How do I stop this? I means that my computer doesn't work till it's emptied, and it's taken a week to identify the culprit...

It is filling up the /var directory  at /log/mysql until there is no space left, then the computer can't do certain things like download or run anything that requires root as there is no space left on the drive.

disable innodb if you're not using it, and delete the bin logs in /var/lib/mysql.
Google it to find more info about this.

Thanks for the reply. I did a full reinstall of Ibex ubuntu and it's ran fine ever since. But I'm glad to see that a solution has been posted for the next guy.