I have tried every possible solution for my php file 30 seconds timeout, but nothing works. Is it possible that my new configurations that I put in my code don't take affect and still works according to the configurations which are in Goddady's default php.ini?
Quick google shows that you can't change that setting on GoDaddy shared servers. Can't be done: http://support.godaddy.com/groups/web-hosting/forum/topic/set-max_execution_time-and-max_input_time/
That was 2 years ago, and so probably not changed. Go virtual or get a new host?