What version of Linuxcnc (EMC2) were you running before the upgrade?
I think there were some changes in how PIDs were handled between v2.5 and 2.7 
that usually require a little servo returning.

----- Original Message -----
> From: "Les Newell" <les.new...@fastmail.co.uk>
> To: emc-users@lists.sourceforge.net
> Sent: Tuesday, June 27, 2017 10:01:34 AM
> Subject: [Emc-users] Rough motion with servos
> 
> I have been running my lathe using EMC for many years and decided to
> upgrade to the latest LinuxCNC. The computer I am using is showing
> it's
> age and the ancient version of Debian I have been running won't even
> boot properly on my new computer.
> 
> The lathe has a 5i20 and a 7i29 to run the servos. Using the same PID
> settings as I had in EMC I get odd random spikes in the Z axis motor
> command signal, roughly about one to two a second. If I look at
> pid.z.output with halscope I can see the spikes. This is on the same
> computer and hardware as I was running EMC, which ran really
> smoothly. I
> changed the computer and the results are the same. I even used
> Pncconf
> to create an absolute minimum spec configuration and it does the same
> thing.
> 
> I tried both LinuxCNC 2.7.9 and Git head. Does anyone have any ideas
> why
> this would be happening?
> 
> Les
> 
> 
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