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revision 1.138 by edhill, Sun Dec 4 13:57:08 2005 UTC revision 1.176 by jmc, Fri Nov 7 04:34:19 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$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
1381          ROOTDIR=".."          ROOTDIR=".."
1382      else      else
1383          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
# Line 1432  fi Line 1562  fi
1562    
1563  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1564        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1565        DEFINES="$DEFINES -DTIME_PER_TIMESTEP"        if test ! "x$FOOLAD" = x ; then
1566                DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1567          else
1568                DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1569          fi
1570          PACKAGES="$PACKAGES showflops"
1571    fi
1572    if test ! "x$PAPIS" = x ; then
1573          echo "  Turning on PAPI flop summary per timestep"
1574          echo "  Please make sure PAPIINC, PAPILIB are defined"
1575          if test ! "x$FOOLAD" = x ; then
1576                DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
1577          else
1578                DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
1579          fi
1580          INCLUDES="$INCLUDES $PAPIINC"
1581          LIBS="$LIBS $PAPILIB"
1582          PACKAGES="$PACKAGES showflops"
1583    fi
1584    if test ! "x$PCLS" = x ; then
1585          echo "  Turning on PCL counter summary per timestep"
1586          echo "  Please make sure PCLINC, PCLLIB are defined"
1587          if test ! "x$FOOLAD" = x ; then
1588                DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
1589          else
1590                DEFINES="$DEFINES -DUSE_PCL_FLOPS"
1591          fi
1592          INCLUDES="$INCLUDES $PCLINC"
1593          LIBS="$LIBS $PCLLIB"
1594          PACKAGES="$PACKAGES showflops"
1595    fi
1596    if test ! "x$PAPI" = x ; then
1597          if test ! "x$PAPIS" = x ; then
1598              echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
1599              echo "  Sticking with PAPI flop summary per timestep!"
1600          else
1601              echo "  Turning on performance analysis with PAPI"
1602              echo "  Please make sure PAPIINC, PAPILIB are defined"
1603              DEFINES="$DEFINES -DUSE_PAPI"
1604              INCLUDES="$INCLUDES $PAPIINC"
1605              LIBS="$LIBS $PAPILIB"
1606          fi
1607    fi
1608    if test ! "x$PCL" = x ; then
1609          if test ! "x$PCLS" = x ; then
1610              echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
1611              echo "  Sticking with PCL flop summary per timestep!"
1612          else
1613              echo "  Turning on performance analysis with PCL"
1614              echo "  Please make sure PCLINC, PCLLIB are defined"
1615              DEFINES="$DEFINES -DUSE_PCL"
1616              INCLUDES="$INCLUDES $PCLINC"
1617              LIBS="$LIBS $PCLLIB"
1618          fi
1619    fi
1620    if test ! "x$HPMT" = x ; then
1621          if test ! "x$PAPI" = x ; then
1622              echo "  PAPI and the HPM Toolkit cannot co-exist!"
1623              echo "  Sticking with PAPI!"
1624          else if test ! "x$PCL" = x ; then
1625              echo "  PCL and the HPM Toolkit cannot co-exist!"
1626              echo "  Sticking with PCL!"
1627          else
1628              echo "  Turning on performance analysis with the HPM Toolkit"
1629              echo "  Please make sure HPMTINC, HPMTLIB are defined"
1630              DEFINES="$DEFINES -DUSE_LIBHPM"
1631              INCLUDES="$INCLUDES $HPMTINC"
1632              LIBS="$LIBS $HPMTLIB"
1633          fi
1634          fi
1635    fi
1636    if test ! "x$GSL" = x ; then
1637          echo "  Turning on use of GSL to control floating point calculations"
1638          echo "  Please make sure GSLINC, GSLLIB are defined"
1639          DEFINES="$DEFINES -DUSE_GSL_IEEE"
1640          INCLUDES="$INCLUDES $GSLINC"
1641          LIBS="$LIBS $GSLLIB"
1642  fi  fi
1643    
1644  printf "\n===  Checking system libraries  ===\n"  printf "\n===  Checking system libraries  ===\n"
# Line 1503  if test "x$HAVE_CLOC" != x ; then Line 1709  if test "x$HAVE_CLOC" != x ; then
1709      echo "yes"      echo "yes"
1710  else  else
1711      echo "no"      echo "no"
1712        if test "x$EMBED_SRC" = xt ; then
1713            echo "    WARNING: you requested file embedding but it has"
1714            echo "      been disabled since C code cannot be called"
1715            EMBED_SRC=
1716        fi
1717  fi  fi
1718  rm -f genmake_t*  rm -f genmake_t*
1719    
1720  printf "  Can we unlimit the stack size using $FC...  "  printf "  Can we unlimit the stack size using $FC...  "
1721  check_HAVE_SETRLSTK  check_HAVE_SETRLSTK
1722  if test "x$HAVE_SETRLSTK" != x ; then  if test "x$HAVE_SETRLSTK" = xt ; then
1723      echo "yes"      echo "yes"
1724  else  else
1725      echo "no"      echo "no"
# Line 1517  rm -f genmake_t* Line 1728  rm -f genmake_t*
1728    
1729  printf "  Can we register a signal handler using $FC...  "  printf "  Can we register a signal handler using $FC...  "
1730  check_HAVE_SIGREG  check_HAVE_SIGREG
1731  if test "x$HAVE_SIGREG" != x ; then  if test "x$HAVE_SIGREG" = xt ; then
1732      echo "yes"      echo "yes"
1733  else  else
1734      echo "no"      echo "no"
# Line 1542  else Line 1753  else
1753  fi  fi
1754  DEFINES="$DEFINES $IGNORE_TIME"  DEFINES="$DEFINES $IGNORE_TIME"
1755    
1756    if test "x$EMBED_SRC" = xt ; then
1757        build_embed_encode
1758    fi
1759    if test "x$EMBED_SRC" = xt ; then
1760        ENABLE="$ENABLE embed_files"
1761    fi
1762    
1763    
1764  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
1765  printf "  Adding MODS directories:  "  printf "  Adding MODS directories:  "
1766  for d in $MODS ; do  for d in $MODS ; do
# Line 1627  if test -r $ROOTDIR"/eesupp/src/Makefile Line 1846  if test -r $ROOTDIR"/eesupp/src/Makefile
1846      fi      fi
1847  fi  fi
1848    
1849  #same for exch2  #same for pkg/exch2 and pkg/regrid
1850  if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then  for pdir in exch2 regrid ; do
1851      echo "  Making source files in exch2 from  templates"      if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
1852      ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1          echo "  Making source files in pkg/${pdir} from templates"
1853      RETVAL=$?          ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
1854      if test "x${RETVAL}" = x0 ; then          RETVAL=$?
1855          rm -f make_exch2.errors          if test "x${RETVAL}" = x0 ; then
1856      else              rm -f make_${pdir}.errors
1857          echo "Error: problem encountered while building source files in exch2:"          else
1858          cat make_exch2.errors 1>&2              echo "Error: problem encountered while building source files in pkg/${pdir}:"
1859          exit 1              cat make_${pdir}.errors 1>&2
1860                exit 1
1861            fi
1862      fi      fi
1863  fi  done
1864    
1865  printf "\n===  Determining package settings  ===\n"  printf "\n===  Determining package settings  ===\n"
1866  if  test "x${PDEPEND}" = x ; then  if  test "x${PDEPEND}" = x ; then
# Line 1750  done Line 1971  done
1971  rm -f ./.tmp_pack  rm -f ./.tmp_pack
1972  echo "    packages are:  $PACKAGES"  echo "    packages are:  $PACKAGES"
1973    
1974  #  Check availability of NetCDF and then either build the MNC template  #  Check for package MNC: if NetCDF is available, then build the MNC
1975  #  files or delete mnc from the list of available packages.  #  template files ; otherwise, delete mnc from the list of packages.
1976  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
1977  RETVAL=$?  RETVAL=$?
1978  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
# Line 1785  EOF Line 2006  EOF
2006      fi      fi
2007  fi  fi
2008    
2009    #  Check for package PROFILES: if NetCDF is not available,
2010    #  then delete profiles from the list of available packages.
2011    echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
2012    RETVAL=$?
2013    if test "x$RETVAL" = x0 ; then
2014        if test "x$HAVE_NETCDF" != xt ; then
2015            cat <<EOF
2016    
2017    *********************************************************************
2018    WARNING: the "profiles" package was enabled but tests failed to
2019      compile NetCDF applications.  Please check that:
2020    
2021      1) NetCDF is correctly installed for this compiler and
2022      2) the LIBS variable (within the "optfile") specifies the correct
2023           NetCDF library to link against.
2024    
2025      Due to this failure, the "profiles" package is now DISABLED.
2026    *********************************************************************
2027    
2028    EOF
2029            PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
2030            DISABLE="$DISABLE profiles"
2031        fi
2032    fi
2033    
2034  echo "  applying package dependency rules"  echo "  applying package dependency rules"
2035  ck=  ck=
2036  while test "x$ck" != xtt ; do  while test "x$ck" != xtt ; do
2037      i=0      i=0
2038      # rtot=${#PNAME[@]}      # rtot=${#PNAME[@]}
2039      rtot=$nname      rtot=$nname
2040      while test $i -lt $rtot ; do      while test $i -le $rtot ; do
2041    
2042          #  Is $pname in the current $PACKAGES list?          #  Is $pname in the current $PACKAGES list?
2043          #  pname=${PNAME[$i]}          #  pname=${PNAME[$i]}
# Line 1825  while test "x$ck" != xtt ; do Line 2071  while test "x$ck" != xtt ; do
2071    
2072          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2073          if test "x$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
2074                #echo "   " $pname ": need to add :" $dname
2075              in_dis="f"              in_dis="f"
2076              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2077                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 1969  fi Line 2216  fi
2216    
2217  #  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
2218  #  compiler.  #  compiler.
2219  if test -f ./ad_files ; then  if test -f ./adSrcFiles.tmp ; then
2220      rm -f ./ad_files      rm -f ./adSrcFiles.tmp
2221  fi  fi
2222  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2223  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2224      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2225      for j in $list_files ; do      for j in $list_files ; do
2226          cat $i/$j >> ad_files          cat $i/$j >> adSrcFiles.tmp
2227      done      done
2228  done  done
2229  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2230      cat ad_files | sed -e "s/\.f/.$FS/g" > ad_files_f      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
2231      mv -f ad_files_f ad_files      mv -f adSrcFiles.tmp_f adSrcFiles.tmp
2232  fi  fi
2233    
2234  echo  echo
# Line 1993  for i in $INCLUDEDIRS ; do Line 2240  for i in $INCLUDEDIRS ; do
2240      fi      fi
2241  done  done
2242    
2243    if test ! "x$DIVA" = x ; then
2244        echo "  Creating the pseudo-MPI include directory"
2245        INCLUDES="-I./mpi_headers $INCLUDES"
2246        rm -rf ./mpi_headers
2247        mkdir -p ./mpi_headers
2248    
2249        if test "x$MPIINCLUDEDIR" = x ; then
2250            if test "x$MPIHOME" = x ; then
2251                MPIHOME='/usr'
2252            fi
2253            MPIINCLUDEDIR='$MPIHOME/include'
2254        fi
2255        
2256        if test -r $MPIINCLUDEDIR/mpif.h ; then
2257            for i in $MPI_HEADER_FILES; do
2258                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
2259            done
2260    
2261            perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
2262        else
2263            echo " We cannot create a copy of mpif.h!"
2264    #       exit -1
2265        fi
2266    fi
2267    
2268  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2269  rm -rf .links.tmp  rm -rf .links.tmp
2270  mkdir .links.tmp  mkdir .links.tmp
2271    touch .links.tmp/foo
2272    if test ! -r ".links.tmp/foo" ; then
2273        echo
2274        echo "ERROR : something is wrong with your directory permissions or"
2275        echo "   your user file-creation mask (\"umask\") since creating a"
2276        echo "   sub-dir, touch-ing a file within it, and then reading it is"
2277        echo "   not working.  Please try setting your umask to something"
2278        echo "   sane such as:"
2279        echo
2280        echo "      umask 0002"
2281        echo
2282        echo "   and please verify that you have the proper permissions for"
2283        echo "   creating sub-directories and then reading files created"
2284        echo "   within them."
2285        echo
2286        exit 1
2287    fi
2288    rm -f .links.tmp/foo
2289    
2290    if test "x$OPENAD" != x ; then
2291        OAD_DONT_COMPILE="/dev/null"
2292        OAD_DONT_TRANSFORM="/dev/null"
2293        OAD_KEEP_ORIGINAL="/dev/null"
2294        OAD_CB2M_FILES="/dev/null"
2295        echo "  looking for dontCompile file:  "
2296        for i in "." $MODS ; do
2297            if test -r $i"/dontCompile" ; then
2298                OAD_DONT_COMPILE=$i"/dontCompile"
2299                echo "     found $OAD_DONT_COMPILE"
2300                break
2301            fi
2302        done
2303        echo "  looking for dontTransform file:  "
2304        for i in "." $MODS ; do
2305            if test -r $i"/dontTransform" ; then
2306                OAD_DONT_TRANSFORM=$i"/dontTransform"
2307                echo "     found $OAD_DONT_TRANSFORM"
2308                break
2309            fi
2310        done
2311        echo "  looking for keepOriginal file:  "
2312        for i in "." $MODS ; do
2313            if test -r $i"/keepOriginal" ; then
2314                OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2315                echo "     found $OAD_KEEP_ORIGINAL"
2316                break
2317            fi
2318        done
2319        echo "  looking for cb2mFiles:  "
2320        for i in "." $MODS ; do
2321            if test -r $i"/cb2mFiles" ; then
2322                OAD_CB2M_FILES=$i"/cb2mFiles"
2323                echo "     found $OAD_CB2M_FILES"
2324                break
2325            fi
2326        done
2327        echo "   OpenAD exceptions:  "
2328    fi
2329    
2330  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > srclinks.tmp
2331  echo "" >> srclinks.tmp  echo "" >> srclinks.tmp
2332  printf 'SRCFILES = '    > srclist.inc  printf 'F77_SRC_FILES = ' > F77srclist.tmp
2333  printf 'CSRCFILES = '   > csrclist.inc  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp
2334  printf 'F90SRCFILES = ' > f90srclist.inc  printf 'C_SRC_FILES = '   > csrclist.tmp
2335  printf 'HEADERFILES = ' > hlist.inc  printf 'F90_SRC_FILES = ' > F90srclist.tmp
2336  printf 'AD_FLOW_FILES = ' > ad_flow_files.inc  printf 'H_SRC_FILES = '   > hsrclist.tmp
2337    printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp
2338  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2339  for d in $alldirs ; do  for d in $alldirs ; do
2340      deplist=      deplist=
2341      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2342      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
2343        if test "x$OPENAD" != x ; then
2344            sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2345        fi
2346      for sf in $sfiles ; do      for sf in $sfiles ; do
2347          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2348              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2349                  ignore_f=f                  ignore_f=f
2350                  case $d/$sf in                  case $d/$sf in
2351                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2352                            ignore_f=t
2353                          ;;                          ;;
2354                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2355                            ignore_f=t
2356                          ;;                          ;;
2357                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2358                            ignore_f=t
2359                          ;;                          ;;
2360                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2361                            ignore_f=t
2362                            ;;
2363                      ./EMBEDDED_FILES.h)
2364                            ignore_f=t
2365                          ;;                          ;;
2366                    *)                    *)
2367                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
# Line 2035  for d in $alldirs ; do Line 2377  for d in $alldirs ; do
2377                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2378                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2379                      case $extn in                      case $extn in
2380                          F)                        F)
2381                              echo    " \\"  >> srclist.inc                          echo    " \\"  >> F77srclist.tmp
2382                              printf " $sf" >> srclist.inc                          printf " $sf" >> F77srclist.tmp
2383                              ;;                          if test "x$OPENAD" != x ; then
2384                          F90)                              basename=${sf%%.F}
2385                              echo    " \\"  >> f90srclist.inc                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2386                              printf " $sf" >> f90srclist.inc                              if test -z "$isAD" ; then
2387                              ;;                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2388                          c)                                  if test -z "$toBeIgnored" ; then
2389                              echo    " \\"  >> csrclist.inc                                      echo    " \\"  >> nonADF77srclist.tmp
2390                              printf " $sf" >> csrclist.inc                                      printf " $sf" >> nonADF77srclist.tmp
2391                              ;;                                  else
2392                          h)                                      echo "    not to be compiled   :  $sf"
2393                              echo    " \\"  >> hlist.inc                                  fi
2394                              printf " $sf" >> hlist.inc                              else # file is initially listed as an AD file we want to exclude it
2395                              ;;                                   # or we want to retain the untransformed version
2396                          flow)                                  notToBeTransformed=`egrep ^$basename'[      ]*' ${OAD_DONT_TRANSFORM}`
2397                              echo    " \\"  >> ad_flow_files.inc                                  untransformedVersionToBeKept=`egrep ^$basename'[      ]*' ${OAD_KEEP_ORIGINAL}`
2398                              printf " $sf" >> ad_flow_files.inc                                  if test -n "$notToBeTransformed"; then
2399                              ;;                                      echo "    not to be transformed:  $sf"
2400                      esac                                  fi
2401                  fi                                  if test -n "$untransformedVersionToBeKept" ; then
2402                                        echo "    original to be kept  :  $sf"
2403                                    fi    
2404                                    if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2405                                        echo    " \\"  >> nonADF77srclist.tmp
2406                                        printf " $sf" >> nonADF77srclist.tmp
2407                                    fi
2408                                fi
2409                            fi
2410                            ;;
2411                        F90)
2412                            echo    " \\"  >> F90srclist.tmp
2413                            printf " $sf" >> F90srclist.tmp
2414                            ;;
2415                        c)
2416                            echo    " \\"  >> csrclist.tmp
2417                            printf " $sf" >> csrclist.tmp
2418                            ;;
2419                        h)
2420                            echo    " \\"  >> hsrclist.tmp
2421                            printf " $sf" >> hsrclist.tmp
2422                            ;;
2423                        flow)
2424                            echo    " \\"  >> ad_flow_files.tmp
2425                            printf " $sf" >> ad_flow_files.tmp
2426                            ;;
2427                       esac
2428                    fi
2429              fi              fi
2430          fi          fi
2431      done      done
2432      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2433          echo "" >> srclinks.tmp        if test "$d" != "." ; then
2434            echo "" >> srclinks.tmp
2435          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> srclinks.tmp
2436          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> srclinks.tmp
2437          printf "\t\$(LN) %s/\$@ \$@\n" $d >> srclinks.tmp  # We need to make sure that the link isn't already there.
2438    # This may happen when make thinks that a header file has to be "remade"
2439    # because a module it depends on has changed.  In this case we do nothing.
2440            printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp
2441          fi
2442      fi      fi
2443  done  done
2444  rm -rf .links.tmp  rm -rf .links.tmp
2445  echo "" >> srclist.inc  echo "" >> F77srclist.tmp
2446  echo "" >> csrclist.inc  echo "" >> nonADF77srclist.tmp
2447  echo "" >> f90srclist.inc  echo "" >> csrclist.tmp
2448  echo "" >> hlist.inc  echo "" >> F90srclist.tmp
2449  echo "" >> ad_flow_files.inc  echo "" >> hsrclist.tmp
2450    echo "" >> ad_flow_files.tmp
2451    
2452  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
2453      mv -f $MAKEFILE "$MAKEFILE.bak"      mv -f $MAKEFILE "$MAKEFILE.bak"
# Line 2132  DISABLED_PACKAGES = ${DISABLED_PACKAGES} Line 2507  DISABLED_PACKAGES = ${DISABLED_PACKAGES}
2507    
2508  # These files are created by Makefile  # These files are created by Makefile
2509  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
   
2510  EOF  EOF
2511    
2512  #  Note: figure out some way to add Hyades JAM libraries here  if test "x$EMBED_SRC" = xt ; then
2513        echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
2514    else
2515        echo "EMBEDDED_FILES = " >>$MAKEFILE
2516    fi
2517    
2518    #  Note: figure out some way to add Hyades JAM libraries here
2519  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2520  # Unix ln (link)  # Unix ln (link)
2521  LN = ${LN}  LN = ${LN}
# Line 2163  INCLUDES = ${INCLUDES} Line 2542  INCLUDES = ${INCLUDES}
2542  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2543  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2544  # Optim./debug for FC  # Optim./debug for FC
2545  FFLAGS = ${FFLAGS}  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
2546  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM}
2547  # Optim./debug for FC  # Optim./debug for FC
2548  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2549  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
2550    F90FIXEDFORMAT = ${F90FIXEDFORMAT}
2551  # Flags for CC  # Flags for CC
2552  CFLAGS = ${CFLAGS}  CFLAGS = ${CFLAGS}
2553  # Files that should not be optimized  # Files that should not be optimized
# Line 2180  MAKEFILE=${MAKEFILE} Line 2560  MAKEFILE=${MAKEFILE}
2560    
2561  EOF  EOF
2562    
2563  cat srclist.inc       >> $MAKEFILE  cat F77srclist.tmp      >> $MAKEFILE
2564  cat csrclist.inc      >> $MAKEFILE  cat nonADF77srclist.tmp >> $MAKEFILE
2565  cat f90srclist.inc    >> $MAKEFILE  cat csrclist.tmp        >> $MAKEFILE
2566  cat hlist.inc         >> $MAKEFILE  cat F90srclist.tmp      >> $MAKEFILE
2567  cat ad_flow_files.inc >> $MAKEFILE  cat hsrclist.tmp        >> $MAKEFILE
2568    cat ad_flow_files.tmp   >> $MAKEFILE
2569    
2570    rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp
2571    
2572  echo >> $MAKEFILE  echo >> $MAKEFILE
2573  echo 'F77FILES =  $(SRCFILES:.F=.'$FS')'      >> $MAKEFILE  
2574  echo 'F90FILES =  $(F90SRCFILES:.F90=.'$FS90')' >> $MAKEFILE  # add definitions for preprocessed sources
2575  echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE  # and note that not all systems allow case sensitive extensions
2576    # hence the $FS and $FS90 here.
2577    # for fixed format f90 files we use ff90 or FF90 resp
2578    # but these are not expected to be the original source files
2579    
2580    echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2581    echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2582    echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
2583    echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2584  echo >> $MAKEFILE  echo >> $MAKEFILE
2585  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2586  echo '.SUFFIXES: .o .'$FS' .p .F .c .'$FS90' .F90' >> $MAKEFILE  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
 rm -f srclist.inc csrclist.inc hlist.inc flist.tmp clist.tmp f90srclist.inc  
 rm -f ad_flow_files.inc  
2587    
2588  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2589    
2590  all: \$(EXECUTABLE)  all: \$(EXECUTABLE)
2591  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2592          @echo Creating \$@ ...          @echo Creating \$@ ...
2593          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2594  depend:  depend:
2595          @make links          @make links
2596          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(SRCFILES)          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2597          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2598          -rm -f makedepend.out          -rm -f makedepend.out
2599    
# Line 2211  lib: libmitgcmuv.a Line 2601  lib: libmitgcmuv.a
2601    
2602  libmitgcmuv.a: \$(OBJFILES)  libmitgcmuv.a: \$(OBJFILES)
2603          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
2604            ar d   libmitgcmuv.a main.o
2605    
2606  links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
2607    
2608  small_f: \$(F77FILES) \$(F90FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2609    
2610  output.txt: \$(EXECUTABLE)  output.txt: \$(EXECUTABLE)
2611          @printf 'running ... '          @printf 'running ... '
2612          @\$(EXECUTABLE) > \$@          @\$(EXECUTABLE) > \$@
2613    
2614  clean:  clean:
2615          -rm -rf *.o *.$FS *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
2616            -rm -rf *.o
2617            -rm -rf *.$FS *.flowdir
2618            -rm -rf *.f$FS90 *_mod.h *_mod.F90 *.FF90 *.mod-whirl ad_input*
2619            -rm -rf temp.sed reslice.dat
2620  Clean:  Clean:
2621          @make clean          @make clean
2622          @make cleanlinks          @make cleanlinks
2623          -rm -f \$(SPECIAL_FILES)          -rm -f \$(SPECIAL_FILES)
2624          -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
2625            -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
2626  CLEAN:  CLEAN:
2627          @make Clean          @make Clean
2628          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2629          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2630          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2631          -rm -f \$(EXECUTABLE) output.txt STD*          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
2632            -rm -f *_MIT_CE_000.opt0000 costfunction*0000
2633            -rm -rf mnc_test_*
2634    
2635  #eh3 Makefile: makefile  #eh3 Makefile: makefile
2636  makefile:  makefile:
# Line 2240  makefile: Line 2638  makefile:
2638  cleanlinks:  cleanlinks:
2639          -find . -type l -exec rm {} \;          -find . -type l -exec rm {} \;
2640    
2641  # Special targets (SPECIAL_FILES) which are create by make  # Special targets (SPECIAL_FILES) which are created by make
2642  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
2643          @echo Creating \$@ ...          @echo Creating \$@ ...
2644          @$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 2658  test ! "x$THISUSER" = x && echo "      -echo
2658  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE  test ! "x$THISDATE" = x && echo "       -echo \"#define THISDATE '$THISDATE'\" >> \$@" >> $MAKEFILE
2659  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE  test ! "x$THISHOST" = x && echo "       -echo \"#define THISHOST '$THISHOST'\" >> \$@" >> $MAKEFILE
2660    
2661    if test "x$EMBED_SRC" = xt ; then
2662        cat >>$MAKEFILE <<EOF
2663    
2664    decode_files.o : EMBEDDED_FILES.h
2665    
2666    ##  \$(F77_PP_SRC_FILES)
2667    all_fF.tar.gz : \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2668            @echo Creating \$@ ...
2669            -tar -hcf all_fF.tar \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(F77_PP_SRC_FILES) Makefile
2670            -rm -f all_fF.tar.gz
2671            -gzip all_fF.tar
2672    
2673    EMBEDDED_FILES.h : all_fF.tar.gz
2674            @echo Creating \$@ ...
2675            -\${ROOTDIR}/tools/embed_encode/encode_files EMBEDDED_FILES.h all_fF.tar.gz
2676    
2677    EOF
2678    fi
2679    
2680  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2681    
2682  # The normal chain of rules is (  .F - .$FS - .o  )  # The normal chain of rules is (  .F - .$FS - .o  )
2683    
2684  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
2685  ## %.o : %.F  %.o : %.F
2686    
2687  .F.$FS:  .F.$FS:
2688          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
# Line 2273  cat >>$MAKEFILE <<EOF Line 2690  cat >>$MAKEFILE <<EOF
2690          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2691  .F90.$FS90:  .F90.$FS90:
2692          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2693    .FF90.f$FS90:
2694            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2695  .$FS90.o:  .$FS90.o:
2696          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
2697    .f$FS90.o:
2698            cp \$< \$(basename  \$<).f90
2699            \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$(basename  \$<).f90
2700  .c.o:  .c.o:
2701          \$(CC) \$(CFLAGS) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
2702    .flow.flowdir:
2703            \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2704    
2705  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
2706  .F.p:  .F.p:
# Line 2284  cat >>$MAKEFILE <<EOF Line 2708  cat >>$MAKEFILE <<EOF
2708  .p.$FS:  .p.$FS:
2709          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
2710    
2711    EOF
2712    
2713  #=========================================  #=========================================
2714  #===  Automatic Differentiation Rules  ===  #===  Automatic Differentiation Rules  ===
2715    #===  for TAMC/TAF  ======================
2716    
2717    if test "x$OPENAD" == x ; then
2718    
2719    cat >>$MAKEFILE <<EOF
2720    
2721  TAMC           = ${TAMC}  TAMC           = ${TAMC}
2722  TAF            = ${TAF}  TAF            = ${TAF}
# Line 2300  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF Line 2731  ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF
2731  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"  ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
2732  for i in $ad_vars ; do  for i in $ad_vars ; do
2733      name=$i      name=$i
2734      t1="t2=\$"`echo $i`      t1="t2=\$"`echo "$i"`
2735      eval $t1      eval $t1
2736      printf "%-20s = " $name >> $MAKEFILE      printf "%-20s = " $name >> $MAKEFILE
2737      echo $t2 >> $MAKEFILE      echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
2738  done  done
2739    
2740  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
2741  echo >> $MAKEFILE  echo >> $MAKEFILE
2742  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
2743  AD_FILES=`cat ad_files`  AD_FILES=`cat adSrcFiles.tmp`
2744  for i in $AD_FILES ; do  for i in $AD_FILES ; do
2745      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
2746      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
2747  done  done
2748  echo >> $MAKEFILE  echo >> $MAKEFILE
2749  rm -f ad_files  rm -f adSrcFiles.tmp
2750    
2751  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2752    
2753  # ... AD ...  # ... AD ...
2754  adall: ad_taf  adall: \$(EXE_AD)
2755  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
2756  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
2757    
2758  ad_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2759          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
2760          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2761          -rm -f ad_config.template          -rm -f ad_config.template
2762          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2763          @make \$(AD_FLOW_FILES)          @make \$(FLOFILES)
2764          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.$FS          cat \$(FLOFILES) \$(AD_FILES) > ad_input_code.$FS
2765    
2766  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
2767          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2768            ls -l ad_input_code_ad.$FS
2769          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
2770    
2771  adtafonly:  adtafonly:
2772          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
2773            ls -l ad_input_code_ad.$FS
2774          cat ad_input_code_ad.$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
2775    
2776  ad_taf: ad_taf_output.o \$(OBJFILES)  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)
2777          \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
2778    
2779  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
2780          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 2361  ftlall: ftl_taf Line 2794  ftlall: ftl_taf
2794  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
2795  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
2796    
2797  ftl_input_code.$FS: \$(AD_FILES) \$(HEADERFILES)  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
2798          @$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          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
2799          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2800          -rm -f ftl_config.template          -rm -f ftl_config.template
2801          @make \$(F77FILES)          @make \$(F77_PP_SRC_FILES)
2802          @make \$(AD_FLOW_FILES)          @make \$(AD_FLOW_FILES)
2803          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
2804    
2805  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
2806          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2807            ls -l ftl_input_code_ftl.$FS
2808          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
2809    
2810  ftltafonly:  ftltafonly:
2811          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
2812            ls -l ftl_input_code_ftl.$FS
2813          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
2814    
2815  ftl_taf: ftl_taf_output.o \$(OBJFILES)  ftl_taf: ftl_taf_output.o \$(OBJFILES)
# Line 2412  svd_touch: Line 2847  svd_touch:
2847          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
2848          -rm -f ftl_config.template          -rm -f ftl_config.template
2849    
2850  #=========================================  EOF
2851    
2852    fi
2853    
2854    #===  for OpenAD  ========================
2855    
2856    if test "x$OPENAD" != x ; then
2857    
2858    # ============ begin OpenAD specific section ==============
2859    
2860    cat >>$MAKEFILE <<EOF
2861    
2862    # all the source files linked from the various locations:
2863    ALL_LINKED_FILES= \
2864    \$(F77_SRC_FILES) \
2865    \$(C_SRC_FILES) \
2866    \$(H_SRC_FILES) \
2867    \$(F90_SRC_FILES) \
2868    \$(SPECIAL_FILES)
2869    
2870    ifndef OPENADROOT
2871      \$(error "Error:  environment variable OPENADROOT not defined!")
2872    endif
2873    
2874    ifndef XAIFSCHEMAROOT
2875      \$(error "Error:  environment variable XAIFSCHEMAROOT not defined!")
2876    endif
2877    
2878    ifndef XAIFBOOSTERROOT
2879      \$(error "Error:  environment variable XAIFBOOSTERROOT not defined!")
2880    endif
2881    
2882  EOF  EOF
2883    
2884    echo "  Add the source list for common block to module conversion "
2885    echo >> $MAKEFILE
2886    printf "CB2M_F90_SRC_NAMES = " >> $MAKEFILE
2887    for i in `cat ${OAD_CB2M_FILES}` ; do
2888      echo    " \\" >> $MAKEFILE
2889      printf " $i" >> $MAKEFILE
2890    done
2891    echo >> $MAKEFILE
2892    
2893    echo "  Add the source list for AD code generation"
2894    echo >> $MAKEFILE
2895    printf "AD_FILES = " >> $MAKEFILE
2896    for i in `cat ${OAD_CB2M_FILES}` ; do
2897      echo    " \\" >> $MAKEFILE
2898      printf " ${i}_mod.f$FS90" >> $MAKEFILE
2899    done
2900    AD_FILES=`cat adSrcFiles.tmp`
2901    for i in $AD_FILES ; do
2902      basename=${i%%.f}
2903      toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
2904      if test -z "$toBeIgnored" ; then
2905        echo    " \\" >> $MAKEFILE
2906        printf " $i" >> $MAKEFILE
2907      fi
2908    done
2909    echo >> $MAKEFILE
2910    rm -f adSrcFiles.tmp
2911    
2912    cat >>$MAKEFILE <<EOF
2913    
2914    adAll: \$(EXE_AD)
2915    .PHONY: adAll
2916    
2917    CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
2918    
2919    .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
2920    
2921    .PHONY: adDepend
2922    adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
2923            \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
2924            \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2925            -rm -f makedepend.out
2926    
2927    OPENAD_SUPPORT_F90_SRC_FILES = \
2928    w2f__types.F90 \
2929    OAD_active.F90 \
2930    OAD_cp.F90 \
2931    OAD_rev.F90 \
2932    OAD_tape.F90        
2933    
2934    OPENAD_SUPPORT_C_SRC_FILES = \
2935    iaddr.c \
2936    timeRatio.c
2937    
2938    f95_test_mods.f90: \$(OPENAD_SUPPORT_F90_SRC_FILES:F90=$FS90)
2939            cat \$^ > \$@
2940    
2941    f95_test.f90: all_mods.xb.x2w.w2f.pp.f$FS90 \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90) ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90
2942            cat \$^ > \$@
2943    
2944    f95_test.out: f95_test_mods.f90 f95_test.f90
2945            f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
2946            f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
2947    
2948    AD_OBJ_FILES=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) all_mods.xb.x2w.w2f.pp.o  ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.o \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
2949    
2950    \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(AD_OBJ_FILES)
2951            @echo Creating \$@ ...
2952            \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES) \$(LIBS)
2953    
2954    # makefile debug rule
2955    openad: ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90
2956    .PHONY: openad
2957    
2958    # create the module files
2959    %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
2960            ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
2961    
2962    # create the header files
2963    %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
2964            ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
2965    
2966    # change everybody else to use the new module files:
2967    %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
2968            ../OAD_support/cb2mUseModules.bash $< ${MPI}
2969    
2970    # makefile debug rule
2971    small_f: \$(CB2M_F90_PP_SRC_FILES)
2972    .PHONY: small_f
2973    
2974    ad_output.txt: \$(EXE_AD)
2975            @printf 'linking data files ... '
2976            \$(LN) -f ../input_ad/data* ../input_ad/eedata .
2977            \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
2978            @printf 'running ... '
2979            @./\$(EXE_AD) > \$@
2980    
2981    CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
2982    ad_input_code.f$FS90: ../OAD_support/maxMinDefs.f \$(CB2M_AD_FILES)
2983            cat \$^ > \$@
2984    
2985    # strip all comments and blanks to reduce
2986    # the file size in order to reduce perl's memory requirements
2987    ad_input_code_sf.f$FS90 : ad_input_code.f$FS90
2988            cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@
2989    
2990    # mfef90 preprocessing
2991    # expand statement functions
2992    # expose mfef90 specific substring handling
2993    # add the w2f__types module
2994    ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
2995            ./mfef90 -r8 -z -F -N132 \$<
2996            mv \$<.B \$(basename \$<).B
2997            ./whirl2f -openad \$(basename \$<).B
2998            cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
2999    
3000    # canonicalizer
3001    ad_input_code_sf.w2f.canon.f$FS90: ad_input_code_sf.w2f.f$FS90 canon.v1.py
3002            python canon.v1.py --r8 \$< > \$@
3003    
3004    # F -> WHIRL
3005    # note that the canonicalized version cuts off at col 72
3006    # doing this also for string constants which is ok as long
3007    # as we are in fixed mode and cut of exactly there.
3008    # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)
3009    # characters respectively.
3010    ad_input_code_sf.w2f.canon.B: ad_input_code_sf.w2f.canon.f$FS90 mfef90
3011            ./mfef90 -r8 -z -F \$<
3012            mv \$<.B \$@
3013    
3014    # WHIRL -> XAIF
3015    ad_input_code_sf.w2f.canon.xaif : ad_input_code_sf.w2f.canon.B whirl2xaif
3016            ./whirl2xaif -s -n --debug 1 -o \$@ \$<
3017    
3018    # XAIF -> XAIF'
3019    ad_input_code_sf.w2f.canon.xb.xaif : ad_input_code_sf.w2f.canon.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd openad_adm
3020            ./openad_adm -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3021    
3022    # XAIF' -> WHIRL'
3023    ad_input_code_sf.w2f.canon.xb.x2w.B : ad_input_code_sf.w2f.canon.xb.xaif xaif2whirl
3024            ./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.canon.B \$<
3025    
3026    # WHIRL' -> F'
3027    ad_input_code_sf.w2f.canon.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.canon.xb.x2w.B whirl2f whirl2f_be
3028            ./whirl2f -FLIST:ftn_file=\$@ -openad \$<
3029    
3030    # undo slice hiding
3031    # insert template directives
3032    ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.f$FS90: ad_input_code_sf.w2f.canon.xb.x2w.w2f.f$FS90 reslicer.py ../OAD_support/insertTemplateDir.bash
3033            python reslicer.py \$< > \$<.1
3034            ../OAD_support/insertTemplateDir.bash \$<.1  \$@
3035            rm \$<.1
3036    
3037    # postprocess F'
3038    ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.f$FS90 multi-pp.pl ../OAD_support/ad_inline.f \$(wildcard ../OAD_support/ad_template.*.f)
3039            perl multi-pp.pl -inline=../OAD_support/ad_inline.f \$<
3040            # the postprocessor still gets the name wrong
3041            cat \$<.pp | sed 's/RETURN//' > \$@
3042    
3043    # extract all transformed modules
3044    all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90
3045            cat \$< | sed -n '/MODULE /,/END MODULE/p' > \$@
3046    
3047    # remove the transformed globals module from the
3048    # transformed ad_input_code file
3049    # and remove for now the duplicate variables
3050    # and fix 2 data statements
3051    ad_input_code.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90: ad_input_code_sf.w2f.canon.xb.x2w.w2f.rs.pp.f$FS90
3052            cat \$< | sed '/MODULE /,/END MODULE/d' | sed '/^      INTEGER(w2f__i4) DOLOOP_UB/d' > \$@
3053    
3054    # setup some links
3055    %.xsd:
3056            \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3057    
3058    mfef90:
3059            \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .
3060    
3061    # link the support files:
3062    \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
3063            \$(LN) ../OAD_support/\$@ .
3064    
3065    whirl2xaif xaif2whirl:
3066            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3067    
3068    %.pl:
3069            \$(LN) \${OPENADFORTTK}/bin/\$@ .
3070    
3071    %.py:
3072            \$(LN) \${OPENADROOT}/OpenADFortTk/tools/canonicalize/\$@ .
3073    
3074    whirl2f whirl2f_be:
3075            \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
3076    
3077    openad_adm:
3078            \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/test/t \$@
3079    
3080    # ============ end OpenAD specific section ==============
3081    
3082    EOF
3083    
3084    fi
3085    
3086    #=========================================
3087    
3088  if test "x$EXEHOOK" != x ; then  if test "x$EXEHOOK" != x ; then
3089      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE      printf "\nexehook:\n\t%s\n" $EXEHOOK >> $MAKEFILE
3090  fi  fi

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