# 2023-10-03 <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 resources](#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)

Chris Trevelyan - FBS Molecular Cellular biology
## 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://arctraining.github.io/rc-slides/hpc0.html#/meta-code

## Further reading

Linux crib sheet that covers lots of idea from today and beyond - https://leeds365.sharepoint.com/\:b:/s/TEAM-ResearchSoftwareEngineering/EYW4b7LarU9MrLwg8-xDtZ0B6XjeSBHiiBFSmSbUbgpe3A?e=AFtP8d

## Agenda

| Time | Agenda |
| -------- | ------------------------------- |
| 0930 | Introduction, connecting to ARC |
| 1020 | Break |
| 1030 | Navigating the shell |
| 1120 | Break and Exercise 1 |
| 1130 | Data transformation in the shell|
| 1220 | 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?

- Ollie Clark, RSE - Python, databases, software engineering
- Tianyi Pan, RSE - CFD, HPC, Python, Fortran
- Abi Buchan, PGR in SEE - CLaimte modelling
-Majed Melibary PhD Mechnical Engineering
- Jennifer McLauchlan, PhD in Food Science - MD simulations
- Bianca Hazt, PhD in Food Science - coarse-grained simulations
- Darren Greenwood, School of Medicine, using MCMC methods, hoping to call JAGS from within R, modelling long covid trajectories
- Abi, PhD in atmospheric chemistry
- Amin Atashgaran, Neuroscience MBiol student - R, genomic data analysis
- Lucy Fothergill,PGR Artificial Intelligence - Python
- BAN A-Jassani - Research Fellow - School of Mechanic / Computing . Interested area Matlab - C - C++.
- PGR -
- Rebecca Chandler-Bostock, Biological Sciences interested in viral assembly and NGS data analysis, R, C#,
- Jack Smith - PhD School of Earth and Environment, Python for deep learning (Pytorch)
- Peter King - Postdoc, economics, R.
- Nasrollah Hajaliakbari Computing
- Chris Trevelyan - FBS Molecular and Cellular Biology
- Hao Guo, PGR in EE, Matlab, Python, C++
- Rossana Escanilla, PGR SoG, Python, R
- Sinead - LITE (absolutely no programming background, sorry!)

## Feedback
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