Abstract: A control system for a film deposition apparatus having a plurality of processing chambers. The control system includes a plurality of control processors, each of the plurality of processors including a memory, being coupled to a subset of the plurality of chambers and controlling processing in said subset of the plurality of chambers. Each processor includes a data structure, provided in said memory, having configuration data for said plurality of processing chambers, and control routines for controlling processing in the apparatus. In a second aspect, the system includes a facility for determining the position of the substrate in the system. The transport system of the deposition apparatus includes hardware position sensors which indicate the presence or absence of a substrate at said sensor. The facility determines the position of substrates when the output of one or more of the hardware sensors is unavailable.