Access to the supercomputer
Access Ngarrgu Tindebeek
Access to the supercomputer is available through Secure Shell (SSH) to nt.swin.edu.au for all users. i.e:
ssh [your-username]@nt.swin.edu.au
Important
After logging in you will be assigned to one of the two login nodes: tooarrana1 or tooarrana2.
From these nodes you can submit jobs to the queue nodes using Slurm. You may also use the login nodes as interactive nodes to run short jobs directly, compile code, or test your application.
Note
Do not use these login nodes to run long jobs or jobs with big computational requirements. Running such jobs in interactive mode can be done by requesting interactive nodes from the queue.
From each of tooarrana1/2 you can access the other with ssh t1 or ssh t2. tooarrana1/2 are also available for direct login via eg. ssh [your-username]@tooarrana1.hpc.swin.edu.au.
From tooarrana1/2 you can also SSH into farnarkle1/2, the login nodes for the previous supercomputer OzSTAR, with ssh f1 or ssh f2.
Direct access to farmarkle1/2 is still available via
ssh [your-username]@ozstar.swin.edu.au
Note
Jobs submitted on tooarrana1/2 will run on the new AMD Milan nodes, whereas jobs submitted on farnarkle1/2 will run on the older Intel Skylake nodes.
Tip
If you want to avoid having to type the rather long [your-username]@ozstar.swin.edu.au every time you want to connect to the supercomputer, you can set a shortcut in your SSH config.
For example, you can set the following in ~/.ssh/config:
Host nt
HostName nt.swin.edu.au
User your-username
Once set, you can use this shortcut to SSH into the supercomputer. The following commands will produce the same outcome:
Connect to supercomputer:
ssh [your-username]@nt.swin.edu.au
ssh nt
Copy a local file to supercomputer:
scp myfile.txt [your-username]@nt.swin.edu.au:path/to/location/
scp myfile.txt nt:path/to/location/
Client Requirements
Terminal
A terminal is required to access OzSTAR via Secure Shell (SSH) and issue command line instructions.
Operating System |
Terminal |
|---|---|
Mac |
Available by default via Applications > Utilities > Terminal |
Linux |
Available by default |
Windows |
The recommended method is to use the Windows Subsystem for Linux (WSL). More information available at the Microsoft documentation. If you are using an older version of Windows that does not provide WSL, you will need to install PuTTY. |
X11 Windows Forwarding
If you need to use a graphical screen of your application rather than a terminal, the ability to forward a graphical screen from the application back to your home computer is available via X11 Windows Forwarding.
Note
Graphical workflows are inherently unsuitable the queue-based job submission model of the supercomputer. However, having a graphical window can still be useful for examining the results of your jobs.
With Linux and MacOS this can be done by login from the command line Secure Shell with the -Y option:
ssh -Y [username]@ozstar.swin.edu.au
For MacOS you will first need to install XQuartz.
For modern Windows installations, you can use the Windows Subsystem for Linux (WSL), which provides a Linux command prompt. This is the recommended method. From there, the steps are the same as for Linux. Please refer to Microsoft's documentation on how to configure your system to run Linux GUI applications: https://learn.microsoft.com/en-us/windows/wsl/tutorials/gui-apps
For older Windows installations that do not provide WSL, you will need to install an X11 Server implementation. The following options can be used:
If you are using PuTTY, you will also need to enable X11 forwarding before connecting, This can be done through connection > SSH > X11 by selecting “Enable X11 Forwarding”.
VNC Sessions
In some instances, you may need to run a graphical application that requires a full desktop environment. In these cases, you can use a Virtual Network Computing (VNC) session.
VNC is also more efficient than X11 forwarding, so it can be useful for X11 applications that are slow to forward, especially over high-latency network connections -- any applications that show detailed 2D images or 3D graphics will benefit from it.
1. Setup and launch a VNC server on OzSTAR
Choose a login node to run the VNC server on.
You cannot rely on the generic ozstar or nt logins as a destination for remote persistent processes, since they are both round-robin addresses.
You need to pick one of tooarrana1/2 or farnarkle1/2 and stick to it.
# Connect via ssh to a login node
ssh [username]@tooarrana1.hpc.swin.edu.au
# Ensure you have no modules loaded
ml purge
# Select up a vnc password
vncpasswd
# Start a vnc server
vncserver
The VNC server will start on the first available port, e.g. :1. It should say something like:
New 'tooarrana1:1 (username)' desktop is tooarrana1:1
Starting applications specified in /home/username/.vnc/xstartup
Log file is /home/username/.vnc/tooarrana1:1.log
You only need to do this once. Running vncserver again will start a new session on the next available port, e.g. :2.
2. Use SSH tunneling to forward a port from your local machine to your VNC server
From your local machine, setup up an SSH tunnel:
ssh -L 5901:localhost:5901 -N [username]@tooarrana1.hpc.swin.edu.au
This will forward port 5901 on your local machine to port 5901 on the login node.
If you started the VNC server on a different port, adjust the port number accordingly, e.g. for port :2 use 5902.
3. Connect to your VNC server from your local machine with a VNC client
You can use any VNC client to connect to the VNC server on the login node. Some popular clients include:
In each client, you just simply connect to localhost:5901 (or whichever port you forwarded) and enter the password you set up with vncpasswd.
You should then have a desktop window from the login node on your local machine. You can run graphical applications from the terminal in this window.
4. Tidying up
When you are finished, remember to stop the VNC server on the login node
vncserver -kill :X
where X is the number of the VNC server you started, e.g. 1 or 2.
You can see what servers are running with:
vncserver -list