--- MITgcm/tools/genmake2	2011/11/03 22:46:47	1.227
+++ MITgcm/tools/genmake2	2012/01/17 22:55:39	1.228
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.227 2011/11/03 22:46:47 utke Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.228 2012/01/17 22:55:39 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
@@ -2658,7 +2658,7 @@
 NOOPTFLAGS = ${NOOPTFLAGS}
 # Flags and libraries needed for linking
 LIBS = ${LIBS}
-# Name of the Mekfile
+# Name of the makefile
 MAKEFILE=${MAKEFILE}
 
 EOF
@@ -2696,7 +2696,7 @@
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 
 depend:
-	@make links
+	@make -f \$(MAKEFILE) links
 	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
@@ -2726,8 +2726,8 @@
 
 # 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 +2735,7 @@
 # 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 $LOGFILE genmake_state genmake_*optfile
 	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
@@ -2874,8 +2874,8 @@
 	@$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
-	@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
@@ -2915,8 +2915,8 @@
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
-	@make \$(F77_PP_SRC_FILES)
-	@make \$(AD_FLOW_FILES)
+	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@make -f \$(MAKEFILE) \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.$FS
 
 ftl_taf_output.$FS: ftl_input_code.$FS