This is the same bug mentioned above (e13) -
https://bugs.launchpad.net/ubuntu/+bug/361123

The issue is the fan speed. NOT that the processor is working at
capacity (set to performance, etc). My Lenovo T61 frequently serves as a
desktop replacement. Even with the cpu throttled it runs not. Overnight
backups, or software like BOINC or even a flashy screen saver can all
send the laptop into thermal shutdown. If I want to run my cpu at it's
full speed, the laptop should be capable of that without overheating.
Dumbing it down is not the answer.

Here is the workaround for Lenovo, which involves disengaging acpi
control of the fan so that it runs at the correct speed. If you look at
your fan speed, you will see that it is *slow* and that it gets
*delayed* turning on when the cpu overheats. This is why the cpu
overheats - the fan is too slow and does not turn on soon enough - at
least in my case.

A person should be able to run cpu intensive applications overnight
without causing their laptop to go into thermal shutdown!

 I found a work around, which is to let the fan run full speed all the
time. (This can also be adjusted easily)

The laptop is now running at 44C as I surf and write this post, and goes
to 94-95C under a cpu stress test but no higher.

1. you can monitor your fan speed from the thinkpad-acpi module: cat
/proc/acpi/ibm/fan (check path under /proc for your laptop)

2. you can adjust the fan speed to stay on at full speed by executing
the following command as root: echo level disengaged >
/proc/acpi/ibm/fan

(you will need to uninstall any other fan control applications or
scripts you may have tried, including tpfand)

One I did that, the fan kicked up to 4000+ rpm and stayed there. The CPU
temp stays at 94C under full load and goes no higher. There are
additional options, and scripts you can run if you wish to control the
fan based on temperature and load.

With the fan running between 4000-5000 rpm cooling is not a problem.

When fan control is engaged in the thinkpad-acpi module, the fan spins
*only* between 0 and about 3000 rpm and takes quite a while to kick in -
usually too late

Note that I tested the same software on my wife's T61 running 8.04 and
did *NOT* have any thermal issue. I have replicated my heat problem on
the T61 using both the 64-bit and 32-bit kernels.


For more info, see the following: 
http://www.thinkwiki.org/wiki/How_to_control_fan_speed

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Ubuntu 9.04 laptop overheat and shutdown
https://bugs.launchpad.net/bugs/370173
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