https://github.com/mschubert/r-hpc

https://github.com/mschubert/r-hpc

Last synced: about 12 hours ago
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• Host: GitHub
• URL: https://github.com/mschubert/r-hpc
• Owner: mschubert
• Created: 2022-03-04T20:29:01.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2022-04-04T13:10:49.000Z (almost 3 years ago)
• Last Synced: 2023-03-13T18:12:50.740Z (almost 2 years ago)
• Language: Makefile
• Homepage: https://mschubert.github.io/R-hpc
• Size: 16.3 MB
• Stars: 1
• Watchers: 2
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# High Performance Computing with the R programming language

Below is a brief overview of the course content.

## Day 1

#### Morning: Technical Introduction by HPC admins

* Capabilities of the computing cluster

* How to connect

* Starting a basic job

#### Afternoon: [Quick Start](https://mschubert.github.io/R-hpc/articles/quickstart.html)

* Copying and editing files via the command-line

* Interactive jobs, batch jobs

* `parallel` package, cluster objects, and `future`

#### Afternoon: [Neovim as IDE](https://mschubert.github.io/R-hpc/articles/neovim-ide.html)

* The `Nvim-R` plugin to interactively develop in a remote session

* Persistent server sessions using `tmux`

## Day 2

#### Morning: [Breakpoint example](https://mschubert.github.io/R-hpc/articles/breakpt-ex.html)

* An MCMC breakpoint detection method as example

* Tasks vs. threads for bigger jobs

* R packages for HPC use: `slurmR` and `clustermq`

#### Afternoon: [Workflows](https://mschubert.github.io/R-hpc/articles/workflows.html)

* GNU parallel and GNU make

* Snakemake

* The `targets` R package

#### Afternoon: 

* Possibility for attendees to work on their own projects with help from the instructors