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revision 1.113 by edhill, Sun Dec 26 16:38:20 2004 UTC revision 1.152 by jmc, Thu Jun 15 17:11:37 2006 UTC
# Line 13  Line 13 
13  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
14      cpp_options=$1      cpp_options=$1
15      pkg=$2      pkg=$2
16      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
17      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
18      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
19      test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
20        test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
21        test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
22        test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
23        test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
24  }  }
25    
26  # Search for particular CPP #cmds associated with MPI  # Search for particular CPP #cmds associated with MPI
27  # usage: test_for_mpi_in_cpp_eeoptions CPP_file  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
28  test_for_mpi_in_cpp_eeoptions() {  test_for_mpi_in_cpp_eeoptions() {
29      cpp_options=$1      cpp_options=$1
30      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
31      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
32      test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
33      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
34        test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
35        test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
36        test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
37        test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
38  }  }
39    
40  # 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 39  test_for_string_in_file() { Line 47  test_for_string_in_file() {
47      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
48          printf "Error: In $file there is an illegal line: "          printf "Error: In $file there is an illegal line: "
49          grep -i "$strng" $file          grep -i "$strng" $file
50          return 1          exit 99
51      fi      fi
52      return 0      return 0
53  }  }
# Line 122  EOF Line 130  EOF
130        stop        stop
131        end        end
132  EOF  EOF
133      test -f Makefile  &&  mv -f Makefile Makefile.bak      test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
134      cat <<EOF >> Makefile      cat <<EOF >> $MAKEFILE
135  .SUFFIXES:  .SUFFIXES:
136  .SUFFIXES: .$tfs .F  .SUFFIXES: .$tfs .F
137  .F.$tfs:  .F.$tfs:
# Line 148  EOF Line 156  EOF
156              return              return
157          fi          fi
158      fi      fi
159      rm -f genmake_hello.* Makefile      rm -f genmake_hello.* $MAKEFILE
160      test -f Makefile  &&  mv -f Makefile.bak Makefile      test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
161    
162      #  If we make it here, use the extensions      #  If we make it here, use the extensions
163      FS=$tfs      FS=$tfs
# Line 181  look_for_makedepend()  { Line 189  look_for_makedepend()  {
189      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
190          which makedepend > /dev/null 2>&1          which makedepend > /dev/null 2>&1
191          RV0=$?          RV0=$?
192            test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
193            #  echo 'MAKEFILE="'$MAKEFILE'"'
194            cat <<EOF >> $MAKEFILE
195    #   THIS IS A TEST MAKEFILE GENERATED BY "genmake2"
196    #
197    #   Some "makedepend" implementations will die if they cannot
198    #   find a Makefile -- so this file is here to gives them an
199    #   empty one to find and parse.
200    EOF
201          cat <<EOF >> genmake_tc.f          cat <<EOF >> genmake_tc.f
202        program test        program test
203        write(*,*) 'test'        write(*,*) 'test'
# Line 189  look_for_makedepend()  { Line 206  look_for_makedepend()  {
206  EOF  EOF
207          makedepend genmake_tc.f > /dev/null 2>&1          makedepend genmake_tc.f > /dev/null 2>&1
208          RV1=$?          RV1=$?
209            test -f $MAKEFILE  &&  rm -f $MAKEFILE
210            test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
211          if test "x${RV0}${RV1}" = x00 ; then          if test "x${RV0}${RV1}" = x00 ; then
212              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
213          else          else
# Line 237  build_cyrus_makedepend()  { Line 256  build_cyrus_makedepend()  {
256      fi      fi
257  }  }
258    
259    
260    build_embed_encode()
261    {
262        printf "  building the embed-encode utility...  "
263        if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
264            if test ! -d "$ROOTDIR/tools/embed_encode" ; then
265                echo
266                echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
267                echo
268                EMBED_SRC=f
269                return 1
270            fi
271            clist="cc gcc c89 $CC"
272            for ic in $clist ; do
273                comm="$ic -o encode_files encode_files.c"
274                ( cd $ROOTDIR/tools/embed_encode && $comm ) > /dev/null 2>&1
275                RETVAL=$?
276                if test "x$RETVAL" = x0 ; then
277                    echo "OK"
278                    DEFINES="$DEFINES -DHAVE_EMBED_SRC"
279                    return 0
280                fi
281            done
282            echo
283            echo "    Error: unable to build $ROOTDIR/embed_encode/encode_files"
284            echo "      so it has been disabled"
285            echo
286            EMBED_SRC=f
287            return 1
288        fi
289        echo "OK"
290        DEFINES="$DEFINES -DHAVE_EMBED_SRC"
291    }
292    
293    
294  # Guess possible config options for this host  # Guess possible config options for this host
295  find_possible_configs()  {  find_possible_configs()  {
296    
# Line 310  EOF Line 364  EOF
364    
365      #================================================================      #================================================================
366      #  look for possible FORTRAN compilers      #  look for possible FORTRAN compilers
367      tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"      tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95 gfortran"
368      p_FC=      p_FC=
369      for c in $tmp ; do      for c in $tmp ; do
370          rm -f ./hello.f ./hello          rm -f ./hello.f ./hello
# Line 342  EOF Line 396  EOF
396      else      else
397          echo "  The possible FORTRAN compilers found in your path are:"          echo "  The possible FORTRAN compilers found in your path are:"
398          echo "   "$p_FC          echo "   "$p_FC
399          if test "x$FC" = x ; then      fi
400              FC=`echo $p_FC | $AWK '{print $1}'`  
401              echo "  Setting FORTRAN compiler to: "$FC      #  Use the first of the compilers found in the current PATH
402          fi      #  that has a correctly-named optfile
403        if test "x$OPTFILE" = x  -a  "x$FC" = x ; then
404            for i in $p_FC ; do
405                OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
406                if test -r $OPTFILE ; then
407                    echo "  Setting OPTFILE to: "$OPTFILE
408                    break
409                fi
410            done
411      fi      fi
412    
413      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
# Line 516  Usage: "$0" [OPTIONS] Line 578  Usage: "$0" [OPTIONS]
578            *only* works if it is supported by the OPTFILE that            *only* works if it is supported by the OPTFILE that
579            is being used.            is being used.
580    
581        -ignoretime | -ignore_time | --ignoretime | --ignore_time
582              Ignore all the "wall clock" routines entirely.  This will
583              not in any way hurt the model results -- it simply means
584              that the code that checks how long the model spends in
585              various routines will give junk values.
586    
587        -ts | --ts
588              Produce timing information per timestep
589        -papis | --papis
590              Produce summary MFlop/s (and IPC) with PAPI per timestep
591        -pcls | --pcls
592              Produce summary MFlop/s etc. with PCL per timestep
593        -foolad | --foolad
594              Fool the AD code generator
595        -papi | --papi
596              Performance analysis with PAPI
597        -pcl | --pcl
598              Performance analysis with PCL
599        -hpmt | --hpmt
600              Performance analysis with the HPM Toolkit
601    
602        -gsl | --gsl
603              Use GSL to control floating point rounding and precision
604    
605      -mpi | --mpi      -mpi | --mpi
606            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
607      -mpi=PATH | --mpi=PATH      -mpi=PATH | --mpi=PATH
# Line 523  Usage: "$0" [OPTIONS] Line 609  Usage: "$0" [OPTIONS]
609            set to PATH. i.e. Include files from \$PATH/include, link to libraries            set to PATH. i.e. Include files from \$PATH/include, link to libraries
610            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
611    
612        -es | --es | -embed-source | --embed-source
613              Embed a tarball containing the full source code
614              (including the Makefile, etc.) used to build the
615              executable [off by default]
616    
617      -bash NAME      -bash NAME
618            Explicitly specify the Bourne or BASH shell to use            Explicitly specify the Bourne or BASH shell to use
619    
# Line 581  WARNING: Please contact <MITgcm-support@ Line 672  WARNING: Please contact <MITgcm-support@
672  EOF  EOF
673          return 1          return 1
674      fi      fi
675      cat > genmake_tcomp.f <<EOF      cat > genmake_tcomp.$FS <<EOF
676        subroutine tcall( string )        subroutine tcall( string )
677        character*(*) string        character*(*) string
678        call tsub( string )        call tsub( string )
679        end        end
680  EOF  EOF
681      $FC $FFLAGS $DEFINES -c genmake_tcomp.f >> genmake_warnings 2>&1      $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
682      RETVAL=$?      RETVAL=$?
683      if test "x$RETVAL" != x0 ; then      if test "x$RETVAL" != x0 ; then
684          FC_NAMEMANGLE=$default_nm          FC_NAMEMANGLE=$default_nm
# Line 653  void FC_NAMEMANGLE(cloc) ( double *curti Line 744  void FC_NAMEMANGLE(cloc) ( double *curti
744   *curtim = *curtim/1.E6;   *curtim = *curtim/1.E6;
745  }  }
746  EOF  EOF
747      make genmake_tc_1.o >> genmake_tc.log 2>&1      make genmake_tc_1.o >> genmake_warnings 2>&1
748      RET_C=$?      RET_C=$?
749      cat <<EOF > genmake_tc_2.f      cat <<EOF > genmake_tc_2.$FS
750        program hello        program hello
751        Real*8 wtime        REAL*8 wtime
752        external cloc        external cloc
753        call cloc(wtime)        call cloc(wtime)
754        print *," HELLO WORLD", wtime        print *," HELLO WORLD", wtime
755        end program hello        end
756  EOF  EOF
757      $FC $FFLAGS -o genmake_tc genmake_tc_2.f genmake_tc_1.o >> genmake_tc.log 2>&1      $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_warnings 2>&1
758      RET_F=$?      RET_F=$?
759      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
760      RETVAL=$?      RETVAL=$?
761      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
762          HAVE_CLOC=t          HAVE_CLOC=t
# Line 675  EOF Line 766  EOF
766  }  }
767    
768    
769    check_HAVE_SIGREG()  {
770        if test ! "x$HAVE_SIGREG" = x ; then
771            return
772        fi
773        get_fortran_c_namemangling
774        cat <<EOF > genmake_tc_1.c
775    $FC_NAMEMANGLE
776    #include <stdlib.h>
777    #include <stdio.h>
778    #include <signal.h>
779    #include <errno.h>
780    #include <ucontext.h>
781    
782    int * ip;
783    
784    static void killhandler(
785        unsigned int sn, siginfo_t  si, struct ucontext *sc )
786    {
787        *ip = *ip + 1;
788        return;
789    }
790    
791    void FC_NAMEMANGLE(sigreg) (int * aip)
792    {
793        struct sigaction s;
794        ip = aip;
795        s.sa_flags = SA_SIGINFO;
796        s.sa_sigaction = (void *)killhandler;
797        if(sigaction (SIGTERM,&s,(struct sigaction *)NULL)) {
798            printf("Sigaction returned error = %d\n", errno);
799            exit(0);
800        }
801        return;
802    }
803    EOF
804        make genmake_tc_1.o >> genmake_warnings 2>&1
805        RET_C=$?
806        cat <<EOF > genmake_tc_2.$FS
807          program hello
808          integer anint
809          common /iv/ anint
810          external sigreg
811          call sigreg(anint)
812          end
813    EOF
814        echo >> genmake_warnings
815        echo "running: check_HAVE_SIGREG()" >> genmake_warnings
816        cat genmake_tc_2.$FS >> genmake_warnings
817        COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
818        echo $COMM >> genmake_warnings
819        $COMM >> genmake_warnings 2>&1
820        RETVAL=$?
821        if test "x$RETVAL" = x0 ; then
822            HAVE_SIGREG=t
823            DEFINES="$DEFINES -DHAVE_SIGREG"
824        fi
825        rm -f genmake_tc*
826    }
827    
828    
829    check_HAVE_SETRLSTK()  {
830        if test "x$HAVE_SETRLSTK" = xt ; then
831            DEFINES="$DEFINES -DHAVE_SETRLSTK"
832            return
833        fi  
834        if test ! "x$HAVE_SETRLSTK" = x ; then
835            return
836        fi
837        get_fortran_c_namemangling
838        cat <<EOF > genmake_tc_1.c
839    $FC_NAMEMANGLE
840    #include <sys/time.h>
841    #include <sys/resource.h>
842    #include <unistd.h>
843    void FC_NAMEMANGLE(setrlstk) ()
844    {
845        struct rlimit rls;
846        rls.rlim_cur = RLIM_INFINITY;
847        rls.rlim_max = RLIM_INFINITY;
848        setrlimit(RLIMIT_STACK, &rls);
849        return;
850    }
851    EOF
852        make genmake_tc_1.o >> genmake_warnings 2>&1
853        RET_C=$?
854        cat <<EOF > genmake_tc_2.$FS
855          program hello
856          external setrlstk
857          call setrlstk()
858          end
859    EOF
860        echo >> genmake_warnings
861        echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
862        cat genmake_tc_2.$FS >> genmake_warnings
863        COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
864        echo $COMM >> genmake_warnings
865        $COMM >> genmake_warnings 2>&1
866        RETVAL=$?
867        if test "x$RETVAL" = x0 ; then
868            HAVE_SETRLSTK=t
869            DEFINES="$DEFINES -DHAVE_SETRLSTK"
870        fi
871        rm -f genmake_tc*
872    }
873    
874    
875  check_HAVE_STAT()  {  check_HAVE_STAT()  {
876      get_fortran_c_namemangling      get_fortran_c_namemangling
877      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
# Line 698  void FC_NAMEMANGLE(tfsize) ( int *nbyte Line 895  void FC_NAMEMANGLE(tfsize) ( int *nbyte
895  EOF  EOF
896      make genmake_tc_1.o >> genmake_tc.log 2>&1      make genmake_tc_1.o >> genmake_tc.log 2>&1
897      RET_C=$?      RET_C=$?
898      cat <<EOF > genmake_tc_2.f      cat <<EOF > genmake_tc_2.$FS
899        program hello        program hello
900        integer nbyte        integer nbyte
901        call tfsize(nbyte)        call tfsize(nbyte)
902        print *," HELLO WORLD", nbyte        print *," HELLO WORLD", nbyte
903        end program hello        end
904  EOF  EOF
905      $FC $FFLAGS -o genmake_tc genmake_tc_2.f genmake_tc_1.o >> genmake_tc.log 2>&1      echo >> genmake_warnings
906      RET_F=$?      echo "running: check_HAVE_STAT()" >> genmake_warnings
907      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1      cat genmake_tc_2.$FS >> genmake_warnings
908        COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
909        echo $COMM >> genmake_warnings
910        $COMM >> genmake_tc.log 2>&1
911      RETVAL=$?      RETVAL=$?
912      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
913          HAVE_STAT=t          HAVE_STAT=t
# Line 721  check_netcdf_libs()  { Line 921  check_netcdf_libs()  {
921      if test ! "x$SKIP_NETCDF_CHECK" = x ; then      if test ! "x$SKIP_NETCDF_CHECK" = x ; then
922          return          return
923      fi      fi
924      echo "" > genmake_tnc.log      echo >> genmake_warnings
925      cat <<EOF > genmake_tnc.for      echo "running: check_netcdf_libs()" >> genmake_warnings
926        cat <<EOF > genmake_tnc.F
927        program fgennc        program fgennc
928  #include "netcdf.inc"  #include "netcdf.inc"
929  EOF  EOF
930      if test ! "x$MPI" = x ; then      if test ! "x$MPI" = x ; then
931          echo '#include "mpif.h"' >> genmake_tnc.for          echo '#include "mpif.h"' >> genmake_tnc.F
932      fi      fi
933      cat <<EOF >> genmake_tnc.for      cat <<EOF >> genmake_tnc.F
934        integer iret, ncid, xid        integer iret, ncid, xid
935        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
936        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
# Line 739  EOF Line 940  EOF
940        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
941        end        end
942  EOF  EOF
943      echo "Executing:" > genmake_tnc.log      echo "===  genmake_tnc.F  ===" > genmake_tnc.log
944      echo "  $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f" \      cat genmake_tnc.F >> genmake_tnc.log
945          > genmake_tnc.log      echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
946      RET_CPP=f      RET_CPP=f
947      $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \      COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
948          &&  RET_CPP=t      echo "$COMM" >> genmake_tnc.log
949        $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
950      if test "x$RET_CPP" = xf ; then      if test "x$RET_CPP" = xf ; then
951          echo "  WARNING: CPP failed to pre-process the netcdf test." \          echo "  WARNING: CPP failed to pre-process the netcdf test." \
952              > genmake_tnc.log              >> genmake_tnc.log
953          echo "    Please check that \$INCLUDES is properly set." \          echo "    Please check that \$INCLUDES is properly set." \
954              > genmake_tnc.log              >> genmake_tnc.log
955      fi      fi
956      echo "Executing:" > genmake_tnc.log      echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
957      echo "  $FC $FFLAGS $FOPTIM -c genmake_tnc.f" > genmake_tnc.log      echo "  &&  $LINK -o genmake_tnc.o $LIBS" >> genmake_tnc.log
958      echo "  $LINK -o genmake_tnc.o $LIBS" > genmake_tnc.log      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
     $FC $FFLAGS $FOPTIM -c genmake_tnc.f >> genmake_tnc.log 2>&1  \  
959          &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1          &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
960      RET_COMPILE=$?      RET_COMPILE=$?
961        cat genmake_tnc.log >> genmake_warnings
962    
963      #EH3  Remove test program execution for machines that either disallow      #EH3  Remove test program execution for machines that either disallow
964      #EH3  execution or cannot support it (eg. cross-compilers)      #EH3  execution or cannot support it (eg. cross-compilers)
# Line 769  EOF Line 971  EOF
971          HAVE_NETCDF=t          HAVE_NETCDF=t
972      else      else
973          # try again with "-lnetcdf" added to the libs          # try again with "-lnetcdf" added to the libs
974          $CPP $DEFINES $INCLUDES genmake_tnc.for > genmake_tnc.f 2>/dev/null  \          echo "try again with added '-lnetcdf'" > genmake_tnc.log
975              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.f >> genmake_tnc.log 2>&1  \          echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
976            echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
977            echo " &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
978            cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
979                &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
980              &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1              &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
981          RET_COMPILE=$?          RET_COMPILE=$?
982            cat genmake_tnc.log >> genmake_warnings
983          if test "x$RET_COMPILE" = x0 ; then          if test "x$RET_COMPILE" = x0 ; then
984              LIBS="$LIBS -lnetcdf"              LIBS="$LIBS -lnetcdf"
985              HAVE_NETCDF=t              HAVE_NETCDF=t
         else  
             cat genmake_tnc.log >> genmake_warnings  
986          fi          fi
987      fi      fi
988      rm -f genmake_tnc*      rm -f genmake_tnc*
# Line 796  PLATFORM= Line 1001  PLATFORM=
1001  LN=  LN=
1002  S64=  S64=
1003  KPP=  KPP=
1004  FC=  #FC=
1005  #CC=gcc  #CC=gcc
1006  CPP=  #CPP=
1007  LINK=  LINK=
1008  DEFINES=  DEFINES=
1009  PACKAGES=  PACKAGES=
1010  ENABLE=  ENABLE=
1011  DISABLE=  DISABLE=
1012  MAKEFILE=  # MAKEFILE=
1013  #MAKEDEPEND=  # MAKEDEPEND=
1014  PDEPEND=  PDEPEND=
1015  DUMPSTATE=t  DUMPSTATE=t
1016  PDEFAULT=  PDEFAULT=
# Line 823  NOOPTFILES= Line 1028  NOOPTFILES=
1028  NOOPTFLAGS=  NOOPTFLAGS=
1029  MPI=  MPI=
1030  MPIPATH=  MPIPATH=
1031    TS=
1032    PAPIS=
1033    PCLS=
1034    FOOLAD=
1035    PAPI=
1036    PCL=
1037    HPMT=
1038    GSL=
1039    HAVE_TEST_L=
1040    
1041  # DEFINES checked by test compilation  # DEFINES checked by test compilation or command-line
1042  HAVE_SYSTEM=  HAVE_SYSTEM=
1043  HAVE_FDATE=  HAVE_FDATE=
1044  FC_NAMEMANGLE=  FC_NAMEMANGLE=
1045  HAVE_CLOC=  HAVE_CLOC=
1046    # HAVE_SETRLSTK=
1047  HAVE_STAT=  HAVE_STAT=
1048  HAVE_NETCDF=  HAVE_NETCDF=
1049  HAVE_ETIME=  HAVE_ETIME=
1050    IGNORE_TIME=
1051    
1052  MODS=  MODS=
1053  TOOLSDIR=  TOOLSDIR=
# Line 842  STANDARDDIRS="USE_THE_DEFAULT" Line 1058  STANDARDDIRS="USE_THE_DEFAULT"
1058  G2ARGS=  G2ARGS=
1059  BASH=  BASH=
1060  PWD=`pwd`  PWD=`pwd`
1061  MAKE=make  test "x$MAKE" = x  &&  MAKE=make
1062  AWK=awk  test "x$AWK" = x   &&  AWK=awk
1063    EMBED_SRC=
1064  THISHOST=`hostname`  THISHOST=`hostname`
1065  THISCWD=`pwd`  THISCWD=`pwd`
1066  THISDATE=`date`  THISDATE=`date`
# Line 877  TAMC_EXTRA= Line 1094  TAMC_EXTRA=
1094    
1095  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1096  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
1097  gm_s2="FC CPP IEEE MPI JAM DUMPSTATE STANDARDDIRS"  gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL MPI JAM DUMPSTATE STANDARDDIRS"
1098    
1099  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1100  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
# Line 1057  for ac_option in "$@" ; do Line 1274  for ac_option in "$@" ; do
1274          -noieee | --noieee)          -noieee | --noieee)
1275              IEEE= ;;              IEEE= ;;
1276    
1277            -ts | --ts)
1278                TS=true ;;
1279            -papis | --papis)
1280                PAPIS=true ;;
1281            -pcls | --pcls)
1282                PCLS=true ;;
1283            -foolad | --foolad)
1284                FOOLAD=true ;;
1285            -papi | --papi)
1286                PAPI=true ;;
1287            -pcl | --pcl)
1288                PCL=true ;;
1289            -hpmt | --hpmt)
1290                HPMT=true ;;
1291    
1292            -gsl | --gsl)
1293                GSL=true ;;
1294    
1295          -mpi | --mpi)          -mpi | --mpi)
1296              MPI=true ;;              MPI=true ;;
1297          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
# Line 1080  for ac_option in "$@" ; do Line 1315  for ac_option in "$@" ; do
1315              ac_prev=TAMC_EXTRA ;;              ac_prev=TAMC_EXTRA ;;
1316          -tamc_extra=* | --tamc_extra=*)          -tamc_extra=* | --tamc_extra=*)
1317              TAMC_EXTRA=$ac_optarg ;;              TAMC_EXTRA=$ac_optarg ;;
1318            
1319            -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1320                IGNORE_TIME="-DIGNORE_TIME" ;;
1321    
1322            -es | --es | -embed-source | --embed-source)
1323                EMBED_SRC=t ;;
1324    
1325          -*)          -*)
1326              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
# Line 1095  for ac_option in "$@" ; do Line 1336  for ac_option in "$@" ; do
1336            
1337  done  done
1338    
1339    
1340  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1341      echo      echo
1342      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
# Line 1136  fi Line 1378  fi
1378    
1379  #  Find the MITgcm ${THISVER}  #  Find the MITgcm ${THISVER}
1380  if test -f "${ROOTDIR}/doc/tag-index" ; then  if test -f "${ROOTDIR}/doc/tag-index" ; then
1381      THISVER=`grep checkpoint ${ROOTDIR}/doc/tag-index | head -1`      THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`
1382    fi
1383    
1384    if test "x$MAKEFILE" = x ; then
1385        MAKEFILE="Makefile"
1386  fi  fi
1387    
1388  echo "  getting OPTFILE information:  "  echo "  getting OPTFILE information:  "
# Line 1168  if test "x$OPTFILE" != xNONE ; then Line 1414  if test "x$OPTFILE" != xNONE ; then
1414      fi      fi
1415  fi  fi
1416    
 #  Check for broken systems that cannot correctly distinguish *.F and *.f files  
 # check_for_broken_Ff  
   
1417  echo "  getting AD_OPTFILE information:  "  echo "  getting AD_OPTFILE information:  "
1418  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1419      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" = x ; then
# Line 1198  if test "x${AD_OPTFILE}" != xNONE ; then Line 1441  if test "x${AD_OPTFILE}" != xNONE ; then
1441      fi      fi
1442  fi  fi
1443    
1444    #====================================================================
1445    #  Set default values if not set by the optfile
1446    #
1447  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
1448  #  either set defaults or complain and abort!  #  either set defaults or complain and abort!
1449  if test ! "x$BASH" = x ; then  if test ! "x$BASH" = x ; then
# Line 1274  Error: The command "ln -s" failed -- ple Line 1520  Error: The command "ln -s" failed -- ple
1520  EOF  EOF
1521      exit 1      exit 1
1522  fi  fi
1523    test -L genmake_tlink > /dev/null 2>&1
1524    RETVAL=$?
1525    if test "x$RETVAL" = x0 ; then
1526        HAVE_TEST_L=t
1527    fi
1528  rm -f genmake_test_ln genmake_tlink  rm -f genmake_test_ln genmake_tlink
1529    
1530  #  Check for broken *.F/*.f handling and fix if possible  #  Check for broken *.F/*.f handling and fix if possible
# Line 1284  if test ! "x$MPI" = x ; then Line 1535  if test ! "x$MPI" = x ; then
1535        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
1536  fi  fi
1537    
1538    if test ! "x$TS" = x ; then
1539          echo "  Turning on timing per timestep"
1540          if test ! "x$FOOLAD" = x ; then
1541                DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1542          else
1543                DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1544          fi
1545    fi
1546    if test ! "x$PAPIS" = x ; then
1547          echo "  Turning on PAPI flop summary per timestep"
1548          echo "  Please make sure PAPIINC, PAPILIB are defined"
1549          if test ! "x$FOOLAD" = x ; then
1550                DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
1551          else
1552                DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
1553          fi
1554          INCLUDES="$INCLUDES $PAPIINC"
1555          LIBS="$LIBS $PAPILIB"
1556    fi
1557    if test ! "x$PCLS" = x ; then
1558          echo "  Turning on PCL counter summary per timestep"
1559          echo "  Please make sure PCLINC, PCLLIB are defined"
1560          if test ! "x$FOOLAD" = x ; then
1561                DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
1562          else
1563                DEFINES="$DEFINES -DUSE_PCL_FLOPS"
1564          fi
1565          INCLUDES="$INCLUDES $PCLINC"
1566          LIBS="$LIBS $PCLLIB"
1567    fi
1568    if test ! "x$PAPI" = x ; then
1569          if test ! "x$PAPIS" = x ; then
1570              echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
1571              echo "  Sticking with PAPI flop summary per timestep!"
1572          else
1573              echo "  Turning on performance analysis with PAPI"
1574              echo "  Please make sure PAPIINC, PAPILIB are defined"
1575              DEFINES="$DEFINES -DUSE_PAPI"
1576              INCLUDES="$INCLUDES $PAPIINC"
1577              LIBS="$LIBS $PAPILIB"
1578          fi
1579    fi
1580    if test ! "x$PCL" = x ; then
1581          if test ! "x$PCLS" = x ; then
1582              echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
1583              echo "  Sticking with PCL flop summary per timestep!"
1584          else
1585              echo "  Turning on performance analysis with PCL"
1586              echo "  Please make sure PCLINC, PCLLIB are defined"
1587              DEFINES="$DEFINES -DUSE_PCL"
1588              INCLUDES="$INCLUDES $PCLINC"
1589              LIBS="$LIBS $PCLLIB"
1590          fi
1591    fi
1592    if test ! "x$HPMT" = x ; then
1593          if test ! "x$PAPI" = x ; then
1594              echo "  PAPI and the HPM Toolkit cannot co-exist!"
1595              echo "  Sticking with PAPI!"
1596          else if test ! "x$PCL" = x ; then
1597              echo "  PCL and the HPM Toolkit cannot co-exist!"
1598              echo "  Sticking with PCL!"
1599          else
1600              echo "  Turning on performance analysis with the HPM Toolkit"
1601              echo "  Please make sure HPMTINC, HPMTLIB are defined"
1602              DEFINES="$DEFINES -DUSE_LIBHPM"
1603              INCLUDES="$INCLUDES $HPMTINC"
1604              LIBS="$LIBS $HPMTLIB"
1605          fi
1606          fi
1607    fi
1608    if test ! "x$GSL" = x ; then
1609          echo "  Turning on use of GSL to control floating point calculations"
1610          echo "  Please make sure GSLINC, GSLLIB are defined"
1611          DEFINES="$DEFINES -DUSE_GSL_IEEE"
1612          INCLUDES="$INCLUDES $GSLINC"
1613          LIBS="$LIBS $GSLLIB"
1614    fi
1615    
1616  printf "\n===  Checking system libraries  ===\n"  printf "\n===  Checking system libraries  ===\n"
1617  printf "  Do we have the system() command using $FC...  "  printf "  Do we have the system() command using $FC...  "
1618  cat > genmake_tcomp.f <<EOF  cat > genmake_tcomp.$FS <<EOF
1619        program hello        program hello
1620        call system('echo hi')        call system('echo hi')
1621        end        end
1622  EOF  EOF
1623  $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1  $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
1624  RETVAL=$?  RETVAL=$?
1625  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1626      HAVE_SYSTEM=t      HAVE_SYSTEM=t
# Line 1304  fi Line 1633  fi
1633  rm -f genmake_tcomp*  rm -f genmake_tcomp*
1634    
1635  printf "  Do we have the fdate() command using $FC...  "  printf "  Do we have the fdate() command using $FC...  "
1636  cat > genmake_tcomp.f <<EOF  cat > genmake_tcomp.$FS <<EOF
1637        program hello        program hello
1638        CHARACTER(128) string        CHARACTER*(128) string
1639        string = ' '        string = ' '
1640        call fdate( string )        call fdate( string )
1641        print *, string        print *, string
1642        end        end
1643  EOF  EOF
1644  $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1  $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
1645  RETVAL=$?  RETVAL=$?
1646  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1647      HAVE_FDATE=t      HAVE_FDATE=t
# Line 1325  fi Line 1654  fi
1654  rm -f genmake_tcomp*  rm -f genmake_tcomp*
1655    
1656  printf "  Do we have the etime() command using $FC...  "  printf "  Do we have the etime() command using $FC...  "
1657  cat > genmake_tcomp.f <<EOF  cat > genmake_tcomp.$FS <<EOF
1658        program hello        program hello
1659        REAL*4 ACTUAL, TARRAY(2)        REAL*4 ACTUAL, TARRAY(2)
1660        EXTERNAL ETIME        EXTERNAL ETIME
# Line 1334  cat > genmake_tcomp.f <<EOF Line 1663  cat > genmake_tcomp.f <<EOF
1663        print *, tarray        print *, tarray
1664        end        end
1665  EOF  EOF
1666  $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1  $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
1667  RETVAL=$?  RETVAL=$?
1668  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1669      HAVE_ETIME=t      HAVE_ETIME=t
# Line 1352  if test "x$HAVE_CLOC" != x ; then Line 1681  if test "x$HAVE_CLOC" != x ; then
1681      echo "yes"      echo "yes"
1682  else  else
1683      echo "no"      echo "no"
1684        if test "x$EMBED_SRC" = xt ; then
1685            echo "    WARNING: you requested file embedding but it has"
1686            echo "      been disabled since C code cannot be called"
1687            EMBED_SRC=
1688        fi
1689    fi
1690    rm -f genmake_t*
1691    
1692    printf "  Can we unlimit the stack size using $FC...  "
1693    check_HAVE_SETRLSTK
1694    if test "x$HAVE_SETRLSTK" = xt ; then
1695        echo "yes"
1696    else
1697        echo "no"
1698    fi
1699    rm -f genmake_t*
1700    
1701    printf "  Can we register a signal handler using $FC...  "
1702    check_HAVE_SIGREG
1703    if test "x$HAVE_SIGREG" = xt ; then
1704        echo "yes"
1705    else
1706        echo "no"
1707  fi  fi
1708  rm -f genmake_t*  rm -f genmake_t*
1709    
# Line 1371  if test "x$HAVE_NETCDF" != x ; then Line 1723  if test "x$HAVE_NETCDF" != x ; then
1723  else  else
1724      echo "no"      echo "no"
1725  fi  fi
1726    DEFINES="$DEFINES $IGNORE_TIME"
1727    
1728    if test "x$EMBED_SRC" = xt ; then
1729        build_embed_encode
1730    fi
1731    if test "x$EMBED_SRC" = xt ; then
1732        ENABLE="$ENABLE embed_files"
1733    fi
1734    
1735    
1736  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
# Line 1388  for d in $MODS ; do Line 1748  for d in $MODS ; do
1748  done  done
1749  echo  echo
1750    
 if test "x$MAKEFILE" = x ; then  
     MAKEFILE="Makefile"  
 fi  
1751  if test "x${PLATFORM}" = x ; then  if test "x${PLATFORM}" = x ; then
1752      PLATFORM=$p_PLATFORM      PLATFORM=$p_PLATFORM
1753  fi  fi
# Line 1722  for n in $names ; do Line 2079  for n in $names ; do
2079              fi              fi
2080          done          done
2081          if test "x$has_pack" = xf ; then          if test "x$has_pack" = xf ; then
2082              undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2083              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
2084          fi          fi
2085      fi      fi
2086  done  done
2087  ENABLED_PACKAGES=  ENABLED_PACKAGES=
2088  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2089      def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`      def=`echo "ALLOW_$i" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2090      ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"      ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"
2091  #eh3 DEFINES="$DEFINES -D$def"  #eh3 DEFINES="$DEFINES -D$def"
2092    
# Line 1813  for i in $SOURCEDIRS ; do Line 2170  for i in $SOURCEDIRS ; do
2170          cat $i/$j >> ad_files          cat $i/$j >> ad_files
2171      done      done
2172  done  done
2173    if test ! "x"$FS = "x.f" ; then
2174        cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f
2175        mv -f ad_files_f ad_files
2176    fi
2177    
2178  echo  echo
2179  echo "===  Creating the Makefile  ==="  echo "===  Creating the Makefile  ==="
# Line 1824  for i in $INCLUDEDIRS ; do Line 2184  for i in $INCLUDEDIRS ; do
2184      fi      fi
2185  done  done
2186    
2187    if test ! "x$DIVA" = x ; then
2188        echo "  Creating the pseudo-MPI include directory"
2189        INCLUDES="-I./mpi_headers $INCLUDES"
2190        rm -rf ./mpi_headers
2191        mkdir -p ./mpi_headers
2192    
2193        if test "x$MPIINCLUDEDIR" = x ; then
2194            if test "x$MPIHOME" = x ; then
2195                MPIHOME='/usr'
2196            fi
2197            MPIINCLUDEDIR='$MPIHOME/include'
2198        fi
2199        
2200        if test -r $MPIINCLUDEDIR/mpif.h ; then
2201            for i in $MPI_HEADER_FILES; do
2202                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
2203            done
2204    
2205            perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
2206        else
2207            echo " We cannot create a copy of mpif.h!"
2208            exit -1
2209        fi
2210    fi
2211    
2212  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2213  rm -rf .links.tmp  rm -rf .links.tmp
2214  mkdir .links.tmp  mkdir .links.tmp
2215    touch .links.tmp/foo
2216    if test ! -r ".links.tmp/foo" ; then
2217        echo
2218        echo "ERROR : something is wrong with your directory permissions or"
2219        echo "   your user file-creation mask (\"umask\") since creating a"
2220        echo "   sub-dir, touch-ing a file within it, and then reading it is"
2221        echo "   not working.  Please try setting your umask to something"
2222        echo "   sane such as:"
2223        echo
2224        echo "      umask 0002"
2225        echo
2226        echo "   and please verify that you have the proper permissions for"
2227        echo "   creating sub-directories and then reading files created"
2228        echo "   within them."
2229        echo
2230        exit 1
2231    fi
2232    rm -f .links.tmp/foo
2233  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > srclinks.tmp
2234  echo "" >> srclinks.tmp  echo "" >> srclinks.tmp
2235  printf 'SRCFILES = '    > srclist.inc  printf 'SRCFILES = '    > srclist.inc
# Line 1842  for d in $alldirs ; do Line 2245  for d in $alldirs ; do
2245      for sf in $sfiles ; do      for sf in $sfiles ; do
2246          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2247              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2248                    ignore_f=f
2249                  case $d/$sf in                  case $d/$sf in
2250                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2251                            ignore_f=t
2252                          ;;                          ;;
2253                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2254                            ignore_f=t
2255                          ;;                          ;;
2256                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2257                            ignore_f=t
2258                          ;;                          ;;
2259                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2260                            ignore_f=t
2261                            ;;
2262                      ./EMBEDDED_FILES.h)
2263                            ignore_f=t
2264                          ;;                          ;;
2265                    *)                    *)
2266                          touch .links.tmp/$sf                          #  For the local directory *ONLY*,
2267                          deplist="$deplist $sf"                          #  ignore all soft-links
2268                            if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
2269                                ignore_f=t
2270                            else
2271                                touch .links.tmp/$sf
2272                                deplist="$deplist $sf"
2273                            fi
2274                          ;;                          ;;
2275                  esac                  esac
2276                  extn=`echo $sf | $AWK -F '.' '{print $NF}'`                  if test "x$ignore_f" = xf ; then
2277                  case $extn in                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2278                      F)                      case $extn in
2279                          echo    " \\"  >> srclist.inc                          F)
2280                          printf " $sf" >> srclist.inc                              echo    " \\"  >> srclist.inc
2281                          ;;                              printf " $sf" >> srclist.inc
2282                      F90)                              ;;
2283                          echo    " \\"  >> f90srclist.inc                          F90)
2284                          printf " $sf" >> f90srclist.inc                              echo    " \\"  >> f90srclist.inc
2285                          ;;                              printf " $sf" >> f90srclist.inc
2286                      c)                              ;;
2287                          echo    " \\"  >> csrclist.inc                          c)
2288                          printf " $sf" >> csrclist.inc                              echo    " \\"  >> csrclist.inc
2289                          ;;                              printf " $sf" >> csrclist.inc
2290                      h)                              ;;
2291                          echo    " \\"  >> hlist.inc                          h)
2292                          printf " $sf" >> hlist.inc                              echo    " \\"  >> hlist.inc
2293                          ;;                              printf " $sf" >> hlist.inc
2294                      flow)                              ;;
2295                          echo    " \\"  >> ad_flow_files.inc                          flow)
2296                          printf " $sf" >> ad_flow_files.inc                              echo    " \\"  >> ad_flow_files.inc
2297                          ;;                              printf " $sf" >> ad_flow_files.inc
2298                  esac                              ;;
2299                        esac
2300                    fi
2301              fi              fi
2302          fi          fi
2303      done      done
# Line 1954  DISABLED_PACKAGES = ${DISABLED_PACKAGES} Line 2373  DISABLED_PACKAGES = ${DISABLED_PACKAGES}
2373    
2374  # These files are created by Makefile  # These files are created by Makefile
2375  SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h  SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h
   
2376  EOF  EOF
2377    
2378  #  Note: figure out some way to add Hyades JAM libraries here  if test "x$EMBED_SRC" = xt ; then
2379        echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
2380    else
2381        echo "EMBEDDED_FILES = " >>$MAKEFILE
2382    fi
2383    
2384    #  Note: figure out some way to add Hyades JAM libraries here
2385  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2386  # Unix ln (link)  # Unix ln (link)
2387  LN = ${LN}  LN = ${LN}
# Line 2009  cat hlist.inc         >> $MAKEFILE Line 2432  cat hlist.inc         >> $MAKEFILE
2432  cat ad_flow_files.inc >> $MAKEFILE  cat ad_flow_files.inc >> $MAKEFILE
2433  echo >> $MAKEFILE  echo >> $MAKEFILE
2434  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE
2435  echo 'F90FILES =  $(F90SRCFILES:.F=.'$FS90')' >> $MAKEFILE  echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE
2436  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
2437  echo >> $MAKEFILE  echo >> $MAKEFILE
2438  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
# Line 2020  rm -f ad_flow_files.inc Line 2443  rm -f ad_flow_files.inc
2443  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2444    
2445  all: \$(EXECUTABLE)  all: \$(EXECUTABLE)
2446  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2447          @echo Creating \$@ ...          @echo Creating \$@ ...
2448          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2449  depend:  depend:
# Line 2029  depend: Line 2452  depend:
2452          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2453          -rm -f makedepend.out          -rm -f makedepend.out
2454    
2455    lib: libmitgcmuv.a
2456    
2457    libmitgcmuv.a: \$(OBJFILES)
2458            ar rcv libmitgcmuv.a \$(OBJFILES)
2459    
2460  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
2461    
2462  small_f: \$(F77FILES) \$(F90FILES)  small_f: \$(F77FILES) \$(F90FILES)
# Line 2049  CLEAN: Line 2477  CLEAN:
2477          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2478          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2479          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2480          -rm -f \$(EXECUTABLE) output.txt STD*          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
2481            -rm -rf mnc_test_*
2482    
2483  #eh3 Makefile: makefile  #eh3 Makefile: makefile
2484  makefile:  makefile:
# Line 2077  test ! "x$THISUSER" = x && echo "      -echo Line 2506  test ! "x$THISUSER" = x && echo "      -echo
2506  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
2507  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
2508    
2509    if test "x$EMBED_SRC" = xt ; then
2510        cat >>$MAKEFILE <<EOF
2511    
2512    decode_files.o : EMBEDDED_FILES.h
2513    
2514    ##  \$(F77FILES)
2515    all_fF.tar.gz : \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile
2516            @echo Creating \$@ ...
2517            -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(F77FILES) Makefile
2518            -rm -f all_fF.tar.gz
2519            -gzip all_fF.tar
2520    
2521    EMBEDDED_FILES.h : all_fF.tar.gz
2522            @echo Creating \$@ ...
2523            -\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
2524    
2525    EOF
2526    fi
2527    
2528  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2529    
2530  # The normal chain of rules is (  .F - .$FS - .o  )  # The normal chain of rules is (  .F - .$FS - .o  )
# Line 2093  cat >>$MAKEFILE <<EOF Line 2541  cat >>$MAKEFILE <<EOF
2541  .$FS90.o:  .$FS90.o:
2542          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
2543  .c.o:  .c.o:
2544          \$(CC) \$(CFLAGS) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
2545    
2546  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
2547  .F.p:  .F.p:
# Line 2117  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF Line 2565  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF
2565  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
2566  for i in $ad_vars ; do  for i in $ad_vars ; do
2567      name=$i      name=$i
2568      t1="t2=\$"`echo $i`      t1="t2=\$"`echo "$i"`
2569      eval $t1      eval $t1
2570      printf "%-20s = " $name >> $MAKEFILE      printf "%-20s = " $name >> $MAKEFILE
2571      echo $t2 >> $MAKEFILE      echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
2572  done  done
2573    
2574  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
# Line 2137  rm -f ad_files Line 2585  rm -f ad_files
2585  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2586    
2587  # ... AD ...  # ... AD ...
2588  adall: ad_taf  adall: \$(EXE_AD)
2589  adtaf: ad_taf_output.f  adtaf: ad_taf_output.$FS
2590  adtamc: ad_tamc_output.f  adtamc: ad_tamc_output.$FS
2591    
2592  ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)  ad_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)
2593          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
2594          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
2595          -rm -f ad_config.template          -rm -f ad_config.template
2596          @make \$(F77FILES)          @make \$(F77FILES)
2597          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2598          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS
2599    
2600  ad_taf_output.f: ad_input_code.f  ad_taf_output.$FS: ad_input_code.$FS
2601          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2602          cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
2603    
2604  adtafonly:  adtafonly:
2605          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2606          cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
2607    
2608  ad_taf: ad_taf_output.o \$(OBJFILES)  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
2609          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
2610    
2611  ad_tamc_output.f: ad_input_code.f  ad_tamc_output.$FS: ad_input_code.$FS
2612          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
2613          cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.f          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
2614    
2615  ad_tamc: ad_tamc_output.o \$(OBJFILES)  ad_tamc: ad_tamc_output.o \$(OBJFILES)
2616          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
# Line 2175  adtrick: Line 2623  adtrick:
2623    
2624  # ... FTL ...  # ... FTL ...
2625  ftlall: ftl_taf  ftlall: ftl_taf
2626  ftltaf: ftl_taf_output.f  ftltaf: ftl_taf_output.$FS
2627  ftltamc: ftl_tamc_output.f  ftltamc: ftl_tamc_output.$FS
2628    
2629  ftl_input_code.f: \$(AD_FILES) \$(HEADERFILES)  ftl_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)
2630          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2631          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2632          -rm -f ftl_config.template          -rm -f ftl_config.template
2633          @make \$(F77FILES)          @make \$(F77FILES)
2634          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2635          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
2636    
2637  ftl_taf_output.f: ftl_input_code.f  ftl_taf_output.$FS: ftl_input_code.$FS
2638          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2639          cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2640    
2641  ftltafonly:  ftltafonly:
2642          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2643          cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2644    
2645  ftl_taf: ftl_taf_output.o \$(OBJFILES)  ftl_taf: ftl_taf_output.o \$(OBJFILES)
2646          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
2647    
2648  ftl_tamc_output.f: ftl_input_code.f  ftl_tamc_output.$FS: ftl_input_code.$FS
2649          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.f          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
2650          cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.f          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
2651    
2652  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
2653          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
2654    
2655    
2656  # ... SVD ...  # ... SVD ...
2657  svdtaf: ad_taf_output.f ftl_taf_output.f  svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
2658          @echo "--->>> Only ran TAF to generate SVD code!    <<<---"          @echo "--->>> Only ran TAF to generate SVD code!    <<<---"
2659          @echo "--->>> Do make svdall afterwards to compile. <<<---"          @echo "--->>> Do make svdall afterwards to compile. <<<---"
2660  svdall: svd_touch svd_taf  svdall: svd_touch svd_taf
# Line 2222  svd_touch: Line 2670  svd_touch:
2670          @echo "--->>> Only COMPILE svd code! <<<---"          @echo "--->>> Only COMPILE svd code! <<<---"
2671          @echo "--->>> Assumes you previously <<<---"          @echo "--->>> Assumes you previously <<<---"
2672          @echo "--->>> did make svdtaf        <<<---"          @echo "--->>> did make svdtaf        <<<---"
2673          touch ad_taf_output.f ftl_taf_output.f          touch ad_taf_output.$FS ftl_taf_output.$FS
2674          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.f          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
2675          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.f          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
2676          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2677          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2678          -rm -f ftl_config.template          -rm -f ftl_config.template

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