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That was actually I thought which came to mind since you recently kicked off all those VN sites. Though it would mean that one of the other hosted sites which remains must be very I/O intensive with horrible caching to have such a large effect on disk load and latency. Though if you're still stuck in a completely filled 1U, I assume it's not possible to kick the hosted sites off the RAID since there is no room for adding a separate physical drive.

If this really is the case, I guess the only good news to take from it is yande.re traffic isn't the primary cause of the I/O bottleneck on your server which emerged out of nowhere this past month. Probably says a lot for how well yande.re has been optimized over the years.