Purdue University

cannot connect to X server / cannot open display

Link to section 'Problem' of 'cannot connect to X server / cannot open display' Problem

You receive the following message after entering a command to bring up a graphical window

cannot connect to X server cannot open display

Link to section 'Solution' of 'cannot connect to X server / cannot open display' Solution

This can happen due to multiple reasons:

1. Reason: Your SSH client software does not support graphical display by itself (e.g. SecureCRT or PuTTY).
   • Solution: Try using a client software like Thinlinc or MobaXterm as described in the SSH X11 Forwarding guide.

2. Reason: You did not enable X11 forwarding in your SSH connection.

   • Solution: If you are in a Windows environment, make sure that X11 forwarding is enabled in your connection settings (e.g. in MobaXterm or PuTTY). If you are in a Linux environment, try

     ssh -Y -l username hostname

3. Reason: If you are trying to open a graphical window within an interactive PBS job, make sure you are using the -X option with qsub after following the previous step(s) for connecting to the front-end. Please see the example in the Interactive Jobs guide.
4. Reason: If none of the above apply, make sure that you are within quota of your home directory.

bash: command not found

Link to section 'Problem' of 'bash: command not found' Problem

You receive the following message after typing a command

bash: command not found

Link to section 'Solution' of 'bash: command not found' Solution

This means the system doesn't know how to find your command. Typically, you need to load a module to do it.

bash: module command not found

Link to section 'Problem' of 'bash: module command not found' Problem

You receive the following message after typing a command, e.g. module load intel

bash: module command not found

Link to section 'Solution' of 'bash: module command not found' Solution

The system cannot find the module command. You need to source the modules.sh file as below

source /etc/profile.d/modules.sh

or

#!/bin/bash -i

Close Firefox / Firefox is already running but not responding

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You receive the following message after trying to launch Firefox browser inside your graphics desktop:

Close Firefox

Firefox is already running, but not responding.  To open a new window,
you  must first close the existing Firefox process, or restart your system.

Link to section 'Solution' of 'Close Firefox / Firefox is already running but not responding' Solution

When Firefox runs, it creates several lock files in the Firefox profile directory (inside ~/.mozilla/firefox/ folder in your home directory). If a newly-started Firefox instance detects the presence of these lock files, it complains.

This error can happen due to multiple reasons:

1. Reason: You had a single Firefox process running, but it terminated abruptly without a chance to clean its lock files (e.g. the job got terminated, session ended, node crashed or rebooted, etc).
   • Solution: If you are certain you do not have any other Firefox processes running elsewhere, please use the following command in a terminal window to detect and remove the lock files:

     $ unlock-firefox

2. Reason: You may indeed have another Firefox process (in another Thinlinc or Gateway session on this or other cluster, another front-end or compute node). With many clusters sharing common home directory, a running Firefox instance on one can affect another.
   • Solution: Try finding and closing running Firefox process(es) on other nodes and clusters.
   • Solution: If you must have multiple Firefoxes running simultaneously, you may be able to create separate Firefox profiles and select which one to use for each instance.

Jupyter: database is locked / can not load notebook format

Link to section 'Problem' of 'Jupyter: database is locked / can not load notebook format' Problem

You receive the following message after trying to load existing Jupyter notebooks inside your JupyterHub session:

Error loading notebook

An unknown error occurred while loading this notebook.  This version can load notebook formats or earlier. See the server log for details.

Alternatively, the notebook may open but present an error when creating or saving a notebook:

Autosave Failed!

Unexpected error while saving file:  MyNotebookName.ipynb database is locked

Link to section 'Solution' of 'Jupyter: database is locked / can not load notebook format' Solution

When Jupyter notebooks are opened, the server keeps track of their state in an internal database (located inside ~/.local/share/jupyter/ folder in your home directory). If a Jupyter process gets terminated abruptly (e.g. due to an out-of-memory error or a host reboot), the database lock is not cleared properly, and future instances of Jupyter detect the lock and complain.

Please follow these steps to resolve:

1. Fully exit from your existing Jupyter session (close all notebooks, terminate Jupyter, log out from JupyterHub or JupyterLab, terminate OnDemand gateway's Jupyter app, etc).
2. In a terminal window (SSH, Thinlinc or OnDemand gateway's terminal app) use the following command to clean up stale database locks:

   $ unlock-jupyter

3. Start a new Jupyter session as usual.