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Some environments are currently not working well with Preempt-RT. Here is an overview of known limitations and workarounds.
The Raspberry PI 3 is currently not part of the mainline kernel and requires an out of tree patch for its Support. This support also includes an USB driver which may lock up the RT System. Possible workarounds:
dwc_otg.fiq_enable=0 dwc_otg.fiq_fsm_enable=0