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Any idea of what is happening? It's swapping, but why the 30 mysql instances?

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What OS / version? I suspect those are threads of a single MYSQL process. – HTTP500 Feb 18 '13 at 16:35
Also see if you have some long running queries. e.g. mysqladmin processlist – HTTP500 Feb 18 '13 at 16:49
thank you for the long queries suggestion, i will check that once that the load returns to abnormal. I don't really think mysql to be the bottleneck, but i will try to debug that. – cedivad Feb 18 '13 at 17:41

As htop indicates, you system seems to hang into huge iowait. The 30 mysql instances are probably because you got 30 connections to your mysql server.

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It's a ssd only server, I don't understand how that is possible. – cedivad Feb 18 '13 at 16:08
Can you maybe post output of iotop and/or vmstat, iostat? – Henrik Feb 18 '13 at 16:16

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