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Would a 10% increase in visitors really explain a 325% increase in disk latency, 25% increase in disk utilization, along with an entirely different performance profile? Unless an entire country worth of abusive traffic decided to not access the site for a few days, I'd still find the sudden change of performance on that Tueday suspicious.

Peak time performance before RAID scrub:
13k packets/sec
1.9k connections
200M traffic
80% Disk Utilization
200ms latency

Off-Peak time performance before RAID scrub:
7k packets/sec
0.8k connections
100Mbps traffic
50% Disk Utilization
200ms latency

to

Peak time performance after RAID scrub:
14k packets/sec
2.1k connections
220Mbps traffic
100% Disk Utilization
650ms latency

Semi-Peak time performance after RAID scrub (for comparison):
12k packets/sec
1.6k connections
180Mbps traffic
70% Disk Utilization
400ms latency

Off-Peak time performance after RAID scrub:
7k packets/sec
0.8k connections
100Mbps traffic
60% Disk Utilization
300ms latency

I'd suspect that yande.re has a mostly random access pattern, so how you increased the read-ahead may account for some of the performance degradation, but it still wouldn't explain the change which occurred on that Tuesday.