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

== Login to Cypress using port forwarding ==

See for example [wiki: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, but this time you'll need to include port forwarding in order to connect to the RStudio server running on the compute node from your browser on your local machine.

'''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 server web 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 your choice for '''8888''' as needed.

{{{
localhost:8888/
}}}

 * Use RStudio server web interface in your browser

 Shown below is RStudio server web interface loading in your browser.

 Note that this and all future graphical responses to your actions in the browser may be slow due to your particular network latency.

[[Image(RStudioInBrowserStartup.png, center, 30%)]]

----

 Shown below is RStudio server web 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 [wiki:InstallingRPackages Installing R Packages on Cypress].

[[Image(RStudioInBrowserRunning.png, center, 30%)]]

----

 When you're done, go to '''File''' -> '''Quit Session...''' , then with '''R Session Ended''' showing, simply close the browser tab.

[[Image(RStudioInBrowserEnded.png, center, 30%)]]