Prevent nginx 504 Gateway timeout using PHP set_time_limit()

I am getting 504 timeouts message from nginx when my PHP script is running longer than usual. `set_time_limit(0)` does not seem to prevent that! Does it not work when running php5-fpm on nginx? If so, whats the proper way of setting the time limit? **Error:** 504 Gateway Time-out nginx/1.2.7