--- MITgcm/tools/genmake2	2010/11/01 00:20:28	1.209
+++ MITgcm/tools/genmake2	2010/11/02 22:45:07	1.211
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.209 2010/11/01 00:20:28 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.211 2010/11/02 22:45:07 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -656,17 +656,18 @@
     if test ! "x$FC_NAMEMANGLE" = x ; then
         return 0
     fi
+    echo "running: get_fortran_c_namemangling()" >> $LOGFILE
 
     default_nm="#define FC_NAMEMANGLE(X) X ## _"
 
     cat > genmake_test.c <<EOF
 void tcall( char * string ) { tsub( string ); }
 EOF
-    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    $MAKE genmake_test.o >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_errors
+	cat <<EOF>> $LOGFILE
 
 WARNING: C test compile fails
 WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
@@ -678,7 +679,7 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
 WARNING: The "nm" command failed.
 WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
@@ -692,13 +693,13 @@
       call tsub( string )
       end
 EOF
-    $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+    $FC $FFLAGS -c genmake_tcomp.$FS >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+WARNING: FORTRAN test compile fails -- please see '$LOGFILE'
 WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
 WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
 EOF
@@ -708,7 +709,7 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
 WARNING: The "nm" command failed.
 WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
@@ -742,6 +743,8 @@
 
 
 check_HAVE_CLOC()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_CLOC()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -759,8 +762,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -771,10 +774,10 @@
       end
 EOF
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_F=$?
-    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
+    test -x ./genmake_tc  &&  ./genmake_tc >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_CLOC=t
@@ -788,6 +791,8 @@
     if test ! "x$HAVE_SIGREG" = x ; then
 	return
     fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SIGREG()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -820,8 +825,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -831,12 +836,10 @@
       call sigreg(anint)
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_SIGREG()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SIGREG=t
@@ -854,6 +857,8 @@
     if test ! "x$HAVE_SETRLSTK" = x ; then
 	return
     fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SETRLSTK()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -870,8 +875,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -879,12 +884,10 @@
       call setrlstk()
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SETRLSTK=t
@@ -895,6 +898,8 @@
 
 
 check_HAVE_STAT()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_STAT()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -916,7 +921,7 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
+    echo $COMM >> $LOGFILE
     $COMM >> genmake_tc.log 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
@@ -926,11 +931,9 @@
       print *," HELLO WORLD", nbyte
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_STAT()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
+    echo $COMM >> $LOGFILE
     $COMM >> genmake_tc.log 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
@@ -945,8 +948,8 @@
     if test ! "x$SKIP_NETCDF_CHECK" = x ; then
 	return
     fi
-    echo >> genmake_warnings
-    echo "running: check_netcdf_libs()" >> genmake_warnings
+    echo >> $LOGFILE
+    echo "running: check_netcdf_libs()" >> $LOGFILE
     cat <<EOF > genmake_tnc.F
       program fgennc
 #include "netcdf.inc"
@@ -964,9 +967,9 @@
       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
       end
 EOF
-    echo "===  genmake_tnc.F  ===" > genmake_tnc.log
+    echo "===  genmake_tnc.F  >>>" > genmake_tnc.log
     cat genmake_tnc.F >> genmake_tnc.log
-    echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
+    echo "<<<  genmake_tnc.F  ===" >> genmake_tnc.log
     RET_CPP=f
     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
     echo "$COMM" >> genmake_tnc.log
@@ -982,7 +985,7 @@
     $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 	&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
     RET_COMPILE=$?
-    cat genmake_tnc.log >> genmake_warnings
+    cat genmake_tnc.log >> $LOGFILE
 
     #EH3  Remove test program execution for machines that either disallow
     #EH3  execution or cannot support it (eg. cross-compilers)
@@ -993,9 +996,10 @@
 
     if test "x$RET_COMPILE" = x0 ; then
 	HAVE_NETCDF=t
+	echo "check_netcdf: successful" >> $LOGFILE
     else
 	# try again with "-lnetcdf" added to the libs
-	echo "try again with added '-lnetcdf'" > genmake_tnc.log
+	echo "==> try again with added '-lnetcdf'" > genmake_tnc.log
 	echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
 	echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
 	echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
@@ -1003,13 +1007,15 @@
 	    &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
-	cat genmake_tnc.log >> genmake_warnings
+	echo >> $LOGFILE
+	cat genmake_tnc.log >> $LOGFILE
 	if test "x$RET_COMPILE" = x0 ; then
 	    LIBS="$LIBS -lnetcdf"
 	    HAVE_NETCDF=t
+	    echo "check_netcdf: successful" >> $LOGFILE
 	else
 	# try again with "-lnetcdff" added to the libs
-	    echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+	    echo "==> try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
 	    echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
 	    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
 	    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
@@ -1017,10 +1023,12 @@
 		&&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 		&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
 	    RET_COMPILE=$?
-	    cat genmake_tnc.log >> genmake_warnings
+	    echo >> $LOGFILE
+	    cat genmake_tnc.log >> $LOGFILE
 	    if test "x$RET_COMPILE" = x0 ; then
 		LIBS="$LIBS -lnetcdff -lnetcdf"
 		HAVE_NETCDF=t
+		echo "check_netcdf: successful" >> $LOGFILE
 	    fi
 	fi
     fi
@@ -1052,7 +1060,7 @@
 # MAKEDEPEND=
 PKG_DEPEND=
 PKG_GROUPS=
-DUMPSTATE=t
+DUMPSTATE=f
 OPTFILE=
 INCLUDES="-I. $INCLUDES"
 FFLAGS=
@@ -1160,15 +1168,16 @@
 
 GENMAKE :
 
-A program for GENerating MAKEfiles for the MITgcm project.  For a
-quick list of options, use "genmake -h" or for more detail see:
-
-  http://mitgcm.org/devel_HOWTO/
+A program for GENerating MAKEfiles for the MITgcm project.
+   For a quick list of options, use "genmake2 -h"
+or for more detail see the Developer's HOWTO manual at:
+   http://mitgcm.org/public/docs.html
 
 EOF
 
-#- clean-up previous genmake logfiles: 
-rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
+LOGFILE="genmake.log"
+#- clean-up previous genmake logfiles:
+rm -f genmake_state genmake_*optfile $LOGFILE
 
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
@@ -1450,7 +1459,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $OPTFILE "genmake_optfile"
 	fi
     else
@@ -1477,7 +1486,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $AD_OPTFILE "genmake_ad_optfile"
 	fi
     else
@@ -2689,28 +2698,34 @@
 	@printf 'running ... '
 	@\$(EXECUTABLE) > \$@
 
+# remove most of the files that "make" generates
 clean:
 	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 	-rm -rf *.o
 	-rm -rf *.$FS *.flowdir
 	-rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
+
+# remove most of the files that "make" and "make depend" generate
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f \$(SPECIAL_FILES)
-	-rm -f make.log run.log f90mkdepend.log *.bak "$MAKEFILE.old"
+	-rm -f \$(SPECIAL_FILES) f90mkdepend.log
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log
+	-rm -f genmake_warnings genmake_errors make.log
+
+# remove also the executable, files that "genmake2" generates (except Makefile)
+#         and output from a run (plus log files from testreport)
 CLEAN:
 	@make Clean
-	-rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak $MAKEFILE.old
+	-rm -f $LOGFILE genmake_state genmake_*optfile genmake.tr_log make.tr_log
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+	-rm -f *.txt STD* *diagnostics.log datetime
 	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
 	-rm -rf mnc_test_*
 
-#eh3 Makefile: makefile
 makefile:
 	$THIS_SCRIPT $G2ARGS
 cleanlinks:
@@ -3226,7 +3241,7 @@
 
 
 #  Write the "state" for future records
-if test "x$DUMPSTATE" != xf ; then
+if test "x$DUMPSTATE" = xt ; then
     printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"