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I am running 12.04 LTS on Apple mini hardware (about 4 years old).

The fan seems to run non-stop. "ThinkFan" is installed but I do not know how to use it in order to modulate fan speed. The software says that it can be used with systems other than ThinkPads through sysfs hwmon interface. I have no idea what that is.

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Try to use fancontrol. It might help.
You could then edit your config file /etc/fancontrol or run pwmconfig (sudo su - -c /usr/sbin/pwmconfig). You can also edit the config file like this one, but bear in mind that you have different hardware:
Taken from

DEVPATH=hwmon0=devices/platform/coretemp.0 hwmon2=devices/platform/w83627ehf.656
DEVNAME=hwmon0=coretemp hwmon2=w83627dhg
FCFANS= hwmon0/device/pwm1=hwmon0/device/fan1_input

INTERVAL: how often the daemon should poll CPU temps and adjust fan speeds. INTERVAL is in seconds.

The rest of the configuration file is split into (at least) two values per configuration option. Each configuration option first points to a PWM device which is written to which sets the fan speed. The second "field" is the actual value to set. This allows monitoring and controlling multiple fans and temperatures.

FCTEMPS: The temperature input device to read for CPU temperature. The above example corresponds to /sys/class/hwmon/hwmon0/device/temp1_input.
FCFANS: The current fan speed, which can be read (like the temperature) in /sys/class/hwmon/hwmon0/device/fan1_input
MINTEMP: The temperature (°C) at which to SHUT OFF the CPU fan. Efficient CPUs often will not need a fan while idling. Be sure to set this to a temperature that you know is safe. Setting this to 0 is not recommended and may ruin your hardware!
MAXTEMP: The temperature (°C) at which to spin the fan at its MAXIMUM speed. This should be probably be set to perhaps 10 or 20 degrees (°C) below your CPU's critical/shutdown temperature. Setting it closer to MINTEMP will result in higher fan speeds overall.
MINSTOP: The PWM value at which your fan stops spinning. Each fan is a little different. Power tweakers can echo different values (between 0 and 255) to /sys/class/hwmon/hwmon0/device/pwm1 and then watch the CPU fan. When the CPU fan stops, use this value.
MINSTART: The PWM value at which your fan starts to spin again. This is often a higher value than MINSTOP as more voltage is required to overcome inertia.

There are also two settings fancontrol needs to verify the configuration file is still up to date. The lines start with the setting name and a equality sign, followed by groups of hwmon-class-device=setting, seperated by spaces. You need to specify each setting for each hwmon class device you use anywhere in the config, or fancontrol will not work.

DEVPATH: Sets the physical device. You can determine this by executing the command

You should have these values set accordingly to the values of the the command sensors.

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I recommend expanding this answer to explain specifically how to use fancontrol for this purpose. Also, if you're unsure if it will work (or work well enough), I recommend including an explanation of the relevant issues. – Eliah Kagan Apr 25 '15 at 21:15

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