Celeb Glow
updates | February 26, 2026

PuTTY Network Timeout Error

I'm using PuTTY on my Windows machine to use SSH on my university server. I run analyses that take up to 3 days to complete. I can connect and start the analyses but eventually get an error message 'PuTTY Network Error: Software caused connection abort'. I have problem solved this - the issue lies with the period of inactivity on PuTTY where it is running the analyses. The network connections ect are all fine. At the moment the only way I can get the analyses to complete is to press enter every couple of hours. This really is annoying as I have to get up during the night!

I'm not a computer whizz whatsoever and would really apprentice if anyone could suggest a solution.

Thanks :)

2 Answers

Either of the following methods (I prefer the second but YMMV)

  1. Prevent timeout
    • Fiddle with Putty's settings such as Enable TCP Keepalives and seconds between keepalives.
    • Tell the shell not to get bored (unset TMOUT)
  2. Change what you are doing so you don't hold a session open while inactive for several days

e.g.

nohup ./my_analysis > analysis.out 2> analysis.err &; exit;

You can check progress by e.g. logging in again and using

tail -f analysis.out

More complicated needs can often be accomodated using named pipes.


Other references

2

You could also use screen if it's available.

It would allow you do run whatever command within a screen session (which wouldn't timeout) and you'd be able to reconnect it later. A basic use could look like the following:

  1. Run screen
  2. Start analysis
  3. Detach (Ctrl+A D) the screen (or wait for the timeout)
  4. Reconnect later using screen -r

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