# flux-reconcile — A Flux resource has failed to reconcile for 15 minutes **Alert:** `FluxReconciliationFailure` (warning, 15m) **File:** `platform/monitoring/alerts.yaml`, group `platform-health.flux` **Expression:** `max by (namespace, name, kind) (gotk_reconcile_condition{type="Ready", status="False"}) == 1` ## What this means here Something in the GitOps chain is stuck at Ready=False. On this cluster that is more consequential than it sounds, because **`git push origin main` IS the deploy** — there is no other apply step. A stuck Kustomization means git and the cluster have diverged and nothing will close the gap. The chain has **14 tiers**: `flux-system` → `cilium` → `platform` → `platform-config` → `platform-config-cdi` → `apps-wave-0/1/2`, plus the non-gating leaves `apps-vms`, `oauth2-proxy`, `headlamp`, `homepage`, `crafty`, `runbooks`, `backup`. Which tier is failing decides the blast radius: - **`flux-system`, `cilium`, `platform`, `platform-config` are gating (`wait: true`).** One Failed HelmRelease in the `platform` tier stalls **everything downstream** on "dependency not ready". That is not theoretical: a crashlooping Headlamp HelmRelease once stalled `platform-config`, `oauth2-proxy` and every apps wave (the "Headlamp gating stall"), and oauth2-proxy twice deadlocked by **blocking its own fix** — it sat in the gating tier while needing Keycloak + trusted TLS + split-horizon DNS, so `platform-config`, which applies the fix, could never reconcile. Both were resolved by moving the leaf into its own `wait: false` tier. - **The leaf tiers are `wait: false`** precisely so their unhealth can never gate anything. Prod's source is `http://gitea.gitea.svc.cluster.local:3000` — the **in-cluster Service**, on purpose. It used to be a public hostname, and the apex flip taught the expensive version of that lesson: the HTTPRoute serving the source's own hostname lives in a downstream tier that cannot reconcile while the source is down, so `srcReady=False` / *"unable to list remote"* became a **deadlock**. If you are tempted to point the GitRepository at a public name, don't. **This alert is currently INERT.** `count(gotk_reconcile_condition)` and `count(gotk_suspend_status)` both returned **0 series** on prod on 2026-09-13: there is no scrape job for the Flux controllers in Prometheus's 19 jobs, so every `gotk_*`-based rule (`FluxReconciliationFailure`, `FluxResourceSuspended`, `ImageUpdateAutomationFailing`, `ImagePolicyStalled`, `UpdateHealthGateFailed`) evaluates against nothing. **Flux health is therefore unmonitored today** and must be read from the CRs directly, with the commands below. See `/runbooks/targets-down` for the full list of inert rule groups. Adding the Flux controllers' ServiceMonitor is open work. ## Running the commands in this runbook `kubectl` does not work on the operator workstation. The toolchain lives only in the pinned dev container, and the host's `k3s-oidc` context hangs on a browser prompt once its token expires — that hang is not the cluster being down. Every command below runs as: infra/devcontainer/dev.sh run bash -c 'kubectl --context k3s-prod get nodes' Always pass `--context k3s-prod` explicitly. `dev.sh` merges BOTH clusters into one kubeconfig and picks a current-context per invocation, and **that default has already changed once** — it was k3s-dev until dev was decommissioned on 2026-09-13, and is k3s-prod now. A command that names its context means the same thing next month as it does today; one that relies on the default does not, and the failure is silent (it answers confidently about the other cluster). `CLUSTER=prod infra/devcontainer/dev.sh run kubectl ...` selects it explicitly, and every invocation prints a banner naming the cluster it is about to talk to — read it. Do not run two `dev.sh` invocations at once; they share one container and interfere. USE FULLY-QUALIFIED RESOURCE NAMES, ALWAYS. Three CRDs on this cluster register the kind `Backup`: `longhorn.io/v1beta2`, `postgresql.cnpg.io/v1` and `velero.io/v1`. The bare short name resolves to Longhorn's, which holds zero objects — so `kubectl get backup -A` prints **"No resources found"** on a cluster holding 6 Velero backups and 27 CNPG backups. Verified on prod 2026-09-13. Reading that as "the backups are gone" and acting on it turns a false negative into real data loss. Write `backups.velero.io`, `backups.postgresql.cnpg.io`, `clusters.postgresql.cnpg.io`, `settings.longhorn.io`, `volumes.longhorn.io`, `nodes.longhorn.io`. Mutating kubectl (`apply`, `patch`, `annotate`, `rollout`) and `flux reconcile` are blocked for agents here: every durable change goes through git (`git push origin main` **is** the deploy). Where this runbook gives a mutating command it is for an operator, and it says so. ## First commands The whole chain at a glance — this is the command to run first, every time: ``` infra/devcontainer/dev.sh run bash -c \ 'kubectl --context k3s-prod get kustomizations.kustomize.toolkit.fluxcd.io -A \ -o custom-columns=NAME:.metadata.name,PATH:.spec.path,READY:.status.conditions[?\(@.type==\"Ready\"\)].status,MSG:.status.conditions[?\(@.type==\"Ready\"\)].message,REV:.status.lastAppliedRevision' ``` Is the SOURCE healthy? If not, nothing downstream can be: ``` infra/devcontainer/dev.sh run bash -c \ 'kubectl --context k3s-prod -n flux-system get gitrepositories.source.toolkit.fluxcd.io \ -o custom-columns=NAME:.metadata.name,URL:.spec.url,READY:.status.conditions[?\(@.type==\"Ready\"\)].status,MSG:.status.conditions[?\(@.type==\"Ready\"\)].message' ``` HelmReleases (the usual culprit inside `platform`): ``` infra/devcontainer/dev.sh run bash -c \ 'kubectl --context k3s-prod get helmreleases.helm.toolkit.fluxcd.io -A \ -o custom-columns=NS:.metadata.namespace,NAME:.metadata.name,READY:.status.conditions[?\(@.type==\"Ready\"\)].status,MSG:.status.conditions[?\(@.type==\"Ready\"\)].message' ``` The controller's own view, with the real error text: ``` infra/devcontainer/dev.sh run bash -c \ 'kubectl --context k3s-prod -n flux-system logs deploy/kustomize-controller --tail=80; echo ====; \ kubectl --context k3s-prod -n flux-system logs deploy/helm-controller --tail=80' ``` ## Likely causes, most likely first ### 1. "no matches for kind X" — a CR applied before its CRD The recurring structural failure here. Flux server-side-apply fails the **whole** apply, so a tier that ships both a CRD-installing HelmRelease and CRs of that CRD can never converge — the CRD never gets created because the apply that would create it also contains the CR. Symptoms: `no matches for kind "ClusterIssuer"` / `"PrometheusRule"`. The standing rule: **any component shipping CRs of a CRD it installs must split the CRs into `platform-config`** (`dependsOn: platform`), and second-order CRs whose CRD only appears after a controller reconciles go in `platform-config-cdi`. Remediation is a git change moving the resource; `bootstrap/standup.sh crds` is the belt-and-braces repair for a cluster already wedged. ### 2. A HelmRelease is genuinely failing its install/upgrade Read the message. Known instances: the `headlamp-0.40.1` `-session-ttl` chart/image desync; Grafana 13 OOM-looping after kps 65→88. Note `platform`'s `timeout: 5m` versus Longhorn's HelmRelease `timeout: 15m` — **the tier can time out while a legitimate Longhorn upgrade is still running**. Give it another interval before concluding it is broken. ### 3. A `${TOKEN}` problem in post-build substitution Substitution **fails open**: an undefined variable becomes the empty string and the Kustomization still reports Ready — which is how `k8sServiceHost: ""` broke Cilium on 2 of 3 dev nodes on 2026-09-01. A *parse* error is the loud version and does fail the whole Kustomization (`unable to parse variable name`). If the message mentions envsubst or a variable, run the L0 check: `conformance/tests/l0-static/flux-postbuild-substitution/check.sh`. Note **strict substitution became default-on in kustomize-controller v1.9.0**, so a Flux upgrade flips this behaviour whether or not you opt in. ### 4. A remote kustomize base timed out The kustomize-controller's git fetch has a 27s timeout and remote GitHub bases flake against it. `external-snapshotter` was vendored into the repo for this reason; **`platform/kubevirt` still uses remote bases**, so a `BuildFail` there is probably this. Remediation: vendor it the same way. ### 5. SOPS decryption A tier that carries an encrypted Secret needs its own `decryption` stanza patched in by the overlay, by name. A newly split-out tier that inherited a secret but not the patch fails here. ## Remediation notes - Everything durable is a **git change**. `flux reconcile` only re-triggers; it does not fix a bad manifest, and it is blocked for agents here. - Flux is **level-triggered**: an interrupted reconcile is retried, so a restart of a controller is safe and often the fastest way past a wedged in-flight apply (operator action). - `dependsOn` is **revision-gated**, not merely Ready-gated: a dependent cannot reconcile revision N until its dependency has applied N. That is what makes the chain safe and also what makes one stuck tier so expensive. ## When to escalate or stop - **If `flux-system`, `cilium`, `platform` or `platform-config` is the failing tier, treat it as a platform outage in progress** — everything downstream is frozen, including the fix. Get the operator. - **Do not `flux suspend` a tier to make the alert stop.** That trades a visible failure for `/runbooks/flux-suspended` and silent drift, which is how prod's whole `platform` tier ended up suspended and left that way after the 2026-09-04 external-dns incident. - **Do not enable `driftDetection.mode: enabled` on a CNI.** During the 2026-09-01 Cilium incident the Helm storage manifest *was* the bad render, so drift correction would have actively re-asserted the broken value. - If the GitRepository itself is not Ready, check Gitea before Flux — and remember prod deliberately reads from the in-cluster Service so that public DNS can never be in this path. --- Source of truth: `runbooks/flux-reconcile.md`. Index: `/runbooks/` Records: `DECISIONS-LOG.md` "2026-09-01 — INCIDENT: merging PR #4 briefly broke Cilium" (substitution fails open), the Headlamp gating stall, the oauth2-proxy cold-start deadlock, and the 2026-09-13 GitOps source deadlock.