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Errors and Tricks

.Xauthority locking error

If you get the following error when connecting ssh, your home is certainly overquota: 

/usr/bin/xauth: error in locking authority file /home/login/.Xauthority

You can check your home storage usage with the following command:

du -csh ~

As the home quota is small as it is dedicated to configuration files, please delete some files or move some of them somewhere else. Pay a particular attention to softwares that store data in the home storage.

Unexpected disconnection and Broken pipe message

It is possible that the connection to frontend closes itself when you are idle for too long. You can configure your computer to limit this problem.

echo "ServerAliveInterval 60" >> ~/.ssh/config

Go to Settings -> Configuration -> SSH. There is section titled SSH settings, check the option SSH keepalive.

  • Load your connection session and in the Category pane, click Connection.
  • Under Sending of null packets to keep session active, in the Seconds between keepalives, type 240 (4 min).
  • With this configuration, PuTTY sends a packet to the server every 240 seconds (4 minutes) to keep the connection alive.
  • In the Category pane, click Session and Save.

Create an ssh alias

If you find painful to type ssh <login>@genobioinfo.toulouse.inrae.fr each time you want to connect to cluster, you can add an alias to your ssh configuration file to achieve same result with ssh genobioinfo. Any related to ssh, like scp or rsync, will be able to use this alias without additional configuration.

This tips is only available with openssh client (the default client for Linux and macOS, which is also available for Windows).

On your own computer, you need to edit file ~/.ssh/config(1) ans add the following content (click on (2) to get a comment):

  1. On Windows, you must edit file %userprofile%\.ssh\config, which is, most of the time, the file C:\Users\<My-User>\.ssh\config.
  2. A comment
~/.ssh/config
1
2
3
4
5
Host genobioinfo # (1)!
    Hostname genobioinfo.toulouse.inrae.fr # (2)!
    User <login> # (3)!
    ServerAliveInterval 60 # (4)!
    ServerAliveCountMax 2
  1. Define alias name, here genobioinfo.
  2. Address to which the alias points genobioinfo points, ici genobioinfo.toulouse.inrae.fr.
  3. The login to use to connect. Replace <login> with your cluster login.
  4. Lines 4 & 5 make the connection more resilient to network outages (optional)

When the file is saved, Une fois le fichier enregistré, just type ssh genobioinfo in a terminal to connect. For other commands, the principle is the same: just replace the block <login>@genobioinfo.toulouse.inrae.fr with genobioinfo:

# Syntaxe sans aliasscp my-sequences.fa <login>@genobioinfo.toulouse.inrae.fr:work/# Syntaxe avec aliasscp my-sequences.fa genobioinfo:work/

If you want to go further with the ssh config, you can consult the manual with command man ssh_config in a terminal.