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

HPC Support Docs Training & Technical Essays

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