Add new image for Dask hub #144

jacobtomlinson · 2021-02-22T11:54:56Z

In order for a Docker image to be used with the Daskhub helm chart it needs dask-gateway and jupyterhub-singleuser to be installed.

Neither of our official images have those packages so I propose we either add them to the notebook image or create a new image specifically for Daskhub.

The text was updated successfully, but these errors were encountered:

jrbourbeau · 2021-02-22T22:23:09Z

Sounds good! I have a slight preference for creating a new image, but you probably have a better sense of what makes sense here

chrisroat · 2021-09-17T04:59:13Z

More may be needed than simply adding those packages. I tried to roll my own images and it didn't work - I get 404s. If I use the latest dask-notebook, I see the same -- even when installing dask-gateway and jupyterhub-singleuser

Below is an example config that I installed on a local minikube, including those packages. (If you try to repro, don't use the latest k8s v1.22, which is starting to become the default download -- daskhub chart is not compatible). I also include below the logs from the hub and the user pod.

To note:

user pod gives 404 for /user/<username> url at the very end of the logs
hub logs claim Single-user server has no version header, which means it is likely < 0.8. Expected 1.4.2, though you can clearly see jupyterhub-singleuser 1.4.2 being installed on the user pod.
hub logs show 404 for all static files (e.g. css)

Adding @consideRatio , as this feels a bit like a jhub configuration update is needed, as well. I'd be interested to know what that might be, as I'm not sure how to get more information about what is going wrong.

$ cat config.yaml 
jupyterhub:
  proxy:
    service:
      type: NodePort
  singleuser:
    image:
      name: daskdev/dask-notebook
      tag: 2021.9.0
      pullPolicy: Always
    extraEnv:
      EXTRA_CONDA_PACKAGES: "dask-gateway jupyterhub-singleuser"
$ helm upgrade --install dhub dask/daskhub --values=secrets.yml --values config.yaml

Hub Logs

$ kubectl logs hub-5857bf9fb8-7thrh 
Loading /usr/local/etc/jupyterhub/secret/values.yaml
No config at /usr/local/etc/jupyterhub/existing-secret/values.yaml
Loading extra config: 00-add-dask-gateway-values
Setting DASK_GATEWAY__ADDRESS http://proxy-public/services/dask-gateway
Adding dask-gateway service URL
[I 2021-09-17 04:43:01.183 JupyterHub app:2459] Running JupyterHub version 1.4.2
[I 2021-09-17 04:43:01.183 JupyterHub app:2489] Using Authenticator: jupyterhub.auth.DummyAuthenticator-1.4.2
[I 2021-09-17 04:43:01.183 JupyterHub app:2489] Using Spawner: kubespawner.spawner.KubeSpawner-1.1.0
[I 2021-09-17 04:43:01.183 JupyterHub app:2489] Using Proxy: jupyterhub.proxy.ConfigurableHTTPProxy-1.4.2
[W 2021-09-17 04:43:01.201 JupyterHub app:1808] No admin users, admin interface will be unavailable.
[W 2021-09-17 04:43:01.201 JupyterHub app:1809] Add any administrative users to `c.Authenticator.admin_users` in config.
[I 2021-09-17 04:43:01.201 JupyterHub app:1838] Not using allowed_users. Any authenticated user will be allowed.
[I 2021-09-17 04:43:01.243 JupyterHub provider:576] Updating oauth client service-dask-gateway
[I 2021-09-17 04:43:01.303 JupyterHub reflector:275] watching for pods with label selector='component=singleuser-server' in namespace default
[I 2021-09-17 04:43:01.328 JupyterHub reflector:275] watching for events with field selector='involvedObject.kind=Pod' in namespace default
[W 2021-09-17 04:43:01.344 JupyterHub _version:41] Single-user server has no version header, which means it is likely < 0.8. Expected 1.4.2
[I 2021-09-17 04:43:01.345 JupyterHub app:2186] test still running
[I 2021-09-17 04:43:01.347 JupyterHub app:2526] Initialized 1 spawners in 0.078 seconds
[I 2021-09-17 04:43:01.360 JupyterHub app:2738] Not starting proxy
[I 2021-09-17 04:43:01.364 JupyterHub app:2774] Hub API listening on http://:8081/hub/
[I 2021-09-17 04:43:01.364 JupyterHub app:2776] Private Hub API connect url http://hub:8081/hub/
[I 2021-09-17 04:43:01.364 JupyterHub app:2789] Starting managed service cull-idle
[I 2021-09-17 04:43:01.365 JupyterHub service:339] Starting service 'cull-idle': ['python3', '-m', 'jupyterhub_idle_culler', '--url=http://localhost:8081/hub/api', '--timeout=3600', '--cull-every=600', '--concurrency=10']
[I 2021-09-17 04:43:01.368 JupyterHub service:121] Spawning python3 -m jupyterhub_idle_culler --url=http://localhost:8081/hub/api --timeout=3600 --cull-every=600 --concurrency=10
[I 2021-09-17 04:43:01.378 JupyterHub app:2798] Adding external service dask-gateway at http://traefik-dhub-dask-gateway.default
[I 2021-09-17 04:43:01.387 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:43:01.390 JupyterHub app:2849] JupyterHub is now running at http://:8000
[I 2021-09-17 04:43:01.497 JupyterHub log:189] 200 GET /hub/api/users (cull-idle@127.0.0.1) 28.40ms
[I 2021-09-17 04:43:02.628 JupyterHub log:189] 200 GET /hub/error/503?url=%2Flab (@172.17.0.1) 39.85ms
[I 2021-09-17 04:43:54.143 JupyterHub log:189] 200 GET /hub/error/503?url=%2Flab (@172.17.0.1) 3.30ms
[I 2021-09-17 04:43:54.159 JupyterHub log:189] 302 GET / -> /hub/ (@::ffff:172.17.0.1) 1.77ms
[I 2021-09-17 04:43:54.242 JupyterHub log:189] 302 GET /hub/ -> /user/test/ (test@::ffff:172.17.0.1) 18.78ms
[W 2021-09-17 04:44:01.347 JupyterHub app:2131] User test server stopped with exit code: 1
[I 2021-09-17 04:44:01.347 JupyterHub proxy:309] Removing user test from proxy (/user/test/)
[I 2021-09-17 04:44:01.399 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:44:12.641 JupyterHub log:189] 200 GET /hub/error/503?url=%2Fuser%2Ftest%2F (@172.17.0.1) 3.06ms
[I 2021-09-17 04:44:17.512 JupyterHub log:189] 200 GET /hub/home (test@::ffff:172.17.0.1) 26.76ms
[I 2021-09-17 04:44:21.444 JupyterHub provider:574] Creating oauth client jupyterhub-user-test
[I 2021-09-17 04:44:21.466 JupyterHub spawner:2344] Attempting to create pvc claim-test, with timeout 3
[I 2021-09-17 04:44:21.469 JupyterHub log:189] 302 GET /hub/spawn/test -> /hub/spawn-pending/test (test@::ffff:172.17.0.1) 60.57ms
[I 2021-09-17 04:44:21.489 JupyterHub spawner:2361] PVC claim-test already exists, so did not create new pvc.
[I 2021-09-17 04:44:21.498 JupyterHub spawner:2302] Attempting to create pod jupyter-test, with timeout 3
[I 2021-09-17 04:44:21.525 JupyterHub pages:402] test is pending spawn
[I 2021-09-17 04:44:21.532 JupyterHub log:189] 200 GET /hub/spawn-pending/test (test@::ffff:172.17.0.1) 12.44ms
[W 2021-09-17 04:44:40.970 JupyterHub _version:41] Single-user server has no version header, which means it is likely < 0.8. Expected 1.4.2
[I 2021-09-17 04:44:40.970 JupyterHub base:909] User test took 19.557 seconds to start
[I 2021-09-17 04:44:40.970 JupyterHub proxy:285] Adding user test to proxy /user/test/ => http://172.17.0.10:8888
[I 2021-09-17 04:44:40.975 JupyterHub users:677] Server test is ready
[I 2021-09-17 04:44:40.976 JupyterHub log:189] 200 GET /hub/api/users/test/server/progress (test@::ffff:172.17.0.1) 19131.77ms
[I 2021-09-17 04:44:41.104 JupyterHub log:189] 302 GET /hub/spawn-pending/test -> /user/test/ (test@::ffff:172.17.0.1) 6.18ms
[I 2021-09-17 04:44:41.343 JupyterHub log:189] 302 GET /static/style/bootstrap.min.css?v=0e8a7fbd6de23ad6b27ab95802a0a0915af6693af612bc304d83af445529ce5d95842309ca3405d10f538d45c8a3a261b8cff78b4bd512dd9effb4109a71d0ab -> /hub/static/style/bootstrap.min.css?v=0e8a7fbd6de23ad6b27ab95802a0a0915af6693af612bc304d83af445529ce5d95842309ca3405d10f538d45c8a3a261b8cff78b4bd512dd9effb4109a71d0ab (@::ffff:172.17.0.1) 1.81ms
[I 2021-09-17 04:44:41.346 JupyterHub log:189] 302 GET /static/style/bootstrap-theme.min.css?v=8b2f045cb5b4d5ad346f6e816aa2566829a4f5f2783ec31d80d46a57de8ac0c3d21fe6e53bcd8e1f38ac17fcd06d12088bc9b43e23b5d1da52d10c6b717b22b3 -> /hub/static/style/bootstrap-theme.min.css?v=8b2f045cb5b4d5ad346f6e816aa2566829a4f5f2783ec31d80d46a57de8ac0c3d21fe6e53bcd8e1f38ac17fcd06d12088bc9b43e23b5d1da52d10c6b717b22b3 (@::ffff:172.17.0.1) 2.25ms
[I 2021-09-17 04:44:41.348 JupyterHub log:189] 302 GET /static/style/index.css?v=06e1f33518235bf36a1673b70c8f205bb706470f69d8ec46149d883cf17c53c9719e60341439e57b4057b468037216d7320fcc8afb920fdb6216b37aed5277f6 -> /hub/static/style/index.css?v=06e1f33518235bf36a1673b70c8f205bb706470f69d8ec46149d883cf17c53c9719e60341439e57b4057b468037216d7320fcc8afb920fdb6216b37aed5277f6 (@::ffff:172.17.0.1) 2.83ms
[W 2021-09-17 04:44:41.404 JupyterHub log:189] 404 GET /hub/static/style/bootstrap.min.css?v=0e8a7fbd6de23ad6b27ab95802a0a0915af6693af612bc304d83af445529ce5d95842309ca3405d10f538d45c8a3a261b8cff78b4bd512dd9effb4109a71d0ab (@::ffff:172.17.0.1) 2.54ms
[W 2021-09-17 04:44:41.406 JupyterHub log:189] 404 GET /hub/static/style/bootstrap-theme.min.css?v=8b2f045cb5b4d5ad346f6e816aa2566829a4f5f2783ec31d80d46a57de8ac0c3d21fe6e53bcd8e1f38ac17fcd06d12088bc9b43e23b5d1da52d10c6b717b22b3 (@::ffff:172.17.0.1) 3.13ms
[W 2021-09-17 04:44:41.409 JupyterHub log:189] 404 GET /hub/static/style/index.css?v=06e1f33518235bf36a1673b70c8f205bb706470f69d8ec46149d883cf17c53c9719e60341439e57b4057b468037216d7320fcc8afb920fdb6216b37aed5277f6 (@::ffff:172.17.0.1) 1.65ms
[I 2021-09-17 04:44:41.462 JupyterHub log:189] 302 GET /static/logo/logo.png?v=a2a176ee3cee251ffddf5fa21fe8e43727a9e5f87a06f9c91ad7b776d9e9d3d5e0159c16cc188a3965e00375fb4bc336c16067c688f5040c0c2d4bfdb852a9e4 -> /hub/static/logo/logo.png?v=a2a176ee3cee251ffddf5fa21fe8e43727a9e5f87a06f9c91ad7b776d9e9d3d5e0159c16cc188a3965e00375fb4bc336c16067c688f5040c0c2d4bfdb852a9e4 (@::ffff:172.17.0.1) 1.60ms
[W 2021-09-17 04:44:41.515 JupyterHub log:189] 404 GET /hub/static/logo/logo.png?v=a2a176ee3cee251ffddf5fa21fe8e43727a9e5f87a06f9c91ad7b776d9e9d3d5e0159c16cc188a3965e00375fb4bc336c16067c688f5040c0c2d4bfdb852a9e4 (@::ffff:172.17.0.1) 4.92ms
[I 2021-09-17 04:45:01.413 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:46:01.405 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:47:01.404 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:48:01.404 JupyterHub proxy:347] Checking routes
[I 2021-09-17 04:49:01.403 JupyterHub proxy:347] Checking routes

User Pod Logs

$ kubectl logs jupyter-test
+ '[' 1000 -eq 0 ']'
+ '[' -e /opt/app/environment.yml ']'
+ echo 'no environment.yml'
no environment.yml
+ '[' 'dask-gateway jupyterhub-singleuser' ']'
+ echo 'EXTRA_CONDA_PACKAGES environment variable found.  Installing.'
+ /opt/conda/bin/conda install -y dask-gateway jupyterhub-singleuser
EXTRA_CONDA_PACKAGES environment variable found.  Installing.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - dask-gateway
    - jupyterhub-singleuser


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    dask-gateway-0.9.0         |   py38h578d9bd_2          45 KB  conda-forge
    jupyterhub-singleuser-1.4.2|   py38h578d9bd_0           5 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          50 KB

The following NEW packages will be INSTALLED:

  dask-gateway       conda-forge/linux-64::dask-gateway-0.9.0-py38h578d9bd_2
  jupyterhub-single~ conda-forge/linux-64::jupyterhub-singleuser-1.4.2-py38h578d9bd_0



Downloading and Extracting Packages
dask-gateway-0.9.0   | 45 KB     | ########## | 100% 
jupyterhub-singleuse | 5 KB      | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '[' '' ']'
+ exec start.sh jupyter lab
Executing the command: jupyter lab
[I 2021-09-17 04:44:39.949 ServerApp] dask_labextension | extension was successfully linked.
[I 2021-09-17 04:44:39.949 ServerApp] jupyter_server_proxy | extension was successfully linked.
[I 2021-09-17 04:44:39.957 ServerApp] jupyterlab | extension was successfully linked.
[W 2021-09-17 04:44:39.959 NotebookApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-09-17 04:44:39.959 NotebookApp] 'port' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-09-17 04:44:39.959 NotebookApp] 'port' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[I 2021-09-17 04:44:40.603 ServerApp] nbclassic | extension was successfully linked.
[I 2021-09-17 04:44:40.654 ServerApp] nbclassic | extension was successfully loaded.
[I 2021-09-17 04:44:40.655 ServerApp] dask_labextension | extension was successfully loaded.
[I 2021-09-17 04:44:40.660 ServerApp] jupyter_server_proxy | extension was successfully loaded.
[I 2021-09-17 04:44:40.661 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.8/site-packages/jupyterlab
[I 2021-09-17 04:44:40.661 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 2021-09-17 04:44:40.663 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-09-17 04:44:40.663 ServerApp] Serving notebooks from local directory: /home/jovyan
[I 2021-09-17 04:44:40.663 ServerApp] Jupyter Server 1.10.2 is running at:
[I 2021-09-17 04:44:40.663 ServerApp] http://jupyter-test:8888/lab?token=54c6a9ee2e64588d57492189e6a8ba2f7c0ad8a556a44498
[I 2021-09-17 04:44:40.663 ServerApp]  or http://127.0.0.1:8888/lab?token=54c6a9ee2e64588d57492189e6a8ba2f7c0ad8a556a44498
[I 2021-09-17 04:44:40.663 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2021-09-17 04:44:40.665 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///home/jovyan/.local/share/jupyter/runtime/jpserver-7-open.html
    Or copy and paste one of these URLs:
        http://jupyter-test:8888/lab?token=54c6a9ee2e64588d57492189e6a8ba2f7c0ad8a556a44498
     or http://127.0.0.1:8888/lab?token=54c6a9ee2e64588d57492189e6a8ba2f7c0ad8a556a44498
[W 2021-09-17 04:44:41.225 ServerApp] 404 GET /user/test (172.17.0.12) 28.72ms referer=http://127.0.0.1:8001/hub/spawn-pending/test

consideRatio · 2021-09-17T05:45:55Z

Is jupyterhub-singleuser a conda package? I think jupyterhub-base is one. Are you sure you startup with the latest jupyterhub-singleuser script? The extra package thing must install the extra packages before running the jupyterhub-singleuser script that bundles as an entrypoint part of the python package jupyterhub, and jupyterhub-base contain that without dependecies like node only relevant if you run jh locally etc.

I think w. K8s 1.22, you need a new release of dask-gateway helm chart for several reasons, ive fixed them in current main branch but its not released yet.

There are also other things to fix, such disabling hub.networkPolicy.enabled=false, also fixed in latest main.

All help working towards a release of dask/dask-gateway appreciated.

jacobtomlinson · 2021-09-17T09:31:28Z

When I raised this issue I had successfully created a custom image (based on RAPIDS) which just added dask-gateway and jupyterhub-singleuser. Although I can't seem to find it now.

Is jupyterhub-singleuser a conda package?

Yeah

All help working towards a release of dask/dask-gateway appreciated.

This came up again at the Dask maintainers meeting this week. We are blocked with @jcrist being the only person who can do this. It looks like Jim should have some time for this soon though.

chrisroat · 2021-09-17T12:36:17Z

OK, so it sounds like there is still some work to do here. Deferring discussion of dask-gateway (for the moment -- let's come back to that), what needs to be done just to get jupyter working?

The base-notebook Dockerfile has:

# Configure container startup
ENTRYPOINT ["tini", "-g", "--"]
CMD ["start-notebook.sh"]

On the raw jupyter front, the dask entrypoint runs a prepare.sh script instead of tini, that installs packages and then does:

dask-docker/notebook/prepare.sh

Line 36 in 490c810

exec start.sh jupyter lab ${JUPYTERLAB_ARGS}

It seems tricky to do all 3:

install packages
keep the tini entrypoint
run start-singleuser.sh

Would switching prepare.sh to use exec start-singleuser.sh ${JUPYTERLAB_ARG} be acceptable (it continues to skip tini)?

jacobtomlinson · 2021-09-17T13:04:23Z

Can we not change the entrypoint to prepare.sh start-singleuser.sh ${JUPYTERLAB_ARG}? The prepare script executes $@ anyway. We still lose tini here, but is that a big problem?

chrisroat · 2021-09-17T13:09:01Z

I think you are looking at the wrong prepare script. The one I referenced is in the notebook subdirectory. It's a bit convoluted -- maybe we should cleanup the prepare/entrypoint/cmd here.

chrisroat · 2021-09-17T13:10:32Z

I just verified that switching to exec start-singleuser.sh ${JUPYTERLAB_ARG} makes things work again -- no 404s.

chrisroat · 2021-09-17T13:55:12Z

It seems singleuser.defaultUrl isn't working to set the default to lab. Maybe it's related to
jupyterhub/kubespawner#493

jacobtomlinson mentioned this issue Feb 22, 2021

Inheriting from these images pangeo-data/pangeo-docker-images#187

Closed

jacobtomlinson mentioned this issue Jul 15, 2021

dask-gateway image far behind mainline dask version. dask/dask-gateway#405

Closed

jacobtomlinson added the enhancement label Aug 17, 2021

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Add new image for Dask hub #144

Add new image for Dask hub #144

jacobtomlinson commented Feb 22, 2021

jrbourbeau commented Feb 22, 2021

chrisroat commented Sep 17, 2021 •

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chrisroat commented Sep 17, 2021

Add new image for Dask hub #144

Add new image for Dask hub #144

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