--- MITgcm/tools/genmake2	2004/02/23 21:51:32	1.66
+++ MITgcm/tools/genmake2	2004/03/16 18:20:34	1.73
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.66 2004/02/23 21:51:32 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.73 2004/03/16 18:20:34 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
@@ -80,7 +80,8 @@
     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
     tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
     tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
-    PLATFORM=$tmp2
+    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"
     
@@ -100,13 +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
 
@@ -145,18 +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
 
@@ -215,7 +259,7 @@
     . ./.pd_tmp
     rm -f ./.pd_tmp
 
-    echo -n "PNAME = "${}
+    printf "PNAME = "${}
 }
 
 
@@ -253,6 +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".
@@ -294,6 +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:
 
@@ -476,6 +534,11 @@
 }
 
 
+
+###############################################################################
+#   Sequential part of script starts here
+###############################################################################
+
 #  Set defaults here
 COMMANDL="$0 $@"
 
@@ -486,7 +549,6 @@
 FC=
 CPP=
 LINK=
-# DEFINES="-DWORDLENGTH=4"
 DEFINES=
 PACKAGES=
 ENABLE=
@@ -503,10 +565,13 @@
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
+#LDADD=
 LIBS=
 KPPFILES=
 NOOPTFILES=
 NOOPTFLAGS=
+MPI=
+MPIPATH=
 
 # DEFINES checked by test compilation
 HAVE_SYSTEM=
@@ -521,6 +586,8 @@
 INCLUDEDIRS=
 STANDARDDIRS="USE_THE_DEFAULT"
 
+G2ARGS=
+BASH=
 PWD=`pwd`
 MAKE=make
 AWK=awk
@@ -589,7 +656,7 @@
 	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
@@ -613,6 +680,8 @@
 ac_prev=
 for ac_option ; do
 
+    G2ARGS="$G2ARGS \"$ac_option\""
+
     # If the previous option needs an argument, assign it.
     if test -n "$ac_prev"; then
 	eval "$ac_prev=\$ac_option"
@@ -654,6 +723,16 @@
 	-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=*)
@@ -705,6 +784,12 @@
 	    IEEE=true ;;
 	-noieee | --noieee)
 	    IEEE= ;;
+
+	-mpi | --mpi)
+	    MPI=true ;;
+	-mpi=* | --mpi=*)
+	    MPIPATH=$ac_optarg
+	    MPI=true ;;
 	
 #	-jam | --jam)
 #	    JAM=1 ;;
@@ -757,7 +842,7 @@
 	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 \"$ROOTDIR\" so we'll try it."
 		break
 	    fi
@@ -791,7 +876,7 @@
 	. "$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
@@ -818,7 +903,7 @@
 	. "$AD_OPTFILE"
 	RETVAL=$?
 	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
@@ -833,6 +918,10 @@
 
 #  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
 
@@ -897,9 +986,13 @@
 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')
@@ -917,7 +1010,7 @@
 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
@@ -938,7 +1031,7 @@
 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"
@@ -947,7 +1040,7 @@
 fi
 rm -f genmake_t*
 
-echo -n "  Can we create NetCDF-enabled binaries...  "
+printf "  Can we create NetCDF-enabled binaries...  "
 check_netcdf_libs
 if test "x$HAVE_NETCDF" != x ; then
     echo "yes"
@@ -957,14 +1050,14 @@
 
 
 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
@@ -1089,7 +1182,7 @@
 	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
@@ -1372,11 +1465,11 @@
 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=
@@ -1401,23 +1494,23 @@
 		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
@@ -1446,7 +1539,7 @@
 echo "# This makefile was generated automatically on" >> $MAKEFILE
 echo "#    $THISDATE" >> $MAKEFILE
 echo "# by the command:" >> $MAKEFILE
-echo "#    $0 $@" >> $MAKEFILE
+echo "#    $0 $G2ARGS" >> $MAKEFILE
 echo "# executed by:" >> $MAKEFILE
 echo "#    $USER@${THISHOSTNAME}:${THISCWD}" >> $MAKEFILE
 
@@ -1514,7 +1607,7 @@
 # Fortran compiler
 F90C = ${F90C}
 # Link editor
-LINK = ${LINK}
+LINK = ${LINK} ${LDADD}
 
 # Defines for CPP
 DEFINES = ${DEFINES}
@@ -1567,6 +1660,7 @@
 	@make links
 	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
+	-rm -f makedepend.out
 
 links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
@@ -1592,17 +1686,17 @@
 
 #eh3 Makefile: makefile
 makefile:
-	$THIS_SCRIPT $@
+	$THIS_SCRIPT $G2ARGS
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
 # 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" > \$@
@@ -1649,11 +1743,11 @@
 
 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
@@ -1666,7 +1760,7 @@
 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)
@@ -1698,7 +1792,7 @@
 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)
@@ -1771,7 +1865,7 @@
 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
@@ -1785,13 +1879,13 @@
     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