> I think it's related to your vmware instance. Try moving it to a
> physical machine and see if the problem persists.

Easier said than done...

> Did you have any task/cron running every 30 minutes?

There are some yes. But they should not create heavy load on the 
system. In any case, one should notice it every 30 minutes then 
and not only every 3 hours.

> What is the io wait of that vm?

No problem I guess.

http://img341.imageshack.us/img341/9022/moniiowait.jpg




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