A plurality of target field programmable gate arrays are interconnected in accordance with a connection topology and map portions of a target system. A control module is coupled to the plurality of target field programmable gate arrays. A balanced clock distribution network is configured to distribute a reference clock signal, and a balanced reset distribution network is coupled to the control module and configured to distribute a reset signal to the plurality of target field programmable gate arrays. The control module and the balanced reset distribution network are cooperatively configured to initiate and control a simulation of the target system with the plurality of target field programmable gate arrays. A plurality of local clock control state machines reside in the target field programmable gate arrays. The local clock control state machines are coupled to the balanced clock distribution network and obtain the reference clock signal therefrom. The plurality of local clock control state machines are configured to generate a set of synchronized free-running and stoppable clocks to maintain cycle-accurate and cycle-reproducible execution of the simulation of the target system. A method is also provided.