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Add persistent volume configuration to jupyter #78

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Add persistent volume configuration to jupyter #78

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641ee72
Add persistent volume configuration to jupyter
wabscale Jul 10, 2020
a9bc794
FIX persistent directory permissions with initContainer
wabscale Jul 11, 2020
e256a14
ADD optional initContainer, 755 permissions and default pv path to jo…
wabscale Jul 13, 2020
17c9aad
ADD persistent volume options to README
wabscale Jul 13, 2020
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35 changes: 35 additions & 0 deletions dask/templates/dask-jupyter-deployment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,15 @@ spec:
spec:
imagePullSecrets:
{{- toYaml .Values.jupyter.image.pullSecrets | nindent 8 }}
{{- if .Values.jupyter.persistent.enable }}
initContainers:
- name: {{ .Release.Name }}-jupyter-volume-permissions
image: busybox:1.31.1
command: ["sh", "-c", "chmod -Rv 777 /data/ && chown 0:100 -R /data/"]
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Setting permissions to 777 is generally a bad idea. You may find 755 is more appropriate.

However could you provide a little explaination why this is necessary at all?

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The storage class that I am using is longhorn. The volumes they give you are owned by root by default. That init container sets the permissions so that the jovyan user can read and write to the PV.

I'm not aware of any storage classes that let you explicitly set the default ownership. I will add an option so its easy to disable this init container if desired.

volumeMounts:
- name: jupyter-persistent
mountPath: /data
{{- end }}
containers:
- name: {{ template "dask.fullname" . }}-jupyter
image: "{{ .Values.jupyter.image.repository }}:{{ .Values.jupyter.image.tag }}"
Expand All @@ -43,6 +52,10 @@ spec:
volumeMounts:
- name: config-volume
mountPath: /usr/local/etc/jupyter
{{- if .Values.jupyter.persistent.enable }}
- name: jupyter-persistent
mountPath: {{ .Values.jupyter.persistent.path }}
{{- end }}
env:
- name: DASK_SCHEDULER_ADDRESS
value: {{ template "dask.fullname" . }}-scheduler:{{ .Values.scheduler.servicePort }}
Expand All @@ -53,6 +66,11 @@ spec:
- name: config-volume
configMap:
name: {{ template "dask.fullname" . }}-jupyter-config
{{- if .Values.jupyter.persistent.enable }}
- name: jupyter-persistent
persistentVolumeClaim:
claimName: {{ .Release.Name }}-jupyter-persistent
{{- end }}
{{- with .Values.jupyter.nodeSelector }}
nodeSelector:
{{- toYaml . | nindent 8 }}
Expand All @@ -72,4 +90,21 @@ spec:
{{- if .Values.jupyter.serviceAccountName }}
serviceAccountName: {{ .Values.jupyter.serviceAccountName | quote }}
{{- end }}
{{- if .Values.jupyter.persistent.enable }}
---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: {{ .Release.Name }}-jupyter-persistent
spec:
{{- if (not (eq .Values.jupyter.persistent.storageClass "default")) }}
storageClassName: {{ .Values.jupyter.persistent.storageClass }}
{{- end }}
accessModes:
- ReadWriteOnce
resources:
requests:
storage: {{ .Values.jupyter.persistent.size }}
{{- end }}

{{- end }}
5 changes: 5 additions & 0 deletions dask/values.yaml
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Expand Up @@ -97,6 +97,11 @@ jupyter:
servicePort: 80
# This hash corresponds to the password 'dask'
password: 'sha1:aae8550c0a44:9507d45e087d5ee481a5ce9f4f16f37a0867318c'
persistent:
enable: false
storageClass: "default"
size: 1Gi
path: /home/jovyan/persistent
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I would recommend making this just /home/jovyan

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I was trying to explicitly not overwrite the examples directory with the pv. I see your point though, it would be much clearer to the user if the entire home directory is whats saved.

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The examples are created at runtime. So this should've be a problem.

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When I make the mount path /home/jovyan the examples do not show up.

Checking the Dockerfile from the dask-docker repo shows they are added at build time.

https://github.com/dask/dask-docker/blob/master/notebook/Dockerfile#L47

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Oh interesting. I must be thinking of the Pangeo helm chart.

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I'm wondering how you want to handle this. I can submit a PR to the docker-helm repo to copy the examples to another directory (say /usr/share/doc/dask-examples). That way they would be independent of the PV, and always available.

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Hey @jacobtomlinson how would you wan tot handle this?

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I can submit a PR to the docker-helm repo to copy the examples to another directory (say /usr/share/doc/dask-examples).

The trouble with this is discoverability. Really they need to show up in the sidebar.

Perhaps adding them to that location and then adding a line to the prepare.sh script to create a symbolic link would work?

env:
# - name: EXTRA_CONDA_PACKAGES
# value: "numba xarray -c conda-forge"
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