--- MITgcm/tools/genmake2	2009/01/02 20:32:21	1.181
+++ MITgcm/tools/genmake2	2009/04/21 22:35:41	1.189
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.181 2009/01/02 20:32:21 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.189 2009/04/21 22:35:41 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -611,6 +611,11 @@
           set to PATH. i.e. Include files from \$PATH/include, link to libraries
           from \$PATH/lib and use binaries from \$PATH/bin.
 
+    -omp | --omp
+          Activate OpenMP code + use Compiler option OMPFLAG
+    -omp=OMPFLAG | --omp=OMPFLAG
+          Activate OpenMP code + use Compiler option OMPFLAG
+
     -es | --es | -embed-source | --embed-source
           Embed a tarball containing the full source code 
           (including the Makefile, etc.) used to build the 
@@ -1058,6 +1063,8 @@
 NOOPTFLAGS=
 MPI=
 MPIPATH=
+OMP=
+OMPFLAG=
 TS=
 PAPIS=
 PCLS=
@@ -1125,7 +1132,7 @@
 
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s2="FC CPP IEEE TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
 gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
@@ -1326,10 +1333,11 @@
 	    MPIPATH=$ac_optarg
 	    MPI=true ;;
 	
-#	-jam | --jam)
-#	    JAM=1 ;;
-#	-nojam | --nojam)
-#	    JAM=0 ;;
+ 	-omp | --omp)
+ 	    OMP=true ;;
+	-omp=* | --omp=*)
+	    OMPFLAG=$ac_optarg
+	    OMP=true ;;
 	
 	-ds | --ds)
 	    DUMPSTATE=t ;;
@@ -1567,6 +1575,12 @@
       echo "  Turning on MPI cpp macros"
       DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
 fi
+if test ! "x$OMP" = x ; then
+      echo "  Add OMPFLAG and turn on OpenMP cpp macros"
+      FFLAGS="$FFLAGS $OMPFLAG"
+      F90FLAGS="$F90FLAGS $OMPFLAG"
+      DEFINES="$DEFINES -DUSE_OMP_THREADING"
+fi
 
 if test ! "x$TS" = x ; then
       echo "  Turning on timing per timestep"
@@ -1775,19 +1789,63 @@
 
 
 printf "\n===  Setting defaults  ===\n"
-printf "  Adding MODS directories:  "
+printf "  Adding MODS directories: "
+MPI_LNKF=
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	printf " $d"
+	printf "$d "
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
+	#-------------------------------------------------------
+	# Put special links so that MPI specific files are used
+	MPI_FILES=`(cd $d ; find . -name "*_mpi" -print)`
+	for i in $MPI_FILES ; do
+	  ii=`echo $i | sed 's:^\./::'`
+	  name=`echo $ii | sed 's:_mpi::' `
+	  if test "x$MPI" = x ; then
+	  # NO: We undo an _mpi symbolically linked file
+	    if test -L $name ; then
+	      cmp $name "$d/$ii" > /dev/null 2>&1
+	      RETVAL=$?
+	      if test "x$RETVAL" = x0 ; then
+		printf "Un-linking $name ; "
+		rm -f $name
+	      fi
+	    fi
+	  else
+	  # YES: We symbolically link this file (with conditions if already there)
+	    if test -L $name ; then
+	      cmp $d/$ii $name > /dev/null 2>&1
+	      RETVAL=$?
+	      yy=0 ; 
+	      for xx in $MPI_LNKF ; do if test $xx = $name ; then yy=1 ; fi ; done
+ 	      if test "x$RETVAL" != x0 -a $yy = 0 ; then
+	      # remove sym-link if different and has not just been linked
+		printf "Un-link + "
+		rm -f $name
+	      fi
+	      if test "x$RETVAL" = x0 ; then
+	      # if identical, keep sym-link and keep record of it
+		MPI_LNKF="$MPI_LNKF $name"
+	      fi
+	    fi
+	    if ! test -f $name ; then
+	      # make sym-link and keep record of it
+		printf "Linking $ii to $name ; "
+		ln -sf $d/$ii $name
+		MPI_LNKF="$MPI_LNKF $name"
+	    fi
+	  fi
+	done
+	#-------------------------------------------------------
     fi
 done
 echo
+#echo "MPI_LNKF='$MPI_LNKF'"
 
 if test "x${PLATFORM}" = x ; then
     PLATFORM=$p_PLATFORM
@@ -2528,7 +2586,6 @@
     echo "EMBEDDED_FILES = " >>$MAKEFILE
 fi
 
-#  Note: figure out some way to add Hyades JAM libraries here 
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
@@ -2727,7 +2784,7 @@
 #===  Automatic Differentiation Rules  ===
 #===  for TAMC/TAF  ======================
 
-if test "x$OPENAD" == x ; then 
+if test "x$OPENAD" = x ; then 
 
 cat >>$MAKEFILE <<EOF
 
@@ -2768,7 +2825,7 @@
 adtaf: ad_taf_output.$FS
 adtamc: ad_tamc_output.$FS
 
-ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
 	@$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
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
@@ -3012,7 +3069,7 @@
 
 # canonicalizer
 ad_input_code_sf.w2f.pre.f$FS90: ad_input_code_sf.w2f.f$FS90 preProcess.py
-	./preProcess.py --mode=reverse \$< -o \$@
+	./preProcess.py -H -S \$< -o \$@
 
 # F -> WHIRL
 # note that the canonicalized version cuts off at col 72 
@@ -3029,23 +3086,24 @@
 	./whirl2xaif -s -n --debug 1 -o \$@ \$<
 
 # XAIF -> XAIF'
-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 openad_adm
-	./openad_adm -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
+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
+	./oadDriver -f -t forward_step -i \$< -c \${XAIFSCHEMAROOT}/schema/examples/inlinable_intrinsics.xaif -o \$@ -I -r
 
 # XAIF' -> WHIRL'
 ad_input_code_sf.w2f.pre.xb.x2w.B : ad_input_code_sf.w2f.pre.xb.xaif xaif2whirl
-	./xaif2whirl --debug 1 --structured ad_input_code_sf.w2f.pre.B \$<
+	./xaif2whirl --debug 1 -t OpenADTy_active --structured ad_input_code_sf.w2f.pre.B \$<
 
 # WHIRL' -> F'
 ad_input_code_sf.w2f.pre.xb.x2w.w2f.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.B whirl2f whirl2f_be
-	./whirl2f -FLIST:ftn_file=\$@ -openad \$< 
+	./whirl2f -FLIST:ftn_file=\$@ -openad -openadType OpenADTy_active  \$< 
 
 # insert template directives
 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
 	../OAD_support/insertTemplateDir.bash \$< \$@
 
+PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
 # postprocess F'
-ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl ../OAD_support/ad_inline.f \$(wildcard ../OAD_support/ad_template.*.f)
+ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.f$FS90 multi-pp.pl \$(PPEXTRAS:.F=.f)
 	perl multi-pp.pl -inline=../OAD_support/ad_inline.f \$<
 	# the postprocessor still gets the name wrong
 	cat \$<.pp | sed 's/RETURN//' > \$@
@@ -3084,8 +3142,8 @@
 whirl2f whirl2f_be:
 	\$(LN) \${OPEN64ROOT}/whirl2f/\$@ .
 
-openad_adm:
-	\$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/test/t \$@
+oadDriver:
+	\$(LN) \${XAIFBOOSTERROOT}/xaifBooster/algorithms/BasicBlockPreaccumulationReverse/driver/oadDriver \$@
 
 # ============ end OpenAD specific section ==============