Processor clock signals are generated for each processor in a HPC system, such that all the processor clock signals are of the same frequency. Furthermore, as part of a startup (boot) procedure, a process sets all time stamp counters (TSCs) of the processors, such they indicate identical times. Each blade of the HPC system recovers a recovered clock signal from a synchronous communication network, to which the blade is coupled. The blade generates a processor clock from the recovered clock signal and provides the processor clock to processor(s) on the blade. Each chassis is coupled to a second, system-wide, synchronous communication network, and each chassis synchronizes its chassis synchronous communication network with the system-wide synchronous communication system. Thus, all the processor clock signals are generated with the same frequency.