🚧 Work in Progress

This repository is under active development.
Expected completion: TBD

Docs, tools, and technical resources for research computing at the Kennedy Institute of Rheumatology, University of Oxford

HPC Support Documentation

01

Getting Started

Setup an account & Login

• How to request a BMRC HPC account
• Access the cluster for the first time
• Set up your ssh clients

02

Filesystem Layout

Overview of BMRC Filesystem

• Where to store your raw data
• Where to do your work
• How to share data between the group or non-KIR BMRC groups

03

Software

Managing Software on BMRC

• Search and access software with modules
• Notes on specific software
• How to create your own Python virtual environment
• pixi in favour of conda

04

Batch Computing

Introduction to Slurm

• What is Slurm and Slurm variables
• Using GPUs via Slurm
• Slurm job arrays

05

Interactive Computing

Interactive HPC with OnDemand and srun

• Introduction to OnDemand and it's apps
• Interactive computing with srun

06

Data Transfer

How to transfer data to/from BMRC filesystem

• Data transfer with CLI tools such as scp,rsync
• How to use FileZilla
• Data transfer with Globus

07

Parallel Computing

Parallel Speedup and Scaling

• Scaling Limits

08

Service Status

BMRC Cluster/Data service status

Checking services…

Training Catalogue & Technical Essays

🎓

KIR Research Computing

Browse the Training Catalogue →

• The KIR Research Computing team runs hands-on training workshops covering HPC, bioinformatics workflows, software packaging, and scientific computing. All materials are freely available and self-paced.

✒️

KIR Research Computing

Browse Technical Essays →

• Articles on HPC, bioinformatics, containers, and scientific computing from the KIR research computing team.

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