Can I just repeat that what the OP probably wants is a maximum error of 1ms, not a maximum "offset" of 1ms. If the high latency responses are infrequent, it is actually possible that he is already achieving the first objective!

The other side of this is that, in the general case, ntpd cannot guarantee hard real time behaviour, even if given a couple of days to stabilise. If you want anything better than 90 percentile guarantees, you need to perform a detailed analysis of the scheduling behaviour of all components in the system. It is almost certain that that
information will be trade secrets for some of the components.

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