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I'm using Ubuntu 12.04 LTS. I'm not sure if it is the CPU (i7) fan or the video card fan.

I've tried using lm-sensors & fancontrol

sudo sensors-detect

Now follows a summary of the probes I have just done.
Just press ENTER to continue: 

Driver `w83627ehf':
  * ISA bus, address 0x290
    Chip `Nuvoton NCT6776F Super IO Sensors' (confidence: 9)

Driver `coretemp':
  * Chip `Intel digital thermal sensor' (confidence: 9)

To load everything that is needed, add this to /etc/modules:
# Chip drivers

Like many people, I'm also getting error:

/usr/sbin/pwmconfig: There are no pwm-capable sensor modules installed  

Here is the output of sensors:

# sensors
Adapter: PCI adapter
temp1:        +71.0°C  

Adapter: ISA adapter
Physical id 0:  +44.0°C  (high = +80.0°C, crit = +98.0°C)
Core 0:         +44.0°C  (high = +80.0°C, crit = +98.0°C)
Core 1:         +40.0°C  (high = +80.0°C, crit = +98.0°C)
Core 2:         +43.0°C  (high = +80.0°C, crit = +98.0°C)
Core 3:         +42.0°C  (high = +80.0°C, crit = +98.0°C)

I'm hoping some-one has already solved this for my configuration because this seems to be a problem for many people and there are many different suggestions.

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I've opened up the case and rebooted multiple times, and although it is difficult to tell, I'm pretty sure now it is the fan on the ATI Radeon HD6970 that is the problem, not the CPU fan or 2 chasis fans. – Chris Good Sep 30 '12 at 2:04

I'm answering this myself because I couldn't find any other answers to this in Ask Ubuntu although a work around is mentioned in at least several Ubuntu bug reports.

Refer Bug 748080 + Bug 563156

Unfortunately bug 748080 has now been marked as Won't Fix as it was for Ubuntu 11.04.

First I tried setting power_method to dynpm (dynamic):

sudo echo dynpm > /sys/class/drm/card0/device/power_method

dynpm seems to keep temperature around 64C but there is screen flickering when video card works hard (eg scrolling fast thru a document) and you can hear fan rev'ing up & down. Very annoying...

The best work around for me so far is to set power_method back to profile, then set power_profile to low

sudo echo profile > /sys/class/drm/card0/device/power_method
sudo echo low > /sys/class/drm/card0/device/power_profile

Fan is much quieter now (still makes small noise) and no flickering or fan rev'ing. 'sensors' says temperature is 51C although I've got no confidence this is accurate.

To make permanent put into the /etc/rc.local :

echo low > /sys/class/drm/card0/device/power_profile

NOTE: BEWARE It's possible that forcing power_profile to low could be allowing the display adaptor to overheat. Time will tell...

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