Using R and RStudio on the Cluster
- Simon Alexander
Introduction: This workshop will discuss how the various R related tools and RStudio work together on the cluster and introduce a series of best practices for managing these environments.
Course Goals:
Using R from the command line.
Refresh on creating ‘R’ conda environments.
Where are libraries installed?
Using RStudio via OnDemand.
Using a Conda environment within RStudio
Introduction aspects of using R in parallel on the cluster.
This is not a workshop on learning the R language, but on how to use R on the cluster.
Notes:
The workshop modules work best in a sequential manner as a story introducing concepts and providing examples, but sections can be used separately to focus on a particular concept.
We have tried to make the examples as generic as possible. You will need to replace
<project-name>and<username>with appropriate values that apply to you.This tutorial is available for download as a PDF here.
Where are R Packages Installed on the Cluster? Understand where R installs packages and where libraries are located, as well as inspecting general R system configuration.
R Conda Environments and Installed Packages: Understand R environments build with Conda.
R Packages and System Modules: Installing some R packages requires understanding what libraries are available on the System.
Creating a Shared Library of R Packages: Demonstrate how to use an R library to create a shared set of R packages.
Using R and RStudio within OnDemand: Detail the process of using R and RStudio via the OnDemand service.
Using an R Conda Environment with RStudio: Detail how to use an R Conda Environment within RStudio.
Create an R Kernel for a Jupyter Notebook: Detail how to update an R Conda environment so it can be used as a kernel within ARCC’s Jupyter service.
R Environments and Reproducibility: Introduce ideas and practices to assist in managing the reproducibility of R environments.
Parallel R: Introduction: Introduction some high-level aspects of using R in parallel relating to the cluster.
Using R/RStudio on the Cluster: Summary: Summarize the concepts covered across the workshop.
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