If you own a ThinkPad, there's a piece of software called thinkfan that does exactly this. As the name obviously suggests, it is specifically made for ThinkPads (thinkpad_acpi).

The thinkfan software is available in the standard ubuntu software repositories, but it does require a few steps to configure.

Here is an easy step-by-step guide, which is basically a translated version of this German guide.

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1. Install the thinkfan software and the sensors:

   sudo apt-get install thinkfan lm-sensors
   

2. Make sure that the daemon controls the fan by editing the thinkpad.conf file:

   sudo nano /etc/modprobe.d/thinkfan.conf
   

   by adding the following line:

   options thinkpad_acpi fan_control=1
   

3. Make the daemon load automatically at start-up by editing the file:

   sudo nano /etc/default/thinkfan
   

   making sure that the START key is set to yes, i.e., there should be a line that says:

   START=yes
   

4. Detect your laptop's sensors:

   sudo sensors-detect
   

   and just choose the default answers whenever you're prompted by hitting Enter.

5. Load the new modules. From Ubuntu 13.10 this done by:

   sudo service kmod start
   

   while for previous versions like 13.04 you instead will need to do:

   sudo service module-init-tools start
   

6. Figure out which sensors are in use:

   sensors
   

   (the ones that indicate 0 degrees are not in use, I don't know why those are "detected" too). Remember which ones are in use.

7. Find out the full paths of these sensors:

   find /sys/devices -type f -name "temp*_input"
   

   The output should be a list of paths like /sys/devices/...

8. Copy-paste the paths to the sensors into the configuration file /etc/thinkpad.conf. To do this, first open up the file:

   sudo nano /etc/thinkfan.conf
   

   There should already be a line like

   #sensor /proc/acpi/ibm/thermal (0, 10, 15, 2, 10, 5, 0, 3, 0, 3) 
   

   (the #-symbol means that that line is commented out). Add a line starting with sensor (without the #-symbol) and copy-paste you first sensor. Repeat this if you have more than one sensor. For example, on my machine, the output in step 7 yields

   /sys/devices/virtual/hwmon/hwmon0/temp1_input
   /sys/devices/platform/thinkpad_hwmon/temp3_input
   /sys/devices/platform/thinkpad_hwmon/temp4_input
   /sys/devices/platform/thinkpad_hwmon/temp5_input
   /sys/devices/platform/thinkpad_hwmon/temp6_input
   /sys/devices/platform/thinkpad_hwmon/temp7_input
   /sys/devices/platform/thinkpad_hwmon/temp1_input
   /sys/devices/platform/thinkpad_hwmon/temp8_input
   /sys/devices/platform/thinkpad_hwmon/temp2_input
   /sys/devices/platform/coretemp.0/temp4_input
   /sys/devices/platform/coretemp.0/temp2_input 
   

   The ones that are in use in my machine are the ones in the first and the last two lines, so I added the three lines:

   sensor /sys/devices/virtual/hwmon/hwmon0/temp1_input
   sensor /sys/devices/platform/coretemp.0/temp4_input
   sensor /sys/devices/platform/coretemp.0/temp2_input 
   

9. Finally, we can set the fan speed levels in the configuration file. Open the /etc/thinkpad.conf file if it wasn't open already.

   sudo nano /etc/thinkfan.conf
   

   The fan levels I use on my ThinkPad x201 are:

   (0, 0, 51)
   (1, 50, 52)
   (2, 51, 55)
   (3, 54, 58)
   (4, 56, 63)
   (5, 60, 70)
   (6, 66, 79)
   (7, 74, 92)
   (127, 85, 32767) 
   

   The last line ensures full fan speed (127 = "disengaged" i.e. unregulated). You can fiddle with these levels to fit your needs/wishes, but PLEASE BE CAREFUL!

10. Reboot. Everything should work now. In order to check whether thinkpad is running correctly, use:

    sudo thinkfan -n
    

    Which starts thinkfan in verbose mode. You might want to stop the thinkfan daemon first:

    sudo /etc/init.d/thinkfan stop
    

    If you want to start the thinkfan daemon again, type:

    sudo /etc/init.d/thinkfan start
    

Just to be complete, my /etc/thinkfan.conf configuration file is:

# IMPORTANT:
#
# To keep your HD from overheating, you have to specify a correction value for
# the sensor that has the HD's temperature. You need to do this because
# thinkfan uses only the highest temperature it can find in the system, and
# that'll most likely never be your HD, as most HDs are already out of spec
# when they reach 55 °C.
# Correction values are applied from left to right in the same order as the
# temperatures are read from the file.
#
# For example:
# sensor /proc/acpi/ibm/thermal (0, 0, 10)
# will add a fixed value of 10 °C the 3rd value read from that file. Check out
# http://www.thinkwiki.org/wiki/Thermal_Sensors to find out how much you may
# want to add to certain temperatures.

# Syntax:
# (LEVEL, LOW, HIGH)
# LEVEL is the fan level to use (0-7 with thinkpad_acpi)
# LOW is the temperature at which to step down to the previous level
# HIGH is the temperature at which to step up to the next level
# All numbers are integers.
#

# I use this on my T61p:
#sensor /proc/acpi/ibm/thermal (0, 10, 15, 2, 10, 5, 0, 3, 0, 3)

#(0, 0, 55)
#(1, 48, 60)
#(2, 50, 61)
#(3, 52, 63)
#(4, 56, 65)
#(5, 59, 66)
#(7, 63, 32767)


# My settings for my ThinkPad X201: (kris)

sensor /sys/devices/virtual/hwmon/hwmon0/temp1_input
sensor /sys/devices/platform/coretemp.0/temp4_input
sensor /sys/devices/platform/coretemp.0/temp2_input

(0, 0, 51)
(1, 50, 52)
(2, 51, 55)
(3, 54, 58)
(4, 56, 63)
(5, 60, 70)
(6, 66, 79)
(7, 74, 92)
(127, 85, 32767)