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I recently have situation where my laptop can heat to 105 degrees and shut down. I think shutting down is some bios/laptop internal protection, because it doesn't just gracefully shut down the system, but cut the power off.

Anyway, I wonder if I can configure it somehow to throttle-down CPU if it exceeds some threshold, say 100 degree.

I use Ubuntu 11.10.

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It sounds like you need to figure out the reason your system is getting so hot, your cpu is shutting itself off, to protect itself. What your asking goes beyond what software is design to do. If the setting exists it would be in the BIOS but again SOLVE THE OVERHEATING problem. –  Ramhound May 11 '12 at 14:23
    
In fact it's quite reasonable to run the CPU in overdrive at a low duty cycle to get bursty work done faster. Google uses this technique in their data centers. –  joeforker Jun 14 '12 at 13:57

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lm-sensors is a library that should allow you to get your cpu temparature. Conky uses it to do nice little graphs. Once you have the value it should be easy to put a script in the crontab to call the shutdown command which would be cleaner than your bios pull the blug. Not sure about how to throttle a cpu, might be possible not sure might want to google that one.

As a side note, i had the same issue on a dell laptop and it turned out to be the fan clutered with dust, so you might want to open your laptop for a spring clean :)

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