# 2020-11-30 <br> HPC1: Introduction to HPC at Leeds

Welcome to the hack pad for HPC1 course from Research Computing at the University of Leeds!

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## Contents

1. [Links to resource](#Links-to-resources)
2. [Agenda Day 1](#Agenda-Day-1)
3. [Agenda Day 2](#Agenda-Day-2)
4. [What's your name and where do you come from?](#What’s-your-name-and-where-do-you-come-from)
5. [Code along notes](#Code-along-notes)
6. [Questions](#Questions)

## Links to resources

- **Contact Research Computing** - https://bit.ly/arc-help
- **Request HPC account** - https://leeds.service-now.com/it?id=sc_cat_item&sys_id=4c002dd70f235f00a82247ece1050ebc
- **Presentation for today** - https://bit.ly/hpc1intro
- **Exercises for today** - https://docs.google.com/document/d/1SPaZ2kmzYpMFIkiMSi-Qnu-ZqLaW4reSpVal3aOrmmk/edit
- **Github repository** - https://github.com/arctraining/hpc1-files
- **How to transfer files** -https://arcdocs.leeds.ac.uk/getting_started/file_transfer.html

## Agenda Day 1

| Time | Agenda |
| -------- | ------------------------------------------ |
| 0900 | Intro, connecting to ARC, what and why HPC?|
| 0950 | Break |
| 1000 | Login, HOME directory and looking around <br> Exercise 1 |
| 1050 | Break and Answers |
| 1100 | Simple job submission, qstat, qdel |
| 1150 | Questions |
| 1200 | Close |

## Agenda Day 2

| Time | Agenda |
| -------- | ------------------------------------------ |
| 1300 | Intro, Data Transfer, Modules |
| 1350 | Questions and break |
| 1400 | Interactive sessions, ib v smp, node types |
| 1450 | Questions and break |
| 1500 | User guided section, talking through <br> your hopes/fears for HPC |
| 1550 | Wrap up and questions |
| 1600 | Close |

## What's your name and where do you come from? And why do you want to use HPC?

- Alex Coleman, Research Software Engineer, my research has previously been in natural language processing and clustering event descriptions data and simulating crime rates using historic data.

- Nick Rhodes, Research Software Engineer. Working with Alex and John in the Research Computing team. Generalist with a background in operational leadership, development and support of large systems.

- John Hodrien, Research Software Engineer. Particularly into all things Linux. Started off as a Computer Scientist, then have taught, and been a researcher here at Leeds, before moving over to IT.

- Ausrine Marinskaite, 4th year Medicinal Chemistry student, doing my final year MChem project. Will be using ARC to do the computational part of my project :)
- Xuefeng He PDRA in School of Chemistry, want to run COMSOL on HPC to do some finite element analysis simulation
- Emily Dowd, 1st year PhD Student in SEE. Will be using ARC to run a chemical transport model, TOMCAT, to look at atmospheric methane.
- Yunqing Wang, project involves processing of human microbiome data.
- Sherif Zantiba, I am working on building a device for testing meniscus function with the aid of MRI.But I intend to use FEA at some point to build more models
- Lauren Burton, first year PhD student in SEE. Working with climate models to model both the Pliocene epoch (~3 million years ago) and future climate change
- Belen Fadrique, Marie Curie Fellow at the Geography Department. I work with large long-term vegetation census data to understand species long-term trends and their relationship with climate change. Hoping to perform big data analysis from R on the HPC.
- Eve Shalom, Second Year PhD Student (EPSRC-CASE). Working with CFD modelling for applications in improvign liver surgery planning through inversion methods. Hoping to scale up to larger realistic systems that will match DCE-MRI scan data sizes.
- Sophie Hazelden, final year PhD student working with the pig microbiome. Looking to complete bioinformatics/Mothur using the HPC
- Giulia Sindoni, I just finished my PhD in theoretical computer science, and now I'm Teaching Assistant at Leeds Uni.
- Yousef Alghamdi, PhD student, Cancer Bioinformatics
- Alex Wright, digital pathology research fellow. Applying AI to cancer slide images
- Ahmed Alali, Second year PhD Researcher in the school of civil Engineering
- Fan Qiao- 1st year PhD in SEE. Working with WRF-chem model to simulate chemical process of air pollution
- Adam Gauley, PostDoc working in
- Mojtaba Lashgari, PhD school of computing. Will use HPC for simulation
- Oliver Bramley, First year PhD student in chemistry. Looking to use the HPC for quantum simualtions and electronic structure. Would like to learn how to schedule jobs on the HPC using a python script
## Glossary of Terms

- Core: the basic computation unit of the CPU. This is unit that carries out the actual computations.
- Node: the physical machine/server. In current systems, a node would typically include one or more processors, as well as memory and other hardware.
- Parallel: run across multiple CPU cores, splitting the workload between them and solving the problem faster.
- Processor: the central processing unit (CPU) inside the node, which contains one or more cores.
- Serial: run on a single CPU core, solving one problem at a time
- Batch processing: Jobs that are run as and when the system is able to, rather than jobs run interactively
- Thread: A lightweight logical computation process. If a program is a sequence of instructions, this is the finger that works its way through the list of instructions. There can be many fingers, and you can have many more threads than you have hardware to run them.
- GPU: Graphical Processing Unit. Not necessarily graphical, but this type of hardware is good at some high parallelism problems. We have a small number of these in ARC3/4. Massive speed ups are possible - one GPU can be as powerful as 40 machines.

## Code along

`git clone https://github.com/arctraining/hpc1-files`