RStudio on Pegasus¶
Rstudio is available as a software module on Pegasus utilizing R version 4.1.0. RStudio graphical jobs can be submitted to the LSF scheduler via the interactive queue.
In order to launch an RStudio interactive job, you will need to login to Pegasus with X11 forwarding enabled.
You will also need to install an X11 server on your local machine such as Xming for Windows or XQuartz for Mac.
Please see the following guide on how to achieve this: https://acs-docs.readthedocs.io/services/1-access.html?highlight=x11#connect-with-x11-forwarding
Loading the Module¶
The RStudio module is dependent on the gcc/8.3.0 and R/4.1.0 software modules. These will come pre-loaded once the RStudio module has been loaded
[nra20@login4 ~]$ module load rstudio [nra20@login4 ~]$ module list Currently Loaded Modulefiles: 1) perl/5.18.1(default) 3) gcc/8.3.0 2) R/4.1.0 4) rstudio/2022.05.999
First Time configurations¶
If this is the first time you are using the RStudio module you will need to configure the rendering engine to run in software mode by editing /nethome/caneid/.config/RStudio/desktop.ini
[nra20@login4 ~]$ vi /nethome/nra20/.config/RStudio/desktop.ini
Add the following line under [General]
Launching RStudio jobs through LSF¶
To launch RStudio jobs to the LSF scheduler, you will need to pass the X11 -XF parameter and submit to the interactive queue through the command line.
[nra20@login4 ~]$ bsub -Is -q interactive -P hpc -XF rstudio Job is submitted to <hpc> project. Job <27157788> is submitted to queue <interactive>. <<ssh X11 forwarding job>> <<Waiting for dispatch ...>> Warning: Permanently added '10.10.104.5' (ECDSA) to the list of known hosts. <<Starting on n131>>
The RStudio graphical interface will then appear, from which you can utilize and install any needed packages.
Changing Graphical Backend¶
In order to utilize the graphical features of RStudio, please change the graphical backend to AGG format. You can do after lauching the graphical UI from the previous step.
- Navigate to “Tools > Global Optios”
- Navigate to the “Graphics” tab located towards the top of the menu
- Switch the “Backend” option to “AGG”
This option only has to be configured once. Subsequent RStudio sessions will now have the AGG backend enabled and your sessions can now utilize graphical features.
More information on submitting graphical interactive jobs: https://acs-docs.readthedocs.io/pegasus/jobs/5-interactive.html
If you run into any issues with package installations, please send an email to firstname.lastname@example.org