/[MITgcm]/MITgcm/tools/genmake2

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-revision 1.260 by jmc,
Thu Aug 22 01:10:53 2013 UTC
+revision 1.279 by jmc,
Sat Jan 28 18:37:21 2017 UTC
 Line 19 
 Usage: "$0" [OPTIONS]
      -help | --help | -h | --h
            Print this help message and exit.
+     -oad | --oad
+           Generate a Makefile for an OpenAD built
+     -nocat4ad | -dog4ad | -ncad | -dad
+           do not concatenate (cat) source code sent to TAF
+           resulting in compilation of multiple files
      -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
        -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
            Use "NAME" as the adoptfile.  By default, the file at
+           "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
            "tools/adjoint_options/adjoint_default" will be used.
-     -nooptfile | --nooptfile
+     -optfile NAME | --optfile NAME | -of NAME | --of NAME
-       -optfile NAME | --optfile NAME | -of NAME | --of NAME
        -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
            Use "NAME" as the optfile.  By default, an attempt will be
            made to find an appropriate "standard" optfile in the
-Line 1079 
 EOF
+Line 1086 
 EOF
  }
  check_lapack_libs()  {
-     if test ! "x$SKIP_LAPACK_CHECK" = x ; then
+     if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
-         return
-     fi
      echo >> $LOGFILE
      echo "running: check_lapack_libs()" >> $LOGFILE
      cat <<EOF > genmake_tla.F
-Line 1277 
 GSL=
+Line 1282 
 GSL=
  DEVEL=
  HAVE_TEST_L=
- # comment this line out to enable lapack test
+ # set this to "t" to enable lapack test
- SKIP_LAPACK_CHECK=t
+ CHECK_FOR_LAPACK=f
  # DEFINES checked by test compilation or command-line
  HAVE_SYSTEM=
-Line 1325 
 FS=
+Line 1330 
 FS=
  FS90=
  AUTODIFF_PKG_USED=f
+ OPENAD=
  AD_OPTFILE=
+ CAT_SRC_FOR_TAF=1
  TAF=
  AD_TAF_FLAGS=
  FTL_TAF_FLAGS=
-Line 1355 
 gm_s7="TMP THISHOST THISUSER THISDATE TH
+Line 1362 
 gm_s7="TMP THISHOST THISUSER THISDATE TH
  gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
  #  The following are all related to adjoint/tangent-linear stuff
- gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
+ gm_s10="AUTODIFF_PKG_USED AD_OPTFILE OPENAD TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
  gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
  gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
-Line 1400 
 for ac_option in "$@" ; do
+Line 1407 
 for ac_option in "$@" ; do
          -help | --help | -h | --h)
              usage ;;
-         -nooptfile | --nooptfile)
-             OPTFILE="NONE" ;;
          -optfile | --optfile | -of | --of)
              ac_prev=OPTFILE ;;
          -optfile=* | --optfile=* | -of=* | --of=*)
              OPTFILE=$ac_optarg ;;
+         -oad | --oad)
+             OPENAD="true" ; ALWAYS_USE_F90=1 ;;
+         -nocat4ad | -dog4ad | -ncad | -dad)
+             CAT_SRC_FOR_TAF=0 ;;
          -adoptfile | --adoptfile | -adof | --adof)
              ac_prev=AD_OPTFILE ;;
          -adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
-Line 1576 
 for ac_option in "$@" ; do
+Line 1585 
 for ac_option in "$@" ; do
  done
- TMP=./genmk_$$
+ #TMP=./genmk_$$
  #- try to put temporary files in system-local /tmp dir
- #TMP=/tmp/genmk_$$
+ TMP=/tmp/genmk_${USER}_$$
- #touch $TMP ; retVal=$?
+ touch $TMP ; retVal=$?
- #if [ $retVal -eq 0 ] ; then
+ if [ $retVal -eq 0 ] ; then
- #  if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
+   if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
- #else
+ else
- #  TMP=./genmk_$$
+   TMP=./genmk_$$
- #fi
+ fi
- #rm -f $TMP
+ rm -f $TMP
- ##echo "  temp files: $TMP.*"
+ #echo "  temp files: $TMP.*"
  printf "  getting local config information:  "
  if test -f $gm_local ; then
-Line 1680 
 fi
+Line 1689 
 fi
  echo "  getting AD_OPTFILE information:"
  if test "x${AD_OPTFILE}" = x ; then
-     if test "x$MITGCM_AD_OF" = x ; then
+     if test "x$MITGCM_AD_OF" != x ; then
+         AD_OPTFILE=$MITGCM_AD_OF
+     elif test "x$OPENAD" = x ; then
          AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
      else
-         AD_OPTFILE=$MITGCM_AD_OF
+         AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_oad
      fi
  fi
  if test "x${AD_OPTFILE}" != xNONE ; then
-Line 1706 
 if test "x${AD_OPTFILE}" != xNONE ; then
+Line 1717 
 if test "x${AD_OPTFILE}" != xNONE ; then
  fi
  #====================================================================
+ # Initialize INCLUDEDIRSMK from and optfile INCLUDEDIRS
+ if test "x${INCLUDEDIRS}" != "x" ; then
+  INCLUDEDIRSMK=${INCLUDEDIRS}
+ fi
+ #====================================================================
  #  Set default values if not set by the optfile
  #
  #  Check that FC, CC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
-Line 1950 
 else
+Line 1967 
 else
  fi
  rm -f genmake_tcomp*
- printf "  Do we have the etime() command using $FC...  "
+ printf "  Do we have the etime() command using $FC... "
- cat > genmake_tcomp.$FS <<EOF
+ cat > genmake_tcomp_1.$FS <<EOF
        program hello
-       REAL*4 ACTUAL, TARRAY(2)
+       REAL*4 actual, tarray(2)
        EXTERNAL ETIME
        REAL*4 ETIME
-       actual = etime( tarray )
+       actual = ETIME( tarray )
        print *, tarray
        end
  EOF
- $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
  RETVAL=$?
  if test "x$RETVAL" = x0 ; then
-     HAVE_ETIME=t
+     HAVE_ETIME='Fct'
-     DEFINES="$DEFINES -DHAVE_ETIME"
+     DEFINES="$DEFINES -DHAVE_ETIME_FCT"
-     echo "yes"
+     echo " yes (${HAVE_ETIME})"
  else
+   cat > genmake_tcomp_2.$FS <<EOF
+       program hello
+       REAL*4 actual, tarray(2)
+       actual = -999.
+       call ETIME( tarray, actual )
+       if ( actual.ge.0. ) then
+         print *, 0, tarray, actual
+       else
+         print *, 1, tarray, actual
+       endif
+       end
+ EOF
+   $FC $FFLAGS -o genmake_tcomp_2 genmake_tcomp_2.$FS >> genmake_tcomp.log 2>&1
+   RETVAL=$?
+   if test "x$RETVAL" = x0 ; then
+     echo -n 'c,'
+     ./genmake_tcomp_2 > genmake_tcomp_2.out 2>&1
+     RETVAL=$?
+   fi
+   if test "x$RETVAL" = x0 ; then
+     echo -n 'r:'
+     RETVAL=`cat genmake_tcomp_2.out | $AWK '{print $1}'`
+   fi
+   if test "x$RETVAL" = x0 ; then
+     HAVE_ETIME='SbR'
+     DEFINES="$DEFINES -DHAVE_ETIME_SBR"
+     echo " yes (${HAVE_ETIME})"
+   else
      HAVE_ETIME=
-     echo "no"
+     echo " no"
+   fi
  fi
+ #mkdir chk_etime ; cp -p -f genmake_tcomp* chk_etime
  rm -f genmake_tcomp*
  printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
-Line 2064 
 for d in $MODS ; do
+Line 2111 
 for d in $MODS ; do
          printf "$d "
          SOURCEDIRS="$SOURCEDIRS $d"
          INCLUDEDIRS="$INCLUDEDIRS $d"
+         SOURCEDIRSMK="$SOURCEDIRSMK $d"
+         INCLUDEDIRSMK="$INCLUDEDIRSMK $d"
      fi
  done
  echo
-Line 2087 
 fi
+Line 2136 
 fi
  if test "x${TOOLSDIR}" = x ; then
      TOOLSDIR="$ROOTDIR/tools"
+     TOOLSDIRMK='$(ROOTDIR)'"/tools"
+ else
+     TOOLSDIRMK=${TOOLSDIR}
  fi
  if test ! -d ${TOOLSDIR} ; then
      echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
-Line 2356 
 EOF
+Line 2408 
 EOF
      fi
  fi
- #  Check for package RADTRANS: if LAPACK is not available,
+ #  Make sure the openad package is enabled if using OpenAD
- #  then issue a warning that the direct radtrans solver is not available.
+ if test "x$OPENAD" != x ; then
- if test "x$HAVE_LAPACK" != xt ; then
+     echo " $PACKAGES " | grep ' openad ' > /dev/null 2>&1
-     echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1
      RETVAL=$?
-     if test "x$RETVAL" = x0 ; then
+     if test "x$RETVAL" != x0 ; then
          cat <<EOF
- *********************************************************************
- WARNING: the "radtrans" package was enabled but tests failed to
-   compile LAPACK applications.  This means that the direct radtrans
-   solver is not available and compilation will fail if it is enabled.
-   If you want to use the direct solver, please check that:
-) LAPACK is correctly installed for this compiler and
-) the LIBS variable (within the "optfile") specifies the correct
-      LAPACK library to link against.
  *********************************************************************
+ ERROR: when generating an adjoint with OpenAD, the openad package
+   must be enabled.  Please add it to packages.conf.
+ *********************************************************************
  EOF
+         exit 1
      fi
  fi
-Line 2456 
 if  test "x${PKG_DEPEND}" != x ; then
+Line 2504 
 if  test "x${PKG_DEPEND}" != x ; then
  fi
  for i in $PACKAGES ; do
      adr="$ROOTDIR/pkg/$i"
+     adrmk='$(ROOTDIR)'"/pkg/$i"
      if test -d $adr ; then
          SOURCEDIRS="$SOURCEDIRS $adr"
          INCLUDEDIRS="$INCLUDEDIRS $adr"
+         SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
+         INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
          if test "x$i" = xautodiff ; then
              AUTODIFF_PKG_USED=t
          fi
-Line 2514 
 BUILDDIR=${BUILDDIR:-.}
+Line 2565 
 BUILDDIR=${BUILDDIR:-.}
  if test "x$STANDARDDIRS" != x ; then
      for d in $STANDARDDIRS ; do
          adr="$ROOTDIR/$d/src"
+         adrmk='$(ROOTDIR)/'"$d/src"
          if test ! -d $adr ; then
              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
              echo "  is correct and that you correctly specified the STANDARDDIRS option"
              exit 1
          else
              SOURCEDIRS="$SOURCEDIRS $adr"
+             SOURCEDIRSMK="$SOURCEDIRSMK $adrmk"
          fi
          adr="$ROOTDIR/$d/inc"
+         adrmk='$(ROOTDIR)/'"$d/inc"
          if test ! -d $adr ; then
              echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
              echo "  is correct and that you correctly specified the STANDARDDIRS option"
              exit 1
          else
              INCLUDEDIRS="$INCLUDEDIRS $adr"
+             INCLUDEDIRSMK="$INCLUDEDIRSMK $adrmk"
          fi
      done
  fi
-Line 2627 
 if test "x$OPENAD" != x ; then
+Line 2682 
 if test "x$OPENAD" != x ; then
      OAD_KEEP_ORIGINAL="/dev/null"
      OAD_CB2M_FILES="/dev/null"
      OADTOOLS="$TOOLSDIR/OAD_support"
+     OADTOOLSMK='$(TOOLSDIR)/OAD_support'
      echo "  looking for dontCompile file:  "
-     for i in "." $MODS ; do
+     for i in "." $MODS $OADTOOLS ; do
          if test -r $i"/dontCompile" ; then
              OAD_DONT_COMPILE=$i"/dontCompile"
              echo "     found $OAD_DONT_COMPILE"
-Line 2636 
 if test "x$OPENAD" != x ; then
+Line 2692 
 if test "x$OPENAD" != x ; then
          fi
      done
      echo "  looking for dontTransform file:  "
-     for i in "." $MODS ; do
+     for i in "." $MODS $OADTOOLS ; do
          if test -r $i"/dontTransform" ; then
              OAD_DONT_TRANSFORM=$i"/dontTransform"
              echo "     found $OAD_DONT_TRANSFORM"
-Line 2644 
 if test "x$OPENAD" != x ; then
+Line 2700 
 if test "x$OPENAD" != x ; then
          fi
      done
      echo "  looking for keepOriginal file:  "
-     for i in "." $MODS ; do
+     for i in "." $MODS $OADTOOLS ; do
          if test -r $i"/keepOriginal" ; then
              OAD_KEEP_ORIGINAL=$i"/keepOriginal"
              echo "     found $OAD_KEEP_ORIGINAL"
-Line 2652 
 if test "x$OPENAD" != x ; then
+Line 2708 
 if test "x$OPENAD" != x ; then
          fi
      done
      echo "  looking for cb2mFiles:  "
-     for i in "." $MODS ; do
+     for i in "." $MODS $OADTOOLS ; do
          if test -r $i"/cb2mFiles" ; then
              OAD_CB2M_FILES=$i"/cb2mFiles"
              echo "     found $OAD_CB2M_FILES"
-Line 2671 
 printf 'F90_SRC_FILES = ' > $TMP.F90srcl
+Line 2727 
 printf 'F90_SRC_FILES = ' > $TMP.F90srcl
  printf 'H_SRC_FILES = '   > $TMP.hsrclist
  printf 'AD_FLOW_FILES = ' > $TMP.ad_flow_files
  alldirs="$SOURCEDIRS $INCLUDEDIRS ."
+ alldirsmk=(${SOURCEDIRSMK} ${INCLUDEDIRSMK} ".")
+ nd=0
  for d in $alldirs ; do
+     dmk=${alldirsmk[${nd}]}
+     nd=$((${nd}+1))
      deplist=
      sfiles=`( cd $d; echo *.[h,c,F] *.flow )`
      sfiles=`( echo $sfiles; cd $d; echo *.F90 )`
-Line 2774 
 for d in $alldirs ; do
+Line 2834 
 for d in $alldirs ; do
      if test "x$deplist" != x ; then
        if test "$d" != "." ; then
          echo "" >> $TMP.srclinks
-         echo "#  These files are linked from $d" >> $TMP.srclinks
+         echo "#  These files are linked from $dmk ( aka $d )" >> $TMP.srclinks
          echo "$deplist :" >> $TMP.srclinks
  # We need to make sure that the link isn't already there.
  # This may happen when make thinks that a header file has to be "remade"
  # because a module it depends on has changed.  In this case we do nothing.
-         printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $d >> $TMP.srclinks
+         printf "\tif [ ! -L \$@ ]; then \$(LN) %s/\$@ \$@; fi\n" $dmk >> $TMP.srclinks
        fi
      fi
  done
-Line 2836 
 cat >>$MAKEFILE <<EOF
+Line 2896 
 cat >>$MAKEFILE <<EOF
  ROOTDIR     = ${ROOTDIR}
  BUILDDIR    = ${BUILDDIR}
- SOURCEDIRS  = ${SOURCEDIRS}
+ SOURCEDIRS  = ${SOURCEDIRSMK}
- INCLUDEDIRS = ${INCLUDEDIRS}
+ INCLUDEDIRS = ${INCLUDEDIRSMK}
  EXEDIR      = ${EXEDIR}
  EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
- TOOLSDIR    = ${TOOLSDIR}
+ TOOLSDIR    = ${TOOLSDIRMK}
- OADTOOLS    = ${OADTOOLS}
+ OADTOOLS    = ${OADTOOLSMK}
  #eh3  new defines for the adjoint work
- AUTODIFF    = ${ROOTDIR}/pkg/autodiff
+ AUTODIFF    = \$(ROOTDIR)/pkg/autodiff
  EXE_AD      = ${EXE_AD}
  EXE_FTL     = ${EXE_FTL}
  EXE_SVD     = ${EXE_SVD}
-Line 2891 
 CPPINCLUDES = ${CPPINCLUDES}
+Line 2951 
 CPPINCLUDES = ${CPPINCLUDES}
  KFLAGS1 = ${KFLAGS1}
  KFLAGS2 = ${KFLAGS2}
  # Optim./debug for FC
- FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
+ FFLAGS = ${FFLAGS}
- FOPTIM = ${FOPTIM}
+ FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
  # Optim./debug for FC
  F90FLAGS = ${F90FLAGS}
  F90OPTIM = ${F90OPTIM}
-Line 2958 
 depend:
+Line 3018 
 depend:
  lib: libmitgcmuv.a
- libmitgcmuv.a: \$(OBJFILES)
+ libmitgcmuv.a: \$(SPECIAL_FILES) \$(OBJFILES)
          ar rcv libmitgcmuv.a \$(OBJFILES)
          ar d   libmitgcmuv.a main.o
-Line 2968 
 links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
+Line 3028 
 links: \$(F77_SRC_FILES) \$(C_SRC_FILES)
  small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
- output.txt: \$(EXECUTABLE)
-         @printf 'running ... '
-         @\$(EXECUTABLE) > \$@
  # remove most of the files that "make" generates
  clean:
          -rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
-Line 3123 
 done
+Line 3179 
 done
  echo >> $MAKEFILE
  rm -f $TMP.adSrcFiles
+ if test $CAT_SRC_FOR_TAF = 0 ; then
+ cat >>$MAKEFILE <<EOF
+ # ... Utilities ...
+ remove_comments:
+         sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
+         @-rm -f \$(AD_FILES:.$FS=.$FS.bak)
+ adj_sed:
+         sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
+         @-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
+ ftl_sed:
+         sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
+         @-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
+ adobjfiles: \$(AD_FILES:.$FS=_ad.o)
+ ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
+ EOF
+ fi
  cat >>$MAKEFILE <<EOF
  # ... AD ...
-Line 3145 
 ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
+Line 3219 
 ad_input_code.$FS: \$(AD_FILES) \$(AD_FL
          @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
          cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
- ad_taf_output.$FS: ad_input_code.$FS
+ adtafonly:
-         @-rm -f ad_input_code_ad.$FS ; echo ''
          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
          ls -l ad_input_code_ad.$FS
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
- adtafonly:
+ EOF
+ if test $CAT_SRC_FOR_TAF = 1 ; then
+ cat >>$MAKEFILE <<EOF
+ # ... send 1 file to TAF ...
+ ad_taf_output.$FS: ad_input_code.$FS
+         @-rm -f ad_input_code_ad.$FS ; echo ''
          \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
          ls -l ad_input_code_ad.$FS
          cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
-Line 3159 
 adtafonly:
+Line 3238 
 adtafonly:
  \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
          \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
- ad_tamc_output.$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
- ad_tamc: ad_tamc_output.o \$(OBJFILES)
+ EOF
-         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
+ else
+ cat >>$MAKEFILE <<EOF
+ # ... send multiple files to TAF ...
+ ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+         cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+         @\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
+         @-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
+         \$(MAKE) -f \$(MAKEFILE) remove_comments
+         \$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
+         \$(MAKE) -f \$(MAKEFILE) adj_sed
+         cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
+ \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
+         \$(MAKE) -f \$(MAKEFILE) adobjfiles
+         \$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
+ adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
+         \$(MAKE) -f \$(MAKEFILE) adobjfiles
+ EOF
+ fi
+ cat >>$MAKEFILE <<EOF
  adonlyfwd:
          patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
  adtrick:
          patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
- adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
+ ad_tamc_output.$FS: ad_input_code.$FS
+         \$(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
+ ad_tamc: ad_tamc_output.o \$(OBJFILES)
+         \$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
  # ... FTL ...
  ftlall: ftl_exe_target
-Line 3194 
 ftl_input_code.$FS: \$(AD_FILES)
+Line 3301 
 ftl_input_code.$FS: \$(AD_FILES)
          @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
          cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
- ftl_taf_output.$FS: ftl_input_code.$FS
+ ftltafonly:
-         @-rm -f ftl_input_code_tl.$FS ; echo ''
          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
          ls -l ftl_input_code_tl.$FS
          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
- ftltafonly:
+ EOF
+ if test $CAT_SRC_FOR_TAF = 1 ; then
+ cat >>$MAKEFILE <<EOF
+ # ... send 1 file to TAF ...
+ ftl_taf_output.$FS: ftl_input_code.$FS
+         @-rm -f ftl_input_code_tl.$FS ; echo ''
          \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
          ls -l ftl_input_code_tl.$FS
          cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
-Line 3208 
 ftltafonly:
+Line 3320 
 ftltafonly:
  \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
          \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
+ EOF
+ else
+ cat >>$MAKEFILE <<EOF
+ # ... send multiple files to TAF ...
+ ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+         cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         @\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+         @\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
+         @-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
+         \$(MAKE) -f \$(MAKEFILE) remove_comments
+         \$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
+         \$(MAKE) -f \$(MAKEFILE) ftl_sed
+         cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
+ \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
+         \$(MAKE) -f \$(MAKEFILE) ftlobjfiles
+         \$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
+ EOF
+ fi
+ cat >>$MAKEFILE <<EOF
  ftl_tamc_output.$FS: ftl_input_code.$FS
          \$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
          cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
-Line 3250 
 if test "x$OPENAD" != x ; then
+Line 3387 
 if test "x$OPENAD" != x ; then
  # ============ begin OpenAD specific section ==============
  cat >>$MAKEFILE <<EOF
+ # ... OpenAD ...
  # all the source files linked from the various locations:
  ALL_LINKED_FILES= \
-Line 3303 
 rm -f $TMP.adSrcFiles
+Line 3441 
 rm -f $TMP.adSrcFiles
  cat >>$MAKEFILE <<EOF
- adAll: \$(EXE_AD)
+ adAll: ad_exe_target
  .PHONY: adAll
+ ad_exe_target:
+         @echo Update AD_CONFIG.h and make \$(EXE_AD)
+         @$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
+         @cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+         @-rm -f ad_config.template
+         \$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
  CB2M_F90_PP_SRC_FILES=\$(addsuffix _mod.f$FS90, \$(CB2M_F90_SRC_NAMES))
  .PRECIOUS: \$(CB2M_F90_PP_SRC_FILES) \$(NON_AD_F77_SRC_FILES:.F=_cb2m.f$FS90)
-Line 3322 
 OAD_active.F90 \
+Line 3467 
 OAD_active.F90 \
  OAD_cp.F90 \
  OAD_rev.F90 \
  OAD_tape.F90 \
+ OAD_regular_cp.F90 \
  revolve.F90
  OPENAD_SUPPORT_C_SRC_FILES = \
-Line 3348 
 AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
+Line 3494 
 AD_OBJ_FILES_S2=\$(AD_OBJ_FILES_S1) \$(N
          \$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
  # create sources files modules from header files containing common blocks
- %_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
+ %_mod.FF90 : %.h \$(OADTOOLS)/cb2mGetModules.csh \$(OADTOOLS)/cb2mGetModules.awk
-         \${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
+         \$(OADTOOLS)/cb2mGetModules.csh $< \$(OADTOOLS)/cb2mGetModules.awk
  # create new header files with USE statements for the new modules made above
- %_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
+ %_mod.h : %.h \$(OADTOOLS)/cb2mGetHeaders.csh \$(OADTOOLS)/cb2mGetHeaders.awk
-         \${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+         \$(OADTOOLS)/cb2mGetHeaders.csh $< \$(OADTOOLS)/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
  # change the include directives of everybody to refer to  the new header files with the USE statements
- %_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
+ %_cb2m.FF90 : %.F \$(OADTOOLS)/cb2mUseModules.bash
-         \${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
+         \$(OADTOOLS)/cb2mUseModules.bash $< ${MPI}
  # makefile debug rule
  small_f: \$(CB2M_F90_PP_SRC_FILES)
  .PHONY: small_f
- ad_output.txt: \$(EXE_AD)
-         @printf 'linking data files ... '
-         \$(LN) -f ../input_ad/data* ../input_ad/eedata .
-         \$(LN) -f ../../global_ocean.90x40x15/input/*.bin .
-         @printf 'running ... '
-         @./\$(EXE_AD) > \$@
  ad_input_code.f$FS90:  \$(CB2M_AD_FILES)
          cat \$^ > \$@
-Line 3379 
 ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
+Line 3518 
 ad_input_code_sf.pre.f90 : \$(CB2M_AD_FI
  # replace stop statements (to avoid the implied unstructured control flow)  with print statements
  ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
-         cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
+         cat \$< | sed -f \$(OADTOOLS)/stop2print.sed > ad_input_code_sf.pre.s2p.f90
  # F -> WHIRL
  ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
-Line 3402 
 ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
+Line 3541 
 ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS
          \${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
  # insert template directives
- 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
+ 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
-         \${OADTOOLS}/insertTemplateDir.bash \$< \$@
+         \$(OADTOOLS)/insertTemplateDir.bash \$< \$@
- PPEXTRAS=\$(notdir \$(wildcard \${OADTOOLS}/ad_template.*.F)) ad_inline.F
+ PPEXTRAS=\$(notdir \$(wildcard \$(OADTOOLS)/ad_template.*.F)) ad_inline.F
  # postprocess F'
  postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
          \${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ad_inline.f \$<
-Line 3420 
 OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
+Line 3559 
 OAD_intrinsics_oad.f \$(CB2M_AD_FILES:.f
  # link the support files:
  \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES) \$(PPEXTRAS):
-         \$(LN) \${OADTOOLS}/\$@ .
+         \$(LN) \$(OADTOOLS)/\$@ .
  AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag

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