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I added the pcie_aspm=off and also igb.EEE=0
while running latency-histogram the rt error occurred and the latency shot up massively, see attached.
i then added isolcpus=2,3. I have since done some cutting and not had the error since. Time will tell if that resolved it or not, but the massive increase in latency that came out of nowhere makes me think there is something else happening

 

Please give me more information to be able to help you (e.g. screenshots..)

There it is, that's the name lcec.0.D1.srv-cia-statusword instead of lcec.0.0.cia-statusword you have in the hal file.
Replace in cia402.hal file and you should come one step further, to the next variable.

The index 0x6041, you don't seem to need that now when the naming pattern is so obvious from the listing.

I guess EtherCAT went out of OP mode, to INIT or PREOP. No harm done. You have started linuxcnc in a very rudimentary state. If you like to, you can stop it with "halrun -U". Optional. EtherCAT continues to work and linuxcnc will make it enter the state it needs to be in.