Changes between Version 1 and Version 2 of cypress/RunningRWithSingularity

Timestamp:

01/13/26 16:08:48 (29 hours ago)

Author:

Carl Baribault

Comment:

Filled out content

cypress/RunningRWithSingularity

@@ -1 +1 @@
 [[PageOutline]]
 = Running R with Singularity on Cypress =
-Coming soon
+The [[https://rocker-project.org/ | Rocker Project]] is a website established to provide docker containers in the form of docker files for the R environment.
+
+In order to use any of those docker files on Cypress, we'll need to construct a container file - usually with '''.sif''' file extension - suitable for use with Singularity on Cypress. For reference in the following see [[wiki:Singularity]].
+
+Here's the sequence of commands to create and simply test a container file for the latest available R version - as provided the above website.
+
+== Start the interactive session ==
+First, start an interactive session.
+
+'''For Workshop''' :
+If your account is in the group '''workshop''', please use the following.
+
+{{{
+[tulaneID@cypress1 ~]$idev --partition=workshop7 -c 2 # request 2 cores in the partition workshop7
+Requesting 1 node(s)  task(s) to normal queue of workshop7 partition
+1 task(s)/node, 2 cpu(s)/task, 0 MIC device(s)/node
+Time: 0 (hr) 60 (min).
+0d 0h 60m
+Submitted batch job 3287405
+JOBID=3287405 begin on cypress01-060
+--> Creating interactive terminal session (login) on node cypress01-060.
+--> You have 0 (hr) 60 (min).
+--> Assigned Host List : /tmp/idev_nodes_file_tulaneID
+Last login: Tue Jan 13 11:58:39 2026 from cypress1.cm.cluster
+[tulaneID@cypress01-060 ~]$
+}}}
+
+'''Non-workshop'''
+{{{
+[tulaneID@cypress1 ~]idev --partition=centos7 # 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 container image file ==
+Then proceed as follows to construct the '''.sif''' container image file 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/r-base:latest # takes a few minutes to construct file r-base_latest.sif
+...
+[tulaneID@cypress01-060 ~]$singularity exec r-base_latest.sif R --version # check the version of R
+R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
+Copyright (C) 2025 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under the terms of the
+GNU General Public License versions 2 or 3.
+For more information about these matters see
+https://www.gnu.org/licenses/.
+
+[tulaneID@cypress01-066 rstudio at 15:53:56]$
+}}}