# 2022-11-08 <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 |
| 1200 | Finish |

## 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 executable 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”](https://arc.leeds.ac.uk/help/videos/) and read carefully the [documentation section](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, I like Python and R and data sciencey magic
- John Hodrien, research software engineer. I'm a long term Linux fan, and HPC administrator.
- Rachael Lowe, PhD student in the School of Chemical and Process ENgineering. Looking to run modelling software on ARC
- Alex Derry, I am a PhD student in medicine, but live in chemistry. I came from York, and enjoy some chill games like card games. I will use the HPC for drug protein interactions.
- Tanmay Bhore, theoretical physics PhD student, I simulate quantum systems, mostly with Python.
- Emily Rolfe, I am a PhD student in LICAMM. I am looking at finding ligands from large libraries to treat cardiometabolic disease, hence why I want to use HPC.
- Nan Cui, Geography PhD student, I came from China.
- Emily Byrne, Placement student from York
- Michael Zulyniak, Lecturer, FSN, genomics research
- Kenny Campbell, PhD students, working on quantum communications with the electrical and and electronic engineering department
- Ahmed Ahmed, PhD student in Accounting and Finance, looking to use python to analyze social media posts by investors
- George Alton, Statistical Programmer in Cl. I do R, SAS and STATA. we are looking at HPC as an extension to my role and to potentially help with the simulation of clinical trials.
- Zeke Marshall, Research Asssitant in SRI, working in R and Python. Here to learn how to run a targets workflow on the HPC.
- Majed , Phd, i want to learn how to Submitting multiple jobs in Abaqus using INP files and python.
- Naomi Shakespeare-Rees, PhD student in school of Earth and Environment, Using machine learning methods to study geomagnetic fields :)
- Basudha Basu, Postdoc in the Faculty of Medicine and Health. Modelling retinal disease using patient mutations in stem cells. I do a lot of RNA seq for that and would like to use the HPC to learn how to analyze it myself.
- Gurjit Panesar - Research Storage team understanding more about Arc and linux commands
- Becky Banbury Morgan, PhD Student in School of Geography. Building simulations of forest stand structure and forest responses to changes in growth and mortality rates.
- Cristian Voinea, PhD student in theoretical physics, doing numerical work on quantum many body dynamics
- Arundhati Kalyan, PhD student in Climate science, using linux/HPC to run climate simulations and analyze datasets
- Yiyu Wang, PhD student in CSAP cluster, using HPC to run pedestrian simulation applying ABM and Bayesian game theory
- Arya, pronounced as Rjo. Postdoc from School of Molecular & Cellular Biology.