TECHNOLOGY FOCUS - COMPUTING AND CONTROL - Controlling the operation of purified hydrogen generator includes managing the operation of each of physical subsystems of purified hydrogen generator through a respective subsystem manager, directing state transitions of the subsystem managers from a master control manager, and routing interaction between the subsystem managers from the master control manager.    TECHNOLOGY FOCUS - MECHANICAL ENGINEERING - Preferred Components: The fuel processor includes a fuel subsystem; a water subsystem; an air subsystem; an oxidizer receiving fuel from the fuel subsystem, water from the water subsystem, and air from the air subsystem and producing a process feed stream; an autothermal reactor for generating the reformate from the process feed stream; and a thermal system for providing a coolant to the oxidizer and the autothermal reactor. The hydrogen purifier is a pressure-swing adsorption unit. The control system integrates and controls the operation of fuel processor, pressure-swing adsorption unit, and compressor by integrating their operation. The control system includes a computing device, a bus system, a storage communicating with the computing device over the bus system, and a software application residing on the storage. The software application comprises a first layer including subsystem managers, each subsystem manager controlling a respective one of physical subsystems of the hydrogen generator; a second layer interfacing the subsystem managers to their respective physical subsystems; a third layer interfacing the subsystem managers with the second layer; and a master control manager controlling the fuel processor through the subsystem managers. Each subsystem manager comprises an information exchange module through which the subsystem manager determines the feasibility of requested events and identifies the actions for implementing requested events, a physical module with which the information exchange module consults to identify the actions for implementing requested events, and a control module with which the physical module consults to determine which actions are to be taken to implement a requested event. The compressor and pressure-swing adsorption unit together comprise one of the physical subsystems.