IT HPCC User Guidance
IT Services provides a general purpose Compute Cluster as a resource for researchers within the University.
Request access
Connecting
From the campus network, either LAN connected or via eduroam Wi-Fi network or using VPN. Use a terminal program on your PC to issue the command ssh username@headnode04.cent.gla.ac.uk
For first login, use the password provided to you upon account creation, it must be changed afterwards.
Job scheduling
Scheduler used is PBS + Maui + Torque
Jobs are either:
a) Interactive: qsub -I
b) Batch: qsub myjobscript.sh
A basic example for a job submission script (myjobscript.sh) that requests 1 hour on a CentOS7 server can look like:
#!/bin/bash
#PBS -l cput=01:00:00, walltime=01:00:00, nodes=1:centos7
#PBS –m abe
#PBS –M myemail@glasgow.ac.uk
/path/to/programme_to_run
#OR
module load R
R —version
More info about how to set a job’s time limit and other available job options, how the job script looks like and how to check the status of running jobs can be found in the user manuals.
Compute resources
The resources are a mixture of CentOS 7 and Oracle Linux 9 compute servers, with combined:
- 1020 cores
- 8TB of memory and
- 7 Nvidia GeForce GTX 1080 GPUs
Available storage spaces
a) $HOME/
b) Shared Scratch: /export/scratch/username
Software
Some installations are available as shared modules. Use “module available” to check the full list, “module load <module>” to activate any installation in your current session (can be used also in job scripts).
Please note that Environment Modules are only available on CentOS 7 nodes and not Oracle Linux 9 ones, to ensure you land on these nodes make sure you’re using “centos7” in your job script or in the interactive job allocation command.