---
# System prepended metadata

title: '2022-06-28 <br> HPC1: Introduction to HPC at Leeds'

---

# 2022-06-28 <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, love programming in Python and sometimes R. Interested in data science tools and techniques and software development best practice for reproducible research.

- John Hodrien, research software engineer. Been at the university since 1997, back when I was a Computer Science student, and haven't successfully left. Have taught, and been a researcher working on distributed systems and visualisation. Long time Linux advocate.
- Jon Ward, Lecturer in Applied Maths, have had many students use the HPC but I've not used it personally. Supervising an MSc student this year (Jai, who is also here too) that's using it, so thought I should learn to support him.
- Alex Jones, first year PGR working with HPC to run simulations 
- Xin Zhou, PostDoc at School of Earth and Environment, want to work more efficiently with HPC.
- Yang Li, PostDoc at School of Earth and Environment, using HPC to analyze atmospheric data.
- Dustin Foley, research software engineer. Working on a project for the CDRC creating a transport model, which would benefit from running on an HPC.
- Minh Dang, teaching assistant, would like to use HPC and GPU for deep learning research
- Rachel Taylor, Research Fellow, Centre for Plant Sciences, Faculty of Biological Sciences, using HPC for high throughput sequencing data.
- Chris Winder, first year PhD on AI CDT
- Yiming Hou, second year PhD student from ITS, working on deep-learning-related research.
- Allan Pang, first year PhD student on AI CDT within the School of Computing.  Working with healthcare data to develop risk calculators.
- Ben Keel, first year PhD student on AI CDT, currently using HPC/ARC to train variational autoencoders.
- Maria Koutoulaki, Research fellow at School of Physics and Astronomy, using HPC for running simulations of protoplanetary discs.
- Lewis Howell, first year PhD student on AI CDT. GPU acceleration for deep learning models.
- Hong Wang, PhD, school of geography, using HPC to run python scripts 
- Hong Fu, PhD student of geography, want to use HPC for calculation for large data.
- Jai Prathap, Msc Student, want to use for my dissertation under the guidance of professor Jon.
## 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`
