Using RStudio

Warning

Using RStudio differs between different HPC clusters.

  • We also recommend ThinLinc!

On UPPMAX

There is a system installed version, available via the “rstudio” command (you will get RStudio/1.1.423).

However, we recommend you to use a RStudio module.

Warning

We recommend ThinLinc because the graphics is more effective there!

Using ThinLinc

  • ThinLinc app: <user>@rackham-gui.uppmax.uu.se

  • ThinLinc in web browser: https://rackham-gui.uppmax.uu.se This requires 2FA!

  • Choose Xfce as the desktop environment (faster)

  • start a command line window

Using terminal

  • Remember to have X11 installed!

  • On Mac

    • install XQuartz

  • On Windows

    • Use MobaXterm or

Check for RStudio versions

Check all available versions with:

$ module avail RStudio

Output at UPPMAX as of March 10 2024

[bjornc@rackham5 ~]$ ml av RStudio

------------------------------------- /sw/mf/rackham/applications -------------------------------------
   RStudio/1.0.136    RStudio/1.1.423     RStudio/2022.02.0-443    RStudio/2023.06.0-421
   RStudio/1.0.143    RStudio/1.1.463     RStudio/2022.02.3-492    RStudio/2023.06.2-561
   RStudio/1.0.153    RStudio/1.4.1106    RStudio/2022.07.1-554    RStudio/2023.12.1-402 (D)

  Where:
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

  • load R_packages

  • module load RStudio

  • run rstudio & from the command line, and wait

    • it might take 5-10 minutes for RStudio to start, especially if you loaded R_packages as well, but once it starts, there should be no further delays

    • do not start RStudio through the graphical menu system in ThinLinc, this will not have access to loaded modules.

    • if it takes a long time and might be due to that you have saved a lot of workspace

Example:

Demo

$ module load R/4.1.1
$ module load RStudio/2023.12.1-402
$ rstudio &

If you’re going to run heavier computations within RStudio then you have to remember that you need to do it inside an interactive session on one of the computation nodes, and not on a login node. But if you mostly want to use it as a pretty code editor then you can run it on the login node as well.

To use Rstudio on a compute node, start by asking SLURM for an interactive allocation (within the ThinLink session). E.g.

$ interactive -A naiss2023-22-44 -p devcore -n 4 -t 10:00

On Bianca

When logging onto Bianca, you are placed on a login node, which nowadays has 2 CPU and a few GB of RAM. This is sufficient for doing some light-weight calculations, but interactive sessions and batch jobs provide access to much more resources and should be requested via the SLURM system.

The desktop client version of ThinLinc does not work for Bianca. Instead you run and login to ThinLinc in the browser:

On HPC2N

Rstudio also exists on Kebnekaise but is only installed on the ThinLinc login nodes and not on the compute nodes (and also not on the regular login nodes accessible with SSH). Thus, Rstudio should only be used for development and very light analysis, since there is no way to submit a job to the compute nodes.

Login to ThinLinc desktop application by providing the following

  • server: kebnekaise-tl.hpc2n.umu.se

  • username

  • password

Alternatively, you can use ThinLinc in the browser: https://kebnekaise-tl.hpc2n.umu.se:300/

When in ThinLinc, you can start Rstudio either from the menu (version 4.0.4) or from the command line. If you start it from the command line you first need to load R and its prerequisites, but you can pick between several versions this way.