Programmable photonic integrated circuits have the potential to increase the speed at which photonic applications are developed. However, in order to use these circuits effectively, there is a lack of efficient algorithms that compute an appropriate configuration for a given use case. We discuss a place-and-route algorithm that quickly calculates a solution to this problem. A specialized multi-stage simulated annealing process is introduced that gives a fast and effective way to configure the port-to-port response of programmable photonic integrated circuits.