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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
ARM is using stop_machine() while patching assembly opcodes at run time which can cause high latencies. This means “jump labels” support is deactivated because the may be used for instance by changing scheduler options. kprobe and kgdb is also patching code at run time but are not disabled. They should only be used in a development environment for debug so it should be safe.