---
# System prepended metadata

title: '2021-11-30 <br> HPC1: Introduction to HPC at Leeds'
tags: [teaching, ' hpc1']

---

---
tags: teaching, hpc1
---
# 2021-11-30 <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, helping researchers write reproducible research code. Loves Python and occasionally R.
- John Hodrien, Research Software Engineer.  Long history of using Linux, High performance systems.
- Abigail Byford, PhD student researching the placenta. I have done some courses on RNAseq data analysis and would like to use HPC to try this.
- Nick Rhodes, Research software engineer, all round IT guy, Support/development/Leadership. Likes toast and green tea for breakfast.
- Smail Kechidi, Postdoc, working in the School of Civil Engineering, keen to make the most of what a computer can do for humain.
- Michael Brigham, PhD student at School of Cellular and Molecular Biology, Studying how bugs make drugs - have been carrying out smaller scale comparision of the enzymes that make natural products through Python, want to explore how HPC can help with this
- Samuel Hughes, school of biology, running models faster, also keen to learn about hpc as have never used anything like it before
- Maharani Ummi, Phd Phd Phd Phd Phd Phd Phd Phd Phd Phd 
- Wei-Lun Lee, PhD student at the School of Mechanical Engineering in Leeds University. Good to meet you all :))
- Kin Suen, Postdoc, FBS. EM data analysis
- Ffion Hall, MChem student using Gaussian to calculate potential energy surfaces for reactions I am carrying out in my project

- Ibrahim, I am a PhD student in Applied Maths, using Python data science, 
- Matthew Asker, PGR Applied Maths. Want to use HPC to run stochastic simulations of fluctuating environment population evolutions and match this to analytic solutions.
- Ollie Clark, Research Software Engineer in Research Computing. Background in software engineering, databases and web development.
- Andrew Bate, Math Bio Postdoc based Civil Engineering. Modelling disease risk. Want to run many runs of Python model.
- Jack Lynch, PhD student in Oral Biology. Processing sequencing data and designing in silico modelling.
- Kangyi Zhu, MRes Climate and Atmospheric Science project, need to run a model about ozone.
- Sheridan Few,  
- Anne Braakmann-Folgmann, PhD in Earth and Environment, want to use ARC4 to train a neural network
- Laura Cope, Postdoc in Fluid Dynamics
- Isobel Lloyd, PhD student in Geography, want to use HPC so I can process my data (using EddyPro software) and so my laptop doesn't get destroyed in the process!
* Ashutosh Singh, Lecturer in Marketing, working on big data, need a source with high computational power
-Dave Collins, PhD student in SCaPE, using HPC for DFT structure optimisations. 
- Jose A. Zabala, PhD Student at the ITS, running models faster
- Weiyu Zhang, PhD Student in Earth and Environment, using HPC for data analysis and climate modelling.
- Moneerh Aleedy, PhD student want to run python models in the field of NLP.
- Lena AlMutair, PhD student in School of computing, need hpc to run and process big data.
- Maharani Ummi, Phd student in School of Mathematics, run R for DNA sequencing data analysis
- 
## 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`

