MySQL limits solutions

Hi everyone!
There is a problem, i cannot find answe few month-

I have a server runing on FedoraCore4, running apache+mysql+php on it, its a hosting server, and some of my users run from php to MySQL some very slow queries, i know wait_timeout and interactive_timeout doesnt work on slow queries because they kills only "sleep" queries but dont "executing" queries.

What the answer? i try some Perl cron script that kill process that using more 30 seconds to execute but it doesnt work properly everytime....
Somebody please help me... Thanks.

 

 

 

 

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