Running RStudio with Singularity on Cypress

Login using port forwarding

See for example Jupyter notebook.

Make note of your choice of ports in the above for your use in the following.

Here we assume the choices 8888 and 12345.

Start the interactive session - with port forwarding

First, start an interactive session.

For Workshop : If your account is in the group workshop, please use the following.

[tulaneID@cypress1 ~]$idev --partition=workshop7 -c 2 --port=12345:8888 # request 2 cores in the partition workshop7
Requesting 1 node(s)  task(s) to normal queue of workshop7 partition
1 task(s)/node, 2 cpu(s)/task, 0 MIC device(s)/node
Time: 0 (hr) 60 (min).
0d 0h 60m
Submitted batch job 3287405
JOBID=3287405 begin on cypress01-060
--> Creating interactive terminal session (login) on node cypress01-060.
--> You have 0 (hr) 60 (min).
--> Assigned Host List : /tmp/idev_nodes_file_tulaneID
Last login: Tue Jan 13 11:58:39 2026 from cypress1.cm.cluster
[tulaneID@cypress01-060 ~]$

Non-workshop

[tulaneID@cypress1 ~]idev --partition=centos7 --port=12345:8888 # start an interactive session in the partition centos7
Requesting 1 node(s)  task(s) to normal queue of centos7 partition
1 task(s)/node, 20 cpu(s)/task, 0 MIC device(s)/node
Time: 0 (hr) 60 (min).
0d 0h 60m
Submitted batch job 3288388
JOBID=3288388 begin on cypress01-066
--> Creating interactive terminal session (login) on node cypress01-066.
--> You have 0 (hr) 60 (min).
--> Assigned Host List : /tmp/idev_nodes_file_tulaneID
Last login: Tue Jan 13 14:09:07 2026 from cypress2.cm.cluster
[tulaneID@cypress01-066 ~]$

Construct and check the image file for RStudio

Then proceed as follows to construct the container image file rstudio_latest.sif and check the R version.

[tulaneID@cypress01-060 ~]$module load singularity/3.9.0 # load the singularity module
[tulaneID@cypress01-060 ~]$singularity pull docker://rocker/rstudio:latest # takes a few minutes to construct file r-base_latest.sif
...
[tulaneID@cypress01-060 ~]$singularity exec rstudio_latest.sif R --version # check the version of R
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

[tulaneID@cypress01-066 ~]$

Start the RStudio server

• Setup local authentication

In order to run the RStudio server, you'll first need to construct a local database for authentication - one time only - as in the following.

echo "auto-create=1" > database.conf

• Start the RStudio server

Start the RStudio server, rserver, via the following.

Note the use of the option —www-port to match your choice of local port number in the above.

[tulaneID@cypress01-066 ~]$singularity exec -B /lustre:/lustre --scratch /run,/var/lib/rstudio-server --workdir $(mktemp -d) tidyverse_latest.sif  rserver --www-address=0.0.0.0 --www-port=8888 --server-user=$(whoami) --database-config-file $PWD/database.conf

Use RStudio on your browser

• Go to your browser

You can now use the RStudio interface on your browser.

Using the above, now that you have the RStudio server running in your Cypress interactive session, open a browser window or tab on your local machine and type the following.

Be sure to match your choice of local port number from above, substituting for 8888 as needed.

localhost:8888/

• Use RStudio in your browser

Here is RStudio starting in your browser.

Note that this and all future responses may be slow due to your particular network latency.

Here is RStudio interface finished loading in your browser.

Note that all of your previously installed R packages should also available in your RStudio's R session.

See Installing R Packages on Cypress.

When you're done, go to File → Quit Session… , then simply close the browser tab.