---
# System prepended metadata

title: '2021-11-09 <br> HPC1: Introduction to HPC at Leeds'
tags: [teaching, ' hpc1']

---

---
tags: teaching, hpc1
---
# 2021-11-09 <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
- **Getting connected** - https://arcdocs.leeds.ac.uk/getting_started/logon.html
- **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://i.imgur.com/qM7ckB4.png)

1. Navigate using a web browser to https://mobaxterm.mobatek.net/
2. Select Download 
    ![](https://i.imgur.com/2OWkFeU.png)

3. Click Download Now for the Home Edition
    ![](https://i.imgur.com/z7snaxu.png)
4. Select MobaXTerm Home Edition v21.0 (Portable edition)
    ![](https://i.imgur.com/bmdYrg7.png)
5. This opens a download prompt for a .zip file. Select Save File and click OK
    ![](https://i.imgur.com/jqvN3SW.png)
6. Go to your Download folder and find the .zip file you have just downloaded
    ![](https://i.imgur.com/C9qIoQ5.png)

7. Click Extract in the Ribbon Bar and select Extract All
    ![](https://i.imgur.com/lAJtyXq.png)

8. Using the Wizard window extract the folder at the suggested location
    ![](https://i.imgur.com/rwAEDT2.png)

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
    ![](https://i.imgur.com/aYjt8bf.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?

- John Hodrien, Research Software Engineer.  Long history of using parallel processing systems, starting back in 2000.
- Aiden Daniel, PhD student from the School of Physics and Astronomy. Looking to use HPC to look at many-body systems and dynamics.
- Michael Bell, LICAMM, novel reconstruction for medical imaging.
- Janet Richardson, SEE - for faster modelling using SD-Topmodel 
- Justin Clarke, FBS, amplicon and RNA sequencing
- Benjamin Mills, Earth and Environment, running HadCM3 climate model
- Andrew Merdith, Earth and Environment, running HadCM3
- Alhanof Alolyan, School of Computing, crowd analysis 
- Rosie Knapp, School of Biology, RNA sequencing
- Michael Zulyniak, FSN
- Tom Allcock, School of Computing, Medical Image Analysis
- Sofia Biffi, School of Geography, bird ID with cnn
- Yatin Darbar, School of Computing, Simulation Droplet Coalesence
- Natalie Chaddock, LIDA, Genetic Epidemiology (Bioinformatics) PhD
- Zac Paling and Esther Lewis, school of Biology, Cryo-EM
- Jess Snelson, SCAPE PhD Student - using HPC to queue big coding jobs to model materials
- Sarah Miller, AI Med CDT NLP on health data
- Violet Patterson, Earth and Environment, climate-ice modelling
- Jo Egan, School of Chemistry, running LMD Venus climate model
- Alaa Alhumaisan, School of Computing. I am taking this course to help me with training my models.
- Andrew Pretorius, SEE, Speeding up seismic location algorithms using GPUs
- Thomas Nussle, School of Physics and Astronomy, developing a Path integral spin dynamics model
- Beth Soanes, PhD candidate, School of Biology, RNA-seq/splice isoform analysis 
- Jaime Pitts, FBS, structural biology using crosslinking MS to study kinases 
- Giulia Fedrizzi, PhD in Fluid Dynamics, running simulations of fluids in rocks
- Chris Field, EPS, MRes Project based on atomistic (and possibly course-grained) molecular dynamics simulations of Microtubules
- Tamara Fletcher, School of Earth and Environment, using statistical modelling to develop a proxy to reconstruct cloud in deep time. 
- Menwa Alshammeri, School of Computing, In my research, I train deep learning models that requires high power computing.

## 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`

### 2_Python 

Create a job submission file for the `example1.py` file.

1. Copying from the 1_R to 2_Python

```bash=
cd ~/hpc1-files/2_Python/

cp ../1_R/submit-r.sh submit-python.sh
```

2. Use nano to edit the file:

```bash
nano submit-python.sh
```

3. Edit the file as you say fit and save and exit

Change the bottom line to:

```bash=
python example1.py
```


Save and exit using the following keyboard combinations:
`CTRL+O, Enter, CTRL+X`

4. Submitting a job to the queue:

```
qsub submit-python.sh
```

Check your job in the queue with:

```
watch qstat
```

Using `q` to quit from the watch command.

### 3_Parrallel_Executables

