O2portal - Shiny on O2

This application aims to simplify the process of running your R Shiny application on O2 via O2Portal. It also enable collaborations among O2Portal users who can interact with the app and source code without the need to deploy the content to a third-party service (e.g., shinyapps.io or RStudio Connect). The Shiny app you create will NOT be visible to people outside the O2 environment, for information on publishing a Shiny app visible to the world email us at rchelp@hms.harvard.edu. The application requires two elements, (i) the path to your R Shiny application on O2 and (ii) the path to the R Personal Library also on O2.

Open

The R Shiny Application on OOD provides the flexibility of customizing the job submission. Below is a brief description of each field.

Account:

This is the Slurm Account associated with your Slurm User. You can find your Slurm account by running the command sshare -U -u $USER from a shell within the O2 cluster.

Partition:

This is the partition you can use to submit the OOD R-Shiny job. You can use most standard O2 partitions, with the exception of "interactive". We highly recommend using the "priority" partition. 

Wall Time requested in hours:

This is the allocated time, in hours, to run the OOD R-Shiny job. The maximum value admissible depends on the partition you selected. 

Number of cores:

This is the number of CPU cores to allocate for the OOD R-Shiny job.

GPUs (optional):

If you selected a GPU partition, then specify the GPUs to allocate for the job.

GPU card type (optional):

If you selected a GPU partition, then select a GPU card type

Total Memory in GB:

This is the amount of memory (RAM) in GB you want to allocate for your job. 

Modules to be loaded:

Enter the modules required to run the Shiny app on O2.

Shiny app to run:

Enter the path to the Shiny App on O2 (e.g., ~/myshiny-app). The path must include the app.R or server.R file.

R Personal Library:

Enter the path to the R Personal Library on O2 (e.g., ~/R-4.0.1/library). The path must include all the R packages needed for the Shiny app.

Slurm Custom Arguments

This is an optional text field that can be used to pass additional flags to the Slurm scheduler when submitting the job.

After clicking on “Launch”, a job will be submitted to O2 to run the Shiny application. While the job is pending, you will see the following on display:

Open

The Session ID can be used to open a new window with the log files associated with the current job.

Once the job starts, the display tile changes to green, and a “Connect to Shiny” option appears in the lower-left corner.

After clicking on the “Connect to Shiny” button, a new browser tab opens with your R Shiny application.

Please click the Delete button from the O2Portal to finish the job. 

Note: Closing the internet browser does not stop or kill the job. The job will be running for the specified Wall Time before launching the application.