/[MITgcm]/MITgcm_contrib/heimbach/OpenAD/code_regress/genmake2

Diff of /MITgcm_contrib/heimbach/OpenAD/code_regress/genmake2

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-revision 1.3 by utke,
Tue Dec 18 06:44:50 2007 UTC
+revision 1.6 by utke,
Fri Jun 20 20:29:59 2008 UTC
 Line 1
  #! /usr/bin/env bash
  #
  # $Header$
-Line 14
+Line 13
  test_for_package_in_cpp_options() {
      cpp_options=$1
      pkg=$2
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
  }
  # Search for particular CPP #cmds associated with MPI
  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
  test_for_mpi_in_cpp_eeoptions() {
      cpp_options=$1
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
-     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
+     test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
  }
  # Search for particular string in a file. Return 1 if detected, 0 if not
-Line 40 
 test_for_string_in_file() {
+Line 47 
 test_for_string_in_file() {
      if test "x${RETVAL}" = x0 ; then
          printf "Error: In $file there is an illegal line: "
          grep -i "$strng" $file
-         return 1
+         exit 99
      fi
      return 0
  }
-Line 249 
 build_cyrus_makedepend()  {
+Line 256 
 build_cyrus_makedepend()  {
      fi
  }
+ build_embed_encode()
+ {
+     printf "  building the embed-encode utility...  "
+     if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
+         if test ! -d "$ROOTDIR/tools/embed_encode" ; then
+             echo
+             echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
+             echo
+             EMBED_SRC=f
+             return 1
+         fi
+         clist="cc gcc c89 $CC"
+         for ic in $clist ; do
+             comm="$ic -o encode_files encode_files.c"
+             ( cd $ROOTDIR/tools/embed_encode && $comm ) > /dev/null 2>&1
+             RETVAL=$?
+             if test "x$RETVAL" = x0 ; then
+                 echo "OK"
+                 DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+                 return 0
+             fi
+         done
+         echo
+         echo "    Error: unable to build $ROOTDIR/embed_encode/encode_files"
+         echo "      so it has been disabled"
+         echo
+         EMBED_SRC=f
+         return 1
+     fi
+     echo "OK"
+     DEFINES="$DEFINES -DHAVE_EMBED_SRC"
+ }
  # Guess possible config options for this host
  find_possible_configs()  {
-Line 283 
 find_possible_configs()  {
+Line 325 
 find_possible_configs()  {
      #================================================================
      #  look for possible C compilers
-     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc"
+     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
      p_CC=
      for c in $tmp ; do
          rm -f ./genmake_hello.c  ./genmake_hello
-Line 322 
 EOF
+Line 364 
 EOF
      #================================================================
      #  look for possible FORTRAN compilers
-     tmp="$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"
      p_FC=
      for c in $tmp ; do
          rm -f ./hello.f ./hello
-Line 354 
 EOF
+Line 396 
 EOF
      else
          echo "  The possible FORTRAN compilers found in your path are:"
          echo "   "$p_FC
-         if test "x$FC" = x ; then
+     fi
-             FC=`echo $p_FC | $AWK '{print $1}'`
-             echo "  Setting FORTRAN compiler to: "$FC
+     #  Use the first of the compilers found in the current PATH
-         fi
+     #  that has a correctly-named optfile
+     if test "x$OPTFILE" = x  -a  "x$FC" = x ; then
+         for i in $p_FC ; do
+             OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+             if test -r $OPTFILE ; then
+                 echo "  Setting OPTFILE to: "$OPTFILE
+                 break
+             fi
+         done
      fi
      if test "x$OPTFILE" = x ; then
-Line 528 
 Usage: "$0" [OPTIONS]
+Line 578 
 Usage: "$0" [OPTIONS]
            *only* works if it is supported by the OPTFILE that
            is being used.
+     -ignoretime | -ignore_time | --ignoretime | --ignore_time
+           Ignore all the "wall clock" routines entirely.  This will
+           not in any way hurt the model results -- it simply means
+           that the code that checks how long the model spends in
+           various routines will give junk values.
      -ts | --ts
            Produce timing information per timestep
+     -papis | --papis
+           Produce summary MFlop/s (and IPC) with PAPI per timestep
+     -pcls | --pcls
+           Produce summary MFlop/s etc. with PCL per timestep
+     -foolad | --foolad
+           Fool the AD code generator
+     -papi | --papi
+           Performance analysis with PAPI
+     -pcl | --pcl
+           Performance analysis with PCL
+     -hpmt | --hpmt
+           Performance analysis with the HPM Toolkit
+     -gsl | --gsl
+           Use GSL to control floating point rounding and precision
+     -devel | --devel
+           Add additional warning and debugging flags for development
      -mpi | --mpi
            Include MPI header files and link to MPI libraries
-Line 538 
 Usage: "$0" [OPTIONS]
+Line 611 
 Usage: "$0" [OPTIONS]
            set to PATH. i.e. Include files from \$PATH/include, link to libraries
            from \$PATH/lib and use binaries from \$PATH/bin.
+     -es | --es | -embed-source | --embed-source
+           Embed a tarball containing the full source code
+           (including the Makefile, etc.) used to build the
+           executable [off by default]
      -bash NAME
            Explicitly specify the Bourne or BASH shell to use
-Line 602 
 EOF
+Line 680 
 EOF
        call tsub( string )
        end
  EOF
-     $FC $FFLAGS $DEFINES -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+     $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
      RETVAL=$?
      if test "x$RETVAL" != x0 ; then
          FC_NAMEMANGLE=$default_nm
-Line 668 
 void FC_NAMEMANGLE(cloc) ( double *curti
+Line 746 
 void FC_NAMEMANGLE(cloc) ( double *curti
   *curtim = *curtim/1.E6;
  }
  EOF
-     make genmake_tc_1.o >> genmake_warnings 2>&1
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
        program hello
-       Real*8 wtime
+       REAL*8 wtime
        external cloc
        call cloc(wtime)
        print *," HELLO WORLD", wtime
-       end program hello
+       end
  EOF
-     $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"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
      RET_F=$?
      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
      RETVAL=$?
-Line 690 
 EOF
+Line 772 
 EOF
  }
+ check_HAVE_SIGREG()  {
+     if test ! "x$HAVE_SIGREG" = x ; then
+         return
+     fi
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include <signal.h>
+ #include <errno.h>
+ #include <ucontext.h>
+ int * ip;
+ static void killhandler(
+     unsigned int sn, siginfo_t  si, struct ucontext *sc )
+ {
+     *ip = *ip + 1;
+     return;
+ }
+ void FC_NAMEMANGLE(sigreg) (int * aip)
+ {
+     struct sigaction s;
+     ip = aip;
+     s.sa_flags = SA_SIGINFO;
+     s.sa_sigaction = (void *)killhandler;
+     if(sigaction (SIGTERM,&s,(struct sigaction *)NULL)) {
+         printf("Sigaction returned error = %d\n", errno);
+         exit(0);
+     }
+     return;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       integer anint
+       common /iv/ anint
+       external sigreg
+       call sigreg(anint)
+       end
+ EOF
+     echo >> genmake_warnings
+     echo "running: check_HAVE_SIGREG()" >> genmake_warnings
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_SIGREG=t
+         DEFINES="$DEFINES -DHAVE_SIGREG"
+     fi
+     rm -f genmake_tc*
+ }
+ check_HAVE_SETRLSTK()  {
+     if test "x$HAVE_SETRLSTK" = xt ; then
+         DEFINES="$DEFINES -DHAVE_SETRLSTK"
+         return
+     fi
+     if test ! "x$HAVE_SETRLSTK" = x ; then
+         return
+     fi
+     get_fortran_c_namemangling
+     cat <<EOF > genmake_tc_1.c
+ $FC_NAMEMANGLE
+ #include <sys/time.h>
+ #include <sys/resource.h>
+ #include <unistd.h>
+ void FC_NAMEMANGLE(setrlstk) ()
+ {
+     struct rlimit rls;
+     rls.rlim_cur = RLIM_INFINITY;
+     rls.rlim_max = RLIM_INFINITY;
+     setrlimit(RLIMIT_STACK, &rls);
+     return;
+ }
+ EOF
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RET_C=$?
+     cat <<EOF > genmake_tc_2.$FS
+       program hello
+       external setrlstk
+       call setrlstk()
+       end
+ EOF
+     echo >> genmake_warnings
+     echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+     RETVAL=$?
+     if test "x$RETVAL" = x0 ; then
+         HAVE_SETRLSTK=t
+         DEFINES="$DEFINES -DHAVE_SETRLSTK"
+     fi
+     rm -f genmake_tc*
+ }
  check_HAVE_STAT()  {
      get_fortran_c_namemangling
      cat <<EOF > genmake_tc_1.c
-Line 711 
 void FC_NAMEMANGLE(tfsize) ( int *nbyte
+Line 903 
 void FC_NAMEMANGLE(tfsize) ( int *nbyte
          *nbyte = -1;
  }
  EOF
-     make genmake_tc_1.o >> genmake_tc.log 2>&1
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_tc.log 2>&1
      RET_C=$?
      cat <<EOF > genmake_tc_2.$FS
        program hello
        integer nbyte
        call tfsize(nbyte)
        print *," HELLO WORLD", nbyte
-       end program hello
+       end
  EOF
-     $FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o >> genmake_tc.log 2>&1
+     echo >> genmake_warnings
-     RET_F=$?
+     echo "running: check_HAVE_STAT()" >> genmake_warnings
-     test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1
+     cat genmake_tc_2.$FS >> genmake_warnings
+     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_tc.log 2>&1
      RETVAL=$?
      if test "x$RETVAL" = x0 ; then
          HAVE_STAT=t
-Line 736 
 check_netcdf_libs()  {
+Line 933 
 check_netcdf_libs()  {
      if test ! "x$SKIP_NETCDF_CHECK" = x ; then
          return
      fi
-     echo "" > genmake_tnc.log
+     echo >> genmake_warnings
+     echo "running: check_netcdf_libs()" >> genmake_warnings
      cat <<EOF > genmake_tnc.F
        program fgennc
  #include "netcdf.inc"
-Line 754 
 EOF
+Line 952 
 EOF
        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
        end
  EOF
-     echo "Executing:" > genmake_tnc.log
+     echo "===  genmake_tnc.F  ===" > genmake_tnc.log
-     echo "  $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS" \
+     cat genmake_tnc.F >> genmake_tnc.log
-         > genmake_tnc.log
+     echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
      RET_CPP=f
-     $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS 2>/dev/null  \
+     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
-         &&  RET_CPP=t
+     echo "$COMM" >> genmake_tnc.log
+     eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
      if test "x$RET_CPP" = xf ; then
          echo "  WARNING: CPP failed to pre-process the netcdf test." \
-             > genmake_tnc.log
+             >> genmake_tnc.log
          echo "    Please check that \$INCLUDES is properly set." \
-             > genmake_tnc.log
+             >> genmake_tnc.log
      fi
-     echo "Executing:" > genmake_tnc.log
+     echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
-     echo "  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS" > genmake_tnc.log
+     echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc.o $LIBS" >> genmake_tnc.log
-     echo "  $LINK -o genmake_tnc.o $LIBS" > genmake_tnc.log
      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
-         &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
+         &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
      RET_COMPILE=$?
+     cat genmake_tnc.log >> genmake_warnings
      #EH3  Remove test program execution for machines that either disallow
      #EH3  execution or cannot support it (eg. cross-compilers)
-Line 784 
 EOF
+Line 983 
 EOF
          HAVE_NETCDF=t
      else
          # try again with "-lnetcdf" added to the libs
-         $CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS 2>/dev/null  \
+         echo "try again with added '-lnetcdf'" > genmake_tnc.log
+         echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
+         echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
+         echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+         cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
-             &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
+             &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
          RET_COMPILE=$?
+         cat genmake_tnc.log >> genmake_warnings
          if test "x$RET_COMPILE" = x0 ; then
              LIBS="$LIBS -lnetcdf"
              HAVE_NETCDF=t
          else
+         # try again with "-lnetcdff" added to the libs
+             echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+             echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
+             echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
+             echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+             cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
+                 &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
+                 &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
+             RET_COMPILE=$?
              cat genmake_tnc.log >> genmake_warnings
+             if test "x$RET_COMPILE" = x0 ; then
+                 LIBS="$LIBS -lnetcdff -lnetcdf"
+                 HAVE_NETCDF=t
+             fi
          fi
      fi
      rm -f genmake_tnc*
-Line 828 
 OPTFILE=
+Line 1045 
 OPTFILE=
  INCLUDES="-I. $INCLUDES"
  FFLAGS=
  FOPTIM=
+ FEXTRAFLAGS=
  CFLAGS=
  KFLAGS1=
  KFLAGS2=
-Line 839 
 NOOPTFLAGS=
+Line 1057 
 NOOPTFLAGS=
  MPI=
  MPIPATH=
  TS=
+ PAPIS=
+ PCLS=
+ FOOLAD=
+ PAPI=
+ PCL=
+ HPMT=
+ GSL=
+ DEVEL=
+ HAVE_TEST_L=
  # DEFINES checked by test compilation or command-line
  HAVE_SYSTEM=
  HAVE_FDATE=
  FC_NAMEMANGLE=
  HAVE_CLOC=
+ # HAVE_SETRLSTK=
  HAVE_STAT=
  HAVE_NETCDF=
  HAVE_ETIME=
-Line 861 
 BASH=
+Line 1089 
 BASH=
  PWD=`pwd`
  test "x$MAKE" = x  &&  MAKE=make
  test "x$AWK" = x   &&  AWK=awk
+ EMBED_SRC=
  THISHOST=`hostname`
  THISCWD=`pwd`
  THISDATE=`date`
-Line 894 
 TAMC_EXTRA=
+Line 1123 
 TAMC_EXTRA=
  #  The following state can be set directly by command-line switches
  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
- 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"
  #  The following state is not directly set by command-line switches
- 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"
  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
-Line 924 
 EOF
+Line 1153 
 EOF
  echo "===  Processing options files and arguments  ==="
  gm_local="genmake_local"
- modsCount=0
- for i in . $MODS ; do
-     if test -r $i/$gm_local ; then
-         . $i/$gm_local
-         break
-     fi
-     let modsCount=modsCount+1
- done
- if test $modsCount -gt 1 ; then
-   echo "ERROR: some uses of MODS break with more than one directory specified"
-   exit -1;
- fi
  printf "  getting local config information:  "
  if test -f $gm_local ; then
      echo "using $gm_local"
-Line 1082 
 for ac_option in "$@" ; do
+Line 1299 
 for ac_option in "$@" ; do
          -ts | --ts)
              TS=true ;;
+         -papis | --papis)
+             PAPIS=true ;;
+         -pcls | --pcls)
+             PCLS=true ;;
+         -foolad | --foolad)
+             FOOLAD=true ;;
+         -papi | --papi)
+             PAPI=true ;;
+         -pcl | --pcl)
+             PCL=true ;;
+         -hpmt | --hpmt)
+             HPMT=true ;;
+         -gsl | --gsl)
+             GSL=true ;;
+         -devel | --devel)
+             DEVEL=true ;;
          -mpi | --mpi)
              MPI=true ;;
-Line 1110 
 for ac_option in "$@" ; do
+Line 1345 
 for ac_option in "$@" ; do
          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
              IGNORE_TIME="-DIGNORE_TIME" ;;
+         -es | --es | -embed-source | --embed-source)
+             EMBED_SRC=t ;;
          -*)
              echo "Error: unrecognized option: "$ac_option
              usage
-Line 1128 
 done
+Line 1366 
 done
  if test -f ./.genmakerc ; then
      echo
      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
-     echo "  file.  This file format is no longer supported.  Please see:"
+     echo "  file.  This file format is no longer supported.  For directions on"
-     echo
+     echo "  how to setup and use the new \"genmake2\" script, please see:"
      echo "    http://mitgcm.org/devel_HOWTO/"
-     echo
+     echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
-     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."
      echo
  fi
  #  Find the MITgcm ${ROOTDIR}
  if test "x${ROOTDIR}" = x ; then
      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
-     if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then
+     if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
          ROOTDIR=".."
      else
          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
-Line 1308 
 Error: The command "ln -s" failed -- ple
+Line 1545 
 Error: The command "ln -s" failed -- ple
  EOF
      exit 1
  fi
+ test -L genmake_tlink > /dev/null 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     HAVE_TEST_L=t
+ fi
  rm -f genmake_test_ln genmake_tlink
  #  Check for broken *.F/*.f handling and fix if possible
-Line 1320 
 fi
+Line 1562 
 fi
  if test ! "x$TS" = x ; then
        echo "  Turning on timing per timestep"
-       DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
+       else
+             DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
+       fi
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PAPIS" = x ; then
+       echo "  Turning on PAPI flop summary per timestep"
+       echo "  Please make sure PAPIINC, PAPILIB are defined"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DUSE_PAPI_FLOPS_SFP"
+       else
+             DEFINES="$DEFINES -DUSE_PAPI_FLOPS"
+       fi
+       INCLUDES="$INCLUDES $PAPIINC"
+       LIBS="$LIBS $PAPILIB"
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PCLS" = x ; then
+       echo "  Turning on PCL counter summary per timestep"
+       echo "  Please make sure PCLINC, PCLLIB are defined"
+       if test ! "x$FOOLAD" = x ; then
+             DEFINES="$DEFINES -DUSE_PCL_FLOPS_SFP"
+       else
+             DEFINES="$DEFINES -DUSE_PCL_FLOPS"
+       fi
+       INCLUDES="$INCLUDES $PCLINC"
+       LIBS="$LIBS $PCLLIB"
+       PACKAGES="$PACKAGES showflops"
+ fi
+ if test ! "x$PAPI" = x ; then
+       if test ! "x$PAPIS" = x ; then
+           echo "  PAPI performance analysis and flop summary per timestep cannot co-exist!"
+           echo "  Sticking with PAPI flop summary per timestep!"
+       else
+           echo "  Turning on performance analysis with PAPI"
+           echo "  Please make sure PAPIINC, PAPILIB are defined"
+           DEFINES="$DEFINES -DUSE_PAPI"
+           INCLUDES="$INCLUDES $PAPIINC"
+           LIBS="$LIBS $PAPILIB"
+       fi
+ fi
+ if test ! "x$PCL" = x ; then
+       if test ! "x$PCLS" = x ; then
+           echo "  PCL performance analysis and flop summary per timestep cannot co-exist!"
+           echo "  Sticking with PCL flop summary per timestep!"
+       else
+           echo "  Turning on performance analysis with PCL"
+           echo "  Please make sure PCLINC, PCLLIB are defined"
+           DEFINES="$DEFINES -DUSE_PCL"
+           INCLUDES="$INCLUDES $PCLINC"
+           LIBS="$LIBS $PCLLIB"
+       fi
+ fi
+ if test ! "x$HPMT" = x ; then
+       if test ! "x$PAPI" = x ; then
+           echo "  PAPI and the HPM Toolkit cannot co-exist!"
+           echo "  Sticking with PAPI!"
+       else if test ! "x$PCL" = x ; then
+           echo "  PCL and the HPM Toolkit cannot co-exist!"
+           echo "  Sticking with PCL!"
+       else
+           echo "  Turning on performance analysis with the HPM Toolkit"
+           echo "  Please make sure HPMTINC, HPMTLIB are defined"
+           DEFINES="$DEFINES -DUSE_LIBHPM"
+           INCLUDES="$INCLUDES $HPMTINC"
+           LIBS="$LIBS $HPMTLIB"
+       fi
+       fi
+ fi
+ if test ! "x$GSL" = x ; then
+       echo "  Turning on use of GSL to control floating point calculations"
+       echo "  Please make sure GSLINC, GSLLIB are defined"
+       DEFINES="$DEFINES -DUSE_GSL_IEEE"
+       INCLUDES="$INCLUDES $GSLINC"
+       LIBS="$LIBS $GSLLIB"
  fi
  printf "\n===  Checking system libraries  ===\n"
-Line 1330 
 cat > genmake_tcomp.$FS <<EOF
+Line 1648 
 cat > genmake_tcomp.$FS <<EOF
        call system('echo hi')
        end
  EOF
- $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+ $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
  RETVAL=$?
  if test "x$RETVAL" = x0 ; then
      HAVE_SYSTEM=t
-Line 1345 
 rm -f genmake_tcomp*
+Line 1663 
 rm -f genmake_tcomp*
  printf "  Do we have the fdate() command using $FC...  "
  cat > genmake_tcomp.$FS <<EOF
        program hello
-       CHARACTER(128) string
+       CHARACTER*(128) string
        string = ' '
        call fdate( string )
        print *, string
        end
  EOF
- $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+ $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
  RETVAL=$?
  if test "x$RETVAL" = x0 ; then
      HAVE_FDATE=t
-Line 1373 
 cat > genmake_tcomp.$FS <<EOF
+Line 1691 
 cat > genmake_tcomp.$FS <<EOF
        print *, tarray
        end
  EOF
- $FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+ $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
  RETVAL=$?
  if test "x$RETVAL" = x0 ; then
      HAVE_ETIME=t
-Line 1391 
 if test "x$HAVE_CLOC" != x ; then
+Line 1709 
 if test "x$HAVE_CLOC" != x ; then
      echo "yes"
  else
      echo "no"
+     if test "x$EMBED_SRC" = xt ; then
+         echo "    WARNING: you requested file embedding but it has"
+         echo "      been disabled since C code cannot be called"
+         EMBED_SRC=
+     fi
+ fi
+ rm -f genmake_t*
+ printf "  Can we unlimit the stack size using $FC...  "
+ check_HAVE_SETRLSTK
+ if test "x$HAVE_SETRLSTK" = xt ; then
+     echo "yes"
+ else
+     echo "no"
+ fi
+ rm -f genmake_t*
+ printf "  Can we register a signal handler using $FC...  "
+ check_HAVE_SIGREG
+ if test "x$HAVE_SIGREG" = xt ; then
+     echo "yes"
+ else
+     echo "no"
  fi
  rm -f genmake_t*
-Line 1412 
 else
+Line 1753 
 else
  fi
  DEFINES="$DEFINES $IGNORE_TIME"
+ if test "x$EMBED_SRC" = xt ; then
+     build_embed_encode
+ fi
+ if test "x$EMBED_SRC" = xt ; then
+     ENABLE="$ENABLE embed_files"
+ fi
  printf "\n===  Setting defaults  ===\n"
  printf "  Adding MODS directories:  "
  for d in $MODS ; do
-Line 1497 
 if test -r $ROOTDIR"/eesupp/src/Makefile
+Line 1846 
 if test -r $ROOTDIR"/eesupp/src/Makefile
      fi
  fi
- #same for exch2
+ #same for pkg/exch2 and pkg/regrid
- if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
+ for pdir in exch2 regrid ; do
-     echo "  Making source files in exch2 from  templates"
+     if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
-     ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
+         echo "  Making source files in pkg/${pdir} from templates"
-     RETVAL=$?
+         ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
-     if test "x${RETVAL}" = x0 ; then
+         RETVAL=$?
-         rm -f make_exch2.errors
+         if test "x${RETVAL}" = x0 ; then
-     else
+             rm -f make_${pdir}.errors
-         echo "Error: problem encountered while building source files in exch2:"
+         else
-         cat make_exch2.errors 1>&2
+             echo "Error: problem encountered while building source files in pkg/${pdir}:"
-         exit 1
+             cat make_${pdir}.errors 1>&2
+             exit 1
+         fi
      fi
- fi
+ done
  printf "\n===  Determining package settings  ===\n"
  if  test "x${PDEPEND}" = x ; then
-Line 1620 
 done
+Line 1971 
 done
  rm -f ./.tmp_pack
  echo "    packages are:  $PACKAGES"
- #  Check availability of NetCDF and then either build the MNC template
+ #  Check for package MNC: if NetCDF is available, then build the MNC
- #  files or delete mnc from the list of available packages.
+ #  template files ; otherwise, delete mnc from the list of packages.
  echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
  RETVAL=$?
  if test "x$RETVAL" = x0 ; then
-Line 1655 
 EOF
+Line 2006 
 EOF
      fi
  fi
+ #  Check for package PROFILES: if NetCDF is not available,
+ #  then delete profiles from the list of available packages.
+ echo $PACKAGES | grep ' profiles ' > /dev/null 2>&1
+ RETVAL=$?
+ if test "x$RETVAL" = x0 ; then
+     if test "x$HAVE_NETCDF" != xt ; then
+         cat <<EOF
+ *********************************************************************
+ WARNING: the "profiles" package was enabled but tests failed to
+   compile NetCDF applications.  Please check that:
+) NetCDF is correctly installed for this compiler and
+) the LIBS variable (within the "optfile") specifies the correct
+        NetCDF library to link against.
+   Due to this failure, the "profiles" package is now DISABLED.
+ *********************************************************************
+ EOF
+         PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
+         DISABLE="$DISABLE profiles"
+     fi
+ fi
  echo "  applying package dependency rules"
  ck=
  while test "x$ck" != xtt ; do
      i=0
      # rtot=${#PNAME[@]}
      rtot=$nname
-     while test $i -lt $rtot ; do
+     while test $i -le $rtot ; do
          #  Is $pname in the current $PACKAGES list?
          #  pname=${PNAME[$i]}
-Line 1695 
 while test "x$ck" != xtt ; do
+Line 2071 
 while test "x$ck" != xtt ; do
          #  Do we need to add $dname according to the dependency rules?
          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
+             #echo "   " $pname ": need to add :" $dname
              in_dis="f"
              for dis in $DISABLE ; do
                  if test "x$dis" = "x$dname" ; then
-Line 1849 
 for i in $SOURCEDIRS ; do
+Line 2226 
 for i in $SOURCEDIRS ; do
          cat $i/$j >> adSrcFiles.tmp
      done
  done
  if test ! "x"$FS = "x.f" ; then
      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f
      mv -f adSrcFiles.tmp_f adSrcFiles.tmp
-Line 1864 
 for i in $INCLUDEDIRS ; do
+Line 2240 
 for i in $INCLUDEDIRS ; do
      fi
  done
+ if test ! "x$DIVA" = x ; then
+     echo "  Creating the pseudo-MPI include directory"
+     INCLUDES="-I./mpi_headers $INCLUDES"
+     rm -rf ./mpi_headers
+     mkdir -p ./mpi_headers
+     if test "x$MPIINCLUDEDIR" = x ; then
+         if test "x$MPIHOME" = x ; then
+             MPIHOME='/usr'
+         fi
+         MPIINCLUDEDIR='$MPIHOME/include'
+     fi
+     if test -r $MPIINCLUDEDIR/mpif.h ; then
+         for i in $MPI_HEADER_FILES; do
+             cp -p $MPIINCLUDEDIR/$i ./mpi_headers
+         done
+         perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
+     else
+         echo " We cannot create a copy of mpif.h!"
+ #       exit -1
+     fi
+ fi
  echo "  Determining the list of source and include files"
  rm -rf .links.tmp
  mkdir .links.tmp
+ touch .links.tmp/foo
+ if test ! -r ".links.tmp/foo" ; then
+     echo
+     echo "ERROR : something is wrong with your directory permissions or"
+     echo "   your user file-creation mask (\"umask\") since creating a"
+     echo "   sub-dir, touch-ing a file within it, and then reading it is"
+     echo "   not working.  Please try setting your umask to something"
+     echo "   sane such as:"
+     echo
+     echo "      umask 0002"
+     echo
+     echo "   and please verify that you have the proper permissions for"
+     echo "   creating sub-directories and then reading files created"
+     echo "   within them."
+     echo
+     exit 1
+ fi
+ rm -f .links.tmp/foo
  echo "# This section creates symbolic links" > srclinks.tmp
  echo "" >> srclinks.tmp
  printf 'F77_SRC_FILES = ' > F77srclist.tmp
-Line 1892 
 for d in $alldirs ; do
+Line 2311 
 for d in $alldirs ; do
                    ./BUILD_INFO.h)
                          ;;
                    *)
-                         touch .links.tmp/$sf
+                         #  For the local directory *ONLY*,
-                         deplist="$deplist $sf"
+                         #  ignore all soft-links
+                         if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
+                             ignore_f=t
+                         else
+                             touch .links.tmp/$sf
+                             deplist="$deplist $sf"
+                         fi
                          ;;
                  esac
                  extn=`echo $sf | $AWK -F. '{print $NF}'`
-Line 1959 
 echo "" >> hsrclist.tmp
+Line 2384 
 echo "" >> hsrclist.tmp
  if test -f $MAKEFILE ; then
      mv -f $MAKEFILE "$MAKEFILE.bak"
  fi
  echo "  Writing makefile: $MAKEFILE"
  echo "# Multithreaded + multi-processing makefile for:" > $MAKEFILE
  echo "#    $MACHINE" >> $MAKEFILE
  echo "# This makefile was generated automatically on" >> $MAKEFILE
-Line 2011 
 EXE_AD      = ${EXE_AD}
+Line 2434 
 EXE_AD      = ${EXE_AD}
  EXE_FTL     = ${EXE_FTL}
  EXE_SVD     = ${EXE_SVD}
- ENABLED_PACKAGES  = ${ENABLED_PACKAGES}
+ ENABLED_PACKAGES = ${ENABLED_PACKAGES}
  DISABLED_PACKAGES = ${DISABLED_PACKAGES}
  # These files are created by Makefile
  SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h BUILD_INFO.h
  EOF
- #  Note: figure out some way to add Hyades JAM libraries here
+ if test "x$EMBED_SRC" = xt ; then
+     echo "EMBEDDED_FILES = EMBEDDED_FILES.h" >>$MAKEFILE
+ else
+     echo "EMBEDDED_FILES = " >>$MAKEFILE
+ fi
+ #  Note: figure out some way to add Hyades JAM libraries here
  cat >>$MAKEFILE <<EOF
  # Unix ln (link)
  LN = ${LN}
-Line 2047 
 INCLUDES = ${INCLUDES}
+Line 2474 
 INCLUDES = ${INCLUDES}
  KFLAGS1 = ${KFLAGS1}
  KFLAGS2 = ${KFLAGS2}
  # Optim./debug for FC
- FFLAGS = ${FFLAGS}
+ FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
  FOPTIM = ${FOPTIM}
- # Optim./debug/format for FC
+ # Optim./debug for FC
  F90FLAGS = ${F90FLAGS}
  F90OPTIM = ${F90OPTIM}
  F90FIXEDFORMAT = ${F90FIXEDFORMAT}
-Line 2156 
 cat >>$MAKEFILE <<EOF
+Line 2583 
 cat >>$MAKEFILE <<EOF
  .f$FS90.o:
          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$(F90FIXEDFORMAT) \$<
  .c.o:
-         \$(CC) \$(CFLAGS) -c \$<
+         \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
  .F.p:
-Line 2268 
 GLOBAL_SUM \
+Line 2695 
 GLOBAL_SUM \
  GMREDI \
  GMREDI_TAVE \
  GRID \
+ MNC_BUFF \
+ MNC_COMMON \
+ MNC_PARAMS \
  MPI_INFO \
  RESTART \
+ SIGREG \
  SOLVE_FOR_PRESSURE3D \
  SOLVE_FOR_PRESSURE \
  SURFACE \
-Line 2366 
 ad_input_code_sf.f$FS90 : ad_input_code.
+Line 2797 
 ad_input_code_sf.f$FS90 : ad_input_code.
  ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90
          ./mfef90 -z -F -N132 \$<
          mv \$<.B \$(basename \$<).B
-         ./whirl2f \$(basename \$<).B
+         ./whirl2f -openad \$(basename \$<).B
          cat w2f__types.f90 \$(basename \$<).w2f.f > \$@
  # canonicalizer
-Line 2440 
 ncheckLev.conf :
+Line 2871 
 ncheckLev.conf :
  whirl2xaif xaif2whirl:
-         \$(LN) \${OPENADROOT}/OpenADFortTk/OpenADFortTk-x86-Linux/bin/\$@ .
+         \$(LN) \${OPENADFORTTK}/bin/\$@ .
  %.pl:
-         \$(LN) \${OPENADROOT}/OpenADFortTk/OpenADFortTk-x86-Linux/bin/\$@ .
+         \$(LN) \${OPENADFORTTK}/bin/\$@ .
  %.py:
          \$(LN) \${OPENADROOT}/OpenADFortTk/tools/canonicalize/\$@ .

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Added in v.1.6
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Added in v.1.6
-Removed from v.1.3
+Added in v.1.6

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