RStudio on Biowulf

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. We recommend using the Graphical Session on HPC OnDemand.

RStudio Server is also available through HPC OnDemand web interface. For more information, check out the documentation here.

Common pitfalls

top

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 a Graphical Session on HPC OnDemand 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.

Running RStudio interactively

Connect to Biowulf using a Graphical Session on HPC OnDemand, then open a terminal:

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 15323416
salloc.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 &

Documentation