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. RStudio Server is used interactively and requires an SSH tunnel connection to biowulf. Please use an sinteractive tunnel to create the tunnel necessary to access RStudio Server.
This module is currently experimental and may change or disappear without warning. Please contact staff@hpc.nih.gov if you run into issues while following the below steps.
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