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revision 1.234 by jmc, Fri Aug 17 17:27:57 2012 UTC revision 1.265 by jmc, Fri Apr 4 21:34:01 2014 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        -oad | --oad
23              Generate a Makefile for an OpenAD built
24    
25      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
26        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
27            Use "NAME" as the adoptfile.  By default, the file at            Use "NAME" as the adoptfile.  By default, the file at
28            "tools/adjoint_options/adjoint_default" will be used.            "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
29              "tools/adjoint_options/adjoint_default" will be used.
30    
31      -nooptfile | --nooptfile      -nooptfile | --nooptfile
32        -optfile NAME | --optfile NAME | -of NAME | --of NAME        -optfile NAME | --optfile NAME | -of NAME | --of NAME
33        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
34            Use "NAME" as the optfile.  By default, an attempt will be            Use "NAME" as the optfile.  By default, an attempt will be
35            made to find an appropriate "standard" optfile in the            made to find an appropriate "standard" optfile in the
36            tools/build_options/ directory.            tools/build_options/ directory.
37    
38      -pdepend NAME | --pdepend NAME      -pdepend NAME | --pdepend NAME
39        -pdepend=NAME | --pdepend=NAME        -pdepend=NAME | --pdepend=NAME
40            Get package dependency information from "NAME".            Get package dependency information from "NAME".
41    
42      -pgroups NAME | --pgroups NAME      -pgroups NAME | --pgroups NAME
43        -pgroups=NAME | --pgroups=NAME        -pgroups=NAME | --pgroups=NAME
44            Get the package groups information from "NAME".            Get the package groups information from "NAME".
45    
46      -bash NAME      -bash NAME
47            Explicitly specify the Bourne or BASH shell to use            Explicitly specify the Bourne or BASH shell to use
48    
49      -make NAME | -m NAME      -make NAME | -m NAME
50        --make=NAME | -m=NAME        --make=NAME | -m=NAME
51            Use "NAME" for the MAKE program. The default is "make" but            Use "NAME" for the MAKE program. The default is "make" but
52            many platforms, "gmake" is the preferred choice.            many platforms, "gmake" is the preferred choice.
53    
54      -makefile NAME | -mf NAME      -makefile NAME | -mf NAME
55        --makefile=NAME | -mf=NAME        --makefile=NAME | -mf=NAME
56            Call the makefile "NAME".  The default is "Makefile".            Call the makefile "NAME".  The default is "Makefile".
57    
58      -makedepend NAME | -md NAME      -makedepend NAME | -md NAME
59        --makedepend=NAME | -md=NAME        --makedepend=NAME | -md=NAME
60            Use "NAME" for the MAKEDEPEND program.            Use "NAME" for the MAKEDEPEND program.
61    
62      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
63        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
64            Specify the location of the MITgcm ROOTDIR as "NAME".            Specify the location of the MITgcm ROOTDIR as "NAME".
65            By default, genamke will try to find the location by            By default, genamke will try to find the location by
66            looking in parent directories (up to the 5th parent).            looking in parent directories (up to the 5th parent).
67    
68      -mods NAME | --mods NAME | -mo NAME | --mo NAME      -mods NAME | --mods NAME | -mo NAME | --mo NAME
69        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
70            Here, "NAME" specifies a list of directories that are            Here, "NAME" specifies a list of directories that are
71            used for additional source code.  Files found in the            used for additional source code.  Files found in the
72            "mods list" are given preference over files of the same            "mods list" are given preference over files of the same
73            name found elsewhere.            name found elsewhere.
74    
75      -disable NAME | --disable NAME      -disable NAME | --disable NAME
76        -disable=NAME | --disable=NAME        -disable=NAME | --disable=NAME
77            Here "NAME" specifies a list of packages that we don't            Here "NAME" specifies a list of packages that we don't
78            want to use.  If this violates package dependencies,            want to use.  If this violates package dependencies,
79            genamke will exit with an error message.            genamke will exit with an error message.
80    
81      -enable NAME | --enable NAME      -enable NAME | --enable NAME
82        -enable=NAME | --enable=NAME        -enable=NAME | --enable=NAME
83            Here "NAME" specifies a list of packages that we wish            Here "NAME" specifies a list of packages that we wish
84            to specifically enable.  If this violates package            to specifically enable.  If this violates package
85            dependencies, genamke will exit with an error message.            dependencies, genamke will exit with an error message.
86    
87      -standarddirs NAME | --standarddirs NAME      -standarddirs NAME | --standarddirs NAME
88        -standarddirs=NAME | --standarddirs=NAME        -standarddirs=NAME | --standarddirs=NAME
89            Here, "NAME" specifies a list of directories to be            Here, "NAME" specifies a list of directories to be
90            used as the "standard" code.            used as the "standard" code.
91    
92      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
93        -fc=NAME | --fc=NAME        -fc=NAME | --fc=NAME
94            Use "NAME" as the fortran compiler.  By default, genmake            Use "NAME" as the fortran compiler.  By default, genmake
95            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
96            "usual suspects" such as g77, f77, etc.            "usual suspects" such as g77, f77, etc.
97    
98      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
99            Use "NAME" as the C compiler.  By default, genmake            Use "NAME" as the C compiler.  By default, genmake
100            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
101            "usual suspects" such as gcc, c89, cc, etc.            "usual suspects" such as gcc, c89, cc, etc.
102    
103      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
104            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
105            *only* works if CPP_EEOPTIONS.h allows this.            *only* works if CPP_EEOPTIONS.h allows this.
106    
107      -ignoretime | -ignore_time | --ignoretime | --ignore_time      -ignoretime | -ignore_time | --ignoretime | --ignore_time
108            Ignore all the "wall clock" routines entirely.  This will            Ignore all the "wall clock" routines entirely.  This will
109            not in any way hurt the model results -- it simply means            not in any way hurt the model results -- it simply means
110            that the code that checks how long the model spends in            that the code that checks how long the model spends in
111            various routines will give junk values.            various routines will give junk values.
112    
113      -ts | --ts      -ts | --ts
114            Produce timing information per timestep            Produce timing information per timestep
115      -papis | --papis      -papis | --papis
116            Produce summary MFlop/s (and IPC) with PAPI per timestep            Produce summary MFlop/s (and IPC) with PAPI per timestep
117      -pcls | --pcls      -pcls | --pcls
118            Produce summary MFlop/s etc. with PCL per timestep            Produce summary MFlop/s etc. with PCL per timestep
119      -foolad | --foolad      -foolad | --foolad
120            Fool the AD code generator            Fool the AD code generator
121      -papi | --papi      -papi | --papi
122            Performance analysis with PAPI            Performance analysis with PAPI
123      -pcl | --pcl      -pcl | --pcl
124            Performance analysis with PCL            Performance analysis with PCL
125      -hpmt | --hpmt      -hpmt | --hpmt
126            Performance analysis with the HPM Toolkit            Performance analysis with the HPM Toolkit
127    
128      -ieee | --ieee      -ieee | --ieee
129            use IEEE numerics.  Note that this option *only* works            use IEEE numerics.  Note that this option *only* works
130            if it is supported by the OPTFILE that is being used.            if it is supported by the OPTFILE that is being used.
131      -devel | --devel      -devel | --devel
132            Add additional warning and debugging flags for development            Add additional warning and debugging flags for development
133            (if supported by the OPTFILE); also switch to IEEE numerics.            (if supported by the OPTFILE); also switch to IEEE numerics.
134      -gsl | --gsl      -gsl | --gsl
135            Use GSL to control floating point rounding and precision            Use GSL to control floating point rounding and precision
136    
137      -mpi | --mpi      -mpi | --mpi
138            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
139      -mpi=PATH | --mpi=PATH      -mpi=PATH | --mpi=PATH
140            Include MPI header files and link to MPI libraries using MPI_ROOT            Include MPI header files and link to MPI libraries using MPI_ROOT
141            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
142            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
143    
144      -omp | --omp      -omp | --omp
145            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
146      -omp=OMPFLAG | --omp=OMPFLAG      -omp=OMPFLAG | --omp=OMPFLAG
147            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
148    
149      -es | --es | -embed-source | --embed-source      -es | --es | -embed-source | --embed-source
150            Embed a tarball containing the full source code            Embed a tarball containing the full source code
151            (including the Makefile, etc.) used to build the            (including the Makefile, etc.) used to build the
152            executable [off by default]            executable [off by default]
153    
154      -ds | --ds      -ds | --ds
155            Report genmake internal variables status (DUMPSTATE)            Report genmake internal variables status (DUMPSTATE)
156            to file "genmake_state" (for debug purpose)            to file "genmake_state" (for debug purpose)
157    
158    While it is most often a single word, the "NAME" variables specified    While it is most often a single word, the "NAME" variables specified
159    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 174  EOF Line 178  EOF
178  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
179      cpp_options=$1      cpp_options=$1
180      pkg=$2      pkg=$2
181      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
182      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
183      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
184      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$"  
185  }  }
186    
187  # Search for particular CPP #cmds associated with MPI  # Search for particular CPP #cmds associated with MPI
188  # usage: test_for_mpi_in_cpp_eeoptions CPP_file  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
189  test_for_mpi_in_cpp_eeoptions() {  test_for_mpi_in_cpp_eeoptions() {
190      cpp_options=$1      cpp_options=$1
191      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
192      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 $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"  
193  }  }
194    
195  # 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 203  test_for_mpi_in_cpp_eeoptions() { Line 197  test_for_mpi_in_cpp_eeoptions() {
197  test_for_string_in_file() {  test_for_string_in_file() {
198      file=$1      file=$1
199      strng=$2      strng=$2
200      grep -i "$strng" $file > /dev/null 2>&1      grep "$strng" $file > /dev/null 2>&1
201      RETVAL=$?      RETVAL=$?
202      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
203          printf "Error: In $file there is an illegal line: "          printf "Error: In $file there is an illegal line: "
204          grep -i "$strng" $file          grep -i "$strng" $file
205          exit 99          exit 99
206      fi      fi
207      return 0      return 0
# Line 218  test_for_string_in_file() { Line 212  test_for_string_in_file() {
212  expand_pkg_groups() {  expand_pkg_groups() {
213      new_packages=      new_packages=
214      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
215          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp          cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > $TMP.p1
216          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
217          matched=0          matched=0
218          for i in $PACKAGES ; do          for i in $PACKAGES ; do
219              line=`grep "^ *$i" ./p2.tmp`              line=`grep "^ *$i" $TMP.p2`
220              RETVAL=$?              RETVAL=$?
221              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
222                  matched=1                  matched=1
# Line 234  expand_pkg_groups() { Line 228  expand_pkg_groups() {
228              fi              fi
229          done          done
230          PACKAGES=$new_packages          PACKAGES=$new_packages
231          rm -f ./p[1,2].tmp          rm -f $TMP.p[1,2]
232          return $matched          return $matched
233      else      else
234          echo "Warning: can't read package groups definition file: $PKG_GROUPS"          echo "Warning: can't read package groups definition file: $PKG_GROUPS"
# Line 305  EOF Line 299  EOF
299              FS90='fr9'              FS90='fr9'
300              check_for_broken_Ff              check_for_broken_Ff
301          else          else
302              cat <<EOF 2>&1              echo "ERROR: test: '$MAKE -f $MAKEFILE genmake_hello.$tfs' Failed"
303  ERROR: Your file system cannot distinguish between *.F and *.f files              echo "       see simple makefile: '$MAKEFILE' (left here)"
304    (fails the "make/ln" test) and this program cannot find a suitable              echo "  Please check (1) your '$MAKE' command, (2) your '$LN' command"
305    replacement extension.  Please try a different build environment or              echo "           and (3) the allowed sufix '.F' and '.$tfs' in makefile"
306    contact the <MITgcm-support@mitgcm.org> list for help.              echo "  or contact the <MITgcm-support@mitgcm.org> list for help."
307                echo ""
 EOF  
308              exit -1              exit -1
309              return              return
310          fi          fi
# Line 335  look_for_makedepend()  { Line 328  look_for_makedepend()  {
328      #      #
329      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
330      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
331      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
332      #      #
333      #  So the choices are, in order:      #  So the choices are, in order:
     #  
334      #    1) use the user-specified program      #    1) use the user-specified program
335      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
336      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
337      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
338        #             (faster, but can miss some dependencies)
339      #      #
340      echo >> $LOGFILE      echo >> $LOGFILE
341      echo "running: look_for_makedepend()" >> $LOGFILE      echo "running: look_for_makedepend()" >> $LOGFILE
# Line 354  look_for_makedepend()  { Line 346  look_for_makedepend()  {
346              build_cyrus_makedepend              build_cyrus_makedepend
347              RETVAL=$?              RETVAL=$?
348              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
349                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
350                  MAKEDEPEND=                  MAKEDEPEND=
351              fi              fi
352          else          else
# Line 367  look_for_makedepend()  { Line 359  look_for_makedepend()  {
359          fi          fi
360      fi      fi
361      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
362          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
363          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
364          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 384  EOF Line 374  EOF
374        stop        stop
375        end        end
376  EOF  EOF
377          makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
378          RV1=$?          RV1=$?
379            which makedepend > /dev/null 2>&1
380            RV2=$?
381            if test "x${RV2}" = x0 ; then
382                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
383                RV3=$? ; loc_msg='not working.'
384            else RV3=$RV2 ; loc_msg='not found.'
385            fi
386          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
387          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
388          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
389            if test "x${RV1}" = x0 ; then
390                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
391                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
392            elif test "x${RV3}" = x0 ; then
393                echo "    local tools/xmakedepend not working. Use system-default makedepend"
394              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
395              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
396          else          else
397              echo "    system-default makedepend not found. Try to build cyrus-makedepend"              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
398                echo -n "    Try to build cyrus-makedepend ..."
399              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
400              build_cyrus_makedepend              build_cyrus_makedepend
401              RETVAL=$?              RETVAL=$?
402              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
403                  echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"                  echo "  Works"
404                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'              else
405                  echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE                  echo "  Fails" ; echo "" >> $LOGFILE
406                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
407                    echo ""
408                    exit -1
409                    return
410              fi              fi
411          fi          fi
412      fi      fi
# Line 412  build_cyrus_makedepend()  { Line 419  build_cyrus_makedepend()  {
419      (      (
420          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
421              &&  ./configure > /dev/null 2>&1  \              &&  ./configure > /dev/null 2>&1  \
422              &&  make > /dev/null 2>&1              &&  $MAKE > /dev/null 2>&1
423          if test -x ./makedepend.exe ; then          if test -x ./makedepend.exe ; then
424              $LN ./makedepend.exe ./makedepend              $LN ./makedepend.exe ./makedepend
425          fi          fi
# Line 436  build_embed_encode() Line 443  build_embed_encode()
443  {  {
444      printf "  building the embed-encode utility...  "      printf "  building the embed-encode utility...  "
445      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
446          if test ! -d "$ROOTDIR/tools/embed_encode" ; then          if test ! -d "$ROOTDIR/tools/embed_encode" ; then
447              echo              echo
448              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
449              echo              echo
450              EMBED_SRC=f              EMBED_SRC=f
451              return 1              return 1
452          fi          fi
453          clist="cc gcc c89 $CC"          clist="cc gcc c89 $CC"
454          for ic in $clist ; do          for ic in $clist ; do
455              comm="$ic -o encode_files encode_files.c"              comm="$ic -o encode_files encode_files.c"
# Line 578  EOF Line 585  EOF
585      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
586          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
587          if test ! -r $OPTFILE ; then          if test ! -r $OPTFILE ; then
588               echo "  I looked for the file "$OPTFILE" but did not find it"               echo "  I looked for the file "$OPTFILE" but did not find it"
589          fi          fi
590      fi      fi
591    
592      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
# Line 597  Error: No options file was found in:  $R Line 604  Error: No options file was found in:  $R
604  EOF  EOF
605          exit 1          exit 1
606      fi      fi
607    }
608    
609    #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
610    #  checking for additional included headers (in case of chain of included header)
611    mpi_headers_do_local_copy() {
612    
613        dBug=0
614        rm -rf ./mpi_headers
615        if test -d $MPIINCLUDEDIR ; then
616    
617  #     # look for possible MPI libraries          #----- check for additional headers (chain of included headers)
618  #     mpi_libs=          echo -n '  Check MPI headers ... '
619  #     mpi_fort=`which mpif77 2>/dev/null`          listIni=$MPI_HEADER_FILES
620  #     RETVAL=$?          echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
621  #     if test "x${RETVAL}" = x0 ; then          outp=$?
622  #       cat >>test.f <<EOF          #- always check mpif.h (the only mpi-header included in standard MITgcm code)
623  #       PROGRAM HELLO          if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
624  #       DO 10, I=1,10          if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
625  #       PRINT *,'Hello World'  
626  #    10 CONTINUE          doCheck=1 ; list2copy='' ; list2check=$listIni
627  #       STOP          while test $doCheck = 1 ; do
628  #       END            newList=''
629  # EOF            for i in $list2check ; do
630  #       eval "$mpi_fort -showme test.f > out"              if test -f $MPIINCLUDEDIR/$i ; then
631  #       RETVAL=$?                newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
632  #       if test "x${RETVAL}" = x0 ; then                  sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
633  #           a=`cat out`                if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
634  #           for i in $a ; do                for j in $newInc ; do
635  #               case $i in                  echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
636  #                   -*)                  outp=$?
637  #                       mpi_libs="$mpi_libs $i" ;;                  if test $outp != 0 ; then
638  #               esac                    if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
639  #           done                    newList="$newList $j"
640  #           echo "The MPI libs appear to be:"                  fi
641  #           echo "  "$mpi_libs                done
642  #       fi                if test $dBug = 1 ; then echo "" ; fi
643  #       rm -f test.f out              fi
644  #     fi            done
645              if test "x$newList" = x ; then doCheck=0
646              else list2check=$newList ; list2copy="$list2copy $newList"
647              fi
648            done
649            list2copy="$MPI_HEADER_FILES $list2copy"
650            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
651    
652            #----- create local mpi_headers dir if we have files to copy
653            mkListInc=`echo $list2copy | wc -w`
654            if test $mkListInc != 0 ; then
655              echo 'create local "./mpi_headers" dir'
656              mkdir -p ./mpi_headers
657              INCLUDES="-I./mpi_headers $INCLUDES"
658              mkListInc=1
659            fi
660            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
661    
662            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
663            for i in $list2copy ; do
664              if test -f $MPIINCLUDEDIR/$i ; then
665                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
666                if test $i = 'mpif.h' ; then
667                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
668                fi
669                if test $mkListInc = 2 ; then
670                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
671                fi
672                if test $mkListInc = 1 ; then
673                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
674                fi
675              fi
676            done
677        else
678            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
679            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
680    #       exit -1
681        fi
682  }  }
683    
684  #  Parse the package dependency information  #  Parse the package dependency information
# Line 650  get_fortran_c_namemangling()  { Line 703  get_fortran_c_namemangling()  {
703    
704      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
705      if test ! "x$FC_NAMEMANGLE" = x ; then      if test ! "x$FC_NAMEMANGLE" = x ; then
706          return 0          return 0
707      fi      fi
708      echo " running: get_fortran_c_namemangling()" >> $LOGFILE      echo " running: get_fortran_c_namemangling()" >> $LOGFILE
709    
# Line 947  check_netcdf_libs()  { Line 1000  check_netcdf_libs()  {
1000        program fgennc        program fgennc
1001  #include "netcdf.inc"  #include "netcdf.inc"
1002  EOF  EOF
1003      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1004          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1005      fi     #fi
1006      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1007        integer iret, ncid, xid        integer iret, ncid, xid
1008        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1037  check_lapack_libs()  { Line 1090  check_lapack_libs()  {
1090      echo "running: check_lapack_libs()" >> $LOGFILE      echo "running: check_lapack_libs()" >> $LOGFILE
1091      cat <<EOF > genmake_tla.F      cat <<EOF > genmake_tla.F
1092        program fgenla        program fgenla
1093        integer info        integer info
1094        integer ipiv( 2 )        integer ipiv( 2 )
1095        double precision ab( 4, 2 ), b( 2 )        double precision ab( 4, 2 ), b( 2 )
1096        data ab / 0., 0., 1., 2., 0., 2., 1., 0. /        data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
# Line 1108  EOF Line 1161  EOF
1161                  LIBS="$LIBS -llapack -lf77blas -lcblas"                  LIBS="$LIBS -llapack -lf77blas -lcblas"
1162                  HAVE_LAPACK=t                  HAVE_LAPACK=t
1163                  echo "check_lapack: successful" >> $LOGFILE                  echo "check_lapack: successful" >> $LOGFILE
1164              else              else
1165              # try again with "-latlas" added to the libs              # try again with "-latlas" added to the libs
1166                  echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log                  echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
1167                  echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log                  echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1168                  echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log                  echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1169                  echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log                  echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
1170                  cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \                  cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1171                      &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \                      &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1172                      &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1                      &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
1173                  RET_COMPILE=$?                  RET_COMPILE=$?
1174                  echo >> $LOGFILE                  echo >> $LOGFILE
1175                  cat genmake_tla.log >> $LOGFILE                  cat genmake_tla.log >> $LOGFILE
1176                  if test "x$RET_COMPILE" = x0 ; then                  if test "x$RET_COMPILE" = x0 ; then
1177                      LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"                      LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
1178                      HAVE_LAPACK=t                      HAVE_LAPACK=t
1179                      echo "check_lapack: successful" >> $LOGFILE                      echo "check_lapack: successful" >> $LOGFILE
1180                  fi                  fi
1181              fi              fi
1182          fi          fi
1183      fi      fi
# Line 1132  EOF Line 1185  EOF
1185      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1186  }  }
1187    
1188    check_HAVE_FLUSH()  {
1189        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1190            return
1191        fi
1192        echo >> $LOGFILE
1193        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1194        cat <<EOF > genmake_tflsh.$FS
1195          program fgenflsh
1196          integer iounit
1197          character*9 fname
1198          iounit = 26
1199          fname = 'tmp.tflsh'
1200          open(iounit,FILE=fname,STATUS='unknown')
1201          write(iounit,*) 'genmake_tflsh: hello'
1202          call flush(iounit)
1203          close(iounit)
1204          end
1205    EOF
1206        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1207        cat genmake_tflsh.$FS >> genmake_tflsh.log
1208        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1209    
1210        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1211        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1212        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1213            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1214        RET_COMPILE=$?
1215    
1216        if test "x$RET_COMPILE" = x0 ; then
1217            HAVE_FLUSH=t
1218            #cat genmake_tflsh.log >> $LOGFILE
1219            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1220        else
1221            HAVE_FLUSH=f
1222            cat genmake_tflsh.log >> $LOGFILE
1223        fi
1224        rm -f genmake_tflsh*
1225        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1226    }
1227    
1228  ###############################################################################  ###############################################################################
1229  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1189  GSL= Line 1281  GSL=
1281  DEVEL=  DEVEL=
1282  HAVE_TEST_L=  HAVE_TEST_L=
1283    
1284    # comment this line out to enable lapack test
1285    SKIP_LAPACK_CHECK=t
1286    
1287  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1288  HAVE_SYSTEM=  HAVE_SYSTEM=
1289  HAVE_FDATE=  HAVE_FDATE=
# Line 1200  HAVE_NETCDF= Line 1295  HAVE_NETCDF=
1295  HAVE_ETIME=  HAVE_ETIME=
1296  IGNORE_TIME=  IGNORE_TIME=
1297  HAVE_LAPACK=  HAVE_LAPACK=
1298    HAVE_FLUSH=
1299    
1300  MODS=  MODS=
1301  TOOLSDIR=  TOOLSDIR=
# Line 1207  SOURCEDIRS= Line 1303  SOURCEDIRS=
1303  INCLUDEDIRS=  INCLUDEDIRS=
1304  STANDARDDIRS="USE_THE_DEFAULT"  STANDARDDIRS="USE_THE_DEFAULT"
1305    
1306    #- local config file
1307    gm_local="genmake_local"
1308    
1309  G2ARGS=  G2ARGS=
1310  BASH=  BASH=
1311  PWD=`pwd`  PWD=`pwd`
# Line 1230  FS= Line 1329  FS=
1329  FS90=  FS90=
1330    
1331  AUTODIFF_PKG_USED=f  AUTODIFF_PKG_USED=f
1332    OPENAD=
1333  AD_OPTFILE=  AD_OPTFILE=
1334  TAF=  TAF=
1335  AD_TAF_FLAGS=  AD_TAF_FLAGS=
# Line 1242  FTL_TAF_FLAGS= Line 1342  FTL_TAF_FLAGS=
1342  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1343  TAMC_EXTRA=  TAMC_EXTRA=
1344    
1345    DIVA=
1346    MPIINCLUDEDIR=
1347    MPI_HEADER_FILES=
1348    LOCAL_MPI_HEADERS=
1349    
1350  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1351  gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS DISABLE ENABLE MAKEFILE MAKEDEPEND PLATFORM"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1352  gm_s2="FC CC MPI OMP USE_R4 TS PAPIS PCLS PAPI PCL HPMT IEEE DEVEL GSL FEXTRAFLAGS"  gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
1353  gm_s3="ROOTDIR STANDARDDIRS MODS DUMPSTATE"  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
1354    
1355  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1356  gm_s4="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1357  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1358  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1359  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1360  gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK"  gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
1361    
1362  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1363  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"  gm_s10="AUTODIFF_PKG_USED AD_OPTFILE OPENAD TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
1364  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"
1365  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1366    
1367  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"  gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
1368  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1278  LOGFILE="genmake.log" Line 1383  LOGFILE="genmake.log"
1383  rm -f genmake_state genmake_*optfile $LOGFILE  rm -f genmake_state genmake_*optfile $LOGFILE
1384    
1385  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  
1386    
1387  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
1388  #parse_options  #parse_options
# Line 1306  for ac_option in "$@" ; do Line 1401  for ac_option in "$@" ; do
1401      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
1402    
1403      case $ac_option in      case $ac_option in
1404            
1405          -help | --help | -h | --h)          -help | --help | -h | --h)
1406              usage ;;              usage ;;
1407            
1408          -nooptfile | --nooptfile)          -nooptfile | --nooptfile)
1409              OPTFILE="NONE" ;;              OPTFILE="NONE" ;;
1410          -optfile | --optfile | -of | --of)          -optfile | --optfile | -of | --of)
1411              ac_prev=OPTFILE ;;              ac_prev=OPTFILE ;;
1412          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1413              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1414            
1415            -oad | --oad)
1416                OPENAD="true" ;;
1417          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1418              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1419          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
1420              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1421            
1422          -pdepend | --pdepend)          -pdepend | --pdepend)
1423              ac_prev=PKG_DEPEND ;;              ac_prev=PKG_DEPEND ;;
1424          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
1425              PKG_DEPEND=$ac_optarg ;;              PKG_DEPEND=$ac_optarg ;;
1426            
1427          -pgroups | --pgroups)          -pgroups | --pgroups)
1428              ac_prev=PKG_GROUPS ;;              ac_prev=PKG_GROUPS ;;
1429          -pgroups=* | --pgroups=*)          -pgroups=* | --pgroups=*)
1430              PKG_GROUPS=$ac_optarg ;;              PKG_GROUPS=$ac_optarg ;;
1431            
1432          -make | --make | -m | --m)          -make | --make | -m | --m)
1433              ac_prev=MAKE ;;              ac_prev=MAKE ;;
1434          -make=* | --make=* | -m=* | --m=*)          -make=* | --make=* | -m=* | --m=*)
1435              MAKE=$ac_optarg ;;              MAKE=$ac_optarg ;;
1436            
1437          -bash | --bash)          -bash | --bash)
1438              ac_prev=BASH ;;              ac_prev=BASH ;;
1439          -bash=* | --bash=*)          -bash=* | --bash=*)
1440              BASH=$ac_optarg ;;              BASH=$ac_optarg ;;
1441            
1442          -makedepend | --makedepend | -md | --md)          -makedepend | --makedepend | -md | --md)
1443              ac_prev=MAKEDEPEND ;;              ac_prev=MAKEDEPEND ;;
1444          -makedepend=* | --makedepend=* | -md=* | --md=*)          -makedepend=* | --makedepend=* | -md=* | --md=*)
1445              MAKEDEPEND=$ac_optarg ;;              MAKEDEPEND=$ac_optarg ;;
1446            
1447          -makefile | --makefile | -ma | --ma)          -makefile | --makefile | -mf | --mf)
1448              ac_prev=MAKEFILE ;;              ac_prev=MAKEFILE ;;
1449          -makefile=* | --makefile=* | -ma=* | --ma=*)          -makefile=* | --makefile=* | -mf=* | --mf=*)
1450              MAKEFILE=$ac_optarg ;;              MAKEFILE=$ac_optarg ;;
1451            
1452          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
1453              echo "ERROR: The platform option has been removed.  Please specify"              echo "ERROR: The platform option has been removed.  Please specify"
1454              echo "  the build options using the \"optfile\" mechanism."              echo "  the build options using the \"optfile\" mechanism."
1455              echo              echo
1456              usage              usage
1457              ;;              ;;
1458            
1459          -rootdir | --rootdir | -rd | --rd)          -rootdir | --rootdir | -rd | --rd)
1460              ac_prev=ROOTDIR ;;              ac_prev=ROOTDIR ;;
1461          -rootdir=* | --rootdir=* | -rd=* | --rd=*)          -rootdir=* | --rootdir=* | -rd=* | --rd=*)
1462              ROOTDIR=$ac_optarg ;;              ROOTDIR=$ac_optarg ;;
1463            
1464          -mods | --mods | -mo | --mo)          -mods | --mods | -mo | --mo)
1465              ac_prev=MODS ;;              ac_prev=MODS ;;
1466          -mods=* | --mods=* | -mo=* | --mo=*)          -mods=* | --mods=* | -mo=* | --mo=*)
1467              MODS=$ac_optarg ;;              MODS=$ac_optarg ;;
1468            
1469          -disable | --disable)          -disable | --disable)
1470              ac_prev=DISABLE ;;              ac_prev=DISABLE ;;
1471          -disable=* | --disable=*)          -disable=* | --disable=*)
1472              DISABLE=$ac_optarg ;;              DISABLE=$ac_optarg ;;
1473            
1474          -enable | --enable)          -enable | --enable)
1475              ac_prev=ENABLE ;;              ac_prev=ENABLE ;;
1476          -enable=* | --enable=*)          -enable=* | --enable=*)
1477              ENABLE=$ac_optarg ;;              ENABLE=$ac_optarg ;;
1478            
1479          -standarddirs | --standarddirs)          -standarddirs | --standarddirs)
1480              ac_prev=STANDARDDIRS ;;              ac_prev=STANDARDDIRS ;;
1481          -standarddirs=* | --standarddirs=*)          -standarddirs=* | --standarddirs=*)
# Line 1388  for ac_option in "$@" ; do Line 1485  for ac_option in "$@" ; do
1485  #               ac_prev=cpp ;;  #               ac_prev=cpp ;;
1486  #           -cpp=* | --cpp=*)  #           -cpp=* | --cpp=*)
1487  #               CPP=$ac_optarg ;;  #               CPP=$ac_optarg ;;
1488            
1489          -cc | --cc)          -cc | --cc)
1490              ac_prev=CC ;;              ac_prev=CC ;;
1491          -cc=* | --cc=*)          -cc=* | --cc=*)
1492              CC=$ac_optarg ;;              CC=$ac_optarg ;;
1493            
1494          -fortran | --fortran | -fc | --fc)          -fortran | --fortran | -fc | --fc)
1495              ac_prev=FC ;;              ac_prev=FC ;;
1496          -fc=* | --fc=*)          -fc=* | --fc=*)
1497              FC=$ac_optarg ;;              FC=$ac_optarg ;;
1498            
1499          -fs | --fs)          -fs | --fs)
1500              ac_prev=FS ;;              ac_prev=FS ;;
1501          -fs=* | --fs=*)          -fs=* | --fs=*)
1502              FS=$ac_optarg ;;              FS=$ac_optarg ;;
1503            
1504          -fs90 | --fs90)          -fs90 | --fs90)
1505              ac_prev=FS90 ;;              ac_prev=FS90 ;;
1506          -fs90=* | --fs90=*)          -fs90=* | --fs90=*)
1507              FS90=$ac_optarg ;;              FS90=$ac_optarg ;;
1508            
1509          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1510              USE_R4=true ;;              USE_R4=true ;;
1511    
# Line 1416  for ac_option in "$@" ; do Line 1513  for ac_option in "$@" ; do
1513              IEEE=true ;;              IEEE=true ;;
1514          -noieee | --noieee)          -noieee | --noieee)
1515              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
1516          -devel | --devel)          -devel | --devel)
1517              IEEE=true ; DEVEL=true ;;              IEEE=true ; DEVEL=true ;;
1518          -gsl | --gsl)          -gsl | --gsl)
1519              GSL=true ;;              GSL=true ;;
1520    
1521          -ts | --ts)          -ts | --ts)
# Line 1441  for ac_option in "$@" ; do Line 1538  for ac_option in "$@" ; do
1538          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
1539              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1540              MPI=true ;;              MPI=true ;;
1541            
1542          -omp | --omp)          -omp | --omp)
1543              OMP=true ;;              OMP=true ;;
1544          -omp=* | --omp=*)          -omp=* | --omp=*)
1545              OMPFLAG=$ac_optarg              OMPFLAG=$ac_optarg
1546              OMP=true ;;              OMP=true ;;
1547            
1548          -ds | --ds)          -ds | --ds)
1549              DUMPSTATE=t ;;              DUMPSTATE=t ;;
1550            
1551          -extra_flag | --extra_flag)          -extra_flag | --extra_flag)
1552              ac_prev=FEXTRAFLAGS ;;              ac_prev=FEXTRAFLAGS ;;
1553          -extra_flag=* | --extra_flag=*)          -extra_flag=* | --extra_flag=*)
1554              FEXTRAFLAGS=$ac_optarg ;;              FEXTRAFLAGS=$ac_optarg ;;
1555            
1556          -taf_extra | --taf_extra)          -taf_extra | --taf_extra)
1557              ac_prev=TAF_EXTRA ;;              ac_prev=TAF_EXTRA ;;
1558          -taf_extra=* | --taf_extra=*)          -taf_extra=* | --taf_extra=*)
# Line 1465  for ac_option in "$@" ; do Line 1562  for ac_option in "$@" ; do
1562              ac_prev=TAMC_EXTRA ;;              ac_prev=TAMC_EXTRA ;;
1563          -tamc_extra=* | --tamc_extra=*)          -tamc_extra=* | --tamc_extra=*)
1564              TAMC_EXTRA=$ac_optarg ;;              TAMC_EXTRA=$ac_optarg ;;
1565            
1566          -ignoretime | -ignore_time | --ignoretime | --ignore_time)          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1567              IGNORE_TIME="-DIGNORE_TIME" ;;              IGNORE_TIME="-DIGNORE_TIME" ;;
1568    
# Line 1476  for ac_option in "$@" ; do Line 1573  for ac_option in "$@" ; do
1573              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
1574              usage              usage
1575              ;;              ;;
1576            
1577          *)          *)
1578              echo "Error: unrecognized argument: "$ac_option              echo "Error: unrecognized argument: "$ac_option
1579              usage              usage
1580              ;;              ;;
1581            
1582      esac      esac
1583    
1584  done  done
1585    
1586    #TMP=./genmk_$$
1587    #- try to put temporary files in system-local /tmp dir
1588    TMP=/tmp/genmk_$$
1589    touch $TMP ; retVal=$?
1590    if [ $retVal -eq 0 ] ; then
1591      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1592    else
1593      TMP=./genmk_$$
1594    fi
1595    rm -f $TMP
1596    #echo "  temp files: $TMP.*"
1597    
1598    printf "  getting local config information:  "
1599    if test -f $gm_local ; then
1600        echo "using $gm_local"
1601        . $gm_local
1602    else
1603        echo "none found"
1604    fi
1605    
1606  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1607      echo      echo
1608      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
# Line 1570  fi Line 1687  fi
1687    
1688  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1689  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1690      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1691            AD_OPTFILE=$MITGCM_AD_OF
1692        elif test "x$OPENAD" = x ; then
1693          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1694      else      else
1695          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1696      fi      fi
1697  fi  fi
1698  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1697  check_for_broken_Ff Line 1816  check_for_broken_Ff
1816    
1817  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1818        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1819        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1820    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1821    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1822  fi  fi
1823  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1824        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1714  fi Line 1835  fi
1835  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1836        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1837        if test ! "x$FOOLAD" = x ; then        if test ! "x$FOOLAD" = x ; then
1838              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1839        else        else
1840              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1841        fi        fi
# Line 1750  if test ! "x$PAPI" = x ; then Line 1871  if test ! "x$PAPI" = x ; then
1871            echo "  Sticking with PAPI flop summary per timestep!"            echo "  Sticking with PAPI flop summary per timestep!"
1872        else        else
1873            echo "  Turning on performance analysis with PAPI"            echo "  Turning on performance analysis with PAPI"
1874            echo "  Please make sure PAPIINC, PAPILIB are defined"            echo "  Please make sure PAPIINC, PAPILIB are defined"
1875            DEFINES="$DEFINES -DUSE_PAPI"            DEFINES="$DEFINES -DUSE_PAPI"
1876            INCLUDES="$INCLUDES $PAPIINC"            INCLUDES="$INCLUDES $PAPIINC"
1877            LIBS="$LIBS $PAPILIB"            LIBS="$LIBS $PAPILIB"
# Line 1762  if test ! "x$PCL" = x ; then Line 1883  if test ! "x$PCL" = x ; then
1883            echo "  Sticking with PCL flop summary per timestep!"            echo "  Sticking with PCL flop summary per timestep!"
1884        else        else
1885            echo "  Turning on performance analysis with PCL"            echo "  Turning on performance analysis with PCL"
1886            echo "  Please make sure PCLINC, PCLLIB are defined"            echo "  Please make sure PCLINC, PCLLIB are defined"
1887            DEFINES="$DEFINES -DUSE_PCL"            DEFINES="$DEFINES -DUSE_PCL"
1888            INCLUDES="$INCLUDES $PCLINC"            INCLUDES="$INCLUDES $PCLINC"
1889            LIBS="$LIBS $PCLLIB"            LIBS="$LIBS $PCLLIB"
# Line 1772  if test ! "x$HPMT" = x ; then Line 1893  if test ! "x$HPMT" = x ; then
1893        if test ! "x$PAPI" = x ; then        if test ! "x$PAPI" = x ; then
1894            echo "  PAPI and the HPM Toolkit cannot co-exist!"            echo "  PAPI and the HPM Toolkit cannot co-exist!"
1895            echo "  Sticking with PAPI!"            echo "  Sticking with PAPI!"
1896        else if test ! "x$PCL" = x ; then        else
1897            if test ! "x$PCL" = x ; then
1898            echo "  PCL and the HPM Toolkit cannot co-exist!"            echo "  PCL and the HPM Toolkit cannot co-exist!"
1899            echo "  Sticking with PCL!"            echo "  Sticking with PCL!"
1900        else          else
1901            echo "  Turning on performance analysis with the HPM Toolkit"            echo "  Turning on performance analysis with the HPM Toolkit"
1902            echo "  Please make sure HPMTINC, HPMTLIB are defined"            echo "  Please make sure HPMTINC, HPMTLIB are defined"
1903            DEFINES="$DEFINES -DUSE_LIBHPM"            DEFINES="$DEFINES -DUSE_LIBHPM"
1904            INCLUDES="$INCLUDES $HPMTINC"            INCLUDES="$INCLUDES $HPMTINC"
1905            LIBS="$LIBS $HPMTLIB"            LIBS="$LIBS $HPMTLIB"
1906        fi          fi
1907        fi        fi
1908  fi  fi
1909  if test ! "x$GSL" = x ; then  if test ! "x$GSL" = x ; then
# Line 1921  if test "x$HAVE_LAPACK" != x ; then Line 2043  if test "x$HAVE_LAPACK" != x ; then
2043  else  else
2044      echo "no"      echo "no"
2045  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2046    
2047    printf "  Can we call FLUSH intrinsic subroutine...  "
2048    check_HAVE_FLUSH
2049    if test "x$HAVE_FLUSH" = xt ; then
2050        DEFINES="$DEFINES -DHAVE_FLUSH"
2051        echo "yes"
2052    else
2053        echo "no"
2054    fi
2055    
2056    DEFINES="$DEFINES $IGNORE_TIME"
2057  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2058      build_embed_encode      build_embed_encode
2059  fi  fi
# Line 2106  else Line 2237  else
2237          exit 1          exit 1
2238      else      else
2239          echo "    using PKG_LIST=\"$PKG_LIST\""          echo "    using PKG_LIST=\"$PKG_LIST\""
2240          #  Strip the comments and add all the names          #  Strip the comments and add all the names
2241          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 $0}'`
2242          RETVAL=$?          RETVAL=$?
2243          if test "x${RETVAL}" != x0 ; then          if test "x${RETVAL}" != x0 ; then
# Line 2127  if test "x${PKG_GROUPS}" != x ; then Line 2258  if test "x${PKG_GROUPS}" != x ; then
2258  fi  fi
2259    
2260  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2261  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2262  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2263      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2264  done  done
2265  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2266      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2267      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2268  done  done
# Line 2149  for p in $PACKAGES ; do Line 2280  for p in $PACKAGES ; do
2280  done  done
2281  PACKAGES="$pack"  PACKAGES="$pack"
2282  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2283  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2284  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2285  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2286  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2287      j=`echo $i | sed 's/[-+]//'`      j=`echo $i | sed 's/[-+]//'`
2288      if test ! -d "$ROOTDIR/pkg/$j" ; then      if test ! -d "$ROOTDIR/pkg/$j" ; then
2289          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2290          exit 1          exit 1
2291      fi      fi
2292      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2293  done  done
2294  PACKAGES=  PACKAGES=
2295  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2296      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2297  done  done
2298  rm -f ./.tmp_pack  rm -f $TMP.pack
2299  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2300    
2301  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2201  else Line 2332  else
2332          echo "Error: problem encountered while building source files in pkg/mnc:"          echo "Error: problem encountered while building source files in pkg/mnc:"
2333          cat make_mnc.errors 1>&2          cat make_mnc.errors 1>&2
2334          if test "x$mnc_in" = x0 ; then          if test "x$mnc_in" = x0 ; then
2335              exit 1              exit 1
2336          else          else
2337              DISABLE="$DISABLE mnc"              DISABLE="$DISABLE mnc"
2338          fi          fi
# Line 2234  EOF Line 2365  EOF
2365      fi      fi
2366  fi  fi
2367    
2368  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2369  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2370  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2371      RETVAL=$?      RETVAL=$?
2372      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2373          cat <<EOF          cat <<EOF
 *********************************************************************  
 WARNING: the "radtrans" package was enabled but tests failed to  
   compile LAPACK applications.  This means that the direct radtrans  
   solver is not available and compilation will fail if it is enabled.  
   If you want to use the direct solver, please check that:  
2374    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2375  *********************************************************************  *********************************************************************
2376    ERROR: when generating an adjoint with OpenAD, the openad package
2377      must be enabled.  Please add it to packages.conf.
2378    *********************************************************************
2379    
2380  EOF  EOF
2381            exit 1
2382      fi      fi
2383  fi  fi
2384    
# Line 2300  if  test "x${PKG_DEPEND}" != x ; then Line 2427  if  test "x${PKG_DEPEND}" != x ; then
2427    
2428          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2429          if test "x$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
2430              #echo "   " $pname ": need to add :" $dname              #echo "   " $pname ": need to add :" $dname
2431              in_dis="f"              in_dis="f"
2432              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2433                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 2325  if  test "x${PKG_DEPEND}" != x ; then Line 2452  if  test "x${PKG_DEPEND}" != x ; then
2452              echo "  the dependency rules for \"$dname\""              echo "  the dependency rules for \"$dname\""
2453              exit 1              exit 1
2454          fi          fi
2455          i=`echo "$i + 1" | bc -l`          i=`echo "$i + 1" | bc -l`
2456          #i=$(( $i + 1 ))          #i=$(( $i + 1 ))
2457      done      done
2458      ck=$ck"t"      ck=$ck"t"
# Line 2366  for n in $names ; do Line 2493  for n in $names ; do
2493          done          done
2494          if test "x$has_pack" = xf ; then          if test "x$has_pack" = xf ; then
2495              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2496              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
2497          fi          fi
2498      fi      fi
2499  done  done
# Line 2379  for i in $PACKAGES ; do Line 2506  for i in $PACKAGES ; do
2506  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
2507      case $i in      case $i in
2508          aim_v23)          aim_v23)
2509              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
2510              echo "Warning: ALLOW_AIM is set to enable aim_v23."              echo "Warning: ALLOW_AIM is set to enable aim_v23."
2511              ;;              ;;
2512      esac      esac
# Line 2421  for i in $spaths ; do Line 2548  for i in $spaths ; do
2548      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
2549          echo "    found CPP_OPTIONS=\"$try\""          echo "    found CPP_OPTIONS=\"$try\""
2550          CPP_OPTIONS="$try"          CPP_OPTIONS="$try"
2551          # 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
2552          for n in $names ; do          for n in $names ; do
2553              test_for_package_in_cpp_options $CPP_OPTIONS $n              test_for_package_in_cpp_options $CPP_OPTIONS $n
2554          done          done
2555      fi      fi
2556      try="$i/CPP_EEOPTIONS.h"      try="$i/CPP_EEOPTIONS.h"
2557      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
2558          echo "    found CPP_EEOPTIONS=\"$try\""          echo "    found CPP_EEOPTIONS=\"$try\""
2559          # 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
2560  #**** not yet enabled ****  #**** not yet enabled ****
2561  #        test_for_mpi_in_cpp_eeoptions $try  #        test_for_mpi_in_cpp_eeoptions $try
2562  #**** not yet enabled ****  #**** not yet enabled ****
# Line 2443  fi Line 2570  fi
2570    
2571  #  Here, we build the list of files to be "run through" the adjoint  #  Here, we build the list of files to be "run through" the adjoint
2572  #  compiler.  #  compiler.
2573  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2574      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2575  fi  fi
2576  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2577  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2578  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2579      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2580      for j in $list_files ; do      for j in $list_files ; do
2581          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2582      done      done
2583  done  done
2584  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2585      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2586      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2587  fi  fi
2588    
2589  echo  echo
# Line 2468  for i in $INCLUDEDIRS ; do Line 2595  for i in $INCLUDEDIRS ; do
2595      fi      fi
2596  done  done
2597    
2598  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2599      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2600      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2601      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2602      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2603            mpi_headers_do_local_copy
     if test "x$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  
2604      fi      fi
2605  fi  fi
2606    
2607  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2608  rm -rf .links.tmp  rm -rf $TMP.links
2609  mkdir .links.tmp  mkdir $TMP.links
2610  touch .links.tmp/foo  touch $TMP.links/foo
2611  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2612      echo      echo
2613      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2614      echo "   your user file-creation mask (\"umask\") since creating a"      echo "   your user file-creation mask (\"umask\") since creating a"
# Line 2513  if test ! -r ".links.tmp/foo" ; then Line 2624  if test ! -r ".links.tmp/foo" ; then
2624      echo      echo
2625      exit 1      exit 1
2626  fi  fi
2627  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2628    
2629  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2630      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2631      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2632      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2633      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2634        OADTOOLS="$TOOLSDIR/OAD_support"
2635      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2636      for i in "." $MODS ; do      for i in "." $MODS ; do
2637          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
# Line 2555  if test "x$OPENAD" != x ; then Line 2667  if test "x$OPENAD" != x ; then
2667      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2668  fi  fi
2669    
2670  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2671  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2672  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2673  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2674  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2675  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2676  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2677  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2678  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2679  for d in $alldirs ; do  for d in $alldirs ; do
2680      deplist=      deplist=
# Line 2572  for d in $alldirs ; do Line 2684  for d in $alldirs ; do
2684          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2685      fi      fi
2686      for sf in $sfiles ; do      for sf in $sfiles ; do
2687          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2688              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2689                  ignore_f=f                  ignore_f=f
2690                  case $d/$sf in                  case $d/$sf in
2691                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2692                          ignore_f=t                          ignore_f=t
2693                          ;;                          ;;
2694                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2695                          ignore_f=t                          ignore_f=t
2696                          ;;                          ;;
2697                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2698                          ignore_f=t                          ignore_f=t
2699                          ;;                          ;;
2700                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2701                          ignore_f=t                          ignore_f=t
2702                          ;;                          ;;
2703                    ./EMBEDDED_FILES.h)                    ./EMBEDDED_FILES.h)
2704                          ignore_f=t                          ignore_f=t
2705                          ;;                          ;;
2706                    *)                    *)
2707                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
2708                          #  ignore all soft-links                          #  ignore all soft-links
2709                          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 $sf ; then
2710                              ignore_f=t                              ignore_f=t
2711                          else                          else
2712                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2713                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2714                          fi                          fi
2715                          ;;                          ;;
2716                  esac                  esac
2717                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2718                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2719                      case $extn in                      case $extn in
2720                        F)                        F)
2721                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2722                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2723                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2724                              basename=${sf%%.F}                              basename=${sf%%.F}
2725                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2726                                if test -z "$isAD" ; then
2727                                    echo    " \\"  >> $TMP.nonADF77srclist
2728                                    printf " $sf" >> $TMP.nonADF77srclist
2729                                fi
2730                            else #- OpenAD case:
2731                                basename=${sf%%.F}
2732                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2733                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2734                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2735                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2736                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2737                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2738                                  else                                  else
2739                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2740                                  fi                                  fi
# Line 2630  for d in $alldirs ; do Line 2749  for d in $alldirs ; do
2749                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2750                                  fi                                  fi
2751                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2752                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2753                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2754                                  fi                                  fi
2755                              fi                              fi
2756                          fi                          fi
2757                          ;;                          ;;
2758                      F90)                      F90)
2759                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2760                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2761                          ;;                          ;;
2762                      c)                      c)
2763                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2764                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2765                          ;;                          ;;
2766                      h)                      h)
2767                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2768                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2769                          ;;                          ;;
2770                      flow)                      flow)
2771                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2772                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2773                          ;;                          ;;
2774                     esac                     esac
2775                  fi                  fi
# Line 2659  for d in $alldirs ; do Line 2778  for d in $alldirs ; do
2778      done      done
2779      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2780        if test "$d" != "." ; then        if test "$d" != "." ; then
2781          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2782          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2783          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2784  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2785  # This may happen when make thinks that a header file has to be "remade"  # This may happen when make thinks that a header file has to be "remade"
2786  # because a module it depends on has changed.  In this case we do nothing.  # because a module it depends on has changed.  In this case we do nothing.
2787          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2788        fi        fi
2789      fi      fi
2790  done  done
2791  rm -rf .links.tmp  rm -rf $TMP.links
2792  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2793  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2794  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2795  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2796  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2797  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2798    
2799  CMDLINE=$0  CMDLINE=$0
2800  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
2801      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2802                          else CMDLINE="$CMDLINE '$xx'" ; fi                          else CMDLINE="$CMDLINE '$xx'" ; fi
2803  done  done
2804    
2805  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
# Line 2714  cat >>$MAKEFILE <<EOF Line 2833  cat >>$MAKEFILE <<EOF
2833  # INCLUDES     : Directories searched for header files  # INCLUDES     : Directories searched for header files
2834  # DEFINES      : Macro definitions for CPP  # DEFINES      : Macro definitions for CPP
2835  # MAKEDEPEND   : Dependency generator  # MAKEDEPEND   : Dependency generator
 # KPP          : Special preprocessor command (specific to platform)  
 # KFLAGS       : Flags for KPP  
2836  # FC           : Fortran compiler command  # FC           : Fortran compiler command
2837  # FFLAGS       : Configuration/debugging options for FC  # FFLAGS       : Configuration/debugging options for FC
2838  # FOPTIM       : Optimization options for FC  # FOPTIM       : Optimization options for FC
# Line 2729  INCLUDEDIRS = ${INCLUDEDIRS} Line 2846  INCLUDEDIRS = ${INCLUDEDIRS}
2846  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2847  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2848  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2849    OADTOOLS    = ${OADTOOLS}
2850    
2851  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2852  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2749  else Line 2867  else
2867      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2868  fi  fi
2869    
2870    # extract default cpp search path so we can pass it to makedepend
2871    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2872    
2873  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2874  # Unix ln (link)  # Unix ln (link)
2875  LN = ${LN}  LN = ${LN}
 # C preprocessor  
 CPP = cat \$< | ${S64} | ${CPP}  
2876  # Dependency generator  # Dependency generator
2877  MAKEDEPEND = ${MAKEDEPEND}  MAKEDEPEND = ${MAKEDEPEND}
2878  # Special preprocessor (KAP on DECs, FPP on Crays)  # Special preprocessor (KAP on DECs, FPP on Crays)
# Line 2771  LINK = ${LINK} ${LDADD} Line 2890  LINK = ${LINK} ${LDADD}
2890  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2891  # Includes for CPP  # Includes for CPP
2892  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2893    # default CPP includes for makedepend
2894    CPPINCLUDES = ${CPPINCLUDES}
2895  # Flags for KPP  # Flags for KPP
2896  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2897  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
# Line 2789  NOOPTFLAGS = ${NOOPTFLAGS} Line 2910  NOOPTFLAGS = ${NOOPTFLAGS}
2910  # Flags and libraries needed for linking  # Flags and libraries needed for linking
2911  LIBS = ${LIBS}  LIBS = ${LIBS}
2912  # Name of the makefile  # Name of the makefile
2913  MAKEFILE=${MAKEFILE}  MAKEFILE = ${MAKEFILE}
2914    # Name of the make program
2915    MAKE = ${MAKE}
2916    
2917  EOF  EOF
2918    
2919  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2920  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2921  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2922  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2923  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2924  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2925    
2926  rm -f F77srclist.tmp nonADF77srclist.tmp csrclist.tmp F90srclist.tmp hsrclist.tmp ad_flow_files.tmp  rm -f $TMP.F77srclist $TMP.nonADF77srclist $TMP.csrclist $TMP.F90srclist $TMP.hsrclist $TMP.ad_flow_files
2927    
2928  echo >> $MAKEFILE  echo >> $MAKEFILE
2929    
# Line 2813  echo >> $MAKEFILE Line 2936  echo >> $MAKEFILE
2936  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2937  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2938  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
2939  echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE  echo 'FLOWFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2940  echo >> $MAKEFILE  echo >> $MAKEFILE
2941  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2942  echo '.SUFFIXES: .o .'$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' >> $MAKEFILE
2943    
2944  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2945    
2946  all: \$(EXECUTABLE)  all: fwd_exe_target
2947    fwd_exe_target:
2948            @echo Update AD_CONFIG.h and make \$(EXECUTABLE)
2949            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
2950            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2951            @-rm -f ad_config.template
2952            \$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
2953    
2954  \$(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)
2955          @echo Creating \$@ ...          @echo Creating \$@ ...
2956          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2957    
2958  depend:  depend:
2959          @make -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2960          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2961          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2962          -rm -f makedepend.out          -rm -f makedepend.out
2963    
# Line 2843  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 2973  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
2973    
2974  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2975    
2976  output.txt: \$(EXECUTABLE)  # output.txt: \$(EXECUTABLE)
2977          @printf 'running ... '  #       @printf 'running ... '
2978          @\$(EXECUTABLE) > \$@  #       @\$(EXECUTABLE) > \$@
2979    
2980  # remove most of the files that "make" generates  # remove most of the files that "make" generates
2981  clean:  clean:
# Line 2856  clean: Line 2986  clean:
2986    
2987  # remove most of the files that "make" and "make depend" generate  # remove most of the files that "make" and "make depend" generate
2988  Clean:  Clean:
2989          @make -f \$(MAKEFILE) clean          @\$(MAKE) -f \$(MAKEFILE) clean
2990          @make -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
2991          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
2992          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.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  
2993    
2994  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
2995  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
2996  CLEAN:  CLEAN:
2997          @make -f \$(MAKEFILE) Clean          @\$(MAKE) -f \$(MAKEFILE) Clean
2998          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
2999          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3000          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3001            -rm -rf mpi_headers mnc_test_*
3002          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3003          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3004          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3005          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3006            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3007          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3008          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3009    
3010  makefile:  makefile:
3011          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2884  cleanlinks: Line 3015  cleanlinks:
3015  # Special targets (SPECIAL_FILES) which are created by make  # Special targets (SPECIAL_FILES) which are created by make
3016  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
3017          @echo Creating \$@ ...          @echo Creating \$@ ...
3018          @$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) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
3019  AD_CONFIG.h:  AD_CONFIG.h:
3020          @echo Creating \$@ ...          @echo Creating \$@ ...
3021          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
3022  FC_NAMEMANGLE.h:  FC_NAMEMANGLE.h:
3023          @echo Creating \$@ ...          @echo Creating \$@ ...
3024          echo "$FC_NAMEMANGLE" > \$@          echo "$FC_NAMEMANGLE" > \$@
# Line 2927  cat >>$MAKEFILE <<EOF Line 3058  cat >>$MAKEFILE <<EOF
3058  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3059  ## %.o : %.F  ## %.o : %.F
3060    
3061    # C preprocessing and replacing the _d in constants:
3062    CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3063    
3064  .F.$FS:  .F.$FS:
3065          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3066  .$FS.o:  .$FS.o:
3067          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3068  .F.o:  .F.o:
3069          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3070  .F90.$FS90:  .F90.$FS90:
3071          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3072  .FF90.f$FS90:  .FF90.f$FS90:
3073          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3074  .$FS90.o:  .$FS90.o:
3075          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
3076  .f$FS90.o:  .f$FS90.o:
# Line 2945  cat >>$MAKEFILE <<EOF Line 3079  cat >>$MAKEFILE <<EOF
3079  .c.o:  .c.o:
3080          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
3081  .flow.flowdir:  .flow.flowdir:
3082          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3083    
3084  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
3085  .F.p:  .F.p:
3086          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3087  .p.$FS:  .p.$FS:
3088          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
3089    
# Line 2968  TAF            = ${TAF} Line 3102  TAF            = ${TAF}
3102    
3103  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3104  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3105    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3106    
3107  EOF  EOF
3108    
# Line 2985  done Line 3120  done
3120  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3121  echo >> $MAKEFILE  echo >> $MAKEFILE
3122  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3123  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3124  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3125      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3126      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3127  done  done
3128  echo >> $MAKEFILE  echo >> $MAKEFILE
3129  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3130    
3131  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3132    
3133  # ... AD ...  # ... AD ...
3134  adall: \$(EXE_AD)  adall: ad_exe_target
3135  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
3136  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
3137    
3138  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)  ad_exe_target:
3139          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template          @echo Update AD_CONFIG.h and make \$(EXE_AD)
3140            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3141            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3142            @-rm -f ad_config.template
3143            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3144    
3145    ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
3146            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3147          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
3148          -rm -f ad_config.template          @-rm -f ad_config.template
3149          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3150          @make -f \$(MAKEFILE) \$(FLOFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3151          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
3152    
3153  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
3154            @-rm -f ad_input_code_ad.$FS ; echo ''
3155          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3156          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3157          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
# Line 3018  adtafonly: Line 3161  adtafonly:
3161          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3162          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3163    
3164  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3165          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3166    
3167  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
3168          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 3034  adonlyfwd: Line 3177  adonlyfwd:
3177  adtrick:  adtrick:
3178          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3179    
3180  adobj: ad_taf_output.o \$(OBJFILES)  adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3181    
3182  # ... FTL ...  # ... FTL ...
3183  ftlall: \$(EXE_FTL)  ftlall: ftl_exe_target
3184  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
3185  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
3186    
3187  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)  ftl_exe_target:
3188          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template          @echo Update AD_CONFIG.h and make \$(EXE_FTL)
3189          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3190          -rm -f ftl_config.template          @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3191          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @-rm -f ad_config.template
3192          @make -f \$(MAKEFILE) \$(AD_FLOW_FILES)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
3193    
3194    ftl_input_code.$FS: \$(AD_FILES)
3195            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3196            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3197            @-rm -f ad_config.template
3198            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3199            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3200          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3201    
3202  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
3203            @-rm -f ftl_input_code_tl.$FS ; echo ''
3204          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3205          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3206          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3207    
3208  ftltafonly:  ftltafonly:
3209          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3210          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3211          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3212    
3213  \${EXE_FTL}: ftl_taf_output.o \$(OBJFILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3214          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3215    
3216  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3217          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
# Line 3089  svd_touch: Line 3240  svd_touch:
3240          touch ad_taf_output.$FS ftl_taf_output.$FS          touch ad_taf_output.$FS ftl_taf_output.$FS
3241          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
3242          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
3243          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3244          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3245          -rm -f ftl_config.template          @-rm -f ad_config.template
3246    
3247  EOF  EOF
3248    
# Line 3104  if test "x$OPENAD" != x ; then Line 3255  if test "x$OPENAD" != x ; then
3255  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3256    
3257  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3258    # ... OpenAD ...
3259    
3260  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3261  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3143  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3295  for i in `cat ${OAD_CB2M_FILES}` ; do
3295    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3296    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3297  done  done
3298  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3299  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3300    basename=${i%%.f}    basename=${i%%.f}
3301    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
# Line 3153  for i in $AD_FILES ; do Line 3305  for i in $AD_FILES ; do
3305    fi    fi
3306  done  done
3307  echo >> $MAKEFILE  echo >> $MAKEFILE
3308  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3309    
3310  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3311    
3312  adAll: \$(EXE_AD)  adAll: ad_exe_target
3313  .PHONY: adAll  .PHONY: adAll
3314    
3315    ad_exe_target:
3316            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3317            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3318            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3319            @-rm -f ad_config.template
3320            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3321    
3322  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
3323    
3324  .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)  .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
# Line 3175  w2f__types.F90 \ Line 3334  w2f__types.F90 \
3334  OAD_active.F90 \  OAD_active.F90 \
3335  OAD_cp.F90 \  OAD_cp.F90 \
3336  OAD_rev.F90 \  OAD_rev.F90 \
3337  OAD_tape.F90  OAD_tape.F90 \
3338    revolve.F90
3339    
3340  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3341  iaddr.c \  iaddr.c \
# Line 3191  f95_test.out: f95_test_mods.f90 f95_test Line 3351  f95_test.out: f95_test_mods.f90 f95_test
3351          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
3352          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
3353    
3354  # the file included below is created by the  CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
 # postProcessor and its inclusion sets the  
 # variable POSTPROCESSEDFILES  
 # used below. Because the file is made during  
 # make it won't be read until the second (recursive)  
 # invocation in the rule below  
 -include postProcess.make  
3355    
3356  AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$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)
3357    
3358  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)
3359    
3360  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)  
3361          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
 else  
         touch \$@  
 endif  
3362    
3363  # makefile debug rule  # create sources files modules from header files containing common blocks
3364  openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3365  .PHONY: openad          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3366    
3367  # create the module files  # create new header files with USE statements for the new modules made above
3368  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3369          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3370    
3371  # create the header files  # change the include directives of everybody to refer to  the new header files with the USE statements
3372  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3373          ../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 $< ${MPI}  
3374    
3375  # makefile debug rule  # makefile debug rule
3376  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3377  .PHONY: small_f  .PHONY: small_f
3378    
3379  ad_output.txt: \$(EXE_AD)  # ad_output.txt: \$(EXE_AD)
3380          @printf 'linking data files ... '  #       @printf 'linking data files ... '
3381          \$(LN) -f ../input_ad/data* ../input_ad/eedata .  #       \$(LN) -f ../input_ad/data* ../input_ad/eedata .
3382          \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .  #       \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
3383          @printf 'running ... '  #       @printf 'running ... '
3384          @./\$(EXE_AD) > \$@  #       @./\$(EXE_AD) > \$@
3385    
 CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)  
3386  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3387          cat \$^ > \$@          cat \$^ > \$@
3388    
 # 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 > \$@  
   
3389  # canonicalizer  # canonicalizer
3390  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)
3391          ./preProcess.py --timing --r8 -H -S \$< -o \$@          \${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
3392    
3393    # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3394    ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3395            cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3396    
3397  # F -> WHIRL  # F -> WHIRL
3398  # note that the canonicalized version cuts off at col 72  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
3399  # 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$FS90 mfef90  
         ./mfef90 -r8 -z -F \$<  
         mv \$<.B \$@  
3400    
3401  # WHIRL -> XAIF  # WHIRL -> XAIF
3402  ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif  ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
3403          ./whirl2xaif -s -n --debug 1 -o \$@ \$<          \${OPENADFORTTK}/bin/whirl2xaif -s -n --debug 1 -o \$@ \$<
3404    
3405  # XAIF -> XAIF'  # XAIF -> XAIF'
3406  ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver  ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
3407          ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r          \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3408    
3409  # XAIF' -> WHIRL'  # XAIF' -> WHIRL'
3410  ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl  ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
3411          ./xaif2whirl --debug 1 ad_input_code_sf.w2f.pre.B \$<          \${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
3412    
3413  # WHIRL' -> F'  # WHIRL' -> F'
3414  ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
3415          ./whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3416    
3417  # insert template directives  # insert template directives
3418  ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$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$FS90 \${OADTOOLS}/insertTemplateDir.bash
3419          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3420    
3421  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3422  # postprocess F'  # postprocess F'
3423  postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
3424          # the target is a placeholder to signal execution of the rule          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
3425            # the target is a placeholder to trigger a single execution of the rule
3426          touch \$@          touch \$@
3427          # this step also creates the file postProcess.make but we cannot  # put this so make knows about the postprocessing output
3428          # name it as the target or else make will try to remake it for  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$FS90=_oad.f): postProcess.tag
         # the include directive above for any rule, e.g. make clean  
         ./postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<  
3429    
3430  # setup some links  # link the XAIF schema files
3431  %.xsd:  %.xsd:
3432          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3433    
 mfef90:  
         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .  
   
3434  # link the support files:  # link the support files:
3435  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3436          \$(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 \$@  
3437    
3438  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
3439    
3440  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3441    
# Line 3366  for i in $NOOPTFILES ; do Line 3471  for i in $NOOPTFILES ; do
3471  done  done
3472    
3473  echo "  Add rules for links"  echo "  Add rules for links"
3474  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3475  rm -f srclinks.tmp  rm -f $TMP.srclinks
3476    
3477  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3478  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE
# Line 3375  printf "\n\n# DO NOT DELETE\n" >> $MAKEF Line 3480  printf "\n\n# DO NOT DELETE\n" >> $MAKEF
3480  printf "\n===  Done  ===\n"  printf "\n===  Done  ===\n"
3481    
3482  # Create special header files  # Create special header files
3483  $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"
3484  if test ! -f $PACKAGES_DOT_H ; then  if test ! -f $PACKAGES_DOT_H ; then
3485      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
3486  else  else
# Line 3389  else Line 3494  else
3494      fi      fi
3495  fi  fi
3496  if test ! -f AD_CONFIG.h ; then  if test ! -f AD_CONFIG.h ; then
3497      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
3498  fi  fi
3499    
3500  #  Write the "state" for future records  #  Write the "state" for future records

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