Problem running RStudio server with podman

[bernt-matthias]

I'm trying to get rocker running with podman (our HPC does only support podman).

podman run     --rm     -ti     -p 8787:8787     -e DISABLE_AUTH=true     rocker/rstudio:latest-daily

This gives me the following output:

s6-supervise s6-fdholderd: fatal: unable to mkfifodir event: Value too large for data type
s6-supervise s6-fdholderd: fatal: unable to mkfifodir event: Permission denied
s6-supervise s6-fdholderd: fatal: unable to mkfifodir event: Permission denied
s6-supervise s6-fdholderd: fatal: unable to mkfifodir event: Permission denied
s6-supervise s6-fdholderd: fatal: unable to mkfifodir event: Permission denied

Any ideas that help me understand / solve the issue?

As far as I see (curl http://localhost:8787/ gives me curl: (56) Recv failure: Connection reset by peer) the RStudio server is not up.

[cboettig]

can you try with rocker/rstudio:latest instead? (unfortunately the daily tag is not successfully building at this time, cc @eitsupi )

[bernt-matthias]

Thanks for the fast reply. Same problem with rocker/rstudio:latest (stumbled over this problem when I tried to get this running .. so it was unlikely that latest works).

[eitsupi]

unfortunately the daily tag is not successfully building at this time

The latest-daily tag is obsolete.

[cboettig]

@bernt-matthias looks like you may be running in an environment where root is blocked? Can you test rocker/binder instead?

podman run --rm -p 8888:8888 docker.io/rocker/binder

(apologies for all the suggestions, shooting a bit in the dark here. binder runs without root via jupyterhub and may thus sidestep the issue).

[bernt-matthias]

@bernt-matthias looks like you may be running in an environment where root is blocked?

I would guess so. Given that our HPC system (or its admins) is quiet restrictive.

Can you test rocker/binder instead?

podman run --rm -p 8888:8888 docker.io/rocker/binder

This gives me.

Writing manifest to image destination
WARN[0411] Additional gid=50 is not present in the user namespace, skip setting it 
Error: OCI runtime error: crun: cannot setresgid to `1000`: Invalid argument

So I guess that means that you are right?

(apologies for all the suggestions, shooting a bit in the dark here. binder runs without root via jupyterhub and may thus sidestep the issue).

Nothing to worry about. Anything is highly appreciated and I'm happy to try any suggestion.

[benz0li]

@bernt-matthias Does podman run -ti --rm debian work?

You could give glcr.b-data.ch/jupyterlab/r/geospatial a try, i.e.

podman run --rm \
  -p 8888:8888 \
  glcr.b-data.ch/jupyterlab/r/geospatial

or

podman run --rm \
  -p 8888:8888 \
  -u root \
  -e NB_USER=root \
  -e NB_UID=0 \
  -e NB_GID=0 \
  -e NOTEBOOK_ARGS="--allow-root" \
  glcr.b-data.ch/jupyterlab/r/geospatial

[bernt-matthias]

Does podman run -ti --rm debian work?

Yes.

You could give glcr.b-data.ch/jupyterlab/r/geospatial a try, i.e.

podman run --rm \
  -p 8888:8888 \
  glcr.b-data.ch/jupyterlab/r/geospatial

This just gives me: Error: OCI runtime error: crun: cannot setresgid to 100: Invalid argument

podman run --rm \
  -p 8888:8888 \
  -u root \
  -e NB_USER=root \
  -e NB_UID=0 \
  -e NB_GID=0 \
  -e NOTEBOOK_ARGS="--allow-root" \
  glcr.b-data.ch/jupyterlab/r/geospatial

This seems to do much more:

Entered start.sh with args: start-notebook.sh
Running hooks in: /usr/local/bin/start-notebook.d as uid: 0 gid: 0
Sourcing shell script: /usr/local/bin/start-notebook.d/10-populate.sh
Done running hooks in: /usr/local/bin/start-notebook.d
Updated the jovyan user:
- username: jovyan       -> root
- home dir: /home/jovyan -> /home/root
Attempting to copy /home/jovyan to /home/root...
Success!
Changing working directory to /home/root/
Running hooks in: /usr/local/bin/before-notebook.d as uid: 0 gid: 0
Sourcing shell script: /usr/local/bin/before-notebook.d/10-env.sh
Sourcing shell script: /usr/local/bin/before-notebook.d/11-home.sh

But there is an error in the "end": runuser: cannot set groups: Operation not permitted