diff --git a/_data/sidebars/merlin6_sidebar.yml b/_data/sidebars/merlin6_sidebar.yml index e3180f5..f6d17e2 100644 --- a/_data/sidebars/merlin6_sidebar.yml +++ b/_data/sidebars/merlin6_sidebar.yml @@ -67,6 +67,8 @@ entries: url: /merlin6/jupyter-extensions.html - title: Jupyterlab url: /merlin6/jupyterlab.html + - title: Jupyterhub Troubleshooting + url: /merlin6/jupyterhub-trouble.html - title: - title: Announcements folderitems: diff --git a/pages/merlin6/04 jupyterhub/jupyterhub-trouble.md b/pages/merlin6/04 jupyterhub/jupyterhub-trouble.md new file mode 100644 index 0000000..768968a --- /dev/null +++ b/pages/merlin6/04 jupyterhub/jupyterhub-trouble.md @@ -0,0 +1,63 @@ +--- +title: Jupyterhub Troubleshooting +#tags: +#keywords: +last_updated: 18 February 2020 +#summary: "" +sidebar: merlin6_sidebar +permalink: /merlin6/jupyterhub-trouble.html +--- + +In case of problems or requests, please either submit a **[PSI Service Now](https://psi.service-now.com/psisp)** incident containing *"Merlin Jupyterhub"* as part of the subject, or contact us by mail through . + +## General steps for troubleshooting + +### Investigate the Slurm output file +Your jupyterhub session runs as a normal batch job on the cluster, and each launch will create a slurm output file in your HOME directory named like `jupyterhub_batchspawner_{$JOBID}.log`, where the $JOBID part is the slurm job ID of your job. After a failed launch, investigate the contents of that file. An error message will usually be found towards the end of the file, often including a python backtrace. + +### Investigate python environment interferences +Jupyterhub just runs a jupyter notebook executable as your user inside the batch job. A frequent source of errors consists of a user's local python environment definitions getting mixed up with the environment that jupyter needs to launch. + + - setting PYTHONPATH inside of the ~/.bash_profile or any other startup script + - having installed packages to your local user area (e.g. using `pip install --user `). Such installation will interfere with the environment offered by the `module` system on our cluster (based on anaconda). You can list such packages by executing + `pip list user`. They are usually located in `~/.local/lib/pythonX.Y/...`. + +You can investigate the launching of a notebook interactively, by logging in to Merlin6 and running a jupyter command in the correct environment. + +``` + module use unstable + module load anaconda/2019.07 + conda activate jupyterhub-1.0.0_py36 + jupyter --paths +``` + +## Known Problems and workarounds +### Spawner times out +If the cluster is very full, it may be difficult to launch a session. We always reserve some slots for interactive Jupyterhub use, but it may be that these slots have been taken or that the resources you requested are currently not available. + +Inside of a Merlin6 terminal shell, you can run the standard commands like `sinfo` and `squeue` to get an overview of how full the cluster is. + +### Your user environment is not among the kernels offered for choice +Refer to our documentation about [using your own custom made +environments with jupyterhub](/merlin6/jupyterhub.html). + + +### Cannot save notebook - _xsrf argument missing_ +You cannot save your notebook anymore and you get this error: + + **'_xsrf' argument missing from POST** + +This issue occurs very seldomly. There exists the following workaround: + +Go to the jupyterhub file browsing window and just open another +notebook using the same kernel in another browser window. The issue +should then go away. For more information refer to [this github +thread](https://github.com/nteract/hydrogen/issues/922#issuecomment-405456346) + + + + + + + + diff --git a/pages/merlin6/04 jupyterhub/jupyterhub.md b/pages/merlin6/04 jupyterhub/jupyterhub.md index 1785d28..7109938 100644 --- a/pages/merlin6/04 jupyterhub/jupyterhub.md +++ b/pages/merlin6/04 jupyterhub/jupyterhub.md @@ -77,7 +77,7 @@ After this, your new kernel will be visible as `my-test-env` inside of your jupy -## Troubleshooting +## Contact +In case of problems or requests, please either submit a **[PSI Service Now](https://psi.service-now.com/psisp)** incident containing *"Merlin Jupyterhub"* as part of the subject, or contact us by mail through . + - In case of problems or request, please either submit a **[PSI Service Now](https://psi.service-now.com/psisp)** incident containing *"Merlin Jupyterhub"* as part of the subject, or contact us by mail through . -