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Running RStudio on the FMRIB cluster

The Open OnDemand server allows you to run RStudio via a cluster job.

To start a session, select RStudio Server from the Interactive Apps menu, this provides a form you can use to setup your RStudio session, and requires the following information:

  • R Studio Server version - 'default' will use the latest version installed, or you can select a specific version (if available) using the drop down menu.
  • Extra modules script - if you need to load any environment modules before starting R, create a text file containing the appropriate `module load` commands and specify the full path to the script here.
  • Cores/RAM - choose an appropriate amount of cores and memory for your task. Try to keep these as low as possible, and aim for a maximum of 16GB for every two CPU cores you request (based on one of those cores being a virtual thread).
  • Enter the number of hours you need the session for - this is subject to the maximum time configured on the interactive (or gpu_short) partition.
  • Finally, if your software requires a CUDA device then you can tick the GPU box. This will add two additional fields allowing you to select a specific GPU type and specfiy that you require more than one GPU (default is one GPU). Please be aware that there are a limited number of GPUs you may have to wait some time for your session to start.

Open OnDemand RStudio ServerOpen OnDemand RStudio Server

 

Once submitted you will be taken to you My Interactive Session page where you can monitor the progress of your job, connect to your session and shut it down.

When your job is running (the card heading has turned green), you can use the Connect to RStudio Server button to open a new web bowser tab with your session within.