I recently applied some new thermal paste to my main server, and am wondering if it is safe to immediately resume high-performance computing applications, or if I need to wait for the paste to "settle" before using the CPU at 100% (I don't overclock it though). I am using an Intel i7 CPU.

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Do read the manual or website of the thermal paste if available. While most pastes will work fine out of the box, some may need a certain amount of time to settle and some may require the computer to cool down and heat up in that period of time. – AndrejaKo Dec 14 '11 at 23:12
The old wax based paste required a few thermal cycles to work at 100%, newer pastes no longer require this break in. – Moab Dec 15 '11 at 2:09
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Yes it is. If you notice that the CPU is overheating though, you may want to redo the paste.

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TECHNICALLY this depends on the paste, but practically everything on the market should be fine even without waiting for it to set. – Shinrai Dec 14 '11 at 21:31
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So it should be fine if I start the HPC application, go away from the computer for a few hours, and it shouldn't degrade the paste? – IDWMaster Dec 14 '11 at 21:31
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Yup, that's how it works. – soandos Dec 14 '11 at 21:32
I would not think twice about it, no (beyond the usual caveat that you should always keep an eye on your temperatures right after remounting a heatsink just in case it's not on correctly) – Shinrai Dec 14 '11 at 21:36
HPC apps have been running for about 5 minutes now (I will accept answer in a minute), and it's so far keeping a steady temperature at 105F. – IDWMaster Dec 14 '11 at 21:41
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