stack.basicstack.de/infrastructure/OS_UPDATE_PROCEDURE.md

Weekly Rolling Ubuntu OS Update Procedure

Purpose: Keep every k3s node's Ubuntu OS patched (kernel, security, package updates) with a rolling, zero-downtime update — one node at a time, drain → update → reboot → verify → uncordon → cluster health check → next node.

Audience: Agents (currently CTO, optionally a dedicated ClusterOps agent). Also usable manually by an operator.

Scope — what this procedure does:

• Runs apt-get update, apt-get -y upgrade, apt-get -y dist-upgrade, apt-get -y autoremove on each cluster node.
• Reboots the node if a reboot is required (kernel/libc updates).
• Drains and cordons each node before touching it, uncordons after verification.
• Verifies the node and cluster are healthy before moving on.

Scope — what this procedure MUST NOT do:

• Never change the Kubernetes / k3s setup. Do not touch /etc/systemd/system/k3s*.service*, /etc/rancher/k3s/*, k3s binary version, k3s config, kube-system manifests, network policies, or any manifest under infrastructure/, apps/, or applied via ArgoCD.
• Do not upgrade k3s here. k3s upgrades are handled separately by system-upgrade-controller (see K3S_OPERATIONS.md and k3s-upgrade/).
• Do not delete PersistentVolumes, PVCs, or workload manifests.
• Do not "fix" application-level problems on a node — that's out of scope. Only fix problems in the OS/apt/reboot layer of the current node being updated. Anything else → stop, report, escalate.

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Cluster topology (context)

Role	Node	Private IP	Public IP	Datacenter	Notes
control-plane	k3s-cp-1	10.42.1.1	178.105.17.239	fsn1	EXCLUDED from os-update.sh — see CP_UPDATE_PROCEDURE.md
control-plane	k3s-cp-2	—	188.245.85.199	fsn1	EXCLUDED — see CP_UPDATE_PROCEDURE.md
control-plane	k3s-cp-3	—	49.13.92.162	fsn1	EXCLUDED — see CP_UPDATE_PROCEDURE.md
worker	k3s-worker-1	10.42.1.2	(via CP)	fsn1
worker	k3s-worker-2	10.42.1.3	(via CP)	fsn1
worker	k3s-worker-3	10.42.1.5	167.233.121.121	fsn1
worker	k3s-worker-4	10.42.1.6	128.140.3.80	nbg1
worker	k3s-worker-5	10.42.1.7	167.233.192.86	fsn1
runner	k3s-update-runner	167.233.79.65	167.233.79.65	fsn1	k3s-upgrade helper, still an updatable node

Always re-derive the live list before running — nodes may have been added/removed:

ssh root@178.105.17.239 'kubectl get nodes -o wide'

Order rule: update workers only. Within workers, update in this order to protect stateful workloads:

1. runner + workers that host no PVs (safest — lowest disruption)
2. remaining workers
3. Stalwart-hosting fsn1 workers last among workers — Stalwart has hard fsn1 affinity, so draining a fsn1 worker while another fsn1 worker is also unavailable can leave Stalwart Pending. Never have two fsn1 workers cordoned/down at the same time.
4. ALL control-plane nodes excluded — os-update.sh selects nodes without the node-role.kubernetes.io/control-plane label, so k3s-cp-1, k3s-cp-2, and k3s-cp-3 are all skipped automatically. CPs have their own procedure (CP_UPDATE_PROCEDURE.md — HA-aware, one CP at a time, leader last).

Concurrency: exactly one node at a time. Never in parallel.

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Kine thundering-herd guardrails (added after 2026-08-16 incident, see DEV-495)

Historical context (single-CP kine era, 2026-08-16). When the cluster ran a single CP with embedded SQLite via kine, draining a worker with many StatefulSets could trigger a self-amplifying eviction-and-slow-SQL cascade: kine backs up on writes → apiserver hangs → node-lease renewals fail → taint-eviction kicks in on more nodes → more writes → kine falls further behind → OOM risk on cp-1.

Current state (HA-etcd era, since DEV-510 on 2026-08-22). The datastore is now embedded etcd 3.6.12 with 3-node quorum across cp-1/cp-2/cp-3. A single-worker drain no longer creates the lone-SQLite writer risk, and etcd tolerates one member being slow or briefly unreachable. Guardrails (1) and (3) below are retained as sanity checks but the failure mode they were named for is much less likely to trigger. Guardrail (2) is largely done (add swap on cp-1/cp-2/cp-3 tracked in the CP update procedure).

All four rules below MUST be observed on every DEV-478 fire. The reference implementation (os-update.sh) does not yet enforce (1)/(3) automatically; the operator must actively watch.

1. Pre-plan drain order for StatefulSets. Before draining any worker, kubectl get pods -n <ns> -o wide against every namespace with StatefulSets and count how many will be evicted from the target node. If a single drain would evict more than 3 StatefulSets at once, redistribute first: cordon+delete individual StatefulSet pods one namespace at a time and wait for each reschedule to settle before draining the whole node.
2. All CPs must have swap before their update cycle. cp-1/cp-2/cp-3 currently all have 0 swap. Add at least 2 GiB (default 4 GiB) of swap on each CP before its OS-update run — see Phase A in CP_UPDATE_PROCEDURE.md. This is a one-off setup task per CP; once done it is a durable capability.
3. Halt on kine slowness. During any drain, keep a time kubectl get nodes running from cp-1. If it exceeds 5 s in real time, halt the cycle immediately (uncordon the current node, do not proceed), verify cluster health, and escalate. The 5 s threshold is the leading indicator that kine has fallen behind and the taint-eviction cascade is about to start.
4. CP updates are a separate design task. With HA etcd across three CPs the risk is now etcd quorum loss (two CPs down simultaneously), not the sole-apiserver reboot. CP updates MUST be planned and board-approved per node; they are NOT covered by the standard os-update.sh cycle. See CP_UPDATE_PROCEDURE.md and scripts/os-update/update-cp-node.sh (DEV-515). The old cp-1-only doc CP1_UPDATE_PROCEDURE.md is a redirect stub.

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Access

Prereqs are the same as CLUSTER_ACCESS.md:

• SSH key for root on every node (jump via control plane for private-IP workers).
• kubectl available (either from the operator machine, or by SSH-ing to the control plane and using it there).
• hcloud CLI configured (only needed for firewall-related recovery — not for normal runs).

Environment variables the scripts expect:

• CONTROL_PLANE_HOST — default 178.105.17.239
• CONTROL_PLANE_PRIVATE — default 10.42.1.1
• Drain timeout: DRAIN_TIMEOUT_SECONDS — default 600
• Reboot wait: REBOOT_MAX_WAIT_SECONDS — default 600
• Post-uncordon settle: POST_UNCORDON_WAIT_SECONDS — default 180

---

Preflight (run once per cycle, before touching any node)

1. Cluster is currently healthy. If any of the checks below fail, STOP and open an issue — do not start OS updates on an already-degraded cluster.

   ssh root@$CONTROL_PLANE_HOST bash -s <<'EOF'
   set -e
   kubectl get nodes
   echo "--- Not-ready nodes:"
   kubectl get nodes -o json | jq -r '.items[] | select(.status.conditions[] | select(.type=="Ready" and .status!="True")) | .metadata.name'
   echo "--- Pods not Running/Completed:"
   kubectl get pods -A --field-selector=status.phase!=Running,status.phase!=Succeeded | grep -v 'STATUS' || echo "  (none)"
   echo "--- Non-Ready pods (Running but not Ready):"
   kubectl get pods -A -o json | jq -r '.items[] | select(.status.phase=="Running") | select([.status.conditions[]?|select(.type=="Ready")|.status]|contains(["False"])) | "\(.metadata.namespace)/\(.metadata.name)"'
   EOF
   

   Only proceed if: all nodes Ready, no non-Running/Succeeded pods, no Running-but-not-Ready pods (small transient counts are OK — retry once and continue if it clears).

2. Snapshot k3s datastore (control plane only — this is a checkpoint you can restore etcd from if the control-plane reboot goes badly):

   ssh root@$CONTROL_PLANE_HOST 'k3s etcd-snapshot save --name pre-os-update-$(date +%Y%m%d)'
   ssh root@$CONTROL_PLANE_HOST 'k3s etcd-snapshot list | tail -5'
   

3. List the nodes to update and derive the ordered plan. Persist to /tmp/os-update-plan.txt on the control plane for auditability. See scripts/os-update/os-update.sh for the reference implementation of the ordering rule.

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Per-node procedure

Repeat for each node in the ordered plan. The reference implementation is infrastructure/scripts/os-update/update-node.sh <node-name>; the manual steps below are what that script does.

Throughout: every command's stdout+stderr goes to a per-run log at /tmp/os-update-<node>-<timestamp>.log on the control plane. Attach the log to the issue at the end.

1. Pre-check the node

NODE=<node-name>
kubectl get node "$NODE"
kubectl describe node "$NODE" | grep -A2 Conditions

Confirm: Ready=True, not already cordoned, no DiskPressure/MemoryPressure/PIDPressure.

2. Cordon and drain

kubectl cordon "$NODE"
kubectl drain "$NODE" \
  --ignore-daemonsets \
  --delete-emptydir-data \
  --disable-eviction=false \
  --timeout="${DRAIN_TIMEOUT_SECONDS:-600}s"

If drain fails on a PodDisruptionBudget:

• Do NOT force-delete pods (breaks HA guarantees).
• Log the blocking PDB, uncordon the node, mark the node as SKIPPED_PDB in the plan, and continue with the next node. Escalate the PDB conflict on the issue at the end.

If drain fails on a lone pod without a controller:

• Do NOT --force. Same as above — uncordon, mark SKIPPED_ORPHAN_POD, continue.

3. Update the OS

On the node itself:

ssh -o StrictHostKeyChecking=accept-new root@<node-ssh-target> bash -s <<'REMOTE'
set -euo pipefail
export DEBIAN_FRONTEND=noninteractive
# Refresh package lists
apt-get update
# Configure apt to keep existing config files silently (no interactive prompts)
APT_OPTS='-y -o Dpkg::Options::=--force-confdef -o Dpkg::Options::=--force-confold'
apt-get $APT_OPTS upgrade
apt-get $APT_OPTS dist-upgrade
apt-get $APT_OPTS autoremove --purge
apt-get clean
# Report reboot need
if [ -f /var/run/reboot-required ]; then
  echo "REBOOT_REQUIRED=yes"
  cat /var/run/reboot-required.pkgs 2>/dev/null || true
else
  echo "REBOOT_REQUIRED=no"
fi
REMOTE

For private-IP workers, target them from the control plane (ssh -J root@$CONTROL_PLANE_HOST root@10.42.1.X) or run the whole block after SSH-ing to the control plane first.

Common OS-only fixes the agent MAY perform on the node if apt fails:

• dpkg --configure -a after an interrupted install
• apt-get -f install to resolve broken deps
• Free disk with journalctl --vacuum-time=3d or apt-get clean if / is full
• Restart a system service that is stuck (systemctl restart <unit>) — but NOT k3s, k3s-agent, containerd, flanneld, or any container runtime

Never: change k3s config, delete PVs, uninstall packages the OS didn't schedule, edit /etc/rancher/, or reinstall k3s. If a fix would touch any of those, stop and escalate.

4. Reboot if required

If REBOOT_REQUIRED=yes:

ssh root@<node-ssh-target> 'systemctl reboot' || true
# Wait until SSH responds again (max REBOOT_MAX_WAIT_SECONDS)
deadline=$(( $(date +%s) + ${REBOOT_MAX_WAIT_SECONDS:-600} ))
while [ $(date +%s) -lt $deadline ]; do
  sleep 10
  if ssh -o ConnectTimeout=5 -o StrictHostKeyChecking=accept-new root@<node-ssh-target> 'uptime' 2>/dev/null; then
    echo "Node back up"; break
  fi
done

If the node doesn't come back within the timeout: escalate immediately. Do NOT rebuild the node or touch k3s — a rebuild requires the ADD_WORKER_NODE procedure and is a separate approved action.

5. Wait for k3s-agent / k3s to be ready again

# Wait for kubelet Ready condition (control plane view)
deadline=$(( $(date +%s) + 300 ))
while [ $(date +%s) -lt $deadline ]; do
  READY=$(kubectl get node "$NODE" -o jsonpath='{.status.conditions[?(@.type=="Ready")].status}')
  [ "$READY" = "True" ] && break
  sleep 5
done
kubectl get node "$NODE"

If Ready never returns True: escalate. Do NOT change k3s config.

5b. Reconcile Docker on labeled nodes (before uncordon)

For nodes carrying the basicstack.de/docker=true label (currently the workers that run the Forgejo runner), ensure docker.io is present + running before scheduling resumes. Without this the runner pod comes back ContainerCreating because hostPath requires the docker socket to exist (see DEV-498 and DEV-499).

scripts/os-update/ensure-node-docker.sh "$NODE"

This step is a no-op on nodes without the label. update-node.sh runs it automatically between step 5 and step 6; the script is also safe to run ad-hoc after any manual OS operation. As a defensive extra measure, the apt phase (step 3) now runs apt-mark manual docker.io on any node where it is installed, so apt-get autoremove --purge cannot silently strip it.

6. Uncordon

kubectl uncordon "$NODE"

7. Post-node health verification

Wait for pods to reschedule and settle, then verify:

sleep "${POST_UNCORDON_WAIT_SECONDS:-180}"

# All nodes Ready?
kubectl get nodes
kubectl get nodes -o json | jq -r '.items[] | select(.status.conditions[] | select(.type=="Ready" and .status!="True")) | .metadata.name' | grep . && { echo "NOT-READY NODES"; exit 1; } || true

# Any pod not Running/Succeeded?
BAD=$(kubectl get pods -A --field-selector=status.phase!=Running,status.phase!=Succeeded --no-headers 2>/dev/null | wc -l)
[ "$BAD" -gt 0 ] && { echo "BAD PODS: $BAD"; kubectl get pods -A --field-selector=status.phase!=Running,status.phase!=Succeeded; exit 1; } || true

# Any Deployment/StatefulSet under desired replicas?
kubectl get deploy -A -o json | jq -r '.items[] | select((.status.readyReplicas // 0) < (.spec.replicas // 1)) | "deploy \(.metadata.namespace)/\(.metadata.name) \(.status.readyReplicas // 0)/\(.spec.replicas)"'
kubectl get sts -A -o json | jq -r '.items[] | select((.status.readyReplicas // 0) < (.spec.replicas // 1)) | "sts \(.metadata.namespace)/\(.metadata.name) \(.status.readyReplicas // 0)/\(.spec.replicas)"'

Only proceed to the next node when ALL of the above are green. If not:

• Give it another 3 minutes and re-check (workloads with large images may still be pulling).
• If still not green: STOP the cycle. Uncordon everything, leave the cluster in a stable state, and open a follow-up issue with the failing workloads. Do NOT proceed to update more nodes.

8. Control plane special handling

All three CPs (k3s-cp-1, k3s-cp-2, k3s-cp-3) are NOT updated by the weekly os-update.sh cycle — they have their own dedicated procedure and script: CP_UPDATE_PROCEDURE.md and scripts/os-update/update-cp-node.sh. Reasons:

• CPs are NoSchedule-tainted and host no StatefulSet workloads today, but they are the etcd quorum. Two of three CPs cordoned/rebooting at once = write outage. One CP at a time, leader last.
• All three CPs currently have zero swap. The CP procedure adds a durable 4 GiB swapfile per CP before draining.
• The CP procedure polls the target's /livez from the operator machine and cross-checks etcdctl endpoint status --cluster from a peer CP to confirm the just-rebooted member rejoined.

os-update.sh excludes any node carrying the node-role.kubernetes.io/control-plane label (see --dry-run output) and prints a pointer to the CP procedure.

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Finalization

After all nodes are done:

1. Final cluster health snapshot (same preflight commands as at the start).
2. Print apt history summary per node so the audit trail has "what changed":

   for host in <all-nodes>; do
     echo "=== $host ==="
     ssh root@$host 'zgrep -h "Commandline\|Install\|Upgrade\|Remove" /var/log/apt/history.log* 2>/dev/null | tail -60'
   done
   

3. Optional: prune old etcd snapshots to keep disk in check:

   ssh root@$CONTROL_PLANE_HOST 'k3s etcd-snapshot list'
   # delete anything older than 14 days if desired (manual review)
   

4. Attach the per-run logs to the Paperclip issue that triggered this run.
5. Update the issue with:
   • Nodes updated (list)
   • Nodes skipped (list + reason)
   • Any package that required manual intervention
   • Reboots performed
   • Final kubectl get nodes output

If everything is clean → mark the issue done. If a node was skipped or errored → mark blocked with the unblock action, or open a child issue for the specific failure.

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Recovery / what to do when it goes wrong

Node stuck cordoned after failure: kubectl uncordon <node> — always leave the cluster back in its normal scheduling state.

Node fails to boot after reboot:

• Check Hetzner console for boot errors (kernel panic, initramfs).
• Try hcloud server reboot <name> from hcloud CLI.
• If the node cannot recover: escalate. Do NOT delete or rebuild the Hetzner server without board approval; that is the ADD_WORKER_NODE flow.

k3s-agent won't start after reboot:

• Check journalctl -u k3s-agent -n 100.
• Do NOT edit the k3s-agent unit file. Do NOT re-run the k3s installer.
• Escalate. This is out of scope for the OS-update procedure.

Pods CrashLoopBackOff after node came back:

• Not an OS-update problem to fix — the node is healthy, apt succeeded. Leave the node uncordoned, stop the cycle, and open an application-level issue.

PDB blocked drain:

• Never --force the drain. Leave the node uncordoned, skip it, note in the report which PDB blocked and which workload owns it.

Datastore snapshot restore (last resort — CP only):

• Only if the control plane is broken beyond repair. See K3S_OPERATIONS.md for the --cluster-reset --cluster-reset-restore-path=<snapshot> procedure. Requires board approval — do NOT execute unattended.

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Automation entry points

• infrastructure/scripts/os-update/os-update.sh — full cycle runner (preflight → per-node loop → finalization). Idempotent, resumable via --start-from <node>. Use --dry-run to print the plan without touching anything. Explicitly skips k3s-cp-1.
• infrastructure/scripts/os-update/update-node.sh <node> — single-node update (all 7 per-node steps). Callable standalone for retry. Not for k3s-cp-1.
• infrastructure/scripts/os-update/update-cp-node.sh <node> — HA-aware CP update flow (add swap, preflight, drain, apt, reboot, finalize). Accepts k3s-cp-1, k3s-cp-2, or k3s-cp-3. See CP_UPDATE_PROCEDURE.md.
• infrastructure/scripts/os-update/update-cp-1.sh — thin wrapper (calls update-cp-node.sh k3s-cp-1 "$@"). Kept for backwards compat.
• infrastructure/scripts/os-update/cluster-health.sh — the preflight/post-node health check as a standalone command; exits non-zero on any failure.

Read the script sources for the exact behavior before running them. They mirror this procedure step for step.

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Weekly schedule

A Paperclip routine (see infrastructure/OS_UPDATE_ROUTINE.md) fires this procedure once per week. The routine creates a task whose description points here. The assigned agent reads this document and executes the automation.

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Change history

Date	Change	By
2026-08-09	Initial procedure + automation scripts	CTO agent (DEV-462)
2026-08-16	Added kine thundering-herd guardrails after DEV-495 incident (worker-3 drain caused CP kine cascade + near-OOM on cp-1). Four new rules: pre-plan StatefulSet drain order, swap on cp-1, halt on kubectl >5 s, cp-1 update as separate design task.	CTO agent (DEV-478/DEV-495)
2026-08-23	Downgraded the kine cascade section for the HA-etcd era (DEV-510 migrated cp-1 from kine SQLite to embedded etcd, cp-2/cp-3 joined as full members). Pointed §8 and the "Automation entry points" list at the new HA-aware CP_UPDATE_PROCEDURE.md / update-cp-node.sh. Old CP1_UPDATE_PROCEDURE.md and update-cp-1.sh are now redirect stubs.	CTO agent (DEV-515)