I think this has been reported on the RTAI mailing list some while ago,
there are machines where the TSC is not the most reliable source.
Try looking at rtai_calibrate, that is supposed to help in some cases
(but I'm not sure if only for userspace RT).

Regards,
Alex

On Mon, 2008-05-05 at 09:34 -0500, Jeff Epler wrote:
> On Sun, May 04, 2008 at 06:10:08PM -0400, Kenneth Lerman wrote:
> > Googling: pit clocksource had been installed
> > 
> > Got me to: http://lists.opensuse.org/opensuse-bugs/2008-01/msg00541.html
> > 
> > It appears from the above that you may be able to choose your clock. Choose 
> > wisely.
> 
> Regardless of what clocksource the kernel uses, emc *always* uses the
> TSC for its internal time accounting (e.g., motion.servo-last-period).
> This could potentially be changed, someone "simply" needs to re-write
> rtai_rtapi.c:rtapi_get_clocks().
> 
> Jeff
> 
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