Base image with python version equal or greater than 3.7

[jonDel]

From now, the last version of the minimal notebook is based on python 3.6, s2i-minimal-notebook-py36
How about a s2i-minimal-notebook-py37, s2i-minimal-notebook-py38, etc?
I tried to search the s2i-minimal-notebook-py36 Dockerfile for building my own container with python 3.8, but couldn't find it. Any clues here?

[GrahamDumpleton]

Use the Jupyter Project images:

• https://github.com/jupyter-on-openshift/jupyterhub-quickstart#using-the-jupyter-project-notebook-images

[jonDel]

I tried the tutorial using the official images from jupyter project, but that did not work. The notebook container did not go up, complaining that some shelI script is not present. I then ran containers from both images, s2i-minimal-notebook-py36 and jupyter/minimal-notebook and took a peek inside them. It saw that indeed, the jupyter folder is very different comparing s2i-minimal-notebook-py36 and jupyter/minimal-notebook. A lot of files missing from jupyter/minimal-notebook that breaks the deployment.

[GrahamDumpleton]

You are not providing sufficient information about what you are trying to do. If you are trying to use the Jupyter project images as an S2I builder with the mechanism described with this repository, you can't. For using S2I with Jupyter project images see:

• https://github.com/jupyter/docker-stacks/tree/master/examples/source-to-image

Also see:

• https://github.com/jupyter/docker-stacks/tree/master/examples/openshift

for general details of standalone deployment of Jupyter project images on OpenShift.

The link I provided above previously is specifically related to using the Jupyter project images with JupyterHub on OpenShift. I provided that since had to guess what it is you are trying to do due to the lack of details provided.

[jonDel]

I am trying to follow the tutorial in https://github.com/jupyter-on-openshift/jupyterhub-quickstart , more specifically using the Multi User Developer Workspace template. I do get successful using the s2i-minimal-notebook-py36 as a base image for the notebooks. But I want to use a python 3.8 base image, so I tried https://github.com/jupyter-on-openshift/jupyterhub-quickstart#using-the-jupyter-project-notebook-images, using the jupyter/minimal-notebook image with python 3,.8. However, even following the instructions:

If you still want to run the official Jupyter Project notebook images, you can, but you will need to supply additional configuration to the KubeSpawner plugin for these images to have them work. ... The special setting is supplemental_gids, with it needing to be set to include the UNIX group ID of 100.

it wont work, since there are a lot of files missing from jupyter/minimal-notebook that breaks the deployment.

[GrahamDumpleton]

As I already said, you need to properly explain "it wont work". I can't guess what the problem is. You need to explain properly what you added to your configuration and what errors you are getting and where.

[jonDel]

The event log when the hub tries to start a server with the image jupyter/minimal-notebook (https://hub.docker.com/r/jupyter/minimal-notebook) :

Your server is starting up.

You will be redirected automatically when it's ready for you.
Event log
Server requested
2020-08-25 17:51:42+00:00 [Warning] pod has unbound PersistentVolumeClaims (repeated 4 times)
2020-08-25 17:51:42+00:00 [Normal] Successfully assigned jupyterhub/jupyterhub-nb-*** to ****
2020-08-25 17:51:45+00:00 [Normal] pulling image "***/jupyter-minimal-notebook@sha256:***"
2020-08-25 17:52:21+00:00 [Normal] Successfully pulled image "***/jupyter-minimal-notebook@sha256:***"
2020-08-25 17:52:33+00:00 [Normal] Created container
2020-08-25 17:52:34+00:00 [Warning] Error: failed to start container "setup-volume": Error response from daemon: oci runtime 
  error: container_linux.go:247: 
  starting container process caused "exec: \"/opt/app-root/bin/setup-volume.sh\": 
  stat /opt/app-root/bin/setup-volume.sh: no such file or directory"

As I said, the file structure of images jupyter/minimal-notebook and s2i-minimal-notebook-py36 are very different, as jupyter/minimal-notebook uses conda.

Running a container with s2i-minimal-notebook-py36 image:

(app-root) bash-4.2$ ls /opt/app-root/bin/
activate	  dask-submit		 jsonschema		   jupyter-labhub	    mako-render       pip		setup-volume.sh		stop-supervisord.sh
activate.csh	  dask-worker		 jupyter		   jupyter-migrate	    mod_wsgi-express  pip3		start-daskscheduler.sh	supervisorctl
activate.fish	  easy_install		 jupyter-bundlerextension  jupyter-nbconvert	    oc		      pip3.6		start-daskworker.sh	supervisord
activate_this.py  easy_install-3.6	 jupyterhub		   jupyter-nbextension	    oc-3.11	      pygmentize	start-gateway.sh	wheel
alembic		  echo_supervisord_conf  jupyterhub-singleuser	   jupyter-notebook	    oc-4.0	      pyjson5		start-kernelgateway.sh
certipy		  iptest		 jupyter-kernel		   jupyter-run		    oc-4.1	      python		start-lab.sh
chardetect	  iptest3		 jupyter-kernelgateway	   jupyter-serverextension  oc-4.2	      python3		start-notebook.sh
dask-remote	  ipython		 jupyter-kernelspec	   jupyter-troubleshoot     oc-4.3	      python3.6		start.sh
dask-scheduler	  ipython3		 jupyter-lab		   jupyter-trust	    oc-wrapper.sh     python-config	start-singleuser.sh
dask-ssh	  jlpm			 jupyter-labextension	   kustomize		    pidproxy	      setup-environ.sh	start-webdav.sh

(app-root) bash-4.2$

Running a container with jupyter/minimal-notebook image:

jovyan@b605b1da3c86:~$ ls /opt/app-root/bin/
ls: cannot access '/opt/app-root/bin/': No such file or directory
jovyan@b605b1da3c86:~$ ls /opt/conda/bin/
2to3                     c_rehash      infocmp                   jupyter-labhub           ksu       mako-render       pydoc3            tclsh                           xz
2to3-3.8                 curl-config   infotocap                 jupyter-migrate          kswitch   ncurses6-config   pydoc3.8          tclsh8.6                        xzcat
acountry                 curve_keygen  iptest                    jupyter-nbconvert        ktutil    ncursesw6-config  pygmentize        tic                             xzcmp
activate                 deactivate    iptest3                   jupyter-nbextension      kvno      nghttp            pyjson5           tini                            xzdec
adig                     derb          ipython                   jupyter-notebook         lzcat     nghttpd           pyjwt             toe                             xzdiff
ahost                    easy_install  ipython3                  jupyter-run              lzcmp     nghttpx           python            tput                            xzegrep
alembic                  genbrk        jlpm                      jupyter-serverextension  lzdiff    node              python3           tqdm                            xzfgrep
captoinfo                gencfu        jsonschema                jupyter-troubleshoot     lzegrep   npm               python3.8         tset                            xzgrep
certipy                  gencnval      jupyter                   jupyter-trust            lzfgrep   npx               python3.8-config  unlzma                          xzless
chardetect               gendict       jupyter-bundlerextension  k5srvutil                lzgrep    openssl           python3-config    unxz                            xzmore
clear                    genrb         jupyterhub                kadmin                   lzless    pandoc            reset             uuclient
compile_et               gss-client    jupyterhub-singleuser     kdestroy                 lzma      pandoc-citeproc   sclient           wheel
conda                    icu-config    jupyter-kernel            kinit                    lzmadec   pip               sim_client        wish
conda-env                icuinfo       jupyter-kernelspec        klist                    lzmainfo  pip3              sqlite3           wish8.6
configurable-http-proxy  idle3         jupyter-lab               kpasswd                  lzmore    pkgdata           sqlite3_analyzer  x86_64-conda_cos6-linux-gnu-ld
cph                      idle3.8       jupyter-labextension      krb5-config              makeconv  pydoc             tabs              x86_64-conda-linux-gnu-ld

[GrahamDumpleton]

You can't use the latter recipe for persistent storage in:

• https://github.com/jupyter-on-openshift/jupyterhub-quickstart#allocating-persistent-storage-to-users

with the Jupyter project images. That is, the one relying on setup-volume.sh.

For Jupyter project images, you also need to change the first recipe to:

c.KubeSpawner.user_storage_pvc_ensure = True

c.KubeSpawner.pvc_name_template = '%s-nb-{username}' % c.KubeSpawner.hub_connect_ip
c.KubeSpawner.user_storage_capacity = '1Gi'

c.KubeSpawner.volumes = [
    {
        'name': 'data',
        'persistentVolumeClaim': {
            'claimName': c.KubeSpawner.pvc_name_template
        }
    }
]

c.KubeSpawner.volume_mounts = [
    {
        'name': 'data',
        'mountPath': '/home/jovyan'
    }
]

That is, different mount point for persistent volume.

[jonDel]

Thank you Graham, I will give it a try and come back as soon as I have a result.

[jonDel]

I still got the same error. I seems the KubeSpawner always tries to execute the "setup-volume.sh" command, even when I explicitly declare "c.KubeSpawner.cmd" in the jupyterhub_config,py file.

[GrahamDumpleton]

It isn't c.KubeSpawner.cmd that is going to be the problem. It is going to be because you are setting c.KubeSpawner.singleuser_init_containers.

As I said above, don't use the second recipe which invokes setup-volume.sh listed in:

• https://github.com/jupyter-on-openshift/jupyterhub-quickstart#allocating-persistent-storage-to-users