--- MITgcm/tools/genmake	1998/10/28 03:11:38	1.6
+++ MITgcm/tools/genmake	2001/03/05 19:57:31	1.32
@@ -1,22 +1,30 @@
 #!/bin/csh -f
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/Attic/genmake,v 1.6 1998/10/28 03:11:38 cnh Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/Attic/genmake,v 1.32 2001/03/05 19:57:31 adcroft Exp $
 #
 # Makefile generator for MITgcm UV codes
-#   created by cnh 03/98
-#   adapted by aja 06/98
+#   created  by cnh 03/98
+#   adapted  by aja 06/98
+#   modified by aja 01/00
+
+# Default lists
+set DISABLE = ( aim )
+set ENABLE  = ( )
+set MODS  = ( )
+
+# Grab variables/lists from .genmakerc
+if (-r .genmakerc) source .genmakerc
 
 # Process command-line arguments
 set allargs=( $argv )
 while ($#allargs)
  set arg = $allargs[1]
  switch ($arg)
- case -makefile*:
-   if ($arg == "-makefile") then
-     set mfile = ( Makefile )
-   else
-     set mfile = ( `echo $arg | sed 's/-makefile=//' `)
-   endif
+ case -makefile:
+   set mfile = ( Makefile )
+   breaksw
+ case -makefile=*:
+   set mfile = ( `echo $arg | sed 's/-makefile=//' `)
    breaksw
  case -platform:
  case -platform=:
@@ -25,12 +33,60 @@
    exit
    breaksw
  case -platform*:
+   if ($?platform) then
+    echo Option -platform=dir can only be specified once.; exit 1
+   endif
    set platform = ( `echo $arg | sed 's/-platform=//' `)
    breaksw
+ case -rootdir:
+ case -rootdir=:
+   echo "To specify root directory you must specify one with -rootdir=dir"
+   echo "with NO space eg. -rootdir=../../..  or  -rootdir=/usr/people/joe/src"
+   exit
+   breaksw
+ case -rootdir=*:
+   if ($?ROOTDIR) then
+    echo "***" Warning: variable \$ROOTDIR is already set to $ROOTDIR
+    echo "***" Command line \"$arg\" will override this.
+   endif
+   set ROOTDIR = ( `echo $arg | sed 's/-rootdir=//' `)
+   breaksw
+ case -mods:
+ case -mods=:
+   echo "To specify an additional source directory you must specify one with -mods=dir"
+   echo "with NO space eg. -mods=../code  or  -mods=/usr/people/joe/src"
+   exit
+   breaksw
+ case -mods=*:
+   set MODS = ( $MODS `echo $arg | sed 's/-mods=//' | sed 's/,/ /g' `)
+   breaksw
+ case -disable:
+ case -disable=:
+   echo "To disable packages from compilation use -disable=pkg1,pkg2"
+   echo "with NO spaces eg. -disable=kpp,gmredi or -disable=all (to enable all packages)"
+   exit
+   breaksw
+ case -disable=*:
+   set DISABLE = ( $DISABLE `echo $arg | sed 's/-disable=//' | sed 's/,/ /g' `)
+   breaksw
+ case -enable:
+ case -enable=:
+   echo "To enable packages from compilation use -enable=pkg1,pkg2"
+   echo "with NO spaces eg. -enable=aim or -enable=all (to enable all packages)"
+   echo "-enable overrides -disable, ie. a package listed in both is enabled"
+   exit
+   breaksw
+ case -enable=*:
+   set ENABLE = ( $ENABLE `echo $arg | sed 's/-enable=//' | sed 's/,/ /g' `)
+   breaksw
  case -mpi:
    echo "Enabling MPI options"
    set USEMPI
    breaksw
+ case -jam:
+   set include_jam_libs
+   echo "Including paths to JAM libraries"
+   breaksw
  case -help:
    echo "usage: $0 [-help] [-makefile[=...]] [-platform=...] [-mpi]"
    exit
@@ -44,28 +100,128 @@
  shift allargs
 end
 
-if ($?platform == 0) then
+# Default actions/options
+
+# If platform wasn't specified then determine platform type of the host
+if (! $?platform) then
  set platform = (`uname`)
 endif
-if ($?mfile == 0) set mfile = ( Makefile.$platform )
+# If name of makefile wasn't specified then use default "Makefile"
+if (! $?mfile) set mfile = ( Makefile )
+
 set mach  = ( `uname -a` )
 echo Operating system: $mach
 
+
 # Directories for source, includes, binaries and executables
-# Note
-# o If you prefer/need everything under a single directory
-#   copy everything in ../eesupp/src, ../model/src,
-#   ../eesupp/inc and ../model/inc into a directory and then
-#   edit the paths below to ./
-set SOURCEDIRS  = ( ../eesupp/src/ ../model/src/ ../diags/src/)
-set INCLUDEDIRS = ( ../eesupp/inc/ ../model/inc/ ../diags/inc/)
-set BUILDDIR    = ( ../bin/ )
-set EXEDIR      = ( ../exe/ )
-set EXECUTABLE  = ( mitgcmuv )
+#
+# If -rootdir wasn't specified then assume script is being run from bin
+# but if it was supplied then we should place the executable in the build dir
+if (! $?ROOTDIR) then
+  set pwd=`pwd`
+  if ($pwd:t == bin & -d ../model & -d ../eesupp & -d ../pkg) then
+    set ROOTDIR = ( .. )
+  endif
+endif
+# Scan for logical ROOTDIR
+if (! $?ROOTDIR) then
+  foreach dr (. .. ../.. ../../.. ../../../.. ../../../../..)
+    if (-d $dr/model & -d $dr/eesupp & -d $dr/pkg) then
+      set ROOTDIR = $dr
+      echo ROOTDIR was not specified. Setting ROOTDIR = \"$ROOTDIR\"
+      break
+    endif
+  end
+endif
+if (! $?ROOTDIR) then
+  echo Root directory was not specified and could not be determined.
+  echo Specify the root location of the model source with -rootdir=dir
+  exit 1
+endif
+if (! -d $ROOTDIR) then
+  echo Root directory $ROOTDIR not found.;exit 1
+endif
+# If -mods wasn't specified then we will assume that we can find all the
+# source code in the standard directories
+if (! $?MODS) then
+ set SOURCEDIRS  = ( )
+ set INCLUDEDIRS = ( . )
+else
+ set SOURCEDIRS  = ( $MODS )
+ set INCLUDEDIRS = ( . $MODS )
+endif
+if (! $?BUILDDIR) set BUILDDIR = ( . )
+if (! -d $BUILDDIR) then
+  echo Build directory $BUILDDIR not found.;exit 1
+endif
+if (! $?EXEDIR) then
+  set pwd=`pwd`
+  if ($pwd:t == bin & -d ../exe & $ROOTDIR == ..) then
+   set EXEDIR = ( ../exe )
+  else
+   set EXEDIR = ( . )
+  endif
+endif
+if (! -d $EXEDIR) then
+  echo Executable directory $EXEDIR not found.;exit 1
+endif
+if (! $?TOOLSDIR) set TOOLSDIR = ( $ROOTDIR/tools )
+if (! -d $TOOLSDIR) then
+  echo Tools directory $TOOLSDIR not found.;exit 1
+endif
+if (! $?EXECUTABLE) set EXECUTABLE  = ( mitgcmuv )
+
+# Now scan the standard source code tree
+foreach dr ($SOURCEDIRS)
+  set adr=$dr
+  if (! -d $adr) then
+    echo mods directory $adr not found.; exit 1
+  endif
+  echo Adding mods directory $adr
+end
+if (! $?PACKAGES) then
+  set PACKAGES=(`cd $ROOTDIR/pkg; ls -1 | grep -v CVS`)
+endif
+foreach dr ($PACKAGES)
+  set enable
+  foreach p ($DISABLE)
+   if ($p != 'all' & ! -d $ROOTDIR/pkg/$p) then
+     echo Specified package \"$p\" does not exist.
+     exit 1
+   endif
+   if ($dr == $p) unset enable
+   if ($p == 'all') unset enable
+  end
+  foreach p ($ENABLE)
+   if ($dr == $p) set enable
+  end
+  if ($?enable) then
+    set adr=$ROOTDIR/pkg/$dr
+    if (! -d $adr) then
+      echo Source directory $adr not found.; exit 1
+    endif
+    echo Adding package directory $adr
+    set SOURCEDIRS = ($SOURCEDIRS $adr)
+    set INCLUDEDIRS = ($INCLUDEDIRS $adr)
+  else
+    echo "*" Package \"$dr\" has not been enabled.
+  endif
+end
+if (! $?STANDARDDIRS) set STANDARDDIRS=(eesupp model diags)
+foreach dr ($STANDARDDIRS)
+  set adr=$ROOTDIR/$dr/src
+  if (! -d $adr) then
+    echo Source directory $adr not found.; exit 1
+  endif
+  echo Adding source directory $adr
+  set SOURCEDIRS = ($SOURCEDIRS $adr)
+  set idr = `echo $adr | sed 's/src/inc/'`
+  set INCLUDEDIRS = ($INCLUDEDIRS $idr)
+end
 
 # This is the generic configuration.
 # Platform specific options are chosen below
-set LN         = ( 'ln -sf' )
+set LN         = ( 'ln -s' )
 set CPP        = ( '/lib/cpp -P' )
 set KPP        = (  )
 set FC         = ( 'f77' )
@@ -97,105 +253,184 @@
   case OSF1+mpi:
     echo "Configuring for DEC Alpha"
     set CPP        = ( '/usr/bin/cpp -P' )
-    set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC' )
+    set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
     set KPP        = ( 'kapf' )
     set KPPFILES   = ( 'main.F' )
     set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
     set FC         = ( 'f77' )
-    set FFLAGS     = ( '-convert big_endian -r8 -extend_source -u -automatic -call_shared -notransform_loops -align dcommons' )
+    set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
     set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
     set NOOPTFLAGS = ( '-O0' )
     set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F load_external_fields.F')
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
     set RMFILES    = ( '*.p.out' )
     breaksw
   case IRIX64+mpi:
     echo "Configuring for SGI Mips with MPI"
-    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
     set INCLUDES   = ( '-I/usr/local/mpi/include' )
     set FC         = ( 'mpif77' )
     set LINK       = ( 'mpif77' )
-    set FFLAGS     = ( '-extend_source -bytereclen -r10000' )
+    set FFLAGS     = ( '-extend_source -bytereclen -r10000 -mips4' )
     set FOPTIM     = ( '-O3' )
     set RMFILES    = ( 'rii_files' )
     breaksw
   case IRIX64:
     echo "Configuring for SGI Mips"
-    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
     set INCLUDES   = ( '-I/usr/local/mpi/include' )
     set FFLAGS     = ( '-extend_source -mp -mpio -bytereclen -r10000 -mips4' )
+    set FOPTIM     = ( '-O3' )
+#   set NOOPTFLAGS = ( '-O0' )
+#   set NOOPTFILES = ( 'barrier.F different_multiple.F ' \
+#                      'external_fields_load.F' )
+    set RMFILES    = ( 'rii_files' )
+    breaksw
+  case o2:
+  case IRIX:
+    echo "Configuring for SGI O2 running IRIX 6.5"
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
+    set FFLAGS     = ( '-extend_source -bytereclen -r10000 -mips4' )
     set FOPTIM     = ( '-O2' )
     set NOOPTFLAGS = ( '-O0' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F ' \
-                       'load_external_fields.F' )
-    set RMFILES    = ( 'rii_files' )
+    breaksw
+  case o2+mpi:
+  case IRIX+mpi:
+    echo "Configuring for SGI O2 running IRIX 6.5 with MPI"
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
+    set FFLAGS     = ( '-extend_source -bytereclen -r10000 -mips4' )
+    set FOPTIM     = ( '-O2' )
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F' )
+    set NOOPTFLAGS = ( '-O0' )
+    set LIBS       = ( '-lmpi' )
+    breaksw
+  case o2k+mpi:
+    echo "Configuring for SGI Origin2000 running IRIX 6.5"
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
+    set INCLUDES   = ( '-I/usr/include' )
+    set FFLAGS     = ( '-n32 -extend_source -bytereclen' )
+    set FOPTIM     = ( '-O2' )
+    set NOOPTFILES = ( 'calc_mom_rhs.F' )
+    set NOOPTFLAGS = ( '-O1' )
+    set LIBS       = ( '-lmpi -lscs' )
+    breaksw
+  case onyx:
+  case onyx+mpi:
+    echo "Configuring for SGI ONYX running IRIX64"
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
+    set FFLAGS     = ( '-extend_source -bytereclen -r10000 -64' )
+    set FOPTIM     = ( '-O2' )
+    set NOOPTFLAGS = ( '-O0' )
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F' )
+    set LIBS       = ( '-lmpi' )
     breaksw
   case SunOS:
-    set LN         = ( '/usr/bin/ln -fs' )
+    set LN         = ( '/usr/bin/ln -s' )
     set CPP        = ( '/usr/ccs/lib/cpp -P' )
-    set DEFINES    = ( ${DEFINES} '-DTARGET_SUN' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SUN -DWORDLENGTH=4' )
     set FFLAGS     = ( '-stackvar -explicitpar -vpara -e -u -noautopar')
-    set FOPTIM     = ( '-O5 -fast' )
+    set FOPTIM     = ( '-fast -O3' )
     set NOOPTFLAGS = ( '-O0' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F load_external_fields.F')
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F ini_vertical_grid.F')
     breaksw
   case SunOS+mpi:
-    set LN         = ( '/usr/bin/ln -fs' )
+    set LN         = ( '/usr/bin/ln -s' )
     set CPP        = ( '/usr/ccs/lib/cpp -P' )
-    set DEFINES    = ( ${DEFINES} '-DTARGET_SUN' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SUN -DWORDLENGTH=4' )
     set INCLUDES   = ( '-I/usr/local/mpi/include' )
     set FFLAGS     = ( '-stackvar -explicitpar -vpara -e -u -noautopar')
-    set FOPTIM     = ( '-O5 -fast' )
+    set FOPTIM     = ( '-fast -O3' )
     set NOOPTFLAGS = ( '-O0' )
     set LIBS       = ( '-L/usr/local/mpi/lib/solaris/ch_shmem -lmpi -lthread' \
                        '-lsocket -lnsl' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F load_external_fields.F')
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F ini_vertical_grid.F')
     breaksw
   case IRIX32:
     echo "Configuring for SGI ONYX running IRIX64"
-    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_SGI -DWORDLENGTH=4' )
     set INCLUDES   = ( '-I/usr/include' )
     set FFLAGS     = ( '-extend_source -bytereclen -r10000 -64' )
     set FOPTIM     = ( '-O2' )
     set NOOPTFLAGS = ( '-O0' )
     set NOOPTFILES = ( 'barrier.F different_multiple.F ' \
-                       'load_external_fields.F' )
+                       'external_fields_load.F' )
     set LIBS       = ( '-lmpi' )
     breaksw
-  case HP-UX:
   case HP-UX+mpi:
-    echo "Configuring for HP Exemplar"
-    set CPP        = ( '/usr/ccs/lbin/cpp -P' )
-    set DEFINES    = ( ${DEFINES}  '-DTARGET_HP' )
-    set INCLUDES   = ( '-I/opt/mpi/include' )
     set FC         = ( 'mpif77' )
     set LINK       = ( 'mpif77' )
+    set INCLUDES   = ( '-I/opt/mpi/include' )
+  case HP-UX:
+    echo "Configuring for HP Exemplar"
+    set CPP        = ( '/usr/ccs/lbin/cpp -P' )
+    set DEFINES    = ( ${DEFINES}  '-DTARGET_HP -DWORDLENGTH=4' )
     set FFLAGS     = ( '+es +U77 +Onoautopar +Oexemplar_model' \
                        '+Okernel_threads' )
     set FOPTIM     = ( '+O2' )
     set NOOPTFLAGS = ( '+O0' )
     set NOOPTFILES = ( 'barrier.F different_multiple.F' \
-                       'load_external_fields.F' )
+                       'external_fields_load.F' )
     breaksw
-  case Linux:
-    set LN         = ( '/bin/ln -fs' )
-    set CPP        = ( '/usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P' )
+  case Linux+mpi:
+    set LIBS       = ( '-L/usr/local/lib/LINUX/ch_p4/ -lfmpich -lmpich' )
     set INCLUDES   = ( '-I/usr/local/include' )
+  case Linux:
+    set LN         = ( '/bin/ln -s' )
+    set CPP        = ( '/lib/cpp  -traditional -P' )
+    set DEFINES    = ( ${DEFINES} '-D_BYTESWAPIO -DWORDLENGTH=4' )
     set FC         = ( 'g77' )
-    set FFLAGS     = ( ' ' )
-    set FOPTIM     = ( '  -O3 -funroll-loops ' )
+    set FFLAGS     = ( '-Wimplicit -Wunused -Wuninitialized' )
+    set FOPTIM     = ( '-O3 -malign-double -funroll-loops ' )
     set LINK       = ( 'g77' )
-    set LIBS       = ( '-L/usr/local/lib/LINUX/ch_p4/ -lfmpich -lmpich' )
     breaksw
+  case Linux+pgi+mpi:
+    if ($?include_jam_libs) then
+     set INCLUDES   = ( '-I/usr/local//mpich-cnh-install/include' )
+     set LIBS       = ( '-L/usr/local/mpich-cnh-install/lib/LINUX/ch_p4/ -lfmpich -lmpich' )
+    else
+     set INCLUDES   = ( '-I/usr/local/include' )
+     set LIBS       = ( '-L/usr/local/lib/LINUX/ch_p4/ -lfmpich -lmpich' )
+    endif
   case Linux+pgi:
-    set LN         = ( '/bin/ln -fs' )
-    set CPP        = ( '/usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P' )
-    set INCLUDES   = ( '-I/usr/local/include' )
+    set LN         = ( '/bin/ln -s' )
+    set CPP        = ( '/lib/cpp -traditional -P' )
+    set DEFINES    = ( ${DEFINES} '-DWORDLENGTH=4' )
     set FC         = ( 'pgf77' )
-    set FFLAGS     = ( '-byteswapio' )
+    set FFLAGS     = ( '-byteswapio -r8 -Mnodclchk -Mextend' )
     set FOPTIM     = ( '-tp p6 -v -O2 -Munroll -Mvect=cachesize:512000,transform -Kieee' )
     set LINK       = ( 'pgf77' )
-    set LIBS       = ( '-L/usr/local/lib/LINUX/ch_p4/ -lfmpich -lmpich -Kieee' )
+    breaksw
+  case T3E:
+  case sn6312:
+    set CPP        = ( '/opt/ctl/bin/cpp -P')
+    set DEFINES    = ( ${DEFINES} '-DTARGET_T3E -DWORDLENGTH=4' )
+    set FC         = ( 'f90' )
+    set LINK       = ( 'f90' )
+    set FFLAGS     = ( '-O 2,fusion' )
+    breaksw
+  case T90:
+  case sn7113:
+    set FC         = ( 'f90' )
+    set LINK       = ( 'f90' )
+    set LN         = ( '/bin/ln -s' )
+    set CPP        = ( '/opt/ctl/bin/cpp -N -P' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_CRAY_VECTOR -DWORDLENGTH=4' )
+    set FFLAGS     = ( '-m3 -Rabc -N 132')
+    set FOPTIM     = ( '-O0' )
+    set NOOPTFLAGS = ( '-O0' )
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
+    breaksw
+  case SV1:
+  case sn3002:
+    set FC         = ( 'f90' )
+    set LINK       = ( 'f90' )
+    set LN         = ( '/bin/ln -s' )
+    set CPP        = ( '/opt/ctl/bin/cpp -N -P' )
+    set DEFINES    = ( ${DEFINES} '-DTARGET_CRAY_VECTOR -DWORDLENGTH=4' )
+    set FFLAGS     = ( '-m3 -Rabc -ei -eI -s cf77types -N 132')
+    set FOPTIM     = ( '-O0' )
+    set NOOPTFLAGS = ( '-O0' )
+    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
     breaksw
   default:
     echo "Error: platform not recognized: uname -p = " $platform$USEMPI
@@ -210,55 +445,68 @@
 ##                                                                           ##
 ###############################################################################
 
-# Create list of files
-set flist = `ls -1 ${SOURCEDIRS} | grep '.*\.[F]$'`
-if ( $#flist ) then
- echo -n "SRCFILES = " > srclist.inc
- echo -n "F77FILES = " > f77list.inc
- echo -n "OBJFILES = " > objlist.inc
- foreach ff ( ${flist} )
-  set fname = ( ${ff:t}       )
-  echo ' \' >> srclist.inc
-  echo -n "           " ${fname:r}.F >> srclist.inc
-  echo ' \' >> f77list.inc
-  echo -n "           " ${fname:r}.f >> f77list.inc
-  echo ' \' >> objlist.inc
-  echo -n "           " ${fname:r}.o >> objlist.inc
- end
-else
- echo No source files found...\!
- exit
-endif
-set flist = `ls -1 ${SOURCEDIRS} | grep '.*\.[c]$'`
-if ( $#flist ) then
- foreach ff ( ${flist} )
-  set fname = ( ${ff:t}       )
-  echo ' \' >> objlist.inc
-  echo -n "           " ${fname:r}.o >> objlist.inc
-endif
-echo " " >> srclist.inc
-echo " " >> f77list.inc
-echo " " >> objlist.inc
-
 # Convert lists of directories into command-line options
 foreach inc ($INCLUDEDIRS)
  set INCLUDES = ($INCLUDES -I$inc)
 end
-set SRCSTARS = ( )
+
+# Search for source code
+rm -rf .links.tmp;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 'HEADERFILES = ' > hlist.inc
 foreach dr ($SOURCEDIRS)
- set SRCSTARS = ("${SRCSTARS}" $dr\*.\[Fc\] )
+ set deplist=( )
+ foreach srcfile (`cd $dr; ls *.[hcF]`)
+  if (! -r .links.tmp/$srcfile) then
+   if (-f $dr/$srcfile) then
+    switch ($srcfile:e)
+    case F:
+     touch .links.tmp/$srcfile
+     set deplist=($deplist $srcfile)
+     echo    ' \'                   >> srclist.inc
+     echo -n "           " $srcfile >> srclist.inc
+     breaksw
+    case c:
+     touch .links.tmp/$srcfile
+     set deplist=($deplist $srcfile)
+     echo    ' \'                   >> csrclist.inc
+     echo -n "           " $srcfile >> csrclist.inc
+     breaksw
+    case h:
+#     touch .links.tmp/$srcfile
+#     set deplist=($deplist $srcfile)
+#     echo    ' \'                   >> hlist.inc
+#     echo -n "           " $srcfile >> hlist.inc
+     breaksw
+    endsw
+   endif
+  endif
+ end
+ if ($#deplist != 0) then
+  echo "# These files are linked from $dr" >> srclinks.tmp
+  echo $deplist':' >> srclinks.tmp
+  echo '	$(LN) '$dr'/$@ $@' >> srclinks.tmp
+ endif
 end
+rm -rf .links.tmp
+echo "" >> srclist.inc
+echo "" >> csrclist.inc
+#echo "" >> hlist.inc
 
 set THISHOSTNAME = ( `hostname` )
 set THISCWD = ( `pwd` )
 set THISDATE = ( `date` )
 
+if (-r $mfile) mv -f $mfile $mfile.bak
 ###########################################
 ## This is the template for the makefile ##
 ###########################################
 echo Creating makefile: $mfile
 echo "# Multithreaded + multi-processing makefile for $mach" > ${mfile}
-echo "# This makefile was generated automatically pn" >> ${mfile}
+echo "# This makefile was generated automatically on" >> ${mfile}
 echo "#    $THISDATE" >> ${mfile}
 echo "# by the command:" >> ${mfile}
 echo "#    ${0} $argv" >> ${mfile}
@@ -283,16 +531,55 @@
 # LINK         : Command for link editor program
 # LIBS         : Library flags /or/ additional optimization/debugging flags
 
-BUILDDIR   = ${BUILDDIR}  
-SOURCEDIRS = ${SOURCEDIRS}
+ROOTDIR     = ${ROOTDIR}
+BUILDDIR    = ${BUILDDIR}  
+SOURCEDIRS  = ${SOURCEDIRS}
 INCLUDEDIRS = ${INCLUDEDIRS}
-EXEDIR     = ${EXEDIR}
-EXECUTABLE = \$(EXEDIR)${EXECUTABLE}
+EXEDIR      = ${EXEDIR}
+EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
+TOOLSDIR    = ${TOOLSDIR}
+
+EOF
+
+
+# JAM libraries on Hyades
+if ($?include_jam_libs) then
+cat >> ${mfile} <<EOF
+# extra stuff for Hyades ............................................
+HYADES_DIR = /u/u0/cnh/jam-lib/software
+HYADES_DIR = /u/u0/cnh/jam-lib-twoproc
+WORK_DIR   = \$(HYADES_DIR)
+DEPOSIT_DIR = linux_bin
+
+STARTXOBJDIR = startx_util/\$(DEPOSIT_DIR)
+STARTXOBJ = \$(WORK_DIR)/startx_util/\$(DEPOSIT_DIR)/startx_timer.o \
+            \$(WORK_DIR)/startx_util/\$(DEPOSIT_DIR)/startx_util.o \
+            \$(WORK_DIR)/startx_util/\$(DEPOSIT_DIR)/client.o \
+            \$(WORK_DIR)/startx_util/\$(DEPOSIT_DIR)/csutil.o
+
+JAMOBJDIR  = jam/\$(DEPOSIT_DIR)
+JAMOBJ     = \$(WORK_DIR)/jam/\$(DEPOSIT_DIR)/jam_init.o \
+             \$(WORK_DIR)/jam/\$(DEPOSIT_DIR)/jam_kernel.o \
+             \$(WORK_DIR)/jam/\$(DEPOSIT_DIR)/jam_malloc.o \
+             \$(WORK_DIR)/jam/\$(DEPOSIT_DIR)/jam_vmalloc.o \
+             \$(WORK_DIR)/jam/\$(DEPOSIT_DIR)/jam_mutex.o
+
+JAMCOBJDIR = jam_collective/\$(DEPOSIT_DIR)
+JAMCOBJ    = \$(WORK_DIR)/jam_collective/\$(DEPOSIT_DIR)/jam_collective.o
+
+XLIBS      = \$(STARTXOBJ) \$(JAMOBJ) \$(JAMCOBJ)
 
+# ..................................................................
+
+EOF
+endif
+
+
+cat >> ${mfile} <<EOF
 # Unix ln (link)
 LN = ${LN}
 # C preprocessor
-CPP = cat \$< | ../tools/set64bitConst.sh | ${CPP}
+CPP = cat \$< | \$(TOOLSDIR)/set64bitConst.sh | ${CPP}
 # Special preprocessor (KAP on DECs, FPP on Crays)
 KPP = ${KPP}
 # Fortran compiler
@@ -314,14 +601,16 @@
 NOOPTFILES = ${NOOPTFILES}
 NOOPTFLAGS = ${NOOPTFLAGS}
 # Flags and libraries needed for linking
-LIBS = ${LIBS}
+LIBS = ${LIBS} \$(XLIBS)
 
 EOF
 
-cat srclist.inc >> ${mfile}
-cat f77list.inc >> ${mfile}
-cat objlist.inc >> ${mfile}
-rm -f srclist.inc f77list.inc objlist.inc
+cat srclist.inc  >> ${mfile}
+cat csrclist.inc >> ${mfile}
+echo 'F77FILES =  $(SRCFILES:.F=.f)'                    >> ${mfile}
+echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o)' >> ${mfile}
+
+rm -f srclist.inc csrclist.inc flist.tmp clist.tmp
 
 cat >> ${mfile} <<EOF
 
@@ -331,16 +620,30 @@
 all: \$(EXECUTABLE)
 \$(EXECUTABLE): \$(OBJFILES)
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
-links:
-	@-\$(LN) $SRCSTARS .
 depend:
 	@make links
 	makedepend -o .f \$(INCLUDES) \$(SRCFILES)
+
+links: \$(SRCFILES)
+
+small_f: \$(F77FILES)
+
 clean:
 	-rm -rf *.o *.f *.p ${RMFILES}
 Clean:
 	@make clean
-	-rm -rf *.[Fc]
+	@make cleanlinks
+	-rm -f Makefile.bak
+CLEAN:
+	@make Clean
+	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
+	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
+	-rm -f \$(EXECUTABLE)
+
+makefile:
+	${0} $argv
+cleanlinks:
+	-find . -type l -exec rm {} \;
 
 # The normal chain of rules is (  .F - .f - .o  )
 .F.f:
@@ -365,7 +668,13 @@
  echo "${fname:r}.o: ${fname:r}.f" >> ${mfile}
  echo '	$(FC) $(FFLAGS) $(NOOPTFLAGS) -c $<' >> ${mfile}
 end
-echo >> ${mfile}
+echo "" >> ${mfile}
+
+# Add rules for links
+cat srclinks.tmp >> ${mfile}
+rm -f srclinks.tmp
+
+echo "" >> ${mfile}
 echo "# DO NOT DELETE" >> ${mfile}
 
 exit