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revision 1.238 by jmc, Tue Aug 28 21:11:22 2012 UTC revision 1.274 by jmc, Fri Nov 20 01:22:36 2015 UTC
# Line 19  Usage: "$0" [OPTIONS] Line 19  Usage: "$0" [OPTIONS]
19      -help | --help | -h | --h      -help | --help | -h | --h
20            Print this help message and exit.            Print this help message and exit.
21    
22        -oad | --oad
23              Generate a Makefile for an OpenAD built
24    
25        -nocat4ad | -dog4ad | -ncad | -dad
26              do not concatenate (cat) source code sent to TAF
27              resulting in compilation of multiple files
28    
29      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
30        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
31            Use "NAME" as the adoptfile.  By default, the file at            Use "NAME" as the adoptfile.  By default, the file at
32              "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
33            "tools/adjoint_options/adjoint_default" will be used.            "tools/adjoint_options/adjoint_default" will be used.
34    
35      -nooptfile | --nooptfile      -nooptfile | --nooptfile
# Line 174  EOF Line 182  EOF
182  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
183      cpp_options=$1      cpp_options=$1
184      pkg=$2      pkg=$2
185      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
186      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
187      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
188      test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<DISABLE_$pkg\>"
     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"  
     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"  
     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"  
     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"  
189  }  }
190    
191  # Search for particular CPP #cmds associated with MPI  # Search for particular CPP #cmds associated with MPI
192  # usage: test_for_mpi_in_cpp_eeoptions CPP_file  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
193  test_for_mpi_in_cpp_eeoptions() {  test_for_mpi_in_cpp_eeoptions() {
194      cpp_options=$1      cpp_options=$1
195      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
196      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_USE_MPI\>"
     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"  
     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"  
     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"  
     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"  
     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"  
     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"  
197  }  }
198    
199  # Search for particular string in a file. Return 1 if detected, 0 if not  # Search for particular string in a file. Return 1 if detected, 0 if not
# Line 203  test_for_mpi_in_cpp_eeoptions() { Line 201  test_for_mpi_in_cpp_eeoptions() {
201  test_for_string_in_file() {  test_for_string_in_file() {
202      file=$1      file=$1
203      strng=$2      strng=$2
204      grep -i "$strng" $file > /dev/null 2>&1      grep "$strng" $file > /dev/null 2>&1
205      RETVAL=$?      RETVAL=$?
206      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
207          printf "Error: In $file there is an illegal line: "          printf "Error: In $file there is an illegal line: "
# Line 218  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$RETVAL" = x0 ; then
226                  matched=1                  matched=1
# Line 234  expand_pkg_groups() { Line 232  expand_pkg_groups() {
232              fi              fi
233          done          done
234          PACKAGES=$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 334  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()" >> $LOGFILE
# Line 353  look_for_makedepend()  { Line 350  look_for_makedepend()  {
350              build_cyrus_makedepend              build_cyrus_makedepend
351              RETVAL=$?              RETVAL=$?
352              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
353                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
354                  MAKEDEPEND=                  MAKEDEPEND=
355              fi              fi
356          else          else
# Line 366  look_for_makedepend()  { Line 363  look_for_makedepend()  {
363          fi          fi
364      fi      fi
365      if test "x${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 383  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 598  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='$MPIINCLUDEDIR' is not a directory"
683            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
684    #       exit -1
685        fi
686    }
687    
688  #  Parse the package dependency information  #  Parse the package dependency information
689  get_pdepend_list()  {  get_pdepend_list()  {
690    
# Line 917  check_netcdf_libs()  { Line 1004  check_netcdf_libs()  {
1004        program fgennc        program fgennc
1005  #include "netcdf.inc"  #include "netcdf.inc"
1006  EOF  EOF
1007      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1008          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1009      fi     #fi
1010      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1011        integer iret, ncid, xid        integer iret, ncid, xid
1012        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1000  EOF Line 1087  EOF
1087  }  }
1088    
1089  check_lapack_libs()  {  check_lapack_libs()  {
1090      if test ! "x$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()" >> $LOGFILE
1093      cat <<EOF > genmake_tla.F      cat <<EOF > genmake_tla.F
# Line 1102  EOF Line 1187  EOF
1187      echo " --> set HAVE_LAPACK='$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 1159  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 1170  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 1203  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 1215  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 1223  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 $gm_s12"
# Line 1280  for ac_option in "$@" ; do Line 1415  for ac_option in "$@" ; do
1415          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1416              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1417    
1418            -oad | --oad)
1419                OPENAD="true" ; ALWAYS_USE_F90=1 ;;
1420            -nocat4ad | -dog4ad | -ncad | -dad)
1421                CAT_SRC_FOR_TAF=0 ;;
1422          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1423              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1424          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
# Line 1449  for ac_option in "$@" ; 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 $gm_local"
# Line 1541  fi Line 1692  fi
1692    
1693  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1694  if test "x${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${AD_OPTFILE}" != xNONE ; then
# Line 1668  check_for_broken_Ff Line 1821  check_for_broken_Ff
1821    
1822  if test ! "x$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 -DALWAYS_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 1813  printf "  Do we have the etime() command Line 1968  printf "  Do we have the etime() command
1968  cat > genmake_tcomp.$FS <<EOF  cat > genmake_tcomp.$FS <<EOF
1969        program hello        program hello
1970        REAL*4 ACTUAL, TARRAY(2)        REAL*4 ACTUAL, TARRAY(2)
1971        EXTERNAL ETIME        call etime( tarray, actual )
       REAL*4 ETIME  
       actual = etime( tarray )  
1972        print *, tarray        print *, tarray
1973        end        end
1974  EOF  EOF
# Line 1893  if test "x$HAVE_LAPACK" != x ; then Line 2046  if test "x$HAVE_LAPACK" != x ; then
2046  else  else
2047      echo "no"      echo "no"
2048  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2049    
2050    printf "  Can we call FLUSH intrinsic subroutine...  "
2051    check_HAVE_FLUSH
2052    if test "x$HAVE_FLUSH" = xt ; then
2053        DEFINES="$DEFINES -DHAVE_FLUSH"
2054        echo "yes"
2055    else
2056        echo "no"
2057    fi
2058    
2059    DEFINES="$DEFINES $IGNORE_TIME"
2060  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2061      build_embed_encode      build_embed_encode
2062  fi  fi
# Line 2099  if test "x${PKG_GROUPS}" != x ; then Line 2261  if test "x${PKG_GROUPS}" != x ; then
2261  fi  fi
2262    
2263  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2264  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2265  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2266      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2267  done  done
2268  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2269      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2270      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2271  done  done
# Line 2121  for p in $PACKAGES ; do Line 2283  for p in $PACKAGES ; do
2283  done  done
2284  PACKAGES="$pack"  PACKAGES="$pack"
2285  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2286  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2287  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2288  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2289  for i in $PACKAGES ; do  for i in $PACKAGES ; do
# Line 2130  for i in $PACKAGES ; do Line 2292  for i in $PACKAGES ; do
2292          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2293          exit 1          exit 1
2294      fi      fi
2295      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2296  done  done
2297  PACKAGES=  PACKAGES=
2298  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2299      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2300  done  done
2301  rm -f ./.tmp_pack  rm -f $TMP.pack
2302  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2303    
2304  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2206  EOF Line 2368  EOF
2368      fi      fi
2369  fi  fi
2370    
2371  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2372  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2373  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2374      RETVAL=$?      RETVAL=$?
2375      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2376          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:  
2377    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2378  *********************************************************************  *********************************************************************
2379    ERROR: when generating an adjoint with OpenAD, the openad package
2380      must be enabled.  Please add it to packages.conf.
2381    *********************************************************************
2382    
2383  EOF  EOF
2384            exit 1
2385      fi      fi
2386  fi  fi
2387    
# Line 2415  fi Line 2573  fi
2573    
2574  #  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
2575  #  compiler.  #  compiler.
2576  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2577      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2578  fi  fi
2579  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2580  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2581  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2582      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2583      for j in $list_files ; do      for j in $list_files ; do
2584          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2585      done      done
2586  done  done
2587  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2588      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2589      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2590  fi  fi
2591    
2592  echo  echo
# Line 2440  for i in $INCLUDEDIRS ; do Line 2598  for i in $INCLUDEDIRS ; do
2598      fi      fi
2599  done  done
2600    
2601  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2602      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2603      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2604      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2605      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2606            mpi_headers_do_local_copy
     if test "x$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  
2607      fi      fi
2608  fi  fi
2609    
2610  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2611  rm -rf .links.tmp  rm -rf $TMP.links
2612  mkdir .links.tmp  mkdir $TMP.links
2613  touch .links.tmp/foo  touch $TMP.links/foo
2614  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2615      echo      echo
2616      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2617      echo "   your user file-creation mask (\"umask\") since creating a"      echo "   your user file-creation mask (\"umask\") since creating a"
# Line 2485  if test ! -r ".links.tmp/foo" ; then Line 2627  if test ! -r ".links.tmp/foo" ; then
2627      echo      echo
2628      exit 1      exit 1
2629  fi  fi
2630  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2631    
2632  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2633      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2634      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2635      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2636      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2637        OADTOOLS="$TOOLSDIR/OAD_support"
2638      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2639      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2640          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
2641              OAD_DONT_COMPILE=$i"/dontCompile"              OAD_DONT_COMPILE=$i"/dontCompile"
2642              echo "     found $OAD_DONT_COMPILE"              echo "     found $OAD_DONT_COMPILE"
# Line 2501  if test "x$OPENAD" != x ; then Line 2644  if test "x$OPENAD" != x ; then
2644          fi          fi
2645      done      done
2646      echo "  looking for dontTransform file:  "      echo "  looking for dontTransform file:  "
2647      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2648          if test -r $i"/dontTransform" ; then          if test -r $i"/dontTransform" ; then
2649              OAD_DONT_TRANSFORM=$i"/dontTransform"              OAD_DONT_TRANSFORM=$i"/dontTransform"
2650              echo "     found $OAD_DONT_TRANSFORM"              echo "     found $OAD_DONT_TRANSFORM"
# Line 2509  if test "x$OPENAD" != x ; then Line 2652  if test "x$OPENAD" != x ; then
2652          fi          fi
2653      done      done
2654      echo "  looking for keepOriginal file:  "      echo "  looking for keepOriginal file:  "
2655      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2656          if test -r $i"/keepOriginal" ; then          if test -r $i"/keepOriginal" ; then
2657              OAD_KEEP_ORIGINAL=$i"/keepOriginal"              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2658              echo "     found $OAD_KEEP_ORIGINAL"              echo "     found $OAD_KEEP_ORIGINAL"
# Line 2517  if test "x$OPENAD" != x ; then Line 2660  if test "x$OPENAD" != x ; then
2660          fi          fi
2661      done      done
2662      echo "  looking for cb2mFiles:  "      echo "  looking for cb2mFiles:  "
2663      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2664          if test -r $i"/cb2mFiles" ; then          if test -r $i"/cb2mFiles" ; then
2665              OAD_CB2M_FILES=$i"/cb2mFiles"              OAD_CB2M_FILES=$i"/cb2mFiles"
2666              echo "     found $OAD_CB2M_FILES"              echo "     found $OAD_CB2M_FILES"
# Line 2527  if test "x$OPENAD" != x ; then Line 2670  if test "x$OPENAD" != x ; then
2670      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2671  fi  fi
2672    
2673  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2674  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2675  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2676  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2677  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2678  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2679  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2680  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2681  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2682  for d in $alldirs ; do  for d in $alldirs ; do
2683      deplist=      deplist=
# Line 2544  for d in $alldirs ; do Line 2687  for d in $alldirs ; do
2687          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2688      fi      fi
2689      for sf in $sfiles ; do      for sf in $sfiles ; do
2690          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2691              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2692                  ignore_f=f                  ignore_f=f
2693                  case $d/$sf in                  case $d/$sf in
# Line 2569  for d in $alldirs ; do Line 2712  for d in $alldirs ; do
2712                          if test "x$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 $sf ; then
2713                              ignore_f=t                              ignore_f=t
2714                          else                          else
2715                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2716                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2717                          fi                          fi
2718                          ;;                          ;;
# Line 2578  for d in $alldirs ; do Line 2721  for d in $alldirs ; do
2721                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2722                      case $extn in                      case $extn in
2723                        F)                        F)
2724                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2725                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2726                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2727                                basename=${sf%%.F}
2728                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2729                                if test -z "$isAD" ; then
2730                                    echo    " \\"  >> $TMP.nonADF77srclist
2731                                    printf " $sf" >> $TMP.nonADF77srclist
2732                                fi
2733                            else #- OpenAD case:
2734                              basename=${sf%%.F}                              basename=${sf%%.F}
2735                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2736                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2737                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2738                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2739                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2740                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2741                                  else                                  else
2742                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2743                                  fi                                  fi
# Line 2602  for d in $alldirs ; do Line 2752  for d in $alldirs ; do
2752                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2753                                  fi                                  fi
2754                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2755                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2756                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2757                                  fi                                  fi
2758                              fi                              fi
2759                          fi                          fi
2760                          ;;                          ;;
2761                      F90)                      F90)
2762                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2763                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2764                          ;;                          ;;
2765                      c)                      c)
2766                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2767                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2768                          ;;                          ;;
2769                      h)                      h)
2770                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2771                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2772                          ;;                          ;;
2773                      flow)                      flow)
2774                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2775                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2776                          ;;                          ;;
2777                     esac                     esac
2778                  fi                  fi
# Line 2631  for d in $alldirs ; do Line 2781  for d in $alldirs ; do
2781      done      done
2782      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2783        if test "$d" != "." ; then        if test "$d" != "." ; then
2784          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2785          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2786          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2787  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2788  # 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"
2789  # 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.
2790          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2791        fi        fi
2792      fi      fi
2793  done  done
2794  rm -rf .links.tmp  rm -rf $TMP.links
2795  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2796  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2797  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2798  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2799  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2800  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2801    
2802  CMDLINE=$0  CMDLINE=$0
2803  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
# Line 2699  INCLUDEDIRS = ${INCLUDEDIRS} Line 2849  INCLUDEDIRS = ${INCLUDEDIRS}
2849  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2850  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2851  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2852    OADTOOLS    = ${OADTOOLS}
2853    
2854  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2855  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2719  else Line 2870  else
2870      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2871  fi  fi
2872    
2873    # extract default cpp search path so we can pass it to makedepend
2874    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2875    
2876  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2877  # Unix ln (link)  # Unix ln (link)
2878  LN = ${LN}  LN = ${LN}
 # C preprocessor  
 CPP = cat \$< | ${S64} | ${CPP}  
2879  # Dependency generator  # Dependency generator
2880  MAKEDEPEND = ${MAKEDEPEND}  MAKEDEPEND = ${MAKEDEPEND}
2881  # Special preprocessor (KAP on DECs, FPP on Crays)  # Special preprocessor (KAP on DECs, FPP on Crays)
# Line 2741  LINK = ${LINK} ${LDADD} Line 2893  LINK = ${LINK} ${LDADD}
2893  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2894  # Includes for CPP  # Includes for CPP
2895  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2896    # default CPP includes for makedepend
2897    CPPINCLUDES = ${CPPINCLUDES}
2898  # Flags for KPP  # Flags for KPP
2899  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2900  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2901  # Optim./debug for FC  # Optim./debug for FC
2902  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}  FFLAGS = ${FFLAGS}
2903  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
2904  # Optim./debug for FC  # Optim./debug for FC
2905  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2906  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
# Line 2765  MAKE = ${MAKE} Line 2919  MAKE = ${MAKE}
2919    
2920  EOF  EOF
2921    
2922  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2923  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2924  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2925  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2926  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2927  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2928    
2929  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
2930    
2931  echo >> $MAKEFILE  echo >> $MAKEFILE
2932    
# Line 2806  fwd_exe_target: Line 2960  fwd_exe_target:
2960    
2961  depend:  depend:
2962          @\$(MAKE) -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2963          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2964          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2965          -rm -f makedepend.out          -rm -f makedepend.out
2966    
# Line 2822  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 2976  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
2976    
2977  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2978    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
2979  # remove most of the files that "make" generates  # remove most of the files that "make" generates
2980  clean:  clean:
2981          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2839  Clean: Line 2989  Clean:
2989          @\$(MAKE) -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
2990          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
2991          -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  
2992    
2993  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
2994  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
# Line 2848  CLEAN: Line 2997  CLEAN:
2997          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
2998          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
2999          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3000            -rm -rf mpi_headers mnc_test_*
3001          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3002          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3003          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3004          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3005            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3006          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3007          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3008    
3009  makefile:  makefile:
3010          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2906  cat >>$MAKEFILE <<EOF Line 3057  cat >>$MAKEFILE <<EOF
3057  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3058  ## %.o : %.F  ## %.o : %.F
3059    
3060    # C preprocessing and replacing the _d in constants:
3061    CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3062    
3063  .F.$FS:  .F.$FS:
3064          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3065  .$FS.o:  .$FS.o:
3066          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3067  .F.o:  .F.o:
3068          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3069  .F90.$FS90:  .F90.$FS90:
3070          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3071  .FF90.f$FS90:  .FF90.f$FS90:
3072          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3073  .$FS90.o:  .$FS90.o:
3074          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
3075  .f$FS90.o:  .f$FS90.o:
# Line 2924  cat >>$MAKEFILE <<EOF Line 3078  cat >>$MAKEFILE <<EOF
3078  .c.o:  .c.o:
3079          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
3080  .flow.flowdir:  .flow.flowdir:
3081          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3082    
3083  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
3084  .F.p:  .F.p:
3085          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3086  .p.$FS:  .p.$FS:
3087          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
3088    
# Line 2947  TAF            = ${TAF} Line 3101  TAF            = ${TAF}
3101    
3102  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3103  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3104    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3105    
3106  EOF  EOF
3107    
# Line 2964  done Line 3119  done
3119  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3120  echo >> $MAKEFILE  echo >> $MAKEFILE
3121  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3122  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3123  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3124      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3125      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3126  done  done
3127  echo >> $MAKEFILE  echo >> $MAKEFILE
3128  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3129    
3130    if test $CAT_SRC_FOR_TAF = 0 ; then
3131    cat >>$MAKEFILE <<EOF
3132    
3133    # ... Utilities ...
3134    remove_comments:
3135            sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
3136            @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
3137    adj_sed:
3138            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
3139            @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
3140    ftl_sed:
3141            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
3142            @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
3143    adobjfiles: \$(AD_FILES:.$FS=_ad.o)
3144    ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
3145    EOF
3146    fi
3147    
3148  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3149    
# Line 2986  ad_exe_target: Line 3159  ad_exe_target:
3159          @-rm -f ad_config.template          @-rm -f ad_config.template
3160          \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3161    
3162  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)  ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
3163          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3164          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3165          @-rm -f ad_config.template          @-rm -f ad_config.template
# Line 2994  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC Line 3167  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC
3167          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3168          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
3169    
3170  ad_taf_output.$FS: ad_input_code.$FS  adtafonly:
3171          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3172          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3173          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
3174    
3175  adtafonly:  EOF
3176    
3177    if test $CAT_SRC_FOR_TAF = 1 ; then
3178    cat >>$MAKEFILE <<EOF
3179    # ... send 1 file to TAF ...
3180    ad_taf_output.$FS: ad_input_code.$FS
3181            @-rm -f ad_input_code_ad.$FS ; echo ''
3182          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3183          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3184          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3185    
3186  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3187          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3188    
3189  ad_tamc_output.$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  
3190    
3191  ad_tamc: ad_tamc_output.o \$(OBJFILES)  EOF
         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)  
3192    
3193    else
3194    cat >>$MAKEFILE <<EOF
3195    # ... send multiple files to TAF ...
3196    ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3197            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3198            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3199            @-rm -f ad_config.template
3200            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3201            @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3202            @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
3203            \$(MAKE) -f \$(MAKEFILE) remove_comments
3204            \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
3205            \$(MAKE) -f \$(MAKEFILE) adj_sed
3206            cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
3207    
3208    \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3209            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3210            \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3211    
3212    adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3213            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3214    
3215    EOF
3216    fi
3217    
3218    cat >>$MAKEFILE <<EOF
3219  adonlyfwd:  adonlyfwd:
3220          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
3221    
3222  adtrick:  adtrick:
3223          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3224    
3225  adobj: ad_taf_output.o \$(OBJFILES)  ad_tamc_output.$FS: ad_input_code.$FS
3226            \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
3227            cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
3228    
3229    ad_tamc: ad_tamc_output.o \$(OBJFILES)
3230            \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
3231    
3232  # ... FTL ...  # ... FTL ...
3233  ftlall: ftl_exe_target  ftlall: ftl_exe_target
# Line 3034  ftl_exe_target: Line 3241  ftl_exe_target:
3241          @-rm -f ad_config.template          @-rm -f ad_config.template
3242          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
3243    
3244  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)  ftl_input_code.$FS: \$(AD_FILES)
3245          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3246          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3247          @-rm -f ad_config.template          @-rm -f ad_config.template
# Line 3042  ftl_input_code.$FS: \$(AD_FILES) \$(H_SR Line 3249  ftl_input_code.$FS: \$(AD_FILES) \$(H_SR
3249          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3250          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3251    
3252  ftl_taf_output.$FS: ftl_input_code.$FS  ftltafonly:
3253          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3254          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3255          cat ftl_input_code_ftl.$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
3256    
3257  ftltafonly:  EOF
3258    
3259    if test $CAT_SRC_FOR_TAF = 1 ; then
3260    cat >>$MAKEFILE <<EOF
3261    # ... send 1 file to TAF ...
3262    ftl_taf_output.$FS: ftl_input_code.$FS
3263            @-rm -f ftl_input_code_tl.$FS ; echo ''
3264          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3265          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3266          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3267    
3268  \${EXE_FTL}: ftl_taf_output.o \$(OBJFILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3269          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3270    
3271    EOF
3272    
3273    else
3274    cat >>$MAKEFILE <<EOF
3275    # ... send multiple files to TAF ...
3276    ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3277            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3278            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3279            @-rm -f ad_config.template
3280            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3281            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3282            @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
3283            \$(MAKE) -f \$(MAKEFILE) remove_comments
3284            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
3285            \$(MAKE) -f \$(MAKEFILE) ftl_sed
3286            cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
3287    
3288    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3289            \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
3290            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3291    
3292    EOF
3293    fi
3294    
3295    cat >>$MAKEFILE <<EOF
3296  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3297          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
3298          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
# Line 3097  if test "x$OPENAD" != x ; then Line 3335  if test "x$OPENAD" != x ; then
3335  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3336    
3337  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3338    # ... OpenAD ...
3339    
3340  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3341  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3136  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3375  for i in `cat ${OAD_CB2M_FILES}` ; do
3375    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3376    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3377  done  done
3378  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3379  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3380    basename=${i%%.f}    basename=${i%%.f}
3381    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
# Line 3146  for i in $AD_FILES ; do Line 3385  for i in $AD_FILES ; do
3385    fi    fi
3386  done  done
3387  echo >> $MAKEFILE  echo >> $MAKEFILE
3388  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3389    
3390  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3391    
3392  adAll: \$(EXE_AD)  adAll: ad_exe_target
3393  .PHONY: adAll  .PHONY: adAll
3394    
3395    ad_exe_target:
3396            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3397            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3398            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3399            @-rm -f ad_config.template
3400            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3401    
3402  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))
3403    
3404  .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 3168  w2f__types.F90 \ Line 3414  w2f__types.F90 \
3414  OAD_active.F90 \  OAD_active.F90 \
3415  OAD_cp.F90 \  OAD_cp.F90 \
3416  OAD_rev.F90 \  OAD_rev.F90 \
3417  OAD_tape.F90  OAD_tape.F90 \
3418    OAD_regular_cp.F90 \
3419    revolve.F90
3420    
3421  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3422  iaddr.c \  iaddr.c \
# Line 3194  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N Line 3442  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
3442          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
3443    
3444  # create sources files modules from header files containing common blocks  # create sources files modules from header files containing common blocks
3445  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3446          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3447    
3448  # 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
3449  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3450          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3451    
3452  # 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
3453  %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3454          ../OAD_support/cb2mUseModules.bash $< ${MPI}          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
3455    
3456  # makefile debug rule  # makefile debug rule
3457  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3458  .PHONY: small_f  .PHONY: small_f
3459    
 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) > \$@  
   
3460  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3461          cat \$^ > \$@          cat \$^ > \$@
3462    
# Line 3225  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI Line 3466  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
3466    
3467  # 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
3468  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
3469          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
3470    
3471  # F -> WHIRL  # F -> WHIRL
3472  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 3248  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS Line 3489  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
3489          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3490    
3491  # insert template directives  # insert template directives
3492  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
3493          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3494    
3495  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3496  # postprocess F'  # postprocess F'
3497  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
3498          \${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 \$<
3499          # 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
3500          touch \$@          touch \$@
3501  # put this so make knows about the postprocessing output  # put this so make knows about the postprocessing output
# Line 3265  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f Line 3506  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
3506          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3507    
3508  # link the support files:  # link the support files:
3509  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3510          \$(LN) ../OAD_support/\$@ .          \$(LN) \${OADTOOLS}/\$@ .
3511    
3512  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
3513    
3514  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3515    
# Line 3304  for i in $NOOPTFILES ; do Line 3545  for i in $NOOPTFILES ; do
3545  done  done
3546    
3547  echo "  Add rules for links"  echo "  Add rules for links"
3548  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3549  rm -f srclinks.tmp  rm -f $TMP.srclinks
3550    
3551  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3552  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE
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