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I have noticed that my i5 4460 after 15-20 minutes of prime95 is making a high pitched sound and it ends in like 5 minutes. The sound is coming from the cpu (not from the psu or gpu)

I am using a thermalright macho 120 sbm and have 30 in idle and 54 maximum in prime95.

Is it a bad sign?

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Could be coil whine, but generally people don't recommend Prime95 for Haswell based CPU's (which your CPU is) and typically recommend Aida64 as a stresstest for it. 

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Don't use p95!

And i'm guessing it's not the cpu but the VRM that's next to the cpu crying for help to end the torture...

 

Try to stress test with aida64 and see if it makes the noise.

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are you sure it is coming from the CPU and not the motherboard? because it looks like there is some coil while coming from your mobo, which is perfectly normal under high load situations 

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As said above, Do not use Prime 95.. Use something else for stressing the cpu

 

Coil whine most likely.. not a point of concern but if it's very bad or happens under normal use then you could return it.

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