Biowulf High Performance Computing at the NIH
RStudio on Biowulf
RStudio Logo

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 to biowulf. Please use the NoMachine NX client to create the graphical connection as it is the most reliable for RStudio.

Common pitfalls
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
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.

Running RStudio interactively

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

rstudio window
rstudio window

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=6g --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 window