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uabrc / researcher_facing_readthedocs

The repository for UAB Research Computing researcher facing read the docs
https://uabrc.readthedocs.io
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Jupyter Notebooks caveat #77

Open wwarriner opened 2 years ago

wwarriner commented 2 years ago

Interactive jupyter jobs can fail to start and "disappear" without warning due to an issue with environments.

If the user supplies a conda activate <env> line in the Environment Setup box, and <env> DOES have jupyter installed but does NOT have nb_conda_kernels installed, the job will fail to start and the job card will disappear from My Interactive Sessions. Other errors crop up for other packages, but they aren't fatal. I will list these below.

I've talked with Louis about rearranging the order of operations, but at this time it isn't feasible. There are users who legitimately need to use custom versions of the jupyter server, such as in the Qiime2 module.

We need to update the docs to include this caveat. Something like

If you need to or want to use `conda activate <env>` in the Environment Setup box of the
Interactive Jupyter Notebook form, and your environment has the `jupyter` package installed,
you will need to install additional packages in your environment. In addition to the usual
`ipykernel`, you will need the following

nb_conda_kernels
nb_anacondacloud
nb_conda
nbpresent
wwarriner commented 2 years ago

Side note, people should probably not be installing jupyter directly into an env. That is the server software and we have that covered on OOD. To use an env as a notebook client they should be installing ipykernel only. This is the "best practice" for using OOD Jupyter