---
# System prepended metadata

title: '2022-11 <br> HPC2: Installing and Managing Applications on the HPC'
tags: [hpc2, ' teaching']

---

---
tags: hpc2, teaching
---

# 2022-11 <br> HPC2: Installing and Managing Applications on the HPC

Welcome to the hack pad for HPC2 course from Research Computing at the University of Leeds!

You can edit this document using [Markdown syntax](https://guides.github.com/features/mastering-markdown/).

## Contents

1. [Links to resource](#Links-to-resources)
2. [Further reading](#Further-reading)
3. [Pre workshop prep](#Pre-workshop-prep)
4. [Agenda](#Agenda)
5. [What's your name and where do you come from?](#What’s-your-name-and-where-do-you-come-from)

## Links to resources

- **Contact Research Computing** - https://bit.ly/arc-help
- **Course website** - https://arctraining.github.io/hpc2-software/welcome.html

## Pre workshop prep

This course requires users to have ARC4 accounts and to be familiar with how to log on and connect to HPC systems.

### Required setup steps

- Users register for HPC accounts using the [HPC account request form](https://leeds.service-now.com/it?id=sc_cat_item&sys_id=4c002dd70f235f00a82247ece1050ebc)
- Set up personal computer for connecting to HPC (HPC account required)
    - An overview can be found [here (including screenshots)](https://hackmd.io/xBKb6Az3QmewUsVF3ab2qg#Pre-workshop-prep)
    - For Windows, downloading MobaXTerm and configuring a session with ssh Gateway settings
    - For MacOS/Linux, creating a `~/.ssh/config` file with ProxyJump rule to `remote-access.leeds.ac.uk`

**You are expected to have experience of connecting to ARC4 before this tutorial, as no time will be made available for walking through connecting to HPC**


## Agenda



### Part 1

| Time     | Agenda                          |
| -------- | ------------------------------- |
| 0930     | Introduction, Theory            |
| 1030     | Break                           |
| 1040     | Conda                           |
| 1130     | Break                           |
| 1140     | Autotools/CMake                 |
| 1220     | Wrap up and questions           |
| 1230     | End                             |

### Part 2


| Time     | Agenda                          |
| -------- | ------------------------------- |
| 0930     | Welcome back and homework       |
| 1000     | Containers                      |
| 1020     | Break and questions             |
| 1030     | Containers (cont.)              |
| 1120     | Break and questions             |
| 1130     | Spack                           |
| 1220     | Wrap up and questions           |
| 1230     | End                             |




## What's your name and where do you come from?

- Alex Coleman, research software engineer, love Python, R, data science and machine learning. But also making web apps!
- Nick Rhodes, Research Software Engineer. Computing generalist, everything from infrastruction, systems to programming to databases to technical leadership.
- John Hodrien, Research Software Engineer.  Have a long Linux history (since '97), and particularly like automation and configuration management.
- Abdullah Alsaleh, PhD student, school of computing. 
- Matthew Yusuf - MPhys student, School of Physics and Astronomy
- Basudha Basu, Research Fellow at St.James's Campus. Here to learn how to use the HPC so I can do RNA sequencing analysis. 
- Shairah Abdul Razak, Postdoctoral Research Fellow  at Faculty of Biological Sciences. Focusing on phylogenomics analyses.
- Eilidh Ward, PhD student, school of molecular and cellular biology, computational biologist/data scientist, interested in transcript/translatomics, python, R, C++, Rust etc, Linux and ML.
- Kenny Campbell, PhD student, working on quantum communication, looking to install NetSquid, an accessible-on-request python library
- Izzy Latimer, Fluids CDT student, bubble growth and migration in sediments using LBM-DEM, waLBerla: libraries, cmake, conda, cuda
- Ross Slater - 2nd Year SENSE CDT PhD Student, School of Earth and Environment 
- Laura Cope, Research Fellow, Fluid Dynamics
- Giulia Fedrizzi, CDT Fluid Dynamics. Install libraries (C++, R)
- Ollie Clark, Research Software Engineer, University of Leeds. Software enginering, databases and web.
- Yousef Alghamdi, PhD student, LIMR institute 
- Rachael Lowe PhD student in SCAPE will be using Ansys Fluent on the HPC
- Jeni Sidwell, PhD student in evolutionary genomics, school of biology
- Hong Wang, School of Geography, PhD
- Modupe Aggreh Research Data Scientist
- Oguz Can Eren, Cardiovascular Engineer, iMBE. Using Abaqus for FEA simulations.
- Susannah Cowtan, PGR in clinical trials methodology, R, git, docker. Ask me about RLadies (gender minorities also welcome, the name is old)!
- Hugh Rice, postdoc in Geography, planning to use Python and R with HPC