Anyone familiar with Linux kernel timekeeping?

I've recently upgraded a server to an AMD 890FX/SB850 based motherboard. After doing so, I observed a large (in time-nut terms) inconsistency in system timing, as seen in the rate of the system's Time Of Day clock.

Sync'ing to a local GPS locked NTP server, I see up to an 80 ppm spread between reboots, which I've documented at http://www.flatsurface.com/AMD_SB850/index.html . I'm running kernel 2.6.32 (Debian squeeze).

I think that kernel timekeeping ("jiffies") are linked to the "8254" timer in the SB850 south bridge, but maybe it's the HPET in the 890FX north bridge. Anyone know how to tell which the kernel is using for timekeeping?

Also, is it possible to restart the Linux kernel without a full reboot (avoiding BIOS initialization), to see if it's a kernel or BIOS issue? I don't believe a simple change of runlevel restarts the kernel from scratch.

I haven't seen this inconsistency on previous Intel or Serverworks based motherboards, but I've seen this behavior on 890FX/SB850 motherboards from two different manufacturers (although I think both use Award BIOS).

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