What roboticus said. CGI applications, as I'm sure you must know, work by writing their output to stdout. If your application spends a long time thinking without generating any traffic on stdout something is bound to give up with the result that at the browser end nothing seems to happen.

Also as roboticus said, if you don't show us some code we can't help a lot. Pare down your code to just the problematic loop. If you need data, fake it. If the database takes a long time in the real code put a delay in the sample where the database code would be called. You should be able to reproduce a sketch of the code in a few dozen runable lines of code.

Most likely you can restructure your code to remove most of the database overhead, but we can't tell without seeing at least a sketch.