# 2020-11-23 <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 |

## Further reading

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

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

- John Hodrien: Research Software Engineer. I have been at the university in some form since 1997. Worked in Distrubuted Systems / Grid Computing, and Visualisation, mostly developing software in C++.

- Alex Coleman, Research Software Engineer

- Ollie Clark: Research Software Engineer. I have been at the University of Leeds since my UG degree in 1996 working mainly on Database and Web Development in Perl and Postgress. Now focusing on Azure, Python and HPC.

- Mojtaba Lashgari, PhD student at computing. I need to some MPI programing for a simulation in part of my research.

- Ausrine Marinskaite, BSc, MChem Medicinal Chemistry student, doing my final year project, will be modelling small molecules

- Rachel Dobson: newbie PhD student in Earth and Environment, crop modelling!

- Emily Dowd: First year PhD Student in SEE ICAS. Looking at atmospheric methane. Will be using ARC to run a Chemical Transport Model, TOMCAT.

- Amy Hyde, Nutrition BSc student, doing some research with Helen Chappell as a vacationship scheme & using computational modelling to construct bone collagen and test with silicon. Hopefully will learn a lot today not sure exactly what specifically :)

- Xuefeng He PDRA from school of chemistry

- Zisong Xu: 1st year PhD student in school of Computing.

- Aidan Johnson: 1st year chemistry PhD student. Primarily need ARC for running molecular docking simulations

- Alex Wright: Postdoc Researcher. School of Computing graduate (2007). PhD in DIgital Pathology and AI (2018). New to HPC.

- Saaduddin: School of Earth and Environment

- Yousef Alghamdi: PhD student, Cancer Bioinformatics

- Beth Soanes: PhD student, molecular bio. Need arc for RNA seq and m6a seq bioinformatics

- Jamie Paterson, Applied Maths PhD Student, need ARC for running high demand model simulations

- Belen Fadrique- Marie Curie Fellow at the Geography Department. Working with large databases of vegetation data in the Andes and Amazon. Need HPC for analyses and data management.

- Sophie Hazelden, 4th year PhD student working with the Pig microbiome. Want to be able to run 16S sequencing data on Mothur, via the HPC

- Yunqing Wang, PhD student who is going to work with human microbiome. My work in short term will involve 16sRNA sequencing and PCR.

- Oliver Bramley, PhD student in chemistry. I will be running some quantum simulations and electronic structure calculations on ARC.

- Lucian Chevallier, Mechanical Engineering Master's student. I am going to be running CFD simulations analysing the use of masks and ventilation to limit virus transmission.

- Natalia Petersen, Precision Medicine MSc student. Using ARC for RNA-seq, DESeq2 etc, would like to better my understanding of the ARC system and using linux.

## 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`