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revision 1.243 by utke, Tue Sep 25 21:16:29 2012 UTC revision 1.279 by jmc, Sat Jan 28 18:37:21 2017 UTC
# Line 19  Usage: "$0" [OPTIONS] Line 19  Usage: "$0" [OPTIONS]
19      -help | --help | -h | --h      -help | --help | -h | --h
20            Print this help message and exit.            Print this help message and exit.
21    
22        -oad | --oad
23              Generate a Makefile for an OpenAD built
24    
25        -nocat4ad | -dog4ad | -ncad | -dad
26              do not concatenate (cat) source code sent to TAF
27              resulting in compilation of multiple files
28    
29      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
30        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
31            Use "NAME" as the adoptfile.  By default, the file at            Use "NAME" as the adoptfile.  By default, the file at
32              "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
33            "tools/adjoint_options/adjoint_default" will be used.            "tools/adjoint_options/adjoint_default" will be used.
34    
35      -nooptfile | --nooptfile      -optfile NAME | --optfile NAME | -of NAME | --of NAME
       -optfile NAME | --optfile NAME | -of NAME | --of NAME  
36        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
37            Use "NAME" as the optfile.  By default, an attempt will be            Use "NAME" as the optfile.  By default, an attempt will be
38            made to find an appropriate "standard" optfile in the            made to find an appropriate "standard" optfile in the
# Line 208  test_for_string_in_file() { Line 215  test_for_string_in_file() {
215  expand_pkg_groups() {  expand_pkg_groups() {
216      new_packages=      new_packages=
217      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
218          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > $TMP.p1
219          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
220          matched=0          matched=0
221          for i in $PACKAGES ; do          for i in $PACKAGES ; do
222              line=`grep "^ *$i" ./p2.tmp`              line=`grep "^ *$i" $TMP.p2`
223              RETVAL=$?              RETVAL=$?
224              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
225                  matched=1                  matched=1
# Line 224  expand_pkg_groups() { Line 231  expand_pkg_groups() {
231              fi              fi
232          done          done
233          PACKAGES=$new_packages          PACKAGES=$new_packages
234          rm -f ./p[1,2].tmp          rm -f $TMP.p[1,2]
235          return $matched          return $matched
236      else      else
237          echo "Warning: can't read package groups definition file: $PKG_GROUPS"          echo "Warning: can't read package groups definition file: $PKG_GROUPS"
# Line 324  look_for_makedepend()  { Line 331  look_for_makedepend()  {
331      #      #
332      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
333      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
334      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
335      #      #
336      #  So the choices are, in order:      #  So the choices are, in order:
     #  
337      #    1) use the user-specified program      #    1) use the user-specified program
338      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
339      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
340      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
341        #             (faster, but can miss some dependencies)
342      #      #
343      echo >> $LOGFILE      echo >> $LOGFILE
344      echo "running: look_for_makedepend()" >> $LOGFILE      echo "running: look_for_makedepend()" >> $LOGFILE
# Line 343  look_for_makedepend()  { Line 349  look_for_makedepend()  {
349              build_cyrus_makedepend              build_cyrus_makedepend
350              RETVAL=$?              RETVAL=$?
351              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
352                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
353                  MAKEDEPEND=                  MAKEDEPEND=
354              fi              fi
355          else          else
# Line 356  look_for_makedepend()  { Line 362  look_for_makedepend()  {
362          fi          fi
363      fi      fi
364      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
365          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
366          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
367          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 373  EOF Line 377  EOF
377        stop        stop
378        end        end
379  EOF  EOF
380          makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
381          RV1=$?          RV1=$?
382            which makedepend > /dev/null 2>&1
383            RV2=$?
384            if test "x${RV2}" = x0 ; then
385                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
386                RV3=$? ; loc_msg='not working.'
387            else RV3=$RV2 ; loc_msg='not found.'
388            fi
389          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
390          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
391          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
392            if test "x${RV1}" = x0 ; then
393                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
394                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
395            elif test "x${RV3}" = x0 ; then
396                echo "    local tools/xmakedepend not working. Use system-default makedepend"
397              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
398              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
399          else          else
400              echo "    system-default makedepend not found. Try to build cyrus-makedepend"              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
401                echo -n "    Try to build cyrus-makedepend ..."
402              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
403              build_cyrus_makedepend              build_cyrus_makedepend
404              RETVAL=$?              RETVAL=$?
405              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
406                  echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"                  echo "  Works"
407                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'              else
408                  echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE                  echo "  Fails" ; echo "" >> $LOGFILE
409                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
410                    echo ""
411                    exit -1
412                    return
413              fi              fi
414          fi          fi
415      fi      fi
# Line 588  EOF Line 609  EOF
609      fi      fi
610  }  }
611    
612    #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
613    #  checking for additional included headers (in case of chain of included header)
614    mpi_headers_do_local_copy() {
615    
616        dBug=0
617        rm -rf ./mpi_headers
618        if test -d $MPIINCLUDEDIR ; then
619    
620            #----- check for additional headers (chain of included headers)
621            echo -n '  Check MPI headers ... '
622            listIni=$MPI_HEADER_FILES
623            echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
624            outp=$?
625            #- always check mpif.h (the only mpi-header included in standard MITgcm code)
626            if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
627            if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
628    
629            doCheck=1 ; list2copy='' ; list2check=$listIni
630            while test $doCheck = 1 ; do
631              newList=''
632              for i in $list2check ; do
633                if test -f $MPIINCLUDEDIR/$i ; then
634                  newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
635                    sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
636                  if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
637                  for j in $newInc ; do
638                    echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
639                    outp=$?
640                    if test $outp != 0 ; then
641                      if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
642                      newList="$newList $j"
643                    fi
644                  done
645                  if test $dBug = 1 ; then echo "" ; fi
646                fi
647              done
648              if test "x$newList" = x ; then doCheck=0
649              else list2check=$newList ; list2copy="$list2copy $newList"
650              fi
651            done
652            list2copy="$MPI_HEADER_FILES $list2copy"
653            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
654    
655            #----- create local mpi_headers dir if we have files to copy
656            mkListInc=`echo $list2copy | wc -w`
657            if test $mkListInc != 0 ; then
658              echo 'create local "./mpi_headers" dir'
659              mkdir -p ./mpi_headers
660              INCLUDES="-I./mpi_headers $INCLUDES"
661              mkListInc=1
662            fi
663            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
664    
665            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
666            for i in $list2copy ; do
667              if test -f $MPIINCLUDEDIR/$i ; then
668                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
669                if test $i = 'mpif.h' ; then
670                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
671                fi
672                if test $mkListInc = 2 ; then
673                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
674                fi
675                if test $mkListInc = 1 ; then
676                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
677                fi
678              fi
679            done
680        else
681            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
682            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
683    #       exit -1
684        fi
685    }
686    
687  #  Parse the package dependency information  #  Parse the package dependency information
688  get_pdepend_list()  {  get_pdepend_list()  {
689    
# Line 907  check_netcdf_libs()  { Line 1003  check_netcdf_libs()  {
1003        program fgennc        program fgennc
1004  #include "netcdf.inc"  #include "netcdf.inc"
1005  EOF  EOF
1006      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1007          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1008      fi     #fi
1009      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1010        integer iret, ncid, xid        integer iret, ncid, xid
1011        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 990  EOF Line 1086  EOF
1086  }  }
1087    
1088  check_lapack_libs()  {  check_lapack_libs()  {
1089      if test ! "x$SKIP_LAPACK_CHECK" = x ; then      if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
         return  
     fi  
1090      echo >> $LOGFILE      echo >> $LOGFILE
1091      echo "running: check_lapack_libs()" >> $LOGFILE      echo "running: check_lapack_libs()" >> $LOGFILE
1092      cat <<EOF > genmake_tla.F      cat <<EOF > genmake_tla.F
# Line 1092  EOF Line 1186  EOF
1186      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1187  }  }
1188    
1189    check_HAVE_FLUSH()  {
1190        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1191            return
1192        fi
1193        echo >> $LOGFILE
1194        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1195        cat <<EOF > genmake_tflsh.$FS
1196          program fgenflsh
1197          integer iounit
1198          character*9 fname
1199          iounit = 26
1200          fname = 'tmp.tflsh'
1201          open(iounit,FILE=fname,STATUS='unknown')
1202          write(iounit,*) 'genmake_tflsh: hello'
1203          call flush(iounit)
1204          close(iounit)
1205          end
1206    EOF
1207        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1208        cat genmake_tflsh.$FS >> genmake_tflsh.log
1209        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1210    
1211        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1212        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1213        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1214            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1215        RET_COMPILE=$?
1216    
1217        if test "x$RET_COMPILE" = x0 ; then
1218            HAVE_FLUSH=t
1219            #cat genmake_tflsh.log >> $LOGFILE
1220            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1221        else
1222            HAVE_FLUSH=f
1223            cat genmake_tflsh.log >> $LOGFILE
1224        fi
1225        rm -f genmake_tflsh*
1226        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1227    }
1228    
1229  ###############################################################################  ###############################################################################
1230  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1149  GSL= Line 1282  GSL=
1282  DEVEL=  DEVEL=
1283  HAVE_TEST_L=  HAVE_TEST_L=
1284    
1285    # set this to "t" to enable lapack test
1286    CHECK_FOR_LAPACK=f
1287    
1288  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1289  HAVE_SYSTEM=  HAVE_SYSTEM=
1290  HAVE_FDATE=  HAVE_FDATE=
# Line 1160  HAVE_NETCDF= Line 1296  HAVE_NETCDF=
1296  HAVE_ETIME=  HAVE_ETIME=
1297  IGNORE_TIME=  IGNORE_TIME=
1298  HAVE_LAPACK=  HAVE_LAPACK=
1299    HAVE_FLUSH=
1300    
1301  MODS=  MODS=
1302  TOOLSDIR=  TOOLSDIR=
# Line 1193  FS= Line 1330  FS=
1330  FS90=  FS90=
1331    
1332  AUTODIFF_PKG_USED=f  AUTODIFF_PKG_USED=f
1333    OPENAD=
1334  AD_OPTFILE=  AD_OPTFILE=
1335    CAT_SRC_FOR_TAF=1
1336  TAF=  TAF=
1337  AD_TAF_FLAGS=  AD_TAF_FLAGS=
1338  FTL_TAF_FLAGS=  FTL_TAF_FLAGS=
# Line 1205  FTL_TAF_FLAGS= Line 1344  FTL_TAF_FLAGS=
1344  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1345  TAMC_EXTRA=  TAMC_EXTRA=
1346    
1347    DIVA=
1348    MPIINCLUDEDIR=
1349    MPI_HEADER_FILES=
1350    LOCAL_MPI_HEADERS=
1351    
1352  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1353  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1354  gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"  gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
# Line 1213  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAP Line 1357  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAP
1357  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1358  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1359  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1360  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1361  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1362  gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK"  gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
1363    
1364  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1365  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE OPENAD TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
1366  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
1367  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1368    
1369  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
1370  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1263  for ac_option in "$@" ; do Line 1407  for ac_option in "$@" ; do
1407          -help | --help | -h | --h)          -help | --help | -h | --h)
1408              usage ;;              usage ;;
1409    
         -nooptfile | --nooptfile)  
             OPTFILE="NONE" ;;  
1410          -optfile | --optfile | -of | --of)          -optfile | --optfile | -of | --of)
1411              ac_prev=OPTFILE ;;              ac_prev=OPTFILE ;;
1412          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1413              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1414    
1415            -oad | --oad)
1416                OPENAD="true" ; ALWAYS_USE_F90=1 ;;
1417            -nocat4ad | -dog4ad | -ncad | -dad)
1418                CAT_SRC_FOR_TAF=0 ;;
1419          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1420              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1421          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
# Line 1439  for ac_option in "$@" ; do Line 1585  for ac_option in "$@" ; do
1585    
1586  done  done
1587    
1588    #TMP=./genmk_$$
1589    #- try to put temporary files in system-local /tmp dir
1590    TMP=/tmp/genmk_${USER}_$$
1591    touch $TMP ; retVal=$?
1592    if [ $retVal -eq 0 ] ; then
1593      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1594    else
1595      TMP=./genmk_$$
1596    fi
1597    rm -f $TMP
1598    #echo "  temp files: $TMP.*"
1599    
1600  printf "  getting local config information:  "  printf "  getting local config information:  "
1601  if test -f $gm_local ; then  if test -f $gm_local ; then
1602      echo "using $gm_local"      echo "using $gm_local"
# Line 1531  fi Line 1689  fi
1689    
1690  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1691  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1692      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1693            AD_OPTFILE=$MITGCM_AD_OF
1694        elif test "x$OPENAD" = x ; then
1695          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1696      else      else
1697          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1698      fi      fi
1699  fi  fi
1700  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1557  if test "x${AD_OPTFILE}" != xNONE ; then Line 1717  if test "x${AD_OPTFILE}" != xNONE ; then
1717  fi  fi
1718    
1719  #====================================================================  #====================================================================
1720    # Initialize INCLUDEDIRSMK from and optfile INCLUDEDIRS
1721    if test "x${INCLUDEDIRS}" != "x" ; then
1722     INCLUDEDIRSMK=${INCLUDEDIRS}
1723    fi
1724    
1725    #====================================================================
1726  #  Set default values if not set by the optfile  #  Set default values if not set by the optfile
1727  #  #
1728  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
# Line 1659  check_for_broken_Ff Line 1825  check_for_broken_Ff
1825  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1826        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1827        DEFINES="$DEFINES -DALLOW_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1828    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1829    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1830  fi  fi
1831  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1832        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1799  else Line 1967  else
1967  fi  fi
1968  rm -f genmake_tcomp*  rm -f genmake_tcomp*
1969    
1970  printf "  Do we have the etime() command using $FC...  "  printf "  Do we have the etime() command using $FC... "
1971  cat > genmake_tcomp.$FS <<EOF  cat > genmake_tcomp_1.$FS <<EOF
1972        program hello        program hello
1973        REAL*4 ACTUAL, TARRAY(2)        REAL*4 actual, tarray(2)
1974        EXTERNAL ETIME        EXTERNAL ETIME
1975        REAL*4 ETIME        REAL*4 ETIME
1976        actual = etime( tarray )        actual = ETIME( tarray )
1977        print *, tarray        print *, tarray
1978        end        end
1979  EOF  EOF
1980  $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1  $FC $FFLAGS -o genmake_tcomp_1 genmake_tcomp_1.$FS > genmake_tcomp.log 2>&1
1981  RETVAL=$?  RETVAL=$?
1982  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1983      HAVE_ETIME=t      HAVE_ETIME='Fct'
1984      DEFINES="$DEFINES -DHAVE_ETIME"      DEFINES="$DEFINES -DHAVE_ETIME_FCT"
1985      echo "yes"      echo " yes (${HAVE_ETIME})"
1986  else  else
1987      cat > genmake_tcomp_2.$FS <<EOF
1988          program hello
1989          REAL*4 actual, tarray(2)
1990          actual = -999.
1991          call ETIME( tarray, actual )
1992          if ( actual.ge.0. ) then
1993            print *, 0, tarray, actual
1994          else
1995            print *, 1, tarray, actual
1996          endif
1997          end
1998    EOF
1999      $FC $FFLAGS -o genmake_tcomp_2 genmake_tcomp_2.$FS >> genmake_tcomp.log 2>&1
2000      RETVAL=$?
2001      if test "x$RETVAL" = x0 ; then
2002        echo -n 'c,'
2003        ./genmake_tcomp_2 > genmake_tcomp_2.out 2>&1
2004        RETVAL=$?
2005      fi
2006      if test "x$RETVAL" = x0 ; then
2007        echo -n 'r:'
2008        RETVAL=`cat genmake_tcomp_2.out | $AWK '{print $1}'`
2009      fi
2010      if test "x$RETVAL" = x0 ; then
2011        HAVE_ETIME='SbR'
2012        DEFINES="$DEFINES -DHAVE_ETIME_SBR"
2013        echo " yes (${HAVE_ETIME})"
2014      else
2015      HAVE_ETIME=      HAVE_ETIME=
2016      echo "no"      echo " no"
2017      fi
2018  fi  fi
2019    #mkdir chk_etime ; cp -p -f genmake_tcomp* chk_etime
2020  rm -f genmake_tcomp*  rm -f genmake_tcomp*
2021    
2022  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
# Line 1883  if test "x$HAVE_LAPACK" != x ; then Line 2081  if test "x$HAVE_LAPACK" != x ; then
2081  else  else
2082      echo "no"      echo "no"
2083  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2084    
2085    printf "  Can we call FLUSH intrinsic subroutine...  "
2086    check_HAVE_FLUSH
2087    if test "x$HAVE_FLUSH" = xt ; then
2088        DEFINES="$DEFINES -DHAVE_FLUSH"
2089        echo "yes"
2090    else
2091        echo "no"
2092    fi
2093    
2094    DEFINES="$DEFINES $IGNORE_TIME"
2095  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2096      build_embed_encode      build_embed_encode
2097  fi  fi
# Line 1904  for d in $MODS ; do Line 2111  for d in $MODS ; do
2111          printf "$d "          printf "$d "
2112          SOURCEDIRS="$SOURCEDIRS $d"          SOURCEDIRS="$SOURCEDIRS $d"
2113          INCLUDEDIRS="$INCLUDEDIRS $d"          INCLUDEDIRS="$INCLUDEDIRS $d"
2114            SOURCEDIRSMK="$SOURCEDIRSMK $d"
2115            INCLUDEDIRSMK="$INCLUDEDIRSMK $d"
2116      fi      fi
2117  done  done
2118  echo  echo
# Line 1927  fi Line 2136  fi
2136    
2137  if test "x${TOOLSDIR}" = x ; then  if test "x${TOOLSDIR}" = x ; then
2138      TOOLSDIR="$ROOTDIR/tools"      TOOLSDIR="$ROOTDIR/tools"
2139        TOOLSDIRMK='$(ROOTDIR)'"/tools"
2140    else
2141        TOOLSDIRMK=${TOOLSDIR}
2142  fi  fi
2143  if test ! -d ${TOOLSDIR} ; then  if test ! -d ${TOOLSDIR} ; then
2144      echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"      echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
# Line 2089  if test "x${PKG_GROUPS}" != x ; then Line 2301  if test "x${PKG_GROUPS}" != x ; then
2301  fi  fi
2302    
2303  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2304  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2305  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2306      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2307  done  done
2308  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2309      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2310      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2311  done  done
# Line 2111  for p in $PACKAGES ; do Line 2323  for p in $PACKAGES ; do
2323  done  done
2324  PACKAGES="$pack"  PACKAGES="$pack"
2325  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2326  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2327  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2328  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2329  for i in $PACKAGES ; do  for i in $PACKAGES ; do
# Line 2120  for i in $PACKAGES ; do Line 2332  for i in $PACKAGES ; do
2332          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2333          exit 1          exit 1
2334      fi      fi
2335      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2336  done  done
2337  PACKAGES=  PACKAGES=
2338  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2339      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2340  done  done
2341  rm -f ./.tmp_pack  rm -f $TMP.pack
2342  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2343    
2344  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2196  EOF Line 2408  EOF
2408      fi      fi
2409  fi  fi
2410    
2411  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2412  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2413  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2414      RETVAL=$?      RETVAL=$?
2415      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2416          cat <<EOF          cat <<EOF
 *********************************************************************  
 WARNING: the "radtrans" package was enabled but tests failed to  
   compile LAPACK applications.  This means that the direct radtrans  
   solver is not available and compilation will fail if it is enabled.  
   If you want to use the direct solver, please check that:  
2417    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2418  *********************************************************************  *********************************************************************
2419    ERROR: when generating an adjoint with OpenAD, the openad package
2420      must be enabled.  Please add it to packages.conf.
2421    *********************************************************************
2422    
2423  EOF  EOF
2424            exit 1
2425      fi      fi
2426  fi  fi
2427    
# Line 2296  if  test "x${PKG_DEPEND}" != x ; then Line 2504  if  test "x${PKG_DEPEND}" != x ; then
2504  fi  fi
2505  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2506      adr="$ROOTDIR/pkg/$i"      adr="$ROOTDIR/pkg/$i"
2507        adrmk='$(ROOTDIR)'"/pkg/$i"
2508      if test -d $adr ; then      if test -d $adr ; then
2509          SOURCEDIRS="$SOURCEDIRS $adr"          SOURCEDIRS="$SOURCEDIRS $adr"
2510          INCLUDEDIRS="$INCLUDEDIRS $adr"          INCLUDEDIRS="$INCLUDEDIRS $adr"
2511            SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
2512            INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
2513          if test "x$i" = xautodiff ; then          if test "x$i" = xautodiff ; then
2514              AUTODIFF_PKG_USED=t              AUTODIFF_PKG_USED=t
2515          fi          fi
# Line 2354  BUILDDIR=${BUILDDIR:-.} Line 2565  BUILDDIR=${BUILDDIR:-.}
2565  if test "x$STANDARDDIRS" != x ; then  if test "x$STANDARDDIRS" != x ; then
2566      for d in $STANDARDDIRS ; do      for d in $STANDARDDIRS ; do
2567          adr="$ROOTDIR/$d/src"          adr="$ROOTDIR/$d/src"
2568            adrmk='$(ROOTDIR)/'"$d/src"
2569          if test ! -d $adr ; then          if test ! -d $adr ; then
2570              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
2571              echo "  is correct and that you correctly specified the STANDARDDIRS option"              echo "  is correct and that you correctly specified the STANDARDDIRS option"
2572              exit 1              exit 1
2573          else          else
2574              SOURCEDIRS="$SOURCEDIRS $adr"              SOURCEDIRS="$SOURCEDIRS $adr"
2575                SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
2576          fi          fi
2577          adr="$ROOTDIR/$d/inc"          adr="$ROOTDIR/$d/inc"
2578            adrmk='$(ROOTDIR)/'"$d/inc"
2579          if test ! -d $adr ; then          if test ! -d $adr ; then
2580              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
2581              echo "  is correct and that you correctly specified the STANDARDDIRS option"              echo "  is correct and that you correctly specified the STANDARDDIRS option"
2582              exit 1              exit 1
2583          else          else
2584              INCLUDEDIRS="$INCLUDEDIRS $adr"              INCLUDEDIRS="$INCLUDEDIRS $adr"
2585                INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
2586          fi          fi
2587      done      done
2588  fi  fi
# Line 2405  fi Line 2620  fi
2620    
2621  #  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
2622  #  compiler.  #  compiler.
2623  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2624      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2625  fi  fi
2626  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2627  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2628  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2629      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2630      for j in $list_files ; do      for j in $list_files ; do
2631          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2632      done      done
2633  done  done
2634  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2635      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2636      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2637  fi  fi
2638    
2639  echo  echo
# Line 2430  for i in $INCLUDEDIRS ; do Line 2645  for i in $INCLUDEDIRS ; do
2645      fi      fi
2646  done  done
2647    
2648  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2649      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2650      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2651      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2652      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2653            mpi_headers_do_local_copy
     if test "x$MPIINCLUDEDIR" = x ; then  
         if test "x$MPIHOME" = x ; then  
             MPIHOME='/usr'  
         fi  
         MPIINCLUDEDIR='$MPIHOME/include'  
     fi  
   
     if test -r $MPIINCLUDEDIR/mpif.h ; then  
         for i in $MPI_HEADER_FILES; do  
             cp -p $MPIINCLUDEDIR/$i ./mpi_headers  
         done  
   
         perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h  
     else  
         echo " We cannot create a copy of mpif.h!"  
 #       exit -1  
2654      fi      fi
2655  fi  fi
2656    
2657  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2658  rm -rf .links.tmp  rm -rf $TMP.links
2659  mkdir .links.tmp  mkdir $TMP.links
2660  touch .links.tmp/foo  touch $TMP.links/foo
2661  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2662      echo      echo
2663      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2664      echo "   your user file-creation mask (\"umask\") since creating a"      echo "   your user file-creation mask (\"umask\") since creating a"
# Line 2475  if test ! -r ".links.tmp/foo" ; then Line 2674  if test ! -r ".links.tmp/foo" ; then
2674      echo      echo
2675      exit 1      exit 1
2676  fi  fi
2677  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2678    
2679  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2680      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
# Line 2483  if test "x$OPENAD" != x ; then Line 2682  if test "x$OPENAD" != x ; then
2682      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2683      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2684      OADTOOLS="$TOOLSDIR/OAD_support"      OADTOOLS="$TOOLSDIR/OAD_support"
2685      test -f "oadtempflile"  &&  \rm -f "oadtempflile"      OADTOOLSMK='$(TOOLSDIR)/OAD_support'
 cat >> "oadtempflile" <<EOF  
 $OADTOOLS  
 EOF  
2686      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2687      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2688          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
2689              OAD_DONT_COMPILE=$i"/dontCompile"              OAD_DONT_COMPILE=$i"/dontCompile"
2690              echo "     found $OAD_DONT_COMPILE"              echo "     found $OAD_DONT_COMPILE"
# Line 2496  EOF Line 2692  EOF
2692          fi          fi
2693      done      done
2694      echo "  looking for dontTransform file:  "      echo "  looking for dontTransform file:  "
2695      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2696          if test -r $i"/dontTransform" ; then          if test -r $i"/dontTransform" ; then
2697              OAD_DONT_TRANSFORM=$i"/dontTransform"              OAD_DONT_TRANSFORM=$i"/dontTransform"
2698              echo "     found $OAD_DONT_TRANSFORM"              echo "     found $OAD_DONT_TRANSFORM"
# Line 2504  EOF Line 2700  EOF
2700          fi          fi
2701      done      done
2702      echo "  looking for keepOriginal file:  "      echo "  looking for keepOriginal file:  "
2703      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2704          if test -r $i"/keepOriginal" ; then          if test -r $i"/keepOriginal" ; then
2705              OAD_KEEP_ORIGINAL=$i"/keepOriginal"              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2706              echo "     found $OAD_KEEP_ORIGINAL"              echo "     found $OAD_KEEP_ORIGINAL"
# Line 2512  EOF Line 2708  EOF
2708          fi          fi
2709      done      done
2710      echo "  looking for cb2mFiles:  "      echo "  looking for cb2mFiles:  "
2711      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2712          if test -r $i"/cb2mFiles" ; then          if test -r $i"/cb2mFiles" ; then
2713              OAD_CB2M_FILES=$i"/cb2mFiles"              OAD_CB2M_FILES=$i"/cb2mFiles"
2714              echo "     found $OAD_CB2M_FILES"              echo "     found $OAD_CB2M_FILES"
# Line 2522  EOF Line 2718  EOF
2718      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2719  fi  fi
2720    
2721  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2722  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2723  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2724  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2725  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2726  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2727  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2728  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2729  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2730    alldirsmk=(${SOURCEDIRSMK} ${INCLUDEDIRSMK} ".")
2731    nd=0
2732  for d in $alldirs ; do  for d in $alldirs ; do
2733        dmk=${alldirsmk[${nd}]}
2734        nd=$((${nd}+1))
2735      deplist=      deplist=
2736      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2737      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
# Line 2539  for d in $alldirs ; do Line 2739  for d in $alldirs ; do
2739          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2740      fi      fi
2741      for sf in $sfiles ; do      for sf in $sfiles ; do
2742          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2743              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2744                  ignore_f=f                  ignore_f=f
2745                  case $d/$sf in                  case $d/$sf in
# Line 2564  for d in $alldirs ; do Line 2764  for d in $alldirs ; do
2764                          if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then                          if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
2765                              ignore_f=t                              ignore_f=t
2766                          else                          else
2767                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2768                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2769                          fi                          fi
2770                          ;;                          ;;
# Line 2573  for d in $alldirs ; do Line 2773  for d in $alldirs ; do
2773                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2774                      case $extn in                      case $extn in
2775                        F)                        F)
2776                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2777                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2778                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2779                              basename=${sf%%.F}                              basename=${sf%%.F}
2780                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2781                                if test -z "$isAD" ; then
2782                                    echo    " \\"  >> $TMP.nonADF77srclist
2783                                    printf " $sf" >> $TMP.nonADF77srclist
2784                                fi
2785                            else #- OpenAD case:
2786                                basename=${sf%%.F}
2787                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2788                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2789                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2790                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2791                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2792                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2793                                  else                                  else
2794                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2795                                  fi                                  fi
# Line 2597  for d in $alldirs ; do Line 2804  for d in $alldirs ; do
2804                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2805                                  fi                                  fi
2806                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2807                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2808                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2809                                  fi                                  fi
2810                              fi                              fi
2811                          fi                          fi
2812                          ;;                          ;;
2813                      F90)                      F90)
2814                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2815                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2816                          ;;                          ;;
2817                      c)                      c)
2818                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2819                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2820                          ;;                          ;;
2821                      h)                      h)
2822                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2823                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2824                          ;;                          ;;
2825                      flow)                      flow)
2826                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2827                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2828                          ;;                          ;;
2829                     esac                     esac
2830                  fi                  fi
# Line 2626  for d in $alldirs ; do Line 2833  for d in $alldirs ; do
2833      done      done
2834      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2835        if test "$d" != "." ; then        if test "$d" != "." ; then
2836          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2837          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $dmk ( aka $d )" >> $TMP.srclinks
2838          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2839  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2840  # This may happen when make thinks that a header file has to be "remade"  # This may happen when make thinks that a header file has to be "remade"
2841  # because a module it depends on has changed.  In this case we do nothing.  # because a module it depends on has changed.  In this case we do nothing.
2842          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $dmk >> $TMP.srclinks
2843        fi        fi
2844      fi      fi
2845  done  done
2846  rm -rf .links.tmp  rm -rf $TMP.links
2847  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2848  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2849  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2850  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2851  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2852  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2853    
2854  CMDLINE=$0  CMDLINE=$0
2855  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
# Line 2689  cat >>$MAKEFILE <<EOF Line 2896  cat >>$MAKEFILE <<EOF
2896    
2897  ROOTDIR     = ${ROOTDIR}  ROOTDIR     = ${ROOTDIR}
2898  BUILDDIR    = ${BUILDDIR}  BUILDDIR    = ${BUILDDIR}
2899  SOURCEDIRS  = ${SOURCEDIRS}  SOURCEDIRS  = ${SOURCEDIRSMK}
2900  INCLUDEDIRS = ${INCLUDEDIRS}  INCLUDEDIRS = ${INCLUDEDIRSMK}
2901  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2902  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2903  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIRMK}
2904  OADTOOLS    = ${OADTOOLS}  OADTOOLS    = ${OADTOOLSMK}
2905    
2906  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2907  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = \$(ROOTDIR)/pkg/autodiff
2908  EXE_AD      = ${EXE_AD}  EXE_AD      = ${EXE_AD}
2909  EXE_FTL     = ${EXE_FTL}  EXE_FTL     = ${EXE_FTL}
2910  EXE_SVD     = ${EXE_SVD}  EXE_SVD     = ${EXE_SVD}
# Line 2715  else Line 2922  else
2922      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2923  fi  fi
2924    
2925    # extract default cpp search path so we can pass it to makedepend
2926    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2927    
2928  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2929  # Unix ln (link)  # Unix ln (link)
2930  LN = ${LN}  LN = ${LN}
# Line 2735  LINK = ${LINK} ${LDADD} Line 2945  LINK = ${LINK} ${LDADD}
2945  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2946  # Includes for CPP  # Includes for CPP
2947  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2948    # default CPP includes for makedepend
2949    CPPINCLUDES = ${CPPINCLUDES}
2950  # Flags for KPP  # Flags for KPP
2951  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2952  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2953  # Optim./debug for FC  # Optim./debug for FC
2954  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}  FFLAGS = ${FFLAGS}
2955  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
2956  # Optim./debug for FC  # Optim./debug for FC
2957  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2958  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
# Line 2759  MAKE = ${MAKE} Line 2971  MAKE = ${MAKE}
2971    
2972  EOF  EOF
2973    
2974  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2975  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2976  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2977  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2978  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2979  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2980    
2981  rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp  rm -f $TMP.F77srclist $TMP.nonADF77srclist $TMP.csrclist $TMP.F90srclist $TMP.hsrclist $TMP.ad_flow_files
2982    
2983  echo >> $MAKEFILE  echo >> $MAKEFILE
2984    
# Line 2800  fwd_exe_target: Line 3012  fwd_exe_target:
3012    
3013  depend:  depend:
3014          @\$(MAKE) -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
3015          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
3016          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
3017          -rm -f makedepend.out          -rm -f makedepend.out
3018    
3019  lib: libmitgcmuv.a  lib: libmitgcmuv.a
3020    
3021  libmitgcmuv.a: \$(OBJFILES)  libmitgcmuv.a: \$(SPECIAL_FILES) \$(OBJFILES)
3022          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
3023          ar d   libmitgcmuv.a main.o          ar d   libmitgcmuv.a main.o
3024    
# Line 2816  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 3028  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
3028    
3029  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
3030    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
3031  # remove most of the files that "make" generates  # remove most of the files that "make" generates
3032  clean:  clean:
3033          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2833  Clean: Line 3041  Clean:
3041          @\$(MAKE) -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
3042          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
3043          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log
         -rm -f genmake_warnings genmake_errors make.log  
3044    
3045  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
3046  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
# Line 2842  CLEAN: Line 3049  CLEAN:
3049          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
3050          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3051          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3052            -rm -rf mpi_headers mnc_test_*
3053          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3054          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3055          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3056          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3057            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3058          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3059          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3060    
3061  makefile:  makefile:
3062          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2900  cat >>$MAKEFILE <<EOF Line 3109  cat >>$MAKEFILE <<EOF
3109  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3110  ## %.o : %.F  ## %.o : %.F
3111    
3112  # C preprocessing and replacing the _d in constants:  # C preprocessing and replacing the _d in constants:
3113  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3114    
3115  .F.$FS:  .F.$FS:
# Line 2944  TAF            = ${TAF} Line 3153  TAF            = ${TAF}
3153    
3154  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3155  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3156    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3157    
3158  EOF  EOF
3159    
# Line 2961  done Line 3171  done
3171  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3172  echo >> $MAKEFILE  echo >> $MAKEFILE
3173  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3174  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3175  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3176      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3177      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3178  done  done
3179  echo >> $MAKEFILE  echo >> $MAKEFILE
3180  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3181    
3182    if test $CAT_SRC_FOR_TAF = 0 ; then
3183    cat >>$MAKEFILE <<EOF
3184    
3185    # ... Utilities ...
3186    remove_comments:
3187            sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
3188            @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
3189    adj_sed:
3190            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
3191            @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
3192    ftl_sed:
3193            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
3194            @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
3195    adobjfiles: \$(AD_FILES:.$FS=_ad.o)
3196    ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
3197    EOF
3198    fi
3199    
3200  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3201    
# Line 2991  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL Line 3219  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
3219          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3220          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
3221    
3222  ad_taf_output.$FS: ad_input_code.$FS  adtafonly:
3223          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3224          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3225          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
3226    
3227  adtafonly:  EOF
3228    
3229    if test $CAT_SRC_FOR_TAF = 1 ; then
3230    cat >>$MAKEFILE <<EOF
3231    # ... send 1 file to TAF ...
3232    ad_taf_output.$FS: ad_input_code.$FS
3233            @-rm -f ad_input_code_ad.$FS ; echo ''
3234          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3235          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3236          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3237    
3238  \$(EXE_AD): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ad_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3239          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3240    
3241  ad_tamc_output.$FS: ad_input_code.$FS  adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
         \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS  
         cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS  
3242    
3243  ad_tamc: ad_tamc_output.o \$(OBJFILES)  EOF
3244          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)  
3245    else
3246    cat >>$MAKEFILE <<EOF
3247    # ... send multiple files to TAF ...
3248    ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3249            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3250            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3251            @-rm -f ad_config.template
3252            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3253            @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3254            @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
3255            \$(MAKE) -f \$(MAKEFILE) remove_comments
3256            \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
3257            \$(MAKE) -f \$(MAKEFILE) adj_sed
3258            cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
3259    
3260    \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3261            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3262            \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3263    
3264    adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3265            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3266    
3267    EOF
3268    fi
3269    
3270    cat >>$MAKEFILE <<EOF
3271  adonlyfwd:  adonlyfwd:
3272          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
3273    
3274  adtrick:  adtrick:
3275          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3276    
3277  adobj: ad_taf_output.o \$(OBJFILES)  ad_tamc_output.$FS: ad_input_code.$FS
3278            \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
3279            cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
3280    
3281    ad_tamc: ad_tamc_output.o \$(OBJFILES)
3282            \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
3283    
3284  # ... FTL ...  # ... FTL ...
3285  ftlall: ftl_exe_target  ftlall: ftl_exe_target
# Line 3039  ftl_input_code.$FS: \$(AD_FILES) Line 3301  ftl_input_code.$FS: \$(AD_FILES)
3301          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3302          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3303    
3304  ftl_taf_output.$FS: ftl_input_code.$FS  ftltafonly:
3305          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3306          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3307          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3308    
3309  ftltafonly:  EOF
3310    
3311    if test $CAT_SRC_FOR_TAF = 1 ; then
3312    cat >>$MAKEFILE <<EOF
3313    # ... send 1 file to TAF ...
3314    ftl_taf_output.$FS: ftl_input_code.$FS
3315            @-rm -f ftl_input_code_tl.$FS ; echo ''
3316          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3317          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3318          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3319    
3320    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3321            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3322    
3323  \$(EXE_FTL): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ftl_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  EOF
         \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)  
3324    
3325    else
3326    cat >>$MAKEFILE <<EOF
3327    # ... send multiple files to TAF ...
3328    ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3329            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3330            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3331            @-rm -f ad_config.template
3332            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3333            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3334            @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
3335            \$(MAKE) -f \$(MAKEFILE) remove_comments
3336            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
3337            \$(MAKE) -f \$(MAKEFILE) ftl_sed
3338            cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
3339    
3340    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3341            \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
3342            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3343    
3344    EOF
3345    fi
3346    
3347    cat >>$MAKEFILE <<EOF
3348  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3349          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
3350          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
# Line 3094  if test "x$OPENAD" != x ; then Line 3387  if test "x$OPENAD" != x ; then
3387  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3388    
3389  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3390    # ... OpenAD ...
3391    
3392  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3393  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3133  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3427  for i in `cat ${OAD_CB2M_FILES}` ; do
3427    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3428    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3429  done  done
3430  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3431  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3432    basename=${i%%.f}    basename=${i%%.f}
3433    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
# Line 3143  for i in $AD_FILES ; do Line 3437  for i in $AD_FILES ; do
3437    fi    fi
3438  done  done
3439  echo >> $MAKEFILE  echo >> $MAKEFILE
3440  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3441    
3442  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3443    
3444  adAll: \$(EXE_AD)  adAll: ad_exe_target
3445  .PHONY: adAll  .PHONY: adAll
3446    
3447    ad_exe_target:
3448            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3449            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3450            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3451            @-rm -f ad_config.template
3452            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3453    
3454  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
3455    
3456  .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)  .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
# Line 3165  w2f__types.F90 \ Line 3466  w2f__types.F90 \
3466  OAD_active.F90 \  OAD_active.F90 \
3467  OAD_cp.F90 \  OAD_cp.F90 \
3468  OAD_rev.F90 \  OAD_rev.F90 \
3469  OAD_tape.F90  OAD_tape.F90 \
3470    OAD_regular_cp.F90 \
3471    revolve.F90
3472    
3473  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3474  iaddr.c \  iaddr.c \
# Line 3191  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N Line 3494  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
3494          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3495    
3496  # create sources files modules from header files containing common blocks  # create sources files modules from header files containing common blocks
3497  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk  %_mod.FF90 : %.h \$(OADTOOLS)/cb2mGetModules.csh \$(OADTOOLS)/cb2mGetModules.awk
3498          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk          \$(OADTOOLS)/cb2mGetModules.csh $< \$(OADTOOLS)/cb2mGetModules.awk
3499    
3500  # create new header files with USE statements for the new modules made above  # create new header files with USE statements for the new modules made above
3501  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk  %_mod.h : %.h \$(OADTOOLS)/cb2mGetHeaders.csh \$(OADTOOLS)/cb2mGetHeaders.awk
3502          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \$(OADTOOLS)/cb2mGetHeaders.csh $< \$(OADTOOLS)/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3503    
3504  # change the include directives of everybody to refer to  the new header files with the USE statements  # change the include directives of everybody to refer to  the new header files with the USE statements
3505  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash  %_cb2m.FF90 : %.F \$(OADTOOLS)/cb2mUseModules.bash
3506          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}          \$(OADTOOLS)/cb2mUseModules.bash $< ${MPI}
3507    
3508  # makefile debug rule  # makefile debug rule
3509  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3510  .PHONY: small_f  .PHONY: small_f
3511    
 ad_output.txt: \$(EXE_AD)  
         @printf 'linking data files ... '  
         \$(LN) -f ../input_ad/data* ../input_ad/eedata .  
         \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .  
         @printf 'running ... '  
         @./\$(EXE_AD) > \$@  
   
3512  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3513          cat \$^ > \$@          cat \$^ > \$@
3514    
# Line 3222  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI Line 3518  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
3518    
3519  # replace stop statements (to avoid the implied unstructured control flow)  with print statements  # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3520  ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90  ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3521          cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90          cat \$< | sed -f \$(OADTOOLS)/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3522    
3523  # F -> WHIRL  # F -> WHIRL
3524  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
# Line 3245  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS Line 3541  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
3541          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3542    
3543  # insert template directives  # insert template directives
3544  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \${OADTOOLS}/insertTemplateDir.bash  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \$(OADTOOLS)/insertTemplateDir.bash
3545          \${OADTOOLS}/insertTemplateDir.bash \$< \$@          \$(OADTOOLS)/insertTemplateDir.bash \$< \$@
3546    
3547  PPEXTRAS=\$(wildcard \${OADTOOLS}/ad_template.*.F) \${OADTOOLS}/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \$(OADTOOLS)/ad_template.*.F)) ad_inline.F
3548  # postprocess F'  # postprocess F'
3549  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
3550          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i \${OADTOOLS}/ad_inline.f \$<          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
3551          # the target is a placeholder to trigger a single execution of the rule          # the target is a placeholder to trigger a single execution of the rule
3552          touch \$@          touch \$@
3553  # put this so make knows about the postprocessing output  # put this so make knows about the postprocessing output
# Line 3262  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f Line 3558  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
3558          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3559    
3560  # link the support files:  # link the support files:
3561  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3562          \$(LN) \${OADTOOLS}/\$@ .          \$(LN) \$(OADTOOLS)/\$@ .
3563    
3564  AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag \$(PPEXTRAS:.F=.f)  AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag
3565    
3566  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3567    
# Line 3301  for i in $NOOPTFILES ; do Line 3597  for i in $NOOPTFILES ; do
3597  done  done
3598    
3599  echo "  Add rules for links"  echo "  Add rules for links"
3600  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3601  rm -f srclinks.tmp  rm -f $TMP.srclinks
3602    
3603  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3604  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE

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