Using the python3 in container for setting up jupyter kernel about sherlock HOT 3 CLOSED

Hi @vsoch
Sorry my post and question were misplaced (I was using a singularity container for running some jobs on my university cluster, but this wasn't related to sherlock).
I finally did solve my issue though: thank you very much for the quick replies!

from sherlock.

Hey @MLbyML ! I'll be able to help you further tomorrow (it's the middle of the night here) but one thing that sticks out is that your home path is incorrect, it's missing a leading slash:

• home/lalit/singularity -> /home/lalit/singularity

But actually, if you are using Singularity on sherlock that wouldn't be the path - it should just point to "singularity" which is at /usr/bin/singularity. You are making a lot of assumptions about the user site being on the path, and it's also not clear to me how you are running this (interactively? from the container? what container?) so what I need from you to debug this further is full information to reproduce your case.

• where are you logged in
• show me what's on your path, what modules are loaded
• where did you pull your container from
• any reason to not use on demand?

Thanks! Be back in a few hours.

from sherlock.

I think it's likely those path errors, but another sanity check you can do is to interact with jupyter to list environments. Here is how I re-created your test case on sherlock (but with fixed paths)

mkdir -p /home/users/vsochat/.local/share/jupyter/kernels/mykernel

# Checking my home and singularity locations
echo $HOME
which singularity

# load jupyter (but are you using one in a container?
module load py-jupyter/1.0.0_py36

# list available kernels
$ jupyter kernelspec list
Available kernels:
  python3     /share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/ipykernel/resources
  mykernel    /home/users/vsochat/.local/share/jupyter/kernels/mykernel

# the jupyter I'm using
$ which jupyter
/share/software/user/open/py-jupyter/1.0.0_py36/bin/jupyter

At this point you'd want to open an interactive (command line) test terminal using it. But I'll stop here because I don't know how to reproduce what you are doing exactly, let me know. I suspect the permissions error just stems from having the wrong path (since the kernels are loaded when you start it up) but it might be something else.

from sherlock.