You can start with:
1) disabling the hyperthreading and
2) dedicating one of Atom's cores to EMC (and other RTAI functions) by
adding "isolcpus=1" to grub

Unfortunately I cannot explain in more detail, how exactly to do it,
so I can only advice asking uncle google.

Viesturs

2011/3/15 Joel Jacobs <j...@sdf.lonestar.org>:
> Hi,
> Is there any way to adjust the sensitivity or suppress this  error?  I
> have an Atom D525 running the latest EMC2 from the repositories
> (Ubuntu 10.04).  I have a Mesa 7I43 and Gecko 320 servo drives.  I
> have no base thread at all, just the servo thread running at 700us. At
> 1ms I would get random 'thunks' from the servo only while jogging the
> X axis in the + direction at 120ipm. Minus X Jogs were smooth.
> After adjusting the servo thread to 700us all motors are super smooth
> no matter what.  Just randomly getting this error - sometimes takes an
> hour to pop up.  Like I said, the motors are running great so I don't
> really want to tweak the hyperthreading and isocpu= stuff.  I don't
> understand why I'm getting this error with no base thread.  Thanks,
> Joel Jacobs
>
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