bds_rstudio_template

This is a template Open OnDemand (OOD) app for using BDS's RStudio Singularity containers.

Description

This template will help users create an OOD app to use RStudio from a singularity container directly in a browser. Originally, RStudio would need to be started from the container in an HPC Desktop app which caused some interface issues. This should solve or mitigate those issues.

Setup

Enable Dev Sandbox Apps

In order to add this as an app on OOD, you will need to enable sandbox apps. You can enable sandbox apps with the following steps:

1. Open a terminal on Cheaha and running the following command: mkdir $USER_DATA/ondemand/dev
2. In OOD, click Help > Restart Web Server in the top right. This should cause a </> Develop dropdown menu to appear
3. Click </> Develop > My Sandbox Apps (Development). This will open a new screen
4. Click the New App button.
5. As of now, the only option is to clone an existing app from a Git repo. Click Clone Existing App
6. On the next screen, enter the following information:
   • Directory Name: the directory name the repo will be saved to. Example: bds_rstudio_singularity. The full path to the app would be $USER_DATA/ondemand/dev/bds_rstudio_singularity in this case.
   • Git remote: https://github.com/mdefende/bds_rstudio_template.git or the path to a personal fork
   • If you'd like to create a totally separate git repo for this project, you can click the Create a new Git Project from this? checkbox. If you're operating off a fork, DO NOT click this.
   • Click Submit

Edit Paths

For the app to work correctly for individual users, some paths in the template/script.sh.erb file need to be changed. Navigate to the app directory in your $USER_DATA/ondemand/dev folder. Make the following changes:

1. Set the path after export RSTUDIO_SERVER_IMAGE= to be the path to the SIF file you're wanting to run. Following the BDS instrucitons, it would be set to "${USER_SCRATCH}/HPC_Container_session/rstudio_ggplot2_3.6.3.sif"
2. Optionally, you can edit the singularity bind paths. By default, these are set to be /data and /scratch which will allow Singularity to access any folder you have permissions for on Cheaha. This can be changed to restrict access if desired

Other optional edits

• To change the name or description of the app, change the name or description entries in the manifest.yml file
• To change the resource options when requesting a job, change the options in the form.yml file
  • Note: Drastically changing the options in the form may necessitate changes in the submit.yml.erb file which defines the sbatch submission.
• By default, the password for the RStudio session is set to NBI. This can be changed in template/before.sh.erb on the line export RSTUDIO_PASSWORD

Running the App

To run the app, refresh your My Interactive Sessions page on OOD. There should be a list of Sandbox Apps highlighted in red below the normal apps. Your BDS RStudio app (or if you changed the name) should show up there. Click the app name, select your resources like a normal HPC Desktop job, and start the job.

You will need to provide a username and password to get into the RStudio session. The username is just your Cheaha account username while the password is NBI. RStudio should open to the main screen at this point

Contributing

While this app, by the barest of definitions, runs, it could be improved. If you have suggestions for improvements, you can file an issue on the github page. If you would like to contribute via code, pelase create a fork in your own github, create a new branch to make and test changes, and then submit a pull request to the main repo. If you would like to create your own fork and use it as the base where OOD pulls from, that's perfectly fine as well.