I used to have "clicking" issue on my thinkpad running Ubuntu 7.04/7.10.
Basically I ignored the issue until I saw this article on /.
http://hardware.slashdot.org/article.pl?sid=07/10/30/1742258


Although the title and summary are wrong the issue is real. Great Job
slashdot editors. Anyway head over here for better info
http://mjg59.livejournal.com/77672.html

The issue: In Laptop Mode, the drive power parameters are probably  read
from the Bios or the Drive Firmware. The default settings are really
aggressive and your harddrive spins down within few minutes of idle
time. Now, this issues props up in some harddrive makes and not in others.

The test: If you have a S.M.A.R.T enabled harddrive(most newer
harddrives do) install smartmontools.
Under ubuntu:
$ sudo apt-get install smartmontools

or you can download the latest build it
http://sourceforge.net/projects/smartmontools/
Once installed,

$sudo smartctl -d ata -a /dev/sda | grep 193
193 Load_Cycle_Count        0x0032   098   098   000    Old_age   Always
      -       47577

What you need to look for in the smartctl output is the Load Cycle
Count. Monitor your Load cycle count over a period of time. Most drives
can sustain 500000 to 600000 load cycles before you start seeing
read/write errors, bad sectors etc. I was seeing 1 loadcycle every
minute. My hard drive is around 2 months old and I already have around
47K Load/Unload cycles.


Temporary Fix: For now, I have disabled APM for the harddrive.

$sudo hdparm -B 255 /dev/sda

This turns off the APM for the harddrive.

I would suggest reading the comments section of slashdot article for
more information.

Karthik






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