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revision 1.232 by jahn, Fri Aug 10 17:59:13 2012 UTC revision 1.266 by jmc, Wed May 7 19:36:22 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:  $R
604  EOF  EOF
605          exit 1          exit 1
606      fi      fi
607    }
608    
609  #     # look for possible MPI libraries  #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
610  #     mpi_libs=  #  checking for additional included headers (in case of chain of included header)
611  #     mpi_fort=`which mpif77 2>/dev/null`  mpi_headers_do_local_copy() {
612  #     RETVAL=$?  
613  #     if test "x${RETVAL}" = x0 ; then      dBug=0
614  #       cat >>test.f <<EOF      rm -rf ./mpi_headers
615  #       PROGRAM HELLO      if test -d $MPIINCLUDEDIR ; then
616  #       DO 10, I=1,10  
617  #       PRINT *,'Hello World'          #----- check for additional headers (chain of included headers)
618  #    10 CONTINUE          echo -n '  Check MPI headers ... '
619  #       STOP          listIni=$MPI_HEADER_FILES
620  #       END          echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
621  # EOF          outp=$?
622  #       eval "$mpi_fort -showme test.f > out"          #- always check mpif.h (the only mpi-header included in standard MITgcm code)
623  #       RETVAL=$?          if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
624  #       if test "x${RETVAL}" = x0 ; then          if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
625  #           a=`cat out`  
626  #           for i in $a ; do          doCheck=1 ; list2copy='' ; list2check=$listIni
627  #               case $i in          while test $doCheck = 1 ; do
628  #                   -*)            newList=''
629  #                       mpi_libs="$mpi_libs $i" ;;            for i in $list2check ; do
630  #               esac              if test -f $MPIINCLUDEDIR/$i ; then
631  #           done                newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
632  #           echo "The MPI libs appear to be:"                  sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
633  #           echo "  "$mpi_libs                if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
634  #       fi                for j in $newInc ; do
635  #       rm -f test.f out                  echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
636  #     fi                  outp=$?
637                    if test $outp != 0 ; then
638                      if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
639                      newList="$newList $j"
640                    fi
641                  done
642                  if test $dBug = 1 ; then echo "" ; fi
643                fi
644              done
645              if test "x$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$MPI" = x ; then
1004          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1005      fi     #fi
1006      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1007        integer iret, ncid, xid        integer iret, ncid, xid
1008        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1030  EOF Line 1083  EOF
1083  }  }
1084    
1085  check_lapack_libs()  {  check_lapack_libs()  {
1086      if test ! "x$SKIP_LAPACK_CHECK" = x ; then      if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
         return  
     fi  
1087      echo >> $LOGFILE      echo >> $LOGFILE
1088      echo "running: check_lapack_libs()" >> $LOGFILE      echo "running: check_lapack_libs()" >> $LOGFILE
1089      cat <<EOF > genmake_tla.F      cat <<EOF > genmake_tla.F
1090        program fgenla        program fgenla
1091        integer info        integer info
1092        integer ipiv( 2 )        integer ipiv( 2 )
1093        double precision ab( 4, 2 ), b( 2 )        double precision ab( 4, 2 ), b( 2 )
1094        data ab / 0., 0., 1., 2., 0., 2., 1., 0. /        data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
# Line 1108  EOF Line 1159  EOF
1159                  LIBS="$LIBS -llapack -lf77blas -lcblas"                  LIBS="$LIBS -llapack -lf77blas -lcblas"
1160                  HAVE_LAPACK=t                  HAVE_LAPACK=t
1161                  echo "check_lapack: successful" >> $LOGFILE                  echo "check_lapack: successful" >> $LOGFILE
1162              else              else
1163              # try again with "-latlas" added to the libs              # try again with "-latlas" added to the libs
1164                  echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log                  echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
1165                  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
1166                  echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log                  echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1167                  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
1168                  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  \
1169                      &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \                      &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1170                      &&  $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 $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
1171                  RET_COMPILE=$?                  RET_COMPILE=$?
1172                  echo >> $LOGFILE                  echo >> $LOGFILE
1173                  cat genmake_tla.log >> $LOGFILE                  cat genmake_tla.log >> $LOGFILE
1174                  if test "x$RET_COMPILE" = x0 ; then                  if test "x$RET_COMPILE" = x0 ; then
1175                      LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"                      LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
1176                      HAVE_LAPACK=t                      HAVE_LAPACK=t
1177                      echo "check_lapack: successful" >> $LOGFILE                      echo "check_lapack: successful" >> $LOGFILE
1178                  fi                  fi
1179              fi              fi
1180          fi          fi
1181      fi      fi
# Line 1132  EOF Line 1183  EOF
1183      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE      echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1184  }  }
1185    
1186    check_HAVE_FLUSH()  {
1187        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1188            return
1189        fi
1190        echo >> $LOGFILE
1191        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1192        cat <<EOF > genmake_tflsh.$FS
1193          program fgenflsh
1194          integer iounit
1195          character*9 fname
1196          iounit = 26
1197          fname = 'tmp.tflsh'
1198          open(iounit,FILE=fname,STATUS='unknown')
1199          write(iounit,*) 'genmake_tflsh: hello'
1200          call flush(iounit)
1201          close(iounit)
1202          end
1203    EOF
1204        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1205        cat genmake_tflsh.$FS >> genmake_tflsh.log
1206        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1207    
1208        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1209        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1210        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1211            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1212        RET_COMPILE=$?
1213    
1214        if test "x$RET_COMPILE" = x0 ; then
1215            HAVE_FLUSH=t
1216            #cat genmake_tflsh.log >> $LOGFILE
1217            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1218        else
1219            HAVE_FLUSH=f
1220            cat genmake_tflsh.log >> $LOGFILE
1221        fi
1222        rm -f genmake_tflsh*
1223        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1224    }
1225    
1226  ###############################################################################  ###############################################################################
1227  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1189  GSL= Line 1279  GSL=
1279  DEVEL=  DEVEL=
1280  HAVE_TEST_L=  HAVE_TEST_L=
1281    
1282    # set this to "t" to enable lapack test
1283    CHECK_FOR_LAPACK=f
1284    
1285  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1286  HAVE_SYSTEM=  HAVE_SYSTEM=
1287  HAVE_FDATE=  HAVE_FDATE=
# Line 1200  HAVE_NETCDF= Line 1293  HAVE_NETCDF=
1293  HAVE_ETIME=  HAVE_ETIME=
1294  IGNORE_TIME=  IGNORE_TIME=
1295  HAVE_LAPACK=  HAVE_LAPACK=
1296    HAVE_FLUSH=
1297    
1298  MODS=  MODS=
1299  TOOLSDIR=  TOOLSDIR=
# Line 1207  SOURCEDIRS= Line 1301  SOURCEDIRS=
1301  INCLUDEDIRS=  INCLUDEDIRS=
1302  STANDARDDIRS="USE_THE_DEFAULT"  STANDARDDIRS="USE_THE_DEFAULT"
1303    
1304    #- local config file
1305    gm_local="genmake_local"
1306    
1307  G2ARGS=  G2ARGS=
1308  BASH=  BASH=
1309  PWD=`pwd`  PWD=`pwd`
# Line 1230  FS= Line 1327  FS=
1327  FS90=  FS90=
1328    
1329  AUTODIFF_PKG_USED=f  AUTODIFF_PKG_USED=f
1330    OPENAD=
1331  AD_OPTFILE=  AD_OPTFILE=
1332  TAF=  TAF=
1333  AD_TAF_FLAGS=  AD_TAF_FLAGS=
# Line 1242  FTL_TAF_FLAGS= Line 1340  FTL_TAF_FLAGS=
1340  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1341  TAMC_EXTRA=  TAMC_EXTRA=
1342    
1343    DIVA=
1344    MPIINCLUDEDIR=
1345    MPI_HEADER_FILES=
1346    LOCAL_MPI_HEADERS=
1347    
1348  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1349  gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS DISABLE ENABLE MAKEFILE MAKEDEPEND PLATFORM"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1350  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"
1351  gm_s3="ROOTDIR STANDARDDIRS MODS DUMPSTATE"  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
1352    
1353  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1354  gm_s4="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1355  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1356  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1357  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1358  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"
1359    
1360  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1361  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"
1362  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"
1363  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1364    
1365  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 $gm_s8"
1366  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1278  LOGFILE="genmake.log" Line 1381  LOGFILE="genmake.log"
1381  rm -f genmake_state genmake_*optfile $LOGFILE  rm -f genmake_state genmake_*optfile $LOGFILE
1382    
1383  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  
1384    
1385  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
1386  #parse_options  #parse_options
# Line 1306  for ac_option in "$@" ; do Line 1399  for ac_option in "$@" ; do
1399      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
1400    
1401      case $ac_option in      case $ac_option in
1402            
1403          -help | --help | -h | --h)          -help | --help | -h | --h)
1404              usage ;;              usage ;;
1405            
1406          -nooptfile | --nooptfile)          -nooptfile | --nooptfile)
1407              OPTFILE="NONE" ;;              OPTFILE="NONE" ;;
1408          -optfile | --optfile | -of | --of)          -optfile | --optfile | -of | --of)
1409              ac_prev=OPTFILE ;;              ac_prev=OPTFILE ;;
1410          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1411              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1412            
1413            -oad | --oad)
1414                OPENAD="true" ;;
1415          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1416              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1417          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
1418              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1419            
1420          -pdepend | --pdepend)          -pdepend | --pdepend)
1421              ac_prev=PKG_DEPEND ;;              ac_prev=PKG_DEPEND ;;
1422          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
1423              PKG_DEPEND=$ac_optarg ;;              PKG_DEPEND=$ac_optarg ;;
1424            
1425          -pgroups | --pgroups)          -pgroups | --pgroups)
1426              ac_prev=PKG_GROUPS ;;              ac_prev=PKG_GROUPS ;;
1427          -pgroups=* | --pgroups=*)          -pgroups=* | --pgroups=*)
1428              PKG_GROUPS=$ac_optarg ;;              PKG_GROUPS=$ac_optarg ;;
1429            
1430          -make | --make | -m | --m)          -make | --make | -m | --m)
1431              ac_prev=MAKE ;;              ac_prev=MAKE ;;
1432          -make=* | --make=* | -m=* | --m=*)          -make=* | --make=* | -m=* | --m=*)
1433              MAKE=$ac_optarg ;;              MAKE=$ac_optarg ;;
1434            
1435          -bash | --bash)          -bash | --bash)
1436              ac_prev=BASH ;;              ac_prev=BASH ;;
1437          -bash=* | --bash=*)          -bash=* | --bash=*)
1438              BASH=$ac_optarg ;;              BASH=$ac_optarg ;;
1439            
1440          -makedepend | --makedepend | -md | --md)          -makedepend | --makedepend | -md | --md)
1441              ac_prev=MAKEDEPEND ;;              ac_prev=MAKEDEPEND ;;
1442          -makedepend=* | --makedepend=* | -md=* | --md=*)          -makedepend=* | --makedepend=* | -md=* | --md=*)
1443              MAKEDEPEND=$ac_optarg ;;              MAKEDEPEND=$ac_optarg ;;
1444            
1445          -makefile | --makefile | -ma | --ma)          -makefile | --makefile | -mf | --mf)
1446              ac_prev=MAKEFILE ;;              ac_prev=MAKEFILE ;;
1447          -makefile=* | --makefile=* | -ma=* | --ma=*)          -makefile=* | --makefile=* | -mf=* | --mf=*)
1448              MAKEFILE=$ac_optarg ;;              MAKEFILE=$ac_optarg ;;
1449            
1450          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
1451              echo "ERROR: The platform option has been removed.  Please specify"              echo "ERROR: The platform option has been removed.  Please specify"
1452              echo "  the build options using the \"optfile\" mechanism."              echo "  the build options using the \"optfile\" mechanism."
1453              echo              echo
1454              usage              usage
1455              ;;              ;;
1456            
1457          -rootdir | --rootdir | -rd | --rd)          -rootdir | --rootdir | -rd | --rd)
1458              ac_prev=ROOTDIR ;;              ac_prev=ROOTDIR ;;
1459          -rootdir=* | --rootdir=* | -rd=* | --rd=*)          -rootdir=* | --rootdir=* | -rd=* | --rd=*)
1460              ROOTDIR=$ac_optarg ;;              ROOTDIR=$ac_optarg ;;
1461            
1462          -mods | --mods | -mo | --mo)          -mods | --mods | -mo | --mo)
1463              ac_prev=MODS ;;              ac_prev=MODS ;;
1464          -mods=* | --mods=* | -mo=* | --mo=*)          -mods=* | --mods=* | -mo=* | --mo=*)
1465              MODS=$ac_optarg ;;              MODS=$ac_optarg ;;
1466            
1467          -disable | --disable)          -disable | --disable)
1468              ac_prev=DISABLE ;;              ac_prev=DISABLE ;;
1469          -disable=* | --disable=*)          -disable=* | --disable=*)
1470              DISABLE=$ac_optarg ;;              DISABLE=$ac_optarg ;;
1471            
1472          -enable | --enable)          -enable | --enable)
1473              ac_prev=ENABLE ;;              ac_prev=ENABLE ;;
1474          -enable=* | --enable=*)          -enable=* | --enable=*)
1475              ENABLE=$ac_optarg ;;              ENABLE=$ac_optarg ;;
1476            
1477          -standarddirs | --standarddirs)          -standarddirs | --standarddirs)
1478              ac_prev=STANDARDDIRS ;;              ac_prev=STANDARDDIRS ;;
1479          -standarddirs=* | --standarddirs=*)          -standarddirs=* | --standarddirs=*)
# Line 1388  for ac_option in "$@" ; do Line 1483  for ac_option in "$@" ; do
1483  #               ac_prev=cpp ;;  #               ac_prev=cpp ;;
1484  #           -cpp=* | --cpp=*)  #           -cpp=* | --cpp=*)
1485  #               CPP=$ac_optarg ;;  #               CPP=$ac_optarg ;;
1486            
1487          -cc | --cc)          -cc | --cc)
1488              ac_prev=CC ;;              ac_prev=CC ;;
1489          -cc=* | --cc=*)          -cc=* | --cc=*)
1490              CC=$ac_optarg ;;              CC=$ac_optarg ;;
1491            
1492          -fortran | --fortran | -fc | --fc)          -fortran | --fortran | -fc | --fc)
1493              ac_prev=FC ;;              ac_prev=FC ;;
1494          -fc=* | --fc=*)          -fc=* | --fc=*)
1495              FC=$ac_optarg ;;              FC=$ac_optarg ;;
1496            
1497          -fs | --fs)          -fs | --fs)
1498              ac_prev=FS ;;              ac_prev=FS ;;
1499          -fs=* | --fs=*)          -fs=* | --fs=*)
1500              FS=$ac_optarg ;;              FS=$ac_optarg ;;
1501            
1502          -fs90 | --fs90)          -fs90 | --fs90)
1503              ac_prev=FS90 ;;              ac_prev=FS90 ;;
1504          -fs90=* | --fs90=*)          -fs90=* | --fs90=*)
1505              FS90=$ac_optarg ;;              FS90=$ac_optarg ;;
1506            
1507          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1508              USE_R4=true ;;              USE_R4=true ;;
1509    
# Line 1416  for ac_option in "$@" ; do Line 1511  for ac_option in "$@" ; do
1511              IEEE=true ;;              IEEE=true ;;
1512          -noieee | --noieee)          -noieee | --noieee)
1513              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
1514          -devel | --devel)          -devel | --devel)
1515              IEEE=true ; DEVEL=true ;;              IEEE=true ; DEVEL=true ;;
1516          -gsl | --gsl)          -gsl | --gsl)
1517              GSL=true ;;              GSL=true ;;
1518    
1519          -ts | --ts)          -ts | --ts)
# Line 1441  for ac_option in "$@" ; do Line 1536  for ac_option in "$@" ; do
1536          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
1537              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1538              MPI=true ;;              MPI=true ;;
1539            
1540          -omp | --omp)          -omp | --omp)
1541              OMP=true ;;              OMP=true ;;
1542          -omp=* | --omp=*)          -omp=* | --omp=*)
1543              OMPFLAG=$ac_optarg              OMPFLAG=$ac_optarg
1544              OMP=true ;;              OMP=true ;;
1545            
1546          -ds | --ds)          -ds | --ds)
1547              DUMPSTATE=t ;;              DUMPSTATE=t ;;
1548            
1549          -extra_flag | --extra_flag)          -extra_flag | --extra_flag)
1550              ac_prev=FEXTRAFLAGS ;;              ac_prev=FEXTRAFLAGS ;;
1551          -extra_flag=* | --extra_flag=*)          -extra_flag=* | --extra_flag=*)
1552              FEXTRAFLAGS=$ac_optarg ;;              FEXTRAFLAGS=$ac_optarg ;;
1553            
1554          -taf_extra | --taf_extra)          -taf_extra | --taf_extra)
1555              ac_prev=TAF_EXTRA ;;              ac_prev=TAF_EXTRA ;;
1556          -taf_extra=* | --taf_extra=*)          -taf_extra=* | --taf_extra=*)
# Line 1465  for ac_option in "$@" ; do Line 1560  for ac_option in "$@" ; do
1560              ac_prev=TAMC_EXTRA ;;              ac_prev=TAMC_EXTRA ;;
1561          -tamc_extra=* | --tamc_extra=*)          -tamc_extra=* | --tamc_extra=*)
1562              TAMC_EXTRA=$ac_optarg ;;              TAMC_EXTRA=$ac_optarg ;;
1563            
1564          -ignoretime | -ignore_time | --ignoretime | --ignore_time)          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1565              IGNORE_TIME="-DIGNORE_TIME" ;;              IGNORE_TIME="-DIGNORE_TIME" ;;
1566    
# Line 1476  for ac_option in "$@" ; do Line 1571  for ac_option in "$@" ; do
1571              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
1572              usage              usage
1573              ;;              ;;
1574            
1575          *)          *)
1576              echo "Error: unrecognized argument: "$ac_option              echo "Error: unrecognized argument: "$ac_option
1577              usage              usage
1578              ;;              ;;
1579            
1580      esac      esac
1581    
1582  done  done
1583    
1584    #TMP=./genmk_$$
1585    #- try to put temporary files in system-local /tmp dir
1586    TMP=/tmp/genmk_$$
1587    touch $TMP ; retVal=$?
1588    if [ $retVal -eq 0 ] ; then
1589      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1590    else
1591      TMP=./genmk_$$
1592    fi
1593    rm -f $TMP
1594    #echo "  temp files: $TMP.*"
1595    
1596    printf "  getting local config information:  "
1597    if test -f $gm_local ; then
1598        echo "using $gm_local"
1599        . $gm_local
1600    else
1601        echo "none found"
1602    fi
1603    
1604  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1605      echo      echo
1606      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
# Line 1570  fi Line 1685  fi
1685    
1686  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1687  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1688      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1689            AD_OPTFILE=$MITGCM_AD_OF
1690        elif test "x$OPENAD" = x ; then
1691          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1692      else      else
1693          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1694      fi      fi
1695  fi  fi
1696  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1697  check_for_broken_Ff Line 1814  check_for_broken_Ff
1814    
1815  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1816        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1817        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1818    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1819    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1820  fi  fi
1821  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1822        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1714  fi Line 1833  fi
1833  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1834        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1835        if test ! "x$FOOLAD" = x ; then        if test ! "x$FOOLAD" = x ; then
1836              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1837        else        else
1838              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1839        fi        fi
# Line 1750  if test ! "x$PAPI" = x ; then Line 1869  if test ! "x$PAPI" = x ; then
1869            echo "  Sticking with PAPI flop summary per timestep!"            echo "  Sticking with PAPI flop summary per timestep!"
1870        else        else
1871            echo "  Turning on performance analysis with PAPI"            echo "  Turning on performance analysis with PAPI"
1872            echo "  Please make sure PAPIINC, PAPILIB are defined"            echo "  Please make sure PAPIINC, PAPILIB are defined"
1873            DEFINES="$DEFINES -DUSE_PAPI"            DEFINES="$DEFINES -DUSE_PAPI"
1874            INCLUDES="$INCLUDES $PAPIINC"            INCLUDES="$INCLUDES $PAPIINC"
1875            LIBS="$LIBS $PAPILIB"            LIBS="$LIBS $PAPILIB"
# Line 1762  if test ! "x$PCL" = x ; then Line 1881  if test ! "x$PCL" = x ; then
1881            echo "  Sticking with PCL flop summary per timestep!"            echo "  Sticking with PCL flop summary per timestep!"
1882        else        else
1883            echo "  Turning on performance analysis with PCL"            echo "  Turning on performance analysis with PCL"
1884            echo "  Please make sure PCLINC, PCLLIB are defined"            echo "  Please make sure PCLINC, PCLLIB are defined"
1885            DEFINES="$DEFINES -DUSE_PCL"            DEFINES="$DEFINES -DUSE_PCL"
1886            INCLUDES="$INCLUDES $PCLINC"            INCLUDES="$INCLUDES $PCLINC"
1887            LIBS="$LIBS $PCLLIB"            LIBS="$LIBS $PCLLIB"
# Line 1772  if test ! "x$HPMT" = x ; then Line 1891  if test ! "x$HPMT" = x ; then
1891        if test ! "x$PAPI" = x ; then        if test ! "x$PAPI" = x ; then
1892            echo "  PAPI and the HPM Toolkit cannot co-exist!"            echo "  PAPI and the HPM Toolkit cannot co-exist!"
1893            echo "  Sticking with PAPI!"            echo "  Sticking with PAPI!"
1894        else if test ! "x$PCL" = x ; then        else
1895            if test ! "x$PCL" = x ; then
1896            echo "  PCL and the HPM Toolkit cannot co-exist!"            echo "  PCL and the HPM Toolkit cannot co-exist!"
1897            echo "  Sticking with PCL!"            echo "  Sticking with PCL!"
1898        else          else
1899            echo "  Turning on performance analysis with the HPM Toolkit"            echo "  Turning on performance analysis with the HPM Toolkit"
1900            echo "  Please make sure HPMTINC, HPMTLIB are defined"            echo "  Please make sure HPMTINC, HPMTLIB are defined"
1901            DEFINES="$DEFINES -DUSE_LIBHPM"            DEFINES="$DEFINES -DUSE_LIBHPM"
1902            INCLUDES="$INCLUDES $HPMTINC"            INCLUDES="$INCLUDES $HPMTINC"
1903            LIBS="$LIBS $HPMTLIB"            LIBS="$LIBS $HPMTLIB"
1904        fi          fi
1905        fi        fi
1906  fi  fi
1907  if test ! "x$GSL" = x ; then  if test ! "x$GSL" = x ; then
# Line 1921  if test "x$HAVE_LAPACK" != x ; then Line 2041  if test "x$HAVE_LAPACK" != x ; then
2041  else  else
2042      echo "no"      echo "no"
2043  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2044    
2045    printf "  Can we call FLUSH intrinsic subroutine...  "
2046    check_HAVE_FLUSH
2047    if test "x$HAVE_FLUSH" = xt ; then
2048        DEFINES="$DEFINES -DHAVE_FLUSH"
2049        echo "yes"
2050    else
2051        echo "no"
2052    fi
2053    
2054    DEFINES="$DEFINES $IGNORE_TIME"
2055  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2056      build_embed_encode      build_embed_encode
2057  fi  fi
# Line 2106  else Line 2235  else
2235          exit 1          exit 1
2236      else      else
2237          echo "    using PKG_LIST=\"$PKG_LIST\""          echo "    using PKG_LIST=\"$PKG_LIST\""
2238          #  Strip the comments and add all the names          #  Strip the comments and add all the names
2239          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 $0}'`
2240          RETVAL=$?          RETVAL=$?
2241          if test "x${RETVAL}" != x0 ; then          if test "x${RETVAL}" != x0 ; then
# Line 2127  if test "x${PKG_GROUPS}" != x ; then Line 2256  if test "x${PKG_GROUPS}" != x ; then
2256  fi  fi
2257    
2258  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2259  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2260  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2261      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2262  done  done
2263  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2264      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2265      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2266  done  done
# Line 2149  for p in $PACKAGES ; do Line 2278  for p in $PACKAGES ; do
2278  done  done
2279  PACKAGES="$pack"  PACKAGES="$pack"
2280  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2281  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2282  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2283  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2284  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2285      j=`echo $i | sed 's/[-+]//'`      j=`echo $i | sed 's/[-+]//'`
2286      if test ! -d "$ROOTDIR/pkg/$j" ; then      if test ! -d "$ROOTDIR/pkg/$j" ; then
2287          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2288          exit 1          exit 1
2289      fi      fi
2290      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2291  done  done
2292  PACKAGES=  PACKAGES=
2293  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2294      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2295  done  done
2296  rm -f ./.tmp_pack  rm -f $TMP.pack
2297  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2298    
2299  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2201  else Line 2330  else
2330          echo "Error: problem encountered while building source files in pkg/mnc:"          echo "Error: problem encountered while building source files in pkg/mnc:"
2331          cat make_mnc.errors 1>&2          cat make_mnc.errors 1>&2
2332          if test "x$mnc_in" = x0 ; then          if test "x$mnc_in" = x0 ; then
2333              exit 1              exit 1
2334          else          else
2335              DISABLE="$DISABLE mnc"              DISABLE="$DISABLE mnc"
2336          fi          fi
# Line 2234  EOF Line 2363  EOF
2363      fi      fi
2364  fi  fi
2365    
2366  #  Check for package RADTRANS: if LAPACK is not available,  #  Make sure the openad package is enabled if using OpenAD
2367  #  then issue a warning that the direct radtrans solver is not available.  if test "x$OPENAD" != x ; then
2368  if test "x$HAVE_LAPACK" != xt ; then      echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1  
2369      RETVAL=$?      RETVAL=$?
2370      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" != x0 ; then
2371          cat <<EOF          cat <<EOF
 *********************************************************************  
 WARNING: the "radtrans" package was enabled but tests failed to  
   compile LAPACK applications.  This means that the direct radtrans  
   solver is not available and compilation will fail if it is enabled.  
   If you want to use the direct solver, please check that:  
2372    
   1) LAPACK is correctly installed for this compiler and  
   2) the LIBS variable (within the "optfile") specifies the correct  
      LAPACK library to link against.  
2373  *********************************************************************  *********************************************************************
2374    ERROR: when generating an adjoint with OpenAD, the openad package
2375      must be enabled.  Please add it to packages.conf.
2376    *********************************************************************
2377    
2378  EOF  EOF
2379            exit 1
2380      fi      fi
2381  fi  fi
2382    
# Line 2300  if  test "x${PKG_DEPEND}" != x ; then Line 2425  if  test "x${PKG_DEPEND}" != x ; then
2425    
2426          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2427          if test "x$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
2428              #echo "   " $pname ": need to add :" $dname              #echo "   " $pname ": need to add :" $dname
2429              in_dis="f"              in_dis="f"
2430              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2431                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 2325  if  test "x${PKG_DEPEND}" != x ; then Line 2450  if  test "x${PKG_DEPEND}" != x ; then
2450              echo "  the dependency rules for \"$dname\""              echo "  the dependency rules for \"$dname\""
2451              exit 1              exit 1
2452          fi          fi
2453          i=`echo "$i + 1" | bc -l`          i=`echo "$i + 1" | bc -l`
2454          #i=$(( $i + 1 ))          #i=$(( $i + 1 ))
2455      done      done
2456      ck=$ck"t"      ck=$ck"t"
# Line 2366  for n in $names ; do Line 2491  for n in $names ; do
2491          done          done
2492          if test "x$has_pack" = xf ; then          if test "x$has_pack" = xf ; then
2493              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2494              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
2495          fi          fi
2496      fi      fi
2497  done  done
# Line 2379  for i in $PACKAGES ; do Line 2504  for i in $PACKAGES ; do
2504  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
2505      case $i in      case $i in
2506          aim_v23)          aim_v23)
2507              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
2508              echo "Warning: ALLOW_AIM is set to enable aim_v23."              echo "Warning: ALLOW_AIM is set to enable aim_v23."
2509              ;;              ;;
2510      esac      esac
# Line 2421  for i in $spaths ; do Line 2546  for i in $spaths ; do
2546      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
2547          echo "    found CPP_OPTIONS=\"$try\""          echo "    found CPP_OPTIONS=\"$try\""
2548          CPP_OPTIONS="$try"          CPP_OPTIONS="$try"
2549          # 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
2550          for n in $names ; do          for n in $names ; do
2551              test_for_package_in_cpp_options $CPP_OPTIONS $n              test_for_package_in_cpp_options $CPP_OPTIONS $n
2552          done          done
2553      fi      fi
2554      try="$i/CPP_EEOPTIONS.h"      try="$i/CPP_EEOPTIONS.h"
2555      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
2556          echo "    found CPP_EEOPTIONS=\"$try\""          echo "    found CPP_EEOPTIONS=\"$try\""
2557          # 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
2558  #**** not yet enabled ****  #**** not yet enabled ****
2559  #        test_for_mpi_in_cpp_eeoptions $try  #        test_for_mpi_in_cpp_eeoptions $try
2560  #**** not yet enabled ****  #**** not yet enabled ****
# Line 2443  fi Line 2568  fi
2568    
2569  #  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
2570  #  compiler.  #  compiler.
2571  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2572      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2573  fi  fi
2574  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2575  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2576  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2577      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2578      for j in $list_files ; do      for j in $list_files ; do
2579          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2580      done      done
2581  done  done
2582  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2583      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2584      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2585  fi  fi
2586    
2587  echo  echo
# Line 2468  for i in $INCLUDEDIRS ; do Line 2593  for i in $INCLUDEDIRS ; do
2593      fi      fi
2594  done  done
2595    
2596  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2597      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2598      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2599      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2600      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2601            mpi_headers_do_local_copy
     if test "x$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  
2602      fi      fi
2603  fi  fi
2604    
2605  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2606  rm -rf .links.tmp  rm -rf $TMP.links
2607  mkdir .links.tmp  mkdir $TMP.links
2608  touch .links.tmp/foo  touch $TMP.links/foo
2609  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2610      echo      echo
2611      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2612      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 2622  if test ! -r ".links.tmp/foo" ; then
2622      echo      echo
2623      exit 1      exit 1
2624  fi  fi
2625  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2626    
2627  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2628      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2629      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2630      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2631      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2632        OADTOOLS="$TOOLSDIR/OAD_support"
2633      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2634      for i in "." $MODS ; do      for i in "." $MODS ; do
2635          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
# Line 2555  if test "x$OPENAD" != x ; then Line 2665  if test "x$OPENAD" != x ; then
2665      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2666  fi  fi
2667    
2668  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2669  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2670  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2671  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2672  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2673  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2674  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2675  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2676  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2677  for d in $alldirs ; do  for d in $alldirs ; do
2678      deplist=      deplist=
# Line 2572  for d in $alldirs ; do Line 2682  for d in $alldirs ; do
2682          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2683      fi      fi
2684      for sf in $sfiles ; do      for sf in $sfiles ; do
2685          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2686              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2687                  ignore_f=f                  ignore_f=f
2688                  case $d/$sf in                  case $d/$sf in
2689                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2690                          ignore_f=t                          ignore_f=t
2691                          ;;                          ;;
2692                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2693                          ignore_f=t                          ignore_f=t
2694                          ;;                          ;;
2695                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2696                          ignore_f=t                          ignore_f=t
2697                          ;;                          ;;
2698                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2699                          ignore_f=t                          ignore_f=t
2700                          ;;                          ;;
2701                    ./EMBEDDED_FILES.h)                    ./EMBEDDED_FILES.h)
2702                          ignore_f=t                          ignore_f=t
2703                          ;;                          ;;
2704                    *)                    *)
2705                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
2706                          #  ignore all soft-links                          #  ignore all soft-links
2707                          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 $sf ; then
2708                              ignore_f=t                              ignore_f=t
2709                          else                          else
2710                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2711                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2712                          fi                          fi
2713                          ;;                          ;;
2714                  esac                  esac
2715                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2716                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2717                      case $extn in                      case $extn in
2718                        F)                        F)
2719                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2720                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2721                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2722                              basename=${sf%%.F}                              basename=${sf%%.F}
2723                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2724                                if test -z "$isAD" ; then
2725                                    echo    " \\"  >> $TMP.nonADF77srclist
2726                                    printf " $sf" >> $TMP.nonADF77srclist
2727                                fi
2728                            else #- OpenAD case:
2729                                basename=${sf%%.F}
2730                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2731                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2732                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2733                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2734                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2735                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2736                                  else                                  else
2737                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2738                                  fi                                  fi
# Line 2630  for d in $alldirs ; do Line 2747  for d in $alldirs ; do
2747                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2748                                  fi                                  fi
2749                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2750                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2751                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2752                                  fi                                  fi
2753                              fi                              fi
2754                          fi                          fi
2755                          ;;                          ;;
2756                      F90)                      F90)
2757                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2758                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2759                          ;;                          ;;
2760                      c)                      c)
2761                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2762                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2763                          ;;                          ;;
2764                      h)                      h)
2765                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2766                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2767                          ;;                          ;;
2768                      flow)                      flow)
2769                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2770                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2771                          ;;                          ;;
2772                     esac                     esac
2773                  fi                  fi
# Line 2659  for d in $alldirs ; do Line 2776  for d in $alldirs ; do
2776      done      done
2777      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2778        if test "$d" != "." ; then        if test "$d" != "." ; then
2779          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2780          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $d" >> $TMP.srclinks
2781          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2782  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2783  # 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"
2784  # 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.
2785          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
2786        fi        fi
2787      fi      fi
2788  done  done
2789  rm -rf .links.tmp  rm -rf $TMP.links
2790  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2791  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2792  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2793  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2794  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2795  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2796    
2797  CMDLINE=$0  CMDLINE=$0
2798  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
2799      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2800                          else CMDLINE="$CMDLINE '$xx'" ; fi                          else CMDLINE="$CMDLINE '$xx'" ; fi
2801  done  done
2802    
2803  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
# Line 2714  cat >>$MAKEFILE <<EOF Line 2831  cat >>$MAKEFILE <<EOF
2831  # INCLUDES     : Directories searched for header files  # INCLUDES     : Directories searched for header files
2832  # DEFINES      : Macro definitions for CPP  # DEFINES      : Macro definitions for CPP
2833  # MAKEDEPEND   : Dependency generator  # MAKEDEPEND   : Dependency generator
 # KPP          : Special preprocessor command (specific to platform)  
 # KFLAGS       : Flags for KPP  
2834  # FC           : Fortran compiler command  # FC           : Fortran compiler command
2835  # FFLAGS       : Configuration/debugging options for FC  # FFLAGS       : Configuration/debugging options for FC
2836  # FOPTIM       : Optimization options for FC  # FOPTIM       : Optimization options for FC
# Line 2729  INCLUDEDIRS = ${INCLUDEDIRS} Line 2844  INCLUDEDIRS = ${INCLUDEDIRS}
2844  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2845  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2846  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIR}
2847    OADTOOLS    = ${OADTOOLS}
2848    
2849  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2850  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = ${ROOTDIR}/pkg/autodiff
# Line 2749  else Line 2865  else
2865      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2866  fi  fi
2867    
2868    # extract default cpp search path so we can pass it to makedepend
2869    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2870    
2871  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2872  # Unix ln (link)  # Unix ln (link)
2873  LN = ${LN}  LN = ${LN}
 # C preprocessor  
 CPP = cat \$< | ${S64} | ${CPP}  
2874  # Dependency generator  # Dependency generator
2875  MAKEDEPEND = ${MAKEDEPEND}  MAKEDEPEND = ${MAKEDEPEND}
2876  # Special preprocessor (KAP on DECs, FPP on Crays)  # Special preprocessor (KAP on DECs, FPP on Crays)
# Line 2771  LINK = ${LINK} ${LDADD} Line 2888  LINK = ${LINK} ${LDADD}
2888  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2889  # Includes for CPP  # Includes for CPP
2890  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2891    # default CPP includes for makedepend
2892    CPPINCLUDES = ${CPPINCLUDES}
2893  # Flags for KPP  # Flags for KPP
2894  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2895  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
# Line 2789  NOOPTFLAGS = ${NOOPTFLAGS} Line 2908  NOOPTFLAGS = ${NOOPTFLAGS}
2908  # Flags and libraries needed for linking  # Flags and libraries needed for linking
2909  LIBS = ${LIBS}  LIBS = ${LIBS}
2910  # Name of the makefile  # Name of the makefile
2911  MAKEFILE=${MAKEFILE}  MAKEFILE = ${MAKEFILE}
2912    # Name of the make program
2913    MAKE = ${MAKE}
2914    
2915  EOF  EOF
2916    
2917  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2918  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2919  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2920  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2921  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2922  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2923    
2924  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
2925    
2926  echo >> $MAKEFILE  echo >> $MAKEFILE
2927    
# Line 2813  echo >> $MAKEFILE Line 2934  echo >> $MAKEFILE
2934  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
2935  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
2936  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
2937  echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE  echo 'FLOWFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
2938  echo >> $MAKEFILE  echo >> $MAKEFILE
2939  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
2940  echo '.SUFFIXES: .o .'$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' >> $MAKEFILE
2941    
2942  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2943    
2944  all: \$(EXECUTABLE)  all: fwd_exe_target
2945    fwd_exe_target:
2946            @echo Update AD_CONFIG.h and make \$(EXECUTABLE)
2947            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
2948            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
2949            @-rm -f ad_config.template
2950            \$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
2951    
2952  \$(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)
2953          @echo Creating \$@ ...          @echo Creating \$@ ...
2954          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
2955    
2956  depend:  depend:
2957          @make -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
2958          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
2959          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
2960          -rm -f makedepend.out          -rm -f makedepend.out
2961    
# Line 2843  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 2971  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
2971    
2972  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
2973    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
2974  # remove most of the files that "make" generates  # remove most of the files that "make" generates
2975  clean:  clean:
2976          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2856  clean: Line 2980  clean:
2980    
2981  # remove most of the files that "make" and "make depend" generate  # remove most of the files that "make" and "make depend" generate
2982  Clean:  Clean:
2983          @make -f \$(MAKEFILE) clean          @\$(MAKE) -f \$(MAKEFILE) clean
2984          @make -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
2985          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
2986          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log          -rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log
         -rm -f genmake_warnings genmake_errors make.log  
2987    
2988  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
2989  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
2990  CLEAN:  CLEAN:
2991          @make -f \$(MAKEFILE) Clean          @\$(MAKE) -f \$(MAKEFILE) Clean
2992          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
2993          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
2994          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
2995            -rm -rf mpi_headers mnc_test_*
2996          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
2997          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
2998          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
2999          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3000            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3001          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3002          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3003    
3004  makefile:  makefile:
3005          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2884  cleanlinks: Line 3009  cleanlinks:
3009  # Special targets (SPECIAL_FILES) which are created by make  # Special targets (SPECIAL_FILES) which are created by make
3010  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
3011          @echo Creating \$@ ...          @echo Creating \$@ ...
3012          @$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) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
3013  AD_CONFIG.h:  AD_CONFIG.h:
3014          @echo Creating \$@ ...          @echo Creating \$@ ...
3015          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
3016  FC_NAMEMANGLE.h:  FC_NAMEMANGLE.h:
3017          @echo Creating \$@ ...          @echo Creating \$@ ...
3018          echo "$FC_NAMEMANGLE" > \$@          echo "$FC_NAMEMANGLE" > \$@
# Line 2927  cat >>$MAKEFILE <<EOF Line 3052  cat >>$MAKEFILE <<EOF
3052  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3053  ## %.o : %.F  ## %.o : %.F
3054    
3055    # C preprocessing and replacing the _d in constants:
3056    CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3057    
3058  .F.$FS:  .F.$FS:
3059          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3060  .$FS.o:  .$FS.o:
3061          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3062  .F.o:  .F.o:
3063          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3064  .F90.$FS90:  .F90.$FS90:
3065          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3066  .FF90.f$FS90:  .FF90.f$FS90:
3067          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3068  .$FS90.o:  .$FS90.o:
3069          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
3070  .f$FS90.o:  .f$FS90.o:
# Line 2945  cat >>$MAKEFILE <<EOF Line 3073  cat >>$MAKEFILE <<EOF
3073  .c.o:  .c.o:
3074          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
3075  .flow.flowdir:  .flow.flowdir:
3076          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3077    
3078  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
3079  .F.p:  .F.p:
3080          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3081  .p.$FS:  .p.$FS:
3082          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
3083    
# Line 2968  TAF            = ${TAF} Line 3096  TAF            = ${TAF}
3096    
3097  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3098  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3099    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3100    
3101  EOF  EOF
3102    
# Line 2985  done Line 3114  done
3114  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3115  echo >> $MAKEFILE  echo >> $MAKEFILE
3116  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3117  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3118  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3119      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3120      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3121  done  done
3122  echo >> $MAKEFILE  echo >> $MAKEFILE
3123  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3124    
3125  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3126    
3127  # ... AD ...  # ... AD ...
3128  adall: \$(EXE_AD)  adall: ad_exe_target
3129  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
3130  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
3131    
3132  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)  ad_exe_target:
3133          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template          @echo Update AD_CONFIG.h and make \$(EXE_AD)
3134            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3135            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3136            @-rm -f ad_config.template
3137            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3138    
3139    ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
3140            @$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          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3142          -rm -f ad_config.template          @-rm -f ad_config.template
3143          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3144          @make -f \$(MAKEFILE) \$(FLOFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3145          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
3146    
3147  ad_taf_output.$FS: ad_input_code.$FS  ad_taf_output.$FS: ad_input_code.$FS
3148            @-rm -f ad_input_code_ad.$FS ; echo ''
3149          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3150          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3151          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
# Line 3018  adtafonly: Line 3155  adtafonly:
3155          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3156          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3157    
3158  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3159          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3160    
3161  ad_tamc_output.$FS: ad_input_code.$FS  ad_tamc_output.$FS: ad_input_code.$FS
3162          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS          \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
# Line 3034  adonlyfwd: Line 3171  adonlyfwd:
3171  adtrick:  adtrick:
3172          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3173    
3174  adobj: ad_taf_output.o \$(OBJFILES)  adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3175    
3176  # ... FTL ...  # ... FTL ...
3177  ftlall: ftl_taf  ftlall: ftl_exe_target
3178  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
3179  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
3180    
3181  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)  ftl_exe_target:
3182          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template          @echo Update AD_CONFIG.h and make \$(EXE_FTL)
3183          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3184          -rm -f ftl_config.template          @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3185          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @-rm -f ad_config.template
3186          @make -f \$(MAKEFILE) \$(AD_FLOW_FILES)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
3187          cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS  
3188    ftl_input_code.$FS: \$(AD_FILES)
3189            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3190            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3191            @-rm -f ad_config.template
3192            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3193            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3194            cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3195    
3196  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_taf_output.$FS: ftl_input_code.$FS
3197            @-rm -f ftl_input_code_tl.$FS ; echo ''
3198          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3199          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3200          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3201    
3202  ftltafonly:  ftltafonly:
3203          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3204          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3205          cat ftl_input_code_ftl.$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
3206    
3207  ftl_taf: ftl_taf_output.o \$(OBJFILES)  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3208          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3209    
3210  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3211          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
# Line 3089  svd_touch: Line 3234  svd_touch:
3234          touch ad_taf_output.$FS ftl_taf_output.$FS          touch ad_taf_output.$FS ftl_taf_output.$FS
3235          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
3236          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
3237          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3238          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3239          -rm -f ftl_config.template          @-rm -f ad_config.template
3240    
3241  EOF  EOF
3242    
# Line 3104  if test "x$OPENAD" != x ; then Line 3249  if test "x$OPENAD" != x ; then
3249  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3250    
3251  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3252    # ... OpenAD ...
3253    
3254  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3255  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3143  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3289  for i in `cat ${OAD_CB2M_FILES}` ; do
3289    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3290    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3291  done  done
3292  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3293  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3294    basename=${i%%.f}    basename=${i%%.f}
3295    toBeIgnored=`egrep ^$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 3299  for i in $AD_FILES ; do
3299    fi    fi
3300  done  done
3301  echo >> $MAKEFILE  echo >> $MAKEFILE
3302  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3303    
3304  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3305    
3306  adAll: \$(EXE_AD)  adAll: ad_exe_target
3307  .PHONY: adAll  .PHONY: adAll
3308    
3309    ad_exe_target:
3310            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3311            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3312            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3313            @-rm -f ad_config.template
3314            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3315    
3316  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))
3317    
3318  .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 3328  w2f__types.F90 \
3328  OAD_active.F90 \  OAD_active.F90 \
3329  OAD_cp.F90 \  OAD_cp.F90 \
3330  OAD_rev.F90 \  OAD_rev.F90 \
3331  OAD_tape.F90  OAD_tape.F90 \
3332    revolve.F90
3333    
3334  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3335  iaddr.c \  iaddr.c \
# Line 3191  f95_test.out: f95_test_mods.f90 f95_test Line 3345  f95_test.out: f95_test_mods.f90 f95_test
3345          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
3346          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
3347    
3348  # the file included below is created by the  CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
 # postProcessor and its inclusion sets the  
 # variable POSTPROCESSEDFILES  
 # used below. Because the file is made during  
 # make it won't be read until the second (recursive)  
 # invocation in the rule below  
 -include postProcess.make  
3349    
3350  AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$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)
3351    
3352  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)
3353    
3354  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)  
3355          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
 else  
         touch \$@  
 endif  
3356    
3357  # makefile debug rule  # create sources files modules from header files containing common blocks
3358  openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90  %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
3359  .PHONY: openad          \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
3360    
3361  # create the module files  # create new header files with USE statements for the new modules made above
3362  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
3363          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3364    
3365  # create the header files  # change the include directives of everybody to refer to  the new header files with the USE statements
3366  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
3367          ../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}  
3368    
3369  # makefile debug rule  # makefile debug rule
3370  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3371  .PHONY: small_f  .PHONY: small_f
3372    
 ad_output.txt: \$(EXE_AD)  
         @printf 'linking data files ... '  
         \$(LN) -f ../input_ad/data* ../input_ad/eedata .  
         \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .  
         @printf 'running ... '  
         @./\$(EXE_AD) > \$@  
   
 CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)  
3373  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3374          cat \$^ > \$@          cat \$^ > \$@
3375    
 # strip all comments and blanks to reduce  
 # the file size in order to reduce perl's memory requirements  
 ad_input_code_sf.f$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 > \$@  
   
3376  # canonicalizer  # canonicalizer
3377  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)
3378          ./preProcess.py --timing --r8 -H -S \$< -o \$@          \${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
3379    
3380    # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3381    ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3382            cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3383    
3384  # F -> WHIRL  # F -> WHIRL
3385  # note that the canonicalized version cuts off at col 72  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
3386  # 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$FS90 mfef90  
         ./mfef90 -r8 -z -F \$<  
         mv \$<.B \$@  
3387    
3388  # WHIRL -> XAIF  # WHIRL -> XAIF
3389  ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif  ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
3390          ./whirl2xaif -s -n --debug 1 -o \$@ \$<          \${OPENADFORTTK}/bin/whirl2xaif -s -n --debug 1 -o \$@ \$<
3391    
3392  # XAIF -> XAIF'  # XAIF -> XAIF'
3393  ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver  ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
3394          ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r          \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3395    
3396  # XAIF' -> WHIRL'  # XAIF' -> WHIRL'
3397  ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl  ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
3398          ./xaif2whirl --debug 1 ad_input_code_sf.w2f.pre.B \$<          \${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
3399    
3400  # WHIRL' -> F'  # WHIRL' -> F'
3401  ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
3402          ./whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3403    
3404  # insert template directives  # insert template directives
3405  ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$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$FS90 \${OADTOOLS}/insertTemplateDir.bash
3406          ../OAD_support/insertTemplateDir.bash \$< \$@          \${OADTOOLS}/insertTemplateDir.bash \$< \$@
3407    
3408  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
3409  # postprocess F'  # postprocess F'
3410  postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
3411          # the target is a placeholder to signal execution of the rule          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
3412            # the target is a placeholder to trigger a single execution of the rule
3413          touch \$@          touch \$@
3414          # this step also creates the file postProcess.make but we cannot  # put this so make knows about the postprocessing output
3415          # name it as the target or else make will try to remake it for  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$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 \$<  
3416    
3417  # setup some links  # link the XAIF schema files
3418  %.xsd:  %.xsd:
3419          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3420    
 mfef90:  
         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .  
   
3421  # link the support files:  # link the support files:
3422  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3423          \$(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 \$@  
3424    
3425  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
3426    
3427  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3428    
# Line 3366  for i in $NOOPTFILES ; do Line 3458  for i in $NOOPTFILES ; do
3458  done  done
3459    
3460  echo "  Add rules for links"  echo "  Add rules for links"
3461  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3462  rm -f srclinks.tmp  rm -f $TMP.srclinks
3463    
3464  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3465  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 3467  printf "\n\n# DO NOT DELETE\n" >> $MAKEF
3467  printf "\n===  Done  ===\n"  printf "\n===  Done  ===\n"
3468    
3469  # Create special header files  # Create special header files
3470  $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"
3471  if test ! -f $PACKAGES_DOT_H ; then  if test ! -f $PACKAGES_DOT_H ; then
3472      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
3473  else  else
# Line 3389  else Line 3481  else
3481      fi      fi
3482  fi  fi
3483  if test ! -f AD_CONFIG.h ; then  if test ! -f AD_CONFIG.h ; then
3484      $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
3485  fi  fi
3486    
3487  #  Write the "state" for future records  #  Write the "state" for future records

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