The kernel appears to have died. It will restart automatically

I use “minimal-notebook” as a base and install some extra packages, like “anndata” and “matplotlib”.

Then, I start the docker by

docker run -m 8g --memory-swap="20g"  --cpus=2 -e NB_USER=jovyan -w /home/jovyan -v /Users/me:/home/jovyan/work -p 8888:8888 -it minimal-notebook_extra:latest

Then I enter Jupyter Notebook and import a library

import anndata as ad

It works well. Then I try to load my data

adata = ad.read("mydata.h5ad")

Then it reports an error

Kernel Restarting
The kernel appears to have died. It will restart automatically.

Without Docker, I could load the data normally. Does anybody have an idea what causes this error?

3 Likes

Have you checked the docker logs to see what the logs show? It might have some helpful information.

docker logs [OPTIONS] CONTAINER

I’ve been facing the same problem with Docker. My code works without Docker…
Did you find the solution? @kridsadakorn
Thanks

1 Like

I am also having this issue.
running Jupyterhub on EKS on AWS (chart jupyterhub-0.8.2)

usually happens when running large loads on the notebook

Likely you are OOMing the container involved. Try running with more resources / looking at your container resources overtime before it dies.