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revision 1.241 by utke, Wed Sep 19 20:46:03 2012 UTC revision 1.272 by heimbach, Fri Jul 3 21:33:55 2015 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      -nooptfile | --nooptfile
# Line 208  test_for_string_in_file() { Line 216  test_for_string_in_file() {
216  expand_pkg_groups() {  expand_pkg_groups() {
217      new_packages=      new_packages=
218      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
219          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
220          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
221          matched=0          matched=0
222          for i in $PACKAGES ; do          for i in $PACKAGES ; do
223              line=`grep "^ *$i" ./p2.tmp`              line=`grep "^ *$i" $TMP.p2`
224              RETVAL=$?              RETVAL=$?
225              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
226                  matched=1                  matched=1
# Line 224  expand_pkg_groups() { Line 232  expand_pkg_groups() {
232              fi              fi
233          done          done
234          PACKAGES=$new_packages          PACKAGES=$new_packages
235          rm -f ./p[1,2].tmp          rm -f $TMP.p[1,2]
236          return $matched          return $matched
237      else      else
238          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 332  look_for_makedepend()  {
332      #      #
333      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
334      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
335      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
336      #      #
337      #  So the choices are, in order:      #  So the choices are, in order:
     #  
338      #    1) use the user-specified program      #    1) use the user-specified program
339      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
340      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
341      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
342        #             (faster, but can miss some dependencies)
343      #      #
344      echo >> $LOGFILE      echo >> $LOGFILE
345      echo "running: look_for_makedepend()" >> $LOGFILE      echo "running: look_for_makedepend()" >> $LOGFILE
# Line 343  look_for_makedepend()  { Line 350  look_for_makedepend()  {
350              build_cyrus_makedepend              build_cyrus_makedepend
351              RETVAL=$?              RETVAL=$?
352              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
353                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
354                  MAKEDEPEND=                  MAKEDEPEND=
355              fi              fi
356          else          else
# Line 356  look_for_makedepend()  { Line 363  look_for_makedepend()  {
363          fi          fi
364      fi      fi
365      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
366          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
367          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
368          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 373  EOF Line 378  EOF
378        stop        stop
379        end        end
380  EOF  EOF
381          makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
382          RV1=$?          RV1=$?
383            which makedepend > /dev/null 2>&1
384            RV2=$?
385            if test "x${RV2}" = x0 ; then
386                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
387                RV3=$? ; loc_msg='not working.'
388            else RV3=$RV2 ; loc_msg='not found.'
389            fi
390          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
391          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
392          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
393            if test "x${RV1}" = x0 ; then
394                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
395                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
396            elif test "x${RV3}" = x0 ; then
397                echo "    local tools/xmakedepend not working. Use system-default makedepend"
398              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
399              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
400          else          else
401              echo "    system-default makedepend not found. Try to build cyrus-makedepend"              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
402                echo -n "    Try to build cyrus-makedepend ..."
403              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
404              build_cyrus_makedepend              build_cyrus_makedepend
405              RETVAL=$?              RETVAL=$?
406              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
407                  echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"                  echo "  Works"
408                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'              else
409                  echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE                  echo "  Fails" ; echo "" >> $LOGFILE
410                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
411                    echo ""
412                    exit -1
413                    return
414              fi              fi
415          fi          fi
416      fi      fi
# Line 588  EOF Line 610  EOF
610      fi      fi
611  }  }
612    
613    #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
614    #  checking for additional included headers (in case of chain of included header)
615    mpi_headers_do_local_copy() {
616    
617        dBug=0
618        rm -rf ./mpi_headers
619        if test -d $MPIINCLUDEDIR ; then
620    
621            #----- check for additional headers (chain of included headers)
622            echo -n '  Check MPI headers ... '
623            listIni=$MPI_HEADER_FILES
624            echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
625            outp=$?
626            #- always check mpif.h (the only mpi-header included in standard MITgcm code)
627            if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
628            if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
629    
630            doCheck=1 ; list2copy='' ; list2check=$listIni
631            while test $doCheck = 1 ; do
632              newList=''
633              for i in $list2check ; do
634                if test -f $MPIINCLUDEDIR/$i ; then
635                  newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
636                    sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
637                  if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
638                  for j in $newInc ; do
639                    echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
640                    outp=$?
641                    if test $outp != 0 ; then
642                      if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
643                      newList="$newList $j"
644                    fi
645                  done
646                  if test $dBug = 1 ; then echo "" ; fi
647                fi
648              done
649              if test "x$newList" = x ; then doCheck=0
650              else list2check=$newList ; list2copy="$list2copy $newList"
651              fi
652            done
653            list2copy="$MPI_HEADER_FILES $list2copy"
654            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
655    
656            #----- create local mpi_headers dir if we have files to copy
657            mkListInc=`echo $list2copy | wc -w`
658            if test $mkListInc != 0 ; then
659              echo 'create local "./mpi_headers" dir'
660              mkdir -p ./mpi_headers
661              INCLUDES="-I./mpi_headers $INCLUDES"
662              mkListInc=1
663            fi
664            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
665    
666            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
667            for i in $list2copy ; do
668              if test -f $MPIINCLUDEDIR/$i ; then
669                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
670                if test $i = 'mpif.h' ; then
671                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
672                fi
673                if test $mkListInc = 2 ; then
674                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
675                fi
676                if test $mkListInc = 1 ; then
677                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
678                fi
679              fi
680            done
681        else
682            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
683            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
684    #       exit -1
685        fi
686    }
687    
688  #  Parse the package dependency information  #  Parse the package dependency information
689  get_pdepend_list()  {  get_pdepend_list()  {
690    
# Line 907  check_netcdf_libs()  { Line 1004  check_netcdf_libs()  {
1004        program fgennc        program fgennc
1005  #include "netcdf.inc"  #include "netcdf.inc"
1006  EOF  EOF
1007      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1008          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1009      fi     #fi
1010      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1011        integer iret, ncid, xid        integer iret, ncid, xid
1012        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 990  EOF Line 1087  EOF
1087  }  }
1088    
1089  check_lapack_libs()  {  check_lapack_libs()  {
1090      if test ! "x$SKIP_LAPACK_CHECK" = x ; then      if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
         return  
     fi  
1091      echo >> $LOGFILE      echo >> $LOGFILE
1092      echo "running: check_lapack_libs()" >> $LOGFILE      echo "running: check_lapack_libs()" >> $LOGFILE
1093      cat <<EOF > genmake_tla.F      cat <<EOF > genmake_tla.F
# Line 1092  EOF Line 1187  EOF
1187      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1188  }  }
1189    
1190    check_HAVE_FLUSH()  {
1191        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1192            return
1193        fi
1194        echo >> $LOGFILE
1195        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1196        cat <<EOF > genmake_tflsh.$FS
1197          program fgenflsh
1198          integer iounit
1199          character*9 fname
1200          iounit = 26
1201          fname = 'tmp.tflsh'
1202          open(iounit,FILE=fname,STATUS='unknown')
1203          write(iounit,*) 'genmake_tflsh: hello'
1204          call flush(iounit)
1205          close(iounit)
1206          end
1207    EOF
1208        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1209        cat genmake_tflsh.$FS >> genmake_tflsh.log
1210        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1211    
1212        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1213        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1214        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1215            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1216        RET_COMPILE=$?
1217    
1218        if test "x$RET_COMPILE" = x0 ; then
1219            HAVE_FLUSH=t
1220            #cat genmake_tflsh.log >> $LOGFILE
1221            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1222        else
1223            HAVE_FLUSH=f
1224            cat genmake_tflsh.log >> $LOGFILE
1225        fi
1226        rm -f genmake_tflsh*
1227        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1228    }
1229    
1230  ###############################################################################  ###############################################################################
1231  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1149  GSL= Line 1283  GSL=
1283  DEVEL=  DEVEL=
1284  HAVE_TEST_L=  HAVE_TEST_L=
1285    
1286    # set this to "t" to enable lapack test
1287    CHECK_FOR_LAPACK=f
1288    
1289  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1290  HAVE_SYSTEM=  HAVE_SYSTEM=
1291  HAVE_FDATE=  HAVE_FDATE=
# Line 1160  HAVE_NETCDF= Line 1297  HAVE_NETCDF=
1297  HAVE_ETIME=  HAVE_ETIME=
1298  IGNORE_TIME=  IGNORE_TIME=
1299  HAVE_LAPACK=  HAVE_LAPACK=
1300    HAVE_FLUSH=
1301    
1302  MODS=  MODS=
1303  TOOLSDIR=  TOOLSDIR=
# Line 1193  FS= Line 1331  FS=
1331  FS90=  FS90=
1332    
1333  AUTODIFF_PKG_USED=f  AUTODIFF_PKG_USED=f
1334    OPENAD=
1335    OPENAD_DIVA=
1336  AD_OPTFILE=  AD_OPTFILE=
1337    CAT_SRC_FOR_TAF=1
1338  TAF=  TAF=
1339  AD_TAF_FLAGS=  AD_TAF_FLAGS=
1340  FTL_TAF_FLAGS=  FTL_TAF_FLAGS=
# Line 1205  FTL_TAF_FLAGS= Line 1346  FTL_TAF_FLAGS=
1346  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1347  TAMC_EXTRA=  TAMC_EXTRA=
1348    
1349    DIVA=
1350    MPIINCLUDEDIR=
1351    MPI_HEADER_FILES=
1352    LOCAL_MPI_HEADERS=
1353    
1354  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1355  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1356  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 1359  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAP
1359  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1360  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1361  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1362  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1363  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1364  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"
1365    
1366  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1367  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"
1368  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"
1369  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1370    
1371  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 $gm_s8"
1372  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1270  for ac_option in "$@" ; do Line 1416  for ac_option in "$@" ; do
1416          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1417              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1418    
1419            -oad | --oad)
1420                OPENAD="true" ; ALWAYS_USE_F90=1 ;;
1421            -nocat4ad | -dog4ad | -ncad | -dad)
1422                CAT_SRC_FOR_TAF=0 ;;
1423          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1424              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1425          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
1426              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1427    
1428            -diva | --diva)
1429                OPENAD_DIVA="ALLOW_OPENAD_DIVA=" ;;
1430    
1431          -pdepend | --pdepend)          -pdepend | --pdepend)
1432              ac_prev=PKG_DEPEND ;;              ac_prev=PKG_DEPEND ;;
1433          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
# Line 1439  for ac_option in "$@" ; do Line 1592  for ac_option in "$@" ; do
1592    
1593  done  done
1594    
1595    #TMP=./genmk_$$
1596    #- try to put temporary files in system-local /tmp dir
1597    TMP=/tmp/genmk_${USER}_$$
1598    touch $TMP ; retVal=$?
1599    if [ $retVal -eq 0 ] ; then
1600      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1601    else
1602      TMP=./genmk_$$
1603    fi
1604    rm -f $TMP
1605    #echo "  temp files: $TMP.*"
1606    
1607  printf "  getting local config information:  "  printf "  getting local config information:  "
1608  if test -f $gm_local ; then  if test -f $gm_local ; then
1609      echo "using $gm_local"      echo "using $gm_local"
# Line 1531  fi Line 1696  fi
1696    
1697  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1698  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1699      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1700            AD_OPTFILE=$MITGCM_AD_OF
1701        elif test "x$OPENAD" = x ; then
1702          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1703      else      else
1704          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1705      fi      fi
1706  fi  fi
1707  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1659  check_for_broken_Ff Line 1826  check_for_broken_Ff
1826  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1827        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1828        DEFINES="$DEFINES -DALLOW_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1829    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1830    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1831  fi  fi
1832  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1833        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1883  if test "x$HAVE_LAPACK" != x ; then Line 2052  if test "x$HAVE_LAPACK" != x ; then
2052  else  else
2053      echo "no"      echo "no"
2054  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2055    
2056    printf "  Can we call FLUSH intrinsic subroutine...  "
2057    check_HAVE_FLUSH
2058    if test "x$HAVE_FLUSH" = xt ; then
2059        DEFINES="$DEFINES -DHAVE_FLUSH"
2060        echo "yes"
2061    else
2062        echo "no"
2063    fi
2064    
2065    DEFINES="$DEFINES $IGNORE_TIME"
2066  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2067      build_embed_encode      build_embed_encode
2068  fi  fi
# Line 2089  if test "x${PKG_GROUPS}" != x ; then Line 2267  if test "x${PKG_GROUPS}" != x ; then
2267  fi  fi
2268    
2269  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2270  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2271  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2272      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2273  done  done
2274  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2275      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2276      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2277  done  done
# Line 2111  for p in $PACKAGES ; do Line 2289  for p in $PACKAGES ; do
2289  done  done
2290  PACKAGES="$pack"  PACKAGES="$pack"
2291  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2292  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2293  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2294  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2295  for i in $PACKAGES ; do  for i in $PACKAGES ; do
# Line 2120  for i in $PACKAGES ; do Line 2298  for i in $PACKAGES ; do
2298          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2299          exit 1          exit 1
2300      fi      fi
2301      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2302  done  done
2303  PACKAGES=  PACKAGES=
2304  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2305      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2306  done  done
2307  rm -f ./.tmp_pack  rm -f $TMP.pack
2308  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2309    
2310  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2196  EOF Line 2374  EOF
2374      fi      fi
2375  fi  fi
2376    
2377  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2378  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2379  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2380      RETVAL=$?      RETVAL=$?
2381      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2382          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:  
2383    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2384  *********************************************************************  *********************************************************************
2385    ERROR: when generating an adjoint with OpenAD, the openad package
2386      must be enabled.  Please add it to packages.conf.
2387    *********************************************************************
2388    
2389  EOF  EOF
2390            exit 1
2391      fi      fi
2392  fi  fi
2393    
# Line 2405  fi Line 2579  fi
2579    
2580  #  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
2581  #  compiler.  #  compiler.
2582  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2583      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2584  fi  fi
2585  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2586  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2587  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2588      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2589      for j in $list_files ; do      for j in $list_files ; do
2590          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2591      done      done
2592  done  done
2593  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2594      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2595      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2596  fi  fi
2597    
2598  echo  echo
# Line 2430  for i in $INCLUDEDIRS ; do Line 2604  for i in $INCLUDEDIRS ; do
2604      fi      fi
2605  done  done
2606    
2607  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2608      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2609      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2610      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2611      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2612            mpi_headers_do_local_copy
     if test "x$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  
2613      fi      fi
2614  fi  fi
2615    
2616  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2617  rm -rf .links.tmp  rm -rf $TMP.links
2618  mkdir .links.tmp  mkdir $TMP.links
2619  touch .links.tmp/foo  touch $TMP.links/foo
2620  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2621      echo      echo
2622      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2623      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 2633  if test ! -r ".links.tmp/foo" ; then
2633      echo      echo
2634      exit 1      exit 1
2635  fi  fi
2636  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2637    
2638  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2639      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2640      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2641      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2642      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2643        OADTOOLS="$TOOLSDIR/OAD_support"
2644      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2645      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2646          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
2647              OAD_DONT_COMPILE=$i"/dontCompile"              OAD_DONT_COMPILE=$i"/dontCompile"
2648              echo "     found $OAD_DONT_COMPILE"              echo "     found $OAD_DONT_COMPILE"
# Line 2491  if test "x$OPENAD" != x ; then Line 2650  if test "x$OPENAD" != x ; then
2650          fi          fi
2651      done      done
2652      echo "  looking for dontTransform file:  "      echo "  looking for dontTransform file:  "
2653      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2654          if test -r $i"/dontTransform" ; then          if test -r $i"/dontTransform" ; then
2655              OAD_DONT_TRANSFORM=$i"/dontTransform"              OAD_DONT_TRANSFORM=$i"/dontTransform"
2656              echo "     found $OAD_DONT_TRANSFORM"              echo "     found $OAD_DONT_TRANSFORM"
# Line 2499  if test "x$OPENAD" != x ; then Line 2658  if test "x$OPENAD" != x ; then
2658          fi          fi
2659      done      done
2660      echo "  looking for keepOriginal file:  "      echo "  looking for keepOriginal file:  "
2661      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2662          if test -r $i"/keepOriginal" ; then          if test -r $i"/keepOriginal" ; then
2663              OAD_KEEP_ORIGINAL=$i"/keepOriginal"              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2664              echo "     found $OAD_KEEP_ORIGINAL"              echo "     found $OAD_KEEP_ORIGINAL"
# Line 2507  if test "x$OPENAD" != x ; then Line 2666  if test "x$OPENAD" != x ; then
2666          fi          fi
2667      done      done
2668      echo "  looking for cb2mFiles:  "      echo "  looking for cb2mFiles:  "
2669      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2670          if test -r $i"/cb2mFiles" ; then          if test -r $i"/cb2mFiles" ; then
2671              OAD_CB2M_FILES=$i"/cb2mFiles"              OAD_CB2M_FILES=$i"/cb2mFiles"
2672              echo "     found $OAD_CB2M_FILES"              echo "     found $OAD_CB2M_FILES"
# Line 2517  if test "x$OPENAD" != x ; then Line 2676  if test "x$OPENAD" != x ; then
2676      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2677  fi  fi
2678    
2679  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2680  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2681  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2682  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2683  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2684  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2685  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2686  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2687  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2688  for d in $alldirs ; do  for d in $alldirs ; do
2689      deplist=      deplist=
# Line 2534  for d in $alldirs ; do Line 2693  for d in $alldirs ; do
2693          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2694      fi      fi
2695      for sf in $sfiles ; do      for sf in $sfiles ; do
2696          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2697              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2698                  ignore_f=f                  ignore_f=f
2699                  case $d/$sf in                  case $d/$sf in
# Line 2559  for d in $alldirs ; do Line 2718  for d in $alldirs ; do
2718                          if test "x$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 $sf ; then
2719                              ignore_f=t                              ignore_f=t
2720                          else                          else
2721                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2722                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2723                          fi                          fi
2724                          ;;                          ;;
# Line 2568  for d in $alldirs ; do Line 2727  for d in $alldirs ; do
2727                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2728                      case $extn in                      case $extn in
2729                        F)                        F)
2730                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2731                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2732                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2733                                basename=${sf%%.F}
2734                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2735                                if test -z "$isAD" ; then
2736                                    echo    " \\"  >> $TMP.nonADF77srclist
2737                                    printf " $sf" >> $TMP.nonADF77srclist
2738                                fi
2739                            else #- OpenAD case:
2740                              basename=${sf%%.F}                              basename=${sf%%.F}
2741                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2742                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2743                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2744                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2745                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2746                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2747                                  else                                  else
2748                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2749                                  fi                                  fi
# Line 2592  for d in $alldirs ; do Line 2758  for d in $alldirs ; do
2758                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2759                                  fi                                  fi
2760                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2761                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2762                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2763                                  fi                                  fi
2764                              fi                              fi
2765                          fi                          fi
2766                          ;;                          ;;
2767                      F90)                      F90)
2768                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2769                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2770                          ;;                          ;;
2771                      c)                      c)
2772                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2773                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2774                          ;;                          ;;
2775                      h)                      h)
2776                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2777                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2778                          ;;                          ;;
2779                      flow)                      flow)
2780                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2781                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2782                          ;;                          ;;
2783                     esac                     esac
2784                  fi                  fi
# Line 2621  for d in $alldirs ; do Line 2787  for d in $alldirs ; do
2787      done      done
2788      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2789        if test "$d" != "." ; then        if test "$d" != "." ; then
2790          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2791          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2792          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2793  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2794  # 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"
2795  # 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.
2796          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2797        fi        fi
2798      fi      fi
2799  done  done
2800  rm -rf .links.tmp  rm -rf $TMP.links
2801  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2802  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2803  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2804  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2805  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2806  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2807    
2808  CMDLINE=$0  CMDLINE=$0
2809  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
# Line 2689  INCLUDEDIRS = ${INCLUDEDIRS} Line 2855  INCLUDEDIRS = ${INCLUDEDIRS}
2855  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2856  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2857  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2858    OADTOOLS    = ${OADTOOLS}
2859    
2860  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2861  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2709  else Line 2876  else
2876      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2877  fi  fi
2878    
2879    # extract default cpp search path so we can pass it to makedepend
2880    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2881    
2882  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2883  # Unix ln (link)  # Unix ln (link)
2884  LN = ${LN}  LN = ${LN}
# Line 2724  F90C = ${F90C} Line 2894  F90C = ${F90C}
2894  CC = ${CC}  CC = ${CC}
2895  # Link editor  # Link editor
2896  LINK = ${LINK} ${LDADD}  LINK = ${LINK} ${LDADD}
2897    export $OPENAD_DIVA
2898    
2899  # Defines for CPP  # Defines for CPP
2900  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2901  # Includes for CPP  # Includes for CPP
2902  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2903    # default CPP includes for makedepend
2904    CPPINCLUDES = ${CPPINCLUDES}
2905  # Flags for KPP  # Flags for KPP
2906  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2907  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2908  # Optim./debug for FC  # Optim./debug for FC
2909  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}  FFLAGS = ${FFLAGS}
2910  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
2911  # Optim./debug for FC  # Optim./debug for FC
2912  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2913  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
# Line 2753  MAKE = ${MAKE} Line 2926  MAKE = ${MAKE}
2926    
2927  EOF  EOF
2928    
2929  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2930  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2931  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2932  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2933  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2934  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2935    
2936  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
2937    
2938  echo >> $MAKEFILE  echo >> $MAKEFILE
2939    
# Line 2794  fwd_exe_target: Line 2967  fwd_exe_target:
2967    
2968  depend:  depend:
2969          @\$(MAKE) -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2970          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2971          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2972          -rm -f makedepend.out          -rm -f makedepend.out
2973    
# Line 2810  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 2983  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
2983    
2984  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2985    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
2986  # remove most of the files that "make" generates  # remove most of the files that "make" generates
2987  clean:  clean:
2988          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2827  Clean: Line 2996  Clean:
2996          @\$(MAKE) -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
2997          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
2998          -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  
2999    
3000  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
3001  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
# Line 2836  CLEAN: Line 3004  CLEAN:
3004          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
3005          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3006          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3007            -rm -rf mpi_headers mnc_test_*
3008          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3009          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3010          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3011          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3012            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3013          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3014          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3015    
3016  makefile:  makefile:
3017          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2894  cat >>$MAKEFILE <<EOF Line 3064  cat >>$MAKEFILE <<EOF
3064  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3065  ## %.o : %.F  ## %.o : %.F
3066    
3067  # C preprocessing and replacing the _d in constants:  # C preprocessing and replacing the _d in constants:
3068  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3069    
3070  .F.$FS:  .F.$FS:
# Line 2938  TAF            = ${TAF} Line 3108  TAF            = ${TAF}
3108    
3109  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3110  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3111    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3112    
3113  EOF  EOF
3114    
# Line 2955  done Line 3126  done
3126  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3127  echo >> $MAKEFILE  echo >> $MAKEFILE
3128  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3129  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3130  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3131      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3132      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3133  done  done
3134  echo >> $MAKEFILE  echo >> $MAKEFILE
3135  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3136    
3137    if test $CAT_SRC_FOR_TAF = 0 ; then
3138    cat >>$MAKEFILE <<EOF
3139    
3140    # ... Utilities ...
3141    remove_comments:
3142            sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
3143            @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
3144    adj_sed:
3145            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
3146            @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
3147    ftl_sed:
3148            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
3149            @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
3150    adobjfiles: \$(AD_FILES:.$FS=_ad.o)
3151    ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
3152    EOF
3153    fi
3154    
3155  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3156    
# Line 2985  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL Line 3174  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
3174          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3175          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
3176    
3177  ad_taf_output.$FS: ad_input_code.$FS  adtafonly:
3178          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3179          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3180          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
3181    
3182  adtafonly:  EOF
3183    
3184    if test $CAT_SRC_FOR_TAF = 1 ; then
3185    cat >>$MAKEFILE <<EOF
3186    # ... send 1 file to TAF ...
3187    ad_taf_output.$FS: ad_input_code.$FS
3188            @-rm -f ad_input_code_ad.$FS ; echo ''
3189          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3190          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3191          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3192    
3193  \$(EXE_AD): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ad_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3194          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3195    
3196  ad_tamc_output.$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  
3197    
3198  ad_tamc: ad_tamc_output.o \$(OBJFILES)  EOF
         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)  
3199    
3200    else
3201    cat >>$MAKEFILE <<EOF
3202    # ... send multiple files to TAF ...
3203    ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3204            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3205            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3206            @-rm -f ad_config.template
3207            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3208            @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3209            @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
3210            \$(MAKE) -f \$(MAKEFILE) remove_comments
3211            \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
3212            \$(MAKE) -f \$(MAKEFILE) adj_sed
3213            cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
3214    
3215    \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3216            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3217            \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3218    
3219    adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3220            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3221    
3222    EOF
3223    fi
3224    
3225    cat >>$MAKEFILE <<EOF
3226  adonlyfwd:  adonlyfwd:
3227          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
3228    
3229  adtrick:  adtrick:
3230          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3231    
3232  adobj: ad_taf_output.o \$(OBJFILES)  ad_tamc_output.$FS: ad_input_code.$FS
3233            \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
3234            cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
3235    
3236    ad_tamc: ad_tamc_output.o \$(OBJFILES)
3237            \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
3238    
3239  # ... FTL ...  # ... FTL ...
3240  ftlall: ftl_exe_target  ftlall: ftl_exe_target
# Line 3033  ftl_input_code.$FS: \$(AD_FILES) Line 3256  ftl_input_code.$FS: \$(AD_FILES)
3256          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3257          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3258    
3259  ftl_taf_output.$FS: ftl_input_code.$FS  ftltafonly:
3260          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3261          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3262          cat ftl_input_code_ftl.$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
3263    
3264  ftltafonly:  EOF
3265    
3266    if test $CAT_SRC_FOR_TAF = 1 ; then
3267    cat >>$MAKEFILE <<EOF
3268    # ... send 1 file to TAF ...
3269    ftl_taf_output.$FS: ftl_input_code.$FS
3270            @-rm -f ftl_input_code_tl.$FS ; echo ''
3271          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3272          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3273          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3274    
3275  \$(EXE_FTL): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ftl_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3276          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3277    
3278    EOF
3279    
3280    else
3281    cat >>$MAKEFILE <<EOF
3282    # ... send multiple files to TAF ...
3283    ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3284            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3285            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3286            @-rm -f ad_config.template
3287            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3288            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3289            @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
3290            \$(MAKE) -f \$(MAKEFILE) remove_comments
3291            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
3292            \$(MAKE) -f \$(MAKEFILE) ftl_sed
3293            cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
3294    
3295    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3296            \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
3297            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3298    
3299    EOF
3300    fi
3301    
3302    cat >>$MAKEFILE <<EOF
3303  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3304          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
3305          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
# Line 3088  if test "x$OPENAD" != x ; then Line 3342  if test "x$OPENAD" != x ; then
3342  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3343    
3344  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3345    # ... OpenAD ...
3346    
3347  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3348  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3127  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3382  for i in `cat ${OAD_CB2M_FILES}` ; do
3382    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3383    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3384  done  done
3385  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3386  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3387    basename=${i%%.f}    basename=${i%%.f}
3388    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
# Line 3137  for i in $AD_FILES ; do Line 3392  for i in $AD_FILES ; do
3392    fi    fi
3393  done  done
3394  echo >> $MAKEFILE  echo >> $MAKEFILE
3395  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3396    
3397  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3398    
3399  adAll: \$(EXE_AD)  adAll: ad_exe_target
3400  .PHONY: adAll  .PHONY: adAll
3401    
3402    ad_exe_target:
3403            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3404            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3405            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3406            @-rm -f ad_config.template
3407            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3408    
3409  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))
3410    
3411  .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 3159  w2f__types.F90 \ Line 3421  w2f__types.F90 \
3421  OAD_active.F90 \  OAD_active.F90 \
3422  OAD_cp.F90 \  OAD_cp.F90 \
3423  OAD_rev.F90 \  OAD_rev.F90 \
3424  OAD_tape.F90  OAD_tape.F90 \
3425    OAD_regular_cp.F90 \
3426    revolve.F90
3427    
3428  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3429  iaddr.c \  iaddr.c \
# Line 3185  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N Line 3449  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
3449          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3450    
3451  # create sources files modules from header files containing common blocks  # create sources files modules from header files containing common blocks
3452  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3453          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3454    
3455  # 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
3456  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3457          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3458    
3459  # 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
3460  %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3461          ../OAD_support/cb2mUseModules.bash $< ${MPI}          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
3462    
3463  # makefile debug rule  # makefile debug rule
3464  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3465  .PHONY: small_f  .PHONY: small_f
3466    
 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) > \$@  
   
3467  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3468          cat \$^ > \$@          cat \$^ > \$@
3469    
# Line 3216  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI Line 3473  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
3473    
3474  # 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
3475  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
3476          cat \$< | sed -f ../OAD_support/stop2print.sed > ad_input_code_sf.pre.s2p.f90          cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3477    
3478  # F -> WHIRL  # F -> WHIRL
3479  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 3239  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS Line 3496  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
3496          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3497    
3498  # insert template directives  # insert template directives
3499  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \${OADTOOLS}/insertTemplateDir.bash
3500          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3501    
3502  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3503  # postprocess F'  # postprocess F'
3504  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
3505          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ../OAD_support/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 \$<
3506          # 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
3507          touch \$@          touch \$@
3508  # put this so make knows about the postprocessing output  # put this so make knows about the postprocessing output
# Line 3256  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f Line 3513  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
3513          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3514    
3515  # link the support files:  # link the support files:
3516  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3517          \$(LN) ../OAD_support/\$@ .          \$(LN) \${OADTOOLS}/\$@ .
3518    
3519  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
3520    
3521  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3522    
# Line 3295  for i in $NOOPTFILES ; do Line 3552  for i in $NOOPTFILES ; do
3552  done  done
3553    
3554  echo "  Add rules for links"  echo "  Add rules for links"
3555  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3556  rm -f srclinks.tmp  rm -f $TMP.srclinks
3557    
3558  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3559  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE

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