Share data between JupyterHub users with Manila shares


December 5, 2022

This work has been supported by Indiana University and is cross-posted on the Jetstream 2 official documentation website.

In the standard deployment of JupyterHub on top of Kubernetes on Jetstream 2, each user has access to their own home folder, but there is no built-in way to share data between users.

One option is to install a NFS server as a service in Kubernetes. However, Jetstream offers a managed service, named Manila, that offers the sharing capability out-of-the-box.

Therefore we can lower the maintenance burden by creating a shared volume inside Manila and then mount it on any Kubernetes or JupyterHub pod, so that users can access shared data read-only or read-write.

Create a Share in Manila

Create a share in Horizon following the instructions in the Jetstream documentation:

  • for access to choose “$USER-manila-share”
  • note down “Path” and “Access Key”

Test in a Pod

First we want to test the connection with a pod, which is also useful to perform administrative tasks on the volume.

You can find all the necessary files in this Github repository.

Copy the access key into ceph-secret.yml, then create the secret with:

kubectl create -f ceph-secret.yml

Then split the “Path” string you copied from Horizon into the different servers and the path and copy them to ceph-pod.yml and:

kubectl create -f ceph-pod.yml

Access the shared volume with:

kubectl exec --stdin -n jhub --tty ceph -- /bin/bash
cd /mnt/cephfs

This container executes as root, so you should have write access to the share, instead, the JupyterHub users use the jovyan user, so we need to create a folder owned by jovyan to give them write access, all other folders will be read-only:

mkdir readonly
mkdir readwrite
chown 1000:100 readwrite

so we should have:

root@cephfs-pod:/mnt/cephfs# ls -la
total 6
drwxr-xr-x 4  119   126    0 Dec  1 00:48 .
drwxr-xr-x 1 root root  4096 Nov 30 23:50 ..
drwxr-xr-x 2 root root     0 Dec  1 00:04 readonly
drwxr-xr-x 2 1000 users    0 Dec  1 00:07 readwrite

Configure JupyterHub

We can finally configure JupyterHub to mount this volume, if you have followed the JupyterHub deployment tutorial, you should have your script, edit it to also add an additional configuration file:


helm upgrade --install $RELEASE jupyterhub/jupyterhub \
      --namespace $NAMESPACE  \
      --create-namespace \
      --version 1.2.0 \
      --debug \
      --values config_standard_storage.yaml --values secrets.yaml \
      --values manila/jupyterhub_manila.yaml

manila/jupyterhub_manila.yaml contains the same configuration of ceph-pod.yml, so you can copy-paste from there.

Now you should be able to access the shared folders from a JupyterHub single user session:

jovyan@jupyter-zonca:~$ cd /share
jovyan@jupyter-zonca:/share$ ls -lah
total 5.5K
drwxr-xr-x 4    119   126    0 Dec  1 00:48 .
drwxr-xr-x 1 root   root  4.0K Nov 30 23:48 ..
drwxr-xr-x 2 root   root     0 Dec  1 00:04 readonly
drwxr-xr-x 2 jovyan users    0 Dec  1 00:07 readwrite
jovyan@jupyter-zonca:/share$ touch readwrite/myfile
jovyan@jupyter-zonca:/share$ touch readonly/myfile
touch: cannot touch 'readonly/myfile': Permission denied