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I am using InnoDB instead of MyISAM for a couple of months right now, and it has really optimized my game database-wise. I was aware of the danger of deadlocks, but hadn't had any problems with it, until about a week ago.

I've had a deadlock because two cronjobs were clashing with each other, I believe. Anyway, we've got that fixed by killing both queries and running the cronjobs after each other manually.

All seemed good, except for the fact that the server load is peeking a lot since then (about every 5 minutes) which I don't really know why. I've checked the running queries at those moments and they seem fine.

Do you have any tips where to look on how to fix this? Couldn't find too many information about this on the internet. Thanks in advance.

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The timing of the deadlock and higher CPU usage is likely coincidental, or at least there's no reason for CPU usage to be higher following a deadlock. – James Lupolt Jul 28 '13 at 9:36
I'm assuming you've confirmed that the high CPU usage is from MySQL. Some potentially helpful things to try to figure out what's causing the high CPU: review this post about pt-query-digest, maybe have a look at a profiler like PMP, run ANALYZE TABLE on tables that might have out-of-date statistics. The question is a bit too general to answer well as-is, I'm afraid. – James Lupolt Jul 28 '13 at 9:37

may be you need to clear or reload various internal caches use these commands flush tables ; flush logs ; you can find more details about flush command in this link

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