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:
-
Request an interactive job:
RStudio and Apptainer can only run on a compute node, not on a login node.
qrsh -l h_data=10G
- 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
- Load Apptainer module:
module load apptainer
- 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.
- 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
- 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.
- Display usage statement:
./h2_rstudio.sh -h
- 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:
- Remove RStudio temporary directories:
rm -rf $SCRATCH/rstudiotmp
- 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.