You should be able to prevent or at least strictly limit interrupts if you run a modern kernel, have a single threaded test process and cpu pin your test process to core X, while you've pinned everything else to not core X (and not core X's cpu threads if enabled), and you have no hardware interrupts routed to that core, either.

You might have to look into tickless kernels too, but I think that's pretty mainstream now. Tldr, if there's no contention for the core and there's no hardware interrupts, there's no need for a timer/scheduler tick on that core.

Yeah. I don't know how often interrupts happen to know how easy this would be to control for, but it certainly sounds like it could be tough. I suppose one way to mitigate these though is e.g. taking a min() of the execution times rather than the average?