--- MITgcm/tools/genmake2	2003/12/04 15:00:01	1.52
+++ MITgcm/tools/genmake2	2004/03/12 15:50:06	1.72
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.52 2003/12/04 15:00:01 adcroft Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.72 2004/03/12 15:50:06 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -37,7 +37,7 @@
     grep -i "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
-	echo -n "Error: In $file there is an illegal line: "
+	printf "Error: In $file there is an illegal line: "
         grep -i "$strng" $file
 	return 1
     fi
@@ -78,7 +78,10 @@
     tmp1=`uname`"_"`uname -m`
     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-    PLATFORM=`echo $tmp3 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
+    tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
+    PLATFORM=$tmp3
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
     echo "  The platform appears to be:  $PLATFORM"
     
@@ -98,13 +101,47 @@
 	CPP="cpp -traditional -P"
     fi
 
-    # makedepend is not always available
+    #  The "original" makedepend is part of the Imake system that is
+    #  most often distributed with XFree86 or with an XFree86 source
+    #  package.  As a result, many machines (eg. generic Linux) do not
+    #  have a system-default "makedepend" available.  For those
+    #  systems, we have two fall-back options:
+    #
+    #    1) a makedepend implementation shipped with the cyrus-imapd
+    #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
+    #
+    #    2) a known-buggy xmakedpend shell script
+    #
+    #  So the choices are, in order:
+    #
+    #    1) use the user-specified program
+    #    2) use a system-wide default
+    #    3) locally build and use the cyrus implementation
+    #    4) fall back to the buggy local xmakedpend script
+    #
     if test "x${MAKEDEPEND}" = x ; then
-      which makedepend >& /dev/null
+      which makedepend > /dev/null 2>&1
       RETVAL=$?
-      if test "x${RETVAL}" = x1 ; then
-         echo "    makedepend was not found. Using xmakedpend instead."
-         MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+      if test ! "x${RETVAL}" = x0 ; then
+         echo "    a system-default makedepend was not found."
+
+	 #  Try to build the cyrus impl
+	 rm -f ./genmake_cy_md
+	 (
+	     cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
+		 &&  ./configure > /dev/null 2>&1  \
+		 &&  make > /dev/null 2>&1  \
+		 &&  ./makedepend ifparser.c > /dev/null 2>&1  \
+		 &&  echo "true"
+	 ) > ./genmake_cy_md
+	 grep true ./genmake_cy_md > /dev/null 2>&1
+	 RETVAL=$?
+	 if test "x$RETVAL" = x0 ; then
+	     MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+	 else
+	     MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	 fi
+	 rm -f ./genmake_cy_md
       fi
     fi
 
@@ -143,18 +180,27 @@
 	echo "   "$p_FC
 	if test "x$FC" = x ; then
 	    FC=`echo $p_FC | $AWK '{print $1}'`
+	    echo "  Setting FORTRAN compiler to: "$FC
 	fi
     fi
 
-    for i in $p_FC ; do
-	p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
-	if test -r $p_OF ; then
-	    OPTFILE=$p_OF
-	    echo "  The options file:  $p_OF"
-	    echo "    appears to match so we'll use it."
-	    break
-	fi
-    done
+    if test "x$OPTFILE" = x ; then
+	OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$FC
+	if test ! -r $OPTFILE ; then
+             echo "  I looked for the file "$OPTFILE" but did not find it"
+        fi
+    fi
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#   for i in $p_FC ; do
+#p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
+#if test -r $p_OF ; then
+#    OPTFILE=$p_OF
+#    echo "  The options file:  $p_OF"
+#    echo "    appears to match so we'll use it."
+#    break
+#fi
+#   done
     if test "x$OPTFILE" = x ; then
 	cat 1>&2 <<EOF
 
@@ -213,7 +259,7 @@
     . ./.pd_tmp
     rm -f ./.pd_tmp
 
-    echo -n "PNAME = "${}
+    printf "PNAME = "${}
 }
 
 
@@ -251,6 +297,10 @@
       --makefile=NAME | -mf=NAME
           Call the makefile "NAME".  The default is "Makefile".
 
+    -makedepend NAME | -md NAME
+      --makedepend=NAME | -md=NAME
+          Use "NAME" for the MAKEDEPEND program.
+
     -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
       -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
           Specify the location of the MITgcm ROOTDIR as "NAME".
@@ -292,6 +342,16 @@
           *only* works if it is supported by the OPTFILE that 
           is being used.
 
+    -mpi | --mpi
+          Include MPI header files and link to MPI libraries
+    -mpi=PATH | --mpi=PATH
+          Include MPI header files and link to MPI libraries using MPI_ROOT
+          set to PATH. i.e. Include files from $PATH/include, link to libraries
+          from $PATH/lib and use binaries from $PATH/bin.
+
+    -bash NAME
+          Explicitly specify the Bourne or BASH shell to use
+
   While it is most often a single word, the "NAME" variables specified 
   above can in many cases be a space-delimited string such as:
 
@@ -435,6 +495,50 @@
 }
 
 
+check_netcdf_libs()  {
+    cat <<EOF > genmake_tnc.F
+      program fgennc
+#include "netcdf.inc"
+      integer iret, ncid, xid
+      iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_def_dim(ncid, 'X', 11, xid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_close(ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      end
+EOF
+    $CPP genmake_tnc.F > genmake_tnc.f  \
+	&&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f $LIBS >> genmake_tnc.log 2>&1
+    RET_COMPILE=$?
+    test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    RETVAL=$?
+    if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	HAVE_NETCDF=t
+    else
+	# try again with "-lnetcdf" added to the libs
+	$CPP genmake_tnc.F > genmake_tnc.f  \
+	    &&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f \
+	    $LIBS -lnetcdf >> genmake_tnc_2.log 2>&1
+	RET_COMPILE=$?
+	test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+	RETVAL=$?
+	if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	    LIBS="$LIBS -lnetcdf"
+	    HAVE_NETCDF=t
+	else
+	    cat genmake_tnc.log >> genmake_warnings
+	fi
+    fi
+    rm -f genmake_tnc*
+}
+
+
+
+###############################################################################
+#   Sequential part of script starts here
+###############################################################################
+
 #  Set defaults here
 COMMANDL="$0 $@"
 
@@ -443,8 +547,8 @@
 S64=
 KPP=
 FC=
+CPP=
 LINK=
-# DEFINES="-DWORDLENGTH=4"
 DEFINES=
 PACKAGES=
 ENABLE=
@@ -461,23 +565,28 @@
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
 
 # DEFINES checked by test compilation
 HAVE_SYSTEM=
 HAVE_FDATE=
 FC_NAMEMANGLE=
 HAVE_CLOC=
+HAVE_NETCDF=
 
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
 INCLUDEDIRS=
-STANDARDDIRS=
+STANDARDDIRS="USE_THE_DEFAULT"
 
+BASH=
 PWD=`pwd`
 MAKE=make
 AWK=awk
@@ -510,7 +619,7 @@
 
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s2="FC CPP IEEE MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
 gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
@@ -546,7 +655,7 @@
 	break
     fi
 done
-echo -n "  getting local config information:  "
+printf "  getting local config information:  "
 if test -e $gm_local ; then
     echo "using $gm_local"
     . $gm_local
@@ -611,6 +720,16 @@
 	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$ac_optarg ;;
 	
+	-bash | --bash)
+	    ac_prev=BASH ;;
+	-bash=* | --bash=*)
+	    BASH=$ac_optarg ;;
+	
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MAKEDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MAKEDEPEND=$ac_optarg ;;
+	
 	-makefile | --makefile | -ma | --ma)
 	    ac_prev=MAKEFILE ;;
 	-makefile=* | --makefile=* | -ma=* | --ma=*)
@@ -662,6 +781,12 @@
 	    IEEE=true ;;
 	-noieee | --noieee)
 	    IEEE= ;;
+
+	-mpi | --mpi)
+	    MPI=true ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
 #	-jam | --jam)
 #	    JAM=1 ;;
@@ -714,7 +839,7 @@
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
 	    if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
 		ROOTDIR=$d
-		echo -n "Warning:  ROOTDIR was not specified but there appears to be"
+		printf "Warning:  ROOTDIR was not specified but there appears to be"
 		echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
 		break
 	    fi
@@ -748,7 +873,7 @@
 	. "$OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source OPTFILE \"$OPTFILE\""
+	    printf "Error: failed to source OPTFILE \"$OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -775,7 +900,7 @@
 	. "$AD_OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
+	    printf "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
@@ -790,6 +915,10 @@
 
 #  Check that FC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
 #  either set defaults or complain and abort!
+if test ! "x$BASH" = x ; then
+    # add a trailing space so that it works within the Makefile syntax (see below)
+    BASH="$BASH "
+fi
 if test "x$FC" = x ; then
     cat <<EOF 1>&2
 
@@ -803,12 +932,21 @@
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
-if test "x$CPP" = x ; then
-    CPP="cpp"
-fi
 if test "x$MAKE" = x ; then
     MAKE="make"
 fi
+if test "x$CPP" = x ; then
+    CPP=cpp
+fi
+#EH3 === UGLY ===
+#  The following an ugly little hack to check for $CPP in /lib/ and it
+#  should eventually be replaced with a more general function that
+#  searches a combo of the user's path and a list of "usual suspects"
+#  to find the correct location for binaries such as $CPP.
+for i in " " "/lib/" ; do
+    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
+done
+#EH3 === UGLY ===
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -845,9 +983,13 @@
 fi
 rm -f genmake_test_ln genmake_tlink
 
+if test ! "x$MPI" = x ; then
+      echo "  Turning on MPI cpp macros"
+      DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
+fi
 
 printf "\n===  Checking system libraries  ===\n"
-echo -n "  Do we have the system() command using $FC...  "
+printf "  Do we have the system() command using $FC...  "
 cat > genmake_tcomp.f <<EOF
       program hello
       call system('echo hi')
@@ -865,7 +1007,7 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Do we have the fdate() command using $FC...  "
+printf "  Do we have the fdate() command using $FC...  "
 cat > genmake_tcomp.f <<EOF
       program hello
       CHARACTER(128) string
@@ -886,7 +1028,7 @@
 fi
 rm -f genmake_tcomp*
 
-echo -n "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
 check_HAVE_CLOC
 if test "x$HAVE_CLOC" != x ; then
     echo "yes"
@@ -895,16 +1037,24 @@
 fi
 rm -f genmake_t*
 
+printf "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+
 
 printf "\n===  Setting defaults  ===\n"
-echo -n "  Adding MODS directories:  "
+printf "  Adding MODS directories:  "
 for d in $MODS ; do
     if test ! -d $d ; then
 	echo
 	echo "Error: MODS directory \"$d\" not found!"
 	exit 1
     else
-	echo -n " $d"
+	printf " $d"
 	SOURCEDIRS="$SOURCEDIRS $d"
 	INCLUDEDIRS="$INCLUDEDIRS $d"
     fi
@@ -934,7 +1084,7 @@
     TOOLSDIR="$ROOTDIR/tools"
 fi
 if test ! -d ${TOOLSDIR} ; then
-    echo "Error: the specified $TOOLSDIR (\"$TOOLSDIR\") does not exist!"
+    echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
     exit 1
 fi
 if test "x$S64" = x ; then
@@ -955,11 +1105,25 @@
 	rm -f make_eesupp.errors
     else
 	echo "Error: problem encountered while building source files in eesupp:"
-	cat make_eesupp.errors
+	cat make_eesupp.errors 1>&2
 	exit 1
     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${RETVAL}" = x0 ; then
+        rm -f make_exch2.errors
+    else
+        echo "Error: problem encountered while building source files in exch2:"
+        cat make_exch2.errors 1>&2
+        exit 1
+    fi
+fi
+
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
@@ -1015,7 +1179,7 @@
 	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
 	if test "x${RETVAL}" != x0 ; then
-	    echo -n "Error: can't parse default package list "
+	    printf "Error: can't parse default package list "
 	    echo "-- please check PDEFAULT=\"$PDEFAULT\""
 	    exit 1
 	fi
@@ -1143,6 +1307,32 @@
     fi
 done
 
+#  Build MNC templates and check for ability to build and use NetCDF
+echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    ( cd $ROOTDIR"/pkg/mnc" && $MAKE templates ) > make_mnc.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+	rm -f make_mnc.errors
+    else
+	echo "Error: problem encountered while building source files in pkg/mnc:"
+	cat make_mnc.errors 1>&2
+	exit 1
+    fi
+    if test "x$HAVE_NETCDF" != xt ; then
+	cat <<EOF
+
+WARNING: the "mnc" package has been enabled but tests failed to 
+  compile and/or execute NetCDF applications.  Please check that:
+
+  1) NetCDF is installed for your compiler and
+  2) the LIBS variable (within the 'optfile") specifies the correct 
+       NetCDF library to link against.
+  
+EOF
+    fi
+fi
 
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
@@ -1177,9 +1367,8 @@
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
     case $i in 
 	aim_v23)
-	    DEFINES="$DEFINES -DALLOW_AIM"
             ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
-	    echo "Warning: ALLOW_AIM is set to enable aim_v23. This is REALLY ugly Jean-Michel :-)"
+	    echo "Warning: ALLOW_AIM is set to enable aim_v23."
 	    ;;
     esac
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
@@ -1188,27 +1377,29 @@
 
 echo "  Adding STANDARDDIRS"
 BUILDDIR=${BUILDDIR:-.}
-if test "x$STANDARDDIRS" = x ; then
+if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
     STANDARDDIRS="eesupp model"
 fi
-for d in $STANDARDDIRS ; do
-    adr="$ROOTDIR/$d/src"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	SOURCEDIRS="$SOURCEDIRS $adr"
-    fi
-    adr="$ROOTDIR/$d/inc"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	INCLUDEDIRS="$INCLUDEDIRS $adr"
-    fi
-done
+if test "x$STANDARDDIRS" != x ; then
+    for d in $STANDARDDIRS ; do
+	adr="$ROOTDIR/$d/src"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    SOURCEDIRS="$SOURCEDIRS $adr"
+	fi
+	adr="$ROOTDIR/$d/inc"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    INCLUDEDIRS="$INCLUDEDIRS $adr"
+	fi
+    done
+fi
 
 echo "  Searching for *OPTIONS.h files in order to warn about the presence"
 echo "    of \"#define \"-type statements that are no longer allowed:"
@@ -1218,7 +1409,7 @@
 names=`ls -1 "$ROOTDIR/pkg"`
 for i in $spaths ; do
     try="$i/CPP_OPTIONS.h"
-    if test -f $try -a -r $try -a "x$CPP_OPTIONS" == x ; then
+    if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
         # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
@@ -1227,7 +1418,7 @@
         done
     fi
     try="$i/CPP_EEOPTIONS.h"
-    if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" == x ; then
+    if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
 	echo "    found CPP_EEOPTIONS=\"$try\""
         # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
 #**** not yet enabled ****
@@ -1254,6 +1445,7 @@
     done
 done
 
+
 echo
 echo "===  Creating the Makefile  ==="
 echo "  setting INCLUDES"
@@ -1270,11 +1462,11 @@
 mkdir .links.tmp
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
-echo -n 'SRCFILES = '    > srclist.inc
-echo -n 'CSRCFILES = '   > csrclist.inc
-echo -n 'F90SRCFILES = ' > f90srclist.inc
-echo -n 'HEADERFILES = ' > hlist.inc
-echo -n 'AD_FLOW_FILES = ' > ad_flow_files.inc
+printf 'SRCFILES = '    > srclist.inc
+printf 'CSRCFILES = '   > csrclist.inc
+printf 'F90SRCFILES = ' > f90srclist.inc
+printf 'HEADERFILES = ' > hlist.inc
+printf 'AD_FLOW_FILES = ' > ad_flow_files.inc
 alldirs="$SOURCEDIRS $INCLUDEDIRS ."
 for d in $alldirs ; do
     deplist=
@@ -1299,23 +1491,23 @@
 		case $extn in
 		    F)
 			echo    " \\"  >> srclist.inc
-			echo -n " $sf" >> srclist.inc
+			printf " $sf" >> srclist.inc
 			;;
 		    F90)
 			echo    " \\"  >> f90srclist.inc
-			echo -n " $sf" >> f90srclist.inc
+			printf " $sf" >> f90srclist.inc
 			;;
 		    c)
 			echo    " \\"  >> csrclist.inc
-			echo -n " $sf" >> csrclist.inc
+			printf " $sf" >> csrclist.inc
 			;;
 		    h)
 			echo    " \\"  >> hlist.inc
-			echo -n " $sf" >> hlist.inc
+			printf " $sf" >> hlist.inc
 			;;
 		    flow)
 			echo    " \\"  >> ad_flow_files.inc
-			echo -n " $sf" >> ad_flow_files.inc
+			printf " $sf" >> ad_flow_files.inc
 			;;
 		esac
 	    fi
@@ -1353,6 +1545,8 @@
 EXE_SVD=$EXECUTABLE"_svd"
 
 cat >>$MAKEFILE <<EOF
+#
+# OPTFILE="$OPTFILE"
 # 
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
@@ -1410,7 +1604,7 @@
 # Fortran compiler
 F90C = ${F90C}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1463,6 +1657,7 @@
 	@make links
 	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
 
 links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
@@ -1495,10 +1690,10 @@
 # Special targets ($SPECIAL_FILES) which are create by make
 ${PACKAGES_DOT_H}:
 	@echo Creating \$@ ...
-	@\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
 AD_CONFIG.h:
 	@echo Creating \$@ ...
-	@\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
 FC_NAMEMANGLE.h:
 	@echo Creating \$@ ...
 	echo "$FC_NAMEMANGLE" > \$@
@@ -1545,11 +1740,11 @@
 
 echo "  Add the source list for AD code generation"
 echo >> $MAKEFILE
-echo -n "AD_FILES = " >> $MAKEFILE
+printf "AD_FILES = " >> $MAKEFILE
 AD_FILES=`cat ad_files`
 for i in $AD_FILES ; do
     echo    " \\" >> $MAKEFILE
-    echo -n " $i" >> $MAKEFILE
+    printf " $i" >> $MAKEFILE
 done
 echo >> $MAKEFILE
 rm -f ad_files
@@ -1562,7 +1757,7 @@
 adtamc: ad_tamc_output.f
 
 ad_input_code.f: \$(AD_FILES) \$(HEADERFILES)
-	@\$(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
+	@$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 \$(F77FILES)
@@ -1594,7 +1789,7 @@
 ftltamc: ftl_tamc_output.f
 
 ftl_input_code.f: \$(AD_FILES) \$(HEADERFILES)
-	@\$(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
+	@$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 \$(F77FILES)
@@ -1667,11 +1862,11 @@
 printf "\n===  Done  ===\n"
 
 # Create special header files
-$TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp" 
+$BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" $DISABLED_PACKAGES " " "Enabled packages:" $ENABLED_PACKAGES > $PACKAGES_DOT_H".tmp" 
 if test ! -f $PACKAGES_DOT_H ; then
     mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
 else
-    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H > /dev/null 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	rm -f $PACKAGES_DOT_H".tmp"
@@ -1681,13 +1876,13 @@
     fi
 fi
 if test ! -f AD_CONFIG.h ; then
-    $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
+    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
 fi
 
 
 #  Write the "state" for future records
 if test "x$DUMPSTATE" != xf ; then
-    echo -n "" > genmake_state
+    printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"
 	eval $t1