Accessing Parallel R tutorial

This  document will guide you on how to launch Rstudio App and acess Parallel R workshop material through OSC onDemand.

Step 1: Log on to https://ondemand.osc.edu. Please see this guide on how to use OnDemand service.

Step 2: Launch Rstudio App

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Accessing through OnDemand

All the interactive apps can be found within the 'Interactive Apps' dropdown in our OnDemand web portal as shown in the image below:

Image of OnDemand Desktop Apps Dropdown

After selecting RStudio Server, you will arrive at this job submission page:

Image of how to setup RStudio

Here you can select the resources you would like your RStudio session to have using the menu on the lefthand side of the page. Please pick R/3.6.1 to access the tutorial material. Please provide your project ID as PZS0687 if you have registered for the workshop. If not, use your default project ID. Please contact oschelp@osc.edu if you dont have a project ID yet. Please make sure you check on the box that says Include access to OSC tutorial/workshop material. After you click "Launch", a new session will be queued. Once the session is active you page will look like the image below:

Image of launchable RStudio Session

Click on "Connect to RStudio Server" to begin using RStudio.

Using RStudio

Once you have entered your session, you should see the RStudio page below:

Image of an active RStudio session

This is a typical RStudio interface that should be familiar to most users. Please note that  Rstudio session for accessing the tutorial materials will start with a clean environment. While running in tutorial mode you will not have access to the files your $HOME.

  • Top Left panel: code editer
  • Bottom Left panel: The console where you can type commands and see the output.
  • Top right panel:
    • Environment tab: Shows all the active objects
    • History tab: Shows a list of commands used so far.
  • Bottom right panel:
    • Files tab: Shows all the files and and folders in your home directory
    • Plots tab: Shows all your graphs
    • Packages tab: Lists a series of packages or add-ons needed to run certain processes
    • Help tab: Can be used to find additional info
    • Viewer tab: Used to view local web content

More info on RStudio and its use can be found on the RStudio official support page.

From the bottom right panel, please click on parallelR.rmd markdown file. This will open the training material in the code editer window as shown below.

Image of an active RStudio session

This ParallelR.rmd material is prepared using the “rmarkdown” library. To view this in html format, select “Preview in Viewer Pane” option in the setting of “Knit” button top of the code editer window and then press “Knit”.

Image of an active RStudio session

This will open html version of the rmd document in the Veiwer pane of bottom right panel. 

Image of an active RStudio session

You can read though the html document in the Viewer Pane and execute codes in the Code editor. Press the Run/play button on the top right of each code block to run the code. 

Please reachout to soottikkal@osc.edu if you have questions.

 

Supercomputer: 
Owens
Service: 
Portal