Using a vector-based emulation technique, a hardware-based prototyping system reduces time-consuming recompilation and reduces the iteration time for a verification run. The vector-based emulation technique takes advantage of information derived from user-defined probe points, automatically generated probe points and low-latency snapshots. Using a bounded-cycle simulation technique, the hardware-based prototyping system can provide complete or partial simulation traces covering interested signals and can efficiently evaluates assertions. A user is therefore able to debug in a real system test and to identify causes of fault conditions interactively under a controlled vector debugging environment.