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A long-standing shortcoming in the realtime_tools::RealtimeBuffer is an inability to provide lock-free writes from the RT context. (See ros-controls/realtime_tools#14).
The joint_trajectory_controller in particular is currently using writeFromNonRT() within the RT loop due to this limitation. Either through an upstream change (maybe ros-controls/realtime_tools#73? I haven't had a chance to look into it yet) or some restructuring of the JTC, we need a lock-free write.