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?