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revision 1.241 by utke, Wed Sep 19 20:46:03 2012 UTC revision 1.277 by jmc, Tue Jan 12 20:43:00 2016 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  AD_OPTFILE=  AD_OPTFILE=
1336    CAT_SRC_FOR_TAF=1
1337  TAF=  TAF=
1338  AD_TAF_FLAGS=  AD_TAF_FLAGS=
1339  FTL_TAF_FLAGS=  FTL_TAF_FLAGS=
# Line 1205  FTL_TAF_FLAGS= Line 1345  FTL_TAF_FLAGS=
1345  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1346  TAMC_EXTRA=  TAMC_EXTRA=
1347    
1348    DIVA=
1349    MPIINCLUDEDIR=
1350    MPI_HEADER_FILES=
1351    LOCAL_MPI_HEADERS=
1352    
1353  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1354  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1355  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 1358  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAP
1358  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1359  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1360  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1361  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1362  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1363  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"
1364    
1365  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1366  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"
1367  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"
1368  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1369    
1370  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 $gm_s8"
1371  gm_state="$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 1415  for ac_option in "$@" ; do
1415          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1416              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1417    
1418            -oad | --oad)
1419                OPENAD="true" ; ALWAYS_USE_F90=1 ;;
1420            -nocat4ad | -dog4ad | -ncad | -dad)
1421                CAT_SRC_FOR_TAF=0 ;;
1422          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1423              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1424          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
# Line 1439  for ac_option in "$@" ; do Line 1588  for ac_option in "$@" ; do
1588    
1589  done  done
1590    
1591    #TMP=./genmk_$$
1592    #- try to put temporary files in system-local /tmp dir
1593    TMP=/tmp/genmk_${USER}_$$
1594    touch $TMP ; retVal=$?
1595    if [ $retVal -eq 0 ] ; then
1596      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1597    else
1598      TMP=./genmk_$$
1599    fi
1600    rm -f $TMP
1601    #echo "  temp files: $TMP.*"
1602    
1603  printf "  getting local config information:  "  printf "  getting local config information:  "
1604  if test -f $gm_local ; then  if test -f $gm_local ; then
1605      echo "using $gm_local"      echo "using $gm_local"
# Line 1531  fi Line 1692  fi
1692    
1693  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1694  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1695      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1696            AD_OPTFILE=$MITGCM_AD_OF
1697        elif test "x$OPENAD" = x ; then
1698          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1699      else      else
1700          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1701      fi      fi
1702  fi  fi
1703  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1659  check_for_broken_Ff Line 1822  check_for_broken_Ff
1822  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1823        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1824        DEFINES="$DEFINES -DALLOW_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1825    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1826    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1827  fi  fi
1828  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1829        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1799  else Line 1964  else
1964  fi  fi
1965  rm -f genmake_tcomp*  rm -f genmake_tcomp*
1966    
1967  printf "  Do we have the etime() command using $FC...  "  printf "  Do we have the etime() command using $FC... "
1968  cat > genmake_tcomp.$FS <<EOF  cat > genmake_tcomp_1.$FS <<EOF
1969        program hello        program hello
1970        REAL*4 ACTUAL, TARRAY(2)        REAL*4 actual, tarray(2)
1971        EXTERNAL ETIME        EXTERNAL ETIME
1972        REAL*4 ETIME        REAL*4 ETIME
1973        actual = etime( tarray )        actual = ETIME( tarray )
1974        print *, tarray        print *, tarray
1975        end        end
1976  EOF  EOF
1977  $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
1978  RETVAL=$?  RETVAL=$?
1979  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1980      HAVE_ETIME=t      HAVE_ETIME='Fct'
1981      DEFINES="$DEFINES -DHAVE_ETIME"      DEFINES="$DEFINES -DHAVE_ETIME_FCT"
1982      echo "yes"      echo " yes (${HAVE_ETIME})"
1983  else  else
1984      cat > genmake_tcomp_2.$FS <<EOF
1985          program hello
1986          REAL*4 actual, tarray(2)
1987          actual = -999.
1988          call ETIME( tarray, actual )
1989          if ( actual.ge.0. ) then
1990            print *, 0, tarray, actual
1991          else
1992            print *, 1, tarray, actual
1993          endif
1994          end
1995    EOF
1996      $FC $FFLAGS -o genmake_tcomp_2 genmake_tcomp_2.$FS >> genmake_tcomp.log 2>&1
1997      RETVAL=$?
1998      if test "x$RETVAL" = x0 ; then
1999        echo -n 'c,'
2000        ./genmake_tcomp_2 > genmake_tcomp_2.out 2>&1
2001        RETVAL=$?
2002      fi
2003      if test "x$RETVAL" = x0 ; then
2004        echo -n 'r:'
2005        RETVAL=`cat genmake_tcomp_2.out | $AWK '{print $1}'`
2006      fi
2007      if test "x$RETVAL" = x0 ; then
2008        HAVE_ETIME='SbR'
2009        DEFINES="$DEFINES -DHAVE_ETIME_SBR"
2010        echo " yes (${HAVE_ETIME})"
2011      else
2012      HAVE_ETIME=      HAVE_ETIME=
2013      echo "no"      echo " no"
2014      fi
2015  fi  fi
2016    #mkdir chk_etime ; cp -p -f genmake_tcomp* chk_etime
2017  rm -f genmake_tcomp*  rm -f genmake_tcomp*
2018    
2019  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 2078  if test "x$HAVE_LAPACK" != x ; then
2078  else  else
2079      echo "no"      echo "no"
2080  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2081    
2082    printf "  Can we call FLUSH intrinsic subroutine...  "
2083    check_HAVE_FLUSH
2084    if test "x$HAVE_FLUSH" = xt ; then
2085        DEFINES="$DEFINES -DHAVE_FLUSH"
2086        echo "yes"
2087    else
2088        echo "no"
2089    fi
2090    
2091    DEFINES="$DEFINES $IGNORE_TIME"
2092  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2093      build_embed_encode      build_embed_encode
2094  fi  fi
# Line 2089  if test "x${PKG_GROUPS}" != x ; then Line 2293  if test "x${PKG_GROUPS}" != x ; then
2293  fi  fi
2294    
2295  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2296  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2297  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2298      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2299  done  done
2300  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2301      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2302      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2303  done  done
# Line 2111  for p in $PACKAGES ; do Line 2315  for p in $PACKAGES ; do
2315  done  done
2316  PACKAGES="$pack"  PACKAGES="$pack"
2317  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2318  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2319  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2320  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2321  for i in $PACKAGES ; do  for i in $PACKAGES ; do
# Line 2120  for i in $PACKAGES ; do Line 2324  for i in $PACKAGES ; do
2324          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2325          exit 1          exit 1
2326      fi      fi
2327      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2328  done  done
2329  PACKAGES=  PACKAGES=
2330  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2331      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2332  done  done
2333  rm -f ./.tmp_pack  rm -f $TMP.pack
2334  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2335    
2336  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2196  EOF Line 2400  EOF
2400      fi      fi
2401  fi  fi
2402    
2403  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2404  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2405  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2406      RETVAL=$?      RETVAL=$?
2407      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2408          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:  
2409    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2410  *********************************************************************  *********************************************************************
2411    ERROR: when generating an adjoint with OpenAD, the openad package
2412      must be enabled.  Please add it to packages.conf.
2413    *********************************************************************
2414    
2415  EOF  EOF
2416            exit 1
2417      fi      fi
2418  fi  fi
2419    
# Line 2405  fi Line 2605  fi
2605    
2606  #  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
2607  #  compiler.  #  compiler.
2608  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2609      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2610  fi  fi
2611  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2612  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2613  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2614      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2615      for j in $list_files ; do      for j in $list_files ; do
2616          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2617      done      done
2618  done  done
2619  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2620      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2621      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2622  fi  fi
2623    
2624  echo  echo
# Line 2430  for i in $INCLUDEDIRS ; do Line 2630  for i in $INCLUDEDIRS ; do
2630      fi      fi
2631  done  done
2632    
2633  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2634      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2635      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2636      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2637      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2638            mpi_headers_do_local_copy
     if test "x$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  
2639      fi      fi
2640  fi  fi
2641    
2642  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2643  rm -rf .links.tmp  rm -rf $TMP.links
2644  mkdir .links.tmp  mkdir $TMP.links
2645  touch .links.tmp/foo  touch $TMP.links/foo
2646  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2647      echo      echo
2648      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2649      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 2659  if test ! -r ".links.tmp/foo" ; then
2659      echo      echo
2660      exit 1      exit 1
2661  fi  fi
2662  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2663    
2664  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2665      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2666      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2667      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2668      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2669        OADTOOLS="$TOOLSDIR/OAD_support"
2670      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2671      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2672          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
2673              OAD_DONT_COMPILE=$i"/dontCompile"              OAD_DONT_COMPILE=$i"/dontCompile"
2674              echo "     found $OAD_DONT_COMPILE"              echo "     found $OAD_DONT_COMPILE"
# Line 2491  if test "x$OPENAD" != x ; then Line 2676  if test "x$OPENAD" != x ; then
2676          fi          fi
2677      done      done
2678      echo "  looking for dontTransform file:  "      echo "  looking for dontTransform file:  "
2679      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2680          if test -r $i"/dontTransform" ; then          if test -r $i"/dontTransform" ; then
2681              OAD_DONT_TRANSFORM=$i"/dontTransform"              OAD_DONT_TRANSFORM=$i"/dontTransform"
2682              echo "     found $OAD_DONT_TRANSFORM"              echo "     found $OAD_DONT_TRANSFORM"
# Line 2499  if test "x$OPENAD" != x ; then Line 2684  if test "x$OPENAD" != x ; then
2684          fi          fi
2685      done      done
2686      echo "  looking for keepOriginal file:  "      echo "  looking for keepOriginal file:  "
2687      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2688          if test -r $i"/keepOriginal" ; then          if test -r $i"/keepOriginal" ; then
2689              OAD_KEEP_ORIGINAL=$i"/keepOriginal"              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2690              echo "     found $OAD_KEEP_ORIGINAL"              echo "     found $OAD_KEEP_ORIGINAL"
# Line 2507  if test "x$OPENAD" != x ; then Line 2692  if test "x$OPENAD" != x ; then
2692          fi          fi
2693      done      done
2694      echo "  looking for cb2mFiles:  "      echo "  looking for cb2mFiles:  "
2695      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2696          if test -r $i"/cb2mFiles" ; then          if test -r $i"/cb2mFiles" ; then
2697              OAD_CB2M_FILES=$i"/cb2mFiles"              OAD_CB2M_FILES=$i"/cb2mFiles"
2698              echo "     found $OAD_CB2M_FILES"              echo "     found $OAD_CB2M_FILES"
# Line 2517  if test "x$OPENAD" != x ; then Line 2702  if test "x$OPENAD" != x ; then
2702      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2703  fi  fi
2704    
2705  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2706  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2707  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2708  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2709  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2710  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2711  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2712  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2713  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2714  for d in $alldirs ; do  for d in $alldirs ; do
2715      deplist=      deplist=
# Line 2534  for d in $alldirs ; do Line 2719  for d in $alldirs ; do
2719          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2720      fi      fi
2721      for sf in $sfiles ; do      for sf in $sfiles ; do
2722          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2723              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2724                  ignore_f=f                  ignore_f=f
2725                  case $d/$sf in                  case $d/$sf in
# Line 2559  for d in $alldirs ; do Line 2744  for d in $alldirs ; do
2744                          if test "x$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 $sf ; then
2745                              ignore_f=t                              ignore_f=t
2746                          else                          else
2747                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2748                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2749                          fi                          fi
2750                          ;;                          ;;
# Line 2568  for d in $alldirs ; do Line 2753  for d in $alldirs ; do
2753                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2754                      case $extn in                      case $extn in
2755                        F)                        F)
2756                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2757                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2758                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2759                              basename=${sf%%.F}                              basename=${sf%%.F}
2760                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2761                                if test -z "$isAD" ; then
2762                                    echo    " \\"  >> $TMP.nonADF77srclist
2763                                    printf " $sf" >> $TMP.nonADF77srclist
2764                                fi
2765                            else #- OpenAD case:
2766                                basename=${sf%%.F}
2767                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2768                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2769                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2770                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2771                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2772                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2773                                  else                                  else
2774                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2775                                  fi                                  fi
# Line 2592  for d in $alldirs ; do Line 2784  for d in $alldirs ; do
2784                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2785                                  fi                                  fi
2786                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2787                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2788                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2789                                  fi                                  fi
2790                              fi                              fi
2791                          fi                          fi
2792                          ;;                          ;;
2793                      F90)                      F90)
2794                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2795                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2796                          ;;                          ;;
2797                      c)                      c)
2798                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2799                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2800                          ;;                          ;;
2801                      h)                      h)
2802                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2803                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2804                          ;;                          ;;
2805                      flow)                      flow)
2806                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2807                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2808                          ;;                          ;;
2809                     esac                     esac
2810                  fi                  fi
# Line 2621  for d in $alldirs ; do Line 2813  for d in $alldirs ; do
2813      done      done
2814      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2815        if test "$d" != "." ; then        if test "$d" != "." ; then
2816          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2817          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2818          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2819  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2820  # 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"
2821  # 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.
2822          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2823        fi        fi
2824      fi      fi
2825  done  done
2826  rm -rf .links.tmp  rm -rf $TMP.links
2827  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2828  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2829  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2830  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2831  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2832  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2833    
2834  CMDLINE=$0  CMDLINE=$0
2835  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
# Line 2689  INCLUDEDIRS = ${INCLUDEDIRS} Line 2881  INCLUDEDIRS = ${INCLUDEDIRS}
2881  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2882  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2883  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2884    OADTOOLS    = ${OADTOOLS}
2885    
2886  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2887  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2709  else Line 2902  else
2902      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2903  fi  fi
2904    
2905    # extract default cpp search path so we can pass it to makedepend
2906    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2907    
2908  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2909  # Unix ln (link)  # Unix ln (link)
2910  LN = ${LN}  LN = ${LN}
# Line 2729  LINK = ${LINK} ${LDADD} Line 2925  LINK = ${LINK} ${LDADD}
2925  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2926  # Includes for CPP  # Includes for CPP
2927  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2928    # default CPP includes for makedepend
2929    CPPINCLUDES = ${CPPINCLUDES}
2930  # Flags for KPP  # Flags for KPP
2931  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2932  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2933  # Optim./debug for FC  # Optim./debug for FC
2934  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}  FFLAGS = ${FFLAGS}
2935  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
2936  # Optim./debug for FC  # Optim./debug for FC
2937  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2938  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
# Line 2753  MAKE = ${MAKE} Line 2951  MAKE = ${MAKE}
2951    
2952  EOF  EOF
2953    
2954  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2955  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2956  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2957  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2958  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2959  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2960    
2961  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
2962    
2963  echo >> $MAKEFILE  echo >> $MAKEFILE
2964    
# Line 2794  fwd_exe_target: Line 2992  fwd_exe_target:
2992    
2993  depend:  depend:
2994          @\$(MAKE) -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2995          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2996          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2997          -rm -f makedepend.out          -rm -f makedepend.out
2998    
# Line 2810  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 3008  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
3008    
3009  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
3010    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
3011  # remove most of the files that "make" generates  # remove most of the files that "make" generates
3012  clean:  clean:
3013          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2827  Clean: Line 3021  Clean:
3021          @\$(MAKE) -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
3022          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
3023          -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  
3024    
3025  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
3026  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
# Line 2836  CLEAN: Line 3029  CLEAN:
3029          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
3030          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3031          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3032            -rm -rf mpi_headers mnc_test_*
3033          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3034          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3035          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3036          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3037            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3038          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3039          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3040    
3041  makefile:  makefile:
3042          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2894  cat >>$MAKEFILE <<EOF Line 3089  cat >>$MAKEFILE <<EOF
3089  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3090  ## %.o : %.F  ## %.o : %.F
3091    
3092  # C preprocessing and replacing the _d in constants:  # C preprocessing and replacing the _d in constants:
3093  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3094    
3095  .F.$FS:  .F.$FS:
# Line 2938  TAF            = ${TAF} Line 3133  TAF            = ${TAF}
3133    
3134  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3135  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3136    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3137    
3138  EOF  EOF
3139    
# Line 2955  done Line 3151  done
3151  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3152  echo >> $MAKEFILE  echo >> $MAKEFILE
3153  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3154  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3155  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3156      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3157      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3158  done  done
3159  echo >> $MAKEFILE  echo >> $MAKEFILE
3160  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3161    
3162    if test $CAT_SRC_FOR_TAF = 0 ; then
3163    cat >>$MAKEFILE <<EOF
3164    
3165    # ... Utilities ...
3166    remove_comments:
3167            sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
3168            @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
3169    adj_sed:
3170            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
3171            @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
3172    ftl_sed:
3173            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
3174            @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
3175    adobjfiles: \$(AD_FILES:.$FS=_ad.o)
3176    ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
3177    EOF
3178    fi
3179    
3180  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3181    
# Line 2985  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL Line 3199  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
3199          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3200          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
3201    
3202  ad_taf_output.$FS: ad_input_code.$FS  adtafonly:
3203          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3204          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3205          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
3206    
3207  adtafonly:  EOF
3208    
3209    if test $CAT_SRC_FOR_TAF = 1 ; then
3210    cat >>$MAKEFILE <<EOF
3211    # ... send 1 file to TAF ...
3212    ad_taf_output.$FS: ad_input_code.$FS
3213            @-rm -f ad_input_code_ad.$FS ; echo ''
3214          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3215          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3216          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3217    
3218  \$(EXE_AD): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ad_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3219          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3220    
3221  ad_tamc_output.$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  
3222    
3223  ad_tamc: ad_tamc_output.o \$(OBJFILES)  EOF
3224          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)  
3225    else
3226    cat >>$MAKEFILE <<EOF
3227    # ... send multiple files to TAF ...
3228    ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3229            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3230            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3231            @-rm -f ad_config.template
3232            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3233            @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3234            @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
3235            \$(MAKE) -f \$(MAKEFILE) remove_comments
3236            \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
3237            \$(MAKE) -f \$(MAKEFILE) adj_sed
3238            cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
3239    
3240    \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3241            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3242            \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3243    
3244    adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3245            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3246    
3247    EOF
3248    fi
3249    
3250    cat >>$MAKEFILE <<EOF
3251  adonlyfwd:  adonlyfwd:
3252          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
3253    
3254  adtrick:  adtrick:
3255          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3256    
3257  adobj: ad_taf_output.o \$(OBJFILES)  ad_tamc_output.$FS: ad_input_code.$FS
3258            \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
3259            cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
3260    
3261    ad_tamc: ad_tamc_output.o \$(OBJFILES)
3262            \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
3263    
3264  # ... FTL ...  # ... FTL ...
3265  ftlall: ftl_exe_target  ftlall: ftl_exe_target
# Line 3033  ftl_input_code.$FS: \$(AD_FILES) Line 3281  ftl_input_code.$FS: \$(AD_FILES)
3281          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3282          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3283    
3284  ftl_taf_output.$FS: ftl_input_code.$FS  ftltafonly:
3285          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3286          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3287          cat ftl_input_code_ftl.$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
3288    
3289  ftltafonly:  EOF
3290    
3291    if test $CAT_SRC_FOR_TAF = 1 ; then
3292    cat >>$MAKEFILE <<EOF
3293    # ... send 1 file to TAF ...
3294    ftl_taf_output.$FS: ftl_input_code.$FS
3295            @-rm -f ftl_input_code_tl.$FS ; echo ''
3296          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3297          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3298          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3299    
3300    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3301            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3302    
3303    EOF
3304    
3305    else
3306    cat >>$MAKEFILE <<EOF
3307    # ... send multiple files to TAF ...
3308    ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3309            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3310            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3311            @-rm -f ad_config.template
3312            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3313            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3314            @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
3315            \$(MAKE) -f \$(MAKEFILE) remove_comments
3316            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
3317            \$(MAKE) -f \$(MAKEFILE) ftl_sed
3318            cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
3319    
3320    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3321            \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
3322            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3323    
3324  \$(EXE_FTL): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ftl_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  EOF
3325          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)  fi
3326    
3327    cat >>$MAKEFILE <<EOF
3328  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3329          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
3330          cat ftl_input_code_ftl.$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 3367  if test "x$OPENAD" != x ; then
3367  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3368    
3369  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3370    # ... OpenAD ...
3371    
3372  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3373  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3127  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3407  for i in `cat ${OAD_CB2M_FILES}` ; do
3407    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3408    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3409  done  done
3410  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3411  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3412    basename=${i%%.f}    basename=${i%%.f}
3413    toBeIgnored=`egrep ^$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 3417  for i in $AD_FILES ; do
3417    fi    fi
3418  done  done
3419  echo >> $MAKEFILE  echo >> $MAKEFILE
3420  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3421    
3422  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3423    
3424  adAll: \$(EXE_AD)  adAll: ad_exe_target
3425  .PHONY: adAll  .PHONY: adAll
3426    
3427    ad_exe_target:
3428            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3429            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3430            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3431            @-rm -f ad_config.template
3432            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3433    
3434  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))
3435    
3436  .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 3446  w2f__types.F90 \
3446  OAD_active.F90 \  OAD_active.F90 \
3447  OAD_cp.F90 \  OAD_cp.F90 \
3448  OAD_rev.F90 \  OAD_rev.F90 \
3449  OAD_tape.F90  OAD_tape.F90 \
3450    OAD_regular_cp.F90 \
3451    revolve.F90
3452    
3453  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3454  iaddr.c \  iaddr.c \
# Line 3185  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N Line 3474  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
3474          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3475    
3476  # create sources files modules from header files containing common blocks  # create sources files modules from header files containing common blocks
3477  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3478          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3479    
3480  # 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
3481  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3482          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3483    
3484  # 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
3485  %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3486          ../OAD_support/cb2mUseModules.bash $< ${MPI}          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
3487    
3488  # makefile debug rule  # makefile debug rule
3489  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3490  .PHONY: small_f  .PHONY: small_f
3491    
 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) > \$@  
   
3492  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3493          cat \$^ > \$@          cat \$^ > \$@
3494    
# Line 3216  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI Line 3498  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
3498    
3499  # 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
3500  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
3501          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
3502    
3503  # F -> WHIRL  # F -> WHIRL
3504  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$FS Line 3521  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
3521          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3522    
3523  # insert template directives  # insert template directives
3524  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
3525          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3526    
3527  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3528  # postprocess F'  # postprocess F'
3529  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
3530          \${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 \$<
3531          # 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
3532          touch \$@          touch \$@
3533  # 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 3538  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
3538          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3539    
3540  # link the support files:  # link the support files:
3541  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3542          \$(LN) ../OAD_support/\$@ .          \$(LN) \${OADTOOLS}/\$@ .
3543    
3544  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
3545    
3546  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3547    
# Line 3295  for i in $NOOPTFILES ; do Line 3577  for i in $NOOPTFILES ; do
3577  done  done
3578    
3579  echo "  Add rules for links"  echo "  Add rules for links"
3580  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3581  rm -f srclinks.tmp  rm -f $TMP.srclinks
3582    
3583  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3584  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE

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