A configuration manager identifies a first device and a second device within a simulated system. Each device within the simulated system includes an inbound port and an outbound port. Next, the configuration manager injects a simulation only packet, at an “outbound time,” on the first device's outbound port and detects that the second device's inbound port receives the simulation only packet at an “inbound time.” As such, the configuration manager identifies a direct connection between the first device and the second device and computes a latency time for the connection. In turn, the configuration manager configures one or more first device configuration registers and one or more second device configuration registers based upon the computed latency time.