--- MITgcm/tools/genmake2	2011/09/30 20:03:10	1.226
+++ 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 1.226 2011/09/30 20:03:10 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
@@ -297,7 +297,7 @@
 .F.$tfs:
 	$LN \$< \$@
 EOF
-    $MAKE "genmake_hello."$tfs > /dev/null 2>&1
+    $MAKE -f $MAKEFILE "genmake_hello."$tfs > /dev/null 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 -o ! -f "genmake_hello."$tfs ; then
 	if test "x$FS" = x ; then
@@ -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"
@@ -2658,7 +2654,7 @@
 NOOPTFLAGS = ${NOOPTFLAGS}
 # Flags and libraries needed for linking
 LIBS = ${LIBS}
-# Name of the Mekfile
+# Name of the makefile
 MAKEFILE=${MAKEFILE}
 
 EOF
@@ -2696,8 +2692,8 @@
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 
 depend:
-	@make links
-	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+	@make -f \$(MAKEFILE) links
+	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
@@ -2726,8 +2722,8 @@
 
 # remove most of the files that "make" and "make depend" generate
 Clean:
-	@make clean
-	@make cleanlinks
+	@make -f \$(MAKEFILE) clean
+	@make -f \$(MAKEFILE) cleanlinks
 	-rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
 	-rm -f genmake_warnings genmake_errors make.log
@@ -2735,7 +2731,7 @@
 # remove also the executable, files that "genmake2" generates (except Makefile)
 #         and output from a run (plus log files from testreport)
 CLEAN:
-	@make Clean
+	@make -f \$(MAKEFILE) Clean
 	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak
 	-rm -f $LOGFILE genmake_state genmake_*optfile
 	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
@@ -2757,7 +2753,7 @@
 	@$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 "$FC_NAMEMANGLE" > \$@
@@ -2871,11 +2867,11 @@
 adtamc: ad_tamc_output.$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
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	-rm -f ad_config.template
-	@make \$(F77_PP_SRC_FILES)
-	@make \$(FLOFILES)
+	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@make -f \$(MAKEFILE) \$(FLOFILES)
 	cat \$(FLOFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
 
 ad_taf_output.$FS: ad_input_code.$FS
@@ -2912,11 +2908,11 @@
 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
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
-	@make \$(F77_PP_SRC_FILES)
-	@make \$(AD_FLOW_FILES)
+	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@make -f \$(MAKEFILE) \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
 
 ftl_taf_output.$FS: ftl_input_code.$FS
@@ -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
 
@@ -3175,7 +3171,7 @@
 	# this step also creates the file postProcess.make but we cannot
 	# name it as the target or else make will try to remake it for
 	# the include directive above for any rule, e.g. make clean
-	./postProcess.py --progress --timing --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<
+	./postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed -m r -i ../OAD_support/ad_inline.f --width 4 \$<
 
 # setup some links
 %.xsd:
@@ -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