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Here's a funny one. I ran top the other day on a lightly used server and found MySQL pushing the CPU between 50% and 100%. "Am I under attack?" was my first thought. Oddly, SHOW PROCESSLIST was empty. "High CPU usage but no queries were running? WTF!"
Turns out MySQL's has a bug handling leap seconds. Clearing the condition was as simple as running date -s "`date`"