Are you perhaps associating the wrong run count and run times log entries?  In 
the four-line log snippet you show I believe the middle two entries would be 
associated with each other.  I see the times between divided by runs between to 
be quite stable.  I have run the latency tests and get about 8000 ns on this 
525mw with hyper threading disabled and the other recommended tweaks.

Scott


On Jul 1, 2012, at 11:38 AM, Jon Elson <el...@pico-systems.com> wrote:

> Scott Hasse wrote:
>> Jun 30 17:48:41 scott-desktop kernel: [ 4078.255547] ENCODER runs between:
>> 60
>> Jun 30 17:48:41 scott-desktop kernel: [ 4078.256330] ENCODER time between:
>> 796760
>> Jun 30 17:48:41 scott-desktop kernel: [ 4078.256344] ENCODER runs between:
>> 40
>> Jun 30 17:48:41 scott-desktop kernel: [ 4078.257366] ENCODER time between:
>> 1035788
>> 
> It appears you have really large real time jitter in this system.  It 
> could be either the base thread or the servo
> thread, not completely sure.  But I see about 30% jitter on the time, 
> and 50% on the runs!  That will make any control loop
> malfunction badly.  Have you run the latency tests on this system?
> 
> Jon
> 
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