RStudio Server 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.

This is RStudio Server, a browser-based interface very similar to the standard RStudio desktop environment. RStudio Server can be much more responsive and a generally-better experience when used remotely, especially over a VPN.

This application can be utilized interactively via the HPC OnDemand web interface.

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 workding 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/")
My R sessions are/aren't being restored when I reconnect
R sessions inside RStudio server are persistent within a single sinteractive session. Different sinteractive jobs cannot share R sessions and job sessions are not persistent between jobs. Please save your work to disk or explicitly save your session to an RData file by manually saving the workspace with the Session -> Save Workspace As... menu.
I am getting a permission denied error
R sessions inside RStudio server are persistent within a single sinteractive session. Every time you run rstudio-server, you will receive a new randomized password. Please make sure to use the new link or password each time you restart the server.

Accessing RStudio Server via Open OnDemand

We recommend using HPC OnDemand to access RStudio Server. This uses Open OnDemand to provide a convenient interface to launch and access RStudio sessions in interactive jobs without requiring complex SSH tunneling setup.

To access RStudio Server via Open OnDemand, you navigate to the RStudio Server application page, configure the resources your job requires, and launch your job. You may also select the startup "working directory", equivalent to running cd before launching rstudio-server from the terminal.

Screenshot of the RStudio Server application submission form

For more information about Biowulf's Open OnDemand installation, access, and other services available please see our documentation.

Running RStudio Server interactively

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

It is also required to set up an sinteractive tunnel.

[user@biowulf ~]$ sinteractive --mem=10g --gres=lscratch:5 --tunnel
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

Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.


Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:

    ssh  -L 39689:localhost:39689 user@biowulf.nih.gov

For Windows instructions, see https://hpc.nih.gov/docs/tunneling
[user@cn1640 ~]$ module load rstudio-server
[+] Loading gcc  9.2.0  ...
[-] Unloading gcc  9.2.0  ...
[+] Loading gcc  9.2.0  ...
[+] Loading openmpi 4.0.5  for GCC 9.2.0
[+] Loading ImageMagick  7.0.8  on cn4280
[+] Loading HDF5  1.10.4
[-] Unloading gcc  9.2.0  ...
[+] Loading gcc  9.2.0  ...
[+] Loading NetCDF 4.7.4_gcc9.2.0
[+] Loading pandoc  2.17.1.1  on cn4280
[+] Loading pcre2 10.21  ...
[+] Loading R 4.2.2
[+] Loading rstudio-server  2023.03.0-386
[user@cn1640 dir]$ rstudio-server

Please ensure you have set up the SSH port forwarding as described in the sinteractive instructions.

Please connect to http://localhost:39689/auth-sign-in?user=test2&password=nRmzfPWh_X8Z-03hbDjPz3bm
Use your username 'user' and the pasword 'nRmzfPWh_X8Z-03hbDjPz3bm' to login

If you have set up the SSH tunnel with the command or instructions provided (please make sure to use the specific port/command given by your interactive session) you should be able to load the link and have RStudio Server load in your browser.

If you are presented with a login screen, please use your username and the password provided

Documentation