How to keep a php script from timing out because of a long mysql query

I had the same problem somwhere, and "solved" it with the following code (first two lines of my file):

set_time_limit(0);
ignore_user_abort(1);

According to the manual:

Note: The set_time_limit() function and the configuration directive max_execution_time only affect the execution time of the script itself. Any time spent on activity that happens outside the execution of the script such as system calls using system(), stream operations, database queries, etc. is not included when determining the maximum time that the script has been running.

So it's unlikely to have anything to do with PHP's time limit. What message are you getting when it times out? Perhaps there's a MySQL setting involved.

Is your php running in safe-mode? Quote from PHP manual of set_time_limit:

This function has no effect when PHP is running in safe mode. There is no workaround other than turning off safe mode or changing the time limit in the php.ini.