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grst / rstudio-server-conda

Run Rstudio Server in a conda environment
MIT License
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running rserver on computational node #17

Closed Zepeng-Mu closed 2 years ago

Zepeng-Mu commented 2 years ago

Hi, I'm very new to docker but I already find your repo greatly helpful. I'm using a HPC system that I do not have root privilege, so I installed Singularity using conda. Now I can run rserver in the login node. But what I really want to do is to be able to start a SLURM job and run RStudio server there. When I tried to do this, I got the error:

FATAL:   while extracting rstudio_4.0.5.sif: root filesystem extraction failed: extract command failed: ERROR  : Failed to create user namespace: user namespace disabled
: exit status 1

I have no idea what this means. I tried the solution from rocker project page, and it's the same. Therefore I'm wondering how should I run RStudio server in a computational node?

Thanks so much!

grst commented 2 years ago

In principle I think your approach is fine, but I never encountered this issue before. Maybe it's better to ask this question in the rocker repository, as I don't think it's specific to the conda part.

Zepeng-Mu commented 2 years ago

Hi, thanks for the quick reply. After some reading I found a Singularity issue on it's GitHub page that says this is because security feature after 3.6.4. After downgrading from 3.7.1 to 3.6.3 I no longer see this error message. I will close this issue for now, but maybe this is useful to other people as well.