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May seem like a silly question, but how exactly do you stress test with prime95 and linx?

How long do you run them?

What settings should you use?

What pitfalls to avoid?

I'm looking for the way to ensure your system is rock solid stable with these 2 programs

Well no 2 programs will ever be 100% accurate at proving stability - but Prime95 and LinX combined are a damn good start.

To start, a LinX run with at least 50% of your RAM for an hour should get you a baseline of stability. After you pass that, run Prime95 small FFTs for 4-8 hours (your preference, but I usually run 8 hours). If you can pass both of those tests you're on your way to having a stable system. I've yet to put a system together that could pass those two tests combined and move on to fail something else.