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revision 1.215 by jmc, Mon Dec 6 17:16:06 2010 UTC revision 1.257 by jmc, Sun Aug 11 05:01:47 2013 UTC
# Line 17  Usage: "$0" [OPTIONS] Line 17  Usage: "$0" [OPTIONS]
17    where [OPTIONS] can be:    where [OPTIONS] can be:
18    
19      -help | --help | -h | --h      -help | --help | -h | --h
20            Print this help message and exit.            Print this help message and exit.
21    
22      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
23        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
24            Use "NAME" as the adoptfile.  By default, the file at            Use "NAME" as the adoptfile.  By default, the file at
25            "tools/adjoint_options/adjoint_default" will be used.            "tools/adjoint_options/adjoint_default" will be used.
26    
27      -nooptfile | --nooptfile      -nooptfile | --nooptfile
28        -optfile NAME | --optfile NAME | -of NAME | --of NAME        -optfile NAME | --optfile NAME | -of NAME | --of NAME
29        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
30            Use "NAME" as the optfile.  By default, an attempt will be            Use "NAME" as the optfile.  By default, an attempt will be
31            made to find an appropriate "standard" optfile in the            made to find an appropriate "standard" optfile in the
32            tools/build_options/ directory.            tools/build_options/ directory.
33    
34      -pdepend NAME | --pdepend NAME      -pdepend NAME | --pdepend NAME
35        -pdepend=NAME | --pdepend=NAME        -pdepend=NAME | --pdepend=NAME
36            Get package dependency information from "NAME".            Get package dependency information from "NAME".
37    
38      -pgroups NAME | --pgroups NAME      -pgroups NAME | --pgroups NAME
39        -pgroups=NAME | --pgroups=NAME        -pgroups=NAME | --pgroups=NAME
40            Get the package groups information from "NAME".            Get the package groups information from "NAME".
41    
42      -bash NAME      -bash NAME
43            Explicitly specify the Bourne or BASH shell to use            Explicitly specify the Bourne or BASH shell to use
44    
45      -make NAME | -m NAME      -make NAME | -m NAME
46        --make=NAME | -m=NAME        --make=NAME | -m=NAME
47            Use "NAME" for the MAKE program. The default is "make" but            Use "NAME" for the MAKE program. The default is "make" but
48            many platforms, "gmake" is the preferred choice.            many platforms, "gmake" is the preferred choice.
49    
50      -makefile NAME | -mf NAME      -makefile NAME | -mf NAME
51        --makefile=NAME | -mf=NAME        --makefile=NAME | -mf=NAME
52            Call the makefile "NAME".  The default is "Makefile".            Call the makefile "NAME".  The default is "Makefile".
53    
54      -makedepend NAME | -md NAME      -makedepend NAME | -md NAME
55        --makedepend=NAME | -md=NAME        --makedepend=NAME | -md=NAME
56            Use "NAME" for the MAKEDEPEND program.            Use "NAME" for the MAKEDEPEND program.
57    
58      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
59        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
60            Specify the location of the MITgcm ROOTDIR as "NAME".            Specify the location of the MITgcm ROOTDIR as "NAME".
61            By default, genamke will try to find the location by            By default, genamke will try to find the location by
62            looking in parent directories (up to the 5th parent).            looking in parent directories (up to the 5th parent).
63    
64      -mods NAME | --mods NAME | -mo NAME | --mo NAME      -mods NAME | --mods NAME | -mo NAME | --mo NAME
65        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
66            Here, "NAME" specifies a list of directories that are            Here, "NAME" specifies a list of directories that are
67            used for additional source code.  Files found in the            used for additional source code.  Files found in the
68            "mods list" are given preference over files of the same            "mods list" are given preference over files of the same
69            name found elsewhere.            name found elsewhere.
70    
71      -disable NAME | --disable NAME      -disable NAME | --disable NAME
72        -disable=NAME | --disable=NAME        -disable=NAME | --disable=NAME
73            Here "NAME" specifies a list of packages that we don't            Here "NAME" specifies a list of packages that we don't
74            want to use.  If this violates package dependencies,            want to use.  If this violates package dependencies,
75            genamke will exit with an error message.            genamke will exit with an error message.
76    
77      -enable NAME | --enable NAME      -enable NAME | --enable NAME
78        -enable=NAME | --enable=NAME        -enable=NAME | --enable=NAME
79            Here "NAME" specifies a list of packages that we wish            Here "NAME" specifies a list of packages that we wish
80            to specifically enable.  If this violates package            to specifically enable.  If this violates package
81            dependencies, genamke will exit with an error message.            dependencies, genamke will exit with an error message.
82    
83      -standarddirs NAME | --standarddirs NAME      -standarddirs NAME | --standarddirs NAME
84        -standarddirs=NAME | --standarddirs=NAME        -standarddirs=NAME | --standarddirs=NAME
85            Here, "NAME" specifies a list of directories to be            Here, "NAME" specifies a list of directories to be
86            used as the "standard" code.            used as the "standard" code.
87    
88      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
89        -fc=NAME | --fc=NAME        -fc=NAME | --fc=NAME
90            Use "NAME" as the fortran compiler.  By default, genmake            Use "NAME" as the fortran compiler.  By default, genmake
91            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
92            "usual suspects" such as g77, f77, etc.            "usual suspects" such as g77, f77, etc.
93    
94      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
95            Use "NAME" as the C compiler.  By default, genmake            Use "NAME" as the C compiler.  By default, genmake
96            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
97            "usual suspects" such as gcc, c89, cc, etc.            "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.  
98    
99      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
100            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
101            *only* works if CPP_EEOPTIONS.h allows this.            *only* works if CPP_EEOPTIONS.h allows this.
102    
103      -ignoretime | -ignore_time | --ignoretime | --ignore_time      -ignoretime | -ignore_time | --ignoretime | --ignore_time
104            Ignore all the "wall clock" routines entirely.  This will            Ignore all the "wall clock" routines entirely.  This will
105            not in any way hurt the model results -- it simply means            not in any way hurt the model results -- it simply means
106            that the code that checks how long the model spends in            that the code that checks how long the model spends in
107            various routines will give junk values.            various routines will give junk values.
108    
109      -ts | --ts      -ts | --ts
110            Produce timing information per timestep            Produce timing information per timestep
111      -papis | --papis      -papis | --papis
112            Produce summary MFlop/s (and IPC) with PAPI per timestep            Produce summary MFlop/s (and IPC) with PAPI per timestep
113      -pcls | --pcls      -pcls | --pcls
114            Produce summary MFlop/s etc. with PCL per timestep            Produce summary MFlop/s etc. with PCL per timestep
115      -foolad | --foolad      -foolad | --foolad
116            Fool the AD code generator            Fool the AD code generator
117      -papi | --papi      -papi | --papi
118            Performance analysis with PAPI            Performance analysis with PAPI
119      -pcl | --pcl      -pcl | --pcl
120            Performance analysis with PCL            Performance analysis with PCL
121      -hpmt | --hpmt      -hpmt | --hpmt
122            Performance analysis with the HPM Toolkit            Performance analysis with the HPM Toolkit
123    
124      -gsl | --gsl      -ieee | --ieee
125            Use GSL to control floating point rounding and precision            use IEEE numerics.  Note that this option *only* works
126              if it is supported by the OPTFILE that is being used.
127      -devel | --devel      -devel | --devel
128            Add additional warning and debugging flags for development            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      -mpi | --mpi
134            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
135      -mpi=PATH | --mpi=PATH      -mpi=PATH | --mpi=PATH
136            Include MPI header files and link to MPI libraries using MPI_ROOT            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            set to PATH. i.e. Include files from \$PATH/include, link to libraries
138            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
139    
140      -omp | --omp      -omp | --omp
141            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
142      -omp=OMPFLAG | --omp=OMPFLAG      -omp=OMPFLAG | --omp=OMPFLAG
143            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
144    
145      -es | --es | -embed-source | --embed-source      -es | --es | -embed-source | --embed-source
146            Embed a tarball containing the full source code            Embed a tarball containing the full source code
147            (including the Makefile, etc.) used to build the            (including the Makefile, etc.) used to build the
148            executable [off by default]            executable [off by default]
149    
150      -ds | --ds      -ds | --ds
151            Report genmake internal variables status (DUMPSTATE)            Report genmake internal variables status (DUMPSTATE)
152            to file "genmake_state" (for debug purpose)            to file "genmake_state" (for debug purpose)
153    
154    While it is most often a single word, the "NAME" variables specified    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:    above can in many cases be a space-delimited string such as:
# Line 175  EOF Line 174  EOF
174  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
175      cpp_options=$1      cpp_options=$1
176      pkg=$2      pkg=$2
177      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
178      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
179      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
180      test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"      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$"  
181  }  }
182    
183  # Search for particular CPP #cmds associated with MPI  # Search for particular CPP #cmds associated with MPI
184  # usage: test_for_mpi_in_cpp_eeoptions CPP_file  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
185  test_for_mpi_in_cpp_eeoptions() {  test_for_mpi_in_cpp_eeoptions() {
186      cpp_options=$1      cpp_options=$1
187      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
188      test_for_string_in_file $cpp_options "^[ ]*#undef.*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[ ]"  
     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 $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"  
189  }  }
190    
191  # Search for particular string in a file. Return 1 if detected, 0 if not  # Search for particular string in a file. Return 1 if detected, 0 if not
# Line 204  test_for_mpi_in_cpp_eeoptions() { Line 193  test_for_mpi_in_cpp_eeoptions() {
193  test_for_string_in_file() {  test_for_string_in_file() {
194      file=$1      file=$1
195      strng=$2      strng=$2
196      grep -i "$strng" $file > /dev/null 2>&1      grep "$strng" $file > /dev/null 2>&1
197      RETVAL=$?      RETVAL=$?
198      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
199          printf "Error: In $file there is an illegal line: "          printf "Error: In $file there is an illegal line: "
200          grep -i "$strng" $file          grep -i "$strng" $file
201          exit 99          exit 99
202      fi      fi
203      return 0      return 0
# Line 298  EOF Line 287  EOF
287  .F.$tfs:  .F.$tfs:
288          $LN \$< \$@          $LN \$< \$@
289  EOF  EOF
290      $MAKE "genmake_hello."$tfs > /dev/null 2>&1      $MAKE -f $MAKEFILE "genmake_hello."$tfs > /dev/null 2>&1
291      RETVAL=$?      RETVAL=$?
292      if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then      if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
293          if test "x$FS" = x ; then          if test "x$FS" = x ; then
# Line 306  EOF Line 295  EOF
295              FS90='fr9'              FS90='fr9'
296              check_for_broken_Ff              check_for_broken_Ff
297          else          else
298              cat <<EOF 2>&1              echo "ERROR: test: '$MAKE -f $MAKEFILE genmake_hello.$tfs' Failed"
299  ERROR: Your file system cannot distinguish between *.F and *.f files              echo "       see simple makefile: '$MAKEFILE' (left here)"
300    (fails the "make/ln" test) and this program cannot find a suitable              echo "  Please check (1) your '$MAKE' command, (2) your '$LN' command"
301    replacement extension.  Please try a different build environment or              echo "           and (3) the allowed sufix '.F' and '.$tfs' in makefile"
302    contact the <MITgcm-support@mitgcm.org> list for help.              echo "  or contact the <MITgcm-support@mitgcm.org> list for help."
303                echo ""
 EOF  
304              exit -1              exit -1
305              return              return
306          fi          fi
# Line 336  look_for_makedepend()  { Line 324  look_for_makedepend()  {
324      #      #
325      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
326      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
327      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
328      #      #
329      #  So the choices are, in order:      #  So the choices are, in order:
     #  
330      #    1) use the user-specified program      #    1) use the user-specified program
331      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
332      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
333      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
334        #             (faster, but can miss some dependencies)
335      #      #
336        echo >> $LOGFILE
337        echo "running: look_for_makedepend()" >> $LOGFILE
338        if test "x${MAKEDEPEND}" != x ; then
339            echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
340            RETVAL=$?
341            if test x"$RETVAL" = x0 ; then
342                build_cyrus_makedepend
343                RETVAL=$?
344                if test "x$RETVAL" != x0 ; then
345                    echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
346                    MAKEDEPEND=
347                fi
348            else
349                echo "${MAKEDEPEND}" | grep 'tools.xmakedepend' > /dev/null 2>&1
350                RETVAL=$?
351                if test "x$RETVAL" = x0 ; then
352                    MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
353                fi
354                echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
355            fi
356        fi
357      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
358          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
359          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
360          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 364  EOF Line 370  EOF
370        stop        stop
371        end        end
372  EOF  EOF
373          makedepend genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
374          RV1=$?          RV1=$?
375            which makedepend > /dev/null 2>&1
376            RV2=$?
377            if test "x${RV2}" = x0 ; then
378                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
379                RV3=$? ; loc_msg='not working.'
380            else RV3=$RV2 ; loc_msg='not found.'
381            fi
382          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
383          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
384          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
385            if test "x${RV1}" = x0 ; then
386                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
387                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
388            elif test "x${RV3}" = x0 ; then
389                echo "    local tools/xmakedepend not working. Use system-default makedepend"
390              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
391                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
392          else          else
393              echo "    a system-default makedepend was not found."              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
394                echo -n "    Try to build cyrus-makedepend ..."
395              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
396              build_cyrus_makedepend              build_cyrus_makedepend
397              RETVAL=$?              RETVAL=$?
398              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
399                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'                  echo "  Works"
400                else
401                    echo "  Fails" ; echo "" >> $LOGFILE
402                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
403                    echo ""
404                    exit -1
405                    return
406              fi              fi
             rm -f ./genmake_cy_md  
         fi  
     else  
         #  echo "MAKEDEPEND=${MAKEDEPEND}"  
         echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1  
         RETVAL=$?  
         if test x"$RETVAL" = x0 ; then  
             build_cyrus_makedepend  
407          fi          fi
408      fi      fi
409  }  }
410    
411  build_cyrus_makedepend()  {  build_cyrus_makedepend()  {
412        echo >> $LOGFILE
413        echo "running: build_cyrus_makedepend()" >> $LOGFILE
414      rm -f ./genmake_cy_md      rm -f ./genmake_cy_md
415      (      (
416          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
417              &&  ./configure > /dev/null 2>&1  \              &&  ./configure > /dev/null 2>&1  \
418              &&  make > /dev/null 2>&1              &&  $MAKE > /dev/null 2>&1
419          if test -x ./makedepend.exe ; then          if test -x ./makedepend.exe ; then
420              $LN ./makedepend.exe ./makedepend              $LN ./makedepend.exe ./makedepend
421          fi          fi
# Line 407  build_cyrus_makedepend()  { Line 427  build_cyrus_makedepend()  {
427      rm -f ./genmake_cy_md      rm -f ./genmake_cy_md
428      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
429          MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'          MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
430            echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
431          return 0          return 0
432      else      else
433          echo "WARNING: unable to build cyrus-imapd-makedepend"          echo "WARNING: fail to build cyrus-imapd-makedepend" >> $LOGFILE
434          return 1          return 1
435      fi      fi
436  }  }
# Line 418  build_embed_encode() Line 439  build_embed_encode()
439  {  {
440      printf "  building the embed-encode utility...  "      printf "  building the embed-encode utility...  "
441      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
442          if test ! -d "$ROOTDIR/tools/embed_encode" ; then          if test ! -d "$ROOTDIR/tools/embed_encode" ; then
443              echo              echo
444              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
445              echo              echo
446              EMBED_SRC=f              EMBED_SRC=f
447              return 1              return 1
448          fi          fi
449          clist="cc gcc c89 $CC"          clist="cc gcc c89 $CC"
450          for ic in $clist ; do          for ic in $clist ; do
451              comm="$ic -o encode_files encode_files.c"              comm="$ic -o encode_files encode_files.c"
# Line 432  build_embed_encode() Line 453  build_embed_encode()
453              RETVAL=$?              RETVAL=$?
454              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
455                  echo "OK"                  echo "OK"
                 DEFINES="$DEFINES -DHAVE_EMBED_SRC"  
456                  return 0                  return 0
457              fi              fi
458          done          done
# Line 444  build_embed_encode() Line 464  build_embed_encode()
464          return 1          return 1
465      fi      fi
466      echo "OK"      echo "OK"
     DEFINES="$DEFINES -DHAVE_EMBED_SRC"  
467  }  }
468    
469  #  look for possible C compilers  #  look for possible C compilers
# Line 562  EOF Line 581  EOF
581      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
582          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
583          if test ! -r $OPTFILE ; then          if test ! -r $OPTFILE ; then
584               echo "  I looked for the file "$OPTFILE" but did not find it"               echo "  I looked for the file "$OPTFILE" but did not find it"
585          fi          fi
586      fi      fi
587    
588      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
# Line 581  Error: No options file was found in:  $R Line 600  Error: No options file was found in:  $R
600  EOF  EOF
601          exit 1          exit 1
602      fi      fi
603    }
604    
605    #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
606    #  checking for additional included headers (in case of chain of included header)
607    mpi_headers_do_local_copy() {
608    
609  #     # look for possible MPI libraries      dBug=0
610  #     mpi_libs=      rm -rf ./mpi_headers
611  #     mpi_fort=`which mpif77 2>/dev/null`      if test -d $MPIINCLUDEDIR ; then
612  #     RETVAL=$?  
613  #     if test "x${RETVAL}" = x0 ; then          #----- check for additional headers (chain of included headers)
614  #       cat >>test.f <<EOF          echo -n '  Check MPI headers ... '
615  #       PROGRAM HELLO          listIni=$MPI_HEADER_FILES
616  #       DO 10, I=1,10          echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
617  #       PRINT *,'Hello World'          outp=$?
618  #    10 CONTINUE          #- always check mpif.h (the only mpi-header included in standard MITgcm code)
619  #       STOP          if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
620  #       END          if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
621  # EOF  
622  #       eval "$mpi_fort -showme test.f > out"          doCheck=1 ; list2copy='' ; list2check=$listIni
623  #       RETVAL=$?          while test $doCheck = 1 ; do
624  #       if test "x${RETVAL}" = x0 ; then            newList=''
625  #           a=`cat out`            for i in $list2check ; do
626  #           for i in $a ; do              if test -f $MPIINCLUDEDIR/$i ; then
627  #               case $i in                newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
628  #                   -*)                  sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
629  #                       mpi_libs="$mpi_libs $i" ;;                if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
630  #               esac                for j in $newInc ; do
631  #           done                  echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
632  #           echo "The MPI libs appear to be:"                  outp=$?
633  #           echo "  "$mpi_libs                  if test $outp != 0 ; then
634  #       fi                    if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
635  #       rm -f test.f out                    newList="$newList $j"
636  #     fi                  fi
637                  done
638                  if test $dBug = 1 ; then echo "" ; fi
639                fi
640              done
641              if test "x$newList" = x ; then doCheck=0
642              else list2check=$newList ; list2copy="$list2copy $newList"
643              fi
644            done
645            list2copy="$MPI_HEADER_FILES $list2copy"
646            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
647    
648            #----- create local mpi_headers dir if we have files to copy
649            mkListInc=`echo $list2copy | wc -w`
650            if test $mkListInc != 0 ; then
651              echo 'create local "./mpi_headers" dir'
652              mkdir -p ./mpi_headers
653              INCLUDES="-I./mpi_headers $INCLUDES"
654              mkListInc=1
655            fi
656            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
657    
658            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
659            for i in $list2copy ; do
660              if test -f $MPIINCLUDEDIR/$i ; then
661                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
662                if test $i = 'mpif.h' ; then
663                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
664                fi
665                if test $mkListInc = 2 ; then
666                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
667                fi
668                if test $mkListInc = 1 ; then
669                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
670                fi
671              fi
672            done
673        else
674            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
675            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
676    #       exit -1
677        fi
678  }  }
679    
680  #  Parse the package dependency information  #  Parse the package dependency information
# Line 634  get_fortran_c_namemangling()  { Line 699  get_fortran_c_namemangling()  {
699    
700      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
701      if test ! "x$FC_NAMEMANGLE" = x ; then      if test ! "x$FC_NAMEMANGLE" = x ; then
702          return 0          return 0
703      fi      fi
704      echo " running: get_fortran_c_namemangling()" >> $LOGFILE      echo " running: get_fortran_c_namemangling()" >> $LOGFILE
705    
# Line 766  EOF Line 831  EOF
831      RETVAL=$?      RETVAL=$?
832      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
833          HAVE_CLOC=t          HAVE_CLOC=t
         DEFINES="$DEFINES -DHAVE_CLOC"  
834      fi      fi
835      rm -f genmake_tc*      rm -f genmake_tc*
836      echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE      echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
# Line 828  EOF Line 892  EOF
892      RETVAL=$?      RETVAL=$?
893      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
894          HAVE_SIGREG=t          HAVE_SIGREG=t
         DEFINES="$DEFINES -DHAVE_SIGREG"  
895      fi      fi
896      rm -f genmake_tc*      rm -f genmake_tc*
897      echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE      echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
898  }  }
899    
900  check_HAVE_SETRLSTK()  {  check_HAVE_SETRLSTK()  {
     if test "x$HAVE_SETRLSTK" = xt ; then  
         DEFINES="$DEFINES -DHAVE_SETRLSTK"  
         return  
     fi    
901      if test ! "x$HAVE_SETRLSTK" = x ; then      if test ! "x$HAVE_SETRLSTK" = x ; then
902          return          return
903      fi      fi
# Line 876  EOF Line 935  EOF
935      RETVAL=$?      RETVAL=$?
936      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
937          HAVE_SETRLSTK=t          HAVE_SETRLSTK=t
         DEFINES="$DEFINES -DHAVE_SETRLSTK"  
938      fi      fi
939      rm -f genmake_tc*      rm -f genmake_tc*
940      echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE      echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
# Line 923  EOF Line 981  EOF
981      RETVAL=$?      RETVAL=$?
982      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
983          HAVE_STAT=t          HAVE_STAT=t
         DEFINES="$DEFINES -DHAVE_STAT"  
984      fi      fi
985      rm -f genmake_tc*      rm -f genmake_tc*
986      echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE      echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
# Line 939  check_netcdf_libs()  { Line 996  check_netcdf_libs()  {
996        program fgennc        program fgennc
997  #include "netcdf.inc"  #include "netcdf.inc"
998  EOF  EOF
999      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1000          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1001      fi     #fi
1002      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1003        integer iret, ncid, xid        integer iret, ncid, xid
1004        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1021  EOF Line 1078  EOF
1078      echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE      echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
1079  }  }
1080    
1081    check_lapack_libs()  {
1082        if test ! "x$SKIP_LAPACK_CHECK" = x ; then
1083            return
1084        fi
1085        echo >> $LOGFILE
1086        echo "running: check_lapack_libs()" >> $LOGFILE
1087        cat <<EOF > genmake_tla.F
1088          program fgenla
1089          integer info
1090          integer ipiv( 2 )
1091          double precision ab( 4, 2 ), b( 2 )
1092          data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
1093          data b / 1., 1. /
1094          call dgbsv( 2, 1, 1, 1, ab, 4, ipiv, b, 2, info )
1095          IF (info .NE. 0) write(*,*) 'Error:', info
1096          write(*,*) b
1097          end
1098    EOF
1099        echo "===  genmake_tla.F  >>>" > genmake_tla.log
1100        cat genmake_tla.F >> genmake_tla.log
1101        echo "<<<  genmake_tla.F  ===" >> genmake_tla.log
1102        RET_CPP=f
1103        COMM="cat genmake_tla.F | $CPP $DEFINES $INCLUDES"
1104        echo "$COMM" >> genmake_tla.log
1105        eval $COMM > genmake_tla.$FS 2>/dev/null  &&  RET_CPP=t
1106        if test "x$RET_CPP" = xf ; then
1107            echo "  WARNING: CPP failed to pre-process the lapack test." \
1108                >> genmake_tla.log
1109            echo "    Please check that \$INCLUDES is properly set." \
1110                >> genmake_tla.log
1111        fi
1112        echo "$FC $FFLAGS $FOPTIM -c genmake_tla.$FS  \ " >> genmake_tla.log
1113        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tla.o $LIBS" >> genmake_tla.log
1114        $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1115            &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS >> genmake_tla.log 2>&1
1116        RET_COMPILE=$?
1117        cat genmake_tla.log >> $LOGFILE
1118    
1119        # test program execution not always possible (see check_netcdf_libs)
1120        #
1121        #test -x ./genmake_tla  &&  ./genmake_tla >> genmake_tla.log 2>&1
1122        #RETVAL=$?
1123        #if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
1124    
1125        if test "x$RET_COMPILE" = x0 ; then
1126            HAVE_LAPACK=t
1127            echo "check_lapack: successful" >> $LOGFILE
1128        else
1129            # try again with "-llapack" added to the libs
1130            echo "==> try again with added '-llapack'" > genmake_tla.log
1131            echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1132            echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1133            echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack" >> genmake_tla.log
1134            cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1135                &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1136                &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack >> genmake_tla.log 2>&1
1137            RET_COMPILE=$?
1138            echo >> $LOGFILE
1139            cat genmake_tla.log >> $LOGFILE
1140            if test "x$RET_COMPILE" = x0 ; then
1141                LIBS="$LIBS -llapack"
1142                HAVE_LAPACK=t
1143                echo "check_lapack: successful" >> $LOGFILE
1144            else
1145            # try again with "-lf77blas -lcblas" added to the libs
1146                echo "==> try again with added '-llapack -lf77blas -lcblas'" > genmake_tla.log
1147                echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1148                echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1149                echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas" >> genmake_tla.log
1150                cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1151                    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1152                    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas >> genmake_tla.log 2>&1
1153                RET_COMPILE=$?
1154                echo >> $LOGFILE
1155                cat genmake_tla.log >> $LOGFILE
1156                if test "x$RET_COMPILE" = x0 ; then
1157                    LIBS="$LIBS -llapack -lf77blas -lcblas"
1158                    HAVE_LAPACK=t
1159                    echo "check_lapack: successful" >> $LOGFILE
1160                else
1161                # try again with "-latlas" added to the libs
1162                    echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
1163                    echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1164                    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1165                    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
1166                    cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1167                        &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1168                        &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
1169                    RET_COMPILE=$?
1170                    echo >> $LOGFILE
1171                    cat genmake_tla.log >> $LOGFILE
1172                    if test "x$RET_COMPILE" = x0 ; then
1173                        LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
1174                        HAVE_LAPACK=t
1175                        echo "check_lapack: successful" >> $LOGFILE
1176                    fi
1177                fi
1178            fi
1179        fi
1180        rm -f genmake_tla*
1181        echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1182    }
1183    
1184    check_HAVE_FLUSH()  {
1185        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1186            return
1187        fi
1188        echo >> $LOGFILE
1189        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1190        cat <<EOF > genmake_tflsh.$FS
1191          program fgenflsh
1192          integer iounit
1193          character*9 fname
1194          iounit = 26
1195          fname = 'tmp.tflsh'
1196          open(iounit,FILE=fname,STATUS='unknown')
1197          write(iounit,*) 'genmake_tflsh: hello'
1198          call flush(iounit)
1199          close(iounit)
1200          end
1201    EOF
1202        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1203        cat genmake_tflsh.$FS >> genmake_tflsh.log
1204        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1205    
1206        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1207        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1208        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1209            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1210        RET_COMPILE=$?
1211    
1212        if test "x$RET_COMPILE" = x0 ; then
1213            HAVE_FLUSH=t
1214            #cat genmake_tflsh.log >> $LOGFILE
1215            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1216        else
1217            HAVE_FLUSH=f
1218            cat genmake_tflsh.log >> $LOGFILE
1219        fi
1220        rm -f genmake_tflsh*
1221        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1222    }
1223    
1224  ###############################################################################  ###############################################################################
1225  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1053  FOPTIM= Line 1252  FOPTIM=
1252  FEXTRAFLAGS=  FEXTRAFLAGS=
1253  USE_EXTENDED_SRC=  USE_EXTENDED_SRC=
1254  EXTENDED_SRC_FLAG=  EXTENDED_SRC_FLAG=
1255    GET_FC_VERSION=
1256  CFLAGS=  CFLAGS=
1257  KFLAGS1=  KFLAGS1=
1258  KFLAGS2=  KFLAGS2=
# Line 1077  GSL= Line 1277  GSL=
1277  DEVEL=  DEVEL=
1278  HAVE_TEST_L=  HAVE_TEST_L=
1279    
1280    # comment this line out to enable lapack test
1281    SKIP_LAPACK_CHECK=t
1282    
1283  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1284  HAVE_SYSTEM=  HAVE_SYSTEM=
1285  HAVE_FDATE=  HAVE_FDATE=
# Line 1087  HAVE_STAT= Line 1290  HAVE_STAT=
1290  HAVE_NETCDF=  HAVE_NETCDF=
1291  HAVE_ETIME=  HAVE_ETIME=
1292  IGNORE_TIME=  IGNORE_TIME=
1293    HAVE_LAPACK=
1294    HAVE_FLUSH=
1295    
1296  MODS=  MODS=
1297  TOOLSDIR=  TOOLSDIR=
# Line 1094  SOURCEDIRS= Line 1299  SOURCEDIRS=
1299  INCLUDEDIRS=  INCLUDEDIRS=
1300  STANDARDDIRS="USE_THE_DEFAULT"  STANDARDDIRS="USE_THE_DEFAULT"
1301    
1302    #- local config file
1303    gm_local="genmake_local"
1304    
1305  G2ARGS=  G2ARGS=
1306  BASH=  BASH=
1307  PWD=`pwd`  PWD=`pwd`
# Line 1109  MACHINE=`uname -a` Line 1317  MACHINE=`uname -a`
1317  EXECUTABLE=  EXECUTABLE=
1318  EXEHOOK=  EXEHOOK=
1319  EXEDIR=  EXEDIR=
 PACKAGES_CONF=  
1320  IEEE=  IEEE=
1321  if test "x$MITGCM_IEEE" != x ; then  if test "x$MITGCM_IEEE" != x ; then
1322      IEEE=$MITGCM_IEEE      IEEE=$MITGCM_IEEE
# Line 1130  FTL_TAF_FLAGS= Line 1337  FTL_TAF_FLAGS=
1337  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1338  TAMC_EXTRA=  TAMC_EXTRA=
1339    
1340    DIVA=
1341    MPIINCLUDEDIR=
1342    MPI_HEADER_FILES=
1343    LOCAL_MPI_HEADERS=
1344    
1345  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1346  gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS MAKEFILE MAKEDEPEND PLATFORM ROOTDIR MODS DISABLE ENABLE"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1347  gm_s2="FC CC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"  gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
1348    gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
1349    
1350  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1351  gm_s3="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1352  gm_s4="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1353  gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1354  gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"  gm_s7="THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1355  gm_s7="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"  gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
1356    
1357  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1358  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"
1359  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
1360  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1361    
1362  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
1363  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
1364    
1365  cat <<EOF  cat <<EOF
# Line 1165  LOGFILE="genmake.log" Line 1378  LOGFILE="genmake.log"
1378  rm -f genmake_state genmake_*optfile $LOGFILE  rm -f genmake_state genmake_*optfile $LOGFILE
1379    
1380  echo "===  Processing options files and arguments  ==="  echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"  
 printf "  getting local config information:  "  
 if test -f $gm_local ; then  
     echo "using $gm_local"  
     . $gm_local  
     # echo "DISABLE=$DISABLE"  
     # echo "ENABLE=$ENABLE"  
 else  
     echo "none found"  
 fi  
1381    
1382  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
1383  #parse_options  #parse_options
# Line 1193  for ac_option in "$@" ; do Line 1396  for ac_option in "$@" ; do
1396      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
1397    
1398      case $ac_option in      case $ac_option in
1399            
1400          -help | --help | -h | --h)          -help | --help | -h | --h)
1401              usage ;;              usage ;;
1402            
1403          -nooptfile | --nooptfile)          -nooptfile | --nooptfile)
1404              OPTFILE="NONE" ;;              OPTFILE="NONE" ;;
1405          -optfile | --optfile | -of | --of)          -optfile | --optfile | -of | --of)
1406              ac_prev=OPTFILE ;;              ac_prev=OPTFILE ;;
1407          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1408              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1409            
1410          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1411              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1412          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
1413              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1414            
1415          -pdepend | --pdepend)          -pdepend | --pdepend)
1416              ac_prev=PKG_DEPEND ;;              ac_prev=PKG_DEPEND ;;
1417          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
1418              PKG_DEPEND=$ac_optarg ;;              PKG_DEPEND=$ac_optarg ;;
1419            
1420          -pgroups | --pgroups)          -pgroups | --pgroups)
1421              ac_prev=PKG_GROUPS ;;              ac_prev=PKG_GROUPS ;;
1422          -pgroups=* | --pgroups=*)          -pgroups=* | --pgroups=*)
1423              PKG_GROUPS=$ac_optarg ;;              PKG_GROUPS=$ac_optarg ;;
1424            
1425          -make | --make | -m | --m)          -make | --make | -m | --m)
1426              ac_prev=MAKE ;;              ac_prev=MAKE ;;
1427          -make=* | --make=* | -m=* | --m=*)          -make=* | --make=* | -m=* | --m=*)
1428              MAKE=$ac_optarg ;;              MAKE=$ac_optarg ;;
1429            
1430          -bash | --bash)          -bash | --bash)
1431              ac_prev=BASH ;;              ac_prev=BASH ;;
1432          -bash=* | --bash=*)          -bash=* | --bash=*)
1433              BASH=$ac_optarg ;;              BASH=$ac_optarg ;;
1434            
1435          -makedepend | --makedepend | -md | --md)          -makedepend | --makedepend | -md | --md)
1436              ac_prev=MAKEDEPEND ;;              ac_prev=MAKEDEPEND ;;
1437          -makedepend=* | --makedepend=* | -md=* | --md=*)          -makedepend=* | --makedepend=* | -md=* | --md=*)
1438              MAKEDEPEND=$ac_optarg ;;              MAKEDEPEND=$ac_optarg ;;
1439            
1440          -makefile | --makefile | -ma | --ma)          -makefile | --makefile | -mf | --mf)
1441              ac_prev=MAKEFILE ;;              ac_prev=MAKEFILE ;;
1442          -makefile=* | --makefile=* | -ma=* | --ma=*)          -makefile=* | --makefile=* | -mf=* | --mf=*)
1443              MAKEFILE=$ac_optarg ;;              MAKEFILE=$ac_optarg ;;
1444            
1445          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
1446              echo "ERROR: The platform option has been removed.  Please specify"              echo "ERROR: The platform option has been removed.  Please specify"
1447              echo "  the build options using the \"optfile\" mechanism."              echo "  the build options using the \"optfile\" mechanism."
1448              echo              echo
1449              usage              usage
1450              ;;              ;;
1451            
1452          -rootdir | --rootdir | -rd | --rd)          -rootdir | --rootdir | -rd | --rd)
1453              ac_prev=ROOTDIR ;;              ac_prev=ROOTDIR ;;
1454          -rootdir=* | --rootdir=* | -rd=* | --rd=*)          -rootdir=* | --rootdir=* | -rd=* | --rd=*)
1455              ROOTDIR=$ac_optarg ;;              ROOTDIR=$ac_optarg ;;
1456            
1457          -mods | --mods | -mo | --mo)          -mods | --mods | -mo | --mo)
1458              ac_prev=MODS ;;              ac_prev=MODS ;;
1459          -mods=* | --mods=* | -mo=* | --mo=*)          -mods=* | --mods=* | -mo=* | --mo=*)
1460              MODS=$ac_optarg ;;              MODS=$ac_optarg ;;
1461            
1462          -disable | --disable)          -disable | --disable)
1463              ac_prev=DISABLE ;;              ac_prev=DISABLE ;;
1464          -disable=* | --disable=*)          -disable=* | --disable=*)
1465              DISABLE=$ac_optarg ;;              DISABLE=$ac_optarg ;;
1466            
1467          -enable | --enable)          -enable | --enable)
1468              ac_prev=ENABLE ;;              ac_prev=ENABLE ;;
1469          -enable=* | --enable=*)          -enable=* | --enable=*)
1470              ENABLE=$ac_optarg ;;              ENABLE=$ac_optarg ;;
1471            
1472          -standarddirs | --standarddirs)          -standarddirs | --standarddirs)
1473              ac_prev=STANDARDDIRS ;;              ac_prev=STANDARDDIRS ;;
1474          -standarddirs=* | --standarddirs=*)          -standarddirs=* | --standarddirs=*)
# Line 1275  for ac_option in "$@" ; do Line 1478  for ac_option in "$@" ; do
1478  #               ac_prev=cpp ;;  #               ac_prev=cpp ;;
1479  #           -cpp=* | --cpp=*)  #           -cpp=* | --cpp=*)
1480  #               CPP=$ac_optarg ;;  #               CPP=$ac_optarg ;;
1481            
1482          -cc | --cc)          -cc | --cc)
1483              ac_prev=CC ;;              ac_prev=CC ;;
1484          -cc=* | --cc=*)          -cc=* | --cc=*)
1485              CC=$ac_optarg ;;              CC=$ac_optarg ;;
1486            
1487          -fortran | --fortran | -fc | --fc)          -fortran | --fortran | -fc | --fc)
1488              ac_prev=FC ;;              ac_prev=FC ;;
1489          -fc=* | --fc=*)          -fc=* | --fc=*)
1490              FC=$ac_optarg ;;              FC=$ac_optarg ;;
1491            
1492          -fs | --fs)          -fs | --fs)
1493              ac_prev=FS ;;              ac_prev=FS ;;
1494          -fs=* | --fs=*)          -fs=* | --fs=*)
1495              FS=$ac_optarg ;;              FS=$ac_optarg ;;
1496            
1497          -fs90 | --fs90)          -fs90 | --fs90)
1498              ac_prev=FS90 ;;              ac_prev=FS90 ;;
1499          -fs90=* | --fs90=*)          -fs90=* | --fs90=*)
1500              FS90=$ac_optarg ;;              FS90=$ac_optarg ;;
           
         -ieee | --ieee)  
             IEEE=true ;;  
         -noieee | --noieee)  
             IEEE= ;;  
1501    
1502          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1503              USE_R4=true ;;              USE_R4=true ;;
1504    
1505            -ieee | --ieee)
1506                IEEE=true ;;
1507            -noieee | --noieee)
1508                echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
1509            -devel | --devel)
1510                IEEE=true ; DEVEL=true ;;
1511            -gsl | --gsl)
1512                GSL=true ;;
1513    
1514          -ts | --ts)          -ts | --ts)
1515              TS=true ;;              TS=true ;;
1516          -papis | --papis)          -papis | --papis)
# Line 1319  for ac_option in "$@" ; do Line 1526  for ac_option in "$@" ; do
1526          -hpmt | --hpmt)          -hpmt | --hpmt)
1527              HPMT=true ;;              HPMT=true ;;
1528    
         -gsl | --gsl)  
             GSL=true ;;  
   
         -devel | --devel)  
             DEVEL=true ;;  
   
1529          -mpi | --mpi)          -mpi | --mpi)
1530              MPI=true ;;              MPI=true ;;
1531          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
1532              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1533              MPI=true ;;              MPI=true ;;
1534            
1535          -omp | --omp)          -omp | --omp)
1536              OMP=true ;;              OMP=true ;;
1537          -omp=* | --omp=*)          -omp=* | --omp=*)
1538              OMPFLAG=$ac_optarg              OMPFLAG=$ac_optarg
1539              OMP=true ;;              OMP=true ;;
1540            
1541          -ds | --ds)          -ds | --ds)
1542              DUMPSTATE=t ;;              DUMPSTATE=t ;;
1543            
1544            -extra_flag | --extra_flag)
1545                ac_prev=FEXTRAFLAGS ;;
1546            -extra_flag=* | --extra_flag=*)
1547                FEXTRAFLAGS=$ac_optarg ;;
1548    
1549          -taf_extra | --taf_extra)          -taf_extra | --taf_extra)
1550              ac_prev=TAF_EXTRA ;;              ac_prev=TAF_EXTRA ;;
1551          -taf_extra=* | --taf_extra=*)          -taf_extra=* | --taf_extra=*)
# Line 1349  for ac_option in "$@" ; do Line 1555  for ac_option in "$@" ; do
1555              ac_prev=TAMC_EXTRA ;;              ac_prev=TAMC_EXTRA ;;
1556          -tamc_extra=* | --tamc_extra=*)          -tamc_extra=* | --tamc_extra=*)
1557              TAMC_EXTRA=$ac_optarg ;;              TAMC_EXTRA=$ac_optarg ;;
1558            
1559          -ignoretime | -ignore_time | --ignoretime | --ignore_time)          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1560              IGNORE_TIME="-DIGNORE_TIME" ;;              IGNORE_TIME="-DIGNORE_TIME" ;;
1561    
# Line 1360  for ac_option in "$@" ; do Line 1566  for ac_option in "$@" ; do
1566              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
1567              usage              usage
1568              ;;              ;;
1569            
1570          *)          *)
1571              echo "Error: unrecognized argument: "$ac_option              echo "Error: unrecognized argument: "$ac_option
1572              usage              usage
1573              ;;              ;;
1574            
1575      esac      esac
1576    
1577  done  done
1578    
1579    printf "  getting local config information:  "
1580    if test -f $gm_local ; then
1581        echo "using $gm_local"
1582        . $gm_local
1583    else
1584        echo "none found"
1585    fi
1586    
1587  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1588      echo      echo
1589      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
1590      echo "  file.  This file format is no longer supported.  For directions on"      echo "  file.  This file format is no longer supported.  For directions on"
1591      echo "  how to setup and use the new \"genmake2\" script, please see:"      echo "  how to setup and use the new \"genmake2\" script, please see:"
1592      echo "    http://mitgcm.org/devel_HOWTO/"      echo "    http://mitgcm.org/public/devel_HOWTO/"
1593      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."      echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
1594      echo "WARNING: ignore \"./.genmakerc\" and continue."      echo "WARNING: ignore \"./.genmakerc\" and continue."
1595      echo      echo
# Line 1390  if test "x${ROOTDIR}" = x ; then Line 1604  if test "x${ROOTDIR}" = x ; then
1604          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do          for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
1605              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then              if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
1606                  ROOTDIR=$d                  ROOTDIR=$d
1607                  printf "Warning:  ROOTDIR was not specified but there appears to be"                  printf "Warning: ROOTDIR was not specified ;"
1608                  echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."                  echo " try using a local copy of MITgcm found at \"$ROOTDIR\""
1609                  break                  break
1610              fi              fi
1611          done          done
# Line 1423  if test "x$MAKEFILE" = x ; then Line 1637  if test "x$MAKEFILE" = x ; then
1637      MAKEFILE="Makefile"      MAKEFILE="Makefile"
1638  fi  fi
1639    
1640  echo "  getting OPTFILE information:  "  echo "  getting OPTFILE information:"
1641  if test "x${OPTFILE}" = x ; then  if test "x${OPTFILE}" = x ; then
1642      if test "x$MITGCM_OF" = x ; then      if test "x$MITGCM_OF" = x ; then
1643          echo "Warning: no OPTFILE specified so we'll look for possible settings"          echo "Warning: no OPTFILE specified so we'll look for possible settings"
# Line 1452  if test "x$OPTFILE" != xNONE ; then Line 1666  if test "x$OPTFILE" != xNONE ; then
1666      fi      fi
1667  fi  fi
1668    
1669  echo "  getting AD_OPTFILE information:  "  echo "  getting AD_OPTFILE information:"
1670  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1671      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" = x ; then
1672          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
# Line 1498  Error: no Fortran compiler: please speci Line 1712  Error: no Fortran compiler: please speci
1712  EOF  EOF
1713      exit 1      exit 1
1714  fi  fi
1715    if test "x$GET_FC_VERSION" != x ; then
1716      echo "Get compiler version using: $FC $GET_FC_VERSION" >> $LOGFILE
1717      ff=`echo $FC | sed 's/ .*//'` ; xx=`echo $ff | sed 's/^./& /' | sed 's/ .*//'`
1718      if test $xx != '/' ; then which $ff >> $LOGFILE ; fi
1719      $FC $GET_FC_VERSION > genmake_fc_vers1 2> genmake_fc_vers2
1720      if test -s genmake_fc_vers1 ; then
1721        cat genmake_fc_vers1 >> $LOGFILE
1722      else
1723        cat genmake_fc_vers2 >> $LOGFILE
1724      fi
1725      echo "<-- compiler version ----" >> $LOGFILE
1726      rm -f genmake_fc_vers1 genmake_fc_vers2
1727    fi
1728    
1729  if test "x$CC" = x ; then  if test "x$CC" = x ; then
1730      look_for_C_compilers      look_for_C_compilers
# Line 1568  check_for_broken_Ff Line 1795  check_for_broken_Ff
1795    
1796  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1797        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1798        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1799    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1800    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1801  fi  fi
1802  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1803        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1585  fi Line 1814  fi
1814  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1815        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1816        if test ! "x$FOOLAD" = x ; then        if test ! "x$FOOLAD" = x ; then
1817              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1818        else        else
1819              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1820        fi        fi
# Line 1621  if test ! "x$PAPI" = x ; then Line 1850  if test ! "x$PAPI" = x ; then
1850            echo "  Sticking with PAPI flop summary per timestep!"            echo "  Sticking with PAPI flop summary per timestep!"
1851        else        else
1852            echo "  Turning on performance analysis with PAPI"            echo "  Turning on performance analysis with PAPI"
1853            echo "  Please make sure PAPIINC, PAPILIB are defined"            echo "  Please make sure PAPIINC, PAPILIB are defined"
1854            DEFINES="$DEFINES -DUSE_PAPI"            DEFINES="$DEFINES -DUSE_PAPI"
1855            INCLUDES="$INCLUDES $PAPIINC"            INCLUDES="$INCLUDES $PAPIINC"
1856            LIBS="$LIBS $PAPILIB"            LIBS="$LIBS $PAPILIB"
# Line 1633  if test ! "x$PCL" = x ; then Line 1862  if test ! "x$PCL" = x ; then
1862            echo "  Sticking with PCL flop summary per timestep!"            echo "  Sticking with PCL flop summary per timestep!"
1863        else        else
1864            echo "  Turning on performance analysis with PCL"            echo "  Turning on performance analysis with PCL"
1865            echo "  Please make sure PCLINC, PCLLIB are defined"            echo "  Please make sure PCLINC, PCLLIB are defined"
1866            DEFINES="$DEFINES -DUSE_PCL"            DEFINES="$DEFINES -DUSE_PCL"
1867            INCLUDES="$INCLUDES $PCLINC"            INCLUDES="$INCLUDES $PCLINC"
1868            LIBS="$LIBS $PCLLIB"            LIBS="$LIBS $PCLLIB"
# Line 1643  if test ! "x$HPMT" = x ; then Line 1872  if test ! "x$HPMT" = x ; then
1872        if test ! "x$PAPI" = x ; then        if test ! "x$PAPI" = x ; then
1873            echo "  PAPI and the HPM Toolkit cannot co-exist!"            echo "  PAPI and the HPM Toolkit cannot co-exist!"
1874            echo "  Sticking with PAPI!"            echo "  Sticking with PAPI!"
1875        else if test ! "x$PCL" = x ; then        else
1876            if test ! "x$PCL" = x ; then
1877            echo "  PCL and the HPM Toolkit cannot co-exist!"            echo "  PCL and the HPM Toolkit cannot co-exist!"
1878            echo "  Sticking with PCL!"            echo "  Sticking with PCL!"
1879        else          else
1880            echo "  Turning on performance analysis with the HPM Toolkit"            echo "  Turning on performance analysis with the HPM Toolkit"
1881            echo "  Please make sure HPMTINC, HPMTLIB are defined"            echo "  Please make sure HPMTINC, HPMTLIB are defined"
1882            DEFINES="$DEFINES -DUSE_LIBHPM"            DEFINES="$DEFINES -DUSE_LIBHPM"
1883            INCLUDES="$INCLUDES $HPMTINC"            INCLUDES="$INCLUDES $HPMTINC"
1884            LIBS="$LIBS $HPMTLIB"            LIBS="$LIBS $HPMTLIB"
1885        fi          fi
1886        fi        fi
1887  fi  fi
1888  if test ! "x$GSL" = x ; then  if test ! "x$GSL" = x ; then
# Line 1733  rm -f genmake_tcomp* Line 1963  rm -f genmake_tcomp*
1963  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
1964  check_HAVE_CLOC  check_HAVE_CLOC
1965  if test "x$HAVE_CLOC" != x ; then  if test "x$HAVE_CLOC" != x ; then
1966        DEFINES="$DEFINES -DHAVE_CLOC"
1967      echo "yes"      echo "yes"
1968  else  else
1969      echo "no"      echo "no"
# Line 1747  rm -f genmake_t* Line 1978  rm -f genmake_t*
1978  printf "  Can we unlimit the stack size using $FC...  "  printf "  Can we unlimit the stack size using $FC...  "
1979  check_HAVE_SETRLSTK  check_HAVE_SETRLSTK
1980  if test "x$HAVE_SETRLSTK" = xt ; then  if test "x$HAVE_SETRLSTK" = xt ; then
1981        DEFINES="$DEFINES -DHAVE_SETRLSTK"
1982      echo "yes"      echo "yes"
1983  else  else
1984      echo "no"      echo "no"
# Line 1756  rm -f genmake_t* Line 1988  rm -f genmake_t*
1988  printf "  Can we register a signal handler using $FC...  "  printf "  Can we register a signal handler using $FC...  "
1989  check_HAVE_SIGREG  check_HAVE_SIGREG
1990  if test "x$HAVE_SIGREG" = xt ; then  if test "x$HAVE_SIGREG" = xt ; then
1991        DEFINES="$DEFINES -DHAVE_SIGREG"
1992      echo "yes"      echo "yes"
1993  else  else
1994      echo "no"      echo "no"
# Line 1765  rm -f genmake_t* Line 1998  rm -f genmake_t*
1998  printf "  Can we use stat() through C calls...  "  printf "  Can we use stat() through C calls...  "
1999  check_HAVE_STAT  check_HAVE_STAT
2000  if test "x$HAVE_STAT" != x ; then  if test "x$HAVE_STAT" != x ; then
2001        DEFINES="$DEFINES -DHAVE_STAT"
2002      echo "yes"      echo "yes"
2003  else  else
2004      echo "no"      echo "no"
# Line 1774  rm -f genmake_t* Line 2008  rm -f genmake_t*
2008  printf "  Can we create NetCDF-enabled binaries...  "  printf "  Can we create NetCDF-enabled binaries...  "
2009  check_netcdf_libs  check_netcdf_libs
2010  if test "x$HAVE_NETCDF" != x ; then  if test "x$HAVE_NETCDF" != x ; then
2011        DEFINES="$DEFINES -DHAVE_NETCDF"
2012        echo "yes"
2013    else
2014        echo "no"
2015    fi
2016    
2017    printf "  Can we create LAPACK-enabled binaries...  "
2018    check_lapack_libs
2019    if test "x$HAVE_LAPACK" != x ; then
2020        DEFINES="$DEFINES -DHAVE_LAPACK"
2021      echo "yes"      echo "yes"
2022  else  else
2023      echo "no"      echo "no"
2024  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2025    
2026    printf "  Can we call FLUSH intrinsic subroutine...  "
2027    check_HAVE_FLUSH
2028    if test "x$HAVE_FLUSH" = xt ; then
2029        DEFINES="$DEFINES -DHAVE_FLUSH"
2030        echo "yes"
2031    else
2032        echo "no"
2033    fi
2034    
2035    DEFINES="$DEFINES $IGNORE_TIME"
2036  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2037      build_embed_encode      build_embed_encode
2038  fi  fi
2039  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2040      ENABLE="$ENABLE embed_files"      ENABLE="$ENABLE embed_files"
2041    #   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
2042  fi  fi
2043    
2044  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
# Line 1962  else Line 2216  else
2216          exit 1          exit 1
2217      else      else
2218          echo "    using PKG_LIST=\"$PKG_LIST\""          echo "    using PKG_LIST=\"$PKG_LIST\""
2219          #  Strip the comments and add all the names          #  Strip the comments and add all the names
2220          pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`          pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
2221          RETVAL=$?          RETVAL=$?
2222          if test "x${RETVAL}" != x0 ; then          if test "x${RETVAL}" != x0 ; then
# Line 2012  for i in $PACKAGES ; do Line 2266  for i in $PACKAGES ; do
2266      j=`echo $i | sed 's/[-+]//'`      j=`echo $i | sed 's/[-+]//'`
2267      if test ! -d "$ROOTDIR/pkg/$j" ; then      if test ! -d "$ROOTDIR/pkg/$j" ; then
2268          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2269          exit 1          exit 1
2270      fi      fi
2271      echo $i >> ./.tmp_pack      echo $i >> ./.tmp_pack
2272  done  done
# Line 2057  else Line 2311  else
2311          echo "Error: problem encountered while building source files in pkg/mnc:"          echo "Error: problem encountered while building source files in pkg/mnc:"
2312          cat make_mnc.errors 1>&2          cat make_mnc.errors 1>&2
2313          if test "x$mnc_in" = x0 ; then          if test "x$mnc_in" = x0 ; then
2314              exit 1              exit 1
2315          else          else
2316              DISABLE="$DISABLE mnc"              DISABLE="$DISABLE mnc"
2317          fi          fi
# Line 2090  EOF Line 2344  EOF
2344      fi      fi
2345  fi  fi
2346    
2347    #  Check for package RADTRANS: if LAPACK is not available,
2348    #  then issue a warning that the direct radtrans solver is not available.
2349    if test "x$HAVE_LAPACK" != xt ; then
2350        echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1
2351        RETVAL=$?
2352        if test "x$RETVAL" = x0 ; then
2353            cat <<EOF
2354    *********************************************************************
2355    WARNING: the "radtrans" package was enabled but tests failed to
2356      compile LAPACK applications.  This means that the direct radtrans
2357      solver is not available and compilation will fail if it is enabled.
2358      If you want to use the direct solver, please check that:
2359    
2360      1) LAPACK is correctly installed for this compiler and
2361      2) the LIBS variable (within the "optfile") specifies the correct
2362         LAPACK library to link against.
2363    *********************************************************************
2364    EOF
2365        fi
2366    fi
2367    
2368  if  test "x${PKG_DEPEND}" != x ; then  if  test "x${PKG_DEPEND}" != x ; then
2369    echo "  applying package dependency rules"    echo "  applying package dependency rules"
2370    ck=    ck=
# Line 2135  if  test "x${PKG_DEPEND}" != x ; then Line 2410  if  test "x${PKG_DEPEND}" != x ; then
2410    
2411          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2412          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then          if test "x$pin" = xt -a "x$plus" = "x+" -a "x$din" = xf ; then
2413              #echo "   " $pname ": need to add :" $dname              #echo "   " $pname ": need to add :" $dname
2414              in_dis="f"              in_dis="f"
2415              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2416                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 2160  if  test "x${PKG_DEPEND}" != x ; then Line 2435  if  test "x${PKG_DEPEND}" != x ; then
2435              echo "  the dependency rules for \"$dname\""              echo "  the dependency rules for \"$dname\""
2436              exit 1              exit 1
2437          fi          fi
2438          i=`echo "$i + 1" | bc -l`          i=`echo "$i + 1" | bc -l`
2439          #i=$(( $i + 1 ))          #i=$(( $i + 1 ))
2440      done      done
2441      ck=$ck"t"      ck=$ck"t"
# Line 2201  for n in $names ; do Line 2476  for n in $names ; do
2476          done          done
2477          if test "x$has_pack" = xf ; then          if test "x$has_pack" = xf ; then
2478              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2479              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
2480          fi          fi
2481      fi      fi
2482  done  done
# Line 2214  for i in $PACKAGES ; do Line 2489  for i in $PACKAGES ; do
2489  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
2490      case $i in      case $i in
2491          aim_v23)          aim_v23)
2492              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
2493              echo "Warning: ALLOW_AIM is set to enable aim_v23."              echo "Warning: ALLOW_AIM is set to enable aim_v23."
2494              ;;              ;;
2495      esac      esac
# Line 2256  for i in $spaths ; do Line 2531  for i in $spaths ; do
2531      if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then      if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
2532          echo "    found CPP_OPTIONS=\"$try\""          echo "    found CPP_OPTIONS=\"$try\""
2533          CPP_OPTIONS="$try"          CPP_OPTIONS="$try"
2534          # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h          # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
2535          for n in $names ; do          for n in $names ; do
2536              test_for_package_in_cpp_options $CPP_OPTIONS $n              test_for_package_in_cpp_options $CPP_OPTIONS $n
2537          done          done
2538      fi      fi
2539      try="$i/CPP_EEOPTIONS.h"      try="$i/CPP_EEOPTIONS.h"
2540      if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then      if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
2541          echo "    found CPP_EEOPTIONS=\"$try\""          echo "    found CPP_EEOPTIONS=\"$try\""
2542          # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h          # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
2543  #**** not yet enabled ****  #**** not yet enabled ****
2544  #        test_for_mpi_in_cpp_eeoptions $try  #        test_for_mpi_in_cpp_eeoptions $try
2545  #**** not yet enabled ****  #**** not yet enabled ****
# Line 2303  for i in $INCLUDEDIRS ; do Line 2578  for i in $INCLUDEDIRS ; do
2578      fi      fi
2579  done  done
2580    
2581  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2582      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2583      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2584      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2585      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2586            mpi_headers_do_local_copy
     if test "x$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  
2587      fi      fi
2588  fi  fi
2589    
# Line 2355  if test "x$OPENAD" != x ; then Line 2614  if test "x$OPENAD" != x ; then
2614      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2615      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2616      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2617        OADTOOLS="$TOOLSDIR/OAD_support"
2618      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2619      for i in "." $MODS ; do      for i in "." $MODS ; do
2620          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
# Line 2410  for d in $alldirs ; do Line 2670  for d in $alldirs ; do
2670          if test ! -r ".links.tmp/$sf" ; then          if test ! -r ".links.tmp/$sf" ; then
2671              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2672                  ignore_f=f                  ignore_f=f
2673                  case $d/$sf in                  case $d/$sf in
2674                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2675                          ignore_f=t                          ignore_f=t
2676                          ;;                          ;;
2677                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2678                          ignore_f=t                          ignore_f=t
2679                          ;;                          ;;
2680                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2681                          ignore_f=t                          ignore_f=t
2682                          ;;                          ;;
2683                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2684                          ignore_f=t                          ignore_f=t
2685                          ;;                          ;;
2686                    ./EMBEDDED_FILES.h)                    ./EMBEDDED_FILES.h)
2687                          ignore_f=t                          ignore_f=t
2688                          ;;                          ;;
2689                    *)                    *)
2690                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
2691                          #  ignore all soft-links                          #  ignore all soft-links
2692                          if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then                          if test "x$HAVE_TEST_L" = xt -a "x$d" = x. -a -L $sf ; then
# Line 2436  for d in $alldirs ; do Line 2696  for d in $alldirs ; do
2696                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2697                          fi                          fi
2698                          ;;                          ;;
2699                  esac                  esac
2700                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2701                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2702                      case $extn in                      case $extn in
2703                        F)                        F)
2704                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> F77srclist.tmp
2705                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> F77srclist.tmp
2706                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2707                                basename=${sf%%.F}
2708                                isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2709                                if test -z "$isAD" ; then
2710                                    echo    " \\"  >> nonADF77srclist.tmp
2711                                    printf " $sf" >> nonADF77srclist.tmp
2712                                fi
2713                            else #- OpenAD case:
2714                              basename=${sf%%.F}                              basename=${sf%%.F}
2715                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`
2716                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
# Line 2483  for d in $alldirs ; do Line 2750  for d in $alldirs ; do
2750                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> hsrclist.tmp
2751                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> hsrclist.tmp
2752                          ;;                          ;;
2753                      flow)                      flow)
2754                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> ad_flow_files.tmp
2755                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> ad_flow_files.tmp
2756                          ;;                          ;;
# Line 2494  for d in $alldirs ; do Line 2761  for d in $alldirs ; do
2761      done      done
2762      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2763        if test "$d" != "." ; then        if test "$d" != "." ; then
2764          echo "" >> srclinks.tmp          echo "" >> srclinks.tmp
2765          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> srclinks.tmp
2766          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> srclinks.tmp
2767  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
# Line 2515  echo "" >> ad_flow_files.tmp Line 2782  echo "" >> ad_flow_files.tmp
2782  CMDLINE=$0  CMDLINE=$0
2783  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
2784      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2785                          else CMDLINE="$CMDLINE '$xx'" ; fi                          else CMDLINE="$CMDLINE '$xx'" ; fi
2786  done  done
2787    
2788  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
# Line 2549  cat >>$MAKEFILE <<EOF Line 2816  cat >>$MAKEFILE <<EOF
2816  # INCLUDES     : Directories searched for header files  # INCLUDES     : Directories searched for header files
2817  # DEFINES      : Macro definitions for CPP  # DEFINES      : Macro definitions for CPP
2818  # MAKEDEPEND   : Dependency generator  # MAKEDEPEND   : Dependency generator
 # KPP          : Special preprocessor command (specific to platform)  
 # KFLAGS       : Flags for KPP  
2819  # FC           : Fortran compiler command  # FC           : Fortran compiler command
2820  # FFLAGS       : Configuration/debugging options for FC  # FFLAGS       : Configuration/debugging options for FC
2821  # FOPTIM       : Optimization options for FC  # FOPTIM       : Optimization options for FC
# Line 2564  INCLUDEDIRS = ${INCLUDEDIRS} Line 2829  INCLUDEDIRS = ${INCLUDEDIRS}
2829  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2830  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2831  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2832    OADTOOLS    = ${OADTOOLS}
2833    
2834  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2835  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2584  else Line 2850  else
2850      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2851  fi  fi
2852    
2853    # extract default cpp search path so we can pass it to makedepend
2854    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2855    
2856  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2857  # Unix ln (link)  # Unix ln (link)
2858  LN = ${LN}  LN = ${LN}
 # C preprocessor  
 CPP = cat \$< | ${S64} | ${CPP}  
2859  # Dependency generator  # Dependency generator
2860  MAKEDEPEND = ${MAKEDEPEND}  MAKEDEPEND = ${MAKEDEPEND}
2861  # Special preprocessor (KAP on DECs, FPP on Crays)  # Special preprocessor (KAP on DECs, FPP on Crays)
# Line 2606  LINK = ${LINK} ${LDADD} Line 2873  LINK = ${LINK} ${LDADD}
2873  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2874  # Includes for CPP  # Includes for CPP
2875  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2876    # default CPP includes for makedepend
2877    CPPINCLUDES = ${CPPINCLUDES}
2878  # Flags for KPP  # Flags for KPP
2879  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2880  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
# Line 2623  NOOPTFILES = ${NOOPTFILES} Line 2892  NOOPTFILES = ${NOOPTFILES}
2892  NOOPTFLAGS = ${NOOPTFLAGS}  NOOPTFLAGS = ${NOOPTFLAGS}
2893  # Flags and libraries needed for linking  # Flags and libraries needed for linking
2894  LIBS = ${LIBS}  LIBS = ${LIBS}
2895  # Name of the Mekfile  # Name of the makefile
2896  MAKEFILE=${MAKEFILE}  MAKEFILE = ${MAKEFILE}
2897    # Name of the make program
2898    MAKE = ${MAKE}
2899    
2900  EOF  EOF
2901    
# Line 2648  echo >> $MAKEFILE Line 2919  echo >> $MAKEFILE
2919  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2920  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2921  echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE  echo 'OBJFILES= $(F77_SRC_FILES:.F=.o) $(C_SRC_FILES:.c=.o) $(F90_SRC_FILES:.F90=.o)' >> $MAKEFILE
2922  echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE  echo 'FLOWFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2923  echo >> $MAKEFILE  echo >> $MAKEFILE
2924  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2925  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE  echo '.SUFFIXES: .o .'$FS' .p .F .c .f'$FS90' .'$FS90' .FF90 .F90 .flowdir .flow' >> $MAKEFILE
2926    
2927  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2928    
2929  all: \$(EXECUTABLE)  all: fwd_exe_target
2930    fwd_exe_target:
2931            @echo Update AD_CONFIG.h and make \$(EXECUTABLE)
2932            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
2933            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2934            @-rm -f ad_config.template
2935            \$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
2936    
2937  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)  \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
2938          @echo Creating \$@ ...          @echo Creating \$@ ...
2939          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2940    
2941  depend:  depend:
2942          @make links          @\$(MAKE) -f \$(MAKEFILE) links
2943          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2944          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2945          -rm -f makedepend.out          -rm -f makedepend.out
2946    
# Line 2671  libmitgcmuv.a: \$(OBJFILES) Line 2950  libmitgcmuv.a: \$(OBJFILES)
2950          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
2951          ar d   libmitgcmuv.a main.o          ar d   libmitgcmuv.a main.o
2952    
2953    obj: \$(OBJFILES)
2954    
2955  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
2956    
2957  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
# Line 2688  clean: Line 2969  clean:
2969    
2970  # remove most of the files that "make" and "make depend" generate  # remove most of the files that "make" and "make depend" generate
2971  Clean:  Clean:
2972          @make clean          @\$(MAKE) -f \$(MAKEFILE) clean
2973          @make cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
2974          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
2975          -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 taf_ftl.log
         -rm -f genmake_warnings genmake_errors make.log  
2976    
2977  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
2978  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
2979  CLEAN:  CLEAN:
2980          @make Clean          @\$(MAKE) -f \$(MAKEFILE) Clean
2981          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
2982          -rm -f $LOGFILE genmake_state genmake_*optfile genmake.tr_log make.tr_log          -rm -f $LOGFILE genmake_state genmake_*optfile
2983            -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
2984            -rm -rf mpi_headers mnc_test_*
2985          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2986          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2987          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2988          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
2989            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
2990          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
2991          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
2992    
2993  makefile:  makefile:
2994          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2715  cleanlinks: Line 2998  cleanlinks:
2998  # Special targets (SPECIAL_FILES) which are created by make  # Special targets (SPECIAL_FILES) which are created by make
2999  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
3000          @echo Creating \$@ ...          @echo Creating \$@ ...
3001          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
3002  AD_CONFIG.h:  AD_CONFIG.h:
3003          @echo Creating \$@ ...          @echo Creating \$@ ...
3004          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
3005  FC_NAMEMANGLE.h:  FC_NAMEMANGLE.h:
3006          @echo Creating \$@ ...          @echo Creating \$@ ...
3007          echo "$FC_NAMEMANGLE" > \$@          echo "$FC_NAMEMANGLE" > \$@
# Line 2758  cat >>$MAKEFILE <<EOF Line 3041  cat >>$MAKEFILE <<EOF
3041  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3042  ## %.o : %.F  ## %.o : %.F
3043    
3044    # C preprocessing and replacing the _d in constants:
3045    CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3046    
3047  .F.$FS:  .F.$FS:
3048          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3049  .$FS.o:  .$FS.o:
3050          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3051  .F.o:  .F.o:
3052          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3053  .F90.$FS90:  .F90.$FS90:
3054          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3055  .FF90.f$FS90:  .FF90.f$FS90:
3056          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3057  .$FS90.o:  .$FS90.o:
3058          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
3059  .f$FS90.o:  .f$FS90.o:
# Line 2776  cat >>$MAKEFILE <<EOF Line 3062  cat >>$MAKEFILE <<EOF
3062  .c.o:  .c.o:
3063          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
3064  .flow.flowdir:  .flow.flowdir:
3065          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3066    
3067  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
3068  .F.p:  .F.p:
3069          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3070  .p.$FS:  .p.$FS:
3071          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
3072    
# Line 2799  TAF            = ${TAF} Line 3085  TAF            = ${TAF}
3085    
3086  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3087  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3088    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3089    
3090  EOF  EOF
3091    
# Line 2827  rm -f adSrcFiles.tmp Line 3114  rm -f adSrcFiles.tmp
3114  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3115    
3116  # ... AD ...  # ... AD ...
3117  adall: \$(EXE_AD)  adall: ad_exe_target
3118  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
3119  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
3120    
3121  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)  ad_exe_target:
3122          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template          @echo Update AD_CONFIG.h and make \$(EXE_AD)
3123            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3124            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3125            @-rm -f ad_config.template
3126            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3127    
3128    ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
3129            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3130          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3131          -rm -f ad_config.template          @-rm -f ad_config.template
3132          @make \$(F77_PP_SRC_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3133          @make \$(FLOFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3134          cat \$(FLOFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
3135    
3136  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
3137          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
# Line 2849  adtafonly: Line 3143  adtafonly:
3143          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3144          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3145    
3146  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3147          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3148    
3149  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
3150          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 2865  adonlyfwd: Line 3159  adonlyfwd:
3159  adtrick:  adtrick:
3160          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3161    
3162    adobj: ad_taf_output.o \$(OBJFILES)
3163    
3164  # ... FTL ...  # ... FTL ...
3165  ftlall: ftl_taf  ftlall: ftl_exe_target
3166  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
3167  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
3168    
3169  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)  ftl_exe_target:
3170          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @echo Update AD_CONFIG.h and make \$(EXE_FTL)
3171          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3172          -rm -f ftl_config.template          @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3173          @make \$(F77_PP_SRC_FILES)          @-rm -f ad_config.template
3174          @make \$(AD_FLOW_FILES)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
3175          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS  
3176    ftl_input_code.$FS: \$(AD_FILES)
3177            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3178            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3179            @-rm -f ad_config.template
3180            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3181            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3182            cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3183    
3184  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
3185          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3186          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3187          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3188    
3189  ftltafonly:  ftltafonly:
3190          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3191          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3192          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3193    
3194  ftl_taf: ftl_taf_output.o \$(OBJFILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3195          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3196    
3197  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3198          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
# Line 2918  svd_touch: Line 3221  svd_touch:
3221          touch ad_taf_output.$FS ftl_taf_output.$FS          touch ad_taf_output.$FS ftl_taf_output.$FS
3222          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
3223          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
3224          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3225          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3226          -rm -f ftl_config.template          @-rm -f ad_config.template
3227    
3228  EOF  EOF
3229    
# Line 2995  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod. Line 3298  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.
3298    
3299  .PHONY: adDepend  .PHONY: adDepend
3300  adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)  adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
3301          \$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
3302          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
3303          -rm -f makedepend.out          -rm -f makedepend.out
3304    
# Line 3004  w2f__types.F90 \ Line 3307  w2f__types.F90 \
3307  OAD_active.F90 \  OAD_active.F90 \
3308  OAD_cp.F90 \  OAD_cp.F90 \
3309  OAD_rev.F90 \  OAD_rev.F90 \
3310  OAD_tape.F90  OAD_tape.F90 \
3311    revolve.F90
3312    
3313  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3314  iaddr.c \  iaddr.c \
# Line 3020  f95_test.out: f95_test_mods.f90 f95_test Line 3324  f95_test.out: f95_test_mods.f90 f95_test
3324          f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1          f95 -fixed -w=unused -maxcontin=132 -c f95_test_mods.f90 > \$@ 2>&1
3325          f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1          f95 -fixed -w=unused -maxcontin=132 -c -fixed f95_test.f90 >> \$@ 2>&1
3326    
3327  # the file included below is created by the  CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
 # postProcessor and its inclusion sets the  
 # variable POSTPROCESSEDFILES  
 # used below. Because the file is made during  
 # make it won't be read until the second (recursive)  
 # invocation in the rule below  
 -include postProcess.make  
3328    
3329  AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$FS90=.o)  AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o)  OAD_intrinsics_oad.o \$(CB2M_AD_FILES:.f$FS90=_oad.o)
3330    
3331  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)  AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.o) \$(C_SRC_FILES:.c=.o) \$(F90_SRC_FILES:.F90=.o)
3332    
3333  postProcess.comp: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S1)  \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.tag \$(AD_OBJ_FILES_S2)
 ifeq (\$(MAKELEVEL),0)  
         \$(MAKE) adAll  
 else  
         touch \$@  
 endif  
   
 \$(EXE_AD): \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) postProcess.comp \$(AD_OBJ_FILES_S2)  
 ifeq (\$(MAKELEVEL),1)  
3334          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
 else  
         touch \$@  
 endif  
3335    
3336  # makefile debug rule  # create sources files modules from header files containing common blocks
3337  openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3338  .PHONY: openad          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3339    
3340  # create the module files  # create new header files with USE statements for the new modules made above
3341  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3342          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3343    
3344  # create the header files  # change the include directives of everybody to refer to  the new header files with the USE statements
3345  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3346          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
   
 # change everybody else to use the new module files:  
 %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  
         ../OAD_support/cb2mUseModules.bash $< ${MPI}  
3347    
3348  # makefile debug rule  # makefile debug rule
3349  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
# Line 3073  ad_output.txt: \$(EXE_AD) Line 3356  ad_output.txt: \$(EXE_AD)
3356          @printf 'running ... '          @printf 'running ... '
3357          @./\$(EXE_AD) > \$@          @./\$(EXE_AD) > \$@
3358    
 CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)  
3359  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3360          cat \$^ > \$@          cat \$^ > \$@
3361    
 # strip all comments and blanks to reduce  
 # the file size in order to reduce perl's memory requirements  
 ad_input_code_sf.f$FS90 : ad_input_code.f$FS90  
         cat \$^ | sed -f ../OAD_support/strip.sed | sed -f ../OAD_support/stop2print.sed > \$@  
   
 # mfef90 preprocessing  
 # expand statement functions  
 # expose mfef90 specific substring handling  
 # add the w2f__types module  
 ad_input_code_sf.w2f.f$FS90: ad_input_code_sf.f$FS90 mfef90 whirl2f whirl2f_be w2f__types.f90  
         ./mfef90 -r8 -z -F -N132 \$<  
         mv \$<.B \$(basename \$<).B  
         ./whirl2f -openad \$(basename \$<).B  
         cat w2f__types.f90 \$(basename \$<).w2f.f > \$@  
   
3362  # canonicalizer  # canonicalizer
3363  ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py  ad_input_code_sf.pre.f90 : \$(CB2M_AD_FILES)
3364          ./preProcess.py --timing --r8 -H -S \$< -o \$@          \${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
3365    
3366    # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3367    ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3368            cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3369    
3370  # F -> WHIRL  # F -> WHIRL
3371  # note that the canonicalized version cuts off at col 72  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
3372  # doing this also for string constants which is ok as long          \${OPEN64ROOT}/crayf90/sgi/mfef90 -r8 -z -F ad_input_code_sf.pre.s2p.f90
 # as we are in fixed mode and cut of exactly there.  
 # Otherwise mfef90 patches in spaces to fill up to 72 (or 132)  
 # characters respectively.  
 ad_input_code_sf.w2f.pre.B: ad_input_code_sf.w2f.pre.f$FS90 mfef90  
         ./mfef90 -r8 -z -F \$<  
         mv \$<.B \$@  
3373    
3374  # WHIRL -> XAIF  # WHIRL -> XAIF
3375  ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif  ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
3376          ./whirl2xaif -s -n --debug 1 -o \$@ \$<          \${OPENADFORTTK}/bin/whirl2xaif -s -n --debug 1 -o \$@ \$<
3377    
3378  # XAIF -> XAIF'  # XAIF -> XAIF'
3379  ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver  ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
3380          ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r          \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3381    
3382  # XAIF' -> WHIRL'  # XAIF' -> WHIRL'
3383  ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl  ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
3384          ./xaif2whirl --debug 1 ad_input_code_sf.w2f.pre.B \$<          \${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
3385    
3386  # WHIRL' -> F'  # WHIRL' -> F'
3387  ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
3388          ./whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3389    
3390  # insert template directives  # insert template directives
3391  ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash  ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \${OADTOOLS}/insertTemplateDir.bash
3392          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3393    
3394  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(wildcard \${OADTOOLS}/ad_template.*.F) \${OADTOOLS}/ad_inline.F
3395  # postprocess F'  # postprocess F'
3396  postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
3397          # the target is a placeholder to signal execution of the rule          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i \${OADTOOLS}/ad_inline.f \$<
3398            # the target is a placeholder to trigger a single execution of the rule
3399          touch \$@          touch \$@
3400          # this step also creates the file postProcess.make but we cannot  # put this so make knows about the postprocessing output
3401          # name it as the target or else make will try to remake it for  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$FS90=_oad.f): postProcess.tag
         # the include directive above for any rule, e.g. make clean  
         ./postProcess.py --progress --timing --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<  
3402    
3403  # setup some links  # link the XAIF schema files
3404  %.xsd:  %.xsd:
3405          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3406    
 mfef90:  
         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .  
   
3407  # link the support files:  # link the support files:
3408  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
3409          \$(LN) ../OAD_support/\$@ .          \$(LN) \${OADTOOLS}/\$@ .
   
 whirl2xaif xaif2whirl:  
         \$(LN) \${OPENADFORTTK}/bin/\$@ .  
   
 preProcess.py postProcess.py:  
         \$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .  
   
 whirl2f whirl2f_be:  
         \$(LN) \${OPEN64ROOT}/whirl2f/\$@ .  
   
 oadDriver:  
         \$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@  
3410    
3411  AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.make postProcess.tag postProcess.comp \$(PPEXTRAS:.F=.f)  AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag \$(PPEXTRAS:.F=.f)
3412    
3413  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3414    
# Line 3204  printf "\n\n# DO NOT DELETE\n" >> $MAKEF Line 3453  printf "\n\n# DO NOT DELETE\n" >> $MAKEF
3453  printf "\n===  Done  ===\n"  printf "\n===  Done  ===\n"
3454    
3455  # Create special header files  # Create special header files
3456  $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp"  $BASH $TOOLSDIR/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp"
3457  if test ! -f $PACKAGES_DOT_H ; then  if test ! -f $PACKAGES_DOT_H ; then
3458      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
3459  else  else
# Line 3218  else Line 3467  else
3467      fi      fi
3468  fi  fi
3469  if test ! -f AD_CONFIG.h ; then  if test ! -f AD_CONFIG.h ; then
3470      $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 $TOOLSDIR/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
3471  fi  fi
3472    
3473  #  Write the "state" for future records  #  Write the "state" for future records
# Line 3227  if test "x$DUMPSTATE" = xt ; then Line 3476  if test "x$DUMPSTATE" = xt ; then
3476      for i in $gm_state ; do      for i in $gm_state ; do
3477          t1="t2=\$$i"          t1="t2=\$$i"
3478          eval $t1          eval $t1
3479          echo "$i='$t2'" >> genmake_state          echo "$i='$t2'" | sed -e 's/  */ /g' >> genmake_state
3480      done      done
3481  fi  fi

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