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I had a similar problem with my Macbook Pro running Ubuntu. The first solution I tried was to write a Bash script that could control the fan speeds (Yes those can be controlled, at least on my computer. Look for text files in /etc/devices/platform or subfolders; in my case they were '/sys/devices/platform/applesmc.768/fan1_manual' and '/sys/devices/platform/applesmc.768/fan1_output'). A better solution, for me, was to switch to a less processor intensive desktop environment. I switched from GNOME to LXDE; LXDE runs much cooler.
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