rstudio
- Simon Alexander
- Declan Emmons (Unlicensed)
Please be aware of our Using R and RStudio on the Cluster workshop.
Overview: Using RStudio on the Cluster
RStudio is available on the cluster, and thus in principle can be loaded and used anywhere. To use it effectively:
Do not load and use on the login nodes. This will affect ALL other users trying to log on and use the cluster.
We recommend to use the OnDemand service using an Interactive Desktop session.
It is recommended to use RStudio to edit and update code in a GUI environment, and test/run simple jobs for debugging purposes. Some R packages, if they have the ability to use multiple cores, will simply use ALL the cores available on a node, so please explicitly define within your scripts to only test against one/two cores. Once you’re happy your code is working then use
salloc/sbatchto use the computation nodes and to submit your much longer runs that use significantly more cores.
Using
Use the module name rstudio to discover versions available and to load the application.
You will need to load a version of R before starting RStudio. If you don’t then you’ll see an error message of the form regards “no R”:
[1240032:1011/144405.782798:ERROR:gl_factory.cc(120)] Requested GL implementation (gl=none,angle=none) not found in allowed implementations: [(gl=egl-angle,angle=default),(gl=egl-gles2,angle=none)].
[1240032:1011/144405.784510:ERROR:viz_main_impl.cc(186)] Exiting GPU process due to errors during initialization
/usr/bin/which: no R in (/apps/u/opt/linux/rstudio/2023.09.0/usr/lib/rstudio:/home/salexan5/bin:/home/salexan5/bin:/apps/s/projects/core_hour_usage/bin:/apps/s/arcc/1.0/bin:/apps/s/slurm/latest/bin:/apps/s/turbovnc/turbovnc-2.2.6/bin:/home/salexan5/bin:/home/salexan5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/salexan5/.local/bin:/home/salexan5/bin:/apps/s/singularity/3.10.3/bin:/home/salexan5/.local/bin:/home/salexan5/bin)