Try to make eWatercycle environment + nbgrader run in kubernetes

apptainer.yaml

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+apiVersion: v1
+kind: Pod
+metadata:
+  name: apptainer
+spec:
+  securityContext:
+    runAsUser: 1000
+    runAsNonRoot: true
+  restartPolicy: Never
+  containers:
+  - name: apptainercontainer
+    image: ghcr.io/ewatercycle/teaching:latest
+    # command: 
+    #   - apptainer
+    #   - run
+    #   - docker://alpine:latest cat /etc/os-release
+    securityContext:
+      allowPrivilegeEscalation: true
+      privileged: true
+    resources:
+      limits:
+        cpu: "1"
+        memory: "4Gi"

rclone.yaml.example

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+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: data-rclone-example
+  labels:
+    name: data-rclone-example
+spec:
+  accessModes:
+  - ReadOnlyMany
+  storageClassName: rclone
+  capacity:
+    storage: 10Gi
+  csi:
+    driver: csi-rclone
+    volumeHandle: data-id
+    volumeAttributes:
+      remote: "my-dcache"
+      remotePath: "/"
+      # TODO pass --read-only and --cache-dir
+      configData: |
+        [my-dcache]
+        type = webdav
+        url = https://webdav.grid.surfsara.nl:2880
+        vendor = other
+        user =
+        pass = 
+        bearer_token = ....
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: data-rclone-example
+spec:
+  accessModes:
+  - ReadOnlyMany
+  resources:
+    requests:
+      storage: 10Gi
+  storageClassName: rclone
+  selector:
+    matchLabels:
+      name: data-rclone-example
+
+# From ewc infra
+# # /usr/bin/rclone mount \
+#             --config=/etc/rclone.conf \
+#             --allow-other \
+#             --read-only \
+#             --cache-dir {{ rclone_cache_dir }} \
+#             --vfs-cache-max-size {{ rclone_max_gsize }}G\
+#             --vfs-cache-mode full \
+#             {{ dcache_rclone_name }}:{{ dcache_root }} {{ data_root }}
+
+# From jupyter server log
+ # rclone mount 
+#  my-dcache:/ 
+#  /var/snap/microk8s/common/var/lib/kubelet/pods/81d7b6af-b58d-4eef-87f3-e97a0afec474/volumes/kubernetes.io~csi/data-rclone-example/mount 
+#  --daemon 
+#  --config /tmp/rclone.conf3139822866 
+#  --dir-cache-time=5s --vfs-cache-mode=writes 
+#  --allow-non-empty=true --allow-other=true 
+#  --cache-info-age=72h --cache-chunk-clean-interval=15m
+
+#   Warning  FailedMount             21s   kubelet                  
+# MountVolume.SetUp failed for volume "data-rclone-example" : rpc error: code = Internal desc = mounting failed: exit status 1 cmd:
+# 'rclone' remote: 'my-dcache:/' targetpath: /var/snap/microk8s/common/var/lib/kubelet/pods/ae09680d-d77b-462a-8146-61d817ac3451/volumes/kubernetes.io~csi/data-rclone-example/mount 
+# output: "2024/02/06 14:36:37 Fatal error: mount not ready\n"

vagrant/.gitignore

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+config.yaml
+.vagrant/
+rclone.yaml

vagrant/Dockerfile

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+# docker build -t ghcr.io/ewatercycle/teaching:latest .
+# docker run -ti --rm --privileged ghcr.io/ewatercycle/teaching:latest bash
+
+# Folowing does not work 
+# docker run -ti --rm --cap-add SYS_ADMIN --cap-add MKNOD --cap-add SYS_CHROOT --cap-add SETFCAP  ghcr.io/ewatercycle/teaching:latest bash
+# apptainer run docker://ghcr.io/ewatercycle/leakybucket-grpc4bmi:v0.0.1
+# FATAL:   container creation failed: mount hook function failure: mount /proc/self/fd/3->/var/lib/apptainer/mnt/session/rootfs error: while mounting image /proc/self/fd/3: squashfuse_ll exited with status 1: fuse: device not found, try 'modprobe fuse' first
+
+# apptainer pull docker://ghcr.io/ewatercycle/leakybucket-grpc4bmi:v0.0.1
+# ipython
+# from grpc4bmi.bmi_client_apptainer import BmiClientApptainer
+# model = BmiClientApptainer('docker://ghcr.io/ewatercycle/leakybucket-grpc4bmi:v0.0.1', work_dir='/tmp')
+# model.get_component_name()
+# del model
+
+# echo $CR_PAT | docker login ghcr.io -u sverhoeven --password-stdin
+# docker push ghcr.io/ewatercycle/teaching:latest
+
+FROM jupyter/minimal-notebook:latest
+
+LABEL org.opencontainers.image.source=https://github.com/eWaterCycle/teaching
+LABEL org.opencontainers.image.description="eWatercycle teaching"
+LABEL org.opencontainers.image.licenses=Apache-2.0
+
+USER root
+
+# install apptainer or podman
+# RUN apt update && apt install -y podman && ln -s /usr/bin/podman /usr/bin/docker
+RUN apt update && apt install -y libfuse2 uidmap squashfs-tools squashfuse fuse2fs fuse-overlayfs fakeroot 
+RUN wget https://github.com/apptainer/apptainer/releases/download/v1.2.5/apptainer_1.2.5_amd64.deb && \
+dpkg -i apptainer_1.2.5_amd64.deb && rm apptainer_1.2.5_amd64.deb
+
+# install ngshare stuff
+COPY nbgrader_config.py /etc/jupyter/nbgrader_config.py
+# need fork of ngshare to work with latest jupyter
+RUN mamba install -y nbgrader && pip install git+https://github.com/lauri3k/ngshare_exchange.git#master
+
+# install ewatercycle + its deps
+RUN mamba install -y esmvaltool-python && pip install ewatercycle-leakybucket
+# TODO other models and utils
+
+# TODO install extra jupyter extensions like lsp
+
+USER 1000