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MySQL process running for long time, slowed server to crawl, how to debug

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http://stackoverflow.com – A system I work on was down to an absolute crawl this morning. I ran ps -eh to see if I could find anything, and there was a mysql process that had been running for over 46 minutes. I restarted MySQL and everything sped right back up, running just like normal. Now I'm keeping an eye on the open processes and I see that MySQL is once again creeping up in time...every time I refresh a few more seconds are added to it, eg an hour ago it said it had been running for 19 seconds, and every few minutes I refresh and there's another second...now it's up to about 50 seconds. It has been consistently (HowTos)