There are several things that could be terminating your script. One could be the maximum execution time set in the php.ini file. If that's the case, you can override it in your script with set_time_limit(0);
where zero means no limit and any number greater than zero is the number of seconds to allow the script to run for before being terminated. It's important to note that this time does NOT include the time it takes for the browser to make the request, so file upload time wouldn't count here.
If you're in a shared hosting environment (like Dreamhost), they have process watches that will kill off any PHP process after a set time limit. You cannot get around these. You would need to contact the hosting provider to see what you need to do to get access to run the script for longer (for Dreamhost, they want you to have a they're PS offering).