OOD FAQ

Q: How do I cut and paste in a VDI session?

A: Some browsers (notably Firefox) block cut and paste between noVNC and your desktop. You can work around this; half-way down the left hand edge of the window there is a little pull-out tab; clicking this and then selecting the 2nd button in the resulting panel will pop out a clipboard area; using this area you can cut and paste between your desktop and your VDI session. Some other browsers (eg recent versions of Chrome) allow you to cut and paste without having to go through this.

Q: I have attempted to connect to OOD, but I'm getting a message "Bad Request Login session expired":

A: This probably means you accidentally connected to the authentication service at https://ood.nci.org.au:8443/ rather than the main service at https://ood.nci.org.au

Try clearing the URL in your browser and make sure it is just https://ood.nci.org.au (no 8443 at the end).

(Sometimes browsers cache URLs and autocomplete them inappropriately)

Q: I have attempted to connect to OOD, but I'm getting a Bad Request message:

Bad Request

Your browser sent a request that this server could not understand.
Size of a request header field exceeds server limit.

A: This one can usually be solved by clearing your cookies, or starting the OOD session in a 'Private Browsing' window. It appears to be caused by the size of the cookies the browser is presenting exceeding some limit. We are looking for a fix for this.

Q: I launch a VDI session, but it goes from queue straight to completed, and I can't connect to it

A: This is usually caused by conda environments. Some conda installs will include libraries which conflict with the system ones, and this will cause your desktop to fail to start.

In order to fix this, you need to edit your .bashrc (or equivalent if you use a shell other than bash). You can do this in a couple of different ways:

• Use the built-in file managed in OOD: select 'Files → Home Directory' from the top menu of the OOD homepage, then enable the 'Show Dotfiles' tickbox at the top right, select .bashrc from the list, and click the edit button
• Start a Jupyterlab session from the main page, connect to it, and then select File → New → Terminal from the Jupyterlab menu bar
• Use the SFTP transfer node to transfer the file to your local machine, edit it and put it back: see 2.2. VDI Resources section 'SFTP Transfer Node'

Once you have it open in an editor, you should see a section like this:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/short/bx82/jpe777/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/short/bx82/jpe777/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/short/bx82/jpe777/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/short/bx82/jpe777/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

You need to modify it to check if the current shell is an interactive shell or not.

For bash and other Bourne-shell derivatives, the following should work:

if [[ $- == *i* ]]
then
    # >>> conda initialize >>>
    # !! Contents within this block are managed by 'conda init' !!
    __conda_setup="$('/short/bx82/jpe777/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
    if [ $? -eq 0 ]; then
        eval "$__conda_setup"
    else
        if [ -f "/short/bx82/jpe777/anaconda3/etc/profile.d/conda.sh" ]; then
            . "/short/bx82/jpe777/anaconda3/etc/profile.d/conda.sh"
        else
            export PATH="/short/bx82/jpe777/anaconda3/bin:$PATH"
        fi
    fi
    unset __conda_setup
    # <<< conda initialize <<<
fi

(So we have wrapped the conda section in an if block which checks if there's an "i" character in the the special environment variable $-)

Q: I try to launch an app, but I get back a page like this:

A: Note the 'Disk quota exceeded' message at the top of the Details section. You have run out of space in your home directory; see the next question.

Q: What if I run out of my home space?

A: You won't be able to start a desktop or anything else at this point. However:

• You should still be able to use the "Files" app within OOD to manage your files (Files → Home Directory on the top menu)
  • Note that you may need to select 'Show Dotfiles' at the top right to show files and directories starting with a . character, which are normally hidden.
• You can transfer your files out of your home space using sftp or apps like Cyberduck.  See the "SFTP Transfer Node" section in "2.2. VDI Resources" page for more information.

Q: Are there limitations on resources when using OOD?

A: When launching apps in OOD (e.g., VDI or JupyterLab) you control the resources available via the Compute Size option.  You will be constrained to at most the selected amount and the system does not over-allocate jobs.  If you attempt to use more CPU resources your processes as a collective will be throttled to this threshold.  If you attempt to use more memory the out of memory killer will kill processes to keep it below the threshold.

Q: What network ports do I need to be able to connect to in order to use OOD?

A: You will need to be able to connect to ood.nci.org.au ports 443 and 8443. If you wish to SSH directly to a node, or use the native VNC connection, you will also need to be able to connect to ood-vnc.nci.org.au port 22.

Q: How do I rsync data to OOD?

A: You will need to set up direct SSH access as per "4. Direct SSH access", and then persuade rsync to use it. Depending exactly which versions of rsync and ssh you have installed, you may be able to use the '-e' option to rsync to specify the extra options to ssh, something like rsync -e 'ssh -J abc123@ood-vnc.nci.org.au' -av abc123@ood-vnXX:/home/123/abc123/stuff-to-copy . (where ood-vnXX is the hostname from the session card within the OOD interface, and should not have nci.org.au appended to it). If your versions of ssh and rsync do not allow this, then you should be able to edit your SSH configuration file as per 4. Direct SSH access.

Q: I'm using the imagemagik "display" command and the colours are all messed up

A: there seems to be a bad interaction between the 'display' command and the virtual X server used by OOD. This happens both running display directly on ood, but also over SSH connections to gadi. The workaround it to add the option '-visual DirectColor' to the display command line, eg

display -visual DirectColor MyImage.jpg