---
# System prepended metadata

title: '2022-10-11 <br> HPC1: Introduction to HPC at Leeds'
tags: [teaching, ' hpc1']

---

---
tags: teaching, hpc1
---
# 2022-10-11 <br> 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://bit.ly/hpc1intro
- **Exercises for today** - https://docs.google.com/document/d/1SPaZ2kmzYpMFIkiMSi-Qnu-ZqLaW4reSpVal3aOrmmk/edit
- **Github repository** - https://github.com/arctraining/hpc1-files
- **How to transfer files** -https://arcdocs.leeds.ac.uk/getting_started/file_transfer.html


## Agenda Day 1

| Time     | Agenda                                     |
| -------- | ------------------------------------------ |
| 0900     | Intro, connecting to ARC, what and why HPC?|
| 0950     | Break                                      |
| 1000     | Login, HOME directory and looking around <br> Exercise 1  |
| 1050     | Break and Answers                          |
| 1100     | Simple job submission, qstat, qdel         |
| 1150     | Questions                   |
| 1200     | Close                                      |

## Agenda Day 2

| Time     | Agenda                                     |
| -------- | ------------------------------------------ |
| 0900     | Intro, Data Transfer, Modules              |
| 0950     | Questions and break                        |
| 1000     | Interactive sessions, ib v smp, node types |
| 1050     | Questions and break                        |
| 1100     | User guided section, talking through <br> your hopes/fears for HPC |
| 1150     | Wrap up and questions                      |
| 1200     | 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.
![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba1.png)

1. Navigate using a web browser to https://mobaxterm.mobatek.net/
2. Select Download 
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba2.png)

3. Click Download Now for the Home Edition
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba3.png)
4. Select MobaXTerm Home Edition v21.0 (Portable edition)
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba4.png)
5. This opens a download prompt for a .zip file. Select Save File and click OK
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba5.png)
6. Go to your Download folder and find the .zip file you have just downloaded
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba6.png)

7. Click Extract in the Ribbon Bar and select Extract All
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba7.png)

8. Using the Wizard window extract the folder at the suggested location
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba8.png)

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
    ![](https://raw.githubusercontent.com/ARCTraining/hackpad-templator/main/static/hpc0/moba9.png)
**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?

- Alex Coleman, Research Software Engineer, I love Python.
- John Hodrien, Research Software Engineer, possibly likes Linux a bit too much.
- Ollie Clark, Research Software Engineer. Background in databases and web applications.
- Samuel Mace, PhD Student of Chemistry, to submit fat quantum chemical calculations to the HPC 
- Eilidh, new PhD student, focused on lncRNA, some wet labs but primarily computational to look at RNA-Seq/Ribo-Seq data, with the aim to have some regression models too.
- Corin Ward, Economics PhD, I want to do some things with NNs and other data science stuff
- Stephanie Harrison, Leeds School or Medicine, I am a first year PhD student needing to use HPC for genetic analysis and genome-wide association data and to generate polygenic risk scores
- Ellen Slay, PhD student, using microfluidic devices, working with COMSOL and CellProlfier
- Oliver Devine, Msc Biochemistry, I want to use HPC for Cryo-EM analysis of amyloid strucutres
- Laura Pinkney, PhD Student, School of Maths, to assist project
- Aron Syversen, Comp Sci PhD first year, hpc for project required 
- Seun Coker, PhD Student, to run machine learning models for fluid dynamics application
- Katie Hawkins, Research Masters in Biological Science
- Trent McLean-Ash, Microbiology PhD, not actually sure yet what I will be using HPC for!
- Tamara Garcia del Toro, working on a project as part of the DSDP with the CDRC
- Declan Fisher, Msc Biochemistry. Useful for RELION
- Pietro Canali, theoretical physics
- Matthew Yusuf, theoretical physics
- Abdullah Alsaleh, PhD student, School of Computing, I'd like to use HPC for my Deep Learning research. ("chmod -R 700" to change the files permission)


## 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.

## Code along

`git clone https://github.com/arctraining/hpc1-files`
