Saving all your work for eventual crashes/freezes/restarts before handling system configuration is always good idea. There is no guarantee that this process will not damage your system permanently, I just think that chance of such critical failure is really really low.
(Potentially, this can damage your system or cause system crash.
In terminal type sudo sensors-detect and answer YES to all YES/no questions. Install the lm-sensors and fancontrol packages. If it does, but the software (aka kernel) doesn't know how to control it, you are without luck. If your hardware doesn't support fan speed controls, or doesn't show them to the OS, it is very likely that you could not use this solution. This functionality depends on both your hardware and software.
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