Dear Gokul,
I have a icicidirect.com a/c. In this a/c if you short sell in margin trading and not able to square off before deadline i.e. 1445 hrs thereafter they will square off automatically thru system. I think most of the trading portal has the same system. Only deadline is different for different trading portals. You have check with your broker about the same. However, if their system does not work and square off not take place it will go for auction and it will attact penalities. Hope it clarifies your query.