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# 2021-04-19 <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. [Muhammad Asif Javed](Im doing Phd in mechanical engineering)

Bushra Alayed, PhD student in School of Medicine.

## 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!

## Who are you and where do you come from:
- Alhanof Alolyan, first year PhD student, School of computing.
- Jacqueline Vater, 3rd year PhD at the School of Design
- Ollie Clark, Research Software Engineer in Research Computing. Software Engineering, web and databases. A bit of cloud.
- Nick Rhodes, Research Software Engineer in Research Computing
- John Hodrien, Research Software Engineer in Research Computing, with a big history in working with Linux and parallel systems.
- Benjamin Mills, associate prof, never used the HPC here (Earth and Environment)
- Tomás Zilhão Borge, 3rd year Bsc MEng Computer Science
- Abrar Mohammed-PhD researcher in the school of computing
- Sicily Fiennes - PhD researcher in the School of Biology, researching using technological aids to monitor bird trade
- Qiuyu Zhu, 1st year PhD in the School of Geography
- Jo Galloway, PDRA, Meldrum Group, Chemistry
- Zoe Hancox, PGR for AI in Medical Diagnosis and Care
- Duncan Ewin - PhD student Microbiology
- Jess Snelson - PhD student Chemical & Process Engineering
- Gabriele Sergalyte- MSc Student Food Science (Dissertation on Computational Chemistry)
- Natalie Chaddock - PhD student Genetic Epidemiology & Bioinformatics
- Michael Bell - PGR in LICAMM looking at medical imaging techniques in CVD
- Francesca Appadoo - PhD student in virology and cryo-EM
- Eszter Kovacs - 2nd year PhD student (aerosol/cloud interactions)
- Shengyin Wang PhD student from school of computing
- afrah alshammari phd in bioinformatics
- Andrew Merdith, Marie Curie Fellow using HPC for GCMs
- Charmaine Normington PhD Medical Microbiology
- Alfensi Faruk, PhD Student in the School of Mathematics
- Brett Hull, PhD student in Data Analytics
- Michael Zulyniak, Lecturer, FSN
- Andrew Jackson, MPhys Physics with Astrophysics
- Ibtisam Alshammari, Phd researcher in Computer Science.