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If you use the CPU scaling options that are now a default part of Ubuntu, you will also see that when folding@home runs or any other process that hits the CPU's hard the CPU frequency will jump up a level or two. Folding@home run as a low priority using nice. To stop any nice process from pushing the CPU to its limits add the following code snippet into the existing file /etc/init.d/ondemand. If will replace the start and background switch commands. I also want to set the minimum for my frequency for CPU too.
Now whenever you boot the file that tells the CPU scaling to ignore nice processes will be set.

Ubuntu documentation on Installing Folding At Home
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