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revision 1.169 by jmc, Fri Feb 15 19:33:34 2008 UTC revision 1.205 by jmc, Sun May 23 03:45:58 2010 UTC
# Line 480  get_pdepend_list()  { Line 480  get_pdepend_list()  {
480      #  strip the comments and then convert the dependency file into      #  strip the comments and then convert the dependency file into
481      #  two arrays: PNAME, DNAME      #  two arrays: PNAME, DNAME
482      cat $1 | sed -e 's/#.*$//g' \      cat $1 | sed -e 's/#.*$//g' \
483          | $AWK 'BEGIN{nn=0;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME["nn"]="$1"\nDNAME["nn"]="$i} }' \          | $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \
484          > ./.pd_tmp          > ./.pd_tmp
485        RETVAL=$?
486        if test ! "x${RETVAL}" = x0 ; then
487          echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$1\""
488          exit 1
489        fi
490      . ./.pd_tmp      . ./.pd_tmp
491      rm -f ./.pd_tmp      rm -f ./.pd_tmp
492    
     printf "PNAME = "${}  
493  }  }
494    
495    
# Line 519  Usage: "$0" [OPTIONS] Line 523  Usage: "$0" [OPTIONS]
523        -pdefault=NAME | --pdefault=NAME        -pdefault=NAME | --pdefault=NAME
524            Get the default package list from "NAME".            Get the default package list from "NAME".
525    
526        -bash NAME
527              Explicitly specify the Bourne or BASH shell to use
528    
529      -make NAME | -m NAME      -make NAME | -m NAME
530        --make=NAME | -m=NAME        --make=NAME | -m=NAME
531            Use "NAME" for the MAKE program. The default is "make" but            Use "NAME" for the MAKE program. The default is "make" but
# Line 578  Usage: "$0" [OPTIONS] Line 585  Usage: "$0" [OPTIONS]
585            *only* works if it is supported by the OPTFILE that            *only* works if it is supported by the OPTFILE that
586            is being used.            is being used.
587    
588        -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
589              Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
590              *only* works if CPP_EEOPTIONS.h allows this.
591    
592      -ignoretime | -ignore_time | --ignoretime | --ignore_time      -ignoretime | -ignore_time | --ignoretime | --ignore_time
593            Ignore all the "wall clock" routines entirely.  This will            Ignore all the "wall clock" routines entirely.  This will
594            not in any way hurt the model results -- it simply means            not in any way hurt the model results -- it simply means
# Line 611  Usage: "$0" [OPTIONS] Line 622  Usage: "$0" [OPTIONS]
622            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
623            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
624    
625        -omp | --omp
626              Activate OpenMP code + use Compiler option OMPFLAG
627        -omp=OMPFLAG | --omp=OMPFLAG
628              Activate OpenMP code + use Compiler option OMPFLAG
629    
630      -es | --es | -embed-source | --embed-source      -es | --es | -embed-source | --embed-source
631            Embed a tarball containing the full source code            Embed a tarball containing the full source code
632            (including the Makefile, etc.) used to build the            (including the Makefile, etc.) used to build the
633            executable [off by default]            executable [off by default]
634    
     -bash NAME  
           Explicitly specify the Bourne or BASH shell to use  
   
635    While it is most often a single word, the "NAME" variables specified    While it is most often a single word, the "NAME" variables specified
636    above can in many cases be a space-delimited string such as:    above can in many cases be a space-delimited string such as:
637    
# Line 630  Usage: "$0" [OPTIONS] Line 643  Usage: "$0" [OPTIONS]
643    
644    For more detailed genmake documentation, please see:    For more detailed genmake documentation, please see:
645    
646      http://mitgcm.org/devel_HOWTO/      http://mitgcm.org/public/devel_HOWTO/
647    
648  EOF  EOF
649    
# Line 1046  INCLUDES="-I. $INCLUDES" Line 1059  INCLUDES="-I. $INCLUDES"
1059  FFLAGS=  FFLAGS=
1060  FOPTIM=  FOPTIM=
1061  FEXTRAFLAGS=  FEXTRAFLAGS=
1062    USE_EXTENDED_SRC=
1063    EXTENDED_SRC_FLAG=
1064  CFLAGS=  CFLAGS=
1065  KFLAGS1=  KFLAGS1=
1066  KFLAGS2=  KFLAGS2=
# Line 1056  NOOPTFILES= Line 1071  NOOPTFILES=
1071  NOOPTFLAGS=  NOOPTFLAGS=
1072  MPI=  MPI=
1073  MPIPATH=  MPIPATH=
1074    OMP=
1075    OMPFLAG=
1076    USE_R4=
1077  TS=  TS=
1078  PAPIS=  PAPIS=
1079  PCLS=  PCLS=
# Line 1123  TAMC_EXTRA= Line 1141  TAMC_EXTRA=
1141    
1142  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1143  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
1144  gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"  gm_s2="FC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
1145    
1146  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1147  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
# Line 1164  else Line 1182  else
1182  fi  fi
1183    
1184  #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=$(( $n + 1 ))  
 #done  
1185  #parse_options  #parse_options
1186  ac_prev=  ac_prev=
1187  for ac_option in "$@" ; do  for ac_option in "$@" ; do
# Line 1297  for ac_option in "$@" ; do Line 1306  for ac_option in "$@" ; do
1306          -noieee | --noieee)          -noieee | --noieee)
1307              IEEE= ;;              IEEE= ;;
1308    
1309            -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1310                USE_R4=true ;;
1311    
1312          -ts | --ts)          -ts | --ts)
1313              TS=true ;;              TS=true ;;
1314          -papis | --papis)          -papis | --papis)
# Line 1324  for ac_option in "$@" ; do Line 1336  for ac_option in "$@" ; do
1336              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1337              MPI=true ;;              MPI=true ;;
1338                    
1339  #       -jam | --jam)          -omp | --omp)
1340  #           JAM=1 ;;              OMP=true ;;
1341  #       -nojam | --nojam)          -omp=* | --omp=*)
1342  #           JAM=0 ;;              OMPFLAG=$ac_optarg
1343                OMP=true ;;
1344                    
1345          -ds | --ds)          -ds | --ds)
1346              DUMPSTATE=t ;;              DUMPSTATE=t ;;
# Line 1402  if test ! -d ${ROOTDIR} ; then Line 1415  if test ! -d ${ROOTDIR} ; then
1415  fi  fi
1416    
1417  #  Find the MITgcm ${THISVER}  #  Find the MITgcm ${THISVER}
1418  if test -f "${ROOTDIR}/doc/tag-index" ; then  version_file="${ROOTDIR}/doc/tag-index"
1419      THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`  if test -f $version_file ; then
1420        THISVER=`$AWK '/^checkpoint/{print $1; exit}' $version_file`
1421    #-  remove ./BUILD_INFO.h file if older than version_file
1422        if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
1423            echo "  remove ./BUILD_INFO.h (older than ${version_file})"
1424            rm -f ./BUILD_INFO.h
1425        fi
1426  fi  fi
1427    
1428  if test "x$MAKEFILE" = x ; then  if test "x$MAKEFILE" = x ; then
# Line 1559  if test ! "x$MPI" = x ; then Line 1578  if test ! "x$MPI" = x ; then
1578        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1579        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
1580  fi  fi
1581    if test ! "x$OMP" = x ; then
1582          echo "  Add OMPFLAG and turn on OpenMP cpp macros"
1583          FFLAGS="$FFLAGS $OMPFLAG"
1584          F90FLAGS="$F90FLAGS $OMPFLAG"
1585          DEFINES="$DEFINES -DUSE_OMP_THREADING"
1586    fi
1587    
1588    if test ! "x$USE_R4" = x ; then
1589          echo "  Turning on LET_RS_BE_REAL4 cpp flag"
1590          DEFINES="$DEFINES -DLET_RS_BE_REAL4"
1591    fi
1592    
1593  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1594        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
# Line 1640  if test ! "x$GSL" = x ; then Line 1670  if test ! "x$GSL" = x ; then
1670        INCLUDES="$INCLUDES $GSLINC"        INCLUDES="$INCLUDES $GSLINC"
1671        LIBS="$LIBS $GSLLIB"        LIBS="$LIBS $GSLLIB"
1672  fi  fi
1673    #- if USE_EXTENDED_SRC is set, add EXTENDED_SRC_FLAG to FFLAGS :
1674    if test ! "x$USE_EXTENDED_SRC" = x ; then
1675          FFLAGS="$FFLAGS $EXTENDED_SRC_FLAG"
1676          F90FIXEDFORMAT="$F90FIXEDFORMAT $EXTENDED_SRC_FLAG"
1677    fi
1678    
1679  printf "\n===  Checking system libraries  ===\n"  printf "\n===  Checking system libraries  ===\n"
1680  printf "  Do we have the system() command using $FC...  "  printf "  Do we have the system() command using $FC...  "
# Line 1762  fi Line 1797  fi
1797    
1798    
1799  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
1800  printf "  Adding MODS directories:  "  printf "  Adding MODS directories: "
1801  for d in $MODS ; do  for d in $MODS ; do
1802      if test ! -d $d ; then      if test ! -d $d ; then
1803          echo          echo
1804          echo "Error: MODS directory \"$d\" not found!"          echo "Error: MODS directory \"$d\" not found!"
1805          exit 1          exit 1
1806      else      else
1807          printf " $d"          printf "$d "
1808          SOURCEDIRS="$SOURCEDIRS $d"          SOURCEDIRS="$SOURCEDIRS $d"
1809          INCLUDEDIRS="$INCLUDEDIRS $d"          INCLUDEDIRS="$INCLUDEDIRS $d"
1810      fi      fi
# Line 1830  THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSD Line 1865  THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSD
1865    
1866  EXECUTABLE=${EXECUTABLE:-mitgcmuv}  EXECUTABLE=${EXECUTABLE:-mitgcmuv}
1867    
1868    #  Set Standard Code Directories:
1869    if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
1870        STANDARDDIRS="eesupp model"
1871    fi
1872    #  if model in Standard-Code-Dir, add eesupp (needed to compile model)
1873    echo " $STANDARDDIRS " | grep ' model ' > /dev/null 2>&1
1874    ckM=$?
1875    echo " $STANDARDDIRS " | grep ' eesupp ' > /dev/null 2>&1
1876    ckE=$?
1877    if test $ckM = 0 -a $ckE = 1 ; then
1878        STANDARDDIRS="$STANDARDDIRS eesupp"
1879    fi
1880    
1881  #  We have a special set of source files in eesupp/src which are  #  We have a special set of source files in eesupp/src which are
1882  #  generated from some template source files. We'll make them first so  #  generated from some template source files. We'll make them first so
1883  #  they appear as regular source code  #  they appear as regular source code
# Line 1880  fi Line 1928  fi
1928  echo "  getting package dependency info from  $PDEPEND"  echo "  getting package dependency info from  $PDEPEND"
1929  #  Strip the comments and then convert the dependency file into  #  Strip the comments and then convert the dependency file into
1930  #  two arrays: PNAME, DNAME  #  two arrays: PNAME, DNAME
1931  cat $PDEPEND | sed -e 's/#.*$//g' \  get_pdepend_list $PDEPEND
     | $AWK 'BEGIN{nn=-1;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME_"nn"="$1"\nDNAME_"nn"="$i}} END{print "nname="nn}' \  
     > ./.pd_tmp  
 RETVAL=$?  
 if test ! "x${RETVAL}" = x0 ; then  
     echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""  
     exit 1  
 fi  
 . ./.pd_tmp  
 rm -f ./.pd_tmp  
1932    
1933  #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"  #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
1934  #  file should eventually be added so that, for convenience, one can  #  file has been added so that, for convenience, one can specify
1935  #  specify groups of packages using names like "ocean" and "atmosphere".  #  groups of packages using names like "ocean" and "atmosphere".
1936  echo "  checking default package list:  "  echo "  checking default package list:  "
1937  if test "x${PDEFAULT}" = x ; then  if test "x${PDEFAULT}" = x ; then
1938      for i in "." $MODS ; do      for i in "." $MODS ; do
# Line 1924  else Line 1963  else
1963          for i in $def ; do          for i in $def ; do
1964              PACKAGES="$PACKAGES $i"              PACKAGES="$PACKAGES $i"
1965          done          done
1966          echo "    before group expansion packages are: $PACKAGES"          echo "    before group expansion packages are:$PACKAGES"
1967          RET=1          RET=1
1968          while test $RET = 1 ; do expand_pkg_groups; RET=$?; done          while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
1969          echo "    after group expansion packages are:  $PACKAGES"          echo "    after group expansion packages are: $PACKAGES"
1970      fi      fi
1971  fi  fi
1972    
1973  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
1974    echo "" > ./.tmp_pack
1975  for i in $PACKAGES ; do  for i in $PACKAGES ; do
1976      echo $i >> ./.tmp_pack      echo $i >> ./.tmp_pack
1977  done  done
# Line 1969  for i in `grep -v "-" ./.tmp_pack | sort Line 2009  for i in `grep -v "-" ./.tmp_pack | sort
2009      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2010  done  done
2011  rm -f ./.tmp_pack  rm -f ./.tmp_pack
2012  echo "    packages are:  $PACKAGES"  echo "    packages are: $PACKAGES"
2013    
2014  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
2015  #  template files ; otherwise, delete mnc from the list of packages.  #  template files ; otherwise, delete mnc from the list of packages.
2016  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1  echo " $PACKAGES " | grep ' mnc ' > /dev/null 2>&1
2017  RETVAL=$?  RETVAL=$?
2018  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
2019      if test "x$HAVE_NETCDF" != xt ; then      if test "x$HAVE_NETCDF" != xt ; then
# Line 2008  fi Line 2048  fi
2048    
2049  #  Check for package PROFILES: if NetCDF is not available,  #  Check for package PROFILES: if NetCDF is not available,
2050  #  then delete profiles from the list of available packages.  #  then delete profiles from the list of available packages.
2051  echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1  echo " $PACKAGES " | grep ' profiles ' > /dev/null 2>&1
2052  RETVAL=$?  RETVAL=$?
2053  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
2054      if test "x$HAVE_NETCDF" != xt ; then      if test "x$HAVE_NETCDF" != xt ; then
# Line 2049  while test "x$ck" != xtt ; do Line 2089  while test "x$ck" != xtt ; do
2089                  pin="t"                  pin="t"
2090              fi              fi
2091          done          done
2092            #  or in the current $STANDARDDIRS list?
2093            for p in $STANDARDDIRS ; do
2094                if test "x$p" = "x$pname" ; then pin="t" ; fi
2095            done
2096    
2097          #  Is the DNAME entry a (+) or (-) rule ?          #  Is the DNAME entry a (+) or (-) rule ?
2098          tmp="dname=\"\$DNAME_$i\""          tmp="dname=\"\$DNAME_$i\""
# Line 2101  while test "x$ck" != xtt ; do Line 2145  while test "x$ck" != xtt ; do
2145      done      done
2146      ck=$ck"t"      ck=$ck"t"
2147  done  done
2148  echo "    packages are:  $PACKAGES"  echo "    packages are: $PACKAGES"
2149  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2150      adr="$ROOTDIR/pkg/$i"      adr="$ROOTDIR/pkg/$i"
2151      if test -d $adr ; then      if test -d $adr ; then
# Line 2157  for i in $PACKAGES ; do Line 2201  for i in $PACKAGES ; do
2201    
2202  done  done
2203    
2204  echo "  Adding STANDARDDIRS"  echo "  Adding STANDARDDIRS='$STANDARDDIRS'"
2205  BUILDDIR=${BUILDDIR:-.}  BUILDDIR=${BUILDDIR:-.}
 if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then  
     STANDARDDIRS="eesupp model"  
 fi  
2206  if test "x$STANDARDDIRS" != x ; then  if test "x$STANDARDDIRS" != x ; then
2207      for d in $STANDARDDIRS ; do      for d in $STANDARDDIRS ; do
2208          adr="$ROOTDIR/$d/src"          adr="$ROOTDIR/$d/src"
# Line 2216  fi Line 2257  fi
2257    
2258  #  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
2259  #  compiler.  #  compiler.
2260  if test -f ./ad_files ; then  if test -f ./adSrcFiles.tmp ; then
2261      rm -f ./ad_files      rm -f ./adSrcFiles.tmp
2262  fi  fi
2263  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2264  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2265      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2266      for j in $list_files ; do      for j in $list_files ; do
2267          cat $i/$j >> ad_files          cat $i/$j >> adSrcFiles.tmp
2268      done      done
2269  done  done
2270  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2271      cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
2272      mv -f ad_files_f ad_files      mv -f adSrcFiles.tmp_f adSrcFiles.tmp
2273  fi  fi
2274    
2275  echo  echo
# Line 2286  if test ! -r ".links.tmp/foo" ; then Line 2327  if test ! -r ".links.tmp/foo" ; then
2327      exit 1      exit 1
2328  fi  fi
2329  rm -f .links.tmp/foo  rm -f .links.tmp/foo
2330    
2331    if test "x$OPENAD" != x ; then
2332        OAD_DONT_COMPILE="/dev/null"
2333        OAD_DONT_TRANSFORM="/dev/null"
2334        OAD_KEEP_ORIGINAL="/dev/null"
2335        OAD_CB2M_FILES="/dev/null"
2336        echo "  looking for dontCompile file:  "
2337        for i in "." $MODS ; do
2338            if test -r $i"/dontCompile" ; then
2339                OAD_DONT_COMPILE=$i"/dontCompile"
2340                echo "     found $OAD_DONT_COMPILE"
2341                break
2342            fi
2343        done
2344        echo "  looking for dontTransform file:  "
2345        for i in "." $MODS ; do
2346            if test -r $i"/dontTransform" ; then
2347                OAD_DONT_TRANSFORM=$i"/dontTransform"
2348                echo "     found $OAD_DONT_TRANSFORM"
2349                break
2350            fi
2351        done
2352        echo "  looking for keepOriginal file:  "
2353        for i in "." $MODS ; do
2354            if test -r $i"/keepOriginal" ; then
2355                OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2356                echo "     found $OAD_KEEP_ORIGINAL"
2357                break
2358            fi
2359        done
2360        echo "  looking for cb2mFiles:  "
2361        for i in "." $MODS ; do
2362            if test -r $i"/cb2mFiles" ; then
2363                OAD_CB2M_FILES=$i"/cb2mFiles"
2364                echo "     found $OAD_CB2M_FILES"
2365                break
2366            fi
2367        done
2368        echo "   OpenAD exceptions:  "
2369    fi
2370    
2371  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > srclinks.tmp
2372  echo "" >> srclinks.tmp  echo "" >> srclinks.tmp
2373  printf 'SRCFILES = '    > srclist.inc  printf 'F77_SRC_FILES = ' > F77srclist.tmp
2374  printf 'CSRCFILES = '   > csrclist.inc  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
2375  printf 'F90SRCFILES = ' > f90srclist.inc  printf 'C_SRC_FILES = '   > csrclist.tmp
2376  printf 'HEADERFILES = ' > hlist.inc  printf 'F90_SRC_FILES = ' > F90srclist.tmp
2377  printf 'AD_FLOW_FILES = ' > ad_flow_files.inc  printf 'H_SRC_FILES = '   > hsrclist.tmp
2378    printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
2379  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2380  for d in $alldirs ; do  for d in $alldirs ; do
2381      deplist=      deplist=
2382      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2383      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
2384        if test "x$OPENAD" != x ; then
2385            sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2386        fi
2387      for sf in $sfiles ; do      for sf in $sfiles ; do
2388          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2389              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
# Line 2332  for d in $alldirs ; do Line 2418  for d in $alldirs ; do
2418                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2419                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2420                      case $extn in                      case $extn in
2421                          F)                        F)
2422                              echo    " \\"  >> srclist.inc                          echo    " \\"  >> F77srclist.tmp
2423                              printf " $sf" >> srclist.inc                          printf " $sf" >> F77srclist.tmp
2424                              ;;                          if test "x$OPENAD" != x ; then
2425                          F90)                              basename=${sf%%.F}
2426                              echo    " \\"  >> f90srclist.inc                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2427                              printf " $sf" >> f90srclist.inc                              if test -z "$isAD" ; then
2428                              ;;                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2429                          c)                                  if test -z "$toBeIgnored" ; then
2430                              echo    " \\"  >> csrclist.inc                                      echo    " \\"  >> nonADF77srclist.tmp
2431                              printf " $sf" >> csrclist.inc                                      printf " $sf" >> nonADF77srclist.tmp
2432                              ;;                                  else
2433                          h)                                      echo "    not to be compiled   :  $sf"
2434                              echo    " \\"  >> hlist.inc                                  fi
2435                              printf " $sf" >> hlist.inc                              else # file is initially listed as an AD file we want to exclude it
2436                              ;;                                   # or we want to retain the untransformed version
2437                          flow)                                  notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
2438                              echo    " \\"  >> ad_flow_files.inc                                  untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
2439                              printf " $sf" >> ad_flow_files.inc                                  if test -n "$notToBeTransformed"; then
2440                              ;;                                      echo "    not to be transformed:  $sf"
2441                      esac                                  fi
2442                  fi                                  if test -n "$untransformedVersionToBeKept" ; then
2443                                        echo "    original to be kept  :  $sf"
2444                                    fi    
2445                                    if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2446                                        echo    " \\"  >> nonADF77srclist.tmp
2447                                        printf " $sf" >> nonADF77srclist.tmp
2448                                    fi
2449                                fi
2450                            fi
2451                            ;;
2452                        F90)
2453                            echo    " \\"  >> F90srclist.tmp
2454                            printf " $sf" >> F90srclist.tmp
2455                            ;;
2456                        c)
2457                            echo    " \\"  >> csrclist.tmp
2458                            printf " $sf" >> csrclist.tmp
2459                            ;;
2460                        h)
2461                            echo    " \\"  >> hsrclist.tmp
2462                            printf " $sf" >> hsrclist.tmp
2463                            ;;
2464                        flow)
2465                            echo    " \\"  >> ad_flow_files.tmp
2466                            printf " $sf" >> ad_flow_files.tmp
2467                            ;;
2468                       esac
2469                    fi
2470              fi              fi
2471          fi          fi
2472      done      done
2473      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2474          echo "" >> srclinks.tmp        if test "$d" != "." ; then
2475            echo "" >> srclinks.tmp
2476          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> srclinks.tmp
2477          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> srclinks.tmp
2478          printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp  # We need to make sure that the link isn't already there.
2479    # This may happen when make thinks that a header file has to be "remade"
2480    # because a module it depends on has changed.  In this case we do nothing.
2481            printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
2482          fi
2483      fi      fi
2484  done  done
2485  rm -rf .links.tmp  rm -rf .links.tmp
2486  echo "" >> srclist.inc  echo "" >> F77srclist.tmp
2487  echo "" >> csrclist.inc  echo "" >> nonADF77srclist.tmp
2488  echo "" >> f90srclist.inc  echo "" >> csrclist.tmp
2489  echo "" >> hlist.inc  echo "" >> F90srclist.tmp
2490  echo "" >> ad_flow_files.inc  echo "" >> hsrclist.tmp
2491    echo "" >> ad_flow_files.tmp
2492    
2493    CMDLINE=$0
2494    for xx in "$@" ; do nw=`echo $xx | wc -w`
2495        if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2496                            else CMDLINE="$CMDLINE '$xx'" ; fi
2497    done
2498    
2499  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
2500      mv -f $MAKEFILE "$MAKEFILE.bak"      mv -f $MAKEFILE "$MAKEFILE.old"
2501  fi  fi
2502  echo "  Writing makefile: $MAKEFILE"  echo "  Writing makefile: $MAKEFILE"
2503  echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE  echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE
# Line 2380  echo "#    $MACHINE" >> $MAKEFILE Line 2505  echo "#    $MACHINE" >> $MAKEFILE
2505  echo "# This makefile was generated automatically on" >> $MAKEFILE  echo "# This makefile was generated automatically on" >> $MAKEFILE
2506  echo "#    $THISDATE" >> $MAKEFILE  echo "#    $THISDATE" >> $MAKEFILE
2507  echo "# by the command:" >> $MAKEFILE  echo "# by the command:" >> $MAKEFILE
2508  echo "#    $0 $G2ARGS" >> $MAKEFILE  echo "#    $CMDLINE"  >> $MAKEFILE
2509  echo "# executed by:" >> $MAKEFILE  echo "# executed by:" >> $MAKEFILE
2510  echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE  echo "#    ${THISUSER}@${THISHOST}:${THISCWD}" >> $MAKEFILE
2511    
# Line 2391  EXE_SVD=$EXECUTABLE"_svd" Line 2516  EXE_SVD=$EXECUTABLE"_svd"
2516  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2517  #  #
2518  # OPTFILE="$OPTFILE"  # OPTFILE="$OPTFILE"
2519  #  #
2520  # BUILDDIR     : Directory where object files are written  # BUILDDIR     : Directory where object files are written
2521  # SOURCEDIRS   : Directories containing the source (.F) files  # SOURCEDIRS   : Directories containing the source (.F) files
2522  # INCLUDEDIRS  : Directories containing the header-source (.h) files  # INCLUDEDIRS  : Directories containing the header-source (.h) files
# Line 2411  cat >>$MAKEFILE <<EOF Line 2536  cat >>$MAKEFILE <<EOF
2536  # LIBS         : Library flags /or/ additional optimization/debugging flags  # LIBS         : Library flags /or/ additional optimization/debugging flags
2537    
2538  ROOTDIR     = ${ROOTDIR}  ROOTDIR     = ${ROOTDIR}
2539  BUILDDIR    = ${BUILDDIR}    BUILDDIR    = ${BUILDDIR}
2540  SOURCEDIRS  = ${SOURCEDIRS}  SOURCEDIRS  = ${SOURCEDIRS}
2541  INCLUDEDIRS = ${INCLUDEDIRS}  INCLUDEDIRS = ${INCLUDEDIRS}
2542  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
# Line 2437  else Line 2562  else
2562      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2563  fi  fi
2564    
 #  Note: figure out some way to add Hyades JAM libraries here  
2565  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2566  # Unix ln (link)  # Unix ln (link)
2567  LN = ${LN}  LN = ${LN}
# Line 2469  FOPTIM = ${FOPTIM} Line 2593  FOPTIM = ${FOPTIM}
2593  # Optim./debug for FC  # Optim./debug for FC
2594  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2595  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
2596    F90FIXEDFORMAT = ${F90FIXEDFORMAT}
2597  # Flags for CC  # Flags for CC
2598  CFLAGS = ${CFLAGS}  CFLAGS = ${CFLAGS}
2599  # Files that should not be optimized  # Files that should not be optimized
# Line 2481  MAKEFILE=${MAKEFILE} Line 2606  MAKEFILE=${MAKEFILE}
2606    
2607  EOF  EOF
2608    
2609  cat srclist.inc       >> $MAKEFILE  cat F77srclist.tmp      >> $MAKEFILE
2610  cat csrclist.inc      >> $MAKEFILE  cat nonADF77srclist.tmp >> $MAKEFILE
2611  cat f90srclist.inc    >> $MAKEFILE  cat csrclist.tmp        >> $MAKEFILE
2612  cat hlist.inc         >> $MAKEFILE  cat F90srclist.tmp      >> $MAKEFILE
2613  cat ad_flow_files.inc >> $MAKEFILE  cat hsrclist.tmp        >> $MAKEFILE
2614    cat ad_flow_files.tmp   >> $MAKEFILE
2615    
2616    rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
2617    
2618  echo >> $MAKEFILE  echo >> $MAKEFILE
2619  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE  
2620  echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE  # add definitions for preprocessed sources
2621  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE  # and note that not all systems allow case sensitive extensions
2622    # hence the $FS and $FS90 here.
2623    # for fixed format f90 files we use ff90 or FF90 resp
2624    # but these are not expected to be the original source files
2625    
2626    echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2627    echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2628    echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
2629    echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2630  echo >> $MAKEFILE  echo >> $MAKEFILE
2631  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2632  echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc  
 rm -f ad_flow_files.inc  
2633    
2634  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2635    
2636  all: \$(EXECUTABLE)  all: \$(EXECUTABLE)
2637  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2638          @echo Creating \$@ ...          @echo Creating \$@ ...
2639          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2640  depend:  depend:
2641          @make links          @make links
2642          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2643          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2644          -rm -f makedepend.out          -rm -f makedepend.out
2645    
# Line 2514  libmitgcmuv.a: \$(OBJFILES) Line 2649  libmitgcmuv.a: \$(OBJFILES)
2649          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
2650          ar d   libmitgcmuv.a main.o          ar d   libmitgcmuv.a main.o
2651    
2652  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
2653    
2654  small_f: \$(F77FILES) \$(F90FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2655    
2656  output.txt: \$(EXECUTABLE)  output.txt: \$(EXECUTABLE)
2657          @printf 'running ... '          @printf 'running ... '
# Line 2525  output.txt: \$(EXECUTABLE) Line 2660  output.txt: \$(EXECUTABLE)
2660  clean:  clean:
2661          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
2662          -rm -rf *.o          -rm -rf *.o
2663          -rm -rf *.$FS          -rm -rf *.$FS *.flowdir
2664            -rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
2665  Clean:  Clean:
2666          @make clean          @make clean
2667          @make cleanlinks          @make cleanlinks
2668          -rm -f \$(SPECIAL_FILES)          -rm -f \$(SPECIAL_FILES)
2669          -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak          -rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
2670            -rm -f make.log run.log f90mkdepend.log *.bak "$MAKEFILE.old"
2671          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
2672  CLEAN:  CLEAN:
2673          @make Clean          @make Clean
# Line 2547  makefile: Line 2684  makefile:
2684  cleanlinks:  cleanlinks:
2685          -find . -type l -exec rm {} \;          -find . -type l -exec rm {} \;
2686    
2687  # Special targets (SPECIAL_FILES) which are create by make  # Special targets (SPECIAL_FILES) which are created by make
2688  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
2689          @echo Creating \$@ ...          @echo Creating \$@ ...
2690          @$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) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
# Line 2572  if test "x$EMBED_SRC" = xt ; then Line 2709  if test "x$EMBED_SRC" = xt ; then
2709    
2710  decode_files.o : EMBEDDED_FILES.h  decode_files.o : EMBEDDED_FILES.h
2711    
2712  ##  \$(F77FILES)  ##  \$(F77_PP_SRC_FILES)
2713  all_fF.tar.gz : \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile  all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2714          @echo Creating \$@ ...          @echo Creating \$@ ...
2715          -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile          -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2716          -rm -f all_fF.tar.gz          -rm -f all_fF.tar.gz
2717          -gzip all_fF.tar          -gzip all_fF.tar
2718    
# Line 2597  cat >>$MAKEFILE <<EOF Line 2734  cat >>$MAKEFILE <<EOF
2734          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2735  .$FS.o:  .$FS.o:
2736          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2737  .F.o:  .F90.$FS90:
2738          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2739  .F90.o:    .FF90.f$FS90:
2740            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2741    .$FS90.o:
2742          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
2743    .f$FS90.o:
2744            cp \$< \$(basename  \$<).f90
2745            \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
2746  .c.o:  .c.o:
2747          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
2748    .flow.flowdir:
2749            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2750    
2751  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
2752  .F.p:  .F.p:
# Line 2610  cat >>$MAKEFILE <<EOF Line 2754  cat >>$MAKEFILE <<EOF
2754  .p.$FS:  .p.$FS:
2755          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
2756    
2757    EOF
2758    
2759  #=========================================  #=========================================
2760  #===  Automatic Differentiation Rules  ===  #===  Automatic Differentiation Rules  ===
2761    #===  for TAMC/TAF  ======================
2762    
2763    if test "x$OPENAD" = x ; then
2764    
2765    cat >>$MAKEFILE <<EOF
2766    
2767  TAMC           = ${TAMC}  TAMC           = ${TAMC}
2768  TAF            = ${TAF}  TAF            = ${TAF}
# Line 2635  done Line 2786  done
2786  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
2787  echo >> $MAKEFILE  echo >> $MAKEFILE
2788  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
2789  AD_FILES=`cat ad_files`  AD_FILES=`cat adSrcFiles.tmp`
2790  for i in $AD_FILES ; do  for i in $AD_FILES ; do
2791      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
2792      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
2793  done  done
2794  echo >> $MAKEFILE  echo >> $MAKEFILE
2795  rm -f ad_files  rm -f adSrcFiles.tmp
2796    
2797  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2798    
# Line 2650  adall: \$(EXE_AD) Line 2801  adall: \$(EXE_AD)
2801  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
2802  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
2803    
2804  ad_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
2805          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
2806          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2807          -rm -f ad_config.template          -rm -f ad_config.template
2808          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2809          @make \$(AD_FLOW_FILES)          @make \$(FLOFILES)
2810          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS          cat \$(FLOFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
2811    
2812  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
2813          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2814            ls -l ad_input_code_ad.$FS
2815          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
2816    
2817  adtafonly:  adtafonly:
2818          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2819            ls -l ad_input_code_ad.$FS
2820          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
2821    
2822  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
# Line 2687  ftlall: ftl_taf Line 2840  ftlall: ftl_taf
2840  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
2841  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
2842    
2843  ftl_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2844          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2845          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2846          -rm -f ftl_config.template          -rm -f ftl_config.template
2847          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2848          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2849          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
2850    
2851  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
2852          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2853            ls -l ftl_input_code_ftl.$FS
2854          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
2855    
2856  ftltafonly:  ftltafonly:
2857          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2858            ls -l ftl_input_code_ftl.$FS
2859          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2860    
2861  ftl_taf: ftl_taf_output.o \$(OBJFILES)  ftl_taf: ftl_taf_output.o \$(OBJFILES)
# Line 2738  svd_touch: Line 2893  svd_touch:
2893          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2894          -rm -f ftl_config.template          -rm -f ftl_config.template
2895    
2896  #=========================================  EOF
2897    
2898    fi
2899    
2900    #===  for OpenAD  ========================
2901    
2902    if test "x$OPENAD" != x ; then
2903    
2904    # ============ begin OpenAD specific section ==============
2905    
2906    cat >>$MAKEFILE <<EOF
2907    
2908    # all the source files linked from the various locations:
2909    ALL_LINKED_FILES= \
2910    \$(F77_SRC_FILES) \
2911    \$(C_SRC_FILES) \
2912    \$(H_SRC_FILES) \
2913    \$(F90_SRC_FILES) \
2914    \$(SPECIAL_FILES)
2915    
2916    ifndef OPENADROOT
2917      \$(error "Error:  environment variable OPENADROOT not defined!")
2918    endif
2919    
2920    ifndef XAIFSCHEMAROOT
2921      \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
2922    endif
2923    
2924    ifndef XAIFBOOSTERROOT
2925      \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
2926    endif
2927    
2928  EOF  EOF
2929    
2930    echo "  Add the source list for common block to module conversion "
2931    echo >> $MAKEFILE
2932    printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
2933    for i in `cat ${OAD_CB2M_FILES}` ; do
2934      echo    " \\" >> $MAKEFILE
2935      printf " $i" >> $MAKEFILE
2936    done
2937    echo >> $MAKEFILE
2938    
2939    echo "  Add the source list for AD code generation"
2940    echo >> $MAKEFILE
2941    printf "AD_FILES = " >> $MAKEFILE
2942    for i in `cat ${OAD_CB2M_FILES}` ; do
2943      echo    " \\" >> $MAKEFILE
2944      printf " ${i}_mod.f$FS90" >> $MAKEFILE
2945    done
2946    AD_FILES=`cat adSrcFiles.tmp`
2947    for i in $AD_FILES ; do
2948      basename=${i%%.f}
2949      toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
2950      if test -z "$toBeIgnored" ; then
2951        echo    " \\" >> $MAKEFILE
2952        printf " $i" >> $MAKEFILE
2953      fi
2954    done
2955    echo >> $MAKEFILE
2956    rm -f adSrcFiles.tmp
2957    
2958    cat >>$MAKEFILE <<EOF
2959    
2960    adAll: \$(EXE_AD)
2961    .PHONY: adAll
2962    
2963    CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
2964    
2965    .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
2966    
2967    .PHONY: adDepend
2968    adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
2969            \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2970            \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2971            -rm -f makedepend.out
2972    
2973    OPENAD_SUPPORT_F90_SRC_FILES = \
2974    w2f__types.F90 \
2975    OAD_active.F90 \
2976    OAD_cp.F90 \
2977    OAD_rev.F90 \
2978    OAD_tape.F90        
2979    
2980    OPENAD_SUPPORT_C_SRC_FILES = \
2981    iaddr.c \
2982    timeRatio.c
2983    
2984    f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
2985            cat \$^ > \$@
2986    
2987    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$FS90
2988            cat \$^ > \$@
2989    
2990    f95_test.out: f95_test_mods.f90 f95_test.f90
2991            f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
2992            f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
2993    
2994    # the file included below is created by the
2995    # postProcessor and its inclusion sets the
2996    # variable POSTPROCESSEDFILES
2997    # used below. Because the file is made during
2998    # make it won't be read until the second (recursive)
2999    # invocation in the rule below
3000    -include postProcess.make
3001    
3002    AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$FS90=.o)
3003    
3004    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)
3005    
3006    postProcess.comp: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S1)
3007    ifeq (\$(MAKELEVEL),0)
3008            \$(MAKE) adAll
3009    else
3010            touch \$@
3011    endif
3012    
3013    \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.comp \$(AD_OBJ_FILES_S2)
3014    ifeq (\$(MAKELEVEL),1)
3015            \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3016    else
3017            touch \$@
3018    endif
3019    
3020    # makefile debug rule
3021    openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
3022    .PHONY: openad
3023    
3024    # create the module files
3025    %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
3026            ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
3027    
3028    # create the header files
3029    %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
3030            ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3031    
3032    # change everybody else to use the new module files:
3033    %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
3034            ../OAD_support/cb2mUseModules.bash $< ${MPI}
3035    
3036    # makefile debug rule
3037    small_f: \$(CB2M_F90_PP_SRC_FILES)
3038    .PHONY: small_f
3039    
3040    ad_output.txt: \$(EXE_AD)
3041            @printf 'linking data files ... '
3042            \$(LN) -f ../input_ad/data* ../input_ad/eedata .
3043            \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
3044            @printf 'running ... '
3045            @./\$(EXE_AD) > \$@
3046    
3047    CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
3048    ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3049            cat \$^ > \$@
3050    
3051    # strip all comments and blanks to reduce
3052    # the file size in order to reduce perl's memory requirements
3053    ad_input_code_sf.f$FS90 : ad_input_code.f$FS90
3054            cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
3055    
3056    # mfef90 preprocessing
3057    # expand statement functions
3058    # expose mfef90 specific substring handling
3059    # add the w2f__types module
3060    ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
3061            ./mfef90 -r8 -z -F -N132 \$<
3062            mv \$<.B \$(basename \$<).B
3063            ./whirl2f -openad \$(basename \$<).B
3064            cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
3065    
3066    # canonicalizer
3067    ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
3068            ./preProcess.py --timing --r8 -H -S \$< -o \$@
3069    
3070    # F -> WHIRL
3071    # note that the canonicalized version cuts off at col 72
3072    # doing this also for string constants which is ok as long
3073    # as we are in fixed mode and cut of exactly there.
3074    # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
3075    # characters respectively.
3076    ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
3077            ./mfef90 -r8 -z -F \$<
3078            mv \$<.B \$@
3079    
3080    # WHIRL -> XAIF
3081    ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif
3082            ./whirl2xaif -s -n --debug 1 -o \$@ \$<
3083    
3084    # XAIF -> XAIF'
3085    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
3086            ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3087    
3088    # XAIF' -> WHIRL'
3089    ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
3090            ./xaif2whirl --debug 1 ad_input_code_sf.w2f.pre.B \$<
3091    
3092    # WHIRL' -> F'
3093    ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
3094            ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
3095    
3096    # insert template directives
3097    ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
3098            ../OAD_support/insertTemplateDir.bash \$< \$@
3099    
3100    PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
3101    # postprocess F'
3102    postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)
3103            # the target is a placeholder to signal execution of the rule
3104            touch \$@
3105            # this step also creates the file postProcess.make but we cannot
3106            # name it as the target or else make will try to remake it for
3107            # the include directive above for any rule, e.g. make clean
3108            ./postProcess.py --progress --timing --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<
3109    
3110    # setup some links
3111    %.xsd:
3112            \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3113    
3114    mfef90:
3115            \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
3116    
3117    # link the support files:
3118    \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
3119            \$(LN) ../OAD_support/\$@ .
3120    
3121    whirl2xaif xaif2whirl:
3122            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3123    
3124    preProcess.py postProcess.py:
3125            \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
3126    
3127    whirl2f whirl2f_be:
3128            \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
3129    
3130    oadDriver:
3131            \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
3132    
3133    AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.make postProcess.tag postProcess.comp \$(PPEXTRAS:.F=.f)
3134    
3135    # ============ end OpenAD specific section ==============
3136    
3137    EOF
3138    
3139    fi
3140    
3141    #=========================================
3142    
3143  if test "x$EXEHOOK" != x ; then  if test "x$EXEHOOK" != x ; then
3144      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
3145  fi  fi

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