Pwmconfig
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Controlling the speed (and sound!) of your CPU fan is easy!
This can ruin your hardware. A CPU fan is needed to cool your CPU and in this howto it will be turned off for a couple of seconds. If you are not comfortable with doing this, don't!'
lm-sensors
First, you need to set up lm-sensors. This is explained here
pwmconfig
(If you are a very cool hacker, you might want to skip this section and write /etc/fancontrol by your own, which also saves you from hearing all your fans at full speed)
Once you have lm sensors properly configured, run pwmconfig to test and configure speed control of your fans:
Follow the instructions in pwmconfig to set up basic speeds.
The default configuration options should create a new file, /etc/fancontrol.
Follow the instructions in pwmconfig to set up speeds.