All of this seems to suggest that the RTO calculation is wrong.

That is a possiblity.  Or at least could be enhanced.

It seems that packets in this network can be delayed several orders of
magnitude longer than the usual round trip as measured by TCP.

What exactly causes such a huge delay?  What is the TCP measured RTO
in these circumstances where spurious RTOs happen and a 3 second
minimum RTO makes things better?

I belive the biggest component comes from link-layer retransmissions. There can also be some short outtages thanks to signal blocking, tunnels, people with big hats and whatnot that the link-layer retransmissions are trying to address. The three seconds seems to be a value that gives the certainty that 99 times out of 10 the segment was indeed lost.

The trace I've been sent shows clean RTTs ranging from ~200 milliseconds to ~7000 milliseconds.

rick

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