HPC-AI-Healthcare-Training

High Performance Cluster (HPC) short tutorial for UCL AI-Enabled Healthcare CDT

Why use the HPC?

• No CUDA enabled GPU on your laptop
• Don’t want your laptop to become a radiator
• Run parallel experiments and get results quicker
• Hyperparameter optimization
• BIG GPU’s
• Free service
• Relatively high freedom to manage your own environment
• Learn key skills for industry
• Secure place to store healthcare data
• Active support

Why not use the HPC?

• Takes time to setup
• Job queue times
• Unix is hard and ugly
• Unfamiliar environment
• I have a huge GPU in my desktop it’s enough for what I want to do
• Prefer to learn commercial cloud services (AWS GCP AZURE)

Getting access

First of all, it's worth checking if your supervisor already has accesss to HPC services and then requesting an account there.

If not you can request an account:

• CS HPC at https://hpc.cs.ucl.ac.uk/account-form/
• UCL Research Center (RC) at https://signup.rc.ucl.ac.uk/computing/requests/new

This guide is going to use the CS HPC cluster but the two are very similar. Worth noting that I have borrowed loads from the much better docs of RC https://www.rc.ucl.ac.uk/docs/.

The IHI is in the process so procuring its own HPC services but we're not there yet :(.

How does it work?

How do I use it?

Most people use something like the following workflow:

• connect to the cluster's "login nodes"
• create a script of commands to run programs
• submit the script to the scheduler
• wait for the scheduler to find available "compute nodes" and run the script
• look at the results in the files the script created

Logging In

Simple way

You will need to either use the UCL Virtual Private Network or ssh in to UCL's gateway tails.ucl.ac.uk first. From tails you can then ssh in.

ssh <your_UCL_user_id>@tails.cs.ucl.ac.uk
ssh <your_UCL_user_id>@<login_node>.cs.ucl.ac.uk

There are a few login nodes availabel but it shouldn't really matter which you use. gamble is the one I use.

Rapidos way

You can setup a

Scheduler

qsub

Submit a job to the scheduler with qsub

qsub /path/to/submission/script/

qstat

Get the status of a job with qstat

qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
6506636 0.00000 testing    jbloggs      qw    21/12/2012 11:11:11                                    1     
qstat -j <job-ID>

q

Submit a job to the scheduler with qsub

qsub /path/to/submission/script/