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The Yorktown Simulation Engine (YSE) is a special-purpose, highly-parallel programmable machine for the gate-level simulation of logic. The YSE has been designed and is being constructed at the IBM T. J. Watson Research Center. It can simulate up to one million gates at a speed of over two billion gate simulations per second; it is estimated that the IBM 3081 processor could have been simulated on the YSE at a rate of 1000 instructions per second. This is far beyond the capabilities of existing register-level software simulators. This paper describes the software support for the YSE.