Rocker project

Running Rstudio server in a Singularityi/Apptainer container

https://rocker-project.org/use/singularity.html

The project builds and shared docker containers but with support to covert and run it with Singularity/Apptainer. Look for more details on the project web page.

# Pull the container locally for convinience
singularity pull docker://rocker/rstudio:4.4.2

# Run the container
singularity exec \
   --scratch /run,/var/lib/rstudio-server \
   --workdir $(mktemp -d) \
   rstudio_4.4.2.sif \
   rserver --www-address=127.0.0.1 --server-user=$(whoami)

This will run rserver in a Singularity container. The --www-address=127.0.0.1 option binds to localhost (the default is 0.0.0.0, or all IP addresses on the host). listening on 127.0.0.1:8787.

Note

If you run on a remote machine, like computer center, the most efficient way to open the remte server is to use ssh port forwarding, for example

ssh -L 8787:localhost:8787  userID@remote.computer.se

Quite often, you will run the R studio server in an interactive session/reserved compute node. Then you need to redirect to that node.

ssh -L 8787:comp_node_xx:8787  userID@remote.computer.se

Finally, it might happen that another user is using the same 8787 port. Take a random number above 1024 and add this option --www-port=9090 at the end of the singularity exec ... line, where 9090 is the port we have chosen in this example.

Look for more details on the web page on how to protect the server with password or submit a SLURM job.