES= Line 1063  NOOPTFILES=
1063  NOOPTFLAGS=  NOOPTFLAGS=
1064  MPI=  MPI=
1065  MPIPATH=  MPIPATH=
1066    OMP=
1067    OMPFLAG=
1068  TS=  TS=
1069  PAPIS=  PAPIS=
1070  PCLS=  PCLS=
# Line 1036  PAPI= Line 1073  PAPI=
1073  PCL=  PCL=
1074  HPMT=  HPMT=
1075  GSL=  GSL=
1076    DEVEL=
1077  HAVE_TEST_L=  HAVE_TEST_L=
1078    
1079  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
# Line 1094  TAMC_EXTRA= Line 1132  TAMC_EXTRA=
1132    
1133  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1134  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
1135  gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL MPI JAM DUMPSTATE STANDARDDIRS"  gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
1136    
1137  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1138  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
1139  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
1140  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
1141  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
# Line 1124  EOF Line 1162  EOF
1162    
1163  echo "===  Processing options files and arguments  ==="  echo "===  Processing options files and arguments  ==="
1164  gm_local="genmake_local"  gm_local="genmake_local"
 for i in . $MODS ; do  
     if test -r $i/$gm_local ; then  
         . $i/$gm_local  
         break  
     fi  
 done  
1165  printf "  getting local config information:  "  printf "  getting local config information:  "
1166  if test -f $gm_local ; then  if test -f $gm_local ; then
1167      echo "using $gm_local"      echo "using $gm_local"
# Line 1141  else Line 1173  else
1173  fi  fi
1174    
1175  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
 #OPTIONS=  
 #n=0  
 #for i ; do  
 #   echo "$i  $n"  
 #   setvar="OPTIONS[$n]='$i'"  
 #   #  echo "  $setvar"  
 #   eval "$setvar"  
 #   n=$(( $n + 1 ))  
 #done  
1176  #parse_options  #parse_options
1177  ac_prev=  ac_prev=
1178  for ac_option in "$@" ; do  for ac_option in "$@" ; do
# Line 1292  for ac_option in "$@" ; do Line 1315  for ac_option in "$@" ; do
1315          -gsl | --gsl)          -gsl | --gsl)
1316              GSL=true ;;              GSL=true ;;
1317    
1318            -devel | --devel)
1319                DEVEL=true ;;
1320    
1321          -mpi | --mpi)          -mpi | --mpi)
1322              MPI=true ;;              MPI=true ;;
1323          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
1324              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1325              MPI=true ;;              MPI=true ;;
1326                    
1327  #       -jam | --jam)          -omp | --omp)
1328  #           JAM=1 ;;              OMP=true ;;
1329  #       -nojam | --nojam)          -omp=* | --omp=*)
1330  #           JAM=0 ;;              OMPFLAG=$ac_optarg
1331                OMP=true ;;
1332                    
1333          -ds | --ds)          -ds | --ds)
1334              DUMPSTATE=t ;;              DUMPSTATE=t ;;
# Line 1340  done Line 1367  done
1367  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1368      echo      echo
1369      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
1370      echo "  file.  This file format is no longer supported.  Please see:"      echo "  file.  This file format is no longer supported.  For directions on"
1371      echo      echo "  how to setup and use the new \"genmake2\" script, please see:"
1372      echo "    http://mitgcm.org/devel_HOWTO/"      echo "    http://mitgcm.org/devel_HOWTO/"
1373      echo      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
1374      echo "  for directions on how to setup and use the new \"genmake2\" input"      echo "WARNING: ignore \"./.genmakerc\" and continue."
     echo "  files and send an email to MITgcm-support@mitgcm.org if you want help."  
1375      echo      echo
1376  fi  fi
1377    
# Line 1377  if test ! -d ${ROOTDIR} ; then Line 1403  if test ! -d ${ROOTDIR} ; then
1403  fi  fi
1404    
1405  #  Find the MITgcm ${THISVER}  #  Find the MITgcm ${THISVER}
1406  if test -f "${ROOTDIR}/doc/tag-index" ; then  version_file="${ROOTDIR}/doc/tag-index"
1407      THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`  if test -f $version_file ; then
1408        THISVER=`grep '^checkpoint' $version_file | head -1`
1409    #-  remove ./BUILD_INFO.h file if older than version_file
1410        if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
1411            echo "  remove ./BUILD_INFO.h (older than ${version_file})"
1412            rm -f ./BUILD_INFO.h
1413        fi
1414  fi  fi
1415    
1416  if test "x$MAKEFILE" = x ; then  if test "x$MAKEFILE" = x ; then
# Line 1534  if test ! "x$MPI" = x ; then Line 1566  if test ! "x$MPI" = x ; then
1566        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1567        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
1568  fi  fi
1569    if test ! "x$OMP" = x ; then
1570          echo "  Add OMPFLAG and turn on OpenMP cpp macros"
1571          FFLAGS="$FFLAGS $OMPFLAG"
1572          F90FLAGS="$F90FLAGS $OMPFLAG"
1573          DEFINES="$DEFINES -DUSE_OMP_THREADING"
1574    fi
1575    
1576  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1577        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
# Line 1542  if test ! "x$TS" = x ; then Line 1580  if test ! "x$TS" = x ; then
1580        else        else
1581              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1582        fi        fi
1583          PACKAGES="$PACKAGES showflops"
1584  fi  fi
1585  if test ! "x$PAPIS" = x ; then  if test ! "x$PAPIS" = x ; then
1586        echo "  Turning on PAPI flop summary per timestep"        echo "  Turning on PAPI flop summary per timestep"
# Line 1553  if test ! "x$PAPIS" = x ; then Line 1592  if test ! "x$PAPIS" = x ; then
1592        fi        fi
1593        INCLUDES="$INCLUDES $PAPIINC"        INCLUDES="$INCLUDES $PAPIINC"
1594        LIBS="$LIBS $PAPILIB"        LIBS="$LIBS $PAPILIB"
1595          PACKAGES="$PACKAGES showflops"
1596  fi  fi
1597  if test ! "x$PCLS" = x ; then  if test ! "x$PCLS" = x ; then
1598        echo "  Turning on PCL counter summary per timestep"        echo "  Turning on PCL counter summary per timestep"
# Line 1564  if test ! "x$PCLS" = x ; then Line 1604  if test ! "x$PCLS" = x ; then
1604        fi        fi
1605        INCLUDES="$INCLUDES $PCLINC"        INCLUDES="$INCLUDES $PCLINC"
1606        LIBS="$LIBS $PCLLIB"        LIBS="$LIBS $PCLLIB"
1607          PACKAGES="$PACKAGES showflops"
1608  fi  fi
1609  if test ! "x$PAPI" = x ; then  if test ! "x$PAPI" = x ; then
1610        if test ! "x$PAPIS" = x ; then        if test ! "x$PAPIS" = x ; then
# Line 1612  if test ! "x$GSL" = x ; then Line 1653  if test ! "x$GSL" = x ; then
1653        INCLUDES="$INCLUDES $GSLINC"        INCLUDES="$INCLUDES $GSLINC"
1654        LIBS="$LIBS $GSLLIB"        LIBS="$LIBS $GSLLIB"
1655  fi  fi
1656    #- if USE_EXTENDED_SRC is set, add EXTENDED_SRC_FLAG to FFLAGS :
1657    if test ! "x$USE_EXTENDED_SRC" = x ; then
1658          FFLAGS="$FFLAGS $EXTENDED_SRC_FLAG"
1659          F90FIXEDFORMAT="$F90FIXEDFORMAT $EXTENDED_SRC_FLAG"
1660    fi
1661    
1662  printf "\n===  Checking system libraries  ===\n"  printf "\n===  Checking system libraries  ===\n"
1663  printf "  Do we have the system() command using $FC...  "  printf "  Do we have the system() command using $FC...  "
# Line 1734  fi Line 1780  fi
1780    
1781    
1782  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
1783  printf "  Adding MODS directories:  "  printf "  Adding MODS directories: "
1784  for d in $MODS ; do  for d in $MODS ; do
1785      if test ! -d $d ; then      if test ! -d $d ; then
1786          echo          echo
1787          echo "Error: MODS directory \"$d\" not found!"          echo "Error: MODS directory \"$d\" not found!"
1788          exit 1          exit 1
1789      else      else
1790          printf " $d"          printf "$d "
1791          SOURCEDIRS="$SOURCEDIRS $d"          SOURCEDIRS="$SOURCEDIRS $d"
1792          INCLUDEDIRS="$INCLUDEDIRS $d"          INCLUDEDIRS="$INCLUDEDIRS $d"
1793      fi      fi
# Line 1943  done Line 1989  done
1989  rm -f ./.tmp_pack  rm -f ./.tmp_pack
1990  echo "    packages are:  $PACKAGES"  echo "    packages are:  $PACKAGES"
1991    
1992  #  Check availability of NetCDF and then either build the MNC template  #  Check for package MNC: if NetCDF is available, then build the MNC
1993  #  files or delete mnc from the list of available packages.  #  template files ; otherwise, delete mnc from the list of packages.
1994  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
1995  RETVAL=$?  RETVAL=$?
1996  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
# Line 1978  EOF Line 2024  EOF
2024      fi      fi
2025  fi  fi
2026    
2027    #  Check for package PROFILES: if NetCDF is not available,
2028    #  then delete profiles from the list of available packages.
2029    echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
2030    RETVAL=$?
2031    if test "x$RETVAL" = x0 ; then
2032        if test "x$HAVE_NETCDF" != xt ; then
2033            cat <<EOF
2034    
2035    *********************************************************************
2036    WARNING: the "profiles" package was enabled but tests failed to
2037      compile NetCDF applications.  Please check that:
2038    
2039      1) NetCDF is correctly installed for this compiler and
2040      2) the LIBS variable (within the "optfile") specifies the correct
2041           NetCDF library to link against.
2042    
2043      Due to this failure, the "profiles" package is now DISABLED.
2044    *********************************************************************
2045    
2046    EOF
2047            PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
2048            DISABLE="$DISABLE profiles"
2049        fi
2050    fi
2051    
2052  echo "  applying package dependency rules"  echo "  applying package dependency rules"
2053  ck=  ck=
2054  while test "x$ck" != xtt ; do  while test "x$ck" != xtt ; do
2055      i=0      i=0
2056      # rtot=${#PNAME[@]}      # rtot=${#PNAME[@]}
2057      rtot=$nname      rtot=$nname
2058      while test $i -lt $rtot ; do      while test $i -le $rtot ; do
2059    
2060          #  Is $pname in the current $PACKAGES list?          #  Is $pname in the current $PACKAGES list?
2061          #  pname=${PNAME[$i]}          #  pname=${PNAME[$i]}
# Line 2018  while test "x$ck" != xtt ; do Line 2089  while test "x$ck" != xtt ; do
2089    
2090          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2091          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
2092                #echo "   " $pname ": need to add :" $dname
2093              in_dis="f"              in_dis="f"
2094              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2095                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 2162  fi Line 2234  fi
2234    
2235  #  Here, we build the list of files to be "run through" the adjoint  #  Here, we build the list of files to be "run through" the adjoint
2236  #  compiler.  #  compiler.
2237  if test -f ./ad_files ; then  if test -f ./adSrcFiles.tmp ; then
2238      rm -f ./ad_files      rm -f ./adSrcFiles.tmp
2239  fi  fi
2240  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2241  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2242      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2243      for j in $list_files ; do      for j in $list_files ; do
2244          cat $i/$j >> ad_files          cat $i/$j >> adSrcFiles.tmp
2245      done      done
2246  done  done
2247  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2248      cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
2249      mv -f ad_files_f ad_files      mv -f adSrcFiles.tmp_f adSrcFiles.tmp
2250  fi  fi
2251    
2252  echo  echo
# Line 2232  if test ! -r ".links.tmp/foo" ; then Line 2304  if test ! -r ".links.tmp/foo" ; then
2304      exit 1      exit 1
2305  fi  fi
2306  rm -f .links.tmp/foo  rm -f .links.tmp/foo
2307    
2308    if test "x$OPENAD" != x ; then
2309        OAD_DONT_COMPILE="/dev/null"
2310        OAD_DONT_TRANSFORM="/dev/null"
2311        OAD_KEEP_ORIGINAL="/dev/null"
2312        OAD_CB2M_FILES="/dev/null"
2313        echo "  looking for dontCompile file:  "
2314        for i in "." $MODS ; do
2315            if test -r $i"/dontCompile" ; then
2316                OAD_DONT_COMPILE=$i"/dontCompile"
2317                echo "     found $OAD_DONT_COMPILE"
2318                break
2319            fi
2320        done
2321        echo "  looking for dontTransform file:  "
2322        for i in "." $MODS ; do
2323            if test -r $i"/dontTransform" ; then
2324                OAD_DONT_TRANSFORM=$i"/dontTransform"
2325                echo "     found $OAD_DONT_TRANSFORM"
2326                break
2327            fi
2328        done
2329        echo "  looking for keepOriginal file:  "
2330        for i in "." $MODS ; do
2331            if test -r $i"/keepOriginal" ; then
2332                OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2333                echo "     found $OAD_KEEP_ORIGINAL"
2334                break
2335            fi
2336        done
2337        echo "  looking for cb2mFiles:  "
2338        for i in "." $MODS ; do
2339            if test -r $i"/cb2mFiles" ; then
2340                OAD_CB2M_FILES=$i"/cb2mFiles"
2341                echo "     found $OAD_CB2M_FILES"
2342                break
2343            fi
2344        done
2345        echo "   OpenAD exceptions:  "
2346    fi
2347    
2348  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > srclinks.tmp
2349  echo "" >> srclinks.tmp  echo "" >> srclinks.tmp
2350  printf 'SRCFILES = '    > srclist.inc  printf 'F77_SRC_FILES = ' > F77srclist.tmp
2351  printf 'CSRCFILES = '   > csrclist.inc  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
2352  printf 'F90SRCFILES = ' > f90srclist.inc  printf 'C_SRC_FILES = '   > csrclist.tmp
2353  printf 'HEADERFILES = ' > hlist.inc  printf 'F90_SRC_FILES = ' > F90srclist.tmp
2354  printf 'AD_FLOW_FILES = ' > ad_flow_files.inc  printf 'H_SRC_FILES = '   > hsrclist.tmp
2355    printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
2356  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2357  for d in $alldirs ; do  for d in $alldirs ; do
2358      deplist=      deplist=
2359      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2360      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
2361        if test "x$OPENAD" != x ; then
2362            sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2363        fi
2364      for sf in $sfiles ; do      for sf in $sfiles ; do
2365          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2366              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
# Line 2278  for d in $alldirs ; do Line 2395  for d in $alldirs ; do
2395                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2396                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2397                      case $extn in                      case $extn in
2398                          F)                        F)
2399                              echo    " \\"  >> srclist.inc                          echo    " \\"  >> F77srclist.tmp
2400                              printf " $sf" >> srclist.inc                          printf " $sf" >> F77srclist.tmp
2401                              ;;                          if test "x$OPENAD" != x ; then
2402                          F90)                              basename=${sf%%.F}
2403                              echo    " \\"  >> f90srclist.inc                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2404                              printf " $sf" >> f90srclist.inc                              if test -z "$isAD" ; then
2405                              ;;                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2406                          c)                                  if test -z "$toBeIgnored" ; then
2407                              echo    " \\"  >> csrclist.inc                                      echo    " \\"  >> nonADF77srclist.tmp
2408                              printf " $sf" >> csrclist.inc                                      printf " $sf" >> nonADF77srclist.tmp
2409                              ;;                                  else
2410                          h)                                      echo "    not to be compiled   :  $sf"
2411                              echo    " \\"  >> hlist.inc                                  fi
2412                              printf " $sf" >> hlist.inc                              else # file is initially listed as an AD file we want to exclude it
2413                              ;;                                   # or we want to retain the untransformed version
2414                          flow)                                  notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
2415                              echo    " \\"  >> ad_flow_files.inc                                  untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
2416                              printf " $sf" >> ad_flow_files.inc                                  if test -n "$notToBeTransformed"; then
2417                              ;;                                      echo "    not to be transformed:  $sf"
2418                      esac                                  fi
2419                  fi                                  if test -n "$untransformedVersionToBeKept" ; then
2420                                        echo "    original to be kept  :  $sf"
2421                                    fi    
2422                                    if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2423                                        echo    " \\"  >> nonADF77srclist.tmp
2424                                        printf " $sf" >> nonADF77srclist.tmp
2425                                    fi
2426                                fi
2427                            fi
2428                            ;;
2429                        F90)
2430                            echo    " \\"  >> F90srclist.tmp
2431                            printf " $sf" >> F90srclist.tmp
2432                            ;;
2433                        c)
2434                            echo    " \\"  >> csrclist.tmp
2435                            printf " $sf" >> csrclist.tmp
2436                            ;;
2437                        h)
2438                            echo    " \\"  >> hsrclist.tmp
2439                            printf " $sf" >> hsrclist.tmp
2440                            ;;
2441                        flow)
2442                            echo    " \\"  >> ad_flow_files.tmp
2443                            printf " $sf" >> ad_flow_files.tmp
2444                            ;;
2445                       esac
2446                    fi
2447              fi              fi
2448          fi          fi
2449      done      done
2450      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2451          echo "" >> srclinks.tmp        if test "$d" != "." ; then
2452            echo "" >> srclinks.tmp
2453          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> srclinks.tmp
2454          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> srclinks.tmp
2455          printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp  # We need to make sure that the link isn't already there.
2456    # This may happen when make thinks that a header file has to be "remade"
2457    # because a module it depends on has changed.  In this case we do nothing.
2458            printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
2459          fi
2460      fi      fi
2461  done  done
2462  rm -rf .links.tmp  rm -rf .links.tmp
2463  echo "" >> srclist.inc  echo "" >> F77srclist.tmp
2464  echo "" >> csrclist.inc  echo "" >> nonADF77srclist.tmp
2465  echo "" >> f90srclist.inc  echo "" >> csrclist.tmp
2466  echo "" >> hlist.inc  echo "" >> F90srclist.tmp
2467  echo "" >> ad_flow_files.inc  echo "" >> hsrclist.tmp
2468    echo "" >> ad_flow_files.tmp
2469    
2470    CMDLINE=$0
2471    for xx in "$@" ; do nw=`echo $xx | wc -w`
2472        if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2473                            else CMDLINE="$CMDLINE '$xx'" ; fi
2474    done
2475    
2476  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
2477      mv -f $MAKEFILE "$MAKEFILE.bak"      mv -f $MAKEFILE "$MAKEFILE.bak"
# Line 2326  echo "#    $MACHINE" >> $MAKEFILE Line 2482  echo "#    $MACHINE" >> $MAKEFILE
2482  echo "# This makefile was generated automatically on" >> $MAKEFILE  echo "# This makefile was generated automatically on" >> $MAKEFILE
2483  echo "#    $THISDATE" >> $MAKEFILE  echo "#    $THISDATE" >> $MAKEFILE
2484  echo "# by the command:" >> $MAKEFILE  echo "# by the command:" >> $MAKEFILE
2485  echo "#    $0 $G2ARGS" >> $MAKEFILE  echo "#    $CMDLINE"  >> $MAKEFILE
2486  echo "# executed by:" >> $MAKEFILE  echo "# executed by:" >> $MAKEFILE
2487  echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE  echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
2488    
# Line 2383  else Line 2539  else
2539      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2540  fi  fi
2541    
 #  Note: figure out some way to add Hyades JAM libraries here  
2542  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2543  # Unix ln (link)  # Unix ln (link)
2544  LN = ${LN}  LN = ${LN}
# Line 2410  INCLUDES = ${INCLUDES} Line 2565  INCLUDES = ${INCLUDES}
2565  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2566  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2567  # Optim./debug for FC  # Optim./debug for FC
2568  FFLAGS = ${FFLAGS}  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
2569  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM}
2570  # Optim./debug for FC  # Optim./debug for FC
2571  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2572  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
2573    F90FIXEDFORMAT = ${F90FIXEDFORMAT}
2574  # Flags for CC  # Flags for CC
2575  CFLAGS = ${CFLAGS}  CFLAGS = ${CFLAGS}
2576  # Files that should not be optimized  # Files that should not be optimized
# Line 2427  MAKEFILE=${MAKEFILE} Line 2583  MAKEFILE=${MAKEFILE}
2583    
2584  EOF  EOF
2585    
2586  cat srclist.inc       >> $MAKEFILE  cat F77srclist.tmp      >> $MAKEFILE
2587  cat csrclist.inc      >> $MAKEFILE  cat nonADF77srclist.tmp >> $MAKEFILE
2588  cat f90srclist.inc    >> $MAKEFILE  cat csrclist.tmp        >> $MAKEFILE
2589  cat hlist.inc         >> $MAKEFILE  cat F90srclist.tmp      >> $MAKEFILE
2590  cat ad_flow_files.inc >> $MAKEFILE  cat hsrclist.tmp        >> $MAKEFILE
2591    cat ad_flow_files.tmp   >> $MAKEFILE
2592    
2593    rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
2594    
2595  echo >> $MAKEFILE  echo >> $MAKEFILE
2596  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE  
2597  echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE  # add definitions for preprocessed sources
2598  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE  # and note that not all systems allow case sensitive extensions
2599    # hence the $FS and $FS90 here.
2600    # for fixed format f90 files we use ff90 or FF90 resp
2601    # but these are not expected to be the original source files
2602    
2603    echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2604    echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2605    echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
2606    echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2607  echo >> $MAKEFILE  echo >> $MAKEFILE
2608  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2609  echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc  
 rm -f ad_flow_files.inc  
2610    
2611  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2612    
2613  all: \$(EXECUTABLE)  all: \$(EXECUTABLE)
2614  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2615          @echo Creating \$@ ...          @echo Creating \$@ ...
2616          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2617  depend:  depend:
2618          @make links          @make links
2619          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2620          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2621          -rm -f makedepend.out          -rm -f makedepend.out
2622    
# Line 2458  lib: libmitgcmuv.a Line 2624  lib: libmitgcmuv.a
2624    
2625  libmitgcmuv.a: \$(OBJFILES)  libmitgcmuv.a: \$(OBJFILES)
2626          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
2627            ar d   libmitgcmuv.a main.o
2628    
2629  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
2630    
2631  small_f: \$(F77FILES) \$(F90FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2632    
2633  output.txt: \$(EXECUTABLE)  output.txt: \$(EXECUTABLE)
2634          @printf 'running ... '          @printf 'running ... '
# Line 2470  output.txt: \$(EXECUTABLE) Line 2637  output.txt: \$(EXECUTABLE)
2637  clean:  clean:
2638          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
2639          -rm -rf *.o          -rm -rf *.o
2640          -rm -rf *.$FS          -rm -rf *.$FS *.flowdir
2641            -rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
2642  Clean:  Clean:
2643          @make clean          @make clean
2644          @make cleanlinks          @make cleanlinks
2645          -rm -f \$(SPECIAL_FILES)          -rm -f \$(SPECIAL_FILES)
2646          -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak          -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log f90mkdepend.log *.bak
2647            -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
2648  CLEAN:  CLEAN:
2649          @make Clean          @make Clean
2650          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2651          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2652          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2653          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
2654            -rm -f *_MIT_CE_000.opt0000 costfunction*0000
2655          -rm -rf mnc_test_*          -rm -rf mnc_test_*
2656    
2657  #eh3 Makefile: makefile  #eh3 Makefile: makefile
# Line 2490  makefile: Line 2660  makefile:
2660  cleanlinks:  cleanlinks:
2661          -find . -type l -exec rm {} \;          -find . -type l -exec rm {} \;
2662    
2663  # Special targets (SPECIAL_FILES) which are create by make  # Special targets (SPECIAL_FILES) which are created by make
2664  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
2665          @echo Creating \$@ ...          @echo Creating \$@ ...
2666          @$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) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
# Line 2515  if test "x$EMBED_SRC" = xt ; then Line 2685  if test "x$EMBED_SRC" = xt ; then
2685    
2686  decode_files.o : EMBEDDED_FILES.h  decode_files.o : EMBEDDED_FILES.h
2687    
2688  ##  \$(F77FILES)  ##  \$(F77_PP_SRC_FILES)
2689  all_fF.tar.gz : \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile  all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2690          @echo Creating \$@ ...          @echo Creating \$@ ...
2691          -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile          -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2692          -rm -f all_fF.tar.gz          -rm -f all_fF.tar.gz
2693          -gzip all_fF.tar          -gzip all_fF.tar
2694    
# Line 2542  cat >>$MAKEFILE <<EOF Line 2712  cat >>$MAKEFILE <<EOF
2712          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2713  .F90.$FS90:  .F90.$FS90:
2714          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2715    .FF90.f$FS90:
2716            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2717  .$FS90.o:  .$FS90.o:
2718          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
2719    .f$FS90.o:
2720            cp \$< \$(basename  \$<).f90
2721            \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
2722  .c.o:  .c.o:
2723          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
2724    .flow.flowdir:
2725            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2726    
2727  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
2728  .F.p:  .F.p:
# Line 2553  cat >>$MAKEFILE <<EOF Line 2730  cat >>$MAKEFILE <<EOF
2730  .p.$FS:  .p.$FS:
2731          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
2732    
2733    EOF
2734    
2735  #=========================================  #=========================================
2736  #===  Automatic Differentiation Rules  ===  #===  Automatic Differentiation Rules  ===
2737    #===  for TAMC/TAF  ======================
2738    
2739    if test "x$OPENAD" = x ; then
2740    
2741    cat >>$MAKEFILE <<EOF
2742    
2743  TAMC           = ${TAMC}  TAMC           = ${TAMC}
2744  TAF            = ${TAF}  TAF            = ${TAF}
# Line 2578  done Line 2762  done
2762  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
2763  echo >> $MAKEFILE  echo >> $MAKEFILE
2764  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
2765  AD_FILES=`cat ad_files`  AD_FILES=`cat adSrcFiles.tmp`
2766  for i in $AD_FILES ; do  for i in $AD_FILES ; do
2767      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
2768      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
2769  done  done
2770  echo >> $MAKEFILE  echo >> $MAKEFILE
2771  rm -f ad_files  rm -f adSrcFiles.tmp
2772    
2773  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2774    
# Line 2593  adall: \$(EXE_AD) Line 2777  adall: \$(EXE_AD)
2777  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
2778  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
2779    
2780  ad_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
2781          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
2782          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2783          -rm -f ad_config.template          -rm -f ad_config.template
2784          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2785          @make \$(AD_FLOW_FILES)          @make \$(FLOFILES)
2786          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS          cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
2787    
2788  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
2789          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2790            ls -l ad_input_code_ad.$FS
2791          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
2792    
2793  adtafonly:  adtafonly:
2794          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2795            ls -l ad_input_code_ad.$FS
2796          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
2797    
2798  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
# Line 2630  ftlall: ftl_taf Line 2816  ftlall: ftl_taf
2816  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
2817  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
2818    
2819  ftl_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2820          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2821          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2822          -rm -f ftl_config.template          -rm -f ftl_config.template
2823          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2824          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2825          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
2826    
2827  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
2828          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2829            ls -l ftl_input_code_ftl.$FS
2830          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2831    
2832  ftltafonly:  ftltafonly:
2833          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2834            ls -l ftl_input_code_ftl.$FS
2835          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2836    
2837  ftl_taf: ftl_taf_output.o \$(OBJFILES)  ftl_taf: ftl_taf_output.o \$(OBJFILES)
# Line 2681  svd_touch: Line 2869  svd_touch:
2869          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2870          -rm -f ftl_config.template          -rm -f ftl_config.template
2871    
2872  #=========================================  EOF
2873    
2874    fi
2875    
2876    #===  for OpenAD  ========================
2877    
2878    if test "x$OPENAD" != x ; then
2879    
2880    # ============ begin OpenAD specific section ==============
2881    
2882    cat >>$MAKEFILE <<EOF
2883    
2884    # all the source files linked from the various locations:
2885    ALL_LINKED_FILES= \
2886    \$(F77_SRC_FILES) \
2887    \$(C_SRC_FILES) \
2888    \$(H_SRC_FILES) \
2889    \$(F90_SRC_FILES) \
2890    \$(SPECIAL_FILES)
2891    
2892    ifndef OPENADROOT
2893      \$(error "Error:  environment variable OPENADROOT not defined!")
2894    endif
2895    
2896    ifndef XAIFSCHEMAROOT
2897      \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
2898    endif
2899    
2900    ifndef XAIFBOOSTERROOT
2901      \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
2902    endif
2903    
2904    EOF
2905    
2906    echo "  Add the source list for common block to module conversion "
2907    echo >> $MAKEFILE
2908    printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
2909    for i in `cat ${OAD_CB2M_FILES}` ; do
2910      echo    " \\" >> $MAKEFILE
2911      printf " $i" >> $MAKEFILE
2912    done
2913    echo >> $MAKEFILE
2914    
2915    echo "  Add the source list for AD code generation"
2916    echo >> $MAKEFILE
2917    printf "AD_FILES = " >> $MAKEFILE
2918    for i in `cat ${OAD_CB2M_FILES}` ; do
2919      echo    " \\" >> $MAKEFILE
2920      printf " ${i}_mod.f$FS90" >> $MAKEFILE
2921    done
2922    AD_FILES=`cat adSrcFiles.tmp`
2923    for i in $AD_FILES ; do
2924      basename=${i%%.f}
2925      toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
2926      if test -z "$toBeIgnored" ; then
2927        echo    " \\" >> $MAKEFILE
2928        printf " $i" >> $MAKEFILE
2929      fi
2930    done
2931    echo >> $MAKEFILE
2932    rm -f adSrcFiles.tmp
2933    
2934    cat >>$MAKEFILE <<EOF
2935    
2936    adAll: \$(EXE_AD)
2937    .PHONY: adAll
2938    
2939    CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
2940    
2941    .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
2942    
2943    .PHONY: adDepend
2944    adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
2945            \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2946            \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2947            -rm -f makedepend.out
2948    
2949    OPENAD_SUPPORT_F90_SRC_FILES = \
2950    w2f__types.F90 \
2951    OAD_active.F90 \
2952    OAD_cp.F90 \
2953    OAD_rev.F90 \
2954    OAD_tape.F90        
2955    
2956    OPENAD_SUPPORT_C_SRC_FILES = \
2957    iaddr.c \
2958    timeRatio.c
2959    
2960    f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
2961            cat \$^ > \$@
2962    
2963    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$FS90
2964            cat \$^ > \$@
2965    
2966    f95_test.out: f95_test_mods.f90 f95_test.f90
2967            f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
2968            f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
2969    
2970    # the file included below is created by the
2971    # postProcessor and its inclusion sets the
2972    # variable POSTPROCESSEDFILES
2973    # used below. Because the file is made during
2974    # make it won't be read until the second (recursive)
2975    # invocation in the rule below
2976    -include postProcess.make
2977    
2978    AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$FS90=.o)
2979    
2980    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)
2981    
2982    postProcess.comp: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S1)
2983    ifeq (\$(MAKELEVEL),0)
2984            \$(MAKE) adAll
2985    else
2986            touch \$@
2987    endif
2988    
2989    \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.comp \$(AD_OBJ_FILES_S2)
2990    ifeq (\$(MAKELEVEL),1)
2991            \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
2992    else
2993            touch \$@
2994    endif
2995    
2996    # makefile debug rule
2997    openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
2998    .PHONY: openad
2999    
3000    # create the module files
3001    %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
3002            ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
3003    
3004    # create the header files
3005    %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
3006            ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3007    
3008    # change everybody else to use the new module files:
3009    %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
3010            ../OAD_support/cb2mUseModules.bash $< ${MPI}
3011    
3012    # makefile debug rule
3013    small_f: \$(CB2M_F90_PP_SRC_FILES)
3014    .PHONY: small_f
3015    
3016    ad_output.txt: \$(EXE_AD)
3017            @printf 'linking data files ... '
3018            \$(LN) -f ../input_ad/data* ../input_ad/eedata .
3019            \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
3020            @printf 'running ... '
3021            @./\$(EXE_AD) > \$@
3022    
3023    CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
3024    ad_input_code.f$FS90:  \$(CB2M_AD_FILES) ../OAD_support/maxMinDefs.f
3025            cat \$^ > \$@
3026    
3027    # strip all comments and blanks to reduce
3028    # the file size in order to reduce perl's memory requirements
3029    ad_input_code_sf.f$FS90 : ad_input_code.f$FS90
3030            cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
3031    
3032    # mfef90 preprocessing
3033    # expand statement functions
3034    # expose mfef90 specific substring handling
3035    # add the w2f__types module
3036    ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
3037            ./mfef90 -r8 -z -F -N132 \$<
3038            mv \$<.B \$(basename \$<).B
3039            ./whirl2f -openad \$(basename \$<).B
3040            cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
3041    
3042    # canonicalizer
3043    ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
3044            ./preProcess.py -H -S \$< -o \$@
3045    
3046    # F -> WHIRL
3047    # note that the canonicalized version cuts off at col 72
3048    # doing this also for string constants which is ok as long
3049    # as we are in fixed mode and cut of exactly there.
3050    # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
3051    # characters respectively.
3052    ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
3053            ./mfef90 -r8 -z -F \$<
3054            mv \$<.B \$@
3055    
3056    # WHIRL -> XAIF
3057    ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif
3058            ./whirl2xaif -s -n --debug 1 -o \$@ \$<
3059    
3060    # XAIF -> XAIF'
3061    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
3062            ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3063    
3064    # XAIF' -> WHIRL'
3065    ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
3066            ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
3067    
3068    # WHIRL' -> F'
3069    ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
3070            ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
3071    
3072    # insert template directives
3073    ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
3074            ../OAD_support/insertTemplateDir.bash \$< \$@
3075    
3076    PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
3077    # postprocess F'
3078    postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)
3079            # the target is a placeholder to signal execution of the rule
3080            touch \$@
3081            # this step also creates the file postProcess.make but we cannot
3082            # name it as the target or else make will try to remake it for
3083            # the include directive above for any rule, e.g. make clean
3084            ./postProcess.py -m r -i ../OAD_support/ad_inline.f --width 4 \$<
3085    
3086    # setup some links
3087    %.xsd:
3088            \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3089    
3090    mfef90:
3091            \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
3092    
3093    # link the support files:
3094    \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
3095            \$(LN) ../OAD_support/\$@ .
3096    
3097    whirl2xaif xaif2whirl:
3098            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3099    
3100    preProcess.py postProcess.py:
3101            \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
3102    
3103    whirl2f whirl2f_be:
3104            \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
3105    
3106    oadDriver:
3107            \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
3108    
3109    AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.make postProcess.tag postProcess.comp
3110    
3111    # ============ end OpenAD specific section ==============
3112    
3113  EOF  EOF
3114    
3115    fi
3116    
3117    #=========================================
3118    
3119  if test "x$EXEHOOK" != x ; then  if test "x$EXEHOOK" != x ; then
3120      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
3121  fi  fi

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