RStudio on Alvis¶
Why is this page at UPPMAX?
It is the intention that this guide is moved to the C3SE documentation. However, it has not been suggested to be added to their documentaton yet.
Introduction¶
RStudio is an IDE specialised for the R programming language.
In this session, we show how to use RStudio on Alvis.
As RStudio is a resource-heavy program, it must be run on an interactive session.
Procedure to start RStudio¶
Below is a step-by-step procedure to start RStudio on Alvis.
Prefer a video?
This procedure is also demonstrated in TODO.
1. Start a Alvis remote desktop environment¶
...
2. Start an interactive session¶
Within the Alvis remote desktop environment, start a terminal. Within that terminal, start an interactive session with 2 cores:
Where:
[naiss_project_id]is your UPPMAX project code[duration]is the duration of the interactive session
Resulting in, For example:
Why two cores?
RStudio is a resource-heavy program. Due to this, we recommend using at least two cores for a more pleasant user experience.
3. Load the modules needed¶
In the terminal of the interactive session, do:
How does that look like?
Your output will be similar to:
[sven@r210 sven]$ module load R/4.3.1 R_packages/4.3.1 RStudio/2023.06.2-561
R/4.3.1: Nearly all CRAN and BioConductor packages are installed and available by loading
the module R_packages/4.3.1
R_packages/4.3.1: Note that loading some spatial analysis packages, especially geo-related packages, might
R_packages/4.3.1: require you to load additional modules prior to use. monocle3 is such a package. See
R_packages/4.3.1: 'module help R_packages/4.3.1'
R_packages/4.3.1: The RStudio packages pane is disabled when loading this module, due to RStudio slowdowns
R_packages/4.3.1: because there are >20000 available packages. *All packages are still available.* For
R_packages/4.3.1: more information and instructions to re-enable the packages pane (not recommended) see
R_packages/4.3.1: 'module help R_packages/4.3.1'
RStudio/2023.12.1-402: Sandboxing is not enabled for RStudio at UPPMAX. See 'module help RStudio/2023.12.1-402' for more information
4. Start RStudio¶
With the modules loaded, start RStudio from the terminal (on the interactive session):
RStudio can be slow to startup, as R has thousands (!) of packages. Additionally, at startup and if enabled, your saved RStudio workspace (with potentially a lot of data!) is read.