--- MITgcm/tools/genmake2	2012/01/17 22:55:39	1.228
+++ MITgcm/tools/genmake2	2012/07/06 18:55:13	1.231
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.228 2012/01/17 22:55:39 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.231 2012/07/06 18:55:13 jmc Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -384,7 +384,7 @@
       stop
       end
 EOF
-	makedepend genmake_tc.f > /dev/null 2>&1
+	makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
 	RV1=$?
 	test -f $MAKEFILE  &&  rm -f $MAKEFILE
 	test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
@@ -450,7 +450,6 @@
 	    RETVAL=$?
 	    if test "x$RETVAL" = x0 ; then
 		echo "OK"
-		DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 		return 0
 	    fi
 	done
@@ -462,7 +461,6 @@
 	return 1
     fi
     echo "OK"
-    DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 }
 
 #  look for possible C compilers
@@ -784,7 +782,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_CLOC=t
-	DEFINES="$DEFINES -DHAVE_CLOC"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
@@ -846,17 +843,12 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SIGREG=t
-	DEFINES="$DEFINES -DHAVE_SIGREG"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
 }
 
 check_HAVE_SETRLSTK()  {
-    if test "x$HAVE_SETRLSTK" = xt ; then
-	DEFINES="$DEFINES -DHAVE_SETRLSTK"
-	return
-    fi	
     if test ! "x$HAVE_SETRLSTK" = x ; then
 	return
     fi
@@ -894,7 +886,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SETRLSTK=t
-	DEFINES="$DEFINES -DHAVE_SETRLSTK"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
@@ -941,7 +932,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_STAT=t
-	DEFINES="$DEFINES -DHAVE_STAT"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
@@ -1768,6 +1758,7 @@
 printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
 check_HAVE_CLOC
 if test "x$HAVE_CLOC" != x ; then
+    DEFINES="$DEFINES -DHAVE_CLOC"
     echo "yes"
 else
     echo "no"
@@ -1782,6 +1773,7 @@
 printf "  Can we unlimit the stack size using $FC...  "
 check_HAVE_SETRLSTK
 if test "x$HAVE_SETRLSTK" = xt ; then
+    DEFINES="$DEFINES -DHAVE_SETRLSTK"
     echo "yes"
 else
     echo "no"
@@ -1791,6 +1783,7 @@
 printf "  Can we register a signal handler using $FC...  "
 check_HAVE_SIGREG
 if test "x$HAVE_SIGREG" = xt ; then
+    DEFINES="$DEFINES -DHAVE_SIGREG"
     echo "yes"
 else
     echo "no"
@@ -1800,6 +1793,7 @@
 printf "  Can we use stat() through C calls...  "
 check_HAVE_STAT
 if test "x$HAVE_STAT" != x ; then
+    DEFINES="$DEFINES -DHAVE_STAT"
     echo "yes"
 else
     echo "no"
@@ -1809,6 +1803,7 @@
 printf "  Can we create NetCDF-enabled binaries...  "
 check_netcdf_libs
 if test "x$HAVE_NETCDF" != x ; then
+    DEFINES="$DEFINES -DHAVE_NETCDF"
     echo "yes"
 else
     echo "no"
@@ -1820,6 +1815,7 @@
 fi
 if test "x$EMBED_SRC" = xt ; then
     ENABLE="$ENABLE embed_files"
+#   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 fi
 
 printf "\n===  Setting defaults  ===\n"
@@ -2697,7 +2693,7 @@
 
 depend:
 	@make -f \$(MAKEFILE) links
-	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
@@ -2757,7 +2753,7 @@
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
 AD_CONFIG.h:
 	@echo Creating \$@ ...
-	@$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 > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
 FC_NAMEMANGLE.h:
 	@echo Creating \$@ ...
 	echo "$FC_NAMEMANGLE" > \$@
@@ -2871,7 +2867,7 @@
 adtamc: ad_tamc_output.$FS
 
 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
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
 	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
@@ -2912,7 +2908,7 @@
 ftltamc: ftl_tamc_output.$FS
 
 ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
-	@$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
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
 	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
@@ -2959,7 +2955,7 @@
 	touch ad_taf_output.$FS ftl_taf_output.$FS
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
-	@$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 "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
 
@@ -3036,7 +3032,7 @@
 
 .PHONY: adDepend
 adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h, \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES)) \$(F77_SRC_FILES:.F=_cb2m.FF90)
-	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
@@ -3259,7 +3255,7 @@
     fi
 fi
 if test ! -f AD_CONFIG.h ; then
-    $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 "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
 fi
 
 #  Write the "state" for future records