---
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