fix(spawner): set fsGroupChangePolicy: OnRootMismatch on singleuser pods#83
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tylerpotts wants to merge 2 commits into
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fix(spawner): set fsGroupChangePolicy: OnRootMismatch on singleuser pods#83tylerpotts wants to merge 2 commits into
tylerpotts wants to merge 2 commits into
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The kubelet's default fsGroupChangePolicy: Always recursively chowns every file on the mounted home PVC to match fsGroup at every spawn. On home PVCs with large pixi envs and model caches (observed: 750k files), this takes 30-150s and times out the spawn at the JupyterHub 60s default. OnRootMismatch only performs the chown when the volume's root GID is wrong, so it runs at most once per PVC and subsequent spawns skip it entirely. Closes #56
The first attempt set securityContext.fsGroupChangePolicy via
extra_pod_config but left fs_gid as a separate KubeSpawner trait,
assuming kubespawner would deep-merge the two into the pod's
securityContext. It doesn't — extra_pod_config does a top-level
attribute overwrite, so the securityContext set here replaced the one
fs_gid produced and pod.spec.securityContext.fsGroup was dropped.
Kubespawner logged exactly this at spawn time:
'pod.spec.security_context' current value: '{'fsGroup': 100}' is
overridden with '{'fsGroupChangePolicy': 'OnRootMismatch'}'
Effect: users no longer had GID 100 as a supplemental group, breaking
shared-storage writes and failing 5 e2e tests on PR #83.
Fix: set fsGroup and fsGroupChangePolicy together in extra_pod_config,
remove the now-redundant fs_gid trait, and document the overwrite
behavior in the comment so this trap doesn't get re-set.
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Summary
securityContext.fsGroupChangePolicy: OnRootMismatchtoc.KubeSpawner.extra_pod_configinconfig/jupyterhub/01-spawner.py.chown(Alwayspolicy) from running on every spawn, which on populated home PVCs (large pixi envs, HuggingFace caches) takes 30–150s and times out the spawn at JupyterHub's 60s default.OnRootMismatchruns the chown at most once per PVC (when the root GID is wrong), so subsequent spawns skip it entirely.The new key is deep-merged into the pod spec alongside the existing
securityContext.fsGroup: 100set byc.KubeSpawner.fs_gid.Closes #56
Test plan
helm lint . --set nebariapp.enabled=falsepassesuvx ruff check config/passeshelm templaterenders bothfsGroup: 100andfsGroupChangePolicy: OnRootMismatchon the rendered hub ConfigMaptests/unit/passkubectl get pod jupyter-<user> -o jsonpath='{.spec.securityContext}'shows bothfsGroupandfsGroupChangePolicykubectl describe pod jupyter-<user>no longer emits the "Setting volume ownership ... is taking longer than expected" warning after the first post-deploy spawnOut of scope
The architectural issue called out in #56 and #54 — that
01-spawner.pydirectly assignsc.KubeSpawner.extra_pod_configand clobbers any operator-providedsingleuser.extraPodConfigfrom values — is not addressed here. That belongs in its own PR.