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........
Everyone should be running with safe_mode on in /etc/php.ini (on Centos) as it makes exploiting your system more difficult is PHPcan't execute anything on the system if a script is exploited.
For example with Safe_Mode on the only executable files on the system are ones in the safe_mode_exec_dir = /safephp
This is crucial, if you must execute anything from PHPthen you have to copy the binary and assign to the user that Apache runs your site under.&........