An apparatus and a method for node synchronization that can be used in a heterogeneous computer system where nodes in the system do not share a common system clock. Time stamps, which are critically important, are attached to transaction requests. Time stamps are based on a “time of day” value, which may simply be a register incremented by a system clock. Since each node has its own system clock, the frequency of these clocks may drift which results in variation in the time stamp values. If the values drift too far apart, data updates may be lost. A frequency synthesizer capable of high resolution and rapid frequency adjustments can be connected to system clock. When a shift in phase between the master and slave time of day values is detected, the frequency synthesizer output can be changed by a small amount to bring the two signals back into phase.