User pvc storage gets deleted on culling

franklin-degirum commented 2 years ago

How can I retain the user storage every time the server is culled and when they login again they get to access their previous runtime files. I tried looking at the jupyterhub_idle_culler.py but not really much options just to delete the server and not the storage. Would like to know if there is an existing feature or any workaround for it.

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consideRatio commented 2 years ago

PVCs are not supposed to be deleted, and I don't think they are when using this Helm chart to deploy JupyterHub with KubeSpawner behind the scenes, but if that happens its a serious bug. Can you describe further how you have configured a deployment of JupyterHub where you experience this?

franklin-degirum commented 2 years ago

I pretty much use the default configuration given in the z2jh documentation except for the Auth0 and LetsEncrypt. I also am using the culling service. when I logout, I'm able to get access to my PVC storage when I login again but when the idle-cull service shuts it down or I manually shut the server down, and try starting the server again its a new empty volume with the same volume name.

manics commented 2 years ago

Can you show us your full configuration, and tell us the version of Z2JH? PVCs may be deleted for named servers, or if the user is deleted (which may be done by the idle-culler, that's why it would be helpful to see your config).

franklin-degirum commented 2 years ago

This is my helm version - version.BuildInfo{Version:"v3.5.0", GitCommit:"32c22239423b3b4ba6706d450bd044baffdcf9e6", GitTreeState:"clean", GoVersion:"go1.15.6"} below is my full configuration except the part for auth0 and letsencrypt:

# fullnameOverride and nameOverride distinguishes blank strings, null values,
# and non-blank strings. For more details, see the configuration reference.
fullnameOverride: ""
nameOverride:

# custom can contain anything you want to pass to the hub pod, as all passed
# Helm template values will be made available there.
custom: {}

# imagePullSecret is configuration to create a k8s Secret that Helm chart's pods
# can get credentials from to pull their images.
imagePullSecret:
  create: false
  automaticReferenceInjection: true
  registry:
  username:
  password:
  email:
# imagePullSecrets is configuration to reference the k8s Secret resources the
# Helm chart's pods can get credentials from to pull their images.
imagePullSecrets: []

# hub relates to the hub pod, responsible for running JupyterHub, its configured
# Authenticator class KubeSpawner, and its configured Proxy class
# ConfigurableHTTPProxy. KubeSpawner creates the user pods, and
# ConfigurableHTTPProxy speaks with the actual ConfigurableHTTPProxy server in
# the proxy pod.
hub:
  config:
    JupyterHub:
      admin_access: true
      authenticator_class: dummy
  service:
    type: ClusterIP
    annotations: {}
    ports:
      nodePort:
    extraPorts: []
    loadBalancerIP:
  baseUrl: /
  cookieSecret:
  initContainers: []
  fsGid: 1000
  nodeSelector: {}
  tolerations: []
  concurrentSpawnLimit: 64
  consecutiveFailureLimit: 5
  activeServerLimit:
  deploymentStrategy:
    ## type: Recreate
    ## - sqlite-pvc backed hubs require the Recreate deployment strategy as a
    ##   typical PVC storage can only be bound to one pod at the time.
    ## - JupyterHub isn't designed to support being run in parallell. More work
    ##   needs to be done in JupyterHub itself for a fully highly available (HA)
    ##   deployment of JupyterHub on k8s is to be possible.
    type: Recreate
  db:
    type: sqlite-pvc
    upgrade:
    pvc:
      annotations: {}
      selector: {}
      accessModes:
        - ReadWriteOnce
      storage: 1Gi
      subPath:
      storageClassName:
    url:
    password:
  labels: {}
  annotations: {}
  command: []
  args: []
  extraConfig: {}
  extraFiles: {}
  extraEnv: {}
  extraContainers: []
  extraVolumes: []
  extraVolumeMounts: []
  image:
    name: jupyterhub/k8s-hub
    tag: "1.2.0"
    pullPolicy:
    pullSecrets: []
  resources: {}
  containerSecurityContext:
    runAsUser: 1000
    runAsGroup: 1000
    allowPrivilegeEscalation: false
  lifecycle: {}
  services: {}
  pdb:
    enabled: false
    maxUnavailable:
    minAvailable: 1
  networkPolicy:
    enabled: true
    ingress: []
    ## egress for JupyterHub already includes Kubernetes internal DNS and
    ## access to the proxy, but can be restricted further, but ensure to allow
    ## access to the Kubernetes API server that couldn't be pinned ahead of
    ## time.
    ##
    ## ref: https://stackoverflow.com/a/59016417/2220152
    egress:
      - to:
          - ipBlock:
              cidr: 0.0.0.0/0
    interNamespaceAccessLabels: ignore
    allowedIngressPorts: []
  allowNamedServers: false
  namedServerLimitPerUser:
  authenticatePrometheus:
  redirectToServer:
  shutdownOnLogout:
  templatePaths: []
  templateVars: {}
  livenessProbe:
    # The livenessProbe's aim to give JupyterHub sufficient time to startup but
    # be able to restart if it becomes unresponsive for ~5 min.
    enabled: true
    initialDelaySeconds: 300
    periodSeconds: 10
    failureThreshold: 30
    timeoutSeconds: 3
  readinessProbe:
    # The readinessProbe's aim is to provide a successful startup indication,
    # but following that never become unready before its livenessProbe fail and
    # restarts it if needed. To become unready following startup serves no
    # purpose as there are no other pod to fallback to in our non-HA deployment.
    enabled: true
    initialDelaySeconds: 0
    periodSeconds: 2
    failureThreshold: 1000
    timeoutSeconds: 1
  existingSecret:
  serviceAccount:
    annotations: {}
  extraPodSpec: {}

rbac:
  enabled: true

# proxy relates to the proxy pod, the proxy-public service, and the autohttps
# pod and proxy-http service.
proxy:
  secretToken:
  annotations: {}
  deploymentStrategy:
    ## type: Recreate
    ## - JupyterHub's interaction with the CHP proxy becomes a lot more robust
    ##   with this configuration. To understand this, consider that JupyterHub
    ##   during startup will interact a lot with the k8s service to reach a
    ##   ready proxy pod. If the hub pod during a helm upgrade is restarting
    ##   directly while the proxy pod is making a rolling upgrade, the hub pod
    ##   could end up running a sequence of interactions with the old proxy pod
    ##   and finishing up the sequence of interactions with the new proxy pod.
    ##   As CHP proxy pods carry individual state this is very error prone. One
    ##   outcome when not using Recreate as a strategy has been that user pods
    ##   have been deleted by the hub pod because it considered them unreachable
    ##   as it only configured the old proxy pod but not the new before trying
    ##   to reach them.
    type: Recreate
    ## rollingUpdate:
    ## - WARNING:
    ##   This is required to be set explicitly blank! Without it being
    ##   explicitly blank, k8s will let eventual old values under rollingUpdate
    ##   remain and then the Deployment becomes invalid and a helm upgrade would
    ##   fail with an error like this:
    ##
    ##     UPGRADE FAILED
    ##     Error: Deployment.apps "proxy" is invalid: spec.strategy.rollingUpdate: Forbidden: may not be specified when strategy `type` is 'Recreate'
    ##     Error: UPGRADE FAILED: Deployment.apps "proxy" is invalid: spec.strategy.rollingUpdate: Forbidden: may not be specified when strategy `type` is 'Recreate'
    rollingUpdate:
  # service relates to the proxy-public service
  service:
    type: LoadBalancer
    labels: {}
    annotations: {}
    nodePorts:
      http:
      https:
    disableHttpPort: false
    extraPorts: []
    loadBalancerIP: <here goes my load balancer IP>
    loadBalancerSourceRanges: []
  # chp relates to the proxy pod, which is responsible for routing traffic based
  # on dynamic configuration sent from JupyterHub to CHP's REST API.
  chp:
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    image:
      name: jupyterhub/configurable-http-proxy
      tag: 4.5.0 # https://github.com/jupyterhub/configurable-http-proxy/releases
      pullPolicy:
      pullSecrets: []
    extraCommandLineFlags: []
    livenessProbe:
      enabled: true
      initialDelaySeconds: 60
      periodSeconds: 10
    readinessProbe:
      enabled: true
      initialDelaySeconds: 0
      periodSeconds: 2
      failureThreshold: 1000
    resources: {}
    defaultTarget:
    errorTarget:
    extraEnv: {}
    nodeSelector: {}
    tolerations: []
    networkPolicy:
      enabled: true
      ingress: []
      egress:
        - to:
            - ipBlock:
                cidr: 0.0.0.0/0
      interNamespaceAccessLabels: ignore
      allowedIngressPorts: [http, https]
    pdb:
      enabled: false
      maxUnavailable:
      minAvailable: 1
    extraPodSpec: {}
  # traefik relates to the autohttps pod, which is responsible for TLS
  # termination when proxy.https.type=letsencrypt.
  traefik:
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    image:
      name: traefik
      tag: 2.6.0 # ref: https://hub.docker.com/_/traefik?tab=tags
      pullPolicy:
      pullSecrets: []
    hsts:
      includeSubdomains: false
      preload: false
      maxAge: 15724800 # About 6 months
    resources: {}
    labels: {}
    extraEnv: {}
    extraVolumes: []
    extraVolumeMounts: []
    extraStaticConfig: {}
    extraDynamicConfig: {}
    nodeSelector: {}
    tolerations: []
    extraPorts: []
    networkPolicy:
      enabled: true
      ingress: []
      egress:
        - to:
            - ipBlock:
                cidr: 0.0.0.0/0
      interNamespaceAccessLabels: ignore
      allowedIngressPorts: [http, https]
    pdb:
      enabled: false
      maxUnavailable:
      minAvailable: 1
    serviceAccount:
      annotations: {}
    extraPodSpec: {}
  secretSync:
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    image:
      name: jupyterhub/k8s-secret-sync
      tag: "1.2.0"
      pullPolicy:
      pullSecrets: []
    resources: {}
  labels: {}
  https:
    enabled: false
    type: letsencrypt
    #type: letsencrypt, manual, offload, secret
    letsencrypt:
      contactEmail: 
      # Specify custom server here (https://acme-staging-v02.api.letsencrypt.org/directory) to hit staging LE
      acmeServer: https://acme-v02.api.letsencrypt.org/directory
    manual:
      key:
      cert:
    secret:
      name:
      key: tls.key
      crt: tls.crt
    hosts: []

# singleuser relates to the configuration of KubeSpawner which runs in the hub
# pod, and its spawning of user pods such as jupyter-myusername.
singleuser:
  podNameTemplate:
  extraTolerations: []
  nodeSelector: {}
  extraNodeAffinity:
    required: []
    preferred: []
  extraPodAffinity:
    required: []
    preferred: []
  extraPodAntiAffinity:
    required: []
    preferred: []
  networkTools:
    image:
      name: jupyterhub/k8s-network-tools
      tag: "1.2.0"
      pullPolicy:
      pullSecrets: []
  cloudMetadata:
    # block set to true will append a privileged initContainer using the
    # iptables to block the sensitive metadata server at the provided ip.
    blockWithIptables: true
    ip: 169.254.169.254
  networkPolicy:
    enabled: true
    ingress: []
    egress:
      # Required egress to communicate with the hub and DNS servers will be
      # augmented to these egress rules.
      #
      # This default rule explicitly allows all outbound traffic from singleuser
      # pods, except to a typical IP used to return metadata that can be used by
      # someone with malicious intent.
      - to:
          - ipBlock:
              cidr: 0.0.0.0/0
              except:
                - 169.254.169.254/32
    interNamespaceAccessLabels: ignore
    allowedIngressPorts: []
  events: true
  extraAnnotations: {}
  extraLabels:
    hub.jupyter.org/network-access-hub: "true"
  extraFiles: {}
  extraEnv: {}
  lifecycleHooks: 
    postStart:
      exec:
        command:
          - "sh"
          - "-c"
          - >
            <a folder copy to /srv/jupyterhub command goes here>

  initContainers: []
  extraContainers: []
  uid: 1000
  fsGid: 100
  serviceAccountName:
  storage:
    type: dynamic
    extraLabels: {}
    extraVolumes: []
    extraVolumeMounts: []
    static:
      pvcName:
      subPath: "{username}"
    capacity: 1Gi
    homeMountPath: /srv/jupyterhub
    dynamic:
      storageClass:
      pvcNameTemplate: claim-{username}{servername}
      volumeNameTemplate: volume-{username}{servername}
      storageAccessModes: [ReadWriteOnce]
  image:
    name: <my modified docker image>
    tag: "latest"
    pullPolicy:
    pullSecrets: []
  startTimeout: 300
  cpu:
    limit:
    guarantee:
  memory:
    limit:
    guarantee: 
  extraResource:
    limits: {}
    guarantees: {}
  cmd: jupyterhub-singleuser
  defaultUrl: /lab/tree/<my landing file>.ipynb
  extraPodConfig: {}
  profileList: []

# scheduling relates to the user-scheduler pods and user-placeholder pods.
scheduling:
  userScheduler:
    enabled: true
    replicas: 2
    logLevel: 4
    # plugins ref: https://kubernetes.io/docs/reference/scheduling/config/#scheduling-plugins-1
    plugins:
      score:
        disabled:
          - name: SelectorSpread
          - name: TaintToleration
          - name: PodTopologySpread
          - name: NodeResourcesBalancedAllocation
          - name: NodeResourcesLeastAllocated
          # Disable plugins to be allowed to enable them again with a different
          # weight and avoid an error.
          - name: NodePreferAvoidPods
          - name: NodeAffinity
          - name: InterPodAffinity
          - name: ImageLocality
        enabled:
          - name: NodePreferAvoidPods
            weight: 161051
          - name: NodeAffinity
            weight: 14631
          - name: InterPodAffinity
            weight: 1331
          - name: NodeResourcesMostAllocated
            weight: 121
          - name: ImageLocality
            weight: 11
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    image:
      # IMPORTANT: Bumping the minor version of this binary should go hand in
      #            hand with an inspection of the user-scheduelrs RBAC resources
      #            that we have forked.
      name: k8s.gcr.io/kube-scheduler
      tag: v1.19.13 # ref: https://github.com/kubernetes/website/blob/main/content/en/releases/patch-releases.md
      pullPolicy:
      pullSecrets: []
    nodeSelector: {}
    tolerations: []
    pdb:
      enabled: true
      maxUnavailable: 1
      minAvailable:
    resources: {}
    serviceAccount:
      annotations: {}
    extraPodSpec: {}
  podPriority:
    enabled: false
    globalDefault: false
    defaultPriority: 0
    userPlaceholderPriority: -10
  userPlaceholder:
    enabled: true
    image:
      name: k8s.gcr.io/pause
      # tag's can be updated by inspecting the output of the command:
      # gcloud container images list-tags k8s.gcr.io/pause --sort-by=~tags
      #
      # If you update this, also update prePuller.pause.image.tag
      tag: "3.5"
      pullPolicy:
      pullSecrets: []
    replicas: 0
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    resources: {}
  corePods:
    tolerations:
      - key: hub.jupyter.org/dedicated
        operator: Equal
        value: core
        effect: NoSchedule
      - key: hub.jupyter.org_dedicated
        operator: Equal
        value: core
        effect: NoSchedule
    nodeAffinity:
      matchNodePurpose: prefer
  userPods:
    tolerations:
      - key: hub.jupyter.org/dedicated
        operator: Equal
        value: user
        effect: NoSchedule
      - key: hub.jupyter.org_dedicated
        operator: Equal
        value: user
        effect: NoSchedule
    nodeAffinity:
      matchNodePurpose: prefer

# prePuller relates to the hook|continuous-image-puller DaemonsSets
prePuller:
  annotations: {}
  resources: {}
  containerSecurityContext:
    runAsUser: 65534 # nobody user
    runAsGroup: 65534 # nobody group
    allowPrivilegeEscalation: false
  extraTolerations: []
  # hook relates to the hook-image-awaiter Job and hook-image-puller DaemonSet
  hook:
    enabled: true
    pullOnlyOnChanges: true
    # image and the configuration below relates to the hook-image-awaiter Job
    image:
      name: jupyterhub/k8s-image-awaiter
      tag: "1.2.0"
      pullPolicy:
      pullSecrets: []
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    podSchedulingWaitDuration: 10
    nodeSelector: {}
    tolerations: []
    resources: {}
    serviceAccount:
      annotations: {}
  continuous:
    enabled: true
  pullProfileListImages: true
  extraImages: {}
  pause:
    containerSecurityContext:
      runAsUser: 65534 # nobody user
      runAsGroup: 65534 # nobody group
      allowPrivilegeEscalation: false
    image:
      name: k8s.gcr.io/pause
      # tag's can be updated by inspecting the output of the command:
      # gcloud container images list-tags k8s.gcr.io/pause --sort-by=~tags
      #
      # If you update this, also update scheduling.userPlaceholder.image.tag
      tag: "3.5"
      pullPolicy:
      pullSecrets: []

ingress:
  enabled: false
  annotations: {}
  hosts: []
  pathSuffix:
  pathType: Prefix
  tls: []

# cull relates to the jupyterhub-idle-culler service, responsible for evicting
# inactive singleuser pods.
#
# The configuration below, except for enabled, corresponds to command-line flags
# for jupyterhub-idle-culler as documented here:
# https://github.com/jupyterhub/jupyterhub-idle-culler#as-a-standalone-script
#
cull:
  enabled: true
  users: false # --cull-users
  removeNamedServers: false # --remove-named-servers
  timeout: 3600 # --timeout
  every: 1200 # --cull-every
  concurrency: 10 # --concurrency
  maxAge: 0 # --max-age

debug:
  enabled: true

global:
  safeToShowValues: false

franklin-degirum commented 2 years ago

If you'd like to know the exact jupyterhub image I am pulling, you can find and pull it from dockerhub - franklinmoses/dghub

consideRatio commented 2 years ago

If you configure this like this:

hub:
  config:
    KubeSpawner:
      delete_pvc: false

And that resolves the issue, then for some reason, either your users are deleted by the jupyterhub-idle-culler, or the JupyterHub Spawner class is incorrectly calling a cleanup function called delete_forever that is associated with deleting users and their associated storage etc.

By the way:

You should not have a copy of all default values of the Helm chart, but you should instead just provide the values you change in a dedicated .yaml file that you pass to helm upgrade --values <your config file.yaml>. If you have a copy of all the previous versions default values, and they change as you upgrade to a new version - you could run into issues. It also makes it very hard for me to guess whats going on, as I cant review specifically what you have changed as all configuration is listed there.
Your culling configuration posted in #2854 had max age set to 12 - which is 12 seconds, see https://github.com/jupyterhub/jupyterhub-idle-culler#readme for details.

consideRatio commented 2 years ago

I figure this is the reason you have issues. It seems like you mount the storage to a location, and then you have a command to copy to that location from somewhere.

singleuser:
  lifecycleHooks: 
    postStart:
      exec:
        command:
          - "sh"
          - "-c"
          - >
            <a folder copy to /srv/jupyterhub command goes here>
  storage:
    homeMountPath: /srv/jupyterhub

I'll go for a close on this issue with that.

jupyterhub / zero-to-jupyterhub-k8s

User pvc storage gets deleted on culling #2848