Bayes Workshop 2025: SCINet setup instructions

How to start an RStudio Server session on Ceres OnDemand

You will need to do this each time.

1. Navigate to Ceres OnDemand and sign in with your credentials.
2. Select RStudio Server from the Interactive Apps dropdown menu at the top of the screen.
3. Start a new job with the following options:
   • Project sea_stats_training
   • Queue scavenger
   • QOS (ignore)
   • R version 4.4.1
   • Number of hours 6 or enough to ensure the job won’t be killed during today’s lesson
   • Number of cores 4
   • Memory required 6000M should be more than enough
4. The job will be queued up and should start within a minute or so. When it starts click the “Connect to RStudio Server” button.

Screenshot - selecting RStudio Server from OnDemand dropdown	Screenshot - options for new RStudio Server session

Initial configuration steps

You will only need to do this once. There is a directory on a shared space that all workshop participants have access to, /project/sea_stats_training/bayes2025. This directory has all the example data, worksheets, pre-fit model objects, and software needed for the workshop including all R packages and an installation of Stan software. You need to copy this directory from the shared space into your home directory as follows:

In RStudio Server, select the “Terminal” tab on the left pane. Type the following command into the terminal and press enter:

cp -r /project/sea_stats_training/bayes2025 ~/bayes2025

Note: it will take 10-15 minutes to copy all the files, 1.4GB in total.

This will create a folder in your home directory on SCINet called bayes2025 that has everything you need in it.

Opening the bayes2025 RStudio project

Once the files have copied, open the bayes2025 folder in the Files tab in RStudio Server. Click the file bayes2025.Rproj to open the bayes2025 RStudio project. This will open the project and automatically configure RStudio to be able to access the installed R packages and Stan software. It will also point you to the folder that contains all the worksheets you will need to participate in the lessons. You are good to go!

Screenshot - entering copy command into RStudio Server terminal	Screenshot - opening RStudio project from Files tab