79 lines
3.1 KiB
Markdown
79 lines
3.1 KiB
Markdown
# Jupyterhub Troubleshooting
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In case of problems or requests, please either submit a **[PSI Service
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Now](https://psi.service-now.com/psisp)** incident containing *"Merlin
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Jupyterhub"* as part of the subject, or contact us by mail through
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<merlin-admins@lists.psi.ch>.
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## General steps for troubleshooting
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### Investigate the Slurm output file
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Your jupyterhub session runs as a normal batch job on the cluster, and each
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launch will create a slurm output file in your *home* directory named like
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`jupyterhub_batchspawner_{$JOBID}.log`, where the `$JOBID` part is the slurm job
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ID of your job. After a failed launch, investigate the contents of that file.
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An error message will usually be found towards the end of the file, often
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including a python backtrace.
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### Investigate python environment interferences
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Jupyterhub just runs a jupyter notebook executable as your user inside the
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batch job. A frequent source of errors consists of a user's local python
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environment definitions getting mixed up with the environment that jupyter
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needs to launch.
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- setting PYTHONPATH inside of the ~/.bash_profile or any other startup script
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- having installed packages to your local user area (e.g. using `pip install
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--user <some-package>`). Such installation will interfere with the
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environment offered by the `module` system on our cluster (based on
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anaconda). You can list such packages by executing `pip list user`.
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They are usually located in `~/.local/lib/pythonX.Y/...`.
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You can investigate the launching of a notebook interactively, by logging in to
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Merlin6 and running a jupyter command in the correct environment.
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```bash
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module use unstable
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module load anaconda/2019.07
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conda activate jupyterhub-1.0.0_py36
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jupyter --paths
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```
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## Known Problems and workarounds
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### Spawner times out
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If the cluster is very full, it may be difficult to launch a session. We always
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reserve some slots for interactive Jupyterhub use, but it may be that these
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slots have been taken or that the resources you requested are currently not
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available.
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Inside of a Merlin6 terminal shell, you can run the standard commands like
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`sinfo` and `squeue` to get an overview of how full the cluster is.
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### Your user environment is not among the kernels offered for choice
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Refer to our documentation about [using your own custom made
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environments with jupyterhub](jupyterhub.md).
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### Cannot save notebook - *xsrf argument missing*
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You cannot save your notebook anymore and you get this error:
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```text
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'_xsrf' argument missing from POST
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```
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This issue occurs very seldomly. There exists the following workaround:
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Go to the jupyterhub file browsing window and just open another
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notebook using the same kernel in another browser window. The issue
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should then go away. For more information refer to [this github
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thread](https://github.com/nteract/hydrogen/issues/922#issuecomment-405456346)
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<!-- ## Error HTTP 500 when starting the spawner -->
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<!-- The spawner screen shows after launching an error message like the following: -->
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<!-- `Internal server error (Spawner failed to start [status=..]. The logs may contain details)` -->
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