First off, there are two separate and interesting threads intertwined in
this discussion.  It would be nice to see them split out.

As to running multiple instances of EMC on a single computer (whether
practical or not), from my perspective, is a less desirable situation.

EMC makes machine control available to many users for little cost.  Adding
complexity with multiple instances on a single motherboard may be a neat
science project, but in an industrial environment will add unnecessary
complexity.  This complexity will increase commissioning time as well as
hamper troubleshooting in the case of hardware problems.  Motherboards are
cheap.  If one instance goes haywire - right of the bat, you know what
machine is the culprit.  If you have a multiple instance machine, one of the
cpu's could cause problems and since there is some integration through the
unified motherboard, you could see ghost issues on the other instances
making troubleshooting more difficult and time consuming. In a multi
motherboard scenario, the offending unit will be obvious, slap in a new
board with a mirrored hard drive and your up and running.

I am with Stuart.  This might be a good time to start looking for a Overhead
software process that can manage multiple and independent instances of EMC.
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