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I have installed Ubuntu 13.04 and Mathematica 9 on a Sony Vaio VPCEA36FG.

When I run a program in Mathematica, CPU usage rises to 100%. This is a normal. But when Mathematica finishes computation, CPU usage remains at 100% for up to 15 minutes.

Can anyone explain why?

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Your CPU might have overheated more than the fan/heatsink could cool it. Ubuntu would then have clocked down the CPU to keep it from burning out. It would then have only been clocked 'back up' once it cooled down again.

You could check to see if the fan/heatsink are not blocked by dust that would cause the cooling to be ineffective and clean the inside every few months from dust.

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