# 2024-04
# HPC1: Introduction to HPC at Leeds
Welcome to the hack pad for HPC1 course from Research Computing at the University of Leeds!
You can edit this document using [Markdown syntax](https://guides.github.com/features/mastering-markdown/).
## 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
- **Presentation for today** - https://arctraining.github.io/rc-slides/hpc1.html
- **Github repository** - https://github.com/arctraining/hpc1-files
- **General ARC Docs** - https://arcdocs.leeds.ac.uk
- [HPC0 Slides](https://arctraining.github.io/rc-slides/hpc0.html)
## Agenda Day 1
| Time | Agenda |
| -------- | ------------------------------------------ |
| 0930 | Intro, connecting to ARC, what and why HPC?|
| 1020 | Break |
| 1030 | Login, HOME directory and looking around <br> Exercise 1 |
| 1120 | Break and Answers |
| 1130 | Simple job submission, qstat, qdel |
| 1230 | Questions |
| 1230 | Close |
## Agenda Day 2
| Time | Agenda |
| -------- | ------------------------------------------ |
| 0930 | Intro, Data Transfer, Modules |
| 1020 | Questions and break |
| 1030 | Interactive sessions, ib v smp, node types |
| 1120 | Questions and break |
| 1130 | User guided section, talking through <br> your hopes/fears for HPC |
| 1220 | Wrap up and questions |
| 1230 | Close |
## 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
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 HPC1!🎉**
### 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/)
- 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.
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)
```bash
$ mkdir ~/.ssh
```
3. Then open a text editor of your choice and create a file called `config` in your `.ssh` directory
```bash
# 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
```bash
Host *.leeds.ac.uk !remote-access.leeds.ac.uk
ProxyJump USERNAME@remote-access.leeds.ac.uk
User USERNAME
```
5. Save this file and attempt to connect using `ssh` to ARC4
```bash
# where USERNAME is your university username
$ ssh USERNAME@arc4.leeds.ac.uk
```
6. The first time you connect you will be prompted with several messages
```bash
The authenticity of host 'remote-access.leeds.ac.uk (129.11.190.34)' can't be established.
RSA key fingerprint is SHA256:SZN1IZ9rL0mhpnxhVG5uxbtVFMZAISg98X9ovHlh8Fg.
Are you sure you want to continue connecting (yes/no)?
```
Type Yes and hit `Enter`. You will then be prompted to enter your password for connecting to remote-access.leeds.ac.uk
```bash
Warning: Permanently added 'remote-access.leeds.ac.uk,129.11.190.34' (RSA) to the list of known hosts.
USERNAME@remote-access.leeds.ac.uk's password:
```
Please enter your password carefully, placeholder `*` characters will not appear but your keystrokes are being recorded. Once you have typed in your password press `Enter`.
You have now connected to remote-access but will now be prompted with similar messages for connecting to ARC4 itself.
```bash
The authenticity of host 'arc4.leeds.ac.uk (<no hostip for proxy command>)' can't be established.
ECDSA key fingerprint is SHA256:lPkw/7SrBqqQkS7lUm+tBN9JIGX9B8Gw7FdkK3MrpLM.
Are you sure you want to continue connecting (yes/no)?
```
Type Yes and hit `Enter`. You will then be prompted to enter your password for connecting to arc4.leeds.ac.uk
```bash
Warning: Permanently added 'arc4.leeds.ac.uk' (ECDSA) to the list of known hosts.
USERNAME@arc4.leeds.ac.uk's password:
```
Again enter your password carefully, placeholder `*` characters will not appear but your keystrokes are being recorded. Once you have typed in your password press `Enter`.
1. Once you have successfully entered your password you will be greeted by the following information on your Terminal
```bash
Advanced Research Computing Node 4 (arc4)
________________________________________________________________________
Information on using this facility may be obtained at the following URL:
http://www.arc.leeds.ac.uk
Please remember to acknowledge the use of ARC facilities in your
papers; details are on the website above.
________________________________________________________________________
[USERNAME@login1.arc4 ~]$
```
And success! You are all connected and ready to go! 🎉
## What's your name and where do you come from? And why do you want to use HPC?
- Andy Turner, Instructor, in a Research Software Engineering role in the Research Computing team in IT Services. I specialised in Computational Geography for over 25 years as a Research Officer based in the School of Geography in Leeds. I have run distributed programs on Tier 0 machines, but have experience of running programs on more local HPC too. I can program in a wide range of computer programming languages and am developing some next generation introductory and intermediate programming courses. I am keen to support researchers and research in the University and am currently enjoying developing a Web application for some researchers in Chemistry.
- Tianyi Pan, RSE
- Tom Hardcastle, RSE. Background in computational chemistry and C++ software development
- Ollie Clark; RSE; Background in software engineering, web development
- Gopal Siingh Phartiyal , India, Research Fellow earth and enviroment
-
* **Rishad Rayyaan**; Research fewllow in composites; need to use ***COMSOL*** to run simulation for 'Heat transfer' in composite materials. The module in COMSOL known as 'Joule Heat Transfer'. I will need to run some files in COMSOL, will then need to tweak those simulation files accordingly.
- Sebastian Croft; Polymer informatics phd student, looking to run a task array of DFT calculations on ARC using Gaussian.
- Claire Taylor. Research Fellow in immunology. Likely to be running next generation sequenging and will need to analyse data
- Shadia Ahmed, PhD student/clinician, I will be doing bioinformatics/metagenomic analysis
- Yushi Guo：I am from computer science as a phd and I need GPU for model training.How should I get GPU resources there are relevant links and tutorials and where to get better GPUs.
- Donald Cummins; Software Development Scientist with Machine Learning Specialisation; recently joined CEMAC; hoping to use ARC for training neural nets and related stuff.
- **Lluís Hernández Navarro**; Postdoctoral researcher; background in Physics; I want to run extensive simulations on stochastic models of eco-evolutionary dynamics in microbial ecosystems, focusing on antimicrobial resistance.
- Ruifan Tang, PhD student from ITS, been coping with a vast amount of data but always got failure on my physical PC.
- Azam Ali, PhD Student at ITS! I want to learn and use HPC to run econometric and ML models.
- Finn O'Sullivan; running ANSYS FLUENT to optimise oil immersion within a dropbox
- Robin Furze; PGR; Developing a multiscale model, initially using python and finite element applications (FEniCS) which will have a high volume of data.
## Glossary of Terms
- Core: the basic computation unit of the CPU. This is unit that carries out the actual computations.
- Node: the physical machine/server. In current systems, a node would typically include one or more processors, as well as memory and other hardware.
- Parallel: run across multiple CPU cores, splitting the workload between them and solving the problem faster.
- Processor: the central processing unit (CPU) inside the node, which contains one or more cores.
- Serial: run on a single CPU core, solving one problem at a time
- Batch processing: Jobs that are run as and when the system is able to, rather than jobs run interactively
- Thread: A lightweight logical computation process. If a program is a sequence of instructions, this is the finger that works its way through the list of instructions. There can be many fingers, and you can have many more threads than you have hardware to run them.
- GPU: Graphical Processing Unit. Not necessarily graphical, but this type of hardware is good at some high parallelism problems. We have a small number of these in ARC3/4. Massive speed ups are possible - one GPU can be as powerful as 40 machines.
## Linux basics
[ArcDocs Linux](https://arcdocs.leeds.ac.uk/getting_started/linuxbasics.html)
## Code along
`git clone https://github.com/arctraining/hpc1-files`
Sign in with Wallet
Connect another wallet