--- MITgcm/tools/genmake2	2003/11/14 19:01:36	1.39
+++ MITgcm/tools/genmake2	2003/12/05 18:09:35	1.54
@@ -1,6 +1,6 @@
-#!/bin/sh
+#! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.39 2003/11/14 19:01:36 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.54 2003/12/05 18:09:35 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,30 +13,35 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    grep -i "#define.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#undef.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#define.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+}
+
+# Search for particular CPP #cmds associated with MPI
+# usage: test_for_mpi_in_cpp_eeoptions CPP_file
+test_for_mpi_in_cpp_eeoptions() {
+    cpp_options=$1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+}
+
+# Search for particular string in a file. Return 1 if detected, 0 if not
+# usage: test_for_string_in_file file string
+test_for_string_in_file() {
+    file=$1
+    strng=$2
+    grep -i "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define DISABLE_$pkg"
-	exit 99
+	echo -n "Error: In $file there is an illegal line: "
+        grep -i "$strng" $file
+	return 1
     fi
-    grep -i "#undef.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef DISABLE_$pkg"
-	exit 99
-   fi
+    return 0
 }
 
 # Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -76,17 +81,6 @@
     PLATFORM=`echo $tmp3 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
     echo "  The platform appears to be:  $PLATFORM"
-#     if test "x$OFLIST" = x ; then
-# 	echo "  No pre-defined options files were found matching this platform"
-# 	echo "  but examples for other platforms can be found in:"
-# 	echo "    $ROOTDIR/tools/build_options"
-#     else
-# 	echo "  Options files (located in $ROOTDIR/tools/build_options) that"
-# 	echo "  may work with this machine are:"
-# 	for i in $OFLIST ; do
-# 	    echo "    $i"
-# 	done
-#     fi
     
     echo "test" > test
     ln -s ./test link
@@ -225,52 +219,94 @@
 
 #  Explain usage
 usage()  {
-    echo
-    echo "Usage: "$0" [OPTIONS]"
-    echo "  where [OPTIONS] can be:"
-    echo
-    echo "    -help | --help | -h | --h"
-    echo "    -nooptfile | --nooptfile"
-    echo "      -optfile NAME | --optfile NAME | -of NAME | --of NAME"
-    echo "      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME"
-    echo "    -pdepend NAME | --pdepend NAME"
-    echo "      -pdepend=NAME | --pdepend=NAME"
-    echo "    -pdefault NAME | --pdefault NAME"
-    echo "      -pdefault=NAME | --pdefault=NAME"
-    echo "    -make NAME | -m NAME"
-    echo "      --make=NAME | -m=NAME"
-    echo "    -makefile NAME | -mf NAME"
-    echo "      --makefile=NAME | -mf=NAME"
-    echo "    -platform NAME | --platform NAME | -pl NAME | --pl NAME"
-    echo "      -platform=NAME | --platform=NAME | -pl=NAME | --pl=NAME"
-    echo "    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME"
-    echo "      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME"
-    echo "    -mods NAME | --mods NAME | -mo NAME | --mo NAME"
-    echo "      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME"
-    echo "    -disable NAME | --disable NAME"
-    echo "      -disable=NAME | --disable=NAME"
-    echo "    -enable NAME | --enable NAME"
-    echo "      -enable=NAME | --enable=NAME"
-    echo "    -standarddirs NAME | --standarddirs NAME"
-    echo "      -standarddirs=NAME | --standarddirs=NAME"
-    echo "    -noopt NAME | --noopt NAME"
-    echo "      -noopt=NAME | --noopt=NAME"
-#    echo "    -cpp NAME | --cpp NAME"
-#    echo "      -cpp=NAME | --cpp=NAME"
-    echo "    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME"
-    echo "      -fc=NAME | --fc=NAME"
-    echo "    -[no]ieee | --[no]ieee"
-    echo "    -[no]mpi | --[no]mpi"
-    echo "    -[no]jam | --[no]jam"
-    echo
-    echo "  and NAME is a string such as:"
-    echo
-    echo "    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'"
-    echo "    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'"
-    echo "    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'"
-    echo
-    echo "  which, depending upon your shell, may need to be single-quoted"
-    echo "  if it contains spaces, dashes, or other special characters."
+cat <<EOF
+
+Usage: "$0" [OPTIONS]
+  where [OPTIONS] can be:
+
+    -help | --help | -h | --h
+          Print this help message and exit.
+
+    -nooptfile | --nooptfile
+      -optfile NAME | --optfile NAME | -of NAME | --of NAME
+      -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
+          Use "NAME" as the optfile.  By default, an attempt will be
+          made to find an appropriate "standard" optfile in the 
+          tools/build_options/ directory.
+
+    -pdepend NAME | --pdepend NAME
+      -pdepend=NAME | --pdepend=NAME
+          Get package dependency information from "NAME".
+
+    -pdefault NAME | --pdefault NAME
+      -pdefault=NAME | --pdefault=NAME
+          Get the default package list from "NAME".
+
+    -make NAME | -m NAME
+      --make=NAME | -m=NAME
+          Use "NAME" for the MAKE program. The default is "make" but 
+          many platforms, "gmake" is the preferred choice.
+
+    -makefile NAME | -mf NAME
+      --makefile=NAME | -mf=NAME
+          Call the makefile "NAME".  The default is "Makefile".
+
+    -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".
+          By default, genamke will try to find the location by 
+          looking in parent directories (up to the 5th parent).
+
+    -mods NAME | --mods NAME | -mo NAME | --mo NAME
+      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
+          Here, "NAME" specifies a list of directories that are 
+          used for additional source code.  Files found in the 
+          "mods list" are given preference over files of the same 
+          name found elsewhere.
+
+    -disable NAME | --disable NAME
+      -disable=NAME | --disable=NAME
+          Here "NAME" specifies a list of packages that we don't 
+          want to use.  If this violates package dependencies, 
+          genamke will exit with an error message.
+
+    -enable NAME | --enable NAME
+      -enable=NAME | --enable=NAME
+          Here "NAME" specifies a list of packages that we wish 
+          to specifically enable.  If this violates package 
+          dependencies, genamke will exit with an error message.
+
+    -standarddirs NAME | --standarddirs NAME
+      -standarddirs=NAME | --standarddirs=NAME
+          Here, "NAME" specifies a list of directories to be 
+          used as the "standard" code.
+
+    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
+      -fc=NAME | --fc=NAME
+          Use "NAME" as the fortran compiler.  By default, genmake 
+          will search for a working compiler by trying a list of
+          "usual suspects" such as g77, f77, etc.
+
+    -[no]ieee | --[no]ieee
+          Do or don't use IEEE numerics.  Note that this option 
+          *only* works if it is supported by the OPTFILE that 
+          is being used.
+
+  While it is most often a single word, the "NAME" variables specified 
+  above can in many cases be a space-delimited string such as:
+
+    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
+    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
+    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
+
+  which, depending upon your shell, may need to be single-quoted.
+
+  For more detailed genmake documentation, please see:
+
+    http://mitgcm.org/devel_HOWTO/
+
+EOF
+
     exit 1
 }
 
@@ -293,7 +329,7 @@
 EOF
 	return 1
     fi
-    c_tcall=`nm genmake_test.o | grep tcall | cut -d ' ' -f 3`
+    c_tcall=`nm genmake_test.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -323,7 +359,7 @@
 EOF
 	return 1
     fi
-    f_tcall=`nm genmake_tcomp.o | grep tcall | cut -d ' ' -f 3`
+    f_tcall=`nm genmake_tcomp.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
@@ -473,7 +509,7 @@
 
 
 #  The following state can be set directly by command-line switches
-gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE NOOPT"
+gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
 gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
@@ -491,8 +527,17 @@
 gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7"
 gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
 
+cat <<EOF
+
+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/
+
+EOF
 
-echo
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
 for i in . $MODS ; do
@@ -546,7 +591,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -571,10 +616,12 @@
 	-makefile=* | --makefile=* | -ma=* | --ma=*)
 	    MAKEFILE=$ac_optarg ;;
 	
-	-platform | --platform | -pl | --pl)
-	    ac_prev=PLATFORM ;;
-	-platform=* | --platform=* | -pl=* | --pl=*)
-	    PLATFORM=$ac_optarg ;;
+	-platform | --platform | -pl | --pl | -platform=* | --platform=* | -pl=* | --pl=*)
+	    echo "ERROR: The platform option has been removed.  Please specify"
+	    echo "  the build options using the \"optfile\" mechanism."
+	    echo
+	    usage
+	    ;;
 	
 	-rootdir | --rootdir | -rd | --rd)
 	    ac_prev=ROOTDIR ;;
@@ -601,11 +648,6 @@
 	-standarddirs=* | --standarddirs=*)
 	    STANDARDDIRS=$ac_optarg ;;
 
-	-noopt | --noopt)
-	    ac_prev=NOOPT ;;
-	-noopt=* | --noopt=*)
-	    NOOPT=$ac_optarg ;;
-	
 #	    -cpp | --cpp)
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
@@ -621,15 +663,10 @@
 	-noieee | --noieee)
 	    IEEE= ;;
 	
-	-mpi | --mpi)
-	    MPI=true ;;
-	-nompi | --nompi)
-	    MPI= ;;
-	
-	-jam | --jam)
-	    JAM=1 ;;
-	-nojam | --nojam)
-	    JAM=0 ;;
+#	-jam | --jam)
+#	    JAM=1 ;;
+#	-nojam | --nojam)
+#	    JAM=0 ;;
 	
 	-ds | --ds)
 	    DUMPSTATE=t ;;
@@ -856,12 +893,6 @@
 else
     echo "no"
 fi
-echo "$FC_NAMEMANGLE" > FC_NAMEMANGLE.h.template
-cmp FC_NAMEMANGLE.h FC_NAMEMANGLE.h.template > /dev/null 2>&1
-RETVAL=$?
-if test "x$RETVAL" != x0 ; then
-    mv -f FC_NAMEMANGLE.h.template FC_NAMEMANGLE.h
-fi
 rm -f genmake_t*
 
 
@@ -909,6 +940,7 @@
 if test "x$S64" = x ; then
     S64='$(TOOLSDIR)/set64bitConst.sh'
 fi
+THIS_SCRIPT=`echo ${0} | sed 's:'$TOOLSDIR':\$(TOOLSDIR):'`
 
 EXECUTABLE=${EXECUTABLE:-mitgcmuv}
 
@@ -960,7 +992,7 @@
 #  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
 #  file should eventually be added so that, for convenience, one can 
 #  specify groups of packages using names like "ocean" and "atmosphere".
-echo  -n "  checking default package list:  "
+echo "  checking default package list:  "
 if test "x${PDEFAULT}" = x ; then
     for i in "." $MODS ; do
 	if test -r $i"/packages.conf" ; then
@@ -973,13 +1005,12 @@
     PDEFAULT="$ROOTDIR/pkg/pkg_default"
 fi
 if test "x${PDEFAULT}" = xNONE ; then
-    echo "default packages file disabled"
+    echo "    default packages file disabled"
 else
     if test ! -r $PDEFAULT ; then
-	echo ""
 	echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
     else
-	echo "  using PDEFAULT=\"$PDEFAULT\""
+	echo "    using PDEFAULT=\"$PDEFAULT\""
         #  Strip the comments and add all the names
 	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
@@ -1115,24 +1146,13 @@
 
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
-cat <<EOF >$PACKAGES_DOT_H".tmp"
-C=== GENMAKE v2 ===
-C  The following defines have been set by GENMAKE, so please do not
-C  edit anything below these comments.  In general, you should
-C  add or remove packages by re-running genmake with different 
-C  "-enable" and/or "-disable" options.
-
-#ifndef PACKAGES_H
-#define PACKAGES_H
-
-C  Packages disabled by genmake:
-EOF
 #  The following UGLY HACK sets multiple "#undef"s and it needs to go 
 #  away.  On 2003-08-12, CNH, JMC, and EH3 agreed that the CPP_OPTIONS.h 
 #  file would eventually be split up so that all package-related #define
 #  statements could be separated and handled only by genmake.
 names=`ls -1 "$ROOTDIR/pkg"`
 all_pack=
+DISABLED_PACKAGES=
 for n in $names ; do
     if test -d "$ROOTDIR/pkg/$n" -a "x$n" != xCVS ; then
 	has_pack="f"
@@ -1144,47 +1164,27 @@
 	done
 	if test "x$has_pack" = xf ; then
 	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
-	    echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
+            DISABLED_PACKAGES="$DISABLED_PACKAGES -U$undef"
 	fi
     fi
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-C  Packages enabled by genmake:
-EOF
+ENABLED_PACKAGES=
 for i in $PACKAGES ; do
     def=`echo "ALLOW_$i" | $AWK '{print toupper($0)}'`
-    echo "#define $def" >> $PACKAGES_DOT_H".tmp"
+    ENABLED_PACKAGES="$ENABLED_PACKAGES -D$def"
 #eh3 DEFINES="$DEFINES -D$def"
 
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
     case $i in 
 	aim_v23)
-	    echo "#define   ALLOW_AIM" >> $PACKAGES_DOT_H".tmp"
 	    DEFINES="$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 :-)"
 	    ;;
     esac
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
 
 done
-cat <<EOF >>$PACKAGES_DOT_H".tmp"
-
-#endif /* PACKAGES_H */
-EOF
-
-if test ! -f $PACKAGES_DOT_H ; then
-    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-else
-    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    RETVAL=$?
-    if test "x$RETVAL" = x0 ; then
-	rm -f $PACKAGES_DOT_H".tmp"
-    else
-	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
-	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
-    fi
-fi
 
 echo "  Adding STANDARDDIRS"
 BUILDDIR=${BUILDDIR:-.}
@@ -1210,29 +1210,36 @@
     fi
 done
 
-echo "  Searching for CPP_OPTIONS.h in order to warn about the presence"
-echo "    of \"#define ALLOW_PKGNAME\"-type statements:"
+echo "  Searching for *OPTIONS.h files in order to warn about the presence"
+echo "    of \"#define \"-type statements that are no longer allowed:"
 CPP_OPTIONS=
+CPP_EEOPTIONS=
 spaths=". $INCLUDEDIRS"
+names=`ls -1 "$ROOTDIR/pkg"`
 for i in $spaths ; do
     try="$i/CPP_OPTIONS.h"
-    #  echo -n "    trying $try : "
-    if test -f $try -a -r $try ; then
+    if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
-	break
+        # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
+        for n in $names ; do
+            test_for_package_in_cpp_options $CPP_OPTIONS $n
+        done
+    fi
+    try="$i/CPP_EEOPTIONS.h"
+    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 ****
+#        test_for_mpi_in_cpp_eeoptions $try
+#**** not yet enabled ****
+	CPP_EEOPTIONS="$try"
     fi
 done
 if test "x$CPP_OPTIONS" = x ; then
     echo "Error: can't find \"CPP_OPTIONS.h\" in the path list: $spaths"
     exit 1
 fi
-# New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
-names=`ls -1 "$ROOTDIR/pkg"`
-for n in $names ; do
-    test_for_package_in_cpp_options $CPP_OPTIONS $n
-done
-
 
 #  Here, we build the list of files to be "run through" the adjoint
 #  compiler.
@@ -1247,18 +1254,6 @@
     done
 done
 
-cat <<EOF > adjoint_sed
-s/call adopen(/call adopen ( mythid,\\
-     \&           /g
-s/call adclose(/call adclose( mythid,\\
-     \&           /g
-s/call adread(/call adread ( mythid,\\
-     \&           /g
-s/call adwrite(/call adwrite( mythid,\\
-     \&           /g
-
-EOF
-
 echo
 echo "===  Creating the Makefile  ==="
 echo "  setting INCLUDES"
@@ -1288,9 +1283,19 @@
     for sf in $sfiles ; do
 	if test ! -r ".links.tmp/$sf" ; then
 	    if test -f "$d/$sf" ; then
+                case $d/$sf in
+                  ./$PACKAGES_DOT_H)
+			;;
+                  ./AD_CONFIG.h)
+			;;
+                  ./FC_NAMEMANGLE.h)
+			;;
+                  *)
+		  	touch .links.tmp/$sf
+		  	deplist="$deplist $sf"
+			;;
+                esac
 		extn=`echo $sf | $AWK -F '.' '{print $NF}'`
-		touch .links.tmp/$sf
-		deplist="$deplist $sf"
 		case $extn in
 		    F)
 			echo    " \\"  >> srclist.inc
@@ -1348,6 +1353,8 @@
 EXE_SVD=$EXECUTABLE"_svd"
 
 cat >>$MAKEFILE <<EOF
+#
+# OPTFILE="$OPTFILE"
 # 
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
@@ -1381,6 +1388,12 @@
 EXE_FTL     = ${EXE_FTL}
 EXE_SVD     = ${EXE_SVD}
 
+ENABLED_PACKAGES = ${ENABLED_PACKAGES}
+DISABLED_PACKAGES = ${DISABLED_PACKAGES}
+
+# These files are created by Makefile
+SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h
+
 EOF
 
 #  Note: figure out some way to add Hyades JAM libraries here
@@ -1445,14 +1458,15 @@
 .SUFFIXES: .o .f .p .F .c .F90 .f90
 
 all: \$(EXECUTABLE)
-\$(EXECUTABLE): \$(OBJFILES)
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)
+	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 depend:
 	@make links
 	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
-	${TOOLSDIR}/f90mkdepend >> \$(MAKEFILE)
+	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES)
+links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77FILES) \$(F90FILES)
 
@@ -1461,12 +1475,12 @@
 	@\$(EXECUTABLE) > \$@
 
 clean:
-	-cat AD_CONFIG.template > AD_CONFIG.h
-	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl}
+	-rm -rf *.o *.f *.p *.f90 *.mod ${RMFILES} work.{pc,pcl} *.template
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f Makefile.bak genmake_state genmake_*optfile make.log
+	-rm -f \$(SPECIAL_FILES)
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
 CLEAN:
 	@make Clean
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
@@ -1476,10 +1490,21 @@
 
 #eh3 Makefile: makefile
 makefile:
-	${0} $@
+	$THIS_SCRIPT $@
 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) > \$@
+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 > \$@
+FC_NAMEMANGLE.h:
+	@echo Creating \$@ ...
+	echo "$FC_NAMEMANGLE" > \$@
+
 # The normal chain of rules is (  .F - .f - .o  )
 .F.f:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
@@ -1539,25 +1564,27 @@
 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
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	-rm -f ad_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ad_input_code.f
 
 ad_taf_output.f: ad_input_code.f
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
 
 adtafonly:
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_taf_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.f
 
 ad_taf: ad_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
 ad_tamc_output.f: ad_input_code.f
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.f
-	cat ad_input_code_ad.f | sed -f adjoint_sed > ad_tamc_output.f
+	cat ad_input_code_ad.f | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.f
 
 ad_tamc: ad_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS) 
@@ -1569,42 +1596,38 @@
 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
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
+	-rm -f ftl_config.template
 	@make \$(F77FILES)
 	@make \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) > ftl_input_code.f
 
 ftl_taf_output.f: ftl_input_code.f
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_taf_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
+
+ftltafonly:
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.f
 
 ftl_taf: ftl_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS) 
 
 ftl_tamc_output.f: ftl_input_code.f
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.f
-	cat ftl_input_code_ftl.f | sed -f adjoint_sed > ftl_tamc_output.f
+	cat ftl_input_code_ftl.f | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.f
 
 ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS) 
 
 
 # ... SVD ...
-svd: svd_taf
-svd_taf_f: svd_taf_output.f
+svdtaf: ad_taf_output.f ftl_taf_output.f
+svdall: svd_taf
 
-svd_input_code.f: \$(SRCFILES)
-	cmp svd_config.template AD_CONFIG.h || cat svd_config.template > AD_CONFIG.h
-	@make \$(F77FILES)
-	@make \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) > svd_input_code.f
-
-svd_taf_output.f: svd_input_code.f
-	\$(TAF) \$(SVD_TAF_FLAGS) \$(TAF_EXTRA) svd_input_code.f
-	cat svd_input_code_ad.f | sed -f adjoint_sed > svd_taf_output.f
-
-svd_taf: svd_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_SVD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) svd_taf_output.o \$(LIBS) 
+svd_taf: ad_taf_output.o ftl_taf_output.o \$(OBJFILES)
+	\$(LINK) -o mitgcmuv_svd \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o ftl_taf_output.o \$(LIBS)
 
 
 #=========================================
@@ -1645,44 +1668,23 @@
 
 printf "\n===  Done  ===\n"
 
-#  Write the "template" files for the adjoint builds
-cat >AD_CONFIG.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >ad_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#define ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >ftl_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#define ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cat >svd_config.template <<EOF
-C  WARNING: This file is automatically generated by genmake2 and 
-C    used by the Makefile rules.  Please DO NOT EDIT this file 
-C    unless you are CERTAIN that you know what you are doing.
-
-#undef ALLOW_ADJOINT_RUN
-#undef ALLOW_TANGENTLINEAR_RUN
-#undef ALLOW_ECCO_OPTIMIZATION
-EOF
-cp AD_CONFIG.template AD_CONFIG.h
+# 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" 
+if test ! -f $PACKAGES_DOT_H ; then
+    mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+else
+    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	rm -f $PACKAGES_DOT_H".tmp"
+    else
+	mv -f $PACKAGES_DOT_H $PACKAGES_DOT_H".bak"
+	mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    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
+fi
 
 
 #  Write the "state" for future records