RStudio is an integrated development environment (IDE)for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. RStudio is used interactively and requires a graphical connection of biowulf. Please use the NoMachine NX client to create the graphical connection as it is the most reliable for RStudio.

There is RStudio Server (a browser-based interface) available through hpcondemand: The HPC OnDemand

working directory is /home

By default, the working directory is /home no matter where the interactive session is started. This could be changed by setwd(), which will set the working directory to desired location.

setwd("/data/somewhere")

Another way (more recommended) is using project, which will set it's own working directory. File -> New Project -> New Directory -> Create New Project (assign directory name, and choose the directory location such as "/data/XXX/")i

XDG_RUNTIME_DIR not set

This is a harmless warning:

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/XXXX/'

Can't open Rstudio

Rstudio requires graphical connection, please use NX to avoid these errors:

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
Unrecognized OpenGL version

or

qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

Connect to Biowulf with NoMachine (NX), then open a terminal inside of NX.

Allocate an sinteractive session. It is generally recommended to allocate at least a small amount of lscratch for temporary storage for R.

[user@biowulf ~]$ sinteractive --mem=10g --gres=lscratch:5
salloc.exe: Pending job allocation 15323416
salloc.exe: job 15323416 queued and waiting for resources
salloc.exe: job 15323416 has been allocated resources
salloc.exe: Granted job allocation 15323416salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1640 are ready for job
[user@cn1640 ~]$ module load rstudio R
[+] Loading Rstudio 1.1.447 
Remember to load an R module before starting Rstudio
...
[user@cn1640 dir]$ rstudio &

• RStudio Web Site
• RStudio Resources