# 2021-03-16 <br> HPC0: Introduction to Linux

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

**Contact Research Computing** - https://bit.ly/arc-help
**Presentation for today** - https://bit.ly/hpc0linux
**Exercises for today** - https://drive.google.com/file/d/1dV8fMS_n6GOFZO_rmFfUBwnuBFGj6C58/view?usp=sharing

**Approximate schedule**

| Time | Agenda |
| -------- | ------------------------------- |
| 1300 | Introduction, connecting to ARC |
| 1350 | Break |
| 1400 | Navigating the shell |
| 1450 | Break and Exercise 1 |
| 1500 | Data transformation in the shell|
| 1550 | Wrap up and questions |

## What's your name and where do you come from? - <br> Make a new line below and write a bit about yourself

- Alex Coleman, Research Software Engineer
- Ollie Clark, Research Software Engineer
- John Hodrien, Research Software Engineer
- Nick Rhodes, Research Software Engineer
- Yasmin Taylor, Mbiol student in Paci lab
- Smail Kechidi, Post-Doc researcher in School of Civil of Engineering
- Josefa Sepúlveda,PhD student in Earth and Environmental School (Volcanology)
- Dan-Adrian Corfar, PhD student in School of Civil Engineering
- ***Lucy Godson***, *PhD student from the school of computing*.
- Esra Ermis, PhD Student in LIMR, I'll use HPC when I analyse RNAseq data.
- William Grant, PhD student in Molecules to Product CDT. Need the HPC for using OpenFOAM.
- **Volodymyr Chapman**, PhD student in the Westhead Group. Investigating AI for diagnosis and prognosis in lymphoma.
- Siti Mohd Noor, PhD student in Chemical Engineering
- Michael Jones, PhD student in Mechanical Engineering. Using HPC to run simulations in COMSOL for corrosion studies in flow cells.
- Moisés Rechy, PhD studend in Structural Biology (Virology)
- Niall Gallop, Research Technician in CRC
- Jessica Haigh, Postdoc in Neuroscience
- Jiaqi Ge, researcher in Geography
- Catherine Hogg, MSc student in Precision Medicine
- Chris Rooney PhD student in LIMR
- Panos Tsoleridis, PhD student, Institute for Transport Studies
- Manir Ali, LIMR, Supervise students who use ARC. Research interests include next generation sequencing.
- Connor Clayton, PhD Student in the School of Earth & Environment
- Shradhanjali Sahu, PhD student in School of Electronic and Electrical Engineering
- **Abdullah Alsaleh**, PhD student, School of Computing
- John Blacker, Prof. Chemist and Engineer
- Samuel Llanwarne, school of computing
- Paula Avello, post doc, school of biology
-

## Useful commands

* `mkdir`:
* Make a directory - `mkdir example`
* Make a directory and intermediates - `mkdir -p one/two/three`
* `cd`: Change directory - `cd example`
* Go up a directory - `cd ..`
* Go home - `cd`
* Go back to where you were previously - `cd -`
* `pwd`: Print Working Directory - `pwd`
* `ls`: list files in a directory - `ls`
* `nano`: simple editor - `nano example.txt`
* `cat`: Print a file - `cat example.txt`
* `less`: Show a file letting you browse/search - `less example.txt`
* `^C`: How to abort a program (Control-C)
* `mv`: Move/rename a file
* Move to a another directory - `mv example somedir`
* Rename - `mv example.txt other.txt`
* Move and rename - `mv example.txt somedir/other.txt`
* `rm`:
* Delete a file - `rm file`
* Delete a directory and contents - `rm -r directory`
* `cut`: Select a bit of text - `echo "one,two" | cut -d, -f2`
* `awk`: For when you don't want cut - `echo "one,two" | awk -F, '{print $2}'`
* `>`: Redirect to file - `echo rabbits > some-file`
* `>>`: Redirect and append to file - `echo rabbits >> some-file`
* `<`: Redirect from file - `cat < some-file`
* `sort`: Sort a file - `sort some-file`
* `head`: Show the top lines from a file - `head some-file`
* `tail`: Show the last lines in a file - `tail some-file`