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What's best for profiling brief performance stuttering?

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I'm currently trying to use VTune Amplifier XE 2015 to drill down on some stuttering that I'm experiencing in this one open-source emulator.

The problem that I have is that the application's performance is not consistently good or bad across the board - instead, it runs full speed for about a second or two, then has a few frames of bad performance, followed by another second or two of full speed, and so on.

This is causing me some issues in figuring out what specifically is causing those brief performance spikes, because whatever it is is getting lost in the overall statistical noise of the rest of the application.

What sort of profiling settings should I be using in order to best pinpoint where the bottleneck is in my code for these particular frames?

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