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revision 1.229 by jmc, Tue Jan 24 14:54:57 2012 UTC revision 1.281 by jmc, Thu Feb 16 23:27:08 2017 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        -nocat4ad | -dog4ad | -ncad | -dad
26              do not concatenate (cat) source code sent to TAF
27              resulting in compilation of multiple files
28    
29      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
30        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
31            Use "NAME" as the adoptfile.  By default, the file at            Use "NAME" as the adoptfile.  By default, the file at
32            "tools/adjoint_options/adjoint_default" will be used.            "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
33              "tools/adjoint_options/adjoint_default" will be used.
34    
35      -nooptfile | --nooptfile      -optfile NAME | --optfile NAME | -of NAME | --of NAME
       -optfile NAME | --optfile NAME | -of NAME | --of NAME  
36        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
37            Use "NAME" as the optfile.  By default, an attempt will be            Use "NAME" as the optfile.  By default, an attempt will be
38            made to find an appropriate "standard" optfile in the            made to find an appropriate "standard" optfile in the
39            tools/build_options/ directory.            tools/build_options/ directory.
40    
41      -pdepend NAME | --pdepend NAME      -pdepend NAME | --pdepend NAME
42        -pdepend=NAME | --pdepend=NAME        -pdepend=NAME | --pdepend=NAME
43            Get package dependency information from "NAME".            Get package dependency information from "NAME".
44    
45      -pgroups NAME | --pgroups NAME      -pgroups NAME | --pgroups NAME
46        -pgroups=NAME | --pgroups=NAME        -pgroups=NAME | --pgroups=NAME
47            Get the package groups information from "NAME".            Get the package groups information from "NAME".
48    
49      -bash NAME      -bash NAME
50            Explicitly specify the Bourne or BASH shell to use            Explicitly specify the Bourne or BASH shell to use
51    
52      -make NAME | -m NAME      -make NAME | -m NAME
53        --make=NAME | -m=NAME        --make=NAME | -m=NAME
54            Use "NAME" for the MAKE program. The default is "make" but            Use "NAME" for the MAKE program. The default is "make" but
55            many platforms, "gmake" is the preferred choice.            many platforms, "gmake" is the preferred choice.
56    
57      -makefile NAME | -mf NAME      -makefile NAME | -mf NAME
58        --makefile=NAME | -mf=NAME        --makefile=NAME | -mf=NAME
59            Call the makefile "NAME".  The default is "Makefile".            Call the makefile "NAME".  The default is "Makefile".
60    
61      -makedepend NAME | -md NAME      -makedepend NAME | -md NAME
62        --makedepend=NAME | -md=NAME        --makedepend=NAME | -md=NAME
63            Use "NAME" for the MAKEDEPEND program.            Use "NAME" for the MAKEDEPEND program.
64    
65      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME      -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
66        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME        -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
67            Specify the location of the MITgcm ROOTDIR as "NAME".            Specify the location of the MITgcm ROOTDIR as "NAME".
68            By default, genamke will try to find the location by            By default, genamke will try to find the location by
69            looking in parent directories (up to the 5th parent).            looking in parent directories (up to the 5th parent).
70    
71      -mods NAME | --mods NAME | -mo NAME | --mo NAME      -mods NAME | --mods NAME | -mo NAME | --mo NAME
72        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME        -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
73            Here, "NAME" specifies a list of directories that are            Here, "NAME" specifies a list of directories that are
74            used for additional source code.  Files found in the            used for additional source code.  Files found in the
75            "mods list" are given preference over files of the same            "mods list" are given preference over files of the same
76            name found elsewhere.            name found elsewhere.
77    
78      -disable NAME | --disable NAME      -disable NAME | --disable NAME
79        -disable=NAME | --disable=NAME        -disable=NAME | --disable=NAME
80            Here "NAME" specifies a list of packages that we don't            Here "NAME" specifies a list of packages that we don't
81            want to use.  If this violates package dependencies,            want to use.  If this violates package dependencies,
82            genamke will exit with an error message.            genamke will exit with an error message.
83    
84      -enable NAME | --enable NAME      -enable NAME | --enable NAME
85        -enable=NAME | --enable=NAME        -enable=NAME | --enable=NAME
86            Here "NAME" specifies a list of packages that we wish            Here "NAME" specifies a list of packages that we wish
87            to specifically enable.  If this violates package            to specifically enable.  If this violates package
88            dependencies, genamke will exit with an error message.            dependencies, genamke will exit with an error message.
89    
90      -standarddirs NAME | --standarddirs NAME      -standarddirs NAME | --standarddirs NAME
91        -standarddirs=NAME | --standarddirs=NAME        -standarddirs=NAME | --standarddirs=NAME
92            Here, "NAME" specifies a list of directories to be            Here, "NAME" specifies a list of directories to be
93            used as the "standard" code.            used as the "standard" code.
94    
95      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME      -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
96        -fc=NAME | --fc=NAME        -fc=NAME | --fc=NAME
97            Use "NAME" as the fortran compiler.  By default, genmake            Use "NAME" as the fortran compiler.  By default, genmake
98            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
99            "usual suspects" such as g77, f77, etc.            "usual suspects" such as g77, f77, etc.
100    
101      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME      -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
102            Use "NAME" as the C compiler.  By default, genmake            Use "NAME" as the C compiler.  By default, genmake
103            will search for a working compiler by trying a list of            will search for a working compiler by trying a list of
104            "usual suspects" such as gcc, c89, cc, etc.            "usual suspects" such as gcc, c89, cc, etc.
105    
106      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4      -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
107            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)            Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
108            *only* works if CPP_EEOPTIONS.h allows this.            *only* works if CPP_EEOPTIONS.h allows this.
109    
110      -ignoretime | -ignore_time | --ignoretime | --ignore_time      -ignoretime | -ignore_time | --ignoretime | --ignore_time
111            Ignore all the "wall clock" routines entirely.  This will            Ignore all the "wall clock" routines entirely.  This will
112            not in any way hurt the model results -- it simply means            not in any way hurt the model results -- it simply means
113            that the code that checks how long the model spends in            that the code that checks how long the model spends in
114            various routines will give junk values.            various routines will give junk values.
115    
116      -ts | --ts      -ts | --ts
117            Produce timing information per timestep            Produce timing information per timestep
118      -papis | --papis      -papis | --papis
119            Produce summary MFlop/s (and IPC) with PAPI per timestep            Produce summary MFlop/s (and IPC) with PAPI per timestep
120      -pcls | --pcls      -pcls | --pcls
121            Produce summary MFlop/s etc. with PCL per timestep            Produce summary MFlop/s etc. with PCL per timestep
122      -foolad | --foolad      -foolad | --foolad
123            Fool the AD code generator            Fool the AD code generator
124      -papi | --papi      -papi | --papi
125            Performance analysis with PAPI            Performance analysis with PAPI
126      -pcl | --pcl      -pcl | --pcl
127            Performance analysis with PCL            Performance analysis with PCL
128      -hpmt | --hpmt      -hpmt | --hpmt
129            Performance analysis with the HPM Toolkit            Performance analysis with the HPM Toolkit
130    
131      -ieee | --ieee      -ieee | --ieee
132            use IEEE numerics.  Note that this option *only* works            use IEEE numerics.  Note that this option *only* works
133            if it is supported by the OPTFILE that is being used.            if it is supported by the OPTFILE that is being used.
134      -devel | --devel      -devel | --devel
135            Add additional warning and debugging flags for development            Add additional warning and debugging flags for development
136            (if supported by the OPTFILE); also switch to IEEE numerics.            (if supported by the OPTFILE); also switch to IEEE numerics.
137      -gsl | --gsl      -gsl | --gsl
138            Use GSL to control floating point rounding and precision            Use GSL to control floating point rounding and precision
139    
140      -mpi | --mpi      -mpi | --mpi
141            Include MPI header files and link to MPI libraries            Include MPI header files and link to MPI libraries
142      -mpi=PATH | --mpi=PATH      -mpi=PATH | --mpi=PATH
143            Include MPI header files and link to MPI libraries using MPI_ROOT            Include MPI header files and link to MPI libraries using MPI_ROOT
144            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
145            from \$PATH/lib and use binaries from \$PATH/bin.            from \$PATH/lib and use binaries from \$PATH/bin.
146    
147      -omp | --omp      -omp | --omp
148            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
149      -omp=OMPFLAG | --omp=OMPFLAG      -omp=OMPFLAG | --omp=OMPFLAG
150            Activate OpenMP code + use Compiler option OMPFLAG            Activate OpenMP code + use Compiler option OMPFLAG
151    
152      -es | --es | -embed-source | --embed-source      -es | --es | -embed-source | --embed-source
153            Embed a tarball containing the full source code            Embed a tarball containing the full source code
154            (including the Makefile, etc.) used to build the            (including the Makefile, etc.) used to build the
155            executable [off by default]            executable [off by default]
156    
157      -ds | --ds      -ds | --ds
158            Report genmake internal variables status (DUMPSTATE)            Report genmake internal variables status (DUMPSTATE)
159            to file "genmake_state" (for debug purpose)            to file "genmake_state" (for debug purpose)
160    
161    While it is most often a single word, the "NAME" variables specified    While it is most often a single word, the "NAME" variables specified
162    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 181  EOF
181  test_for_package_in_cpp_options() {  test_for_package_in_cpp_options() {
182      cpp_options=$1      cpp_options=$1
183      pkg=$2      pkg=$2
184      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
185      test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
186      test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
187      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$"  
188  }  }
189    
190  # Search for particular CPP #cmds associated with MPI  # Search for particular CPP #cmds associated with MPI
191  # usage: test_for_mpi_in_cpp_eeoptions CPP_file  # usage: test_for_mpi_in_cpp_eeoptions CPP_file
192  test_for_mpi_in_cpp_eeoptions() {  test_for_mpi_in_cpp_eeoptions() {
193      cpp_options=$1      cpp_options=$1
194      test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"      test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
195      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 $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"  
196  }  }
197    
198  # 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 200  test_for_mpi_in_cpp_eeoptions() {
200  test_for_string_in_file() {  test_for_string_in_file() {
201      file=$1      file=$1
202      strng=$2      strng=$2
203      grep -i "$strng" $file > /dev/null 2>&1      grep "$strng" $file > /dev/null 2>&1
204      RETVAL=$?      RETVAL=$?
205      if test "x${RETVAL}" = x0 ; then      if test "x${RETVAL}" = x0 ; then
206          printf "Error: In $file there is an illegal line: "          printf "Error: In $file there is an illegal line: "
207          grep -i "$strng" $file          grep -i "$strng" $file
208          exit 99          exit 99
209      fi      fi
210      return 0      return 0
# Line 218  test_for_string_in_file() { Line 215  test_for_string_in_file() {
215  expand_pkg_groups() {  expand_pkg_groups() {
216      new_packages=      new_packages=
217      if test -r $PKG_GROUPS ; then      if test -r $PKG_GROUPS ; then
218          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
219          cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp          cat $TMP.p1 | $AWK '(NF>2 && $2==":"){ print $0 }' > $TMP.p2
220          matched=0          matched=0
221          for i in $PACKAGES ; do          for i in $PACKAGES ; do
222              line=`grep "^ *$i" ./p2.tmp`              line=`grep "^ *$i" $TMP.p2`
223              RETVAL=$?              RETVAL=$?
224              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
225                  matched=1                  matched=1
# Line 234  expand_pkg_groups() { Line 231  expand_pkg_groups() {
231              fi              fi
232          done          done
233          PACKAGES=$new_packages          PACKAGES=$new_packages
234          rm -f ./p[1,2].tmp          rm -f $TMP.p[1,2]
235          return $matched          return $matched
236      else      else
237          echo "Warning: can't read package groups definition file: $PKG_GROUPS"          echo "Warning: can't read package groups definition file: $PKG_GROUPS"
# Line 305  EOF Line 302  EOF
302              FS90='fr9'              FS90='fr9'
303              check_for_broken_Ff              check_for_broken_Ff
304          else          else
305              cat <<EOF 2>&1              echo "ERROR: test: '$MAKE -f $MAKEFILE genmake_hello.$tfs' Failed"
306  ERROR: Your file system cannot distinguish between *.F and *.f files              echo "       see simple makefile: '$MAKEFILE' (left here)"
307    (fails the "make/ln" test) and this program cannot find a suitable              echo "  Please check (1) your '$MAKE' command, (2) your '$LN' command"
308    replacement extension.  Please try a different build environment or              echo "           and (3) the allowed sufix '.F' and '.$tfs' in makefile"
309    contact the <MITgcm-support@mitgcm.org> list for help.              echo "  or contact the <MITgcm-support@mitgcm.org> list for help."
310                echo ""
 EOF  
311              exit -1              exit -1
312              return              return
313          fi          fi
# Line 335  look_for_makedepend()  { Line 331  look_for_makedepend()  {
331      #      #
332      #    1) a makedepend implementation shipped with the cyrus-imapd      #    1) a makedepend implementation shipped with the cyrus-imapd
333      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/      #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
334      #      #    2) a local tools/xmakedepend shell script
     #    2) a known-buggy xmakedpend shell script  
335      #      #
336      #  So the choices are, in order:      #  So the choices are, in order:
     #  
337      #    1) use the user-specified program      #    1) use the user-specified program
338      #    2) use a system-wide default      #    2) use the local xmakedepend script (get all dependencies, but slower)
339      #    3) locally build and use the cyrus implementation      #    3) use a system-wide default
340      #    4) fall back to the buggy local xmakedpend script      #    4) locally build and use the cyrus makedepend
341        #             (faster, but can miss some dependencies)
342      #      #
343      echo >> $LOGFILE      echo >> $LOGFILE
344      echo "running: look_for_makedepend()" >> $LOGFILE      echo "running: look_for_makedepend()" >> $LOGFILE
# Line 354  look_for_makedepend()  { Line 349  look_for_makedepend()  {
349              build_cyrus_makedepend              build_cyrus_makedepend
350              RETVAL=$?              RETVAL=$?
351              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" != x0 ; then
352                  echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"                  echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
353                  MAKEDEPEND=                  MAKEDEPEND=
354              fi              fi
355          else          else
# Line 367  look_for_makedepend()  { Line 362  look_for_makedepend()  {
362          fi          fi
363      fi      fi
364      if test "x${MAKEDEPEND}" = x ; then      if test "x${MAKEDEPEND}" = x ; then
         which makedepend > /dev/null 2>&1  
         RV0=$?  
365          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"          test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
366          #  echo 'MAKEFILE="'$MAKEFILE'"'          #  echo 'MAKEFILE="'$MAKEFILE'"'
367          cat <<EOF >> $MAKEFILE          cat <<EOF >> $MAKEFILE
# Line 384  EOF Line 377  EOF
377        stop        stop
378        end        end
379  EOF  EOF
380          makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1          $ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
381          RV1=$?          RV1=$?
382            which makedepend > /dev/null 2>&1
383            RV2=$?
384            if test "x${RV2}" = x0 ; then
385                makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
386                RV3=$? ; loc_msg='not working.'
387            else RV3=$RV2 ; loc_msg='not found.'
388            fi
389          test -f $MAKEFILE  &&  rm -f $MAKEFILE          test -f $MAKEFILE  &&  rm -f $MAKEFILE
390          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE          test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
391          if test "x${RV0}${RV1}" = x00 ; then          echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
392            if test "x${RV1}" = x0 ; then
393                MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
394                echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
395            elif test "x${RV3}" = x0 ; then
396                echo "    local tools/xmakedepend not working. Use system-default makedepend"
397              MAKEDEPEND=makedepend              MAKEDEPEND=makedepend
398              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE              echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
399          else          else
400              echo "    system-default makedepend not found. Try to build cyrus-makedepend"              echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
401                echo -n "    Try to build cyrus-makedepend ..."
402              #  Try to build the cyrus implementation              #  Try to build the cyrus implementation
403              build_cyrus_makedepend              build_cyrus_makedepend
404              RETVAL=$?              RETVAL=$?
405              if test "x$RETVAL" != x0 ; then              if test "x$RETVAL" = x0 ; then
406                  echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"                  echo "  Works"
407                  MAKEDEPEND='$(TOOLSDIR)/xmakedepend'              else
408                  echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE                  echo "  Fails" ; echo "" >> $LOGFILE
409                    echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
410                    echo ""
411                    exit -1
412                    return
413              fi              fi
414          fi          fi
415      fi      fi
# Line 412  build_cyrus_makedepend()  { Line 422  build_cyrus_makedepend()  {
422      (      (
423          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \          cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
424              &&  ./configure > /dev/null 2>&1  \              &&  ./configure > /dev/null 2>&1  \
425              &&  make > /dev/null 2>&1              &&  $MAKE > /dev/null 2>&1
426          if test -x ./makedepend.exe ; then          if test -x ./makedepend.exe ; then
427              $LN ./makedepend.exe ./makedepend              $LN ./makedepend.exe ./makedepend
428          fi          fi
# Line 436  build_embed_encode() Line 446  build_embed_encode()
446  {  {
447      printf "  building the embed-encode utility...  "      printf "  building the embed-encode utility...  "
448      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then      if test ! -e "$ROOTDIR/tools/embed_encode/encode_files" ; then
449          if test ! -d "$ROOTDIR/tools/embed_encode" ; then          if test ! -d "$ROOTDIR/tools/embed_encode" ; then
450              echo              echo
451              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""              echo "    Error: can't locate \"$ROOTDIR/tools/embed_encode\""
452              echo              echo
453              EMBED_SRC=f              EMBED_SRC=f
454              return 1              return 1
455          fi          fi
456          clist="cc gcc c89 $CC"          clist="cc gcc c89 $CC"
457          for ic in $clist ; do          for ic in $clist ; do
458              comm="$ic -o encode_files encode_files.c"              comm="$ic -o encode_files encode_files.c"
# Line 450  build_embed_encode() Line 460  build_embed_encode()
460              RETVAL=$?              RETVAL=$?
461              if test "x$RETVAL" = x0 ; then              if test "x$RETVAL" = x0 ; then
462                  echo "OK"                  echo "OK"
                 DEFINES="$DEFINES -DHAVE_EMBED_SRC"  
463                  return 0                  return 0
464              fi              fi
465          done          done
# Line 462  build_embed_encode() Line 471  build_embed_encode()
471          return 1          return 1
472      fi      fi
473      echo "OK"      echo "OK"
     DEFINES="$DEFINES -DHAVE_EMBED_SRC"  
474  }  }
475    
476  #  look for possible C compilers  #  look for possible C compilers
# Line 580  EOF Line 588  EOF
588      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
589          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC          OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
590          if test ! -r $OPTFILE ; then          if test ! -r $OPTFILE ; then
591               echo "  I looked for the file "$OPTFILE" but did not find it"               echo "  I looked for the file "$OPTFILE" but did not find it"
592          fi          fi
593      fi      fi
594    
595      if test "x$OPTFILE" = x ; then      if test "x$OPTFILE" = x ; then
# Line 599  Error: No options file was found in:  $R Line 607  Error: No options file was found in:  $R
607  EOF  EOF
608          exit 1          exit 1
609      fi      fi
610    }
611    
612  #     # look for possible MPI libraries  #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
613  #     mpi_libs=  #  checking for additional included headers (in case of chain of included header)
614  #     mpi_fort=`which mpif77 2>/dev/null`  mpi_headers_do_local_copy() {
615  #     RETVAL=$?  
616  #     if test "x${RETVAL}" = x0 ; then      dBug=0
617  #       cat >>test.f <<EOF      rm -rf ./mpi_headers
618  #       PROGRAM HELLO      if test -d $MPIINCLUDEDIR ; then
619  #       DO 10, I=1,10  
620  #       PRINT *,'Hello World'          #----- check for additional headers (chain of included headers)
621  #    10 CONTINUE          echo -n '  Check MPI headers ... '
622  #       STOP          listIni=$MPI_HEADER_FILES
623  #       END          echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
624  # EOF          outp=$?
625  #       eval "$mpi_fort -showme test.f > out"          #- always check mpif.h (the only mpi-header included in standard MITgcm code)
626  #       RETVAL=$?          if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
627  #       if test "x${RETVAL}" = x0 ; then          if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
628  #           a=`cat out`  
629  #           for i in $a ; do          doCheck=1 ; list2copy='' ; list2check=$listIni
630  #               case $i in          while test $doCheck = 1 ; do
631  #                   -*)            newList=''
632  #                       mpi_libs="$mpi_libs $i" ;;            for i in $list2check ; do
633  #               esac              if test -f $MPIINCLUDEDIR/$i ; then
634  #           done                newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
635  #           echo "The MPI libs appear to be:"                  sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
636  #           echo "  "$mpi_libs                if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
637  #       fi                for j in $newInc ; do
638  #       rm -f test.f out                  echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
639  #     fi                  outp=$?
640                    if test $outp != 0 ; then
641                      if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
642                      newList="$newList $j"
643                    fi
644                  done
645                  if test $dBug = 1 ; then echo "" ; fi
646                fi
647              done
648              if test "x$newList" = x ; then doCheck=0
649              else list2check=$newList ; list2copy="$list2copy $newList"
650              fi
651            done
652            list2copy="$MPI_HEADER_FILES $list2copy"
653            if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
654    
655            #----- create local mpi_headers dir if we have files to copy
656            mkListInc=`echo $list2copy | wc -w`
657            if test $mkListInc != 0 ; then
658              echo 'create local "./mpi_headers" dir'
659              mkdir -p ./mpi_headers
660              INCLUDES="-I./mpi_headers $INCLUDES"
661              mkListInc=1
662            fi
663            if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
664    
665            #----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
666            for i in $list2copy ; do
667              if test -f $MPIINCLUDEDIR/$i ; then
668                cp -p $MPIINCLUDEDIR/$i ./mpi_headers
669                if test $i = 'mpif.h' ; then
670                    perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
671                fi
672                if test $mkListInc = 2 ; then
673                    LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
674                fi
675                if test $mkListInc = 1 ; then
676                    LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
677                fi
678              fi
679            done
680        else
681            echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
682            echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
683    #       exit -1
684        fi
685  }  }
686    
687  #  Parse the package dependency information  #  Parse the package dependency information
# Line 643  get_pdepend_list()  { Line 697  get_pdepend_list()  {
697        echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""        echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
698        exit 1        exit 1
699      fi      fi
700        #echo "---- content of tmp file '.pd_tmp' :" ; cat .pd_tmp ; echo "---- end of file"
701      . ./.pd_tmp      . ./.pd_tmp
702      rm -f ./.pd_tmp      rm -f ./.pd_tmp
703  }  }
# Line 652  get_fortran_c_namemangling()  { Line 707  get_fortran_c_namemangling()  {
707    
708      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""      #echo "FC_NAMEMANGLE = \"$FC_NAMEMANGLE\""
709      if test ! "x$FC_NAMEMANGLE" = x ; then      if test ! "x$FC_NAMEMANGLE" = x ; then
710          return 0          return 0
711      fi      fi
712      echo " running: get_fortran_c_namemangling()" >> $LOGFILE      echo " running: get_fortran_c_namemangling()" >> $LOGFILE
713    
# Line 784  EOF Line 839  EOF
839      RETVAL=$?      RETVAL=$?
840      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
841          HAVE_CLOC=t          HAVE_CLOC=t
         DEFINES="$DEFINES -DHAVE_CLOC"  
842      fi      fi
843      rm -f genmake_tc*      rm -f genmake_tc*
844      echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE      echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
# Line 846  EOF Line 900  EOF
900      RETVAL=$?      RETVAL=$?
901      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
902          HAVE_SIGREG=t          HAVE_SIGREG=t
         DEFINES="$DEFINES -DHAVE_SIGREG"  
903      fi      fi
904      rm -f genmake_tc*      rm -f genmake_tc*
905      echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE      echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
906  }  }
907    
908  check_HAVE_SETRLSTK()  {  check_HAVE_SETRLSTK()  {
     if test "x$HAVE_SETRLSTK" = xt ; then  
         DEFINES="$DEFINES -DHAVE_SETRLSTK"  
         return  
     fi    
909      if test ! "x$HAVE_SETRLSTK" = x ; then      if test ! "x$HAVE_SETRLSTK" = x ; then
910          return          return
911      fi      fi
# Line 894  EOF Line 943  EOF
943      RETVAL=$?      RETVAL=$?
944      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
945          HAVE_SETRLSTK=t          HAVE_SETRLSTK=t
         DEFINES="$DEFINES -DHAVE_SETRLSTK"  
946      fi      fi
947      rm -f genmake_tc*      rm -f genmake_tc*
948      echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE      echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
# Line 941  EOF Line 989  EOF
989      RETVAL=$?      RETVAL=$?
990      if test "x$RETVAL" = x0 ; then      if test "x$RETVAL" = x0 ; then
991          HAVE_STAT=t          HAVE_STAT=t
         DEFINES="$DEFINES -DHAVE_STAT"  
992      fi      fi
993      rm -f genmake_tc*      rm -f genmake_tc*
994      echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE      echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
# Line 957  check_netcdf_libs()  { Line 1004  check_netcdf_libs()  {
1004        program fgennc        program fgennc
1005  #include "netcdf.inc"  #include "netcdf.inc"
1006  EOF  EOF
1007      if test ! "x$MPI" = x ; then     #if test ! "x$MPI" = x ; then
1008          echo '#include "mpif.h"' >> genmake_tnc.F     #    echo '#include "mpif.h"' >> genmake_tnc.F
1009      fi     #fi
1010      cat <<EOF >> genmake_tnc.F      cat <<EOF >> genmake_tnc.F
1011        integer iret, ncid, xid        integer iret, ncid, xid
1012        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)        iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
# Line 1039  EOF Line 1086  EOF
1086      echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE      echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
1087  }  }
1088    
1089    check_lapack_libs()  {
1090        if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
1091        echo >> $LOGFILE
1092        echo "running: check_lapack_libs()" >> $LOGFILE
1093        cat <<EOF > genmake_tla.F
1094          program fgenla
1095          integer info
1096          integer ipiv( 2 )
1097          double precision ab( 4, 2 ), b( 2 )
1098          data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
1099          data b / 1., 1. /
1100          call dgbsv( 2, 1, 1, 1, ab, 4, ipiv, b, 2, info )
1101          IF (info .NE. 0) write(*,*) 'Error:', info
1102          write(*,*) b
1103          end
1104    EOF
1105        echo "===  genmake_tla.F  >>>" > genmake_tla.log
1106        cat genmake_tla.F >> genmake_tla.log
1107        echo "<<<  genmake_tla.F  ===" >> genmake_tla.log
1108        RET_CPP=f
1109        COMM="cat genmake_tla.F | $CPP $DEFINES $INCLUDES"
1110        echo "$COMM" >> genmake_tla.log
1111        eval $COMM > genmake_tla.$FS 2>/dev/null  &&  RET_CPP=t
1112        if test "x$RET_CPP" = xf ; then
1113            echo "  WARNING: CPP failed to pre-process the lapack test." \
1114                >> genmake_tla.log
1115            echo "    Please check that \$INCLUDES is properly set." \
1116                >> genmake_tla.log
1117        fi
1118        echo "$FC $FFLAGS $FOPTIM -c genmake_tla.$FS  \ " >> genmake_tla.log
1119        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tla.o $LIBS" >> genmake_tla.log
1120        $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1121            &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS >> genmake_tla.log 2>&1
1122        RET_COMPILE=$?
1123        cat genmake_tla.log >> $LOGFILE
1124    
1125        # test program execution not always possible (see check_netcdf_libs)
1126        #
1127        #test -x ./genmake_tla  &&  ./genmake_tla >> genmake_tla.log 2>&1
1128        #RETVAL=$?
1129        #if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
1130    
1131        if test "x$RET_COMPILE" = x0 ; then
1132            HAVE_LAPACK=t
1133            echo "check_lapack: successful" >> $LOGFILE
1134        else
1135            # try again with "-llapack" added to the libs
1136            echo "==> try again with added '-llapack'" > genmake_tla.log
1137            echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1138            echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1139            echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack" >> genmake_tla.log
1140            cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1141                &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1142                &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack >> genmake_tla.log 2>&1
1143            RET_COMPILE=$?
1144            echo >> $LOGFILE
1145            cat genmake_tla.log >> $LOGFILE
1146            if test "x$RET_COMPILE" = x0 ; then
1147                LIBS="$LIBS -llapack"
1148                HAVE_LAPACK=t
1149                echo "check_lapack: successful" >> $LOGFILE
1150            else
1151            # try again with "-lf77blas -lcblas" added to the libs
1152                echo "==> try again with added '-llapack -lf77blas -lcblas'" > genmake_tla.log
1153                echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1154                echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1155                echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas" >> genmake_tla.log
1156                cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1157                    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1158                    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas >> genmake_tla.log 2>&1
1159                RET_COMPILE=$?
1160                echo >> $LOGFILE
1161                cat genmake_tla.log >> $LOGFILE
1162                if test "x$RET_COMPILE" = x0 ; then
1163                    LIBS="$LIBS -llapack -lf77blas -lcblas"
1164                    HAVE_LAPACK=t
1165                    echo "check_lapack: successful" >> $LOGFILE
1166                else
1167                # try again with "-latlas" added to the libs
1168                    echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
1169                    echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
1170                    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
1171                    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
1172                    cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
1173                        &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
1174                        &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
1175                    RET_COMPILE=$?
1176                    echo >> $LOGFILE
1177                    cat genmake_tla.log >> $LOGFILE
1178                    if test "x$RET_COMPILE" = x0 ; then
1179                        LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
1180                        HAVE_LAPACK=t
1181                        echo "check_lapack: successful" >> $LOGFILE
1182                    fi
1183                fi
1184            fi
1185        fi
1186        rm -f genmake_tla*
1187        echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
1188    }
1189    
1190    check_HAVE_FLUSH()  {
1191        if test ! "x$SKIP_CHECK_FLUSH" = x ; then
1192            return
1193        fi
1194        echo >> $LOGFILE
1195        echo "running: check_HAVE_FLUSH()" >> $LOGFILE
1196        cat <<EOF > genmake_tflsh.$FS
1197          program fgenflsh
1198          integer iounit
1199          character*9 fname
1200          iounit = 26
1201          fname = 'tmp.tflsh'
1202          open(iounit,FILE=fname,STATUS='unknown')
1203          write(iounit,*) 'genmake_tflsh: hello'
1204          call flush(iounit)
1205          close(iounit)
1206          end
1207    EOF
1208        echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
1209        cat genmake_tflsh.$FS >> genmake_tflsh.log
1210        echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
1211    
1212        echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
1213        echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
1214        $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
1215            &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
1216        RET_COMPILE=$?
1217    
1218        if test "x$RET_COMPILE" = x0 ; then
1219            HAVE_FLUSH=t
1220            #cat genmake_tflsh.log >> $LOGFILE
1221            echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
1222        else
1223            HAVE_FLUSH=f
1224            cat genmake_tflsh.log >> $LOGFILE
1225        fi
1226        rm -f genmake_tflsh*
1227        echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
1228    }
1229    
1230  ###############################################################################  ###############################################################################
1231  #   Sequential part of script starts here  #   Sequential part of script starts here
# Line 1096  GSL= Line 1283  GSL=
1283  DEVEL=  DEVEL=
1284  HAVE_TEST_L=  HAVE_TEST_L=
1285    
1286    # set this to "t" to enable lapack test
1287    CHECK_FOR_LAPACK=f
1288    
1289  # DEFINES checked by test compilation or command-line  # DEFINES checked by test compilation or command-line
1290  HAVE_SYSTEM=  HAVE_SYSTEM=
1291  HAVE_FDATE=  HAVE_FDATE=
# Line 1106  HAVE_STAT= Line 1296  HAVE_STAT=
1296  HAVE_NETCDF=  HAVE_NETCDF=
1297  HAVE_ETIME=  HAVE_ETIME=
1298  IGNORE_TIME=  IGNORE_TIME=
1299    HAVE_LAPACK=
1300    HAVE_FLUSH=
1301    
1302  MODS=  MODS=
1303  TOOLSDIR=  TOOLSDIR=
# Line 1113  SOURCEDIRS= Line 1305  SOURCEDIRS=
1305  INCLUDEDIRS=  INCLUDEDIRS=
1306  STANDARDDIRS="USE_THE_DEFAULT"  STANDARDDIRS="USE_THE_DEFAULT"
1307    
1308    #- local config file
1309    gm_local="genmake_local"
1310    
1311  G2ARGS=  G2ARGS=
1312  BASH=  BASH=
1313  PWD=`pwd`  PWD=`pwd`
# Line 1136  FS= Line 1331  FS=
1331  FS90=  FS90=
1332    
1333  AUTODIFF_PKG_USED=f  AUTODIFF_PKG_USED=f
1334    OPENAD=
1335  AD_OPTFILE=  AD_OPTFILE=
1336    CAT_SRC_FOR_TAF=1
1337  TAF=  TAF=
1338  AD_TAF_FLAGS=  AD_TAF_FLAGS=
1339  FTL_TAF_FLAGS=  FTL_TAF_FLAGS=
# Line 1148  FTL_TAF_FLAGS= Line 1345  FTL_TAF_FLAGS=
1345  SVD_TAMC_FLAGS=  SVD_TAMC_FLAGS=
1346  TAMC_EXTRA=  TAMC_EXTRA=
1347    
1348    DIVA=
1349    MPIINCLUDEDIR=
1350    MPI_HEADER_FILES=
1351    LOCAL_MPI_HEADERS=
1352    
1353  #  The following state can be set directly by command-line switches  #  The following state can be set directly by command-line switches
1354  gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS DISABLE ENABLE MAKEFILE MAKEDEPEND PLATFORM"  gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
1355  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"
1356  gm_s3="ROOTDIR STANDARDDIRS MODS DUMPSTATE"  gm_s3="FEXTRAFLAGS IEEE DEVEL GSL TS PAPIS PCLS PAPI PCL HPMT DUMPSTATE"
1357    
1358  #  The following state is not directly set by command-line switches  #  The following state is not directly set by command-line switches
1359  gm_s4="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM"  gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
1360  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"  gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
1361  gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"  gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
1362  gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"  gm_s7="TMP THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
1363  gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"  gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
1364    
1365  #  The following are all related to adjoint/tangent-linear stuff  #  The following are all related to adjoint/tangent-linear stuff
1366  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"
1367  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"
1368  gm_s12="TAF_EXTRA TAMC_EXTRA"  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
1369    
1370  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 $gm_s8"
1371  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"  gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
# Line 1184  LOGFILE="genmake.log" Line 1386  LOGFILE="genmake.log"
1386  rm -f genmake_state genmake_*optfile $LOGFILE  rm -f genmake_state genmake_*optfile $LOGFILE
1387    
1388  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  
1389    
1390  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"  #echo "$0::$1:$2:$3:$4:$5:$6:$7:"
1391  #parse_options  #parse_options
# Line 1212  for ac_option in "$@" ; do Line 1404  for ac_option in "$@" ; do
1404      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`      ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
1405    
1406      case $ac_option in      case $ac_option in
1407            
1408          -help | --help | -h | --h)          -help | --help | -h | --h)
1409              usage ;;              usage ;;
1410            
         -nooptfile | --nooptfile)  
             OPTFILE="NONE" ;;  
1411          -optfile | --optfile | -of | --of)          -optfile | --optfile | -of | --of)
1412              ac_prev=OPTFILE ;;              ac_prev=OPTFILE ;;
1413          -optfile=* | --optfile=* | -of=* | --of=*)          -optfile=* | --optfile=* | -of=* | --of=*)
1414              OPTFILE=$ac_optarg ;;              OPTFILE=$ac_optarg ;;
1415            
1416            -oad | --oad)
1417                OPENAD="true" ; ALWAYS_USE_F90=1 ;;
1418            -nocat4ad | -dog4ad | -ncad | -dad)
1419                CAT_SRC_FOR_TAF=0 ;;
1420          -adoptfile | --adoptfile | -adof | --adof)          -adoptfile | --adoptfile | -adof | --adof)
1421              ac_prev=AD_OPTFILE ;;              ac_prev=AD_OPTFILE ;;
1422          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
1423              AD_OPTFILE=$ac_optarg ;;              AD_OPTFILE=$ac_optarg ;;
1424            
1425          -pdepend | --pdepend)          -pdepend | --pdepend)
1426              ac_prev=PKG_DEPEND ;;              ac_prev=PKG_DEPEND ;;
1427          -pdepend=* | --pdepend=*)          -pdepend=* | --pdepend=*)
1428              PKG_DEPEND=$ac_optarg ;;              PKG_DEPEND=$ac_optarg ;;
1429            
1430          -pgroups | --pgroups)          -pgroups | --pgroups)
1431              ac_prev=PKG_GROUPS ;;              ac_prev=PKG_GROUPS ;;
1432          -pgroups=* | --pgroups=*)          -pgroups=* | --pgroups=*)
1433              PKG_GROUPS=$ac_optarg ;;              PKG_GROUPS=$ac_optarg ;;
1434            
1435          -make | --make | -m | --m)          -make | --make | -m | --m)
1436              ac_prev=MAKE ;;              ac_prev=MAKE ;;
1437          -make=* | --make=* | -m=* | --m=*)          -make=* | --make=* | -m=* | --m=*)
1438              MAKE=$ac_optarg ;;              MAKE=$ac_optarg ;;
1439            
1440          -bash | --bash)          -bash | --bash)
1441              ac_prev=BASH ;;              ac_prev=BASH ;;
1442          -bash=* | --bash=*)          -bash=* | --bash=*)
1443              BASH=$ac_optarg ;;              BASH=$ac_optarg ;;
1444            
1445          -makedepend | --makedepend | -md | --md)          -makedepend | --makedepend | -md | --md)
1446              ac_prev=MAKEDEPEND ;;              ac_prev=MAKEDEPEND ;;
1447          -makedepend=* | --makedepend=* | -md=* | --md=*)          -makedepend=* | --makedepend=* | -md=* | --md=*)
1448              MAKEDEPEND=$ac_optarg ;;              MAKEDEPEND=$ac_optarg ;;
1449            
1450          -makefile | --makefile | -ma | --ma)          -makefile | --makefile | -mf | --mf)
1451              ac_prev=MAKEFILE ;;              ac_prev=MAKEFILE ;;
1452          -makefile=* | --makefile=* | -ma=* | --ma=*)          -makefile=* | --makefile=* | -mf=* | --mf=*)
1453              MAKEFILE=$ac_optarg ;;              MAKEFILE=$ac_optarg ;;
1454            
1455          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)          -platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
1456              echo "ERROR: The platform option has been removed.  Please specify"              echo "ERROR: The platform option has been removed.  Please specify"
1457              echo "  the build options using the \"optfile\" mechanism."              echo "  the build options using the \"optfile\" mechanism."
1458              echo              echo
1459              usage              usage
1460              ;;              ;;
1461            
1462          -rootdir | --rootdir | -rd | --rd)          -rootdir | --rootdir | -rd | --rd)
1463              ac_prev=ROOTDIR ;;              ac_prev=ROOTDIR ;;
1464          -rootdir=* | --rootdir=* | -rd=* | --rd=*)          -rootdir=* | --rootdir=* | -rd=* | --rd=*)
1465              ROOTDIR=$ac_optarg ;;              ROOTDIR=$ac_optarg ;;
1466            
1467          -mods | --mods | -mo | --mo)          -mods | --mods | -mo | --mo)
1468              ac_prev=MODS ;;              ac_prev=MODS ;;
1469          -mods=* | --mods=* | -mo=* | --mo=*)          -mods=* | --mods=* | -mo=* | --mo=*)
1470              MODS=$ac_optarg ;;              MODS=$ac_optarg ;;
1471            
1472          -disable | --disable)          -disable | --disable)
1473              ac_prev=DISABLE ;;              ac_prev=DISABLE ;;
1474          -disable=* | --disable=*)          -disable=* | --disable=*)
1475              DISABLE=$ac_optarg ;;              DISABLE=$ac_optarg ;;
1476            
1477          -enable | --enable)          -enable | --enable)
1478              ac_prev=ENABLE ;;              ac_prev=ENABLE ;;
1479          -enable=* | --enable=*)          -enable=* | --enable=*)
1480              ENABLE=$ac_optarg ;;              ENABLE=$ac_optarg ;;
1481            
1482          -standarddirs | --standarddirs)          -standarddirs | --standarddirs)
1483              ac_prev=STANDARDDIRS ;;              ac_prev=STANDARDDIRS ;;
1484          -standarddirs=* | --standarddirs=*)          -standarddirs=* | --standarddirs=*)
# Line 1294  for ac_option in "$@" ; do Line 1488  for ac_option in "$@" ; do
1488  #               ac_prev=cpp ;;  #               ac_prev=cpp ;;
1489  #           -cpp=* | --cpp=*)  #           -cpp=* | --cpp=*)
1490  #               CPP=$ac_optarg ;;  #               CPP=$ac_optarg ;;
1491            
1492          -cc | --cc)          -cc | --cc)
1493              ac_prev=CC ;;              ac_prev=CC ;;
1494          -cc=* | --cc=*)          -cc=* | --cc=*)
1495              CC=$ac_optarg ;;              CC=$ac_optarg ;;
1496            
1497          -fortran | --fortran | -fc | --fc)          -fortran | --fortran | -fc | --fc)
1498              ac_prev=FC ;;              ac_prev=FC ;;
1499          -fc=* | --fc=*)          -fc=* | --fc=*)
1500              FC=$ac_optarg ;;              FC=$ac_optarg ;;
1501            
1502          -fs | --fs)          -fs | --fs)
1503              ac_prev=FS ;;              ac_prev=FS ;;
1504          -fs=* | --fs=*)          -fs=* | --fs=*)
1505              FS=$ac_optarg ;;              FS=$ac_optarg ;;
1506            
1507          -fs90 | --fs90)          -fs90 | --fs90)
1508              ac_prev=FS90 ;;              ac_prev=FS90 ;;
1509          -fs90=* | --fs90=*)          -fs90=* | --fs90=*)
1510              FS90=$ac_optarg ;;              FS90=$ac_optarg ;;
1511            
1512          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )          -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
1513              USE_R4=true ;;              USE_R4=true ;;
1514    
# Line 1322  for ac_option in "$@" ; do Line 1516  for ac_option in "$@" ; do
1516              IEEE=true ;;              IEEE=true ;;
1517          -noieee | --noieee)          -noieee | --noieee)
1518              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;              echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
1519          -devel | --devel)          -devel | --devel)
1520              IEEE=true ; DEVEL=true ;;              IEEE=true ; DEVEL=true ;;
1521          -gsl | --gsl)          -gsl | --gsl)
1522              GSL=true ;;              GSL=true ;;
1523    
1524          -ts | --ts)          -ts | --ts)
# Line 1347  for ac_option in "$@" ; do Line 1541  for ac_option in "$@" ; do
1541          -mpi=* | --mpi=*)          -mpi=* | --mpi=*)
1542              MPIPATH=$ac_optarg              MPIPATH=$ac_optarg
1543              MPI=true ;;              MPI=true ;;
1544            
1545          -omp | --omp)          -omp | --omp)
1546              OMP=true ;;              OMP=true ;;
1547          -omp=* | --omp=*)          -omp=* | --omp=*)
1548              OMPFLAG=$ac_optarg              OMPFLAG=$ac_optarg
1549              OMP=true ;;              OMP=true ;;
1550            
1551          -ds | --ds)          -ds | --ds)
1552              DUMPSTATE=t ;;              DUMPSTATE=t ;;
1553            
1554          -extra_flag | --extra_flag)          -extra_flag | --extra_flag)
1555              ac_prev=FEXTRAFLAGS ;;              ac_prev=FEXTRAFLAGS ;;
1556          -extra_flag=* | --extra_flag=*)          -extra_flag=* | --extra_flag=*)
1557              FEXTRAFLAGS=$ac_optarg ;;              FEXTRAFLAGS=$ac_optarg ;;
1558            
1559          -taf_extra | --taf_extra)          -taf_extra | --taf_extra)
1560              ac_prev=TAF_EXTRA ;;              ac_prev=TAF_EXTRA ;;
1561          -taf_extra=* | --taf_extra=*)          -taf_extra=* | --taf_extra=*)
# Line 1371  for ac_option in "$@" ; do Line 1565  for ac_option in "$@" ; do
1565              ac_prev=TAMC_EXTRA ;;              ac_prev=TAMC_EXTRA ;;
1566          -tamc_extra=* | --tamc_extra=*)          -tamc_extra=* | --tamc_extra=*)
1567              TAMC_EXTRA=$ac_optarg ;;              TAMC_EXTRA=$ac_optarg ;;
1568            
1569          -ignoretime | -ignore_time | --ignoretime | --ignore_time)          -ignoretime | -ignore_time | --ignoretime | --ignore_time)
1570              IGNORE_TIME="-DIGNORE_TIME" ;;              IGNORE_TIME="-DIGNORE_TIME" ;;
1571    
# Line 1382  for ac_option in "$@" ; do Line 1576  for ac_option in "$@" ; do
1576              echo "Error: unrecognized option: "$ac_option              echo "Error: unrecognized option: "$ac_option
1577              usage              usage
1578              ;;              ;;
1579            
1580          *)          *)
1581              echo "Error: unrecognized argument: "$ac_option              echo "Error: unrecognized argument: "$ac_option
1582              usage              usage
1583              ;;              ;;
1584            
1585      esac      esac
1586    
1587  done  done
1588    
1589    #TMP=./genmk_$$
1590    #- try to put temporary files in system-local /tmp dir
1591    TMP=/tmp/genmk_${USER}_$$
1592    touch $TMP ; retVal=$?
1593    if [ $retVal -eq 0 ] ; then
1594      if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
1595    else
1596      TMP=./genmk_$$
1597    fi
1598    rm -f $TMP
1599    #echo "  temp files: $TMP.*"
1600    
1601    printf "  getting local config information:  "
1602    if test -f $gm_local ; then
1603        echo "using $gm_local"
1604        . $gm_local
1605    else
1606        echo "none found"
1607    fi
1608    
1609  if test -f ./.genmakerc ; then  if test -f ./.genmakerc ; then
1610      echo      echo
1611      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""      echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
# Line 1476  fi Line 1690  fi
1690    
1691  echo "  getting AD_OPTFILE information:"  echo "  getting AD_OPTFILE information:"
1692  if test "x${AD_OPTFILE}" = x ; then  if test "x${AD_OPTFILE}" = x ; then
1693      if test "x$MITGCM_AD_OF" = x ; then      if test "x$MITGCM_AD_OF" != x ; then
1694            AD_OPTFILE=$MITGCM_AD_OF
1695        elif test "x$OPENAD" = x ; then
1696          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
1697      else      else
1698          AD_OPTFILE=$MITGCM_AD_OF          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
1699      fi      fi
1700  fi  fi
1701  if test "x${AD_OPTFILE}" != xNONE ; then  if test "x${AD_OPTFILE}" != xNONE ; then
# Line 1502  if test "x${AD_OPTFILE}" != xNONE ; then Line 1718  if test "x${AD_OPTFILE}" != xNONE ; then
1718  fi  fi
1719    
1720  #====================================================================  #====================================================================
1721    # Initialize INCLUDEDIRSMK from and optfile INCLUDEDIRS
1722    if test "x${INCLUDEDIRS}" != "x" ; then
1723     INCLUDEDIRSMK=${INCLUDEDIRS}
1724    fi
1725    
1726    #====================================================================
1727  #  Set default values if not set by the optfile  #  Set default values if not set by the optfile
1728  #  #
1729  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
# Line 1603  check_for_broken_Ff Line 1825  check_for_broken_Ff
1825    
1826  if test ! "x$MPI" = x ; then  if test ! "x$MPI" = x ; then
1827        echo "  Turning on MPI cpp macros"        echo "  Turning on MPI cpp macros"
1828        DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"        DEFINES="$DEFINES -DALLOW_USE_MPI"
1829    #- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
1830    #     DEFINES="$DEFINES -DALWAYS_USE_MPI"
1831  fi  fi
1832  if test ! "x$OMP" = x ; then  if test ! "x$OMP" = x ; then
1833        echo "  Add OMPFLAG and turn on OpenMP cpp macros"        echo "  Add OMPFLAG and turn on OpenMP cpp macros"
# Line 1620  fi Line 1844  fi
1844  if test ! "x$TS" = x ; then  if test ! "x$TS" = x ; then
1845        echo "  Turning on timing per timestep"        echo "  Turning on timing per timestep"
1846        if test ! "x$FOOLAD" = x ; then        if test ! "x$FOOLAD" = x ; then
1847              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP_SFP"
1848        else        else
1849              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"              DEFINES="$DEFINES -DTIME_PER_TIMESTEP"
1850        fi        fi
# Line 1656  if test ! "x$PAPI" = x ; then Line 1880  if test ! "x$PAPI" = x ; then
1880            echo "  Sticking with PAPI flop summary per timestep!"            echo "  Sticking with PAPI flop summary per timestep!"
1881        else        else
1882            echo "  Turning on performance analysis with PAPI"            echo "  Turning on performance analysis with PAPI"
1883            echo "  Please make sure PAPIINC, PAPILIB are defined"            echo "  Please make sure PAPIINC, PAPILIB are defined"
1884            DEFINES="$DEFINES -DUSE_PAPI"            DEFINES="$DEFINES -DUSE_PAPI"
1885            INCLUDES="$INCLUDES $PAPIINC"            INCLUDES="$INCLUDES $PAPIINC"
1886            LIBS="$LIBS $PAPILIB"            LIBS="$LIBS $PAPILIB"
# Line 1668  if test ! "x$PCL" = x ; then Line 1892  if test ! "x$PCL" = x ; then
1892            echo "  Sticking with PCL flop summary per timestep!"            echo "  Sticking with PCL flop summary per timestep!"
1893        else        else
1894            echo "  Turning on performance analysis with PCL"            echo "  Turning on performance analysis with PCL"
1895            echo "  Please make sure PCLINC, PCLLIB are defined"            echo "  Please make sure PCLINC, PCLLIB are defined"
1896            DEFINES="$DEFINES -DUSE_PCL"            DEFINES="$DEFINES -DUSE_PCL"
1897            INCLUDES="$INCLUDES $PCLINC"            INCLUDES="$INCLUDES $PCLINC"
1898            LIBS="$LIBS $PCLLIB"            LIBS="$LIBS $PCLLIB"
# Line 1678  if test ! "x$HPMT" = x ; then Line 1902  if test ! "x$HPMT" = x ; then
1902        if test ! "x$PAPI" = x ; then        if test ! "x$PAPI" = x ; then
1903            echo "  PAPI and the HPM Toolkit cannot co-exist!"            echo "  PAPI and the HPM Toolkit cannot co-exist!"
1904            echo "  Sticking with PAPI!"            echo "  Sticking with PAPI!"
1905        else if test ! "x$PCL" = x ; then        else
1906            if test ! "x$PCL" = x ; then
1907            echo "  PCL and the HPM Toolkit cannot co-exist!"            echo "  PCL and the HPM Toolkit cannot co-exist!"
1908            echo "  Sticking with PCL!"            echo "  Sticking with PCL!"
1909        else          else
1910            echo "  Turning on performance analysis with the HPM Toolkit"            echo "  Turning on performance analysis with the HPM Toolkit"
1911            echo "  Please make sure HPMTINC, HPMTLIB are defined"            echo "  Please make sure HPMTINC, HPMTLIB are defined"
1912            DEFINES="$DEFINES -DUSE_LIBHPM"            DEFINES="$DEFINES -DUSE_LIBHPM"
1913            INCLUDES="$INCLUDES $HPMTINC"            INCLUDES="$INCLUDES $HPMTINC"
1914            LIBS="$LIBS $HPMTLIB"            LIBS="$LIBS $HPMTLIB"
1915        fi          fi
1916        fi        fi
1917  fi  fi
1918  if test ! "x$GSL" = x ; then  if test ! "x$GSL" = x ; then
# Line 1743  else Line 1968  else
1968  fi  fi
1969  rm -f genmake_tcomp*  rm -f genmake_tcomp*
1970    
1971  printf "  Do we have the etime() command using $FC...  "  printf "  Do we have the etime() command using $FC... "
1972  cat > genmake_tcomp.$FS <<EOF  cat > genmake_tcomp_1.$FS <<EOF
1973        program hello        program hello
1974        REAL*4 ACTUAL, TARRAY(2)        REAL*4 actual, tarray(2)
1975        EXTERNAL ETIME        EXTERNAL ETIME
1976        REAL*4 ETIME        REAL*4 ETIME
1977        actual = etime( tarray )        actual = ETIME( tarray )
1978        print *, tarray        print *, tarray
1979        end        end
1980  EOF  EOF
1981  $FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1  $FC $FFLAGS -o genmake_tcomp_1 genmake_tcomp_1.$FS > genmake_tcomp.log 2>&1
1982  RETVAL=$?  RETVAL=$?
1983  if test "x$RETVAL" = x0 ; then  if test "x$RETVAL" = x0 ; then
1984      HAVE_ETIME=t      HAVE_ETIME='Fct'
1985      DEFINES="$DEFINES -DHAVE_ETIME"      DEFINES="$DEFINES -DHAVE_ETIME_FCT"
1986      echo "yes"      echo " yes (${HAVE_ETIME})"
1987  else  else
1988      cat > genmake_tcomp_2.$FS <<EOF
1989          program hello
1990          REAL*4 actual, tarray(2)
1991          actual = -999.
1992          call ETIME( tarray, actual )
1993          if ( actual.ge.0. ) then
1994            print *, 0, tarray, actual
1995          else
1996            print *, 1, tarray, actual
1997          endif
1998          end
1999    EOF
2000      $FC $FFLAGS -o genmake_tcomp_2 genmake_tcomp_2.$FS >> genmake_tcomp.log 2>&1
2001      RETVAL=$?
2002      if test "x$RETVAL" = x0 ; then
2003        echo -n 'c,'
2004        ./genmake_tcomp_2 > genmake_tcomp_2.out 2>&1
2005        RETVAL=$?
2006      fi
2007      if test "x$RETVAL" = x0 ; then
2008        echo -n 'r:'
2009        RETVAL=`cat genmake_tcomp_2.out | $AWK '{print $1}'`
2010      fi
2011      if test "x$RETVAL" = x0 ; then
2012        HAVE_ETIME='SbR'
2013        DEFINES="$DEFINES -DHAVE_ETIME_SBR"
2014        echo " yes (${HAVE_ETIME})"
2015      else
2016      HAVE_ETIME=      HAVE_ETIME=
2017      echo "no"      echo " no"
2018      fi
2019  fi  fi
2020    #mkdir chk_etime ; cp -p -f genmake_tcomp* chk_etime
2021  rm -f genmake_tcomp*  rm -f genmake_tcomp*
2022    
2023  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
2024  check_HAVE_CLOC  check_HAVE_CLOC
2025  if test "x$HAVE_CLOC" != x ; then  if test "x$HAVE_CLOC" != x ; then
2026        DEFINES="$DEFINES -DHAVE_CLOC"
2027      echo "yes"      echo "yes"
2028  else  else
2029      echo "no"      echo "no"
# Line 1782  rm -f genmake_t* Line 2038  rm -f genmake_t*
2038  printf "  Can we unlimit the stack size using $FC...  "  printf "  Can we unlimit the stack size using $FC...  "
2039  check_HAVE_SETRLSTK  check_HAVE_SETRLSTK
2040  if test "x$HAVE_SETRLSTK" = xt ; then  if test "x$HAVE_SETRLSTK" = xt ; then
2041        DEFINES="$DEFINES -DHAVE_SETRLSTK"
2042      echo "yes"      echo "yes"
2043  else  else
2044      echo "no"      echo "no"
# Line 1791  rm -f genmake_t* Line 2048  rm -f genmake_t*
2048  printf "  Can we register a signal handler using $FC...  "  printf "  Can we register a signal handler using $FC...  "
2049  check_HAVE_SIGREG  check_HAVE_SIGREG
2050  if test "x$HAVE_SIGREG" = xt ; then  if test "x$HAVE_SIGREG" = xt ; then
2051        DEFINES="$DEFINES -DHAVE_SIGREG"
2052      echo "yes"      echo "yes"
2053  else  else
2054      echo "no"      echo "no"
# Line 1800  rm -f genmake_t* Line 2058  rm -f genmake_t*
2058  printf "  Can we use stat() through C calls...  "  printf "  Can we use stat() through C calls...  "
2059  check_HAVE_STAT  check_HAVE_STAT
2060  if test "x$HAVE_STAT" != x ; then  if test "x$HAVE_STAT" != x ; then
2061        DEFINES="$DEFINES -DHAVE_STAT"
2062      echo "yes"      echo "yes"
2063  else  else
2064      echo "no"      echo "no"
# Line 1809  rm -f genmake_t* Line 2068  rm -f genmake_t*
2068  printf "  Can we create NetCDF-enabled binaries...  "  printf "  Can we create NetCDF-enabled binaries...  "
2069  check_netcdf_libs  check_netcdf_libs
2070  if test "x$HAVE_NETCDF" != x ; then  if test "x$HAVE_NETCDF" != x ; then
2071        DEFINES="$DEFINES -DHAVE_NETCDF"
2072      echo "yes"      echo "yes"
2073  else  else
2074      echo "no"      echo "no"
2075  fi  fi
 DEFINES="$DEFINES $IGNORE_TIME"  
2076    
2077    printf "  Can we create LAPACK-enabled binaries...  "
2078    check_lapack_libs
2079    if test "x$HAVE_LAPACK" != x ; then
2080        DEFINES="$DEFINES -DHAVE_LAPACK"
2081        echo "yes"
2082    else
2083        echo "no"
2084    fi
2085    
2086    printf "  Can we call FLUSH intrinsic subroutine...  "
2087    check_HAVE_FLUSH
2088    if test "x$HAVE_FLUSH" = xt ; then
2089        DEFINES="$DEFINES -DHAVE_FLUSH"
2090        echo "yes"
2091    else
2092        echo "no"
2093    fi
2094    
2095    DEFINES="$DEFINES $IGNORE_TIME"
2096  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2097      build_embed_encode      build_embed_encode
2098  fi  fi
2099  if test "x$EMBED_SRC" = xt ; then  if test "x$EMBED_SRC" = xt ; then
2100      ENABLE="$ENABLE embed_files"      ENABLE="$ENABLE embed_files"
2101    #   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
2102  fi  fi
2103    
2104  printf "\n===  Setting defaults  ===\n"  printf "\n===  Setting defaults  ===\n"
# Line 1833  for d in $MODS ; do Line 2112  for d in $MODS ; do
2112          printf "$d "          printf "$d "
2113          SOURCEDIRS="$SOURCEDIRS $d"          SOURCEDIRS="$SOURCEDIRS $d"
2114          INCLUDEDIRS="$INCLUDEDIRS $d"          INCLUDEDIRS="$INCLUDEDIRS $d"
2115            SOURCEDIRSMK="$SOURCEDIRSMK $d"
2116            INCLUDEDIRSMK="$INCLUDEDIRSMK $d"
2117      fi      fi
2118  done  done
2119  echo  echo
# Line 1856  fi Line 2137  fi
2137    
2138  if test "x${TOOLSDIR}" = x ; then  if test "x${TOOLSDIR}" = x ; then
2139      TOOLSDIR="$ROOTDIR/tools"      TOOLSDIR="$ROOTDIR/tools"
2140        TOOLSDIRMK='$(ROOTDIR)'"/tools"
2141    else
2142        TOOLSDIRMK=${TOOLSDIR}
2143  fi  fi
2144  if test ! -d ${TOOLSDIR} ; then  if test ! -d ${TOOLSDIR} ; then
2145      echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"      echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
# Line 1997  else Line 2281  else
2281          exit 1          exit 1
2282      else      else
2283          echo "    using PKG_LIST=\"$PKG_LIST\""          echo "    using PKG_LIST=\"$PKG_LIST\""
2284          #  Strip the comments and add all the names          #  Strip the comments and add all the names
2285          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 $0}'`
2286          RETVAL=$?          RETVAL=$?
2287          if test "x${RETVAL}" != x0 ; then          if test "x${RETVAL}" != x0 ; then
# Line 2018  if test "x${PKG_GROUPS}" != x ; then Line 2302  if test "x${PKG_GROUPS}" != x ; then
2302  fi  fi
2303    
2304  echo "  applying DISABLE settings"  echo "  applying DISABLE settings"
2305  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2306  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2307      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2308  done  done
2309  for i in `grep  "-" ./.tmp_pack` ; do  for i in `grep  "-" $TMP.pack` ; do
2310      j=`echo $i | sed 's/[-]//'`      j=`echo $i | sed 's/[-]//'`
2311      DISABLE="$DISABLE $j"      DISABLE="$DISABLE $j"
2312  done  done
# Line 2040  for p in $PACKAGES ; do Line 2324  for p in $PACKAGES ; do
2324  done  done
2325  PACKAGES="$pack"  PACKAGES="$pack"
2326  echo "  applying ENABLE settings"  echo "  applying ENABLE settings"
2327  echo "" > ./.tmp_pack  echo "" > $TMP.pack
2328  PACKAGES="$PACKAGES $ENABLE"  PACKAGES="$PACKAGES $ENABLE"
2329  # Test if each explicitly referenced package exists  # Test if each explicitly referenced package exists
2330  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2331      j=`echo $i | sed 's/[-+]//'`      j=`echo $i | sed 's/[-+]//'`
2332      if test ! -d "$ROOTDIR/pkg/$j" ; then      if test ! -d "$ROOTDIR/pkg/$j" ; then
2333          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"          echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
2334          exit 1          exit 1
2335      fi      fi
2336      echo $i >> ./.tmp_pack      echo $i >> $TMP.pack
2337  done  done
2338  PACKAGES=  PACKAGES=
2339  for i in `grep -v "-" ./.tmp_pack | sort | uniq` ; do  for i in `grep -v "-" $TMP.pack | sort | uniq` ; do
2340      PACKAGES="$PACKAGES $i"      PACKAGES="$PACKAGES $i"
2341  done  done
2342  rm -f ./.tmp_pack  rm -f $TMP.pack
2343  echo "    packages are: $PACKAGES"  echo "    packages are: $PACKAGES"
2344    
2345  #  Check for package MNC: if NetCDF is available, then build the MNC  #  Check for package MNC: if NetCDF is available, then build the MNC
# Line 2092  else Line 2376  else
2376          echo "Error: problem encountered while building source files in pkg/mnc:"          echo "Error: problem encountered while building source files in pkg/mnc:"
2377          cat make_mnc.errors 1>&2          cat make_mnc.errors 1>&2
2378          if test "x$mnc_in" = x0 ; then          if test "x$mnc_in" = x0 ; then
2379              exit 1              exit 1
2380          else          else
2381              DISABLE="$DISABLE mnc"              DISABLE="$DISABLE mnc"
2382          fi          fi
# Line 2125  EOF Line 2409  EOF
2409      fi      fi
2410  fi  fi
2411    
2412    #  Make sure the openad package is enabled if using OpenAD
2413    if test "x$OPENAD" != x ; then
2414        echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
2415        RETVAL=$?
2416        if test "x$RETVAL" != x0 ; then
2417            cat <<EOF
2418    
2419    *********************************************************************
2420    ERROR: when generating an adjoint with OpenAD, the openad package
2421      must be enabled.  Please add it to packages.conf.
2422    *********************************************************************
2423    
2424    EOF
2425            exit 1
2426        fi
2427    fi
2428    
2429  if  test "x${PKG_DEPEND}" != x ; then  if  test "x${PKG_DEPEND}" != x ; then
2430    echo "  applying package dependency rules"    echo "  applying package dependency rules"
2431    ck=    ck=
# Line 2149  if  test "x${PKG_DEPEND}" != x ; then Line 2450  if  test "x${PKG_DEPEND}" != x ; then
2450              if test "x$p" = "x$pname" ; then pin="t" ; fi              if test "x$p" = "x$pname" ; then pin="t" ; fi
2451          done          done
2452    
2453          #  Is the DNAME entry a (+) or (-) rule ?          #  Is the DNAME entry a (=), (+) or (-) rule ?
2454          tmp="dname=\"\$DNAME_$i\""          tmp="dname=\"\$DNAME_$i\""
2455          eval $tmp          eval $tmp
2456          plus="-"          plus="a"
2457          echo $dname | grep '^+' > /dev/null 2>&1          echo $dname | grep '^+' > /dev/null 2>&1
2458          RETVAL=$?          RETVAL=$?
2459          if test "x$RETVAL" = x0 ; then          if test "x$RETVAL" = x0 ; then plus="+" ; fi
2460              plus="+"          echo $dname | grep '^-' > /dev/null 2>&1
2461          fi          RETVAL=$?
2462            if test "x$RETVAL" = x0 ; then plus="-" ; fi
2463    
2464          #  Is $dname in the current $PACKAGES list?          #  Is $dname in the current $PACKAGES list?
2465          dname=`echo $dname | sed -e 's/^[+-]//'`          dname=`echo $dname | sed -e 's/^[=+-]//'`
2466          din="f"          din="f"
2467          for p in $PACKAGES ; do          for p in $PACKAGES ; do
2468              if test "x$p" = "x$dname" ; then              if test "x$p" = "x$dname" ; then
# Line 2169  if  test "x${PKG_DEPEND}" != x ; then Line 2471  if  test "x${PKG_DEPEND}" != x ; then
2471          done          done
2472    
2473          #  Do we need to add $dname according to the dependency rules?          #  Do we need to add $dname according to the dependency rules?
2474          if test "x$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
2475              #echo "   " $pname ": need to add :" $dname              #echo "   " $pname ": need to add :" $dname
2476              in_dis="f"              in_dis="f"
2477              for dis in $DISABLE ; do              for dis in $DISABLE ; do
2478                  if test "x$dis" = "x$dname" ; then                  if test "x$dis" = "x$dname" ; then
# Line 2178  if  test "x${PKG_DEPEND}" != x ; then Line 2480  if  test "x${PKG_DEPEND}" != x ; then
2480                  fi                  fi
2481              done              done
2482              if test "x$in_dis" = xt ; then              if test "x$in_dis" = xt ; then
2483                  echo "Error: can't satisfy package dependencies:"                  if test "x$plus" = "x+" ; then
2484                  echo "  \"$dname\" is required by the dependency rules"                      echo "Error: can't satisfy package dependencies:"
2485                  echo "  but is disallowed by the DISABLE settings"                      echo "  \"$dname\" is required with pkg \"$pname\" (dependency rules)"
2486                  exit 1                      echo "  but is disallowed by the DISABLE settings"
2487                        exit 1
2488                    elif test "x$ck" = xt ; then
2489                    #- (=) is a weaker dependency rule: warning but no stop
2490                        echo    "Warning: pkg \"$dname\" is set DISABLE (from: \"$PKG_LIST\")"
2491                        echo -n "     but is recommended with pkg \"$pname\" (dependency rules)"
2492                        echo " <- ignores recommendation"
2493                    fi
2494              else              else
2495                  PACKAGES="$PACKAGES $dname"                  PACKAGES="$PACKAGES $dname"
2496                  ck=                  ck=
# Line 2191  if  test "x${PKG_DEPEND}" != x ; then Line 2500  if  test "x${PKG_DEPEND}" != x ; then
2500          #  Do we need to get rid of $dname according to the dependency rules?          #  Do we need to get rid of $dname according to the dependency rules?
2501          if test "x$pin" = xt -a "x$plus" = "x-" -a "x$din" = xt; then          if test "x$pin" = xt -a "x$plus" = "x-" -a "x$din" = xt; then
2502              echo "Error: can't satisfy package dependencies:"              echo "Error: can't satisfy package dependencies:"
2503              echo "  \"$pname\" was requested but is disallowed by"              echo "  \"$dname\" was requested but is disallowed by"
2504              echo "  the dependency rules for \"$dname\""              echo "  the dependency rules for \"$pname\""
2505              exit 1              exit 1
2506          fi          fi
2507          i=`echo "$i + 1" | bc -l`          i=`expr $i + 1`
2508          #i=$(( $i + 1 ))          #i=`echo "$i + 1" | bc -l`
2509      done      done
2510      ck=$ck"t"      ck=$ck"t"
2511    done    done
# Line 2204  if  test "x${PKG_DEPEND}" != x ; then Line 2513  if  test "x${PKG_DEPEND}" != x ; then
2513  fi  fi
2514  for i in $PACKAGES ; do  for i in $PACKAGES ; do
2515      adr="$ROOTDIR/pkg/$i"      adr="$ROOTDIR/pkg/$i"
2516        adrmk='$(ROOTDIR)'"/pkg/$i"
2517      if test -d $adr ; then      if test -d $adr ; then
2518          SOURCEDIRS="$SOURCEDIRS $adr"          SOURCEDIRS="$SOURCEDIRS $adr"
2519          INCLUDEDIRS="$INCLUDEDIRS $adr"          INCLUDEDIRS="$INCLUDEDIRS $adr"
2520            SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
2521            INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
2522          if test "x$i" = xautodiff ; then          if test "x$i" = xautodiff ; then
2523              AUTODIFF_PKG_USED=t              AUTODIFF_PKG_USED=t
2524          fi          fi
# Line 2236  for n in $names ; do Line 2548  for n in $names ; do
2548          done          done
2549          if test "x$has_pack" = xf ; then          if test "x$has_pack" = xf ; then
2550              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`              undef=`echo "ALLOW_$n" | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
2551              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"              DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
2552          fi          fi
2553      fi      fi
2554  done  done
# Line 2249  for i in $PACKAGES ; do Line 2561  for i in $PACKAGES ; do
2561  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!  #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
2562      case $i in      case $i in
2563          aim_v23)          aim_v23)
2564              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"              ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
2565              echo "Warning: ALLOW_AIM is set to enable aim_v23."              echo "Warning: ALLOW_AIM is set to enable aim_v23."
2566              ;;              ;;
2567      esac      esac
# Line 2262  BUILDDIR=${BUILDDIR:-.} Line 2574  BUILDDIR=${BUILDDIR:-.}
2574  if test "x$STANDARDDIRS" != x ; then  if test "x$STANDARDDIRS" != x ; then
2575      for d in $STANDARDDIRS ; do      for d in $STANDARDDIRS ; do
2576          adr="$ROOTDIR/$d/src"          adr="$ROOTDIR/$d/src"
2577            adrmk='$(ROOTDIR)/'"$d/src"
2578          if test ! -d $adr ; then          if test ! -d $adr ; then
2579              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
2580              echo "  is correct and that you correctly specified the STANDARDDIRS option"              echo "  is correct and that you correctly specified the STANDARDDIRS option"
2581              exit 1              exit 1
2582          else          else
2583              SOURCEDIRS="$SOURCEDIRS $adr"              SOURCEDIRS="$SOURCEDIRS $adr"
2584                SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
2585          fi          fi
2586          adr="$ROOTDIR/$d/inc"          adr="$ROOTDIR/$d/inc"
2587            adrmk='$(ROOTDIR)/'"$d/inc"
2588          if test ! -d $adr ; then          if test ! -d $adr ; then
2589              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
2590              echo "  is correct and that you correctly specified the STANDARDDIRS option"              echo "  is correct and that you correctly specified the STANDARDDIRS option"
2591              exit 1              exit 1
2592          else          else
2593              INCLUDEDIRS="$INCLUDEDIRS $adr"              INCLUDEDIRS="$INCLUDEDIRS $adr"
2594                INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
2595          fi          fi
2596      done      done
2597  fi  fi
# Line 2291  for i in $spaths ; do Line 2607  for i in $spaths ; do
2607      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
2608          echo "    found CPP_OPTIONS=\"$try\""          echo "    found CPP_OPTIONS=\"$try\""
2609          CPP_OPTIONS="$try"          CPP_OPTIONS="$try"
2610          # 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
2611          for n in $names ; do          for n in $names ; do
2612              test_for_package_in_cpp_options $CPP_OPTIONS $n              test_for_package_in_cpp_options $CPP_OPTIONS $n
2613          done          done
2614      fi      fi
2615      try="$i/CPP_EEOPTIONS.h"      try="$i/CPP_EEOPTIONS.h"
2616      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
2617          echo "    found CPP_EEOPTIONS=\"$try\""          echo "    found CPP_EEOPTIONS=\"$try\""
2618          # 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
2619  #**** not yet enabled ****  #**** not yet enabled ****
2620  #        test_for_mpi_in_cpp_eeoptions $try  #        test_for_mpi_in_cpp_eeoptions $try
2621  #**** not yet enabled ****  #**** not yet enabled ****
# Line 2313  fi Line 2629  fi
2629    
2630  #  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
2631  #  compiler.  #  compiler.
2632  if test -f ./adSrcFiles.tmp ; then  if test -f $TMP.adSrcFiles ; then
2633      rm -f ./adSrcFiles.tmp      rm -f $TMP.adSrcFiles
2634  fi  fi
2635  echo "  Creating the list of files for the adjoint compiler."  echo "  Creating the list of files for the adjoint compiler."
2636  touch adSrcFiles.tmp  touch $TMP.adSrcFiles
2637  for i in $SOURCEDIRS ; do  for i in $SOURCEDIRS ; do
2638      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`      list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
2639      for j in $list_files ; do      for j in $list_files ; do
2640          cat $i/$j >> adSrcFiles.tmp          cat $i/$j >> $TMP.adSrcFiles
2641      done      done
2642  done  done
2643  if test ! "x"$FS = "x.f" ; then  if test ! "x"$FS = "x.f" ; then
2644      cat adSrcFiles.tmp | sed -e "s/\.f/.$FS/g" > adSrcFiles.tmp_f      cat $TMP.adSrcFiles | sed -e "s/\.f/.$FS/g" > $TMP.adSrcFiles_f
2645      mv -f adSrcFiles.tmp_f adSrcFiles.tmp      mv -f $TMP.adSrcFiles_f $TMP.adSrcFiles
2646  fi  fi
2647    
2648  echo  echo
# Line 2338  for i in $INCLUDEDIRS ; do Line 2654  for i in $INCLUDEDIRS ; do
2654      fi      fi
2655  done  done
2656    
2657  if test ! "x$DIVA" = x ; then  if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
2658      echo "  Creating the pseudo-MPI include directory"      if test ! "x$MPIINCLUDEDIR" = x ; then
2659      INCLUDES="-I./mpi_headers $INCLUDES"          #  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
2660      rm -rf ./mpi_headers          #   checking for additional included headers (in case of chain of included
2661      mkdir -p ./mpi_headers          #   header); also set LOCAL_MPI_HEADERS (if not already set)
2662            mpi_headers_do_local_copy
     if test "x$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  
2663      fi      fi
2664  fi  fi
2665    
2666  echo "  Determining the list of source and include files"  echo "  Determining the list of source and include files"
2667  rm -rf .links.tmp  rm -rf $TMP.links
2668  mkdir .links.tmp  mkdir $TMP.links
2669  touch .links.tmp/foo  touch $TMP.links/foo
2670  if test ! -r ".links.tmp/foo" ; then  if test ! -r "$TMP.links/foo" ; then
2671      echo      echo
2672      echo "ERROR : something is wrong with your directory permissions or"      echo "ERROR : something is wrong with your directory permissions or"
2673      echo "   your user file-creation mask (\"umask\") since creating a"      echo "   your user file-creation mask (\"umask\") since creating a"
# Line 2383  if test ! -r ".links.tmp/foo" ; then Line 2683  if test ! -r ".links.tmp/foo" ; then
2683      echo      echo
2684      exit 1      exit 1
2685  fi  fi
2686  rm -f .links.tmp/foo  rm -f $TMP.links/foo
2687    
2688  if test "x$OPENAD" != x ; then  if test "x$OPENAD" != x ; then
2689      OAD_DONT_COMPILE="/dev/null"      OAD_DONT_COMPILE="/dev/null"
2690      OAD_DONT_TRANSFORM="/dev/null"      OAD_DONT_TRANSFORM="/dev/null"
2691      OAD_KEEP_ORIGINAL="/dev/null"      OAD_KEEP_ORIGINAL="/dev/null"
2692      OAD_CB2M_FILES="/dev/null"      OAD_CB2M_FILES="/dev/null"
2693        OADTOOLS="$TOOLSDIR/OAD_support"
2694        OADTOOLSMK='$(TOOLSDIR)/OAD_support'
2695      echo "  looking for dontCompile file:  "      echo "  looking for dontCompile file:  "
2696      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2697          if test -r $i"/dontCompile" ; then          if test -r $i"/dontCompile" ; then
2698              OAD_DONT_COMPILE=$i"/dontCompile"              OAD_DONT_COMPILE=$i"/dontCompile"
2699              echo "     found $OAD_DONT_COMPILE"              echo "     found $OAD_DONT_COMPILE"
# Line 2399  if test "x$OPENAD" != x ; then Line 2701  if test "x$OPENAD" != x ; then
2701          fi          fi
2702      done      done
2703      echo "  looking for dontTransform file:  "      echo "  looking for dontTransform file:  "
2704      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2705          if test -r $i"/dontTransform" ; then          if test -r $i"/dontTransform" ; then
2706              OAD_DONT_TRANSFORM=$i"/dontTransform"              OAD_DONT_TRANSFORM=$i"/dontTransform"
2707              echo "     found $OAD_DONT_TRANSFORM"              echo "     found $OAD_DONT_TRANSFORM"
# Line 2407  if test "x$OPENAD" != x ; then Line 2709  if test "x$OPENAD" != x ; then
2709          fi          fi
2710      done      done
2711      echo "  looking for keepOriginal file:  "      echo "  looking for keepOriginal file:  "
2712      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2713          if test -r $i"/keepOriginal" ; then          if test -r $i"/keepOriginal" ; then
2714              OAD_KEEP_ORIGINAL=$i"/keepOriginal"              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
2715              echo "     found $OAD_KEEP_ORIGINAL"              echo "     found $OAD_KEEP_ORIGINAL"
# Line 2415  if test "x$OPENAD" != x ; then Line 2717  if test "x$OPENAD" != x ; then
2717          fi          fi
2718      done      done
2719      echo "  looking for cb2mFiles:  "      echo "  looking for cb2mFiles:  "
2720      for i in "." $MODS ; do      for i in "." $MODS $OADTOOLS ; do
2721          if test -r $i"/cb2mFiles" ; then          if test -r $i"/cb2mFiles" ; then
2722              OAD_CB2M_FILES=$i"/cb2mFiles"              OAD_CB2M_FILES=$i"/cb2mFiles"
2723              echo "     found $OAD_CB2M_FILES"              echo "     found $OAD_CB2M_FILES"
# Line 2425  if test "x$OPENAD" != x ; then Line 2727  if test "x$OPENAD" != x ; then
2727      echo "   OpenAD exceptions:  "      echo "   OpenAD exceptions:  "
2728  fi  fi
2729    
2730  echo "# This section creates symbolic links" > srclinks.tmp  echo "# This section creates symbolic links" > $TMP.srclinks
2731  echo "" >> srclinks.tmp  echo "" >> $TMP.srclinks
2732  printf 'F77_SRC_FILES = ' > F77srclist.tmp  printf 'F77_SRC_FILES = ' > $TMP.F77srclist
2733  printf 'NON_AD_F77_SRC_FILES = ' > nonADF77srclist.tmp  printf 'NON_AD_F77_SRC_FILES = ' > $TMP.nonADF77srclist
2734  printf 'C_SRC_FILES = '   > csrclist.tmp  printf 'C_SRC_FILES = '   > $TMP.csrclist
2735  printf 'F90_SRC_FILES = ' > F90srclist.tmp  printf 'F90_SRC_FILES = ' > $TMP.F90srclist
2736  printf 'H_SRC_FILES = '   > hsrclist.tmp  printf 'H_SRC_FILES = '   > $TMP.hsrclist
2737  printf 'AD_FLOW_FILES = ' > ad_flow_files.tmp  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
2738  alldirs="$SOURCEDIRS $INCLUDEDIRS ."  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
2739    alldirsmk=(${SOURCEDIRSMK} ${INCLUDEDIRSMK} ".")
2740    nd=0
2741  for d in $alldirs ; do  for d in $alldirs ; do
2742        dmk=${alldirsmk[${nd}]}
2743        nd=$((${nd}+1))
2744      deplist=      deplist=
2745      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
2746      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
# Line 2442  for d in $alldirs ; do Line 2748  for d in $alldirs ; do
2748          sfiles=`( echo $sfiles | grep -v _cb2m\. )`          sfiles=`( echo $sfiles | grep -v _cb2m\. )`
2749      fi      fi
2750      for sf in $sfiles ; do      for sf in $sfiles ; do
2751          if test ! -r ".links.tmp/$sf" ; then          if test ! -r "$TMP.links/$sf" ; then
2752              if test -f "$d/$sf" ; then              if test -f "$d/$sf" ; then
2753                  ignore_f=f                  ignore_f=f
2754                  case $d/$sf in                  case $d/$sf in
2755                    ./$PACKAGES_DOT_H)                    ./$PACKAGES_DOT_H)
2756                          ignore_f=t                          ignore_f=t
2757                          ;;                          ;;
2758                    ./AD_CONFIG.h)                    ./AD_CONFIG.h)
2759                          ignore_f=t                          ignore_f=t
2760                          ;;                          ;;
2761                    ./FC_NAMEMANGLE.h)                    ./FC_NAMEMANGLE.h)
2762                          ignore_f=t                          ignore_f=t
2763                          ;;                          ;;
2764                    ./BUILD_INFO.h)                    ./BUILD_INFO.h)
2765                          ignore_f=t                          ignore_f=t
2766                          ;;                          ;;
2767                    ./EMBEDDED_FILES.h)                    ./EMBEDDED_FILES.h)
2768                          ignore_f=t                          ignore_f=t
2769                          ;;                          ;;
2770                    *)                    *)
2771                          #  For the local directory *ONLY*,                          #  For the local directory *ONLY*,
2772                          #  ignore all soft-links                          #  ignore all soft-links
2773                          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 $sf ; then
2774                              ignore_f=t                              ignore_f=t
2775                          else                          else
2776                              touch .links.tmp/$sf                              touch $TMP.links/$sf
2777                              deplist="$deplist $sf"                              deplist="$deplist $sf"
2778                          fi                          fi
2779                          ;;                          ;;
2780                  esac                  esac
2781                  if test "x$ignore_f" = xf ; then                  if test "x$ignore_f" = xf ; then
2782                      extn=`echo $sf | $AWK -F. '{print $NF}'`                      extn=`echo $sf | $AWK -F. '{print $NF}'`
2783                      case $extn in                      case $extn in
2784                        F)                        F)
2785                          echo    " \\"  >> F77srclist.tmp                          echo    " \\"  >> $TMP.F77srclist
2786                          printf " $sf" >> F77srclist.tmp                          printf " $sf" >> $TMP.F77srclist
2787                          if test "x$OPENAD" != x ; then                          if test "x$OPENAD" = x ; then
2788                              basename=${sf%%.F}                              basename=${sf%%.F}
2789                              isAD=`egrep ^$basename.f'[  ]*' adSrcFiles.tmp`                              isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2790                                if test -z "$isAD" ; then
2791                                    echo    " \\"  >> $TMP.nonADF77srclist
2792                                    printf " $sf" >> $TMP.nonADF77srclist
2793                                fi
2794                            else #- OpenAD case:
2795                                basename=${sf%%.F}
2796                                isAD=`egrep ^$basename.f'[  ]*' $TMP.adSrcFiles`
2797                              if test -z "$isAD" ; then                              if test -z "$isAD" ; then
2798                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`                                  toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE}`
2799                                  if test -z "$toBeIgnored" ; then                                  if test -z "$toBeIgnored" ; then
2800                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2801                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2802                                  else                                  else
2803                                      echo "    not to be compiled   :  $sf"                                      echo "    not to be compiled   :  $sf"
2804                                  fi                                  fi
# Line 2500  for d in $alldirs ; do Line 2813  for d in $alldirs ; do
2813                                      echo "    original to be kept  :  $sf"                                      echo "    original to be kept  :  $sf"
2814                                  fi                                  fi
2815                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then                                  if test -n "$notToBeTransformed" -o -n "$untransformedVersionToBeKept" ; then
2816                                      echo    " \\"  >> nonADF77srclist.tmp                                      echo    " \\"  >> $TMP.nonADF77srclist
2817                                      printf " $sf" >> nonADF77srclist.tmp                                      printf " $sf" >> $TMP.nonADF77srclist
2818                                  fi                                  fi
2819                              fi                              fi
2820                          fi                          fi
2821                          ;;                          ;;
2822                      F90)                      F90)
2823                          echo    " \\"  >> F90srclist.tmp                          echo    " \\"  >> $TMP.F90srclist
2824                          printf " $sf" >> F90srclist.tmp                          printf " $sf" >> $TMP.F90srclist
2825                          ;;                          ;;
2826                      c)                      c)
2827                          echo    " \\"  >> csrclist.tmp                          echo    " \\"  >> $TMP.csrclist
2828                          printf " $sf" >> csrclist.tmp                          printf " $sf" >> $TMP.csrclist
2829                          ;;                          ;;
2830                      h)                      h)
2831                          echo    " \\"  >> hsrclist.tmp                          echo    " \\"  >> $TMP.hsrclist
2832                          printf " $sf" >> hsrclist.tmp                          printf " $sf" >> $TMP.hsrclist
2833                          ;;                          ;;
2834                      flow)                      flow)
2835                          echo    " \\"  >> ad_flow_files.tmp                          echo    " \\"  >> $TMP.ad_flow_files
2836                          printf " $sf" >> ad_flow_files.tmp                          printf " $sf" >> $TMP.ad_flow_files
2837                          ;;                          ;;
2838                     esac                     esac
2839                  fi                  fi
# Line 2529  for d in $alldirs ; do Line 2842  for d in $alldirs ; do
2842      done      done
2843      if test "x$deplist" != x ; then      if test "x$deplist" != x ; then
2844        if test "$d" != "." ; then        if test "$d" != "." ; then
2845          echo "" >> srclinks.tmp          echo "" >> $TMP.srclinks
2846          echo "#  These files are linked from $d" >> srclinks.tmp          echo "#  These files are linked from $dmk ( aka $d )" >> $TMP.srclinks
2847          echo "$deplist :" >> srclinks.tmp          echo "$deplist :" >> $TMP.srclinks
2848  # We need to make sure that the link isn't already there.  # We need to make sure that the link isn't already there.
2849  # 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"
2850  # 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.
2851          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> srclinks.tmp          printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $dmk >> $TMP.srclinks
2852        fi        fi
2853      fi      fi
2854  done  done
2855  rm -rf .links.tmp  rm -rf $TMP.links
2856  echo "" >> F77srclist.tmp  echo "" >> $TMP.F77srclist
2857  echo "" >> nonADF77srclist.tmp  echo "" >> $TMP.nonADF77srclist
2858  echo "" >> csrclist.tmp  echo "" >> $TMP.csrclist
2859  echo "" >> F90srclist.tmp  echo "" >> $TMP.F90srclist
2860  echo "" >> hsrclist.tmp  echo "" >> $TMP.hsrclist
2861  echo "" >> ad_flow_files.tmp  echo "" >> $TMP.ad_flow_files
2862    
2863  CMDLINE=$0  CMDLINE=$0
2864  for xx in "$@" ; do nw=`echo $xx | wc -w`  for xx in "$@" ; do nw=`echo $xx | wc -w`
2865      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"      if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
2866                          else CMDLINE="$CMDLINE '$xx'" ; fi                          else CMDLINE="$CMDLINE '$xx'" ; fi
2867  done  done
2868    
2869  if test -f $MAKEFILE ; then  if test -f $MAKEFILE ; then
# Line 2584  cat >>$MAKEFILE <<EOF Line 2897  cat >>$MAKEFILE <<EOF
2897  # INCLUDES     : Directories searched for header files  # INCLUDES     : Directories searched for header files
2898  # DEFINES      : Macro definitions for CPP  # DEFINES      : Macro definitions for CPP
2899  # MAKEDEPEND   : Dependency generator  # MAKEDEPEND   : Dependency generator
 # KPP          : Special preprocessor command (specific to platform)  
 # KFLAGS       : Flags for KPP  
2900  # FC           : Fortran compiler command  # FC           : Fortran compiler command
2901  # FFLAGS       : Configuration/debugging options for FC  # FFLAGS       : Configuration/debugging options for FC
2902  # FOPTIM       : Optimization options for FC  # FOPTIM       : Optimization options for FC
# Line 2594  cat >>$MAKEFILE <<EOF Line 2905  cat >>$MAKEFILE <<EOF
2905    
2906  ROOTDIR     = ${ROOTDIR}  ROOTDIR     = ${ROOTDIR}
2907  BUILDDIR    = ${BUILDDIR}  BUILDDIR    = ${BUILDDIR}
2908  SOURCEDIRS  = ${SOURCEDIRS}  SOURCEDIRS  = ${SOURCEDIRSMK}
2909  INCLUDEDIRS = ${INCLUDEDIRS}  INCLUDEDIRS = ${INCLUDEDIRSMK}
2910  EXEDIR      = ${EXEDIR}  EXEDIR      = ${EXEDIR}
2911  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
2912  TOOLSDIR    = ${TOOLSDIR}  TOOLSDIR    = ${TOOLSDIRMK}
2913    OADTOOLS    = ${OADTOOLSMK}
2914    
2915  #eh3  new defines for the adjoint work  #eh3  new defines for the adjoint work
2916  AUTODIFF    = ${ROOTDIR}/pkg/autodiff  AUTODIFF    = \$(ROOTDIR)/pkg/autodiff
2917  EXE_AD      = ${EXE_AD}  EXE_AD      = ${EXE_AD}
2918  EXE_FTL     = ${EXE_FTL}  EXE_FTL     = ${EXE_FTL}
2919  EXE_SVD     = ${EXE_SVD}  EXE_SVD     = ${EXE_SVD}
# Line 2619  else Line 2931  else
2931      echo "EMBEDDED_FILES = " >>$MAKEFILE      echo "EMBEDDED_FILES = " >>$MAKEFILE
2932  fi  fi
2933    
2934    # extract default cpp search path so we can pass it to makedepend
2935    CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
2936    
2937  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
2938  # Unix ln (link)  # Unix ln (link)
2939  LN = ${LN}  LN = ${LN}
 # C preprocessor  
 CPP = cat \$< | ${S64} | ${CPP}  
2940  # Dependency generator  # Dependency generator
2941  MAKEDEPEND = ${MAKEDEPEND}  MAKEDEPEND = ${MAKEDEPEND}
2942  # Special preprocessor (KAP on DECs, FPP on Crays)  # Special preprocessor (KAP on DECs, FPP on Crays)
# Line 2641  LINK = ${LINK} ${LDADD} Line 2954  LINK = ${LINK} ${LDADD}
2954  DEFINES = ${DEFINES}  DEFINES = ${DEFINES}
2955  # Includes for CPP  # Includes for CPP
2956  INCLUDES = ${INCLUDES}  INCLUDES = ${INCLUDES}
2957    # default CPP includes for makedepend
2958    CPPINCLUDES = ${CPPINCLUDES}
2959  # Flags for KPP  # Flags for KPP
2960  KFLAGS1 = ${KFLAGS1}  KFLAGS1 = ${KFLAGS1}
2961  KFLAGS2 = ${KFLAGS2}  KFLAGS2 = ${KFLAGS2}
2962  # Optim./debug for FC  # Optim./debug for FC
2963  FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}  FFLAGS = ${FFLAGS}
2964  FOPTIM = ${FOPTIM}  FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
2965  # Optim./debug for FC  # Optim./debug for FC
2966  F90FLAGS = ${F90FLAGS}  F90FLAGS = ${F90FLAGS}
2967  F90OPTIM = ${F90OPTIM}  F90OPTIM = ${F90OPTIM}
# Line 2659  NOOPTFLAGS = ${NOOPTFLAGS} Line 2974  NOOPTFLAGS = ${NOOPTFLAGS}
2974  # Flags and libraries needed for linking  # Flags and libraries needed for linking
2975  LIBS = ${LIBS}  LIBS = ${LIBS}
2976  # Name of the makefile  # Name of the makefile
2977  MAKEFILE=${MAKEFILE}  MAKEFILE = ${MAKEFILE}
2978    # Name of the make program
2979    MAKE = ${MAKE}
2980    
2981  EOF  EOF
2982    
2983  cat F77srclist.tmp      >> $MAKEFILE  cat $TMP.F77srclist      >> $MAKEFILE
2984  cat nonADF77srclist.tmp >> $MAKEFILE  cat $TMP.nonADF77srclist >> $MAKEFILE
2985  cat csrclist.tmp        >> $MAKEFILE  cat $TMP.csrclist        >> $MAKEFILE
2986  cat F90srclist.tmp      >> $MAKEFILE  cat $TMP.F90srclist      >> $MAKEFILE
2987  cat hsrclist.tmp        >> $MAKEFILE  cat $TMP.hsrclist        >> $MAKEFILE
2988  cat ad_flow_files.tmp   >> $MAKEFILE  cat $TMP.ad_flow_files   >> $MAKEFILE
2989    
2990  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
2991    
2992  echo >> $MAKEFILE  echo >> $MAKEFILE
2993    
# Line 2683  echo >> $MAKEFILE Line 3000  echo >> $MAKEFILE
3000  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE  echo 'F77_PP_SRC_FILES = $(F77_SRC_FILES:.F=.'$FS')'      >> $MAKEFILE
3001  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE  echo 'F90_PP_SRC_FILES = $(F90_SRC_FILES:.F90=.'$FS90')' >> $MAKEFILE
3002  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
3003  echo 'FLOFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE  echo 'FLOWFILES =  $(AD_FLOW_FILES:.flow=.flowdir)' >> $MAKEFILE
3004  echo >> $MAKEFILE  echo >> $MAKEFILE
3005  echo '.SUFFIXES:' >> $MAKEFILE  echo '.SUFFIXES:' >> $MAKEFILE
3006  echo '.SUFFIXES: .o .'$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' >> $MAKEFILE
3007    
3008  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3009    
3010  all: \$(EXECUTABLE)  all: fwd_exe_target
3011    fwd_exe_target:
3012            @echo Update AD_CONFIG.h and make \$(EXECUTABLE)
3013            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Forward version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3014            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3015            @-rm -f ad_config.template
3016            \$(MAKE) -f \$(MAKEFILE) \$(EXECUTABLE)
3017    
3018  \$(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)
3019          @echo Creating \$@ ...          @echo Creating \$@ ...
3020          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
3021    
3022  depend:  depend:
3023          @make -f \$(MAKEFILE) links          @\$(MAKE) -f \$(MAKEFILE) links
3024          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)          \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
3025          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)          \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
3026          -rm -f makedepend.out          -rm -f makedepend.out
3027    
3028  lib: libmitgcmuv.a  lib: libmitgcmuv.a
3029    
3030  libmitgcmuv.a: \$(OBJFILES)  libmitgcmuv.a: \$(SPECIAL_FILES) \$(OBJFILES)
3031          ar rcv libmitgcmuv.a \$(OBJFILES)          ar rcv libmitgcmuv.a \$(OBJFILES)
3032          ar d   libmitgcmuv.a main.o          ar d   libmitgcmuv.a main.o
3033    
# Line 2713  links: \$(F77_SRC_FILES) \$(C_SRC_FILES) Line 3037  links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
3037    
3038  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
3039    
 output.txt: \$(EXECUTABLE)  
         @printf 'running ... '  
         @\$(EXECUTABLE) > \$@  
   
3040  # remove most of the files that "make" generates  # remove most of the files that "make" generates
3041  clean:  clean:
3042          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
# Line 2726  clean: Line 3046  clean:
3046    
3047  # remove most of the files that "make" and "make depend" generate  # remove most of the files that "make" and "make depend" generate
3048  Clean:  Clean:
3049          @make -f \$(MAKEFILE) clean          @\$(MAKE) -f \$(MAKEFILE) clean
3050          @make -f \$(MAKEFILE) cleanlinks          @\$(MAKE) -f \$(MAKEFILE) cleanlinks
3051          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old          -rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
3052          -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  
3053    
3054  # remove also the executable, files that "genmake2" generates (except Makefile)  # remove also the executable, files that "genmake2" generates (except Makefile)
3055  #         and output from a run (plus log files from testreport)  #         and output from a run (plus log files from testreport)
3056  CLEAN:  CLEAN:
3057          @make -f \$(MAKEFILE) Clean          @\$(MAKE) -f \$(MAKEFILE) Clean
3058          -rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak          -rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
3059          -rm -f $LOGFILE genmake_state genmake_*optfile          -rm -f $LOGFILE genmake_state genmake_*optfile
3060          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log          -rm -f SIZE.h.mpi genmake.tr_log make.tr_log
3061            -rm -rf mpi_headers mnc_test_*
3062          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;          -find \$(EXEDIR) -name "*.meta" -exec rm {} \;
3063          -find \$(EXEDIR) -name "*.data" -exec rm {} \;          -find \$(EXEDIR) -name "*.data" -exec rm {} \;
3064          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;          -find \$(EXEDIR) -name "fort.*" -exec rm {} \;
3065          -rm -f *.txt STD* *diagnostics.log datetime          -rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
3066            -rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
3067          -rm -f *_MIT_CE_000.opt0000 costfunction*0000          -rm -f *_MIT_CE_000.opt0000 costfunction*0000
3068          -rm -rf mnc_test_*          -rm -f oad_cp.[0-9][0-9][0-9].?????
3069    
3070  makefile:  makefile:
3071          $THIS_SCRIPT $G2ARGS          $THIS_SCRIPT $G2ARGS
# Line 2754  cleanlinks: Line 3075  cleanlinks:
3075  # Special targets (SPECIAL_FILES) which are created by make  # Special targets (SPECIAL_FILES) which are created by make
3076  ${PACKAGES_DOT_H}:  ${PACKAGES_DOT_H}:
3077          @echo Creating \$@ ...          @echo Creating \$@ ...
3078          @$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) > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
3079  AD_CONFIG.h:  AD_CONFIG.h:
3080          @echo Creating \$@ ...          @echo Creating \$@ ...
3081          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
3082  FC_NAMEMANGLE.h:  FC_NAMEMANGLE.h:
3083          @echo Creating \$@ ...          @echo Creating \$@ ...
3084          echo "$FC_NAMEMANGLE" > \$@          echo "$FC_NAMEMANGLE" > \$@
# Line 2797  cat >>$MAKEFILE <<EOF Line 3118  cat >>$MAKEFILE <<EOF
3118  ## This nullifies any default implicit rules concerning these two file types:  ## This nullifies any default implicit rules concerning these two file types:
3119  ## %.o : %.F  ## %.o : %.F
3120    
3121    # C preprocessing and replacing the _d in constants:
3122    CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
3123    
3124  .F.$FS:  .F.$FS:
3125          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3126  .$FS.o:  .$FS.o:
3127          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3128  .F.o:  .F.o:
3129          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<          \$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
3130  .F90.$FS90:  .F90.$FS90:
3131          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3132  .FF90.f$FS90:  .FF90.f$FS90:
3133          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD)  > \$@
3134  .$FS90.o:  .$FS90.o:
3135          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<          \$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
3136  .f$FS90.o:  .f$FS90.o:
# Line 2815  cat >>$MAKEFILE <<EOF Line 3139  cat >>$MAKEFILE <<EOF
3139  .c.o:  .c.o:
3140          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<          \$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
3141  .flow.flowdir:  .flow.flowdir:
3142          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3143    
3144  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain  # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
3145  .F.p:  .F.p:
3146          \$(CPP) \$(DEFINES) \$(INCLUDES) > \$@          \$(CPPCMD) > \$@
3147  .p.$FS:  .p.$FS:
3148          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<          \$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
3149    
# Line 2838  TAF            = ${TAF} Line 3162  TAF            = ${TAF}
3162    
3163  TAF_EXTRA      = ${TAF_EXTRA}  TAF_EXTRA      = ${TAF_EXTRA}
3164  TAMC_EXTRA     = ${TAMC_EXTRA}  TAMC_EXTRA     = ${TAMC_EXTRA}
3165    LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
3166    
3167  EOF  EOF
3168    
# Line 2855  done Line 3180  done
3180  echo "  Add the source list for AD code generation"  echo "  Add the source list for AD code generation"
3181  echo >> $MAKEFILE  echo >> $MAKEFILE
3182  printf "AD_FILES = " >> $MAKEFILE  printf "AD_FILES = " >> $MAKEFILE
3183  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3184  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3185      echo    " \\" >> $MAKEFILE      echo    " \\" >> $MAKEFILE
3186      printf " $i" >> $MAKEFILE      printf " $i" >> $MAKEFILE
3187  done  done
3188  echo >> $MAKEFILE  echo >> $MAKEFILE
3189  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3190    
3191    if test $CAT_SRC_FOR_TAF = 0 ; then
3192    cat >>$MAKEFILE <<EOF
3193    
3194    # ... Utilities ...
3195    remove_comments:
3196            sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
3197            @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
3198    adj_sed:
3199            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
3200            @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
3201    ftl_sed:
3202            sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
3203            @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
3204    adobjfiles: \$(AD_FILES:.$FS=_ad.o)
3205    ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
3206    EOF
3207    fi
3208    
3209  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3210    
3211  # ... AD ...  # ... AD ...
3212  adall: \$(EXE_AD)  adall: ad_exe_target
3213  adtaf: ad_taf_output.$FS  adtaf: ad_taf_output.$FS
3214  adtamc: ad_tamc_output.$FS  adtamc: ad_tamc_output.$FS
3215    
3216  ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)  ad_exe_target:
3217          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template          @echo Update AD_CONFIG.h and make \$(EXE_AD)
3218            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3219            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3220            @-rm -f ad_config.template
3221            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3222    
3223    ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
3224            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3225          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3226          -rm -f ad_config.template          @-rm -f ad_config.template
3227          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3228          @make -f \$(MAKEFILE) \$(FLOFILES)          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3229          cat \$(FLOFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
3230    
3231  ad_taf_output.$FS: ad_input_code.$FS  adtafonly:
3232          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3233          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3234          cat ad_input_code_ad.$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
3235    
3236  adtafonly:  EOF
3237    
3238    if test $CAT_SRC_FOR_TAF = 1 ; then
3239    cat >>$MAKEFILE <<EOF
3240    # ... send 1 file to TAF ...
3241    ad_taf_output.$FS: ad_input_code.$FS
3242            @-rm -f ad_input_code_ad.$FS ; echo ''
3243          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
3244          ls -l ad_input_code_ad.$FS          ls -l ad_input_code_ad.$FS
3245          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
3246    
3247  \${EXE_AD}: ad_taf_output.o \$(OBJFILES)  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3248          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3249    
3250  ad_tamc_output.$FS: ad_input_code.$FS  adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
         \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS  
         cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS  
3251    
3252  ad_tamc: ad_tamc_output.o \$(OBJFILES)  EOF
         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)  
3253    
3254    else
3255    cat >>$MAKEFILE <<EOF
3256    # ... send multiple files to TAF ...
3257    ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3258            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3259            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3260            @-rm -f ad_config.template
3261            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3262            @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
3263            @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
3264            \$(MAKE) -f \$(MAKEFILE) remove_comments
3265            \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
3266            \$(MAKE) -f \$(MAKEFILE) adj_sed
3267            cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
3268    
3269    \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3270            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3271            \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3272    
3273    adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
3274            \$(MAKE) -f \$(MAKEFILE) adobjfiles
3275    
3276    EOF
3277    fi
3278    
3279    cat >>$MAKEFILE <<EOF
3280  adonlyfwd:  adonlyfwd:
3281          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
3282    
3283  adtrick:  adtrick:
3284          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
3285    
3286  adobj: ad_taf_output.o \$(OBJFILES)  ad_tamc_output.$FS: ad_input_code.$FS
3287            \$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
3288            cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
3289    
3290    ad_tamc: ad_tamc_output.o \$(OBJFILES)
3291            \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
3292    
3293  # ... FTL ...  # ... FTL ...
3294  ftlall: ftl_taf  ftlall: ftl_exe_target
3295  ftltaf: ftl_taf_output.$FS  ftltaf: ftl_taf_output.$FS
3296  ftltamc: ftl_tamc_output.$FS  ftltamc: ftl_tamc_output.$FS
3297    
3298  ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)  ftl_exe_target:
3299          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @echo Update AD_CONFIG.h and make \$(EXE_FTL)
3300          cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3301          -rm -f ftl_config.template          @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3302          @make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)          @-rm -f ad_config.template
3303          @make -f \$(MAKEFILE) \$(AD_FLOW_FILES)          \$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
         cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS  
3304    
3305  ftl_taf_output.$FS: ftl_input_code.$FS  ftl_input_code.$FS: \$(AD_FILES)
3306          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3307          ls -l ftl_input_code_ftl.$FS          cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3308          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS          @-rm -f ad_config.template
3309            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3310            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3311            cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
3312    
3313  ftltafonly:  ftltafonly:
3314          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3315          ls -l ftl_input_code_ftl.$FS          ls -l ftl_input_code_tl.$FS
3316          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
3317    
3318    EOF
3319    
3320    if test $CAT_SRC_FOR_TAF = 1 ; then
3321    cat >>$MAKEFILE <<EOF
3322    # ... send 1 file to TAF ...
3323    ftl_taf_output.$FS: ftl_input_code.$FS
3324            @-rm -f ftl_input_code_tl.$FS ; echo ''
3325            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
3326            ls -l ftl_input_code_tl.$FS
3327            cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
3328    
3329    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3330            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3331    
3332    EOF
3333    
3334    else
3335    cat >>$MAKEFILE <<EOF
3336    # ... send multiple files to TAF ...
3337    ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
3338            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3339            cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3340            @-rm -f ad_config.template
3341            @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
3342            @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
3343            @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
3344            \$(MAKE) -f \$(MAKEFILE) remove_comments
3345            \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
3346            \$(MAKE) -f \$(MAKEFILE) ftl_sed
3347            cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
3348    
3349    \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
3350            \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
3351            \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
3352    
3353  ftl_taf: ftl_taf_output.o \$(OBJFILES)  EOF
3354          \$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)  fi
3355    
3356    cat >>$MAKEFILE <<EOF
3357  ftl_tamc_output.$FS: ftl_input_code.$FS  ftl_tamc_output.$FS: ftl_input_code.$FS
3358          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
3359          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
# Line 2959  svd_touch: Line 3381  svd_touch:
3381          touch ad_taf_output.$FS ftl_taf_output.$FS          touch ad_taf_output.$FS ftl_taf_output.$FS
3382          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
3383          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS          \$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
3384          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template          @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "SVD version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
3385          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
3386          -rm -f ftl_config.template          @-rm -f ad_config.template
3387    
3388  EOF  EOF
3389    
# Line 2974  if test "x$OPENAD" != x ; then Line 3396  if test "x$OPENAD" != x ; then
3396  # ============ begin OpenAD specific section ==============  # ============ begin OpenAD specific section ==============
3397    
3398  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3399    # ... OpenAD ...
3400    
3401  # all the source files linked from the various locations:  # all the source files linked from the various locations:
3402  ALL_LINKED_FILES= \  ALL_LINKED_FILES= \
# Line 3013  for i in `cat ${OAD_CB2M_FILES}` ; do Line 3436  for i in `cat ${OAD_CB2M_FILES}` ; do
3436    echo    " \\" >> $MAKEFILE    echo    " \\" >> $MAKEFILE
3437    printf " ${i}_mod.f$FS90" >> $MAKEFILE    printf " ${i}_mod.f$FS90" >> $MAKEFILE
3438  done  done
3439  AD_FILES=`cat adSrcFiles.tmp`  AD_FILES=`cat $TMP.adSrcFiles`
3440  for i in $AD_FILES ; do  for i in $AD_FILES ; do
3441    basename=${i%%.f}    basename=${i%%.f}
3442    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`    toBeIgnored=`egrep ^$basename'[      ]*' ${OAD_DONT_COMPILE} ${OAD_DONT_TRANSFORM}`
# Line 3023  for i in $AD_FILES ; do Line 3446  for i in $AD_FILES ; do
3446    fi    fi
3447  done  done
3448  echo >> $MAKEFILE  echo >> $MAKEFILE
3449  rm -f adSrcFiles.tmp  rm -f $TMP.adSrcFiles
3450    
3451  cat >>$MAKEFILE <<EOF  cat >>$MAKEFILE <<EOF
3452    
3453  adAll: \$(EXE_AD)  adAll: ad_exe_target
3454  .PHONY: adAll  .PHONY: adAll
3455    
3456    ad_exe_target:
3457            @echo Update AD_CONFIG.h and make \$(EXE_AD)
3458            @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
3459            @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
3460            @-rm -f ad_config.template
3461            \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
3462    
3463  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))
3464    
3465  .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 3045  w2f__types.F90 \ Line 3475  w2f__types.F90 \
3475  OAD_active.F90 \  OAD_active.F90 \
3476  OAD_cp.F90 \  OAD_cp.F90 \
3477  OAD_rev.F90 \  OAD_rev.F90 \
3478  OAD_tape.F90  OAD_tape.F90 \
3479    OAD_regular_cp.F90 \
3480    revolve.F90
3481    
3482  OPENAD_SUPPORT_C_SRC_FILES = \  OPENAD_SUPPORT_C_SRC_FILES = \
3483  iaddr.c \  iaddr.c \
# Line 3061  f95_test.out: f95_test_mods.f90 f95_test Line 3493  f95_test.out: f95_test_mods.f90 f95_test
3493          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
3494          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
3495    
3496  # the file included below is created by the  CB2M_AD_FILES=\$(AD_FILES:.f=_cb2m.f$FS90)
 # postProcessor and its inclusion sets the  
 # variable POSTPROCESSEDFILES  
 # used below. Because the file is made during  
 # make it won't be read until the second (recursive)  
 # invocation in the rule below  
 -include postProcess.make  
3497    
3498  AD_OBJ_FILES_S1=\$(OPENAD_SUPPORT_F90_SRC_FILES:.F90=.o) \$(OPENAD_SUPPORT_C_SRC_FILES:.c=.o) \$(POSTPROCESSEDFILES:.f$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)
3499    
3500  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)
3501    
3502  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)  
3503          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
 else  
         touch \$@  
 endif  
   
 # makefile debug rule  
 openad: ad_input_code.w2f.pre.xb.x2w.w2f.td.pp.f$FS90  
 .PHONY: openad  
3504    
3505  # create the module files  # create sources files modules from header files containing common blocks
3506  %_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk  %_mod.FF90 : %.h \$(OADTOOLS)/cb2mGetModules.csh \$(OADTOOLS)/cb2mGetModules.awk
3507          ../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk          \$(OADTOOLS)/cb2mGetModules.csh $< \$(OADTOOLS)/cb2mGetModules.awk
3508    
3509  # create the header files  # create new header files with USE statements for the new modules made above
3510  %_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk  %_mod.h : %.h \$(OADTOOLS)/cb2mGetHeaders.csh \$(OADTOOLS)/cb2mGetHeaders.awk
3511          ../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)          \$(OADTOOLS)/cb2mGetHeaders.csh $< \$(OADTOOLS)/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
3512    
3513  # change everybody else to use the new module files:  # change the include directives of everybody to refer to  the new header files with the USE statements
3514  %_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash  %_cb2m.FF90 : %.F \$(OADTOOLS)/cb2mUseModules.bash
3515          ../OAD_support/cb2mUseModules.bash $< ${MPI}          \$(OADTOOLS)/cb2mUseModules.bash $< ${MPI}
3516    
3517  # makefile debug rule  # makefile debug rule
3518  small_f: \$(CB2M_F90_PP_SRC_FILES)  small_f: \$(CB2M_F90_PP_SRC_FILES)
3519  .PHONY: small_f  .PHONY: small_f
3520    
 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$FS90)  
3521  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
3522          cat \$^ > \$@          cat \$^ > \$@
3523    
 # strip all comments and blanks to reduce  
 # the file size in order to reduce perl's memory requirements  
 ad_input_code_sf.f$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 > \$@  
   
3524  # canonicalizer  # canonicalizer
3525  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)
3526          ./preProcess.py --timing --r8 -H -S \$< -o \$@          \${OPENADFORTTK_BASE}/tools/SourceProcessing/preProcess.py --timing --r8 -H -S  -o \$@ \$^
3527    
3528    # replace stop statements (to avoid the implied unstructured control flow)  with print statements
3529    ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
3530            cat \$< | sed -f \$(OADTOOLS)/stop2print.sed > ad_input_code_sf.pre.s2p.f90
3531    
3532  # F -> WHIRL  # F -> WHIRL
3533  # note that the canonicalized version cuts off at col 72  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
3534  # 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$FS90 mfef90  
         ./mfef90 -r8 -z -F \$<  
         mv \$<.B \$@  
3535    
3536  # WHIRL -> XAIF  # WHIRL -> XAIF
3537  ad_input_code_sf.w2f.pre.xaif : ad_input_code_sf.w2f.pre.B whirl2xaif  ad_input_code_sf.pre.s2p.xaif : ad_input_code_sf.pre.s2p.B
3538          ./whirl2xaif -s -n --debug 1 -o \$@ \$<          \${OPENADFORTTK}/bin/whirl2xaif -s -n --debug 1 -o \$@ \$<
3539    
3540  # XAIF -> XAIF'  # XAIF -> XAIF'
3541  ad_input_code_sf.w2f.pre.xb.xaif : ad_input_code_sf.w2f.pre.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd oadDriver  ad_input_code_sf.pre.s2p.xb.xaif : ad_input_code_sf.pre.s2p.xaif xaif.xsd xaif_base.xsd xaif_inlinable_intrinsics.xsd xaif_derivative_propagator.xsd xaif_output.xsd
3542          ./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r          \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
3543    
3544  # XAIF' -> WHIRL'  # XAIF' -> WHIRL'
3545  ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl  ad_input_code_sf.pre.s2p.xb.x2w.B : ad_input_code_sf.pre.s2p.xb.xaif
3546          ./xaif2whirl --debug 1 ad_input_code_sf.w2f.pre.B \$<          \${OPENADFORTTK}/bin/xaif2whirl --debug 1 ad_input_code_sf.pre.s2p.B \$<
3547    
3548  # WHIRL' -> F'  # WHIRL' -> F'
3549  ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be  ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.B
3550          ./whirl2f -FLIST:ftn_file=\$@ -openad \$<          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
3551    
3552  # insert template directives  # insert template directives
3553  ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$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$FS90 \$(OADTOOLS)/insertTemplateDir.bash
3554          ../OAD_support/insertTemplateDir.bash \$< \$@          \$(OADTOOLS)/insertTemplateDir.bash \$< \$@
3555    
3556  PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F  PPEXTRAS=\$(notdir \$(wildcard \$(OADTOOLS)/ad_template.*.F)) ad_inline.F
3557  # postprocess F'  # postprocess F'
3558  postProcess.tag: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 postProcess.py \$(PPEXTRAS:.F=.f)  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
3559          # the target is a placeholder to signal execution of the rule          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
3560            # the target is a placeholder to trigger a single execution of the rule
3561          touch \$@          touch \$@
3562          # this step also creates the file postProcess.make but we cannot  # put this so make knows about the postprocessing output
3563          # name it as the target or else make will try to remake it for  OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f$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 \$<  
3564    
3565  # setup some links  # link the XAIF schema files
3566  %.xsd:  %.xsd:
3567          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .          \$(LN) \${XAIFSCHEMAROOT}/schema/\$@ .
3568    
 mfef90:  
         \$(LN) \${OPEN64ROOT}/crayf90/sgi/mfef90 .  
   
3569  # link the support files:  # link the support files:
3570  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
3571          \$(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 \$@  
3572    
3573  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
3574    
3575  # ============ end OpenAD specific section ==============  # ============ end OpenAD specific section ==============
3576    
# Line 3236  for i in $NOOPTFILES ; do Line 3606  for i in $NOOPTFILES ; do
3606  done  done
3607    
3608  echo "  Add rules for links"  echo "  Add rules for links"
3609  cat srclinks.tmp >> $MAKEFILE  cat $TMP.srclinks >> $MAKEFILE
3610  rm -f srclinks.tmp  rm -f $TMP.srclinks
3611    
3612  echo "  Adding makedepend marker"  echo "  Adding makedepend marker"
3613  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE  printf "\n\n# DO NOT DELETE\n" >> $MAKEFILE
# Line 3245  printf "\n\n# DO NOT DELETE\n" >> $MAKEF Line 3615  printf "\n\n# DO NOT DELETE\n" >> $MAKEF
3615  printf "\n===  Done  ===\n"  printf "\n===  Done  ===\n"
3616    
3617  # Create special header files  # Create special header files
3618  $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"
3619  if test ! -f $PACKAGES_DOT_H ; then  if test ! -f $PACKAGES_DOT_H ; then
3620      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H      mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
3621  else  else
# Line 3259  else Line 3629  else
3629      fi      fi
3630  fi  fi
3631  if test ! -f AD_CONFIG.h ; then  if test ! -f AD_CONFIG.h ; then
3632      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h      $BASH $TOOLSDIR/convert_cpp_cmd2defines "Default version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
3633  fi  fi
3634    
3635  #  Write the "state" for future records  #  Write the "state" for future records

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