Permission error when running rstudio inside a singularity instance (Resolved)

Starting in early 2021, I started getting a new error when starting a new Singularity instance based on a rstudio docker image running in an HPC environment on CentOS. This issue was referenced in this thread

Here's the error I was getting:

ERROR database error 7 (sqlite3_statement_backend::loadOne: attempt to write a readonly database) [description: Could not delete expired revoked cookies from the database, description: Could not read revoked cookies from the database]; OCCURRED AT virtual rstudio::core::Error rstudio::core::database::Connection::execute(rstudio::core::database::Query&, bool*) src/cpp/core/Database.cpp:480; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:729

I solved this by binding an address outside the container to /var/lib/rstudio-server when starting the instance as follows:

--bind $RSTUDIO_DB:/var/lib/rstudio-server

where $RSTUDIO_DB is just a path outside the container. I got this idea from this post.

Now my complete instance command looks like this:

singularity instance start \
      --bind $SINGULARITY_LOCALCACHEDIR/tmp:/tmp \
      --bind $SINGULARITY_LOCALCACHEDIR/run:/run \
      --bind $RSTUDIO_DB:/var/lib/rstudio-server \
      $CONTAINER_PATH rserver --www-port ${PORT} --auth-none=0 --auth-pam-helper-path=pam-helper

And it works! I'm just posting here in case this will help someone else figure this out...

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.