--- MITgcm/tools/genmake2	2003/10/30 19:11:45	1.26
+++ MITgcm/tools/genmake2	2003/11/23 20:01:50	1.43
@@ -1,6 +1,6 @@
-#!/bin/bash
+#!/bin/sh
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.26 2003/10/30 19:11:45 heimbach Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.43 2003/11/23 20:01:50 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -76,17 +76,6 @@
     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
@@ -104,6 +93,16 @@
 	CPP="cpp -traditional -P"
     fi
 
+    # makedepend is not always available
+    if test "x${MAKEDEPEND}" = x ; then
+      which makedepend >& /dev/null
+      RETVAL=$?
+      if test "x${RETVAL}" = x1 ; then
+         echo "    makedepend was not found. Using xmakedpend instead."
+         MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+      fi
+    fi
+
     # look for possible fortran compilers
     tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc f90 f95 mpif77 mpf77 mpxlf95"
     p_FC=
@@ -206,7 +205,7 @@
     cat $1 | sed -e 's/#.*$//g' \
 	| $AWK 'BEGIN{nn=0;} (NF>0){ for(i=2;i<=NF;i++){nn++; print "PNAME["nn"]="$1"\nDNAME["nn"]="$i} }' \
 	> ./.pd_tmp
-    source ./.pd_tmp
+    . ./.pd_tmp
     rm -f ./.pd_tmp
 
     echo -n "PNAME = "${}
@@ -215,73 +214,221 @@
 
 #  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
 }
 
-#eh3 # This is the generic configuration.
-#eh3 set LN         = ( 'ln -s' )
-#eh3 set CPP        = ( '/lib/cpp -P' )
-#eh3 set S64        = ( '$(TOOLSDIR)/set64bitConst.sh' )
-#eh3 set KPP        = (  )
-#eh3 set FC         = ( 'f77' )
-#eh3 set LINK       = $FC
-#eh3 set MAKEDEPEND = ( 'makedepend' )
-#eh3 set INCLUDES   = ( -I. )
-#eh3 set FFLAGS     = (  )
-#eh3 set FOPTIM     = (  )
-#eh3 set CFLAGS     = (  )
-#eh3 set KFLAGS1    = (  )
-#eh3 set KFLAGS2    = (  )
-#eh3 set LIBS       = (  )
-#eh3 set KPPFILES   = (  )
-#eh3 if (! $?NOOPTFILES ) set NOOPTFILES = (  )
-#eh3 if (! $?NOOPTFLAGS ) set NOOPTFLAGS = (  )
+#  Build a CPP macro to automate calling C routines from FORTRAN
+get_fortran_c_namemangling()  {
+    default_nm="#define FC_NAMEMANGLE(X) X ## _"
+    
+    cat > genmake_test.c <<EOF
+void tcall( char * string ) { tsub( string ); }
+EOF
+    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_errors
+
+WARNING: C test compile fails
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    c_tcall=`nm genmake_test.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+EOF
+	return 1
+    fi
+    cat > genmake_tcomp.f <<EOF
+      subroutine tcall( string )
+      character*(*) string
+      call tsub( string )
+      end
+EOF
+    $FC $FFLAGS $DEFINES -c genmake_tcomp.f >> genmake_warnings 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: FORTRAN test compile fails -- please see "genmake_errors"
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+    f_tcall=`nm genmake_tcomp.o | grep 'T ' | grep tcall | cut -d ' ' -f 3`
+    RETVAL=$?
+    if test "x$RETVAL" != x0 ; then
+	FC_NAMEMANGLE=$default_nm
+	cat <<EOF>> genmake_warnings
+
+WARNING: The "nm" command failed.
+WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+EOF
+	return 1
+    fi
+
+    c_a=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    f_a=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 1 | sed -e 's|Y||'`
+    c_b=`echo $c_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+    f_b=`echo $f_tcall | sed -e 's|tcall|Y Y|' | cut -d ' ' -f 2 | sed -e 's|Y||'`
+
+    nmangle="X"
+    if test "x$c_a" != "x$f_a" ; then
+	comm="echo x$f_a | sed -e 's|x$c_a||'"
+	a=`eval $comm`
+	nmangle="$a ## $nmangle"
+    fi
+    if test "x$c_b" != "x$f_b" ; then
+	comm="echo x$f_b | sed -e 's|x$c_b||'"
+	b=`eval $comm`
+	nmangle="$nmangle ## $b"
+    fi
+
+    FC_NAMEMANGLE="#define FC_NAMEMANGLE(X)  $nmangle"
+
+    #  cleanup the testing files
+    rm -f genmake_tcomp.* genmake_test.*
+}
+
+
+check_HAVE_CLOC()  {
+    get_fortran_c_namemangling
+    cat <<EOF > genmake_tc_1.c
+$FC_NAMEMANGLE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <assert.h>
+#include <sys/time.h>
+void FC_NAMEMANGLE(cloc) ( double *curtim )
+{
+ struct timeval tv1;
+ gettimeofday(&tv1 , (void *)NULL );
+ *curtim =  (double)((tv1.tv_usec)+(tv1.tv_sec)*1.E6);
+ *curtim = *curtim/1.E6;
+}
+EOF
+    make genmake_tc_1.o >> genmake_tc.log 2>&1
+    RET_C=$?
+    cat <<EOF > genmake_tc_2.f
+      program hello
+      Real*8 wtime
+      external cloc
+      call cloc(wtime)
+      print *," HELLO WORLD", wtime
+      end program hello
+EOF
+    $FC $FFLAGS -o genmake_tc genmake_tc_2.f genmake_tc_1.o >> genmake_tc.log 2>&1
+    RET_F=$?
+    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_tc.log 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	HAVE_CLOC=t
+	DEFINES="$DEFINES -DHAVE_CLOC"
+    fi
+    rm -f genmake_tc*
+}
+
 
 #  Set defaults here
 COMMANDL="$0 $@"
@@ -292,7 +439,8 @@
 KPP=
 FC=
 LINK=
-DEFINES="-DWORDLENGTH=4"
+# DEFINES="-DWORDLENGTH=4"
+DEFINES=
 PACKAGES=
 ENABLE=
 DISABLE=
@@ -313,6 +461,12 @@
 NOOPTFILES=
 NOOPTFLAGS=
 
+# DEFINES checked by test compilation
+HAVE_SYSTEM=
+HAVE_FDATE=
+FC_NAMEMANGLE=
+HAVE_CLOC=
+
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
@@ -350,7 +504,7 @@
 
 
 #  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
@@ -358,28 +512,39 @@
 gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
 gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
+gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE"
 
 #  The following are all related to adjoint/tangent-linear stuff
-gm_s7="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
-gm_s8="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
-gm_s9="TAF_EXTRA TAMC_EXTRA"
+gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
+gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
+gm_s12="TAF_EXTRA TAMC_EXTRA"
 
-gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8 $gm_s9"
+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
     if test -r $i/$gm_local ; then
-	source $i/$gm_local
+	. $i/$gm_local
 	break
     fi
 done
 echo -n "  getting local config information:  "
 if test -e $gm_local ; then
     echo "using $gm_local"
-    source $gm_local
+    . $gm_local
     # echo "DISABLE=$DISABLE"
     # echo "ENABLE=$ENABLE"
 else
@@ -446,10 +611,12 @@
 	-makefile=* | --makefile=* | -ma=* | --ma=*)
 	    MAKEFILE=$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 ;;
@@ -476,11 +643,6 @@
 	-standarddirs=* | --standarddirs=*)
 	    STANDARDDIRS=$ac_optarg ;;
 
-	-noopt | --noopt)
-	    ac_prev=NOOPT ;;
-	-noopt=* | --noopt=*)
-	    NOOPT=$ac_optarg ;;
-	
 #	    -cpp | --cpp)
 #		ac_prev=cpp ;;
 #	    -cpp=* | --cpp=*)
@@ -496,15 +658,10 @@
 	-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 ;;
@@ -583,7 +740,7 @@
 if test "x$OPTFILE" != xNONE ; then
     if test -f "$OPTFILE" -a -r "$OPTFILE" ; then
 	echo "    using OPTFILE=\"$OPTFILE\""
-	source "$OPTFILE"
+	. "$OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
 	    echo -n "Error: failed to source OPTFILE \"$OPTFILE\""
@@ -610,7 +767,7 @@
 if test "x${AD_OPTFILE}" != xNONE ; then
     if test -f "$AD_OPTFILE" -a -r "$AD_OPTFILE" ; then
 	echo "    using AD_OPTFILE=\"$AD_OPTFILE\""
-	source "$AD_OPTFILE"
+	. "$AD_OPTFILE"
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
 	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
@@ -626,8 +783,8 @@
     fi
 fi
 
-#  Check that FC, LINK, CPP, and S64 are defined.  If not, complain 
-#  and abort!
+#  Check that FC, LINK, CPP, S64, LN, and MAKE are defined.  If not,
+#  either set defaults or complain and abort!
 if test "x$FC" = x ; then
     cat <<EOF 1>&2
 
@@ -644,6 +801,9 @@
 if test "x$CPP" = x ; then
     CPP="cpp"
 fi
+if test "x$MAKE" = x ; then
+    MAKE="make"
+fi
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -653,6 +813,7 @@
 
   1) within the options file ("CPP=...") as specified by "-of=OPTFILE"
   2) the "./genmake_local" file
+  3) with the CPP environment variable
 
 EOF
     exit 1
@@ -662,6 +823,79 @@
 if test "x$MAKEDEPEND" = x ; then
     MAKEDEPEND=makedepend
 fi
+if test "x$LN" = x ; then
+    LN="ln -s"
+fi
+echo "test" > genmake_test_ln
+$LN genmake_test_ln genmake_tlink
+RETVAL=$?
+if test "x$RETVAL" != x0 ; then
+    cat <<EOF 1>&2
+
+Error: The command "ln -s" failed -- please specify a working soft-link
+  command in the optfile.
+
+EOF
+    exit 1
+fi
+rm -f genmake_test_ln genmake_tlink
+
+
+printf "\n===  Checking system libraries  ===\n"
+echo -n "  Do we have the system() command using $FC...  "
+cat > genmake_tcomp.f <<EOF
+      program hello
+      call system('echo hi')
+      end
+EOF
+$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_SYSTEM=t
+    DEFINES="$DEFINES -DHAVE_SYSTEM"
+    echo "yes"
+else
+    HAVE_SYSTEM=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
+echo -n "  Do we have the fdate() command using $FC...  "
+cat > genmake_tcomp.f <<EOF
+      program hello
+      CHARACTER(128) string
+      string = ' '
+      call fdate( string )
+      print *, string
+      end
+EOF
+$FC $FFLAGS $DEFINES -o genmake_tcomp genmake_tcomp.f > genmake_tcomp.log 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    HAVE_FDATE=t
+    DEFINES="$DEFINES -DHAVE_FDATE"
+    echo "yes"
+else
+    HAVE_FDATE=
+    echo "no"
+fi
+rm -f genmake_tcomp*
+
+echo -n "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
+check_HAVE_CLOC
+if test "x$HAVE_CLOC" != x ; then
+    echo "yes"
+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*
+
 
 printf "\n===  Setting defaults  ===\n"
 echo -n "  Adding MODS directories:  "
@@ -715,7 +949,7 @@
 #  they appear as regular source code
 if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
     echo "  Making source files in eesupp from templates"
-    $MAKE -C $ROOTDIR"/eesupp/src/" > make_eesupp.errors 2>&1
+    ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	rm -f make_eesupp.errors
@@ -752,13 +986,13 @@
     echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$PDEPEND\""
     exit 1
 fi
-source ./.pd_tmp
+. ./.pd_tmp
 rm -f ./.pd_tmp
 
 #  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 $i"/packages.conf" ; then
@@ -771,13 +1005,12 @@
     PDEFAULT="$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 $0}'`
 	RETVAL=$?
@@ -910,24 +1143,6 @@
     fi
 done
 
-#  This is compatible with the old genmake.  The "DISABLE_*" flags
-#  need to be replaced by the "ALLOW_*" flags set below.
-#
-# echo -n "  Setting package-specific CPP flags:  "
-# pkrm=( mom_fluxform mom_vecinv generic_advdiff )
-# pkrmdef=( -DDISABLE_MOM_FLUXFORM -DDISABLE_MOM_VECINV -DDISABLE_GENERIC_ADVDIFF -DDISABLE_DEBUGMODE )
-# echo -n "  "
-# i=0
-# while test $i -lt "${#pkrm[@]}" ; do
-#     echo "$PACKAGES" | grep "${pk[$i]}" > /dev/null 2>&1
-#     RETVAL=$?
-#     if test "x$RETVAL" = x1 ; then
-# 	DEFINES="$DEFINES ${pkdef[$i]}"
-# 	echo -n " ${pkdef[$i]}"
-#     fi
-#     i=$(( $i + 1 ))
-# done
-# echo
 
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
@@ -961,22 +1176,6 @@
 	if test "x$has_pack" = xf ; then
 	    undef=`echo "ALLOW_$n" | $AWK '{print toupper($0)}'`
 	    echo "#undef $undef" >> $PACKAGES_DOT_H".tmp"
-#           DEFINES="$DEFINES -U$undef"
-
-#EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
-	    case $n in 
-		mom_fluxform)
-		    DEFINES="$DEFINES -DDISABLE_MOM_FLUXFORM"
-		    ;;
-		mom_vecinv)
-		    DEFINES="$DEFINES -DDISABLE_MOM_VECINV"
-		    ;;
-		debug)
-		    DEFINES="$DEFINES -DDISABLE_DEBUGMODE"
-		    ;;
-	    esac
-#EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
-
 	fi
     fi
 done
@@ -1298,7 +1497,7 @@
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f Makefile.bak genmake_state genmake_*optfile make.log
+	-rm -f Makefile.bak genmake_state genmake_*optfile genmake_warnings make.log
 CLEAN:
 	@make Clean
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
@@ -1380,6 +1579,10 @@
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.f
 	cat ad_input_code_ad.f | sed -f 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
+
 ad_taf: ad_taf_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS) 
 
@@ -1406,6 +1609,10 @@
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.f
 	cat ftl_input_code_ftl.f | sed -f 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 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) 
 
@@ -1418,21 +1625,11 @@
 
 
 # ... SVD ...
-svd: svd_taf
-svd_taf_f: svd_taf_output.f
-
-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
+svdtaf: ad_taf_output.f ftl_taf_output.f
+svdall: svd_taf
 
-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)
 
 
 #=========================================