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Compute Modules set with Affinity for SCM1 will ignore SCM2, and anything attached to it, until SCM1 fails.
One last thing. Can the SCMs be used to control a single JBOD chassis like it does with the on board drives to create Storage Pools and virtual drives?
The SCM won't control the external JBOD - it just provides an external pass-through port, making an electrical connection from the JBOD to the compute module. You can't create a virtual drive using anything attached to the external port.