--- MITgcm/tools/genmake2	2009/03/29 19:09:24	1.186
+++ MITgcm/tools/genmake2	2009/04/22 18:35:00	1.190
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.186 2009/03/29 19:09:24 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.190 2009/04/22 18:35:00 utke 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$TS" = x ; then
       echo "  Turning on timing per timestep"
@@ -2572,7 +2586,6 @@
     echo "EMBEDDED_FILES = " >>$MAKEFILE
 fi
 
-#  Note: figure out some way to add Hyades JAM libraries here 
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
@@ -2812,7 +2825,7 @@
 adtaf: ad_taf_output.$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
@@ -3090,10 +3103,8 @@
 
 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 \$(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//' > \$@
+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 postProcess.py \$(PPEXTRAS:.F=.f)
+	./postProcess.py -m r -i ../OAD_support/ad_inline.f -o \$@ \$<
 
 # extract all transformed modules 
 all_mods.xb.x2w.w2f.pp.f$FS90: ad_input_code_sf.w2f.pre.xb.x2w.w2f.td.pp.f$FS90
@@ -3120,10 +3131,7 @@
 whirl2xaif xaif2whirl: 
 	\$(LN) \${OPENADFORTTK}/bin/\$@ .
 
-%.pl: 
-	\$(LN) \${OPENADFORTTK}/bin/\$@ .
-
-preProcess.py: 
+preProcess.py postProcess.py: 
 	\$(LN) \${OPENADFORTTK_BASE}/tools/SourceProcessing/\$@ .
 
 whirl2f whirl2f_be: