added a jupyterhub troubleshooting page

2020-02-18 18:03:07 +01:00 · 2020-02-18 18:03:07 +01:00 · ce66ca0b86
commit ce66ca0b86
parent 5bf1a50c63
3 changed files with 68 additions and 3 deletions
--- 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:
--- a/jupyterhub/jupyterhub-trouble.md
+++ b/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 <merlin-admins@lists.psi.ch>.
+
+## 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 <some-package>`). 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)
+
+
+<!-- ## Error HTTP 500 when starting the spawner -->
+
+<!--    The spawner screen shows after launching an error message like the following: -->
+<!--    `Internal server error (Spawner failed to start [status=..]. The logs may contain details)` -->
+   
+   
--- a/jupyterhub/jupyterhub.md
+++ b/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 <merlin-admins@lists.psi.ch>.
+

-   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 <merlin-admins@lists.psi.ch>.
-