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Merge pull request #1 from baskerville-hpc/pres
Test to create Quarto presidation
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‎.github/workflows/publish.yml‎

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on:
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workflow_dispatch:
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push:
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branches: main
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name: Quarto Publish
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jobs:
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build-deploy:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Render and Publish
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uses: quarto-dev/quarto-actions/publish@v2
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with:
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target: gh-pages
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path: docs
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎docs/HackathonBaskerville/HackathonBaskerville.qmd‎

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---
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title: "Introducton to Baskerville"
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author: "Advanced Research Computing (ARC) Team"
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format:
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revealjs:
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theme: bask2.scss
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footer: Baskerville Hackathon 24/03/2025
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logo: images/BaskervilleW.svg
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---
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# Introduction (*And Welcome*) to Baskerville{.smaller}
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# Baskerville Hackathon
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## Baskerville Content {.smaller}
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::: {}
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1. What is Baskerville
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1. Baskerville resources
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1. How to access Baskerville
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1. How to submit jobs to Baskerville
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:::
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## What is Baskerville {.smaller}
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- Baskerville is a tier 2 HPC (High Performance Computer)
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- It is a GPU focused system with 228 GPUs (57 nodes) in total
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- 46 Nodes with A100 GPUs
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- 11 Nodes A100-80 GPUs
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- Icelake CPUs with 72 cores per node
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- 5.4 PB storage
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::: {.callout-note appearance="simpe"}
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HyperThreading:
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Baskerville has hyperthereading enabled this means that 1 core = 2 threads/tasks
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:::
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## Baskerville Resources {.smaller}{visibility="hidden"}
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Baskerville has a number of resources availible to you:
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::: {.incremental}
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- <https://www.baskerville.ac.uk/> - The homepage for Baskerville, has case studies and papers published by Baskerville users
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- <https://admin.baskerville.ac.uk/> - The admin site is a place to manage your Baskerville account and view user and project information
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- <https://apps.baskerville.ac.uk/> - The apps website contains a list of all the installed applications on Baskerville
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- <https://portal.baskerville.ac.uk/> - The portal site allowds users to use interactive apps in a web browser
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:::
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## Baskerville Resources {.smaller}
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Baskerville has a number of resources availible to you:
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:::: {.columns}
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::: {.column width="50%"}
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::: {.incremental}
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- <https://www.baskerville.ac.uk/> - The homepage for Baskerville, has case studies and papers published by Baskerville users
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- <https://admin.baskerville.ac.uk/> - The admin site is a place to manage your Baskerville account and view user and project information
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:::
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:::
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::: {.column width="50"}
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::: {.incremental}
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- <https://apps.baskerville.ac.uk/> - The apps website contains a list of all the installed applications on Baskerville
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- <https://portal.baskerville.ac.uk/> - The portal site allowds users to use interactive apps in a web browser
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:::
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:::
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::::
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## Baskerville Hackathon {.smaller}
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::: {.incremental}
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- 24th March - 26th March you will have access to Baskerville
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- Reservation of 2 nodes (8 GPUs, 144 cores and 288 threads)
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- A reservation only allows those from seltcted projects to use them this is done through the `--reservation` flag
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- Everyone is part of the project `ranaaaa-hackathon`
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- Other projects have more memory (5 TB) and contain the data.
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:::
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## Baskerville Login {.smaller}
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- Everyone will receive a welcome email when being first added to Baskerville
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- Email points to our documentation and instructions for first time access <https://docs.baskerville.ac.uk/logging-on/>
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- Instructions and video present to show both what to do and what not to do
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- To setup your one time passcode you need an authenticator app please have this open and ready to scan your OTP
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- To login you will need to username, password and OTP to access Baskerville
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- Whilst ssh key option is available this is not recommended during the hackathon
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## Baskerville Login Example
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Insert video here
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## Baskerville Storage {.smaller}
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:::: {.columns}
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::: {.column width="50%"}
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::: {.incremental}
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- **home directory** `/bask/homes/_inital_/_username_`
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- When you first login, this is where you start
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- Only 20 GB of space - this is not where you run jobs
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- Should be for local and cached files
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:::
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:::
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::: {.column width="50%"}
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::: {.incremental}
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- **Project Directory** `/bask/project/_initial_/_projectname_`
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- Has 5 TB space - place where you run jobs
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- Contains you data, job scripts and results
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:::
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:::
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::::
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## Baskerville User Details {.smaller}
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- <https://docs.baskerville.ac.uk/storage/>
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- You can inspect your details either in the [admin site](https://admin.baskerville.ac.uk/) or in the terminal:
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- `my_quota` - This shows how much of your home directory is utilised
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- `my_baskerville` - This gives your project account and QoS details
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## Baskerville User Details Example
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Insert video here
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# Baskerville jobs
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## Login and Compute nodes {.smaller}
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- There are 2 types of nodes on Baskerville
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::: {.incremental}
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- A **login node** is where you start and Baskerville has 3 `bask-pg-login01`, `bask-pg-login02` and `bask-pg-login03`
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- Access to all Baskerville users
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- Intended for simple tasks like managing files
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- Does not have access to GPUs
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- A job submitted goes from a login node to a compute node
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- A **compute node** is the node that does the work nodes do not have login in their name
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- When you submit a job this is where they go
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:::
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## Job script {.smaller}
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- The most common way to run jobs is with the `sbatch` command and the name of you job script
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- Your job script will contain:
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::: {.incremental}
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- Job account
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- Job time
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- Job compute resources (CPUS, GPUs etc)
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- Quality of Service (QoS) for everyone in this hackathon this is `bham`
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- Other options are also availible <https://slurm.schedmd.com/sbatch.html>
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:::
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## Job script example {auto-animate=true}
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```bash
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#!/bin/bash
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#SBATCH --qos=bham
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#SBATCH --account=ranaaaa-hackathon
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#SBATCH --time=1:0:0
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#SBATCH --ntasks=4
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#SBATCH --gres=gpu:1
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#SBATCH --reservation=ranaaaa-hackathon
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module purge
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module load baskerville
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# your commands
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```
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## Job script example {auto-animate=true}
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```bash
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#!/bin/bash <--- run the job using GNU Bourne Again Shell
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#SBATCH --qos=bham
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#SBATCH --account=ranaaaa-hackathon
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#SBATCH --time=1:0:0
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#SBATCH --ntasks=4
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#SBATCH --gres=gpu:1
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#SBATCH --reservation=ranaaaa-hackathon
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module purge
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module load baskerville
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# your commands
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```
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## Job script example {auto-animate=true}
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```bash
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#!/bin/bash
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#SBATCH --qos=bham <--- Using bham job queue
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#SBATCH --account=ranaaaa-hackathon <--- Hackathon project account
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#SBATCH --time=0:20:0 <--- Job to run for 20 minutes
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#SBATCH --ntasks=4 <--- Job requests 4 tasks
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#SBATCH --gres=gpu:1 <--- Requesting 1 GPU
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#SBATCH --reservation=ranaaaa-hackathon <--- Use reserved resources
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module purge
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module load baskerville
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# your commands
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```
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## Job script example {auto-animate=true}
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```bash
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#!/bin/bash
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#SBATCH --qos=bham
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#SBATCH --account=ranaaaa-hackathon
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#SBATCH --time=1:0:0
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#SBATCH --ntasks=4
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#SBATCH --gres=gpu:1
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#SBATCH --reservation=ranaaaa-hackathon
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module purge <--- Purging environemnt
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module load baskerville <--- Loading default Baskerville modules
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<--- Add additional module here
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# your commands <--- Commands you want to run
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```
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## Submitting a job {.smaller}
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When you submit a job you will see:
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```
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sbatch job.sh
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Submitted batch job 992337
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```
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The number (in this case `992337`) is your job id this is a unique job number
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## SLURM {.smaller}
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- SLURM=Simple Linux Utility for Resource Management <https://docs.baskerville.ac.uk/jobs/#slurm-jobs>
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- SLURM is our job sceduler it decides the priority of jobs and when they start
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- Since this has a reservation jobs submitted will be outside of the general queue
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- Batch jobs are submitted with the `sbatch` command and you can monitor the job with `squeue`
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- If your job is in the queue you can use the `sbatch --start` to see an estimate of when your job will start
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- If you want to cancel a job you can use `scancel XXXX` where XXXX is the job id
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## Job results file {.smaller}
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::: {.panel-tabset}
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## Output file .out
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- A file `slurm-XXXXX.out` is created where XXXXX is the job id
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- This file would be the standard output of whatever you would run
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-
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## Stats file .stats
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- A file `slurm-XXXXX.stats` is created where XXXXX is the job id
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- Contains information on resources used (time, memory amount of CPUS and GPUs
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- Will also contain the exit code so you can see if job ended correctly)
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```bash
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+--------------------------------------------------------------------------+
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| Job on the Baskerville cluster:
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| Starting at Tue Sep 28 15:00:30 2021 for auser(123456)
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| Identity jobid 12345 jobname cudaopenmp.sh
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| Running against project ace-project and in partition baskerville-shared
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| Requested cpu=288,mem=864G,node=2,billing=288,gres/gpu=8 - 00:10:00 walltime
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| Assigned to nodes bask-pg0308u30a,bask-pg0308u31a
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| Command /bask/projects/a/ace-project/cudaopenmp.sh
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| WorkDir /bask/projects/a/ace-project
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+--------------------------------------------------------------------------+
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+--------------------------------------------------------------------------+
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| Finished at Tue Sep 28 15:00:35 2021 for auser(123456) on the Baskerville Cluster
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| Required (00:01.942 cputime, 3580K memory used) - 00:00:05 walltime
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| JobState COMPLETING - Reason None
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| Exitcode 0:0
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+--------------------------------------------------------------------------+
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```
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:::
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# Thank You

‎docs/HackathonBaskerville/bask2.scss‎

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/*-- scss:defaults --*/
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$body-bg: #333333;
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$body-color: #fff;
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$body-color: #fafad2;
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$link-color: #42affa;
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$input-panel-bg: rgba(233, 236, 239, 0.2);
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.reveal .footer {
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color: #fafad2 !important;
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}
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.reveal .slide-logo {
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height: 100px !important;
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width: 100px!important;
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max-width: unset !important;
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max-height: unset !important;
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background-image: "images/coding_club_logo2.svg";
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/* background-image: "BC_images/space_back.jpg";*/
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bakcground-opacity: 1;
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}

‎docs/HackathonBaskerville/images/Baskerville2.png‎

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‎docs/HackathonBaskerville/images/BaskervilleW.svg‎

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‎docs/_quarto.yml‎

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project:
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title: "IntroductionToBaskerville"
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