--- MITgcm/tools/genmake2	2006/06/07 22:33:00	1.151
+++ MITgcm/tools/genmake2	2006/10/23 19:40:43	1.156
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.151 2006/06/07 22:33:00 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.156 2006/10/23 19:40:43 heimbach Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -946,7 +946,7 @@
     RET_CPP=f
     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
     echo "$COMM" >> genmake_tnc.log
-    $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
+    eval $COMM > genmake_tnc.$FS 2>/dev/null  &&  RET_CPP=t
     if test "x$RET_CPP" = xf ; then
 	echo "  WARNING: CPP failed to pre-process the netcdf test." \
 	    >> genmake_tnc.log
@@ -954,9 +954,9 @@
 	    >> genmake_tnc.log
     fi
     echo "$FC $FFLAGS $FOPTIM -c genmake_tnc.$FS  \ " >> genmake_tnc.log
-    echo "  &&  $LINK -o genmake_tnc.o $LIBS" >> genmake_tnc.log
+    echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc.o $LIBS" >> genmake_tnc.log
     $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
-	&&  $LINK -o genmake_tnc genmake_tnc.o $LIBS >> 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
 
@@ -974,10 +974,10 @@
 	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 -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
+	echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
 	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
+	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
 	cat genmake_tnc.log >> genmake_warnings
 	if test "x$RET_COMPILE" = x0 ; then
@@ -1352,7 +1352,7 @@
 #  Find the MITgcm ${ROOTDIR}
 if test "x${ROOTDIR}" = x ; then
     tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
-    if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesup -a -d ../pkg ; then
+    if test "x$tmp" = "xbin" -a -d ../model -a -d ../eesupp -a -d ../pkg ; then
 	ROOTDIR=".."
     else
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
@@ -1818,19 +1818,21 @@
     fi
 fi
 
-#same for exch2
-if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
-    echo "  Making source files in exch2 from  templates"
-    ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-        rm -f make_exch2.errors
-    else
-        echo "Error: problem encountered while building source files in exch2:"
-        cat make_exch2.errors 1>&2
-        exit 1
+#same for pkg/exch2 and pkg/regrid
+for pdir in exch2 regrid ; do
+    if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
+	echo "  Making source files in pkg/${pdir} from templates"
+	( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
+	RETVAL=$?
+	if test "x${RETVAL}" = x0 ; then
+	    rm -f make_${pdir}.errors
+	else
+	    echo "Error: problem encountered while building source files in pkg/${pdir}:"
+	    cat make_${pdir}.errors 1>&2
+	    exit 1
+	fi
     fi
-fi
+done
 
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
@@ -2205,7 +2207,7 @@
 	perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
     else
 	echo " We cannot create a copy of mpif.h!"
-	exit -1
+#	exit -1
     fi
 fi
 
@@ -2477,7 +2479,7 @@
 	-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
@@ -2585,7 +2587,7 @@
 cat >>$MAKEFILE <<EOF
 
 # ... AD ...
-adall: ad_taf
+adall: \$(EXE_AD)
 adtaf: ad_taf_output.$FS
 adtamc: ad_tamc_output.$FS
 
@@ -2605,8 +2607,8 @@
 	\$(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