RStudio

Overview

Using on the wi-hpc cluster is tricky, but doable. Using apptainer and The Rocker Project, following this guide, RStudio is available on the wi-hpc cluster and has the ability to access HPC resources.

Warning

Please be warned that this implementation is still very new and not completed tested. Please report any and all issues to the IT Help Desk.

Getting Started

Load the module to prepare your environment

module load R/rocker_4.5.1

Copy the submission script to a location of your choice

cp $ROCKER/rocker.sh path/to/dest

Edit the rocker.sh submission file to your perferences.

nano/vi/emacs rocker.sh

Submit the file with sbatch

sbatch rocker.sh

Note

If you want to use GPUs, you must add the following lines to the rocker.sh script.

...
#SBATCH --partition=gpu
#SBATCH --gres=gpu:x # where x is the number of GPUs you want.
...
# Add the --nv flag to apptainer exec command
apptainer exec --cleanenv \
                -- nv \
                ......

Print out your --error file to see instructions

    1. SSH tunnel from your workstation using the following command:

       ssh -N -L 8787:node_number:external_port aharral@wi-hpc

       and point your web browser to http://localhost:8787

    2. log in to RStudio Server using the following credentials:

       user: username
       password: xxxxxxxxxxxxxxxxxxxxxxxxxx

    When done using RStudio Server, terminate the job by:

    1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
    2. Issue the following command on the login node:

          scancel -f <job-id>

Follow the instructions above closely and start using RStudio inside the wi-hpc cluster.