Computing

RStudio Server

RStudio Server runs on several servers around NCEAS, including Aurora, Mazu, and DataTeam.

Troubleshooting

RStudio Server sessions can become stuck, leaving users unable to access the RStudio web interface via a browser. There seems to be multiple causes so the fix may vary depending on what the user’s doing. Some things to look for include:

• Very large /home/$USER/.RData file: RStudio creates this file by default in order to to save the user’s work and the file can become huge when the user creates variables that take up a large amount of memory. This problem is probably made worse on our HPC hardware because the user, theoretically, can actually load files into memory that RStudio can’t handle unlike on traditional desktop hardware. The user’s RStudio session can hang if this file is large because RStudio, by default, tries to read this file into memory when the session starts.
  • Solution: Rename or delete this file. The user may lose work. Also, advise the user to turn this setting off in their RStudio preferences on the server. The file can still be loaded into an R session if renamed.
• Large numbers of orphaned R processes: In some scenarios, it seems like the RStudio session loses track of the R process(es) it spawns, leaving many R processes running on the system. This isn’t necessarily a cause for a stuck RStudio session but may indicate a problematic workflow.

Beyond the above, it appears that RStudio sessions just get corrupted sometimes. Each user’s RStudio state is stored in /home/$USER/.local/share/rstudio. A two-pass approach to fixing a corrupt session usually works:

• First pass
  1. Tell the user to close any RStudio tabs in their browser
  2. Kill any rstudio-server proccesses (find the pid with ps -ef | grep $USER | grep [r]studio-server)
  3. Delete /home/$USER/.local/share/rstudio/sessions. The user may lose work at this point.
• Second pass (the nuclear option)
  1. Tell the user to close any RStudio tabs in their browser
  2. Kill any rstudio-server proccesses (find the pid with ps -ef | grep $USER | grep [r]studio-server)
  3. Delete /home/$USER/.local/share/rstudio The user may lose work and will lose their RStudio preferences.