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When I ssh using putty into a remote linux server over a site-to-site vpn, I can list certain directories if there's a small number of files/folders. If I try to list a directory like /etc with a large number of files the session hangs. The same thing happens if I run a command that has lots of output like netstat. I've tried setting different MTU settings on both routers. Also tried turning on keepalives within putty.

Anyone have any ideas?

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Complex problem. Most likely TCP ACK stalls causing the socket to timeout. I'd try to get fq_codel installed into the kernel of any devices under your control, for starters. Which VPN solution are you using? – allquixotic Sep 12 '12 at 17:12
Is this a high latency situation? Is there a threshold that determines whether the session times out or keeps going? You could make a series of files with a certain amount of text in it then 'cat' those files to see what the threshold is. – Green Sep 12 '12 at 18:14
You might consider doing a capture with Wireshark. Wireshark will give you some clues about packets being lost, delivered out of order, high latency and you could look at the IO graph to see if there is a certain transfer rate that causes the connection to die. As transfer rate increases so does packet size. With the additional VPN overhead you could be hitting an MTU limit somewhere. – chuck Oct 16 '12 at 12:49

Almost certainly a MTU problem.

Rather than changing MTU on the routers between your client and server, I would rather reduce the MTU on the endpoints : your laptop and (maybe) on the server.

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