2021-04-13
HPC0: Introduction to Linux

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

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Contents

1. Links to resource
2. Further reading
3. Agenda
4. Pre workshop prep
   4.1. Windows Users
   4.2. MacOS/Linux Users
5. 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
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

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?

• Alex Coleman, Research Software Engineer in Research Computing
• John Hodrien, Research Software Engineer in Research Computing
• Ollie Clark, Research Software Engineer in Research Computing
• Holly Foster, PhD Student in Medicinal Chemistry
• Tom Albone, Data Scientist Intern at Leeds Institute for Data Analytics (LIDA)
• Arash Kalatian. Research Fellow, ITS
• Jim McQuaid, Earth and Environment, atmospheric data processing
• Nan Cui, PhD student in School of Geography
• Shuhao Dong, PhD Student in Mechanical Engineering, HPC for machine learning
• Merin Joseph PGR, School of Mathematics
• Elizabeth Young, PhD student medical engineering
• Khatun E Zannat (PGR ITS)
• Maximiliano Lizana - PGR ITS
• Beth Lowe, PhD Student in Medical Engineering, HPC for running ABAQUS jobs
• Maria Luisa Taccari, PhD Student in Civil Engineering
• Marek Kacer, research fellow, LUBS
• Wajiha Rehman, Phd student in Applied Mathematics. I need to learn it because I will do numerically modelling of offshore wind turbine
• Piers Hugill. I am a doctoral student from Earth and Environment studying fire in Siberia.
• Josephina Sampson, Research fellow
• James Vigor, Research fellow in Civil Engineering, I want to try and train neural networks from large datasets
• Rachel Palfrey - PhD student in Earth and Environment - HPC for running spatial analysis in R