Turns out I wasn’t the only one with the problem, and I found a solution here. (Thanks to wieman01 on the Ubuntu forums for this.)

What was happening was Ubuntu’s power management was a bit over zealous and was making the hard drive spin up and down far too often. By changing the power settings this can be fixed, using the command:

hdparm -B 254 /dev/xxx

replacing xxx with your drive name, in my case for my SATA drive it was /dev/sda.

254 here is the lowest level of power management, and 255 is off completely. You can try playing with higher values if you like some kind of power management.

To make this run every time the computer starts, add it to a startup script. For example, save a plain text file containing the above line to:

/etc/init.d/local_settings

Then:


cd /etc/init.d
sudo chmod +x local_settings
sudo ln -s local_settings /etc/rc2.d/S99local_settings


This makes the file executable, and creates a symbolic link to it in the folder which contains the start-up scripts, giving it priority 99.

Hopefully your clicking noise will now be gone!