ucla-oarc-hpc/H2-RStudio

Using RStudio on Hoffman2

RStudio on Hoffman2

Easily run RStudio on Hoffman2 (H2) compute nodes using available containers.

Available RStudio Containers

Find available RStudio containers on Hoffman2 with the following command:

module load apptainer
ls $H2_CONTAINER_LOC/h2-rstudio*sif

To create your own RStudio container or use a different version, visit the UCLA OARC HPC Containers repository.

RStudio Workshop

For more information on using RStudio on Hoffman2, visit the H2HH RStudio Workshop.

Running RStudio: Step-by-Step Guide

Follow these steps to run RStudio using an RStudio container on Hoffman2:

1. Request an interactive job:

   RStudio and Apptainer can only run on a compute node, not on a login node.

qrsh -l h_data=10G

2. Create temporary directories:

RStudio needs these directories to run correctly. Create them in your $SCRATCH directory.

mkdir -pv $SCRATCH/rstudiotmp/var/lib
mkdir -pv $SCRATCH/rstudiotmp/var/run
mkdir -pv $SCRATCH/rstudiotmp/tmp

3. Load Apptainer module:

module load apptainer

4. Start RStudio process:

Do not kill this process until you are finished with RStudio.

apptainer run \
      -B $SCRATCH/rstudiotmp/var/lib:/var/lib/rstudio-server \
      -B $SCRATCH/rstudiotmp/var/run:/var/run/rstudio-server \
      -B $SCRATCH/rstudiotmp/tmp:/tmp \
         $H2_CONTAINER_LOC/h2-rstudio_4.1.0.sif

You can replace $H2_CONTAINER_LOC/h2-rstudio_4.1.0.sif with any rstudio version you find from the available RStudio Containers.

This will display information and an ssh -L ... command to run in a separate terminal.

5. Connect to the compute node's port:

Open a new terminal and run the provided ssh -L ... command.

ssh  -L 8787:nXXX:8787 username@hoffman2.idre.ucla.edu # Or whatever command was displayed earlier 

6. Access RStudio in your web browser:

Enter the following URL in your web browser:

http://localhost:8787 #or whatever port number that was displayed

When finished, exit RStudio and press [Ctrl-C] in the terminal running the RStudio container to exit the job.

Running RStudio: Automated Script

Use the h2_rstudio.sh script on your local machine to automatically set up RStudio on Hoffman2.

1. Display usage statement:

./h2_rstudio.sh -h

2. Start RStudio on Hoffman2:

./h2_rstudio.sh -u H2USERNAME

This will start RStudio as a qrsh job, open a port tunnel, and allow you to access RStudio in your web browser.

Note: This script has been tested on Mac's Terminal, Windows WSL2, and Mobaxterm. It will fail on GitBash due to the lack of the expect command.

Running R in Batch Mode

If you want to use the R version in the container for a batch job, use the rstudio_batch.job script. This example SGE job script submits an R job using the R version inside the RStudio container and uses the installed libraries. This is helpful if you have installed packages with RStudio and want to run an R batch job with the same version of R and R packages.

Troubleshooting Common Issues

If a new RStudio session doesn't start correctly (e.g., due to an improper exit), try the following:

1. Remove RStudio temporary directories:

rm -rf $SCRATCH/rstudiotmp

2. Clear RStudio config files:

rm -rf ~/.config/rstudio

By following these guidelines and solutions, you should be able to easily run RStudio on Hoffman2 compute nodes and troubleshoot any common issues that may arise.