Hello Arun,
It looks like you've been given quite a bit of advice on this already in a different discussion forum:
http://forums.ni.com/ni/board/message?board.id=170&message.id=97865&requireLogin=False
As you've probably found by now, autotuning cannot be done directly in RT. The autotuning is meant to be done first through the host computer to obtain the PID values for the desired performance. Then the autotuning VI can be replaced by the PID.vi or the Advanced PID.vi in the RT VI, as described in the below link.
http://zone.ni.com/devzone/conceptd.nsf/webmain/4ff81745e244e14786256c7e0070d7d8?OpenDocument
Please post a reply on either thread if you have further questions.
Regards,
Kristi H
National Instruments