--- MITgcm/tools/genmake2	2014/01/06 16:49:10	1.263
+++ MITgcm/tools/genmake2	2014/07/15 23:05:54	1.267
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.263 2014/01/06 16:49:10 jahn Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.267 2014/07/15 23:05:54 heimbach Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -19,9 +19,13 @@
     -help | --help | -h | --h
 	  Print this help message and exit.
 
+    -oad | --oad
+	  Generate a Makefile for an OpenAD built
+
     -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
@@ -1079,9 +1083,7 @@
 }
 
 check_lapack_libs()  {
-    if test ! "x$SKIP_LAPACK_CHECK" = x ; then
-	return
-    fi
+    if test "x$CHECK_FOR_LAPACK" = xf ; then return ; fi
     echo >> $LOGFILE
     echo "running: check_lapack_libs()" >> $LOGFILE
     cat <<EOF > genmake_tla.F
@@ -1277,8 +1279,8 @@
 DEVEL=
 HAVE_TEST_L=
 
-# comment this line out to enable lapack test
-SKIP_LAPACK_CHECK=t
+# set this to "t" to enable lapack test
+CHECK_FOR_LAPACK=f
 
 # DEFINES checked by test compilation or command-line
 HAVE_SYSTEM=
@@ -1325,6 +1327,7 @@
 FS90=
 
 AUTODIFF_PKG_USED=f
+OPENAD=
 AD_OPTFILE=
 TAF=
 AD_TAF_FLAGS=
@@ -1355,7 +1358,7 @@
 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"
 
@@ -1407,6 +1410,8 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 
+	-oad | --oad)
+	    OPENAD="true" ;;
 	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
@@ -1680,10 +1685,12 @@
 
 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${AD_OPTFILE}" != xNONE ; then
@@ -2624,7 +2631,7 @@
     OAD_CB2M_FILES="/dev/null"
     OADTOOLS="$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"
@@ -2632,7 +2639,7 @@
 	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"
@@ -2640,7 +2647,7 @@
 	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"
@@ -2648,7 +2655,7 @@
 	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"
@@ -2964,10 +2971,6 @@
 
 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
@@ -3246,6 +3249,7 @@
 # ============ begin OpenAD specific section ==============
 
 cat >>$MAKEFILE <<EOF
+# ... OpenAD ...
 
 # all the source files linked from the various locations:
 ALL_LINKED_FILES= \
@@ -3299,9 +3303,16 @@
 
 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)
@@ -3359,13 +3370,6 @@
 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 \$^ > \$@