FMRIB Open OnDemand Service (OOD)

View your currently running cluster jobs

The Jobs menu has two options, Active Jobs and Job Composer.

The Active Jobs option will present a view of your cluster jobs.

At the top of the view you can change Your Jobs to All Jobs to get an overview of the whole cluster state and use the filter box to identify specific jobs.

Using the trash can icon you can remove jobs that you know to be pointless due to errors in submission.

Open OnDemand cluster job list

The Job Composer allows for the submission of jobs - we would ordinarily recommend the use of the fsl_sub command inside an interactive desktop or shell session, so use of this facility is not covered here.

Running simple shell commands via Open OnDemand

The Clusters menu item allows you to start an interactive text session on our interactive Linux server clint.fmrib.ox.ac.uk.

Warning - this session will only remain running whilst you are connected to VPN/University network and have the browser tab open. Any task left running when the connection is lost will terminate. For long running tasks please use the interactive desktop facility.

Starting and using a Linux remote desktop

When you select the Remote Desktop option from the Interactive Apps menu you will be presented with a form to define the facilities you require for your remote desktop session.

New desktop configuration screen

For most uses, the 'Standard' session will be adequate, if you can use this option please do, as this ensures we can support many more sessions. This session will give you 2 (virtual) cores and 15GB of memory and is fine for running FSLEyes, web browsing, submitting cluster tasks and similar tasks.

Next enter a duration - minimum 0.1 day, maximum 10 days. This is the maximum duration of your session, and fractions allow for the requesting of sessions lasting from 2.4 hours. 

Finally, if you job absolutely requires a CUDA device then you can select the GPU type from the drop-down menu, which will expose an additional option for quantity of GPUs {default 1). The duration of your session will auto-adjust if it is greater than the maximum allowed on a GPU (60 hours) - you will see '3' in the duration box (due to the way the web site works), but this will be reduced automatically to 60 hours when the session is requests.

We have very limited numbers of GPU enabled hosts, so you may experience significant delays in obtaining your session.

Now click on Launch to request a desktop session.

If you see a red box appear titled 'Failed to submit session with the following error' and detail talking about 'Job violates accounting/QOS policy' then you have requested a second desktop session - this is not allowed for fair-share reasons.

If you are certain you need more resources than the default then you can select 'Advanced' from the drop-down, revealing options for RAM and cores/threads. We have limited resources, so the RAM, in particular is in short supply, so any session requesting more than 32GB of RAM may have a significant wait before it can be fulfilled.

Accessing the desktop session

If you have just requested a session you will now be taken to the My Interactive Sessions page. If you are returning to OOD then you can find this page by clicking on the two overlapping squares (on large screens this also has a text label!).
There may be a delay whilst your job starts on the cluster, during this period the pending job will have a blue section header. Once it is running this will turn green.

Open OnDemand Interactive Sessions

In the example here, there are two sessions, a MATLAB one and a FMRIB Desktop, both of which use Virtual Network Computing (VNC) technology to provide the graphical interface. The Interactive sessions card has the following information/links:

• The header shows the job ID (in parentheses) on the left, the number of course and state on the right
• Host details the cluster machine the job is running on, Created at, the start time, a count down of the time remaining for the session.
• The Session ID link takes you to a folder view for the job. This includes logs and files that may assist IT support when diagnosing problems, but ordinarily you don't need to look in here.
• Submit support ticket takes you to the support submission form. The View Only link may be requested by support so that they can follow along with the issue that you are seeing.
• The Delete button terminates this session - any unsaved work will be lost.
• The two sliders along the bottom of the card allow you to adjust the compression level and image quality - increase compression and decrease quality if you are on a slow network link, e.g. WiFi or non-full fibre home internet connections.
  Warning - do NOT set compression to '0' - this is likely to cause 'Incomplete zlib block' errors in the VNC session. 
• The Launch Remote Desktop button begins your VNC session in a new web browser tab.

The VNC session is provided by noVNC and runs a Mate desktop environment.

To the right of the view is the noVNC menu, click the tag to open the icon bar. The icons within are dependent on the device you are accessing from (touch devices get mouse options), but the basic icons are:

• 'A' - a pallete with modifier keys that may not map to keys on your keyboard
• Clipboard - allows for capturing the desktop clipboard or sending your clip board to the remote server
• Cog - settings, ordinarily you don't need to change these, but you may wish to change the Scaling mode and quality sliders.
• The final icon disconnects you from noVNC - once disconnected, your current VNC session is terminated - to return to your desktop you will need to relaunch via the My Interactive Sessions page.

The Mate Desktop

The Mate desktop has two panels by default, the top housing the application menus and application launcher icons (file browser, terminal, Firefox web browser and Thunderbird mail client by default) and on the far right the date and time. The bottom panel has a button to show the desktop and then on the far right, four virtual desktop switchers allowing you to organise your windows by task.

Most interactions with the FMRIB cluster will be via the terminal application which provides a command line from which you can launch FSL applications and submit to the cluster via fsl_sub. Most software packages need activating using environment modules - use the module commands to list/activate/deactive.

How to request and use a dedicated MATLAB session on the FMRIB cluster

The Open OnDemand Interactive Apps/MATLAB option allows you to start an interactive session housing only MATLAB. Whilst you can of course use MATLAB via the Remote Desktop app, this option uses less server resources, and can be considered to be similar to 'ssh -Y' but with session persistence.

The MATLAB app configuration form required the following information:

• Session type/Session duration/GPU and memory/cores (when Advanced selected)- see Interactive Desktop for description of options.
• MATLAB version - 'default' will choose the newest version installed, or you can choose a specific version.
• Extra modules script - this allows you to specify the full path to a text file that will load environment modules before starting MATLAB.

Click Launch to submit your job to the queue.

If you receive a red error box mentioning QOS, then you have requested a second Jupyter session - we do not allow this for fair-share reasons.

This will take you to the My Interactive Sessions page when you can launch the VNC session - see the Interactive Remote Desktop instructions for details on using the VNC viewer.

Running RStudio on the FMRIB cluster

The Open OnDemand server allows you to run RStudio via a cluster job.

To start a session, select RStudio Server from the Interactive Apps menu, this provides a form you can use to setup your RStudio session, and requires the following information:

• Session type/Session duration/GPU (cores and RAM If Advanced selected) - See Remote Desktop for description.
• R Studio Server version - 'default' will use the latest version installed, or you can select a specific version (if available) using the drop down menu.
• Extra modules script - if you need to load any environment modules before starting R, create a text file containing the appropriate `module load` commands and specify the full path to the script here.
• RStudio session request

Click Launch to submit your session to the queues.

If you receive a red error box mentioning QOS, then you have requested a second Jupyter session - we do not allow this for fair-share reasons.

Once submitted you will be taken to you My Interactive Session page where you can monitor the progress of your job, connect to your session and shut it down.

When your job is running (the card heading has turned green), you can use the Connect to RStudio Server button to open a new web bowser tab with your session within.

Launching Jupyter on the FMRIB Cluster

The Jupyter Interactive App allows you to launch a Jupyter session on the FMRIB cluster, which you can then interact with using a web browser.

First select the session type (Advanced will allow you to specify cores and memory), duration and whether you need a GPU - see Remote Desktop for details.

Before you can launch Jupyter you need to prepare a script that will provide the jupyter command. Typically this would be achieved using a conda environment. As a basic example, create a conda environment `jupyter` using a desktop, shell or SSH session:

conda create -y -n jupyter jupyter

create a text file in your home folder called `jupyter.sh` containing:

#!/bin/bash
. $HOME/.bashrc
conda activate jupyter

In the Jupyter form, enter the full path to this file, /home/fs0/<username>/jupyter.sh in the first text field (first red arrow below)

Now choose from Jupyter Notebook, the classic view, or Jupyter Lab, which offers an Integrated Development Environment (IDE) interface.

Specify the startup folder, for example /vols/Scratch/<username>/<myanalysis> in the next field (second red arrow).

Open OnDemand Jupyter

Click Launch to request your session.

If you receive a red error box mentioning QOS, then you have requested a second Jupyter session - we do not allow this for fair-share reasons.

You will now be taken to the My Interactive Sessions page where you can wait for the job to launch.

Once the card heading turns green (from blue), your session has started and you will find a button 'Connect to Jupyter' that will launch your web session.

NB At present, unlike other interactive apps this will not launch a new tab/window - we do not currently understand why this occurs.