Preemption can happen even outside of system calls of course, but I guess my takeaway has been to just avoid calling into the system where a lot of things can happen that I don't really understand or control. That, plus setting my threads to high-priority and possibly pinning them to the right cores.
Language was C, running as root on some Linux 3.x on some ARM/FPGA development board. By setting threads to high-priority I mean something like pthread_setschedparams(... SCHED_FIFO ...).
