Tutorial: Using the HPCC and GitHub through RStudio

Wendy Leuenberger

3/27/2024

[email protected]

This repository goes along with the lecture and demonstration.

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Repository contents

Tutorial

HPCC.*: The R markdown (.Rmd), markdown (.md; easiest viewing on GitHub) and .html documents for setting up your GitHub and HPCC.

Tutorial.*: The R markdown (.Rmd), markdown (.md; easiest viewing on GitHub) and .html documents for using this repository to commit changes and run a job on the HPCC.

Code

WarblerForHPCC.R: Code file used in this tutorial.

Data

warbler-data.rda: Data used in WarblerForHPCC.R

Output

Save your model output here

Placeholder.R: Just here so that I can remove out.RData after running tutorials without deleting the entire folder.

Lecture

Recording

Click here for the recording from IBIO 831

Presentation

HPCC_Presentation.*: Rmd and html files of the brief slides accompanying this tutorial. Formatting isn't great - some images might not show up.

HPCC_diagram.jpeg: Image from lecture depicting the layout of the HPCC. We start on our personal computer, log onto a gateway node, log onto a development node (can run jobs $leq$4 hours), and submit jobs to the clusters. (might not be in the slides)

Submit a job

runWarbler.sb: File used to submit a job to a cluster on the HPCC. I usually place the .sb file in the main part of the repository, and file references are relative to the folder the .sb file is in. Those settings can be changed if you want a different file structure though.