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revision 1.138 by edhill, Sun Dec 4 13:57:08 2005 UTC revision 1.179 by jmc, Fri Nov 21 16:15:00 2008 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" $file
50          return 1          exit 99
51      fi      fi
52      return 0      return 0
53  }  }
# Line 248  build_cyrus_makedepend()  { Line 256  build_cyrus_makedepend()  {
256      fi      fi
257  }  }
258    
259    
260    build_embed_encode()
261    {
262        printf "  building the embed-encode utility...  "
263        if test ! -e "$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 282  find_possible_configs()  { Line 325  find_possible_configs()  {
325    
326      #================================================================      #================================================================
327      #  look for possible C compilers      #  look for possible C compilers
328      tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"      tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
329      p_CC=      p_CC=
330      for c in $tmp ; do      for c in $tmp ; do
331          rm -f ./genmake_hello.c  ./genmake_hello          rm -f ./genmake_hello.c  ./genmake_hello
# Line 321  EOF Line 364  EOF
364    
365      #================================================================      #================================================================
366      #  look for possible FORTRAN compilers      #  look for possible FORTRAN compilers
367      tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95 gfortran"      tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"
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 535  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      -ts | --ts
588            Produce timing information per timestep            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        -devel | --devel
605              Add additional warning and debugging flags for development
606    
607      -mpi | --mpi      -mpi | --mpi
608            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
# Line 545  Usage: "$0" [OPTIONS] Line 611  Usage: "$0" [OPTIONS]
611            set to PATH. i.e. Include files from \$PATH/include, link to libraries            set to PATH. i.e. Include files from \$PATH/include, link to libraries
612            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
613    
614        -es | --es | -embed-source | --embed-source
615              Embed a tarball containing the full source code
616              (including the Makefile, etc.) used to build the
617              executable [off by default]
618    
619      -bash NAME      -bash NAME
620            Explicitly specify the Bourne or BASH shell to use            Explicitly specify the Bourne or BASH shell to use
621    
# Line 675  void FC_NAMEMANGLE(cloc) ( double *curti Line 746  void FC_NAMEMANGLE(cloc) ( double *curti
746   *curtim = *curtim/1.E6;   *curtim = *curtim/1.E6;
747  }  }
748  EOF  EOF
749      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
750        echo $COMM >> genmake_warnings
751        $COMM >> genmake_warnings 2>&1
752      RET_C=$?      RET_C=$?
753      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
754        program hello        program hello
# Line 685  EOF Line 758  EOF
758        print *," HELLO WORLD", wtime        print *," HELLO WORLD", wtime
759        end        end
760  EOF  EOF
761      $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
762        echo $COMM >> genmake_warnings
763        $COMM >> genmake_warnings 2>&1
764      RET_F=$?      RET_F=$?
765      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
766      RETVAL=$?      RETVAL=$?
# Line 698  EOF Line 773  EOF
773    
774    
775  check_HAVE_SIGREG()  {  check_HAVE_SIGREG()  {
776        if test ! "x$HAVE_SIGREG" = x ; then
777            return
778        fi
779      get_fortran_c_namemangling      get_fortran_c_namemangling
780      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
781  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 729  void FC_NAMEMANGLE(sigreg) (int * aip) Line 807  void FC_NAMEMANGLE(sigreg) (int * aip)
807      return;      return;
808  }  }
809  EOF  EOF
810      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
811        echo $COMM >> genmake_warnings
812        $COMM >> genmake_warnings 2>&1
813      RET_C=$?      RET_C=$?
814      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
815        program hello        program hello
# Line 755  EOF Line 835  EOF
835    
836    
837  check_HAVE_SETRLSTK()  {  check_HAVE_SETRLSTK()  {
838        if test "x$HAVE_SETRLSTK" = xt ; then
839            DEFINES="$DEFINES -DHAVE_SETRLSTK"
840            return
841        fi  
842        if test ! "x$HAVE_SETRLSTK" = x ; then
843            return
844        fi
845      get_fortran_c_namemangling      get_fortran_c_namemangling
846      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
847  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 770  void FC_NAMEMANGLE(setrlstk) () Line 857  void FC_NAMEMANGLE(setrlstk) ()
857      return;      return;
858  }  }
859  EOF  EOF
860      make genmake_tc_1.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
861        echo $COMM >> genmake_warnings
862        $COMM >> genmake_warnings 2>&1
863      RET_C=$?      RET_C=$?
864      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
865        program hello        program hello
# Line 814  void FC_NAMEMANGLE(tfsize) ( int *nbyte Line 903  void FC_NAMEMANGLE(tfsize) ( int *nbyte
903          *nbyte = -1;          *nbyte = -1;
904  }  }
905  EOF  EOF
906      make genmake_tc_1.o >> genmake_tc.log 2>&1      COMM="$CC $CFLAGS -c genmake_tc_1.c"
907        echo $COMM >> genmake_warnings
908        $COMM >> genmake_tc.log 2>&1
909      RET_C=$?      RET_C=$?
910      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
911        program hello        program hello
# Line 865  EOF Line 956  EOF
956      cat genmake_tnc.F >> genmake_tnc.log      cat genmake_tnc.F >> genmake_tnc.log
957      echo "===  genmake_tnc.F  ===" >> genmake_tnc.log      echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
958      RET_CPP=f      RET_CPP=f
959      COMM="$CPP $DEFINES $INCLUDES genmake_tnc.F"      COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
960      echo "$COMM" >> genmake_tnc.log      echo "$COMM" >> genmake_tnc.log
961      $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t      eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
962      if test "x$RET_CPP" = xf ; then      if test "x$RET_CPP" = xf ; then
963          echo "  WARNING: CPP failed to pre-process the netcdf test." \          echo "  WARNING: CPP failed to pre-process the netcdf test." \
964              >> genmake_tnc.log              >> genmake_tnc.log
# Line 875  EOF Line 966  EOF
966              >> genmake_tnc.log              >> genmake_tnc.log
967      fi      fi
968      echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log      echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
969      echo "  &&  $LINK -o genmake_tnc.o $LIBS" >> genmake_tnc.log      echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc.o $LIBS" >> genmake_tnc.log
970      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
971          &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1          &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
972      RET_COMPILE=$?      RET_COMPILE=$?
973      cat genmake_tnc.log >> genmake_warnings      cat genmake_tnc.log >> genmake_warnings
974    
# Line 893  EOF Line 984  EOF
984      else      else
985          # try again with "-lnetcdf" added to the libs          # try again with "-lnetcdf" added to the libs
986          echo "try again with added '-lnetcdf'" > genmake_tnc.log          echo "try again with added '-lnetcdf'" > genmake_tnc.log
987          echo "$CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS \ " >> genmake_tnc.log          echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
988          echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log          echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
989          echo " &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log          echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
990          $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS 2>/dev/null  \          cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
991              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
992              &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1              &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
993          RET_COMPILE=$?          RET_COMPILE=$?
994          cat genmake_tnc.log >> genmake_warnings          cat genmake_tnc.log >> genmake_warnings
995          if test "x$RET_COMPILE" = x0 ; then          if test "x$RET_COMPILE" = x0 ; then
996              LIBS="$LIBS -lnetcdf"              LIBS="$LIBS -lnetcdf"
997              HAVE_NETCDF=t              HAVE_NETCDF=t
998            else
999            # try again with "-lnetcdff" added to the libs
1000                echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
1001                echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
1002                echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
1003                echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
1004                cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
1005                    &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
1006                    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
1007                RET_COMPILE=$?
1008                cat genmake_tnc.log >> genmake_warnings
1009                if test "x$RET_COMPILE" = x0 ; then
1010                    LIBS="$LIBS -lnetcdff -lnetcdf"
1011                    HAVE_NETCDF=t
1012                fi
1013          fi          fi
1014      fi      fi
1015      rm -f genmake_tnc*      rm -f genmake_tnc*
# Line 939  OPTFILE= Line 1045  OPTFILE=
1045  INCLUDES="-I. $INCLUDES"  INCLUDES="-I. $INCLUDES"
1046  FFLAGS=  FFLAGS=
1047  FOPTIM=  FOPTIM=
1048    FEXTRAFLAGS=
1049  CFLAGS=  CFLAGS=
1050  KFLAGS1=  KFLAGS1=
1051  KFLAGS2=  KFLAGS2=
# Line 950  NOOPTFLAGS= Line 1057  NOOPTFLAGS=
1057  MPI=  MPI=
1058  MPIPATH=  MPIPATH=
1059  TS=  TS=
1060    PAPIS=
1061    PCLS=
1062    FOOLAD=
1063    PAPI=
1064    PCL=
1065    HPMT=
1066    GSL=
1067    DEVEL=
1068  HAVE_TEST_L=  HAVE_TEST_L=
1069    
1070  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
# Line 957  HAVE_SYSTEM= Line 1072  HAVE_SYSTEM=
1072  HAVE_FDATE=  HAVE_FDATE=
1073  FC_NAMEMANGLE=  FC_NAMEMANGLE=
1074  HAVE_CLOC=  HAVE_CLOC=
1075  HAVE_SETRLSTK=  # HAVE_SETRLSTK=
1076  HAVE_STAT=  HAVE_STAT=
1077  HAVE_NETCDF=  HAVE_NETCDF=
1078  HAVE_ETIME=  HAVE_ETIME=
# Line 974  BASH= Line 1089  BASH=
1089  PWD=`pwd`  PWD=`pwd`
1090  test "x$MAKE" = x  &&  MAKE=make  test "x$MAKE" = x  &&  MAKE=make
1091  test "x$AWK" = x   &&  AWK=awk  test "x$AWK" = x   &&  AWK=awk
1092    EMBED_SRC=
1093  THISHOST=`hostname`  THISHOST=`hostname`
1094  THISCWD=`pwd`  THISCWD=`pwd`
1095  THISDATE=`date`  THISDATE=`date`
# Line 1007  TAMC_EXTRA= Line 1123  TAMC_EXTRA=
1123    
1124  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1125  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
1126  gm_s2="FC CPP IEEE TS MPI JAM DUMPSTATE STANDARDDIRS"  gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"
1127    
1128  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1129  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 FEXTRAFLAGS"
1130  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
1131  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
1132  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
# Line 1037  EOF Line 1153  EOF
1153    
1154  echo "===  Processing options files and arguments  ==="  echo "===  Processing options files and arguments  ==="
1155  gm_local="genmake_local"  gm_local="genmake_local"
 for i in . $MODS ; do  
     if test -r $i/$gm_local ; then  
         . $i/$gm_local  
         break  
     fi  
 done  
1156  printf "  getting local config information:  "  printf "  getting local config information:  "
1157  if test -f $gm_local ; then  if test -f $gm_local ; then
1158      echo "using $gm_local"      echo "using $gm_local"
# Line 1189  for ac_option in "$@" ; do Line 1299  for ac_option in "$@" ; do
1299    
1300          -ts | --ts)          -ts | --ts)
1301              TS=true ;;              TS=true ;;
1302            -papis | --papis)
1303                PAPIS=true ;;
1304            -pcls | --pcls)
1305                PCLS=true ;;
1306            -foolad | --foolad)
1307                FOOLAD=true ;;
1308            -papi | --papi)
1309                PAPI=true ;;
1310            -pcl | --pcl)
1311                PCL=true ;;
1312            -hpmt | --hpmt)
1313                HPMT=true ;;
1314    
1315            -gsl | --gsl)
1316                GSL=true ;;
1317    
1318            -devel | --devel)
1319                DEVEL=true ;;
1320    
1321          -mpi | --mpi)          -mpi | --mpi)
1322              MPI=true ;;              MPI=true ;;
# Line 1217  for ac_option in "$@" ; do Line 1345  for ac_option in "$@" ; do
1345          -ignoretime | -ignore_time | --ignoretime | --ignore_time)          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1346              IGNORE_TIME="-DIGNORE_TIME" ;;              IGNORE_TIME="-DIGNORE_TIME" ;;
1347    
1348            -es | --es | -embed-source | --embed-source)
1349                EMBED_SRC=t ;;
1350    
1351          -*)          -*)
1352              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
1353              usage              usage
# Line 1235  done Line 1366  done
1366  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1367      echo      echo
1368      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
1369      echo "  file.  This file format is no longer supported.  Please see:"      echo "  file.  This file format is no longer supported.  For directions on"
1370      echo      echo "  how to setup and use the new \"genmake2\" script, please see:"
1371      echo "    http://mitgcm.org/devel_HOWTO/"      echo "    http://mitgcm.org/devel_HOWTO/"
1372      echo      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
1373      echo "  for directions on how to setup and use the new \"genmake2\" input"      echo "WARNING: ignore \"./.genmakerc\" and continue."
     echo "  files and send an email to MITgcm-support@mitgcm.org if you want help."  
1374      echo      echo
1375  fi  fi
1376    
1377  #  Find the MITgcm ${ROOTDIR}  #  Find the MITgcm ${ROOTDIR}
1378  if test "x${ROOTDIR}" = x ; then  if test "x${ROOTDIR}" = x ; then
1379      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
1380      if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then      if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
1381          ROOTDIR=".."          ROOTDIR=".."
1382      else      else
1383          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
# Line 1272  if test ! -d ${ROOTDIR} ; then Line 1402  if test ! -d ${ROOTDIR} ; then
1402  fi  fi
1403    
1404  #  Find the MITgcm ${THISVER}  #  Find the MITgcm ${THISVER}
1405  if test -f "${ROOTDIR}/doc/tag-index" ; then  version_file="${ROOTDIR}/doc/tag-index"
1406      THISVER=`grep '^checkpoint' ${ROOTDIR}/doc/tag-index | head -1`  if test -f $version_file ; then
1407        THISVER=`grep '^checkpoint' $version_file | head -1`
1408    #-  remove ./BUILD_INFO.h file if older than version_file
1409        if test -f ./BUILD_INFO.h -a ./BUILD_INFO.h -ot $version_file ; then
1410            echo "  remove ./BUILD_INFO.h (older than ${version_file})"
1411            rm -f ./BUILD_INFO.h
1412        fi
1413  fi  fi
1414    
1415  if test "x$MAKEFILE" = x ; then  if test "x$MAKEFILE" = x ; then
# Line 1432  fi Line 1568  fi
1568    
1569  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1570        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1571        DEFINES="$DEFINES -DTIME_PER_TIMESTEP"        if test ! "x$FOOLAD" = x ; then
1572                DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1573          else
1574                DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1575          fi
1576          PACKAGES="$PACKAGES showflops"
1577    fi
1578    if test ! "x$PAPIS" = x ; then
1579          echo "  Turning on PAPI flop summary per timestep"
1580          echo "  Please make sure PAPIINC, PAPILIB are defined"
1581          if test ! "x$FOOLAD" = x ; then
1582                DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
1583          else
1584                DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
1585          fi
1586          INCLUDES="$INCLUDES $PAPIINC"
1587          LIBS="$LIBS $PAPILIB"
1588          PACKAGES="$PACKAGES showflops"
1589    fi
1590    if test ! "x$PCLS" = x ; then
1591          echo "  Turning on PCL counter summary per timestep"
1592          echo "  Please make sure PCLINC, PCLLIB are defined"
1593          if test ! "x$FOOLAD" = x ; then
1594                DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
1595          else
1596                DEFINES="$DEFINES -DUSE_PCL_FLOPS"
1597          fi
1598          INCLUDES="$INCLUDES $PCLINC"
1599          LIBS="$LIBS $PCLLIB"
1600          PACKAGES="$PACKAGES showflops"
1601    fi
1602    if test ! "x$PAPI" = x ; then
1603          if test ! "x$PAPIS" = x ; then
1604              echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
1605              echo "  Sticking with PAPI flop summary per timestep!"
1606          else
1607              echo "  Turning on performance analysis with PAPI"
1608              echo "  Please make sure PAPIINC, PAPILIB are defined"
1609              DEFINES="$DEFINES -DUSE_PAPI"
1610              INCLUDES="$INCLUDES $PAPIINC"
1611              LIBS="$LIBS $PAPILIB"
1612          fi
1613    fi
1614    if test ! "x$PCL" = x ; then
1615          if test ! "x$PCLS" = x ; then
1616              echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
1617              echo "  Sticking with PCL flop summary per timestep!"
1618          else
1619              echo "  Turning on performance analysis with PCL"
1620              echo "  Please make sure PCLINC, PCLLIB are defined"
1621              DEFINES="$DEFINES -DUSE_PCL"
1622              INCLUDES="$INCLUDES $PCLINC"
1623              LIBS="$LIBS $PCLLIB"
1624          fi
1625    fi
1626    if test ! "x$HPMT" = x ; then
1627          if test ! "x$PAPI" = x ; then
1628              echo "  PAPI and the HPM Toolkit cannot co-exist!"
1629              echo "  Sticking with PAPI!"
1630          else if test ! "x$PCL" = x ; then
1631              echo "  PCL and the HPM Toolkit cannot co-exist!"
1632              echo "  Sticking with PCL!"
1633          else
1634              echo "  Turning on performance analysis with the HPM Toolkit"
1635              echo "  Please make sure HPMTINC, HPMTLIB are defined"
1636              DEFINES="$DEFINES -DUSE_LIBHPM"
1637              INCLUDES="$INCLUDES $HPMTINC"
1638              LIBS="$LIBS $HPMTLIB"
1639          fi
1640          fi
1641    fi
1642    if test ! "x$GSL" = x ; then
1643          echo "  Turning on use of GSL to control floating point calculations"
1644          echo "  Please make sure GSLINC, GSLLIB are defined"
1645          DEFINES="$DEFINES -DUSE_GSL_IEEE"
1646          INCLUDES="$INCLUDES $GSLINC"
1647          LIBS="$LIBS $GSLLIB"
1648  fi  fi
1649    
1650  printf "\n===  Checking system libraries  ===\n"  printf "\n===  Checking system libraries  ===\n"
# Line 1503  if test "x$HAVE_CLOC" != x ; then Line 1715  if test "x$HAVE_CLOC" != x ; then
1715      echo "yes"      echo "yes"
1716  else  else
1717      echo "no"      echo "no"
1718        if test "x$EMBED_SRC" = xt ; then
1719            echo "    WARNING: you requested file embedding but it has"
1720            echo "      been disabled since C code cannot be called"
1721            EMBED_SRC=
1722        fi
1723  fi  fi
1724  rm -f genmake_t*  rm -f genmake_t*
1725    
1726  printf "  Can we unlimit the stack size using $FC...  "  printf "  Can we unlimit the stack size using $FC...  "
1727  check_HAVE_SETRLSTK  check_HAVE_SETRLSTK
1728  if test "x$HAVE_SETRLSTK" != x ; then  if test "x$HAVE_SETRLSTK" = xt ; then
1729      echo "yes"      echo "yes"
1730  else  else
1731      echo "no"      echo "no"
# Line 1517  rm -f genmake_t* Line 1734  rm -f genmake_t*
1734    
1735  printf "  Can we register a signal handler using $FC...  "  printf "  Can we register a signal handler using $FC...  "
1736  check_HAVE_SIGREG  check_HAVE_SIGREG
1737  if test "x$HAVE_SIGREG" != x ; then  if test "x$HAVE_SIGREG" = xt ; then
1738      echo "yes"      echo "yes"
1739  else  else
1740      echo "no"      echo "no"
# Line 1542  else Line 1759  else
1759  fi  fi
1760  DEFINES="$DEFINES $IGNORE_TIME"  DEFINES="$DEFINES $IGNORE_TIME"
1761    
1762    if test "x$EMBED_SRC" = xt ; then
1763        build_embed_encode
1764    fi
1765    if test "x$EMBED_SRC" = xt ; then
1766        ENABLE="$ENABLE embed_files"
1767    fi
1768    
1769    
1770  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
1771  printf "  Adding MODS directories:  "  printf "  Adding MODS directories:  "
1772  for d in $MODS ; do  for d in $MODS ; do
# Line 1627  if test -r $ROOTDIR"/eesupp/src/Makefile Line 1852  if test -r $ROOTDIR"/eesupp/src/Makefile
1852      fi      fi
1853  fi  fi
1854    
1855  #same for exch2  #same for pkg/exch2 and pkg/regrid
1856  if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then  for pdir in exch2 regrid ; do
1857      echo "  Making source files in exch2 from  templates"      if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
1858      ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1          echo "  Making source files in pkg/${pdir} from templates"
1859      RETVAL=$?          ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
1860      if test "x${RETVAL}" = x0 ; then          RETVAL=$?
1861          rm -f make_exch2.errors          if test "x${RETVAL}" = x0 ; then
1862      else              rm -f make_${pdir}.errors
1863          echo "Error: problem encountered while building source files in exch2:"          else
1864          cat make_exch2.errors 1>&2              echo "Error: problem encountered while building source files in pkg/${pdir}:"
1865          exit 1              cat make_${pdir}.errors 1>&2
1866                exit 1
1867            fi
1868      fi      fi
1869  fi  done
1870    
1871  printf "\n===  Determining package settings  ===\n"  printf "\n===  Determining package settings  ===\n"
1872  if  test "x${PDEPEND}" = x ; then  if  test "x${PDEPEND}" = x ; then
# Line 1750  done Line 1977  done
1977  rm -f ./.tmp_pack  rm -f ./.tmp_pack
1978  echo "    packages are:  $PACKAGES"  echo "    packages are:  $PACKAGES"
1979    
1980  #  Check availability of NetCDF and then either build the MNC template  #  Check for package MNC: if NetCDF is available, then build the MNC
1981  #  files or delete mnc from the list of available packages.  #  template files ; otherwise, delete mnc from the list of packages.
1982  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
1983  RETVAL=$?  RETVAL=$?
1984  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
# Line 1785  EOF Line 2012  EOF
2012      fi      fi
2013  fi  fi
2014    
2015    #  Check for package PROFILES: if NetCDF is not available,
2016    #  then delete profiles from the list of available packages.
2017    echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
2018    RETVAL=$?
2019    if test "x$RETVAL" = x0 ; then
2020        if test "x$HAVE_NETCDF" != xt ; then
2021            cat <<EOF
2022    
2023    *********************************************************************
2024    WARNING: the "profiles" package was enabled but tests failed to
2025      compile NetCDF applications.  Please check that:
2026    
2027      1) NetCDF is correctly installed for this compiler and
2028      2) the LIBS variable (within the "optfile") specifies the correct
2029           NetCDF library to link against.
2030    
2031      Due to this failure, the "profiles" package is now DISABLED.
2032    *********************************************************************
2033    
2034    EOF
2035            PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
2036            DISABLE="$DISABLE profiles"
2037        fi
2038    fi
2039    
2040  echo "  applying package dependency rules"  echo "  applying package dependency rules"
2041  ck=  ck=
2042  while test "x$ck" != xtt ; do  while test "x$ck" != xtt ; do
2043      i=0      i=0
2044      # rtot=${#PNAME[@]}      # rtot=${#PNAME[@]}
2045      rtot=$nname      rtot=$nname
2046      while test $i -lt $rtot ; do      while test $i -le $rtot ; do
2047    
2048          #  Is $pname in the current $PACKAGES list?          #  Is $pname in the current $PACKAGES list?
2049          #  pname=${PNAME[$i]}          #  pname=${PNAME[$i]}
# Line 1825  while test "x$ck" != xtt ; do Line 2077  while test "x$ck" != xtt ; do
2077    
2078          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2079          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
2080                #echo "   " $pname ": need to add :" $dname
2081              in_dis="f"              in_dis="f"
2082              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2083                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 1969  fi Line 2222  fi
2222    
2223  #  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
2224  #  compiler.  #  compiler.
2225  if test -f ./ad_files ; then  if test -f ./adSrcFiles.tmp ; then
2226      rm -f ./ad_files      rm -f ./adSrcFiles.tmp
2227  fi  fi
2228  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2229  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2230      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2231      for j in $list_files ; do      for j in $list_files ; do
2232          cat $i/$j >> ad_files          cat $i/$j >> adSrcFiles.tmp
2233      done      done
2234  done  done
2235  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2236      cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
2237      mv -f ad_files_f ad_files      mv -f adSrcFiles.tmp_f adSrcFiles.tmp
2238  fi  fi
2239    
2240  echo  echo
# Line 1993  for i in $INCLUDEDIRS ; do Line 2246  for i in $INCLUDEDIRS ; do
2246      fi      fi
2247  done  done
2248    
2249    if test ! "x$DIVA" = x ; then
2250        echo "  Creating the pseudo-MPI include directory"
2251        INCLUDES="-I./mpi_headers $INCLUDES"
2252        rm -rf ./mpi_headers
2253        mkdir -p ./mpi_headers
2254    
2255        if test "x$MPIINCLUDEDIR" = x ; then
2256            if test "x$MPIHOME" = x ; then
2257                MPIHOME='/usr'
2258            fi
2259            MPIINCLUDEDIR='$MPIHOME/include'
2260        fi
2261        
2262        if test -r $MPIINCLUDEDIR/mpif.h ; then
2263            for i in $MPI_HEADER_FILES; do
2264                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
2265            done
2266    
2267            perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
2268        else
2269            echo " We cannot create a copy of mpif.h!"
2270    #       exit -1
2271        fi
2272    fi
2273    
2274  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2275  rm -rf .links.tmp  rm -rf .links.tmp
2276  mkdir .links.tmp  mkdir .links.tmp
2277    touch .links.tmp/foo
2278    if test ! -r ".links.tmp/foo" ; then
2279        echo
2280        echo "ERROR : something is wrong with your directory permissions or"
2281        echo "   your user file-creation mask (\"umask\") since creating a"
2282        echo "   sub-dir, touch-ing a file within it, and then reading it is"
2283        echo "   not working.  Please try setting your umask to something"
2284        echo "   sane such as:"
2285        echo
2286        echo "      umask 0002"
2287        echo
2288        echo "   and please verify that you have the proper permissions for"
2289        echo "   creating sub-directories and then reading files created"
2290        echo "   within them."
2291        echo
2292        exit 1
2293    fi
2294    rm -f .links.tmp/foo
2295    
2296    if test "x$OPENAD" != x ; then
2297        OAD_DONT_COMPILE="/dev/null"
2298        OAD_DONT_TRANSFORM="/dev/null"
2299        OAD_KEEP_ORIGINAL="/dev/null"
2300        OAD_CB2M_FILES="/dev/null"
2301        echo "  looking for dontCompile file:  "
2302        for i in "." $MODS ; do
2303            if test -r $i"/dontCompile" ; then
2304                OAD_DONT_COMPILE=$i"/dontCompile"
2305                echo "     found $OAD_DONT_COMPILE"
2306                break
2307            fi
2308        done
2309        echo "  looking for dontTransform file:  "
2310        for i in "." $MODS ; do
2311            if test -r $i"/dontTransform" ; then
2312                OAD_DONT_TRANSFORM=$i"/dontTransform"
2313                echo "     found $OAD_DONT_TRANSFORM"
2314                break
2315            fi
2316        done
2317        echo "  looking for keepOriginal file:  "
2318        for i in "." $MODS ; do
2319            if test -r $i"/keepOriginal" ; then
2320                OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2321                echo "     found $OAD_KEEP_ORIGINAL"
2322                break
2323            fi
2324        done
2325        echo "  looking for cb2mFiles:  "
2326        for i in "." $MODS ; do
2327            if test -r $i"/cb2mFiles" ; then
2328                OAD_CB2M_FILES=$i"/cb2mFiles"
2329                echo "     found $OAD_CB2M_FILES"
2330                break
2331            fi
2332        done
2333        echo "   OpenAD exceptions:  "
2334    fi
2335    
2336  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > srclinks.tmp
2337  echo "" >> srclinks.tmp  echo "" >> srclinks.tmp
2338  printf 'SRCFILES = '    > srclist.inc  printf 'F77_SRC_FILES = ' > F77srclist.tmp
2339  printf 'CSRCFILES = '   > csrclist.inc  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
2340  printf 'F90SRCFILES = ' > f90srclist.inc  printf 'C_SRC_FILES = '   > csrclist.tmp
2341  printf 'HEADERFILES = ' > hlist.inc  printf 'F90_SRC_FILES = ' > F90srclist.tmp
2342  printf 'AD_FLOW_FILES = ' > ad_flow_files.inc  printf 'H_SRC_FILES = '   > hsrclist.tmp
2343    printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
2344  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2345  for d in $alldirs ; do  for d in $alldirs ; do
2346      deplist=      deplist=
2347      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2348      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
2349        if test "x$OPENAD" != x ; then
2350            sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2351        fi
2352      for sf in $sfiles ; do      for sf in $sfiles ; do
2353          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2354              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2355                  ignore_f=f                  ignore_f=f
2356                  case $d/$sf in                  case $d/$sf in
2357                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2358                            ignore_f=t
2359                          ;;                          ;;
2360                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2361                            ignore_f=t
2362                          ;;                          ;;
2363                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2364                            ignore_f=t
2365                          ;;                          ;;
2366                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2367                            ignore_f=t
2368                            ;;
2369                      ./EMBEDDED_FILES.h)
2370                            ignore_f=t
2371                          ;;                          ;;
2372                    *)                    *)
2373                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
# Line 2035  for d in $alldirs ; do Line 2383  for d in $alldirs ; do
2383                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2384                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2385                      case $extn in                      case $extn in
2386                          F)                        F)
2387                              echo    " \\"  >> srclist.inc                          echo    " \\"  >> F77srclist.tmp
2388                              printf " $sf" >> srclist.inc                          printf " $sf" >> F77srclist.tmp
2389                              ;;                          if test "x$OPENAD" != x ; then
2390                          F90)                              basename=${sf%%.F}
2391                              echo    " \\"  >> f90srclist.inc                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2392                              printf " $sf" >> f90srclist.inc                              if test -z "$isAD" ; then
2393                              ;;                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2394                          c)                                  if test -z "$toBeIgnored" ; then
2395                              echo    " \\"  >> csrclist.inc                                      echo    " \\"  >> nonADF77srclist.tmp
2396                              printf " $sf" >> csrclist.inc                                      printf " $sf" >> nonADF77srclist.tmp
2397                              ;;                                  else
2398                          h)                                      echo "    not to be compiled   :  $sf"
2399                              echo    " \\"  >> hlist.inc                                  fi
2400                              printf " $sf" >> hlist.inc                              else # file is initially listed as an AD file we want to exclude it
2401                              ;;                                   # or we want to retain the untransformed version
2402                          flow)                                  notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
2403                              echo    " \\"  >> ad_flow_files.inc                                  untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
2404                              printf " $sf" >> ad_flow_files.inc                                  if test -n "$notToBeTransformed"; then
2405                              ;;                                      echo "    not to be transformed:  $sf"
2406                      esac                                  fi
2407                  fi                                  if test -n "$untransformedVersionToBeKept" ; then
2408                                        echo "    original to be kept  :  $sf"
2409                                    fi    
2410                                    if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2411                                        echo    " \\"  >> nonADF77srclist.tmp
2412                                        printf " $sf" >> nonADF77srclist.tmp
2413                                    fi
2414                                fi
2415                            fi
2416                            ;;
2417                        F90)
2418                            echo    " \\"  >> F90srclist.tmp
2419                            printf " $sf" >> F90srclist.tmp
2420                            ;;
2421                        c)
2422                            echo    " \\"  >> csrclist.tmp
2423                            printf " $sf" >> csrclist.tmp
2424                            ;;
2425                        h)
2426                            echo    " \\"  >> hsrclist.tmp
2427                            printf " $sf" >> hsrclist.tmp
2428                            ;;
2429                        flow)
2430                            echo    " \\"  >> ad_flow_files.tmp
2431                            printf " $sf" >> ad_flow_files.tmp
2432                            ;;
2433                       esac
2434                    fi
2435              fi              fi
2436          fi          fi
2437      done      done
2438      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2439          echo "" >> srclinks.tmp        if test "$d" != "." ; then
2440            echo "" >> srclinks.tmp
2441          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> srclinks.tmp
2442          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> srclinks.tmp
2443          printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp  # We need to make sure that the link isn't already there.
2444    # This may happen when make thinks that a header file has to be "remade"
2445    # because a module it depends on has changed.  In this case we do nothing.
2446            printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
2447          fi
2448      fi      fi
2449  done  done
2450  rm -rf .links.tmp  rm -rf .links.tmp
2451  echo "" >> srclist.inc  echo "" >> F77srclist.tmp
2452  echo "" >> csrclist.inc  echo "" >> nonADF77srclist.tmp
2453  echo "" >> f90srclist.inc  echo "" >> csrclist.tmp
2454  echo "" >> hlist.inc  echo "" >> F90srclist.tmp
2455  echo "" >> ad_flow_files.inc  echo "" >> hsrclist.tmp
2456    echo "" >> ad_flow_files.tmp
2457    
2458  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
2459      mv -f $MAKEFILE "$MAKEFILE.bak"      mv -f $MAKEFILE "$MAKEFILE.bak"
# Line 2132  DISABLED_PACKAGES = ${DISABLED_PACKAGES} Line 2513  DISABLED_PACKAGES = ${DISABLED_PACKAGES}
2513    
2514  # These files are created by Makefile  # These files are created by Makefile
2515  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
   
2516  EOF  EOF
2517    
2518  #  Note: figure out some way to add Hyades JAM libraries here  if test "x$EMBED_SRC" = xt ; then
2519        echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
2520    else
2521        echo "EMBEDDED_FILES = " >>$MAKEFILE
2522    fi
2523    
2524    #  Note: figure out some way to add Hyades JAM libraries here
2525  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2526  # Unix ln (link)  # Unix ln (link)
2527  LN = ${LN}  LN = ${LN}
# Line 2163  INCLUDES = ${INCLUDES} Line 2548  INCLUDES = ${INCLUDES}
2548  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2549  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2550  # Optim./debug for FC  # Optim./debug for FC
2551  FFLAGS = ${FFLAGS}  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
2552  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM}
2553  # Optim./debug for FC  # Optim./debug for FC
2554  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2555  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
2556    F90FIXEDFORMAT = ${F90FIXEDFORMAT}
2557  # Flags for CC  # Flags for CC
2558  CFLAGS = ${CFLAGS}  CFLAGS = ${CFLAGS}
2559  # Files that should not be optimized  # Files that should not be optimized
# Line 2180  MAKEFILE=${MAKEFILE} Line 2566  MAKEFILE=${MAKEFILE}
2566    
2567  EOF  EOF
2568    
2569  cat srclist.inc       >> $MAKEFILE  cat F77srclist.tmp      >> $MAKEFILE
2570  cat csrclist.inc      >> $MAKEFILE  cat nonADF77srclist.tmp >> $MAKEFILE
2571  cat f90srclist.inc    >> $MAKEFILE  cat csrclist.tmp        >> $MAKEFILE
2572  cat hlist.inc         >> $MAKEFILE  cat F90srclist.tmp      >> $MAKEFILE
2573  cat ad_flow_files.inc >> $MAKEFILE  cat hsrclist.tmp        >> $MAKEFILE
2574    cat ad_flow_files.tmp   >> $MAKEFILE
2575    
2576    rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
2577    
2578  echo >> $MAKEFILE  echo >> $MAKEFILE
2579  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE  
2580  echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE  # add definitions for preprocessed sources
2581  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE  # and note that not all systems allow case sensitive extensions
2582    # hence the $FS and $FS90 here.
2583    # for fixed format f90 files we use ff90 or FF90 resp
2584    # but these are not expected to be the original source files
2585    
2586    echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2587    echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2588    echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
2589    echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2590  echo >> $MAKEFILE  echo >> $MAKEFILE
2591  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2592  echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc  
 rm -f ad_flow_files.inc  
2593    
2594  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2595    
2596  all: \$(EXECUTABLE)  all: \$(EXECUTABLE)
2597  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2598          @echo Creating \$@ ...          @echo Creating \$@ ...
2599          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2600  depend:  depend:
2601          @make links          @make links
2602          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2603          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2604          -rm -f makedepend.out          -rm -f makedepend.out
2605    
# Line 2211  lib: libmitgcmuv.a Line 2607  lib: libmitgcmuv.a
2607    
2608  libmitgcmuv.a: \$(OBJFILES)  libmitgcmuv.a: \$(OBJFILES)
2609          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
2610            ar d   libmitgcmuv.a main.o
2611    
2612  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
2613    
2614  small_f: \$(F77FILES) \$(F90FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2615    
2616  output.txt: \$(EXECUTABLE)  output.txt: \$(EXECUTABLE)
2617          @printf 'running ... '          @printf 'running ... '
2618          @\$(EXECUTABLE) > \$@          @\$(EXECUTABLE) > \$@
2619    
2620  clean:  clean:
2621          -rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
2622            -rm -rf *.o
2623            -rm -rf *.$FS *.flowdir
2624            -rm -rf *.f$FS90 *_mod.h *_mod.F90 *.FF90 *.mod-whirl ad_input*
2625            -rm -rf temp.sed
2626  Clean:  Clean:
2627          @make clean          @make clean
2628          @make cleanlinks          @make cleanlinks
2629          -rm -f \$(SPECIAL_FILES)          -rm -f \$(SPECIAL_FILES)
2630          -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak          -rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log f90mkdepend.log *.bak
2631            -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
2632  CLEAN:  CLEAN:
2633          @make Clean          @make Clean
2634          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2635          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2636          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2637          -rm -f \$(EXECUTABLE) output.txt STD*          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
2638            -rm -f *_MIT_CE_000.opt0000 costfunction*0000
2639            -rm -rf mnc_test_*
2640    
2641  #eh3 Makefile: makefile  #eh3 Makefile: makefile
2642  makefile:  makefile:
# Line 2240  makefile: Line 2644  makefile:
2644  cleanlinks:  cleanlinks:
2645          -find . -type l -exec rm {} \;          -find . -type l -exec rm {} \;
2646    
2647  # Special targets (SPECIAL_FILES) which are create by make  # Special targets (SPECIAL_FILES) which are created by make
2648  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
2649          @echo Creating \$@ ...          @echo Creating \$@ ...
2650          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
# Line 2260  test ! "x$THISUSER" = x && echo "      -echo Line 2664  test ! "x$THISUSER" = x && echo "      -echo
2664  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
2665  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
2666    
2667    if test "x$EMBED_SRC" = xt ; then
2668        cat >>$MAKEFILE <<EOF
2669    
2670    decode_files.o : EMBEDDED_FILES.h
2671    
2672    ##  \$(F77_PP_SRC_FILES)
2673    all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2674            @echo Creating \$@ ...
2675            -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2676            -rm -f all_fF.tar.gz
2677            -gzip all_fF.tar
2678    
2679    EMBEDDED_FILES.h : all_fF.tar.gz
2680            @echo Creating \$@ ...
2681            -\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
2682    
2683    EOF
2684    fi
2685    
2686  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2687    
2688  # The normal chain of rules is (  .F - .$FS - .o  )  # The normal chain of rules is (  .F - .$FS - .o  )
# Line 2273  cat >>$MAKEFILE <<EOF Line 2696  cat >>$MAKEFILE <<EOF
2696          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2697  .F90.$FS90:  .F90.$FS90:
2698          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2699    .FF90.f$FS90:
2700            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2701  .$FS90.o:  .$FS90.o:
2702          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
2703    .f$FS90.o:
2704            cp \$< \$(basename  \$<).f90
2705            \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
2706  .c.o:  .c.o:
2707          \$(CC) \$(CFLAGS) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
2708    .flow.flowdir:
2709            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2710    
2711  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
2712  .F.p:  .F.p:
# Line 2284  cat >>$MAKEFILE <<EOF Line 2714  cat >>$MAKEFILE <<EOF
2714  .p.$FS:  .p.$FS:
2715          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
2716    
2717    EOF
2718    
2719  #=========================================  #=========================================
2720  #===  Automatic Differentiation Rules  ===  #===  Automatic Differentiation Rules  ===
2721    #===  for TAMC/TAF  ======================
2722    
2723    if test "x$OPENAD" == x ; then
2724    
2725    cat >>$MAKEFILE <<EOF
2726    
2727  TAMC           = ${TAMC}  TAMC           = ${TAMC}
2728  TAF            = ${TAF}  TAF            = ${TAF}
# Line 2300  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF Line 2737  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF
2737  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
2738  for i in $ad_vars ; do  for i in $ad_vars ; do
2739      name=$i      name=$i
2740      t1="t2=\$"`echo $i`      t1="t2=\$"`echo "$i"`
2741      eval $t1      eval $t1
2742      printf "%-20s = " $name >> $MAKEFILE      printf "%-20s = " $name >> $MAKEFILE
2743      echo $t2 >> $MAKEFILE      echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
2744  done  done
2745    
2746  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
2747  echo >> $MAKEFILE  echo >> $MAKEFILE
2748  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
2749  AD_FILES=`cat ad_files`  AD_FILES=`cat adSrcFiles.tmp`
2750  for i in $AD_FILES ; do  for i in $AD_FILES ; do
2751      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
2752      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
2753  done  done
2754  echo >> $MAKEFILE  echo >> $MAKEFILE
2755  rm -f ad_files  rm -f adSrcFiles.tmp
2756    
2757  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2758    
2759  # ... AD ...  # ... AD ...
2760  adall: ad_taf  adall: \$(EXE_AD)
2761  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
2762  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
2763    
2764  ad_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2765          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
2766          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2767          -rm -f ad_config.template          -rm -f ad_config.template
2768          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2769          @make \$(AD_FLOW_FILES)          @make \$(FLOFILES)
2770          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS          cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
2771    
2772  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
2773          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2774            ls -l ad_input_code_ad.$FS
2775          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
2776    
2777  adtafonly:  adtafonly:
2778          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2779            ls -l ad_input_code_ad.$FS
2780          cat ad_input_code_ad.$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
2781    
2782  ad_taf: ad_taf_output.o \$(OBJFILES)  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
2783          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
2784    
2785  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
2786          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 2361  ftlall: ftl_taf Line 2800  ftlall: ftl_taf
2800  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
2801  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
2802    
2803  ftl_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2804          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2805          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2806          -rm -f ftl_config.template          -rm -f ftl_config.template
2807          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2808          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2809          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
2810    
2811  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
2812          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2813            ls -l ftl_input_code_ftl.$FS
2814          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2815    
2816  ftltafonly:  ftltafonly:
2817          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2818            ls -l ftl_input_code_ftl.$FS
2819          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2820    
2821  ftl_taf: ftl_taf_output.o \$(OBJFILES)  ftl_taf: ftl_taf_output.o \$(OBJFILES)
# Line 2412  svd_touch: Line 2853  svd_touch:
2853          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2854          -rm -f ftl_config.template          -rm -f ftl_config.template
2855    
2856  #=========================================  EOF
2857    
2858    fi
2859    
2860    #===  for OpenAD  ========================
2861    
2862    if test "x$OPENAD" != x ; then
2863    
2864    # ============ begin OpenAD specific section ==============
2865    
2866    cat >>$MAKEFILE <<EOF
2867    
2868    # all the source files linked from the various locations:
2869    ALL_LINKED_FILES= \
2870    \$(F77_SRC_FILES) \
2871    \$(C_SRC_FILES) \
2872    \$(H_SRC_FILES) \
2873    \$(F90_SRC_FILES) \
2874    \$(SPECIAL_FILES)
2875    
2876    ifndef OPENADROOT
2877      \$(error "Error:  environment variable OPENADROOT not defined!")
2878    endif
2879    
2880    ifndef XAIFSCHEMAROOT
2881      \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
2882    endif
2883    
2884    ifndef XAIFBOOSTERROOT
2885      \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
2886    endif
2887    
2888  EOF  EOF
2889    
2890    echo "  Add the source list for common block to module conversion "
2891    echo >> $MAKEFILE
2892    printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
2893    for i in `cat ${OAD_CB2M_FILES}` ; do
2894      echo    " \\" >> $MAKEFILE
2895      printf " $i" >> $MAKEFILE
2896    done
2897    echo >> $MAKEFILE
2898    
2899    echo "  Add the source list for AD code generation"
2900    echo >> $MAKEFILE
2901    printf "AD_FILES = " >> $MAKEFILE
2902    for i in `cat ${OAD_CB2M_FILES}` ; do
2903      echo    " \\" >> $MAKEFILE
2904      printf " ${i}_mod.f$FS90" >> $MAKEFILE
2905    done
2906    AD_FILES=`cat adSrcFiles.tmp`
2907    for i in $AD_FILES ; do
2908      basename=${i%%.f}
2909      toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
2910      if test -z "$toBeIgnored" ; then
2911        echo    " \\" >> $MAKEFILE
2912        printf " $i" >> $MAKEFILE
2913      fi
2914    done
2915    echo >> $MAKEFILE
2916    rm -f adSrcFiles.tmp
2917    
2918    cat >>$MAKEFILE <<EOF
2919    
2920    adAll: \$(EXE_AD)
2921    .PHONY: adAll
2922    
2923    CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
2924    
2925    .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
2926    
2927    .PHONY: adDepend
2928    adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
2929            \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2930            \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2931            -rm -f makedepend.out
2932    
2933    OPENAD_SUPPORT_F90_SRC_FILES = \
2934    w2f__types.F90 \
2935    OAD_active.F90 \
2936    OAD_cp.F90 \
2937    OAD_rev.F90 \
2938    OAD_tape.F90        
2939    
2940    OPENAD_SUPPORT_C_SRC_FILES = \
2941    iaddr.c \
2942    timeRatio.c
2943    
2944    f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
2945            cat \$^ > \$@
2946    
2947    f95_test.f90: all_mods.xb.x2w.w2f.pp.f$FS90 \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90) ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
2948            cat \$^ > \$@
2949    
2950    f95_test.out: f95_test_mods.f90 f95_test.f90
2951            f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
2952            f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
2953    
2954    AD_OBJ_FILES=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) all_mods.xb.x2w.w2f.pp.o  ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.o \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
2955    
2956    \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(AD_OBJ_FILES)
2957            @echo Creating \$@ ...
2958            \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES) \$(LIBS)
2959    
2960    # makefile debug rule
2961    openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
2962    .PHONY: openad
2963    
2964    # create the module files
2965    %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
2966            ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
2967    
2968    # create the header files
2969    %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
2970            ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
2971    
2972    # change everybody else to use the new module files:
2973    %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
2974            ../OAD_support/cb2mUseModules.bash $< ${MPI}
2975    
2976    # makefile debug rule
2977    small_f: \$(CB2M_F90_PP_SRC_FILES)
2978    .PHONY: small_f
2979    
2980    ad_output.txt: \$(EXE_AD)
2981            @printf 'linking data files ... '
2982            \$(LN) -f ../input_ad/data* ../input_ad/eedata .
2983            \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
2984            @printf 'running ... '
2985            @./\$(EXE_AD) > \$@
2986    
2987    CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
2988    ad_input_code.f$FS90: ../OAD_support/maxMinDefs.f \$(CB2M_AD_FILES)
2989            cat \$^ > \$@
2990    
2991    # strip all comments and blanks to reduce
2992    # the file size in order to reduce perl's memory requirements
2993    ad_input_code_sf.f$FS90 : ad_input_code.f$FS90
2994            cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
2995    
2996    # mfef90 preprocessing
2997    # expand statement functions
2998    # expose mfef90 specific substring handling
2999    # add the w2f__types module
3000    ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
3001            ./mfef90 -r8 -z -F -N132 \$<
3002            mv \$<.B \$(basename \$<).B
3003            ./whirl2f -openad \$(basename \$<).B
3004            cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
3005    
3006    # canonicalizer
3007    ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
3008            ./preProcess.py -H \$< -o \$@
3009    
3010    # F -> WHIRL
3011    # note that the canonicalized version cuts off at col 72
3012    # doing this also for string constants which is ok as long
3013    # as we are in fixed mode and cut of exactly there.
3014    # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
3015    # characters respectively.
3016    ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90
3017            ./mfef90 -r8 -z -F \$<
3018            mv \$<.B \$@
3019    
3020    # WHIRL -> XAIF
3021    ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif
3022            ./whirl2xaif -s -n --debug 1 -o \$@ \$<
3023    
3024    # XAIF -> XAIF'
3025    ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd openad_adm
3026            ./openad_adm -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3027    
3028    # XAIF' -> WHIRL'
3029    ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
3030            ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
3031    
3032    # WHIRL' -> F'
3033    ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
3034            ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
3035    
3036    # insert template directives
3037    ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
3038            ../OAD_support/insertTemplateDir.bash \$< \$@
3039    
3040    # postprocess F'
3041    ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl ../OAD_support/ad_inline.f \$(wildcard ../OAD_support/ad_template.*.f)
3042            perl multi-pp.pl -inline=../OAD_support/ad_inline.f \$<
3043            # the postprocessor still gets the name wrong
3044            cat \$<.pp | sed 's/RETURN//' > \$@
3045    
3046    # extract all transformed modules
3047    all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
3048            cat \$< | sed -n '/MODULE /,/END MODULE/p' > \$@
3049    
3050    # remove the transformed globals module from the
3051    # transformed ad_input_code file
3052    # and remove for now the duplicate variables
3053    # and fix 2 data statements
3054    ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
3055            cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' > \$@
3056    
3057    # setup some links
3058    %.xsd:
3059            \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3060    
3061    mfef90:
3062            \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
3063    
3064    # link the support files:
3065    \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
3066            \$(LN) ../OAD_support/\$@ .
3067    
3068    whirl2xaif xaif2whirl:
3069            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3070    
3071    %.pl:
3072            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3073    
3074    preProcess.py:
3075            \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
3076    
3077    whirl2f whirl2f_be:
3078            \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
3079    
3080    openad_adm:
3081            \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/test/t \$@
3082    
3083    # ============ end OpenAD specific section ==============
3084    
3085    EOF
3086    
3087    fi
3088    
3089    #=========================================
3090    
3091  if test "x$EXEHOOK" != x ; then  if test "x$EXEHOOK" != x ; then
3092      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
3093  fi  fi

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