Getting Help

Support staff may be contacted via:

Griffith Library and IT Help 3735 5555 or X55555
Email support: eresearch-support@griffith.edu.au
Online Form: https://www.griffith.edu.au/eresearch-services/request-help?hpc

You can log cases on service desk tool Cherwell https://griffith.cherwellondemand.com/CherwellClient/
Note for classifying your request:

To find the current usage, run this command:

du -kh /export/home/snumber

du -kh /scratch/snumber

You may run the following command to check free resources on cluster at any moment:

qstatr

...

Quick Classification: HPC
Service: eResearch
Category: Research Computation, Analysis and Visualisation
Subcategory: High Performance Computing
Team: RSD - eResearch and Specialised Platforms - HPC

eResearch and Specialised Platforms, Griffith University
Email: eresearch-support@griffith.edu.au
Web: https://www.griffith.edu.au/eresearch-services

Getting Started

Logging in.

To log in to the cluster, ssh to

10.250.250.7

clogin1.rcs.griffith.edu.au

What is ssh

SSH Secure Shell provides users with a secure, encrypted mechanism to log into systems and transfer files

ssh clients

windows platform

To install a ssh client e.g. putty, please follow this instruction

Linux platform and mac platform

ssh -Y snumber@clogin1.rcs.griffith.edu.au 

Multi-Factor Authentication (MFA) has been implemented on Griffith HPC as an additional layer of cybersecurity. You will receive this message

Authenticating using PingID...

Please use your pingid authenticator app to approve. After that you will receive this message:

PingID authentication completed successfully

PS: Further information about pingID can be found here.

Transferring files between your desktop and gowonda cluster

Transferring files between your desktop and Griffith HPC cluster

Once you are on the system, have a look around. Your home directory is stored in:
/exports/home/<SNumber>

where you have 50GB of allocated space.

Work space is available at:

/scratch/<snumber>

which is a "scratch" area for short lived data. All data older than one week is deleted from this folder.
You should not read or write directly into your home directory with submitted jobs - they should always use the "/scratch/<snumber>" filesystem

Running Jobs

We provide modules that set up the environments you need to use for specific packages. You can see what modules are available with the command:

module available

and you can load them with the command:

module load MODULENAME

See sample pbs scripts here.

If you don't specify a maximum runtime, you will end up with a maximum runtime as short as 30 minutes, depending on which node your job runs on.

Job Stats

when you run qstat from the command line, you will see your job's state within the queue. The following form lists the possible states and their descriptions

Cluster Status

(When done, you can press "Q" to quit from the below text-based browsers

Use the commands to check the cluster status: pbsnodes, pbsjobs, and pbsqueues

elinks http://localhost:3000/nodes

elinks http://localhost:3000/jobs

elinks http://localhost:3000/queues

Reference:

1. ECDF. 20 July 2011. U of Edinburgh. 7 Oct. 2008 <www.ecdf.ed.ac.uk>