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revision 1.206 by jmc, Sun May 23 18:34:43 2010 UTC revision 1.220 by jmc, Fri Jun 3 19:53:45 2011 UTC
# Line 1  Line 1 
1  #! /usr/bin/env bash  #! /usr/bin/env bash
2  #  #
3  # $Header$  # $Header$
4    # $Name$
5  #  #
6  # Makefile generator for MITgcm UV codes  # Makefile generator for MITgcm UV codes
7  #   created  by cnh 03/98  #   created  by cnh 03/98
# Line 8  Line 9 
9  #   modified by aja 01/00  #   modified by aja 01/00
10  #   rewritten in bash by eh3 08/03  #   rewritten in bash by eh3 08/03
11    
12    #  Explain usage
13    usage()  {
14    cat <<EOF
15    
16    Usage: "$0" [OPTIONS]
17      where [OPTIONS] can be:
18    
19        -help | --help | -h | --h
20              Print this help message and exit.
21    
22        -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
23          -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
24              Use "NAME" as the adoptfile.  By default, the file at
25              "tools/adjoint_options/adjoint_default" will be used.
26    
27        -nooptfile | --nooptfile
28          -optfile NAME | --optfile NAME | -of NAME | --of NAME
29          -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
30              Use "NAME" as the optfile.  By default, an attempt will be
31              made to find an appropriate "standard" optfile in the
32              tools/build_options/ directory.
33    
34        -pdepend NAME | --pdepend NAME
35          -pdepend=NAME | --pdepend=NAME
36              Get package dependency information from "NAME".
37    
38        -pgroups NAME | --pgroups NAME
39          -pgroups=NAME | --pgroups=NAME
40              Get the package groups information from "NAME".
41    
42        -bash NAME
43              Explicitly specify the Bourne or BASH shell to use
44    
45        -make NAME | -m NAME
46          --make=NAME | -m=NAME
47              Use "NAME" for the MAKE program. The default is "make" but
48              many platforms, "gmake" is the preferred choice.
49    
50        -makefile NAME | -mf NAME
51          --makefile=NAME | -mf=NAME
52              Call the makefile "NAME".  The default is "Makefile".
53    
54        -makedepend NAME | -md NAME
55          --makedepend=NAME | -md=NAME
56              Use "NAME" for the MAKEDEPEND program.
57    
58        -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
59          -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
60              Specify the location of the MITgcm ROOTDIR as "NAME".
61              By default, genamke will try to find the location by
62              looking in parent directories (up to the 5th parent).
63    
64        -mods NAME | --mods NAME | -mo NAME | --mo NAME
65          -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
66              Here, "NAME" specifies a list of directories that are
67              used for additional source code.  Files found in the
68              "mods list" are given preference over files of the same
69              name found elsewhere.
70    
71        -disable NAME | --disable NAME
72          -disable=NAME | --disable=NAME
73              Here "NAME" specifies a list of packages that we don't
74              want to use.  If this violates package dependencies,
75              genamke will exit with an error message.
76    
77        -enable NAME | --enable NAME
78          -enable=NAME | --enable=NAME
79              Here "NAME" specifies a list of packages that we wish
80              to specifically enable.  If this violates package
81              dependencies, genamke will exit with an error message.
82    
83        -standarddirs NAME | --standarddirs NAME
84          -standarddirs=NAME | --standarddirs=NAME
85              Here, "NAME" specifies a list of directories to be
86              used as the "standard" code.
87    
88        -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
89          -fc=NAME | --fc=NAME
90              Use "NAME" as the fortran compiler.  By default, genmake
91              will search for a working compiler by trying a list of
92              "usual suspects" such as g77, f77, etc.
93    
94        -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
95              Use "NAME" as the C compiler.  By default, genmake
96              will search for a working compiler by trying a list of
97              "usual suspects" such as gcc, c89, cc, etc.
98    
99        -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
100              Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
101              *only* works if CPP_EEOPTIONS.h allows this.
102    
103        -ignoretime | -ignore_time | --ignoretime | --ignore_time
104              Ignore all the "wall clock" routines entirely.  This will
105              not in any way hurt the model results -- it simply means
106              that the code that checks how long the model spends in
107              various routines will give junk values.
108    
109        -ts | --ts
110              Produce timing information per timestep
111        -papis | --papis
112              Produce summary MFlop/s (and IPC) with PAPI per timestep
113        -pcls | --pcls
114              Produce summary MFlop/s etc. with PCL per timestep
115        -foolad | --foolad
116              Fool the AD code generator
117        -papi | --papi
118              Performance analysis with PAPI
119        -pcl | --pcl
120              Performance analysis with PCL
121        -hpmt | --hpmt
122              Performance analysis with the HPM Toolkit
123    
124        -ieee | --ieee
125              use IEEE numerics.  Note that this option *only* works
126              if it is supported by the OPTFILE that is being used.
127        -devel | --devel
128              Add additional warning and debugging flags for development
129              (if supported by the OPTFILE); also switch to IEEE numerics.
130        -gsl | --gsl
131              Use GSL to control floating point rounding and precision
132    
133        -mpi | --mpi
134              Include MPI header files and link to MPI libraries
135        -mpi=PATH | --mpi=PATH
136              Include MPI header files and link to MPI libraries using MPI_ROOT
137              set to PATH. i.e. Include files from \$PATH/include, link to libraries
138              from \$PATH/lib and use binaries from \$PATH/bin.
139    
140        -omp | --omp
141              Activate OpenMP code + use Compiler option OMPFLAG
142        -omp=OMPFLAG | --omp=OMPFLAG
143              Activate OpenMP code + use Compiler option OMPFLAG
144    
145        -es | --es | -embed-source | --embed-source
146              Embed a tarball containing the full source code
147              (including the Makefile, etc.) used to build the
148              executable [off by default]
149    
150        -ds | --ds
151              Report genmake internal variables status (DUMPSTATE)
152              to file "genmake_state" (for debug purpose)
153    
154      While it is most often a single word, the "NAME" variables specified
155      above can in many cases be a space-delimited string such as:
156    
157        --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
158        -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
159        -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
160    
161      which, depending upon your shell, may need to be single-quoted.
162    
163      For more detailed genmake documentation, please see:
164    
165        http://mitgcm.org/public/devel_HOWTO/
166    
167    EOF
168    
169        exit 1
170    }
171    
172  # Search for particular CPP #cmds associated with packages  # Search for particular CPP #cmds associated with packages
173  # usage: test_for_package_in_cpp_options CPP_file package_name  # usage: test_for_package_in_cpp_options CPP_file package_name
174  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
# Line 56  test_for_string_in_file() { Line 217  test_for_string_in_file() {
217  # the package list.  # the package list.
218  expand_pkg_groups() {  expand_pkg_groups() {
219      new_packages=      new_packages=
     PKG_GROUPS=$ROOTDIR"/pkg/pkg_groups"  
220      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
221          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp
222          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp
# Line 67  expand_pkg_groups() { Line 227  expand_pkg_groups() {
227              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
228                  matched=1                  matched=1
229                  replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`                  replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`
230                  echo "    replacing \"$i\" with: $replace"                  echo "    replacing \"$i\" with:$replace"
231                  new_packages="$new_packages $replace"                  new_packages="$new_packages $replace"
232              else              else
233                  new_packages="$new_packages $i"                  new_packages="$new_packages $i"
# Line 165  EOF Line 325  EOF
325      return      return
326  }  }
327    
   
328  look_for_makedepend()  {  look_for_makedepend()  {
329    
330      #  The "original" makedepend is part of the Imake system that is      #  The "original" makedepend is part of the Imake system that is
# Line 186  look_for_makedepend()  { Line 345  look_for_makedepend()  {
345      #    3) locally build and use the cyrus implementation      #    3) locally build and use the cyrus implementation
346      #    4) fall back to the buggy local xmakedpend script      #    4) fall back to the buggy local xmakedpend script
347      #      #
348        echo >> $LOGFILE
349        echo "running: look_for_makedepend()" >> $LOGFILE
350        if test "x${MAKEDEPEND}" != x ; then
351            echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
352            RETVAL=$?
353            if test x"$RETVAL" = x0 ; then
354                build_cyrus_makedepend
355                RETVAL=$?
356                if test "x$RETVAL" != x0 ; then
357                    echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"
358                    MAKEDEPEND=
359                fi
360            else
361                echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
362            fi
363        fi
364      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
365          which makedepend > /dev/null 2>&1          which makedepend > /dev/null 2>&1
366          RV0=$?          RV0=$?
# Line 210  EOF Line 385  EOF
385          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
386          if test "x${RV0}${RV1}" = x00 ; then          if test "x${RV0}${RV1}" = x00 ; then
387              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
388                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
389          else          else
390              echo "    a system-default makedepend was not found."              echo "    system-default makedepend not found. Try to build cyrus-makedepend"
   
391              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
392              build_cyrus_makedepend              build_cyrus_makedepend
393              RETVAL=$?              RETVAL=$?
394              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
395                    echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"
396                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
397                    echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
398              fi              fi
             rm -f ./genmake_cy_md  
         fi  
     else  
         #  echo "MAKEDEPEND=${MAKEDEPEND}"  
         echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1  
         RETVAL=$?  
         if test x"$RETVAL" = x0 ; then  
             build_cyrus_makedepend  
399          fi          fi
400      fi      fi
401  }  }
402    
   
403  build_cyrus_makedepend()  {  build_cyrus_makedepend()  {
404        echo >> $LOGFILE
405        echo "running: build_cyrus_makedepend()" >> $LOGFILE
406      rm -f ./genmake_cy_md      rm -f ./genmake_cy_md
407      (      (
408          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
# Line 249  build_cyrus_makedepend()  { Line 419  build_cyrus_makedepend()  {
419      rm -f ./genmake_cy_md      rm -f ./genmake_cy_md
420      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
421          MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'          MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
422            echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
423          return 0          return 0
424      else      else
425          echo "WARNING: unable to build cyrus-imapd-makedepend"          echo "WARNING: fail to build cyrus-imapd-makedepend" >> $LOGFILE
426          return 1          return 1
427      fi      fi
428  }  }
429    
   
430  build_embed_encode()  build_embed_encode()
431  {  {
432      printf "  building the embed-encode utility...  "      printf "  building the embed-encode utility...  "
# Line 290  build_embed_encode() Line 460  build_embed_encode()
460      DEFINES="$DEFINES -DHAVE_EMBED_SRC"      DEFINES="$DEFINES -DHAVE_EMBED_SRC"
461  }  }
462    
463    #  look for possible C compilers
464  # Guess possible config options for this host  look_for_C_compilers() {
465  find_possible_configs()  {      echo >> $LOGFILE
466        echo "running: look_for_C_compilers()" >> $LOGFILE
467      tmp1=`uname`"_"`uname -m`      rm -f ./genmake_hello.c  ./genmake_hello
468      tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`      cat >> genmake_hello.c << EOF
     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`  
     tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`  
     tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`  
     tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`  
     PLATFORM=$tmp3  
     echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32  
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`  
     echo "  The platform appears to be:  $PLATFORM"  
   
     echo "test" > test  
     ln -s ./test link  
     RETVAL=$?  
     if test "x${RETVAL}" = x0 ; then  
         LN="ln -s"  
     else  
         echo "Error: \"ln -s\" does not appear to work on this system!"  
         echo "  For help, please contact <MITgcm-support@mitgcm.org>."  
         exit 1  
     fi  
     rm -f test link  
   
     if test "x$CPP" = x ; then  
         CPP="cpp -traditional -P"  
     fi  
   
     look_for_makedepend  
   
     #================================================================  
     #  look for possible C compilers  
     tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"  
     p_CC=  
     for c in $tmp ; do  
         rm -f ./genmake_hello.c  ./genmake_hello  
         cat >> genmake_hello.c << EOF  
469  #include <stdio.h>  #include <stdio.h>
470  int main(int argc, char **argv) {  int main(int argc, char **argv) {
471    printf("Hello!\n");    printf("Hello!\n");
472    return 0;    return 0;
473  }  }
474  EOF  EOF
475          $c -o genmake_hello genmake_hello.c > /dev/null 2>&1      tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
476        p_CC=
477        for c in $tmp ; do
478            COMM="$c $CFLAGS -o genmake_hello genmake_hello.c"
479            echo $COMM >> $LOGFILE
480            $COMM >> $LOGFILE 2>&1
481          RETVAL=$?          RETVAL=$?
482          if test "x${RETVAL}" = x0 ; then          if test "x${RETVAL}" = x0 ; then
483                echo " $c test successful" >> $LOGFILE
484              p_CC="$p_CC $c"              p_CC="$p_CC $c"
485          fi          fi
486      done      done
# Line 354  Error: No C compilers were found in your Line 496  Error: No C compilers were found in your
496  EOF  EOF
497          exit 1          exit 1
498      else      else
499          echo "  The possible C compilers found in your path are:"          echo "  The possible C compilers found in your path are: $p_CC" | tee -a $LOGFILE
         echo "   "$p_CC  
500          if test "x$CC" = x ; then          if test "x$CC" = x ; then
501              CC=`echo $p_CC | $AWK '{print $1}'`              CC=`echo $p_CC | $AWK '{print $1}'`
502              echo "  Setting C compiler to: "$CC              echo "  Setting C compiler to: "$CC
503          fi          fi
504      fi      fi
505        echo " --> set CC='$CC'" >> $LOGFILE
506    }
507    
508    # Guess possible config options for this host
509    find_possible_optfile()  {
510    
511        echo >> $LOGFILE
512        echo "running: find_possible_optfile()" >> $LOGFILE
513        tmp1=`uname`"_"`uname -m`
514        tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
515        tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
516        tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
517        tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
518        tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
519        PLATFORM=$tmp3
520        echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
521        OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
522        echo "  The platform appears to be:  $PLATFORM" | tee -a $LOGFILE
523    
524      #================================================================      #================================================================
525      #  look for possible FORTRAN compilers      #  look for possible FORTRAN compilers
526      tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"      echo "  look for possible FORTRAN compilers" >> $LOGFILE
527        tmp="$MITGCM_FC $FC efc gfortran g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 g95"
528      p_FC=      p_FC=
529      for c in $tmp ; do      rm -f ./genmake_hello.f
530          rm -f ./hello.f ./hello      cat >> genmake_hello.f <<EOF
         cat >> hello.f <<EOF  
531        program hello        program hello
532        do i=1,3        do i=1,3
533          print *, 'hello world : ', i          print *, 'hello world : ', i
534        enddo        enddo
535        end        end
536  EOF  EOF
537          $c -o hello hello.f > /dev/null 2>&1      for f in $tmp ; do
538            COMM="$f -o genmake_hello genmake_hello.f"
539            echo $COMM >> $LOGFILE
540            $COMM >> $LOGFILE 2>&1
541          RETVAL=$?          RETVAL=$?
542          if test "x${RETVAL}" = x0 ; then          if test "x${RETVAL}" = x0 ; then
543              p_FC="$p_FC $c"              echo " $f test successful" >> $LOGFILE
544                p_FC="$p_FC $f"
545          fi          fi
546      done      done
547      rm -f ./hello.f ./hello      rm -f ./genmake_hello.f ./genmake_hello
548      if test "x${p_FC}" = x ; then      if test "x${p_FC}" = x ; then
549          cat 1>&2 <<EOF          cat 1>&2 <<EOF
550    
# Line 394  Error: No Fortran compilers were found i Line 557  Error: No Fortran compilers were found i
557  EOF  EOF
558          exit 1          exit 1
559      else      else
560          echo "  The possible FORTRAN compilers found in your path are:"          echo "  The possible FORTRAN compilers found in your path are: $p_FC" | tee -a $LOGFILE
         echo "   "$p_FC  
561      fi      fi
562    
563      #  Use the first of the compilers found in the current PATH      #  Use the first of the compilers found in the current PATH
# Line 404  EOF Line 566  EOF
566          for i in $p_FC ; do          for i in $p_FC ; do
567              OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i              OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
568              if test -r $OPTFILE ; then              if test -r $OPTFILE ; then
569                  echo "  Setting OPTFILE to: "$OPTFILE                  echo "  Setting OPTFILE to: "$OPTFILE | tee -a $LOGFILE
570                  break                  break
571              fi              fi
572          done          done
# Line 416  EOF Line 578  EOF
578               echo "  I looked for the file "$OPTFILE" but did not find it"               echo "  I looked for the file "$OPTFILE" but did not find it"
579          fi          fi
580      fi      fi
581  #    echo "  The options file:  $p_OF"  
 #    echo "    appears to match so we'll use it."  
 #   for i in $p_FC ; do  
 #p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i  
 #if test -r $p_OF ; then  
 #    OPTFILE=$p_OF  
 #    echo "  The options file:  $p_OF"  
 #    echo "    appears to match so we'll use it."  
 #    break  
 #fi  
 #   done  
582      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
583          cat 1>&2 <<EOF          cat 1>&2 <<EOF
584    
# Line 471  EOF Line 623  EOF
623  #       fi  #       fi
624  #       rm -f test.f out  #       rm -f test.f out
625  #     fi  #     fi
   
626  }  }
627    
628  #  Parse the package dependency information  #  Parse the package dependency information
# Line 484  get_pdepend_list()  { Line 635  get_pdepend_list()  {
635          > ./.pd_tmp          > ./.pd_tmp
636      RETVAL=$?      RETVAL=$?
637      if test ! "x${RETVAL}" = x0 ; then      if test ! "x${RETVAL}" = x0 ; then
638        echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$1\""        echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
639        exit 1        exit 1
640      fi      fi
641      . ./.pd_tmp      . ./.pd_tmp
642      rm -f ./.pd_tmp      rm -f ./.pd_tmp
   
 }  
   
   
 #  Explain usage  
 usage()  {  
 cat <<EOF  
   
 Usage: "$0" [OPTIONS]  
   where [OPTIONS] can be:  
   
     -help | --help | -h | --h  
           Print this help message and exit.  
   
     -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME  
       -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME  
           Use "NAME" as the adoptfile.  By default, the file at  
           "tools/adjoint_options/adjoint_default" will be used.  
   
     -nooptfile | --nooptfile  
       -optfile NAME | --optfile NAME | -of NAME | --of NAME  
       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME  
           Use "NAME" as the optfile.  By default, an attempt will be  
           made to find an appropriate "standard" optfile in the  
           tools/build_options/ directory.  
   
     -pdepend NAME | --pdepend NAME  
       -pdepend=NAME | --pdepend=NAME  
           Get package dependency information from "NAME".  
   
     -pdefault NAME | --pdefault NAME  
       -pdefault=NAME | --pdefault=NAME  
           Get the default package list from "NAME".  
   
     -bash NAME  
           Explicitly specify the Bourne or BASH shell to use  
   
     -make NAME | -m NAME  
       --make=NAME | -m=NAME  
           Use "NAME" for the MAKE program. The default is "make" but  
           many platforms, "gmake" is the preferred choice.  
   
     -makefile NAME | -mf NAME  
       --makefile=NAME | -mf=NAME  
           Call the makefile "NAME".  The default is "Makefile".  
   
     -makedepend NAME | -md NAME  
       --makedepend=NAME | -md=NAME  
           Use "NAME" for the MAKEDEPEND program.  
   
     -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME  
       -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME  
           Specify the location of the MITgcm ROOTDIR as "NAME".  
           By default, genamke will try to find the location by  
           looking in parent directories (up to the 5th parent).  
   
     -mods NAME | --mods NAME | -mo NAME | --mo NAME  
       -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME  
           Here, "NAME" specifies a list of directories that are  
           used for additional source code.  Files found in the  
           "mods list" are given preference over files of the same  
           name found elsewhere.  
   
     -disable NAME | --disable NAME  
       -disable=NAME | --disable=NAME  
           Here "NAME" specifies a list of packages that we don't  
           want to use.  If this violates package dependencies,  
           genamke will exit with an error message.  
   
     -enable NAME | --enable NAME  
       -enable=NAME | --enable=NAME  
           Here "NAME" specifies a list of packages that we wish  
           to specifically enable.  If this violates package  
           dependencies, genamke will exit with an error message.  
   
     -standarddirs NAME | --standarddirs NAME  
       -standarddirs=NAME | --standarddirs=NAME  
           Here, "NAME" specifies a list of directories to be  
           used as the "standard" code.  
   
     -fortran NAME | --fortran NAME | -fc NAME | --fc NAME  
       -fc=NAME | --fc=NAME  
           Use "NAME" as the fortran compiler.  By default, genmake  
           will search for a working compiler by trying a list of  
           "usual suspects" such as g77, f77, etc.  
   
     -cc NAME | --cc NAME | -cc=NAME | --cc=NAME  
           Use "NAME" as the C compiler.  By default, genmake  
           will search for a working compiler by trying a list of  
           "usual suspects" such as gcc, c89, cc, etc.  
   
     -[no]ieee | --[no]ieee  
           Do or don't use IEEE numerics.  Note that this option  
           *only* works if it is supported by the OPTFILE that  
           is being used.  
   
     -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4  
           Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)  
           *only* works if CPP_EEOPTIONS.h allows this.  
   
     -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  
     -mpi=PATH | --mpi=PATH  
           Include MPI header files and link to MPI libraries using MPI_ROOT  
           set to PATH. i.e. Include files from \$PATH/include, link to libraries  
           from \$PATH/lib and use binaries from \$PATH/bin.  
   
     -omp | --omp  
           Activate OpenMP code + use Compiler option OMPFLAG  
     -omp=OMPFLAG | --omp=OMPFLAG  
           Activate OpenMP code + use Compiler option OMPFLAG  
   
     -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]  
   
   While it is most often a single word, the "NAME" variables specified  
   above can in many cases be a space-delimited string such as:  
   
     --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'  
     -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'  
     -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'  
   
   which, depending upon your shell, may need to be single-quoted.  
   
   For more detailed genmake documentation, please see:  
   
     http://mitgcm.org/public/devel_HOWTO/  
   
 EOF  
   
     exit 1  
643  }  }
644    
645  #  Build a CPP macro to automate calling C routines from FORTRAN  #  Build a CPP macro to automate calling C routines from FORTRAN
# Line 657  get_fortran_c_namemangling()  { Line 649  get_fortran_c_namemangling()  {
649      if test ! "x$FC_NAMEMANGLE" = x ; then      if test ! "x$FC_NAMEMANGLE" = x ; then
650          return 0          return 0
651      fi      fi
652        echo " running: get_fortran_c_namemangling()" >> $LOGFILE
653    
654      default_nm="#define FC_NAMEMANGLE(X) X ## _"      default_nm="#define FC_NAMEMANGLE(X) X ## _"
655    
656      cat > genmake_test.c <<EOF      cat > genmake_test.c <<EOF
657  void tcall( char * string ) { tsub( string ); }  void tcall( char * string ) { tsub( string ); }
658  EOF  EOF
659      $MAKE genmake_test.o >> genmake_warnings 2>&1      COMM="$CC $CFLAGS -c genmake_test.c"
660        echo ' '$COMM >> $LOGFILE
661        $COMM >> $LOGFILE 2>&1
662      RETVAL=$?      RETVAL=$?
663      if test "x$RETVAL" != x0 ; then      if test "x$RETVAL" != x0 ; then
664          FC_NAMEMANGLE=$default_nm          FC_NAMEMANGLE=$default_nm
665          cat <<EOF>> genmake_errors          cat <<EOF>> $LOGFILE
666    
667  WARNING: C test compile fails   WARNING: C test compile fails
668  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'   WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
669  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here   WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
670  EOF  EOF
671          return 1          return 1
672      fi      fi
# Line 679  EOF Line 674  EOF
674      RETVAL=$?      RETVAL=$?
675      if test "x$RETVAL" != x0 ; then      if test "x$RETVAL" != x0 ; then
676          FC_NAMEMANGLE=$default_nm          FC_NAMEMANGLE=$default_nm
677          cat <<EOF>> genmake_warnings          cat <<EOF>> $LOGFILE
678    
679  WARNING: The "nm" command failed.   WARNING: The "nm" command failed.
680  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'   WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
681  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here   WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
682  EOF  EOF
683          return 1          return 1
684      fi      fi
# Line 693  EOF Line 688  EOF
688        call tsub( string )        call tsub( string )
689        end        end
690  EOF  EOF
691      $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1      COMM="$FC $FFLAGS -c genmake_tcomp.$FS"
692        echo ' '$COMM >> $LOGFILE
693        $COMM >> $LOGFILE 2>&1
694      RETVAL=$?      RETVAL=$?
695      if test "x$RETVAL" != x0 ; then      if test "x$RETVAL" != x0 ; then
696          FC_NAMEMANGLE=$default_nm          FC_NAMEMANGLE=$default_nm
697          cat <<EOF>> genmake_warnings          cat <<EOF>> $LOGFILE
698    
699  WARNING: FORTRAN test compile fails -- please see "genmake_errors"   WARNING: FORTRAN test compile fails -- please see '$LOGFILE'
700  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'   WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
701  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.   WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
702  EOF  EOF
703          return 1          return 1
704      fi      fi
# Line 709  EOF Line 706  EOF
706      RETVAL=$?      RETVAL=$?
707      if test "x$RETVAL" != x0 ; then      if test "x$RETVAL" != x0 ; then
708          FC_NAMEMANGLE=$default_nm          FC_NAMEMANGLE=$default_nm
709          cat <<EOF>> genmake_warnings          cat <<EOF>> $LOGFILE
710    
711  WARNING: The "nm" command failed.   WARNING: The "nm" command failed.
712  WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'   WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
713  WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.   WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
714  EOF  EOF
715          return 1          return 1
716      fi      fi
# Line 739  EOF Line 736  EOF
736    
737      #  cleanup the testing files      #  cleanup the testing files
738      rm -f genmake_tcomp.* genmake_test.*      rm -f genmake_tcomp.* genmake_test.*
 }  
739    
740        echo " --> set FC_NAMEMANGLE='$FC_NAMEMANGLE'" >> $LOGFILE
741    }
742    
743  check_HAVE_CLOC()  {  check_HAVE_CLOC()  {
744        echo >> $LOGFILE
745        echo "running: check_HAVE_CLOC()" >> $LOGFILE
746      get_fortran_c_namemangling      get_fortran_c_namemangling
747      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
748  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 760  void FC_NAMEMANGLE(cloc) ( double *curti Line 760  void FC_NAMEMANGLE(cloc) ( double *curti
760  }  }
761  EOF  EOF
762      COMM="$CC $CFLAGS -c genmake_tc_1.c"      COMM="$CC $CFLAGS -c genmake_tc_1.c"
763      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
764      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
765      RET_C=$?      RET_C=$?
766      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
767        program hello        program hello
# Line 772  EOF Line 772  EOF
772        end        end
773  EOF  EOF
774      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
775      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
776      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
777      RET_F=$?      RET_F=$?
778      test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1      test -x ./genmake_tc  &&  ./genmake_tc >> $LOGFILE 2>&1
779      RETVAL=$?      RETVAL=$?
780      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
781          HAVE_CLOC=t          HAVE_CLOC=t
782          DEFINES="$DEFINES -DHAVE_CLOC"          DEFINES="$DEFINES -DHAVE_CLOC"
783      fi      fi
784      rm -f genmake_tc*      rm -f genmake_tc*
785        echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
786  }  }
787    
   
788  check_HAVE_SIGREG()  {  check_HAVE_SIGREG()  {
789      if test ! "x$HAVE_SIGREG" = x ; then      if test ! "x$HAVE_SIGREG" = x ; then
790          return          return
791      fi      fi
792        echo >> $LOGFILE
793        echo "running: check_HAVE_SIGREG()" >> $LOGFILE
794      get_fortran_c_namemangling      get_fortran_c_namemangling
795      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
796  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 821  void FC_NAMEMANGLE(sigreg) (int * aip) Line 823  void FC_NAMEMANGLE(sigreg) (int * aip)
823  }  }
824  EOF  EOF
825      COMM="$CC $CFLAGS -c genmake_tc_1.c"      COMM="$CC $CFLAGS -c genmake_tc_1.c"
826      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
827      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
828      RET_C=$?      RET_C=$?
829      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
830        program hello        program hello
# Line 832  EOF Line 834  EOF
834        call sigreg(anint)        call sigreg(anint)
835        end        end
836  EOF  EOF
837      echo >> genmake_warnings      cat genmake_tc_2.$FS >> $LOGFILE
     echo "running: check_HAVE_SIGREG()" >> genmake_warnings  
     cat genmake_tc_2.$FS >> genmake_warnings  
838      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
839      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
840      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
841      RETVAL=$?      RETVAL=$?
842      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
843          HAVE_SIGREG=t          HAVE_SIGREG=t
844          DEFINES="$DEFINES -DHAVE_SIGREG"          DEFINES="$DEFINES -DHAVE_SIGREG"
845      fi      fi
846      rm -f genmake_tc*      rm -f genmake_tc*
847        echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
848  }  }
849    
   
850  check_HAVE_SETRLSTK()  {  check_HAVE_SETRLSTK()  {
851      if test "x$HAVE_SETRLSTK" = xt ; then      if test "x$HAVE_SETRLSTK" = xt ; then
852          DEFINES="$DEFINES -DHAVE_SETRLSTK"          DEFINES="$DEFINES -DHAVE_SETRLSTK"
# Line 855  check_HAVE_SETRLSTK()  { Line 855  check_HAVE_SETRLSTK()  {
855      if test ! "x$HAVE_SETRLSTK" = x ; then      if test ! "x$HAVE_SETRLSTK" = x ; then
856          return          return
857      fi      fi
858        echo >> $LOGFILE
859        echo "running: check_HAVE_SETRLSTK()" >> $LOGFILE
860      get_fortran_c_namemangling      get_fortran_c_namemangling
861      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
862  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 871  void FC_NAMEMANGLE(setrlstk) () Line 873  void FC_NAMEMANGLE(setrlstk) ()
873  }  }
874  EOF  EOF
875      COMM="$CC $CFLAGS -c genmake_tc_1.c"      COMM="$CC $CFLAGS -c genmake_tc_1.c"
876      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
877      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
878      RET_C=$?      RET_C=$?
879      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
880        program hello        program hello
# Line 880  EOF Line 882  EOF
882        call setrlstk()        call setrlstk()
883        end        end
884  EOF  EOF
885      echo >> genmake_warnings      cat genmake_tc_2.$FS >> $LOGFILE
     echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings  
     cat genmake_tc_2.$FS >> genmake_warnings  
886      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
887      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
888      $COMM >> genmake_warnings 2>&1      $COMM >> $LOGFILE 2>&1
889      RETVAL=$?      RETVAL=$?
890      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
891          HAVE_SETRLSTK=t          HAVE_SETRLSTK=t
892          DEFINES="$DEFINES -DHAVE_SETRLSTK"          DEFINES="$DEFINES -DHAVE_SETRLSTK"
893      fi      fi
894      rm -f genmake_tc*      rm -f genmake_tc*
895        echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
896  }  }
897    
   
898  check_HAVE_STAT()  {  check_HAVE_STAT()  {
899        echo >> $LOGFILE
900        echo "running: check_HAVE_STAT()" >> $LOGFILE
901      get_fortran_c_namemangling      get_fortran_c_namemangling
902      cat <<EOF > genmake_tc_1.c      cat <<EOF > genmake_tc_1.c
903  $FC_NAMEMANGLE  $FC_NAMEMANGLE
# Line 917  void FC_NAMEMANGLE(tfsize) ( int *nbyte Line 919  void FC_NAMEMANGLE(tfsize) ( int *nbyte
919  }  }
920  EOF  EOF
921      COMM="$CC $CFLAGS -c genmake_tc_1.c"      COMM="$CC $CFLAGS -c genmake_tc_1.c"
922      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
923      $COMM >> genmake_tc.log 2>&1      $COMM >> genmake_tc.log 2>&1
924      RET_C=$?      RET_C=$?
925      cat <<EOF > genmake_tc_2.$FS      cat <<EOF > genmake_tc_2.$FS
# Line 927  EOF Line 929  EOF
929        print *," HELLO WORLD", nbyte        print *," HELLO WORLD", nbyte
930        end        end
931  EOF  EOF
932      echo >> genmake_warnings      cat genmake_tc_2.$FS >> $LOGFILE
     echo "running: check_HAVE_STAT()" >> genmake_warnings  
     cat genmake_tc_2.$FS >> genmake_warnings  
933      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"      COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
934      echo $COMM >> genmake_warnings      echo $COMM >> $LOGFILE
935      $COMM >> genmake_tc.log 2>&1      $COMM >> genmake_tc.log 2>&1
936      RETVAL=$?      RETVAL=$?
937      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
# Line 939  EOF Line 939  EOF
939          DEFINES="$DEFINES -DHAVE_STAT"          DEFINES="$DEFINES -DHAVE_STAT"
940      fi      fi
941      rm -f genmake_tc*      rm -f genmake_tc*
942        echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
943  }  }
944    
   
945  check_netcdf_libs()  {  check_netcdf_libs()  {
946      if test ! "x$SKIP_NETCDF_CHECK" = x ; then      if test ! "x$SKIP_NETCDF_CHECK" = x ; then
947          return          return
948      fi      fi
949      echo >> genmake_warnings      echo >> $LOGFILE
950      echo "running: check_netcdf_libs()" >> genmake_warnings      echo "running: check_netcdf_libs()" >> $LOGFILE
951      cat <<EOF > genmake_tnc.F      cat <<EOF > genmake_tnc.F
952        program fgennc        program fgennc
953  #include "netcdf.inc"  #include "netcdf.inc"
# Line 965  EOF Line 965  EOF
965        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)        IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
966        end        end
967  EOF  EOF
968      echo "===  genmake_tnc.F  ===" > genmake_tnc.log      echo "===  genmake_tnc.F  >>>" > genmake_tnc.log
969      cat genmake_tnc.F >> genmake_tnc.log      cat genmake_tnc.F >> genmake_tnc.log
970      echo "===  genmake_tnc.F  ===" >> genmake_tnc.log      echo "<<<  genmake_tnc.F  ===" >> genmake_tnc.log
971      RET_CPP=f      RET_CPP=f
972      COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"      COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
973      echo "$COMM" >> genmake_tnc.log      echo "$COMM" >> genmake_tnc.log
# Line 983  EOF Line 983  EOF
983      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \      $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
984          &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1          &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
985      RET_COMPILE=$?      RET_COMPILE=$?
986      cat genmake_tnc.log >> genmake_warnings      cat genmake_tnc.log >> $LOGFILE
987    
988      #EH3  Remove test program execution for machines that either disallow      #EH3  Remove test program execution for machines that either disallow
989      #EH3  execution or cannot support it (eg. cross-compilers)      #EH3  execution or cannot support it (eg. cross-compilers)
# Line 994  EOF Line 994  EOF
994    
995      if test "x$RET_COMPILE" = x0 ; then      if test "x$RET_COMPILE" = x0 ; then
996          HAVE_NETCDF=t          HAVE_NETCDF=t
997            echo "check_netcdf: successful" >> $LOGFILE
998      else      else
999          # try again with "-lnetcdf" added to the libs          # try again with "-lnetcdf" added to the libs
1000          echo "try again with added '-lnetcdf'" > genmake_tnc.log          echo "==> try again with added '-lnetcdf'" > genmake_tnc.log
1001          echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log          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          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          echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
# Line 1004  EOF Line 1005  EOF
1005              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \              &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
1006              &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1              &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
1007          RET_COMPILE=$?          RET_COMPILE=$?
1008          cat genmake_tnc.log >> genmake_warnings          echo >> $LOGFILE
1009            cat genmake_tnc.log >> $LOGFILE
1010          if test "x$RET_COMPILE" = x0 ; then          if test "x$RET_COMPILE" = x0 ; then
1011              LIBS="$LIBS -lnetcdf"              LIBS="$LIBS -lnetcdf"
1012              HAVE_NETCDF=t              HAVE_NETCDF=t
1013                echo "check_netcdf: successful" >> $LOGFILE
1014          else          else
1015          # try again with "-lnetcdff" added to the libs          # try again with "-lnetcdff" added to the libs
1016              echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log              echo "==> try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
1017              echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log              echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
1018              echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log              echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
1019              echo " &&  $LINK $FFLAGS $FOPTIM -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
# Line 1018  EOF Line 1021  EOF
1021                  &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \                  &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
1022                  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1                  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
1023              RET_COMPILE=$?              RET_COMPILE=$?
1024              cat genmake_tnc.log >> genmake_warnings              echo >> $LOGFILE
1025                cat genmake_tnc.log >> $LOGFILE
1026              if test "x$RET_COMPILE" = x0 ; then              if test "x$RET_COMPILE" = x0 ; then
1027                  LIBS="$LIBS -lnetcdff -lnetcdf"                  LIBS="$LIBS -lnetcdff -lnetcdf"
1028                  HAVE_NETCDF=t                  HAVE_NETCDF=t
1029                    echo "check_netcdf: successful" >> $LOGFILE
1030              fi              fi
1031          fi          fi
1032      fi      fi
1033      rm -f genmake_tnc*      rm -f genmake_tnc*
1034        echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
1035  }  }
1036    
1037    
   
1038  ###############################################################################  ###############################################################################
1039  #   Sequential part of script starts here  #   Sequential part of script starts here
1040  ###############################################################################  ###############################################################################
# Line 1051  ENABLE= Line 1056  ENABLE=
1056  DISABLE=  DISABLE=
1057  # MAKEFILE=  # MAKEFILE=
1058  # MAKEDEPEND=  # MAKEDEPEND=
1059  PDEPEND=  PKG_DEPEND=
1060  DUMPSTATE=t  PKG_GROUPS=
1061  PDEFAULT=  DUMPSTATE=f
1062  OPTFILE=  OPTFILE=
1063  INCLUDES="-I. $INCLUDES"  INCLUDES="-I. $INCLUDES"
1064  FFLAGS=  FFLAGS=
# Line 1061  FOPTIM= Line 1066  FOPTIM=
1066  FEXTRAFLAGS=  FEXTRAFLAGS=
1067  USE_EXTENDED_SRC=  USE_EXTENDED_SRC=
1068  EXTENDED_SRC_FLAG=  EXTENDED_SRC_FLAG=
1069    GET_FC_VERSION=
1070  CFLAGS=  CFLAGS=
1071  KFLAGS1=  KFLAGS1=
1072  KFLAGS2=  KFLAGS2=
# Line 1138  FTL_TAF_FLAGS= Line 1144  FTL_TAF_FLAGS=
1144  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1145  TAMC_EXTRA=  TAMC_EXTRA=
1146    
   
1147  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1148  gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS MAKEFILE MAKEDEPEND PLATFORM ROOTDIR MODS DISABLE ENABLE"
1149  gm_s2="FC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"  gm_s2="FC CC USE_R4 TS PAPIS PCLS PAPI PCL HPMT IEEE DEVEL GSL MPI OMP DUMPSTATE STANDARDDIRS"
1150    
1151  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1152  gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"  gm_s3="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
1153  gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s4="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1154  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD THISHOST THISUSER THISDATE THISVER MACHINE"
1155  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
1156  gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"  gm_s7="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"
1157    
1158  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1159  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
# Line 1162  cat <<EOF Line 1167  cat <<EOF
1167    
1168  GENMAKE :  GENMAKE :
1169    
1170  A program for GENerating MAKEfiles for the MITgcm project.  For a  A program for GENerating MAKEfiles for the MITgcm project.
1171  quick list of options, use "genmake -h" or for more detail see:     For a quick list of options, use "genmake2 -h"
1172    or for more detail see the Developer's HOWTO manual at:
1173    http://mitgcm.org/devel_HOWTO/     http://mitgcm.org/public/docs.html
1174    
1175  EOF  EOF
1176    
1177    LOGFILE="genmake.log"
1178    #- clean-up previous genmake logfiles:
1179    rm -f genmake_state genmake_*optfile $LOGFILE
1180    
1181  echo "===  Processing options files and arguments  ==="  echo "===  Processing options files and arguments  ==="
1182  gm_local="genmake_local"  gm_local="genmake_local"
1183  printf "  getting local config information:  "  printf "  getting local config information:  "
# Line 1215  for ac_option in "$@" ; do Line 1224  for ac_option in "$@" ; do
1224              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1225                    
1226          -pdepend | --pdepend)          -pdepend | --pdepend)
1227              ac_prev=PDEPEND ;;              ac_prev=PKG_DEPEND ;;
1228          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
1229              PDEPEND=$ac_optarg ;;              PKG_DEPEND=$ac_optarg ;;
1230                    
1231          -pdefault | --pdefault)          -pgroups | --pgroups)
1232              ac_prev=PDEFAULT ;;              ac_prev=PKG_GROUPS ;;
1233          -pdefault=* | --pdefault=*)          -pgroups=* | --pgroups=*)
1234              PDEFAULT=$ac_optarg ;;              PKG_GROUPS=$ac_optarg ;;
1235                    
1236          -make | --make | -m | --m)          -make | --make | -m | --m)
1237              ac_prev=MAKE ;;              ac_prev=MAKE ;;
# Line 1301  for ac_option in "$@" ; do Line 1310  for ac_option in "$@" ; do
1310          -fs90=* | --fs90=*)          -fs90=* | --fs90=*)
1311              FS90=$ac_optarg ;;              FS90=$ac_optarg ;;
1312                    
1313            -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1314                USE_R4=true ;;
1315    
1316          -ieee | --ieee)          -ieee | --ieee)
1317              IEEE=true ;;              IEEE=true ;;
1318          -noieee | --noieee)          -noieee | --noieee)
1319              IEEE= ;;              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
1320            -devel | --devel)
1321          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )              IEEE=true ; DEVEL=true ;;
1322              USE_R4=true ;;          -gsl | --gsl)
1323                GSL=true ;;
1324    
1325          -ts | --ts)          -ts | --ts)
1326              TS=true ;;              TS=true ;;
# Line 1324  for ac_option in "$@" ; do Line 1337  for ac_option in "$@" ; do
1337          -hpmt | --hpmt)          -hpmt | --hpmt)
1338              HPMT=true ;;              HPMT=true ;;
1339    
         -gsl | --gsl)  
             GSL=true ;;  
   
         -devel | --devel)  
             DEVEL=true ;;  
   
1340          -mpi | --mpi)          -mpi | --mpi)
1341              MPI=true ;;              MPI=true ;;
1342          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
# Line 1375  for ac_option in "$@" ; do Line 1382  for ac_option in "$@" ; do
1382    
1383  done  done
1384    
   
1385  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1386      echo      echo
1387      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
1388      echo "  file.  This file format is no longer supported.  For directions on"      echo "  file.  This file format is no longer supported.  For directions on"
1389      echo "  how to setup and use the new \"genmake2\" script, please see:"      echo "  how to setup and use the new \"genmake2\" script, please see:"
1390      echo "    http://mitgcm.org/devel_HOWTO/"      echo "    http://mitgcm.org/public/devel_HOWTO/"
1391      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
1392      echo "WARNING: ignore \"./.genmakerc\" and continue."      echo "WARNING: ignore \"./.genmakerc\" and continue."
1393      echo      echo
# Line 1396  if test "x${ROOTDIR}" = x ; then Line 1402  if test "x${ROOTDIR}" = x ; then
1402          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
1403              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
1404                  ROOTDIR=$d                  ROOTDIR=$d
1405                  printf "Warning:  ROOTDIR was not specified but there appears to be"                  printf "Warning: ROOTDIR was not specified ;"
1406                  echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."                  echo " try using a local copy of MITgcm found at \"$ROOTDIR\""
1407                  break                  break
1408              fi              fi
1409          done          done
# Line 1434  if test "x${OPTFILE}" = x ; then Line 1440  if test "x${OPTFILE}" = x ; then
1440      if test "x$MITGCM_OF" = x ; then      if test "x$MITGCM_OF" = x ; then
1441          echo "Warning: no OPTFILE specified so we'll look for possible settings"          echo "Warning: no OPTFILE specified so we'll look for possible settings"
1442          printf "\n===  Searching for possible settings for OPTFILE  ===\n"          printf "\n===  Searching for possible settings for OPTFILE  ===\n"
1443          find_possible_configs          find_possible_optfile
1444      else      else
1445          OPTFILE=$MITGCM_OF          OPTFILE=$MITGCM_OF
1446      fi      fi
# Line 1449  if test "x$OPTFILE" != xNONE ; then Line 1455  if test "x$OPTFILE" != xNONE ; then
1455              echo "--please check that variable syntax is bash-compatible"              echo "--please check that variable syntax is bash-compatible"
1456              exit 1              exit 1
1457          fi          fi
1458          if test "x$DUMPSTATE" != xf ; then          if test "x$DUMPSTATE" = xt ; then
1459              cp -f $OPTFILE "genmake_optfile"              cp -f $OPTFILE "genmake_optfile"
1460          fi          fi
1461      else      else
# Line 1476  if test "x${AD_OPTFILE}" != xNONE ; then Line 1482  if test "x${AD_OPTFILE}" != xNONE ; then
1482              echo "--please check that variable syntax is bash-compatible"              echo "--please check that variable syntax is bash-compatible"
1483              exit 1              exit 1
1484          fi          fi
1485          if test "x$DUMPSTATE" != xf ; then          if test "x$DUMPSTATE" = xt ; then
1486              cp -f $AD_OPTFILE "genmake_ad_optfile"              cp -f $AD_OPTFILE "genmake_ad_optfile"
1487          fi          fi
1488      else      else
# Line 1504  Error: no Fortran compiler: please speci Line 1510  Error: no Fortran compiler: please speci
1510  EOF  EOF
1511      exit 1      exit 1
1512  fi  fi
1513    if test "x$GET_FC_VERSION" != x ; then
1514      echo "Get compiler version using: $FC $GET_FC_VERSION" >> $LOGFILE
1515      $FC $GET_FC_VERSION >> $LOGFILE 2>&1
1516      echo "<-- compiler version ----" >> $LOGFILE
1517    fi
1518    
1519  if test "x$CC" = x ; then  if test "x$CC" = x ; then
1520      CC=cc      look_for_C_compilers
 #     cat <<EOF 1>&2  
 # Error: no C compiler: please specify using one of the following:  
 #   1) within the options file ("CC=...") as specified by "-of=OPTFILE"  
 #   2) the "-cc=XXX" command-line option  
 #   3) the "./genmake_local" file  
 # EOF  
 #     exit 1  
1521  fi  fi
1522    
1523  if test "x$LINK" = x ; then  if test "x$LINK" = x ; then
1524      LINK=$FC      LINK=$FC
1525  fi  fi
# Line 1521  if test "x$MAKE" = x ; then Line 1527  if test "x$MAKE" = x ; then
1527      MAKE="make"      MAKE="make"
1528  fi  fi
1529  if test "x$CPP" = x ; then  if test "x$CPP" = x ; then
1530      CPP=cpp      CPP="cpp -traditional -P"
1531  fi  fi
1532  #EH3 === UGLY ===  #EH3 === UGLY ===
1533  #  The following is an ugly little hack to check for $CPP in /lib/ and  #  The following is an ugly little hack to check for $CPP in /lib/ and
# Line 1548  EOF Line 1554  EOF
1554  else  else
1555      rm -f test_cpp      rm -f test_cpp
1556  fi  fi
1557    
1558  look_for_makedepend  look_for_makedepend
1559    
1560    #  Check that soft-link command is set and usable
1561  if test "x$LN" = x ; then  if test "x$LN" = x ; then
1562      LN="ln -s"      LN="ln -s"
1563  fi  fi
# Line 1558  RETVAL=$? Line 1567  RETVAL=$?
1567  if test "x$RETVAL" != x0 ; then  if test "x$RETVAL" != x0 ; then
1568      cat <<EOF 1>&2      cat <<EOF 1>&2
1569    
1570  Error: The command "ln -s" failed -- please specify a working soft-link  Error: The command "$LN" failed -- please specify a working soft-link
1571    command in the optfile.    command in the optfile.
1572    
1573  EOF  EOF
# Line 1795  if test "x$EMBED_SRC" = xt ; then Line 1804  if test "x$EMBED_SRC" = xt ; then
1804      ENABLE="$ENABLE embed_files"      ENABLE="$ENABLE embed_files"
1805  fi  fi
1806    
   
1807  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
1808  printf "  Adding MODS directories: "  printf "  Adding MODS directories: "
1809  for d in $MODS ; do  for d in $MODS ; do
# Line 1811  for d in $MODS ; do Line 1819  for d in $MODS ; do
1819  done  done
1820  echo  echo
1821    
1822  if test "x${PLATFORM}" = x ; then  #if test "x${PLATFORM}" = x ; then
1823      PLATFORM=$p_PLATFORM  #    PLATFORM=$p_PLATFORM
1824  fi  #fi
1825    
1826  if test "x${EXEDIR}" = x ; then  if test "x${EXEDIR}" = x ; then
1827      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`      tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
# Line 1883  fi Line 1891  fi
1891  #  they appear as regular source code  #  they appear as regular source code
1892  if test -r $ROOTDIR"/eesupp/src/Makefile" ; then  if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
1893      echo "  Making source files in eesupp from templates"      echo "  Making source files in eesupp from templates"
1894      ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1      ( cd $ROOTDIR"/eesupp/src/" && $MAKE clean_old && $MAKE \
1895        ) > make_eesupp.errors 2>&1
1896      RETVAL=$?      RETVAL=$?
1897      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
1898          rm -f make_eesupp.errors          rm -f make_eesupp.errors
# Line 1898  fi Line 1907  fi
1907  for pdir in exch2 regrid ; do  for pdir in exch2 regrid ; do
1908      if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then      if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
1909          echo "  Making source files in pkg/${pdir} from templates"          echo "  Making source files in pkg/${pdir} from templates"
1910          ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1          ( cd $ROOTDIR"/pkg/"${pdir} && $MAKE clean_old && $MAKE \
1911            ) > make_${pdir}.errors 2>&1
1912          RETVAL=$?          RETVAL=$?
1913          if test "x${RETVAL}" = x0 ; then          if test "x${RETVAL}" = x0 ; then
1914              rm -f make_${pdir}.errors              rm -f make_${pdir}.errors
# Line 1911  for pdir in exch2 regrid ; do Line 1921  for pdir in exch2 regrid ; do
1921  done  done
1922    
1923  printf "\n===  Determining package settings  ===\n"  printf "\n===  Determining package settings  ===\n"
1924  if  test "x${PDEPEND}" = x ; then  if  test "x${PKG_DEPEND}" = x ; then
1925      tmp=$ROOTDIR"/pkg/pkg_depend"      tmp=$ROOTDIR"/pkg/pkg_depend"
1926      if test -r $tmp ; then      if test -r $tmp ; then PKG_DEPEND=$tmp ; fi
1927          PDEPEND=$tmp  fi
1928      else  if  test "x${PKG_DEPEND}" = x ; then
1929          echo "Warning:  No package dependency information was specified."          echo "Warning:  No package dependency information was specified."
1930          echo "  Please check that ROOTDIR/pkg/pkg_depend exists."          echo "  Please check that ROOTDIR/pkg/pkg_depend exists."
1931    else
1932        if test ! -r ${PKG_DEPEND} ; then
1933            echo "Error:  can't read package dependency info from PKG_DEPEND=\"$PKG_DEPEND\""
1934            exit 1
1935      fi      fi
1936        echo "  getting package dependency info from  $PKG_DEPEND"
1937    #  Strip the comments and then convert the dependency file into arrays: PNAME, DNAME
1938        get_pdepend_list $PKG_DEPEND
1939    fi
1940    
1941    # A default package groups file "$ROOTDIR/pkg/pkg_groups" is provided
1942    #  to define the "default_pkg_list" and package groups (for convenience, one
1943    #  can specify a group of packages using names like "ocean" and "atmosphere").
1944    if test "x${PKG_GROUPS}" = x ; then
1945        tmp=$ROOTDIR"/pkg/pkg_groups"
1946        if test -r $tmp ; then PKG_GROUPS=$tmp ; fi
1947    fi
1948    if test "x${PKG_GROUPS}" = x ; then
1949            echo "Warning:  No package groups information was specified."
1950            echo "  Please check that ROOTDIR/pkg/pkg_groups exists."
1951  else  else
1952      if test ! -r ${PDEPEND} ; then      if test ! -r ${PKG_GROUPS} ; then
1953          echo "Error:  can't read package dependency info from PDEPEND=\"$PDEPEND\""          echo "Error:  can't read package groups info from PKG_GROUPS=\"$PKG_GROUPS\""
1954          exit 1          exit 1
1955      fi      fi
1956        echo "  getting package groups info from      $PKG_GROUPS"
1957  fi  fi
1958  echo "  getting package dependency info from  $PDEPEND"  
1959  #  Strip the comments and then convert the dependency file into  #  Search for packages to compile.
1960  #  two arrays: PNAME, DNAME  echo "  checking list of packages to compile:"
1961  get_pdepend_list $PDEPEND  PKG_LIST=
1962    if test "x${PKG_LIST}" = x ; then
 #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"  
 #  file has been added so that, for convenience, one can specify  
 #  groups of packages using names like "ocean" and "atmosphere".  
 echo "  checking default package list:  "  
 if test "x${PDEFAULT}" = x ; then  
1963      for i in "." $MODS ; do      for i in "." $MODS ; do
1964          if test -r $i"/packages.conf" ; then          if test -r $i"/packages.conf" ; then
1965                  PDEFAULT=$i"/packages.conf"                  PKG_LIST=$i"/packages.conf"
1966                  break                  break
1967          fi          fi
1968      done      done
1969  fi  fi
1970  if test "x${PDEFAULT}" = x ; then  if test "x${PKG_LIST}" = x ; then
1971      PDEFAULT="$ROOTDIR/pkg/pkg_default"      pkg_list='default_pkg_list'
1972  fi      if test "x${PKG_GROUPS}" = x ; then
1973  if test "x${PDEFAULT}" = xNONE ; then          echo "Error:  need package groups info to expand pkg_list=\"$pkg_list\""
1974      echo "    default packages file disabled"          exit 1
1975        fi
1976  else  else
1977      if test ! -r $PDEFAULT ; then      if test ! -r $PKG_LIST ; then
1978          echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""          echo "Error:  can't read package list from PKG_LIST=\"$PKG_LIST\""
1979            exit 1
1980      else      else
1981          echo "    using PDEFAULT=\"$PDEFAULT\""          echo "    using PKG_LIST=\"$PKG_LIST\""
1982          #  Strip the comments and add all the names          #  Strip the comments and add all the names
1983          def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`          pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
1984          RETVAL=$?          RETVAL=$?
1985          if test "x${RETVAL}" != x0 ; then          if test "x${RETVAL}" != x0 ; then
1986              printf "Error: can't parse default package list "              printf "Error: can't parse package list "
1987              echo "-- please check PDEFAULT=\"$PDEFAULT\""              echo "-- please check PKG_LIST=\"$PKG_LIST\""
1988              exit 1              exit 1
1989          fi          fi
         for i in $def ; do  
             PACKAGES="$PACKAGES $i"  
         done  
         echo "    before group expansion packages are:$PACKAGES"  
         RET=1  
         while test $RET = 1 ; do expand_pkg_groups; RET=$?; done  
         echo "    after group expansion packages are: $PACKAGES"  
1990      fi      fi
1991  fi  fi
1992    for i in $pkg_list ; do
1993        PACKAGES="$PACKAGES $i"
1994    done
1995    echo     "    before group expansion packages are:$PACKAGES"
1996    if test "x${PKG_GROUPS}" != x ; then
1997        RET=1
1998        while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
1999        echo "    after group expansion packages are: $PACKAGES"
2000    fi
2001    
2002  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2003  echo "" > ./.tmp_pack  echo "" > ./.tmp_pack
# Line 1999  PACKAGES="$PACKAGES $ENABLE" Line 2028  PACKAGES="$PACKAGES $ENABLE"
2028  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2029      j=`echo $i | sed 's/[-+]//'`      j=`echo $i | sed 's/[-+]//'`
2030      if test ! -d "$ROOTDIR/pkg/$j" ; then      if test ! -d "$ROOTDIR/pkg/$j" ; then
2031          echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2032          exit 1          exit 1
2033      fi      fi
2034      echo $i >> ./.tmp_pack      echo $i >> ./.tmp_pack
# Line 2018  mnc_in=$? Line 2047  mnc_in=$?
2047  if test "x$HAVE_NETCDF" != xt ; then  if test "x$HAVE_NETCDF" != xt ; then
2048      if test "x$mnc_in" = x0 ; then      if test "x$mnc_in" = x0 ; then
2049          cat <<EOF          cat <<EOF
   
2050  *********************************************************************  *********************************************************************
2051  WARNING: the "mnc" package was enabled but tests failed to compile  WARNING: the "mnc" package was enabled but tests failed to compile
2052    NetCDF applications.  Please check that:    NetCDF applications.  Please check that:
# Line 2029  WARNING: the "mnc" package was enabled b Line 2057  WARNING: the "mnc" package was enabled b
2057    
2058    Due to this failure, the "mnc" package is now DISABLED.    Due to this failure, the "mnc" package is now DISABLED.
2059  *********************************************************************  *********************************************************************
   
2060  EOF  EOF
2061          PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`          PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`
2062          DISABLE="$DISABLE mnc"          DISABLE="$DISABLE mnc"
# Line 2061  if test "x$HAVE_NETCDF" != xt ; then Line 2088  if test "x$HAVE_NETCDF" != xt ; then
2088      RETVAL=$?      RETVAL=$?
2089      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
2090          cat <<EOF          cat <<EOF
   
2091  *********************************************************************  *********************************************************************
2092  WARNING: the "profiles" package was enabled but tests failed to  WARNING: the "profiles" package was enabled but tests failed to
2093    compile NetCDF applications.  Please check that:    compile NetCDF applications.  Please check that:
# Line 2072  WARNING: the "profiles" package was enab Line 2098  WARNING: the "profiles" package was enab
2098    
2099    Due to this failure, the "profiles" package is now DISABLED.    Due to this failure, the "profiles" package is now DISABLED.
2100  *********************************************************************  *********************************************************************
   
2101  EOF  EOF
2102          PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`          PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
2103          DISABLE="$DISABLE profiles"          DISABLE="$DISABLE profiles"
# Line 2082  EOF Line 2107  EOF
2107      fi      fi
2108  fi  fi
2109    
2110  echo "  applying package dependency rules"  if  test "x${PKG_DEPEND}" != x ; then
2111  ck=    echo "  applying package dependency rules"
2112  while test "x$ck" != xtt ; do    ck=
2113      while test "x$ck" != xtt ; do
2114      i=0      i=0
2115      # rtot=${#PNAME[@]}      # rtot=${#PNAME[@]}
2116      rtot=$nname      rtot=$nname
# Line 2155  while test "x$ck" != xtt ; do Line 2181  while test "x$ck" != xtt ; do
2181          #i=$(( $i + 1 ))          #i=$(( $i + 1 ))
2182      done      done
2183      ck=$ck"t"      ck=$ck"t"
2184  done    done
2185  echo "    packages are: $PACKAGES"    echo "    packages are: $PACKAGES"
2186    fi
2187  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2188      adr="$ROOTDIR/pkg/$i"      adr="$ROOTDIR/pkg/$i"
2189      if test -d $adr ; then      if test -d $adr ; then
# Line 2272  if test -f ./adSrcFiles.tmp ; then Line 2299  if test -f ./adSrcFiles.tmp ; then
2299      rm -f ./adSrcFiles.tmp      rm -f ./adSrcFiles.tmp
2300  fi  fi
2301  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2302    touch adSrcFiles.tmp
2303  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2304      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2305      for j in $list_files ; do      for j in $list_files ; do
# Line 2668  output.txt: \$(EXECUTABLE) Line 2696  output.txt: \$(EXECUTABLE)
2696          @printf 'running ... '          @printf 'running ... '
2697          @\$(EXECUTABLE) > \$@          @\$(EXECUTABLE) > \$@
2698    
2699    # remove most of the files that "make" generates
2700  clean:  clean:
2701          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
2702          -rm -rf *.o          -rm -rf *.o
2703          -rm -rf *.$FS *.flowdir          -rm -rf *.$FS *.flowdir
2704          -rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*          -rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
2705    
2706    # remove most of the files that "make" and "make depend" generate
2707  Clean:  Clean:
2708          @make clean          @make clean
2709          @make cleanlinks          @make cleanlinks
2710          -rm -f \$(SPECIAL_FILES)          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
         -rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors  
         -rm -f make.log run.log f90mkdepend.log *.bak "$MAKEFILE.old"  
2711          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
2712            -rm -f genmake_warnings genmake_errors make.log
2713    
2714    # remove also the executable, files that "genmake2" generates (except Makefile)
2715    #         and output from a run (plus log files from testreport)
2716  CLEAN:  CLEAN:
2717          @make Clean          @make Clean
2718            -rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak
2719            -rm -f $LOGFILE genmake_state genmake_*optfile
2720            -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
2721          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2722          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2723          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2724          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime          -rm -f *.txt STD* *diagnostics.log datetime
2725          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
2726          -rm -rf mnc_test_*          -rm -rf mnc_test_*
2727    
 #eh3 Makefile: makefile  
2728  makefile:  makefile:
2729          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
2730  cleanlinks:  cleanlinks:
# Line 2745  cat >>$MAKEFILE <<EOF Line 2780  cat >>$MAKEFILE <<EOF
2780          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2781  .$FS.o:  .$FS.o:
2782          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2783    .F.o:
2784            \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
2785  .F90.$FS90:  .F90.$FS90:
2786          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
2787  .FF90.f$FS90:  .FF90.f$FS90:
# Line 2879  ftl_tamc_output.$FS: ftl_input_code.$FS Line 2916  ftl_tamc_output.$FS: ftl_input_code.$FS
2916  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)  ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
2917          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
2918    
   
2919  # ... SVD ...  # ... SVD ...
2920  svdtaf: ad_taf_output.$FS ftl_taf_output.$FS  svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
2921          @echo "--->>> Only ran TAF to generate SVD code!    <<<---"          @echo "--->>> Only ran TAF to generate SVD code!    <<<---"
# Line 3203  if test ! -f AD_CONFIG.h ; then Line 3239  if test ! -f AD_CONFIG.h ; then
3239      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
3240  fi  fi
3241    
   
3242  #  Write the "state" for future records  #  Write the "state" for future records
3243  if test "x$DUMPSTATE" != xf ; then  if test "x$DUMPSTATE" = xt ; then
3244      printf "" > genmake_state      printf "" > genmake_state
3245      for i in $gm_state ; do      for i in $gm_state ; do
3246          t1="t2=\$$i"          t1="t2=\$$i"

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