Yeah, a recent change to Stockfish is that it now defaults to one thread. It sounds like you have a core duo machine if it's using 50% CPU by default. You could go into the engine configuration (see your GUI help instructions) and change the number of threads from one to two, and that should make it use 100% CPU. But be careful; There may not be anything left for your OS or other processes, plus you risk having the PC overheat if it's dusty and dirty inside.
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I just downloaded Stockfish 5 (upgrade from Houdini 1.5a woot!) and it is only using about 50% of my CPU at any time. I know Houdini 1.5a would always gobble up as much CPU as it could get, if I didn't have anything running it might even take as much as 98% of my CPU. Is there a way to allow/make Stockfish 5 use more CPU so I can get deeper evaluations faster?
Thanks for the help!