RStudio Rocker with Singularity

Posit Professional products
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1

Hi,

I'm trying to use RStudio Server on a HPC with Singularity. Following the guidance here (https://www.rocker-project.org/use/singularity/), I run the following:

# Pull the container
singularity pull --name sing_conts/tidyverse.simg docker://rocker/tidyverse:latest
# Then attempt to execute on a node
bsub -Is "singularity exec sing_conts/tidyverse.simg rserver --www-address=127.0.0.1"

And I get the following error:

16 Feb 2021 14:05:15 [rserver] 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

Any assistance would be appreciated.

Ian

2

I think you will need to create a writable image. There are some instructions here:

1 Like
5

@brettellebi Thanks for posting here! I am curious to hear about the HPC grid you are using, if it is possible to share! A few years ago, we introduced the RStudio Job Launcher as a Pro feature that allows launching sessions onto backends like a HPC grid (right now, we only support Slurm). It's always good to hear what our users are using, though!

Also, it'd be great to understand what drives the preference for Singularity containers! Is there a particular reason that you / your organization have standardized on singularity?

I hope you got your problem solved, thanks to @benfulton's great pointer! Please let us know if you have any other questions!

6

Hi Cole.

Our HPC grid is based on Red Hat Enterprise Linux with an LSF job scheduler.

The administrators have installed Singularity on the HPC rather than Docker because of the latter's security issues.

I still haven't managed to get RServer working, but there are a few more avenues yet to pursue.

Cheers,

Ian

1 Like
7

@brettellebi thanks for the background! And sorry to hear about the continued troubles. I'm curious to hear how it goes!