First of all if you're getting this error it is a result of extreme database activity. If you aren't expecting it or it doesn't make sense to you 99% of the time this is a database driven script being exploited (some common examples I see often are things like phpBB being hit by dozens, hundreds or thousands of bots making constant DB write requests).
The easiest way to identify this is to restart MySQL and then run the third party tool "mtop" and you'll see all........
Enter the console as root
mysql -u root -p
Then kill the process (where 1234 = the thread ID)
kill 1234
It's also a good idea to use a tool like "mtop" to monitor which processes and queries are slow, killing them is a temporary fix while you try to isolate the actual problem.........