---
tags: teaching, hpc0
---
# 2021-11-02 <br> HPC0: Introduction to Linux

Welcome to the hack pad for HPC0 course from Research Computing at the University of Leeds!

You can edit this document using [Markdown syntax](https://guides.github.com/features/mastering-markdown/).

## Contents

1. [Links to resource](#Links-to-resources)
2. [Further reading](#Further-reading)
3. [Agenda](#Agenda)
4. [Pre workshop prep](#Pre-workshop-prep)
4.1. [Windows Users](#For-Windows-Users)
4.2. [MacOS/Linux Users](#For-MacLinux-Users)
6. [What's your name and where do you come from?](#What’s-your-name-and-where-do-you-come-from)

## 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
- **Slides for today** - https://bit.ly/hpc0linux
- **Exercises for today** - https://drive.google.com/file/d/1dV8fMS_n6GOFZO_rmFfUBwnuBFGj6C58/view?usp=sharing

## Further reading

Linux crib sheet that covers lots of idea from today and beyond - https://drive.google.com/file/d/0B4hIpRJzq8DPVG5xdEJWcGlRTkU/view?usp=sharing

## Agenda

| Time | Agenda |
| -------- | ------------------------------- |
| 0900 | Introduction, connecting to ARC |
| 0950 | Break |
| 1000 | Navigating the shell |
| 1050 | Break and Exercise 1 |
| 1100 | Data transformation in the shell|
| 1150 | Wrap up and questions |

## Pre workshop prep

***If you haven’t already request an account for the HPC via this link - https://leeds.service-now.com/it?id=sc_cat_item&sys_id=4c002dd70f235f00a82247ece1050ebc***

For Windows users please consult our documentation page and video at https://arcdocs.leeds.ac.uk/getting_started/logon.html#connecting-from-windows

You are required to download the software tool MobaXTerm for this workshop.

1. Navigate using a web browser to https://mobaxterm.mobatek.net/
2. Select Download

3. Click Download Now for the Home Edition
4. Select MobaXTerm Home Edition v21.0 (Portable edition)
5. This opens a download prompt for a .zip file. Select Save File and click OK
6. Go to your Download folder and find the .zip file you have just downloaded

7. Click Extract in the Ribbon Bar and select Extract All

8. Using the Wizard window extract the folder at the suggested location

9. This should open the extracted folder immediately and allow you to double-click on the MobaXTerm_Personal_21.0 executeable to start the application
**And you're all set for HPC0!🎉**

### For Mac/Linux Users:

**MacOS and Linux users do not need MobaXTerm** but can use your builtin Terminal application. You should follow the steps outlined in the bitesize video titled “Connecting to ARC off-campus via Linux/MacOS” on this page (https://arc.leeds.ac.uk/help/videos/) and read carefully the documentation section here (https://arcdocs.leeds.ac.uk/getting_started/logon.html#connecting-from-linux-macos-systems) on connecting from Linux and MacOS, especially the section about configuring SSH for off-campus connections.

Please attempt to read the documentation and watch the videos carefully and attempt the setup steps. If you have any problems don’t worry we will spend the start of the workshop making sure everyone is connected.

In order to connect to ARC when you're off campus you'll need to do some extra configuration so that your SSH connection goes via our `remote-access` server. The following steps outline how to setup this configuration:

1. Open a Terminal on your Linux/macOS machine
2. Create a directory called `.ssh` in your home directory (if one doesn't already exist)

    $ mkdir ~/.ssh

3. Then open a text editor of your choice and create a file called `config` in your `.ssh` directory

    # for instance use the simple nano text editor
    $ nano ~/.ssh/config

4. Within this file include the following contents where `USERNAME` is replaced by your university username

    Host *.leeds.ac.uk !remote-access.leeds.ac.uk
    ProxyJump [e-mail]
    User USERNAME

5. Save this file and your configuration is all set up!

## What's your name and where do you come from?
- Alex Coleman, Research Software Engineer in Research Computing
- Tamara Fletcher, School of Earth and the Environment, Palaeoclimatology, need to run R code on research computers (might be HPC might be a 'smaller' research computer), starting to learn programming outside R.
- John Hodrien, Research Software Engineer in Research Computing (Linux/HPC/Distributed Systems/Visualisation)
- Smail Kechidi, School of Civil Engineering
- Janet Richardson, School of Earth and Environment - here to learn how to speed up some modelling processes for SD-TOPMODEL
- Samuel Hughes, School of Biology- speeding up some modelling, also interested in trying out linux
- Roza Bilas from School of Biology - here to learn how to handle big proteomics datasets
- Alaa Alhumaisan from School of Computing, I am here to learn how to use remote servers in training ML models.
- Aiden Daniel, Research Postgraduate in the School of Physics and Astronomy. Eager to learn how to operate Linux after hearing much about it. Also, HPC is required for a lot of the research work I have to do.
- Iso Hirst, School of Biology, Astbury Centre so I will be using HPC for cryo-electron microscopy data processing
- Matthew Threadgold, PhD Student, School of Mathematics
- Justin Clarke, Faculty of biological sciences, amplicon sequencing
- Harry Barton, School of Chemistry. Natural Sciences Masters student. I'm using HPC for my final project where I'll be using Gaussian and MESMER to obtain theoretical rate coefficients for interstellar chemical reactions.
- Yatin Darbar, School of Computing. I would like to use HPC for my projects
- upasana sykora, faculty of biological sciences, I am using HPC to understand the architecture of hepatitis C virus replication complex. HPC will allow me analyse the data generated by electron microscope.
- Thomas Allcock, School of Computing.
- Billy Hobbs, School of Molecular and Cellular Biology
- Chris Field, School of Physics and Astronomy
- Jo Egan, School of Chemistry
- Ollie Clark, Research Software Engineer in Research Computing. Background in databases, web development and software engineering.
- Sean McMillan, Biochemisty PhD student
- Sarah Miller AI Med Phd from Sheffield.
- Menwa Alshammeri, Schhol of computing at University of Leeds. My PhD research use ML/DL to extract knowledge from texts.
- Zac Paling- School of Biology. Here to navigate HPC for cryo-EM
- Rosie Knapp, PhD student in School of Biology, learning how to use HPC for RNA-seq analysis (looking at gene expression data)
- lena Almutair, School of computing, Phd student
- Ffion Hall, School of Chemistry, MChem student