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NGEET / fates-tutorial

Repository for FATES tutorial and related documentation
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Determine why container notebook saves to local host with a weird user id and group (linux only) #29

Open glemieux opened 2 months ago

glemieux commented 2 months ago

See https://jupyter-docker-stacks.readthedocs.io/en/latest/using/troubleshooting.html#permission-issues-after-changing-the-uid-gid-and-user-in-the-container

glemieux commented 2 months ago

The solution here is to map the host uid and gid to the container during run time. To allow the host local to edit a file created by the container, GB_UMASK needs to be changed from the default read-only.

Note that this option only takes 2 digits as possible entries. Since the permissions don't match the local user, we need to make sure "other" users have write access which requires setting GB_UMASK=1.

glemieux commented 2 months ago

This looks like its really only a problem on linux machines using docker desktop. MacOS docker desktop interacts with mounted volumes through docker-compose fine. That said I've been test running the jupyter notebook using docker run on the CLI instead of compose; maybe compose handles this somehow? If not maybe a newer version of linux docker desktop has fixed this?

UPDATE: docker compose on linux doesn't automatically handle this. Since this isn't an issue with macos, I can simply proceed with that for the time being, but I'll review the docker desktop updates on linux to see if this updates this issue.

~- [ ] review and update docker desktop on linux~

The current version on lobata is the latest available through apt based on the OS version. Postpone this.