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I have APC with my Wordpress website
See my APC summary page here
http://www.animefushigi.com/apc.php
I notice I have a very high amount of fragments (over 10,000)
Is this a bad thing? Will it decrease performance?
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Perhaps your cache entries expire too quickly and thus create the fragmentation.
Your current stats show: "Fragmentation: 0.33% ( 1.2 MBytes out of 349.3 MBytes in 4594 fragments) " so it seems there's no reason to worry about anything.
You might wanna change apc.stat=0 to increase performance but read about it carefully in the documentation before making the change http://php.net/manual/en/apc.configuration.php