[BUG] - permission denied error with datascience-notebook

[verdurin]

What docker image(s) are you using?

datascience-notebook

OS system and architecture running docker image

Fedora CoreOS 35

What Docker command are you running?

Whatever is the default in Zero To JupyterHub version 1.2.0...

How to Reproduce the problem?

1. Launch an R server using the datascience-notebook image
2. Try to run an R command e.g. capabilities()

Command output

No response

Expected behavior

R command is executed and output is shown

Actual behavior

No output visible in the notebook and in the server logs there are errors:

[I 2022-06-13 15:48:33.536 SingleUserLabApp restarter:75] AsyncIOLoopKernelRestarter: restarting kernel (5/5), new random ports
[D 2022-06-13 15:48:33.547 SingleUserLabApp manager:386] Starting kernel: ['R', '--slave', '-e', 'IRkernel::main()', '--args', '/home/jovyan/.local/share/jupyter/runtime/kernel-928c71a4-9525-49a1-a3fd-792974bd24bf.json']
[D 2022-06-13 15:48:33.548 SingleUserLabApp connect:604] Connecting to: tcp://127.0.0.1:37933
OMP: Error #179: Function Can't open SHM2 failed:
OMP: System error #13: Permission denied

Anything else?

Test R commands do work on this same JupyterHub installation using the r-notebook image.

[mathbunnyru]

Hello @verdurin!

Could you reproduce this without Zero To JupyterHub? It will be much easier to debug.

[verdurin]

Hi @mathbunnyru

I've been busily preparing for some teaching that will use a Z2JH cluster next week. As that calms down a bit, I will try to find time for a simpler reproducer, and let you know.

[mathbunnyru]

@verdurin could you check it once again please with latest docker images? (you will have to do docker pull) And if possible, try to reproduce without Zero To JupyterHub.

[mathbunnyru]

@verdurin we're waiting for you response here. Could you please take a look?

[mathbunnyru]

Closing this as no response was received. Please, reopen, if you still see this issue.