We are trying to fully containerize Rstudio however we run the image we get the following error. Is there something we are missing here? Ref: Jun 03 08:09:53 pdlhpc1cn001 rserver[13797]: ERROR Could not change permissions for specified ‘server-data-dir’ - the directory (/var/run/rstudio-server) mus…

I would say next steps are answering these two questions. Can the job find the $RSTUDIO_AUTH in the container (if you’re not mounting home as an example)? Then is the $RSTUDIO_AUTH working as it’s expected? can it find the $RSTUDIO_AUTH file. To debug this, I’d write a simple wrapper like this. T…

This is where it fails after I launch it. [image] I can’t add new posts to this topic so I’m editing this post: I mounted /home I updated the template/bin/auth to include the changes for rstudio server 1.3 support still failing at authorization phase. I installed within the container: R-4.0.0…

I’d ensure that HOME is mounted too. You seem to be passing credentials OK, but can the container find this file `--auth-pam-helper-path "{RSTUDIO_AUTH}"` (It ends up being ~/ondemand/data/sys/dashboard/batch_connect/sys/rstudio/output//bin/auth)?

What version of RStudio Server are you using? We noticed that the new 1.3 version fails to authenticate with “Error: Incorrect or invalid username/password”. We just didn’t get around to posting the issue yet.

Hi, The authentication issue in 1.3 is due to a change in how the auth-pam-helper script is invoked by rserver. Previously, it was called with just one argument, $USERNAME. In 1.3 it is called with three arguments, “$USERNAME rstudio 1”. The test in line 4 of the bin/auth script: #!/usr/bin/env b…

@dugan Thanks for this! I opened an issue to get this merged into bc_osc_rstudio_server here https://github.com/OSC/bc_osc_rstudio_server/issues/34

Onbehalf of eisenfaust (can only do 3 posts atm): I mounted /home I updated the template/bin/auth to include the changes for rstudio server 1.3 support still failing at authorization phase. I installed within the container: R-4.0.0.tar.gz to /R/4.0.0 rstudio-server-rhel-1.3.959-x86_64.rpm to d…

Thanks for this. We’ve now fully remove Singularity from our RStudio Server app.

Try pointing RStudio Server to your /tmp. singularity run -B "$TMPDIR:/tmp" "$RSTUDIO_SERVER_IMAGE" \ --www-port "${port}" \ --auth-none 0 \ --auth-pam-helper-path "${RSTUDIO_AUTH}" \ --auth-encrypt-password 0 \ --rsession-path "${RSESSION_WRAPPER_FILE}" \ --server-data-dir /tmp

Unfortunately that didn’t solve my issue for the authorization issue I’m currently having. It does seem to be a potentially good way to not have to map /tmp:/var/run. If we end up doing this, I think we will need to also supply: --server-pid-file arg (=/var/run/rstudio-server.pid) probably someth…

Hi, are you certain that you need to have this bind? We’re using the Singularity Hub RStudio image https://singularity-hub.org/collections/463 with this configuration https://github.com/bihealth/ood-bih-rstudio-server In this configuration, I’m only binding /fast which is our GPFS file system…

Unable to launch fully containerized Rstudio

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fenz (Fenz) June 17, 2021, 11:47am 22

I think I found a solution: RStudio when launched without Singularity is having strange troubles with authentication - #32 by fenz

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Unable to launch fully containerized Rstudio

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