--- MITgcm/tools/genmake2	2006/05/05 20:04:43	1.148
+++ MITgcm/tools/genmake2	2006/06/15 17:11:37	1.152
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.148 2006/05/05 20:04:43 ce107 Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.152 2006/06/15 17:11:37 jmc Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -767,6 +767,9 @@
 
 
 check_HAVE_SIGREG()  {
+    if test ! "x$HAVE_SIGREG" = x ; then
+	return
+    fi
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -824,6 +827,13 @@
 
 
 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
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -934,7 +944,7 @@
     cat genmake_tnc.F >> genmake_tnc.log
     echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
     RET_CPP=f
-    COMM="$CPP $DEFINES $INCLUDES genmake_tnc.F"
+    COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
     echo "$COMM" >> genmake_tnc.log
     $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
     if test "x$RET_CPP" = xf ; then
@@ -962,10 +972,10 @@
     else
 	# try again with "-lnetcdf" added to the libs
 	echo "try again with added '-lnetcdf'" > genmake_tnc.log
-	echo "$CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS \ " >> 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 -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
-	$CPP $DEFINES $INCLUDES genmake_tnc.F > genmake_tnc.$FS 2>/dev/null  \
+	cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS 2>/dev/null  \
 	    &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 	    &&  $LINK -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
@@ -1033,7 +1043,7 @@
 HAVE_FDATE=
 FC_NAMEMANGLE=
 HAVE_CLOC=
-HAVE_SETRLSTK=
+# HAVE_SETRLSTK=
 HAVE_STAT=
 HAVE_NETCDF=
 HAVE_ETIME=
@@ -1681,7 +1691,7 @@
 
 printf "  Can we unlimit the stack size using $FC...  "
 check_HAVE_SETRLSTK
-if test "x$HAVE_SETRLSTK" != x ; then
+if test "x$HAVE_SETRLSTK" = xt ; then
     echo "yes"
 else
     echo "no"
@@ -1690,7 +1700,7 @@
 
 printf "  Can we register a signal handler using $FC...  "
 check_HAVE_SIGREG
-if test "x$HAVE_SIGREG" != x ; then
+if test "x$HAVE_SIGREG" = xt ; then
     echo "yes"
 else
     echo "no"
@@ -2467,7 +2477,7 @@
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) *.txt STD* *diagnostics.log datetime
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
 	-rm -rf mnc_test_*
 
 #eh3 Makefile: makefile
@@ -2555,10 +2565,10 @@
 ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
 for i in $ad_vars ; do
     name=$i
-    t1="t2=\$"`echo $i`
+    t1="t2=\$"`echo "$i"`
     eval $t1
     printf "%-20s = " $name >> $MAKEFILE
-    echo $t2 >> $MAKEFILE
+    echo "$t2" | sed -e 's| \+| |g' >> $MAKEFILE
 done
 
 echo "  Add the source list for AD code generation"
@@ -2575,7 +2585,7 @@
 cat >>$MAKEFILE <<EOF
 
 # ... AD ...
-adall: ad_taf
+adall: \$(EXE_AD)
 adtaf: ad_taf_output.$FS
 adtamc: ad_tamc_output.$FS
 
@@ -2595,8 +2605,8 @@
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-ad_taf: ad_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
+\${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
 ad_tamc_output.$FS: ad_input_code.$FS
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS