Changes between Version 1 and Version 2 of cypress/RunningRStudioWithSingularity

Timestamp:

02/05/26 14:50:37 (2 days ago)

Author:

Carl Baribault

Comment:

Added content, Work In Progress

cypress/RunningRStudioWithSingularity

@@ -1 +1 @@
 [[PageOutline]]
 = Running RStudio with Singularity on Cypress =
-Coming soon
+
+== 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)]]