[[PageOutline]]
= Running RStudio with Singularity on Cypress =

== Login using port forwarding ==

See for example [[https://wiki.hpc.tulane.edu/trac/wiki/cypress/JupyterNode | 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

With the RStudio server running in your Cypress interactive session, you can now use the RStudio interface on your browser

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 network latency.

[[Image(RStudioInBrowserStartup.png)]]