https://github.com/sodascience/workshop_ossc

This repository contains the code and presentation of the workshop on parallel computing & cluster computing using R in collaboration with SURF.
https://github.com/sodascience/workshop_ossc

agent-based-modeling cluster-computing high-performance-computing odissei parallel-computing r simulation surf

Last synced: about 2 months ago
JSON representation

This repository contains the code and presentation of the workshop on parallel computing & cluster computing using R in collaboration with SURF.

• Host: GitHub
• URL: https://github.com/sodascience/workshop_ossc
• Owner: sodascience
• License: mit
• Created: 2022-03-25T13:06:46.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-09-04T14:27:01.000Z (5 months ago)
• Last Synced: 2024-09-09T02:57:32.224Z (4 months ago)
• Topics: agent-based-modeling, cluster-computing, high-performance-computing, odissei, parallel-computing, r, simulation, surf
• Language: R
• Homepage: https://www.surf.nl/en/agenda/supercomputing-for-social-scientists-with-r
• Size: 45.8 MB
• Stars: 3
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Cluster computing with R for Social Scientists

This repository contains the code and presentation of the workshop on parallel computing & cluster computing using R in collaboration with SURF. More information & sign-up can be found on the website [here](https://www.surf.nl/en/agenda/cluster-computing-for-social-scientists-with-r).

![image](img/abm.png)

## Prerequisites

- Some `R` knowledge & experience :)

- `R`, minimum version `4.2.0` (download [here](https://cran.r-project.org/))

- If you are on Windows: `RTools` (download [here](https://cran.r-project.org/bin/windows/Rtools/))

- Recommended IDE: `RStudio` (download [here](https://www.rstudio.com/products/rstudio/download/#download))

- Install the following packages:

  ```r

  install.packages(c("Rcpp", "tidyverse", "pbapply", "sf", "mgcv"))

  ```

- Download this repository ([link](https://github.com/sodascience/ossc_workshop/archive/refs/heads/main.zip)) and unzip it to a nice location

- Open the project by double-clicking on `ossc_workshop.Rproj` in the folder.

## Schedule

| Time  | Title                                           | Required resource                   |

| :---- | :---------------------------------------------- | :---------------------------------- |

| 09:00 | Introduction to Supercomputing and the OSSC     | [`slides`](./slides/OSSC_SURF.pdf)  |

| 11:00 | Lecture: computational limits in social science | [`slides`](./slides/intro.pdf)      |

| 11:45 | Hands-on: a parallel agent-based model in R     | [`assignment`](./hands_on/intro.md) |

| 12:30 | Break                                           | `lunch`                             |

| 13:30 | Lecture: supercomputing with R                  | [`slides`](./slides/supercomp.pdf)  |

| 14:15 | Hands-on: submitting an R array job             | [`assignment`](./hands_on/super.md) |

| 15:15 | Break                                           | `coffee :)`                         |

| 15:30 | Lecture: combining & analysing the results      | [`slides`](./slides/results.pdf)    |

| 16:15 | Conclusion & Q&A                                | `your remaining attention!`         |

## End result: a map of the Netherlands

The below map would take around 6 months to produce using the naïve implementation on a normal computer. You will learn how to compute it in a few hours on a supercomputer.

![map](img/segr_map.png)

## Contact

This project is developed and maintained by the [ODISSEI Social Data

Science (SoDa)](https://odissei-data.nl/nl/soda/) team.



Do you have questions, suggestions, or remarks? File an issue in the

issue tracker or feel free to contact [Erik-Jan van

Kesteren](https://github.com/vankesteren)

([@ejvankesteren](https://twitter.com/ejvankesteren))