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revision 1.241 by utke, Wed Sep 19 20:46:03 2012 UTC revision 1.262 by jmc, Thu Aug 22 20:49:59 2013 UTC
# Line 208  test_for_string_in_file() { Line 208  test_for_string_in_file() {
208  expand_pkg_groups() {  expand_pkg_groups() {
209      new_packages=      new_packages=
210      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
211          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
212          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
213          matched=0          matched=0
214          for i in $PACKAGES ; do          for i in $PACKAGES ; do
215              line=`grep "^ *$i" ./p2.tmp`              line=`grep "^ *$i" $TMP.p2`
216              RETVAL=$?              RETVAL=$?
217              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
218                  matched=1                  matched=1
# Line 224  expand_pkg_groups() { Line 224  expand_pkg_groups() {
224              fi              fi
225          done          done
226          PACKAGES=$new_packages          PACKAGES=$new_packages
227          rm -f ./p[1,2].tmp          rm -f $TMP.p[1,2]
228          return $matched          return $matched
229      else      else
230          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 324  look_for_makedepend()  {
324      #      #
325      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
326      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
327      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
328      #      #
329      #  So the choices are, in order:      #  So the choices are, in order:
     #  
330      #    1) use the user-specified program      #    1) use the user-specified program
331      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
332      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
333      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
334        #             (faster, but can miss some dependencies)
335      #      #
336      echo >> $LOGFILE      echo >> $LOGFILE
337      echo "running: look_for_makedepend()" >> $LOGFILE      echo "running: look_for_makedepend()" >> $LOGFILE
# Line 343  look_for_makedepend()  { Line 342  look_for_makedepend()  {
342              build_cyrus_makedepend              build_cyrus_makedepend
343              RETVAL=$?              RETVAL=$?
344              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
345                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
346                  MAKEDEPEND=                  MAKEDEPEND=
347              fi              fi
348          else          else
# Line 356  look_for_makedepend()  { Line 355  look_for_makedepend()  {
355          fi          fi
356      fi      fi
357      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
358          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
359          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
360          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 373  EOF Line 370  EOF
370        stop        stop
371        end        end
372  EOF  EOF
373          makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
374          RV1=$?          RV1=$?
375            which makedepend > /dev/null 2>&1
376            RV2=$?
377            if test "x${RV2}" = x0 ; then
378                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
379                RV3=$? ; loc_msg='not working.'
380            else RV3=$RV2 ; loc_msg='not found.'
381            fi
382          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
383          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
384          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
385            if test "x${RV1}" = x0 ; then
386                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
387                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
388            elif test "x${RV3}" = x0 ; then
389                echo "    local tools/xmakedepend not working. Use system-default makedepend"
390              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
391              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
392          else          else
393              echo "    system-default makedepend not found. Try to build cyrus-makedepend"              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
394                echo -n "    Try to build cyrus-makedepend ..."
395              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
396              build_cyrus_makedepend              build_cyrus_makedepend
397              RETVAL=$?              RETVAL=$?
398              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
399                  echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"                  echo "  Works"
400                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'              else
401                  echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE                  echo "  Fails" ; echo "" >> $LOGFILE
402                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
403                    echo ""
404                    exit -1
405                    return
406              fi              fi
407          fi          fi
408      fi      fi
# Line 588  EOF Line 602  EOF
602      fi      fi
603  }  }
604    
605    #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
606    #  checking for additional included headers (in case of chain of included header)
607    mpi_headers_do_local_copy() {
608    
609        dBug=0
610        rm -rf ./mpi_headers
611        if test -d $MPIINCLUDEDIR ; then
612    
613            #----- check for additional headers (chain of included headers)
614            echo -n '  Check MPI headers ... '
615            listIni=$MPI_HEADER_FILES
616            echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
617            outp=$?
618            #- always check mpif.h (the only mpi-header included in standard MITgcm code)
619            if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
620            if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
621    
622            doCheck=1 ; list2copy='' ; list2check=$listIni
623            while test $doCheck = 1 ; do
624              newList=''
625              for i in $list2check ; do
626                if test -f $MPIINCLUDEDIR/$i ; then
627                  newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
628                    sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
629                  if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
630                  for j in $newInc ; do
631                    echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
632                    outp=$?
633                    if test $outp != 0 ; then
634                      if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
635                      newList="$newList $j"
636                    fi
637                  done
638                  if test $dBug = 1 ; then echo "" ; fi
639                fi
640              done
641              if test "x$newList" = x ; then doCheck=0
642              else list2check=$newList ; list2copy="$list2copy $newList"
643              fi
644            done
645            list2copy="$MPI_HEADER_FILES $list2copy"
646            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
647    
648            #----- create local mpi_headers dir if we have files to copy
649            mkListInc=`echo $list2copy | wc -w`
650            if test $mkListInc != 0 ; then
651              echo 'create local "./mpi_headers" dir'
652              mkdir -p ./mpi_headers
653              INCLUDES="-I./mpi_headers $INCLUDES"
654              mkListInc=1
655            fi
656            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
657    
658            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
659            for i in $list2copy ; do
660              if test -f $MPIINCLUDEDIR/$i ; then
661                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
662                if test $i = 'mpif.h' ; then
663                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
664                fi
665                if test $mkListInc = 2 ; then
666                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
667                fi
668                if test $mkListInc = 1 ; then
669                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
670                fi
671              fi
672            done
673        else
674            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
675            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
676    #       exit -1
677        fi
678    }
679    
680  #  Parse the package dependency information  #  Parse the package dependency information
681  get_pdepend_list()  {  get_pdepend_list()  {
682    
# Line 907  check_netcdf_libs()  { Line 996  check_netcdf_libs()  {
996        program fgennc        program fgennc
997  #include "netcdf.inc"  #include "netcdf.inc"
998  EOF  EOF
999      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1000          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1001      fi     #fi
1002      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1003        integer iret, ncid, xid        integer iret, ncid, xid
1004        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1092  EOF Line 1181  EOF
1181      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1182  }  }
1183    
1184    check_HAVE_FLUSH()  {
1185        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1186            return
1187        fi
1188        echo >> $LOGFILE
1189        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1190        cat <<EOF > genmake_tflsh.$FS
1191          program fgenflsh
1192          integer iounit
1193          character*9 fname
1194          iounit = 26
1195          fname = 'tmp.tflsh'
1196          open(iounit,FILE=fname,STATUS='unknown')
1197          write(iounit,*) 'genmake_tflsh: hello'
1198          call flush(iounit)
1199          close(iounit)
1200          end
1201    EOF
1202        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1203        cat genmake_tflsh.$FS >> genmake_tflsh.log
1204        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1205    
1206        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1207        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1208        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1209            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1210        RET_COMPILE=$?
1211    
1212        if test "x$RET_COMPILE" = x0 ; then
1213            HAVE_FLUSH=t
1214            #cat genmake_tflsh.log >> $LOGFILE
1215            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1216        else
1217            HAVE_FLUSH=f
1218            cat genmake_tflsh.log >> $LOGFILE
1219        fi
1220        rm -f genmake_tflsh*
1221        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1222    }
1223    
1224  ###############################################################################  ###############################################################################
1225  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1149  GSL= Line 1277  GSL=
1277  DEVEL=  DEVEL=
1278  HAVE_TEST_L=  HAVE_TEST_L=
1279    
1280    # comment this line out to enable lapack test
1281    SKIP_LAPACK_CHECK=t
1282    
1283  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1284  HAVE_SYSTEM=  HAVE_SYSTEM=
1285  HAVE_FDATE=  HAVE_FDATE=
# Line 1160  HAVE_NETCDF= Line 1291  HAVE_NETCDF=
1291  HAVE_ETIME=  HAVE_ETIME=
1292  IGNORE_TIME=  IGNORE_TIME=
1293  HAVE_LAPACK=  HAVE_LAPACK=
1294    HAVE_FLUSH=
1295    
1296  MODS=  MODS=
1297  TOOLSDIR=  TOOLSDIR=
# Line 1205  FTL_TAF_FLAGS= Line 1337  FTL_TAF_FLAGS=
1337  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1338  TAMC_EXTRA=  TAMC_EXTRA=
1339    
1340    DIVA=
1341    MPIINCLUDEDIR=
1342    MPI_HEADER_FILES=
1343    LOCAL_MPI_HEADERS=
1344    
1345  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1346  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1347  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 1350  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAP
1350  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1351  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1352  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1353  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1354  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1355  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"
1356    
1357  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1358  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
1359  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"
1360  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1361    
1362  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 $gm_s8"
1363  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1439  for ac_option in "$@" ; do Line 1576  for ac_option in "$@" ; do
1576    
1577  done  done
1578    
1579    #TMP=./genmk_$$
1580    #- try to put temporary files in system-local /tmp dir
1581    TMP=/tmp/genmk_$$
1582    touch $TMP ; retVal=$?
1583    if [ $retVal -eq 0 ] ; then
1584      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1585    else
1586      TMP=./genmk_$$
1587    fi
1588    rm -f $TMP
1589    #echo "  temp files: $TMP.*"
1590    
1591  printf "  getting local config information:  "  printf "  getting local config information:  "
1592  if test -f $gm_local ; then  if test -f $gm_local ; then
1593      echo "using $gm_local"      echo "using $gm_local"
# Line 1659  check_for_broken_Ff Line 1808  check_for_broken_Ff
1808  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1809        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1810        DEFINES="$DEFINES -DALLOW_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1811    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1812    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1813  fi  fi
1814  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1815        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1883  if test "x$HAVE_LAPACK" != x ; then Line 2034  if test "x$HAVE_LAPACK" != x ; then
2034  else  else
2035      echo "no"      echo "no"
2036  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2037    
2038    printf "  Can we call FLUSH intrinsic subroutine...  "
2039    check_HAVE_FLUSH
2040    if test "x$HAVE_FLUSH" = xt ; then
2041        DEFINES="$DEFINES -DHAVE_FLUSH"
2042        echo "yes"
2043    else
2044        echo "no"
2045    fi
2046    
2047    DEFINES="$DEFINES $IGNORE_TIME"
2048  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2049      build_embed_encode      build_embed_encode
2050  fi  fi
# Line 2089  if test "x${PKG_GROUPS}" != x ; then Line 2249  if test "x${PKG_GROUPS}" != x ; then
2249  fi  fi
2250    
2251  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2252  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2253  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2254      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2255  done  done
2256  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2257      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2258      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2259  done  done
# Line 2111  for p in $PACKAGES ; do Line 2271  for p in $PACKAGES ; do
2271  done  done
2272  PACKAGES="$pack"  PACKAGES="$pack"
2273  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2274  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2275  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2276  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2277  for i in $PACKAGES ; do  for i in $PACKAGES ; do
# Line 2120  for i in $PACKAGES ; do Line 2280  for i in $PACKAGES ; do
2280          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2281          exit 1          exit 1
2282      fi      fi
2283      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2284  done  done
2285  PACKAGES=  PACKAGES=
2286  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2287      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2288  done  done
2289  rm -f ./.tmp_pack  rm -f $TMP.pack
2290  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2291    
2292  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2217  EOF Line 2377  EOF
2377      fi      fi
2378  fi  fi
2379    
2380    #  Make sure the openad package is enabled if using OpenAD
2381    if test "x$OPENAD" != x ; then
2382        echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
2383        RETVAL=$?
2384        if test "x$RETVAL" != x0 ; then
2385            cat <<EOF
2386    
2387    *********************************************************************
2388    ERROR: when generating an adjoint with OpenAD, the openad package
2389      must be enabled.  Please add it to packages.conf.
2390    *********************************************************************
2391    
2392    EOF
2393            exit 1
2394        fi
2395    fi
2396    
2397  if  test "x${PKG_DEPEND}" != x ; then  if  test "x${PKG_DEPEND}" != x ; then
2398    echo "  applying package dependency rules"    echo "  applying package dependency rules"
2399    ck=    ck=
# Line 2405  fi Line 2582  fi
2582    
2583  #  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
2584  #  compiler.  #  compiler.
2585  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2586      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2587  fi  fi
2588  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2589  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2590  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2591      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2592      for j in $list_files ; do      for j in $list_files ; do
2593          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2594      done      done
2595  done  done
2596  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2597      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2598      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2599  fi  fi
2600    
2601  echo  echo
# Line 2430  for i in $INCLUDEDIRS ; do Line 2607  for i in $INCLUDEDIRS ; do
2607      fi      fi
2608  done  done
2609    
2610  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2611      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2612      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2613      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2614      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2615            mpi_headers_do_local_copy
     if test "x$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  
2616      fi      fi
2617  fi  fi
2618    
2619  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2620  rm -rf .links.tmp  rm -rf $TMP.links
2621  mkdir .links.tmp  mkdir $TMP.links
2622  touch .links.tmp/foo  touch $TMP.links/foo
2623  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2624      echo      echo
2625      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2626      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 2636  if test ! -r ".links.tmp/foo" ; then
2636      echo      echo
2637      exit 1      exit 1
2638  fi  fi
2639  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2640    
2641  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2642      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2643      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2644      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2645      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2646        OADTOOLS="$TOOLSDIR/OAD_support"
2647      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2648      for i in "." $MODS ; do      for i in "." $MODS ; do
2649          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
# Line 2517  if test "x$OPENAD" != x ; then Line 2679  if test "x$OPENAD" != x ; then
2679      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2680  fi  fi
2681    
2682  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2683  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2684  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2685  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2686  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2687  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2688  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2689  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2690  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2691  for d in $alldirs ; do  for d in $alldirs ; do
2692      deplist=      deplist=
# Line 2534  for d in $alldirs ; do Line 2696  for d in $alldirs ; do
2696          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2697      fi      fi
2698      for sf in $sfiles ; do      for sf in $sfiles ; do
2699          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2700              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2701                  ignore_f=f                  ignore_f=f
2702                  case $d/$sf in                  case $d/$sf in
# Line 2559  for d in $alldirs ; do Line 2721  for d in $alldirs ; do
2721                          if test "x$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 $sf ; then
2722                              ignore_f=t                              ignore_f=t
2723                          else                          else
2724                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2725                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2726                          fi                          fi
2727                          ;;                          ;;
# Line 2568  for d in $alldirs ; do Line 2730  for d in $alldirs ; do
2730                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2731                      case $extn in                      case $extn in
2732                        F)                        F)
2733                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2734                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2735                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2736                              basename=${sf%%.F}                              basename=${sf%%.F}
2737                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2738                                if test -z "$isAD" ; then
2739                                    echo    " \\"  >> $TMP.nonADF77srclist
2740                                    printf " $sf" >> $TMP.nonADF77srclist
2741                                fi
2742                            else #- OpenAD case:
2743                                basename=${sf%%.F}
2744                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2745                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2746                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2747                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2748                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2749                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2750                                  else                                  else
2751                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2752                                  fi                                  fi
# Line 2592  for d in $alldirs ; do Line 2761  for d in $alldirs ; do
2761                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2762                                  fi                                  fi
2763                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2764                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2765                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2766                                  fi                                  fi
2767                              fi                              fi
2768                          fi                          fi
2769                          ;;                          ;;
2770                      F90)                      F90)
2771                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2772                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2773                          ;;                          ;;
2774                      c)                      c)
2775                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2776                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2777                          ;;                          ;;
2778                      h)                      h)
2779                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2780                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2781                          ;;                          ;;
2782                      flow)                      flow)
2783                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2784                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2785                          ;;                          ;;
2786                     esac                     esac
2787                  fi                  fi
# Line 2621  for d in $alldirs ; do Line 2790  for d in $alldirs ; do
2790      done      done
2791      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2792        if test "$d" != "." ; then        if test "$d" != "." ; then
2793          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2794          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2795          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2796  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2797  # 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"
2798  # 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.
2799          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2800        fi        fi
2801      fi      fi
2802  done  done
2803  rm -rf .links.tmp  rm -rf $TMP.links
2804  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2805  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2806  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2807  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2808  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2809  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2810    
2811  CMDLINE=$0  CMDLINE=$0
2812  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
# Line 2689  INCLUDEDIRS = ${INCLUDEDIRS} Line 2858  INCLUDEDIRS = ${INCLUDEDIRS}
2858  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2859  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2860  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2861    OADTOOLS    = ${OADTOOLS}
2862    
2863  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2864  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2709  else Line 2879  else
2879      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2880  fi  fi
2881    
2882    # extract default cpp search path so we can pass it to makedepend
2883    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2884    
2885  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2886  # Unix ln (link)  # Unix ln (link)
2887  LN = ${LN}  LN = ${LN}
# Line 2729  LINK = ${LINK} ${LDADD} Line 2902  LINK = ${LINK} ${LDADD}
2902  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2903  # Includes for CPP  # Includes for CPP
2904  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2905    # default CPP includes for makedepend
2906    CPPINCLUDES = ${CPPINCLUDES}
2907  # Flags for KPP  # Flags for KPP
2908  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2909  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
# Line 2753  MAKE = ${MAKE} Line 2928  MAKE = ${MAKE}
2928    
2929  EOF  EOF
2930    
2931  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2932  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2933  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2934  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2935  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2936  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2937    
2938  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
2939    
2940  echo >> $MAKEFILE  echo >> $MAKEFILE
2941    
# Line 2794  fwd_exe_target: Line 2969  fwd_exe_target:
2969    
2970  depend:  depend:
2971          @\$(MAKE) -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2972          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2973          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2974          -rm -f makedepend.out          -rm -f makedepend.out
2975    
# Line 2827  Clean: Line 3002  Clean:
3002          @\$(MAKE) -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
3003          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
3004          -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  
3005    
3006  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
3007  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
# Line 2836  CLEAN: Line 3010  CLEAN:
3010          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
3011          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3012          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3013            -rm -rf mpi_headers mnc_test_*
3014          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3015          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3016          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3017          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3018            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3019          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3020          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3021    
3022  makefile:  makefile:
3023          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2894  cat >>$MAKEFILE <<EOF Line 3070  cat >>$MAKEFILE <<EOF
3070  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3071  ## %.o : %.F  ## %.o : %.F
3072    
3073  # C preprocessing and replacing the _d in constants:  # C preprocessing and replacing the _d in constants:
3074  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}  CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3075    
3076  .F.$FS:  .F.$FS:
# Line 2938  TAF            = ${TAF} Line 3114  TAF            = ${TAF}
3114    
3115  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3116  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3117    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3118    
3119  EOF  EOF
3120    
# Line 2955  done Line 3132  done
3132  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3133  echo >> $MAKEFILE  echo >> $MAKEFILE
3134  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3135  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3136  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3137      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3138      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3139  done  done
3140  echo >> $MAKEFILE  echo >> $MAKEFILE
3141  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3142    
3143  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3144    
# Line 2986  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL Line 3163  ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
3163          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
3164    
3165  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
3166            @-rm -f ad_input_code_ad.$FS ; echo ''
3167          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3168          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3169          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
# Line 2995  adtafonly: Line 3173  adtafonly:
3173          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3174          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
3175    
3176  \$(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)
3177          \$(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)
3178    
3179  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
3180          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 3011  adonlyfwd: Line 3189  adonlyfwd:
3189  adtrick:  adtrick:
3190          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3191    
3192  adobj: ad_taf_output.o \$(OBJFILES)  adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3193    
3194  # ... FTL ...  # ... FTL ...
3195  ftlall: ftl_exe_target  ftlall: ftl_exe_target
# Line 3034  ftl_input_code.$FS: \$(AD_FILES) Line 3212  ftl_input_code.$FS: \$(AD_FILES)
3212          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
3213    
3214  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
3215            @-rm -f ftl_input_code_tl.$FS ; echo ''
3216          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3217          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3218          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3219    
3220  ftltafonly:  ftltafonly:
3221          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3222          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3223          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3224    
3225  \$(EXE_FTL): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ftl_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3226          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3227    
3228  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3229          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
# Line 3127  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3306  for i in `cat ${OAD_CB2M_FILES}` ; do
3306    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3307    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3308  done  done
3309  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3310  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3311    basename=${i%%.f}    basename=${i%%.f}
3312    toBeIgnored=`egrep ^$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 3316  for i in $AD_FILES ; do
3316    fi    fi
3317  done  done
3318  echo >> $MAKEFILE  echo >> $MAKEFILE
3319  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3320    
3321  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3322    
# Line 3159  w2f__types.F90 \ Line 3338  w2f__types.F90 \
3338  OAD_active.F90 \  OAD_active.F90 \
3339  OAD_cp.F90 \  OAD_cp.F90 \
3340  OAD_rev.F90 \  OAD_rev.F90 \
3341  OAD_tape.F90  OAD_tape.F90 \
3342    revolve.F90
3343    
3344  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3345  iaddr.c \  iaddr.c \
# Line 3185  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N Line 3365  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
3365          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3366    
3367  # create sources files modules from header files containing common blocks  # create sources files modules from header files containing common blocks
3368  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3369          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3370    
3371  # 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
3372  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3373          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3374    
3375  # 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
3376  %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3377          ../OAD_support/cb2mUseModules.bash $< ${MPI}          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
3378    
3379  # makefile debug rule  # makefile debug rule
3380  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
# Line 3216  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI Line 3396  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
3396    
3397  # replace stop statements (to avoid the implied unstructured control flow)  with print statements  # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3398  ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90  ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3399          cat \$< | sed -f ../OAD_support/stop2print.sed > ad_input_code_sf.pre.s2p.f90          cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3400    
3401  # F -> WHIRL  # F -> WHIRL
3402  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
# Line 3239  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS Line 3419  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
3419          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3420    
3421  # insert template directives  # insert template directives
3422  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$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$FS90 \${OADTOOLS}/insertTemplateDir.bash
3423          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3424    
3425  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3426  # postprocess F'  # postprocess F'
3427  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$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
3428          \${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 \$<
3429          # 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
3430          touch \$@          touch \$@
3431  # 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 3436  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
3436          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3437    
3438  # link the support files:  # link the support files:
3439  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3440          \$(LN) ../OAD_support/\$@ .          \$(LN) \${OADTOOLS}/\$@ .
3441    
3442  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
3443    
3444  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3445    
# Line 3295  for i in $NOOPTFILES ; do Line 3475  for i in $NOOPTFILES ; do
3475  done  done
3476    
3477  echo "  Add rules for links"  echo "  Add rules for links"
3478  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3479  rm -f srclinks.tmp  rm -f $TMP.srclinks
3480    
3481  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3482  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE

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