--- MITgcm/tools/genmake2	2010/12/26 01:04:45	1.218
+++ MITgcm/tools/genmake2	2011/08/03 18:14:08	1.222
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.218 2010/12/26 01:04:45 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.222 2011/08/03 18:14:08 jmc Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -96,11 +96,6 @@
           will search for a working compiler by trying a list of
           "usual suspects" such as gcc, c89, cc, etc.
 
-    -[no]ieee | --[no]ieee
-          Do or don't use IEEE numerics.  Note that this option
-          *only* works if it is supported by the OPTFILE that
-          is being used.
-
     -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
           Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
           *only* works if CPP_EEOPTIONS.h allows this.
@@ -126,10 +121,14 @@
     -hpmt | --hpmt
           Performance analysis with the HPM Toolkit
 
-    -gsl | --gsl
-          Use GSL to control floating point rounding and precision
+    -ieee | --ieee
+          use IEEE numerics.  Note that this option *only* works
+          if it is supported by the OPTFILE that is being used.
     -devel | --devel
           Add additional warning and debugging flags for development
+          (if supported by the OPTFILE); also switch to IEEE numerics.
+    -gsl | --gsl
+          Use GSL to control floating point rounding and precision
 
     -mpi | --mpi
           Include MPI header files and link to MPI libraries
@@ -359,6 +358,11 @@
 		MAKEDEPEND=
 	    fi
 	else
+	    echo "${MAKEDEPEND}" | grep 'tools.xmakedepend' > /dev/null 2>&1
+	    RETVAL=$?
+	    if test "x$RETVAL" = x0 ; then
+		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	    fi
 	    echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	fi
     fi
@@ -1124,7 +1128,6 @@
 EXECUTABLE=
 EXEHOOK=
 EXEDIR=
-PACKAGES_CONF=
 IEEE=
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
@@ -1146,22 +1149,23 @@
 TAMC_EXTRA=
 
 #  The following state can be set directly by command-line switches
-gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS MAKEFILE MAKEDEPEND PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC CC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
+gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS DISABLE ENABLE MAKEFILE MAKEDEPEND PLATFORM"
+gm_s2="FC CC MPI OMP USE_R4 TS PAPIS PCLS PAPI PCL HPMT IEEE DEVEL GSL FEXTRAFLAGS"
+gm_s3="ROOTDIR STANDARDDIRS MODS DUMPSTATE"
 
 #  The following state is not directly set by command-line switches
-gm_s3="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
-gm_s4="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD THISHOST THISUSER THISDATE THISVER MACHINE"
-gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
-gm_s7="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"
+gm_s4="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM"
+gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
+gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
+gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"
+gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"
 
 #  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_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
 gm_s12="TAF_EXTRA TAMC_EXTRA"
 
-gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
+gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
 gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
 
 cat <<EOF
@@ -1311,13 +1315,17 @@
 	-fs90=* | --fs90=*)
 	    FS90=$ac_optarg ;;
 	
+	-use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
+	    USE_R4=true ;;
+
 	-ieee | --ieee)
 	    IEEE=true ;;
 	-noieee | --noieee)
-	    IEEE= ;;
-
-	-use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4 )
-	    USE_R4=true ;;
+	    echo "Warning: ignore option '$ac_option' (default is already without '-ieee')" ;;
+        -devel | --devel)
+	    IEEE=true ; DEVEL=true ;;
+        -gsl | --gsl)
+	    GSL=true ;;
 
 	-ts | --ts)
 	    TS=true ;;
@@ -1334,12 +1342,6 @@
 	-hpmt | --hpmt)
 	    HPMT=true ;;
 
-        -gsl | --gsl)
-	    GSL=true ;;
-
-        -devel | --devel)
-	    DEVEL=true ;;
-
 	-mpi | --mpi)
 	    MPI=true ;;
 	-mpi=* | --mpi=*)
@@ -1355,6 +1357,11 @@
 	-ds | --ds)
 	    DUMPSTATE=t ;;
 	
+	-extra_flag | --extra_flag)
+	    ac_prev=FEXTRAFLAGS ;;
+	-extra_flag=* | --extra_flag=*)
+	    FEXTRAFLAGS=$ac_optarg ;;
+	
 	-taf_extra | --taf_extra)
 	    ac_prev=TAF_EXTRA ;;
 	-taf_extra=* | --taf_extra=*)
@@ -1390,7 +1397,7 @@
     echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
     echo "  file.  This file format is no longer supported.  For directions on"
     echo "  how to setup and use the new \"genmake2\" script, please see:"
-    echo "    http://mitgcm.org/devel_HOWTO/"
+    echo "    http://mitgcm.org/public/devel_HOWTO/"
     echo "  and send an email to MITgcm-support@mitgcm.org if you need help."
     echo "WARNING: ignore \"./.genmakerc\" and continue."
     echo
@@ -1438,7 +1445,7 @@
     MAKEFILE="Makefile"
 fi
 
-echo "  getting OPTFILE information:  "
+echo "  getting OPTFILE information:"
 if test "x${OPTFILE}" = x ; then
     if test "x$MITGCM_OF" = x ; then
 	echo "Warning: no OPTFILE specified so we'll look for possible settings"
@@ -1467,7 +1474,7 @@
     fi
 fi
 
-echo "  getting AD_OPTFILE information:  "
+echo "  getting AD_OPTFILE information:"
 if test "x${AD_OPTFILE}" = x ; then
     if test "x$MITGCM_AD_OF" = x ; then
 	AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
@@ -2679,6 +2686,7 @@
 \$(EXECUTABLE): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(OBJFILES) \$(EMBEDDED_FILES)
 	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
+
 depend:
 	@make links
 	\$(MAKEDEPEND) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
@@ -2691,6 +2699,8 @@
 	ar rcv libmitgcmuv.a \$(OBJFILES)
 	ar d   libmitgcmuv.a main.o
 
+obj: \$(OBJFILES)
+
 links: \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77_PP_SRC_FILES) \$(F90_PP_SRC_FILES)
@@ -2719,7 +2729,8 @@
 CLEAN:
 	@make Clean
 	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak
-	-rm -f $LOGFILE genmake_state genmake_*optfile genmake.tr_log make.tr_log
+	-rm -f $LOGFILE genmake_state genmake_*optfile
+	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
@@ -3247,6 +3258,6 @@
     for i in $gm_state ; do
 	t1="t2=\$$i"
 	eval $t1
-	echo "$i='$t2'" >> genmake_state
+	echo "$i='$t2'" | sed -e 's/  */ /g' >> genmake_state
     done
 fi