It's possible that on rare occasions Linux will have run a task that used
the FPU so RTL must save FPU state when running your task. That's a very
expensive operation and may account for your occasional longer run-time.
You can test this by dropping some conpr's in the FPU switch code when
Linux owns the fpu. Let me know what it tells you.
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For more information on Real-Time Linux see:
http://www.rtlinux.org/rtlinux/