János Löbb wrote:

How about just using tcpdump during the long delay and see what the machine is doing network wise ?

I have, and network timeout was suggested earlier on this thread. There is no TCP activity of particular interest during the delay. I've hunted for, and not seen, anything to do with the network during the stall. And IPv6 is turned off, by the way. I can't rule out a network cause, but I've seen nothing with tcpdump or netstat associated with the delay to date. And I can't muck with the network much since it's at a remote data center. I can drive out there late at night to take it offline, for example, but I'd need a quick test plan for that to minimize the downtime. (I have gone out there to test memory and disk, both tested fine.)

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