Diagnosing cause of orphaned inodes on Linux, busy MySQL?

Solution 1:

First sanity check your server:

• Are you using ECC memory?
• Are you running RAID? Did you see any RAID cards errors? (dmesg would have shown these at the time, but now you've rebooted they're probably lost)

A high level of cache is desirable and shouldn't corrupt your file-system in any way.

Solution 2:

Orphaned inodes are benign and perfectly normal whenever you have an unclean dismount. They are simply files that had been deleted, but were still open when the fs was remounted read only. They are not the cause, but merely a symptom. You need to check your kernel logs to see what the actual problem was that caused the read only remount. You also might want to run some SMART diagnostics to make sure the drive isn't failing.