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home-network-k3s-impl/platform/monitoring/kube-prometheus-stack.yaml
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jakman85andClaude Opus 4.8 eb31d2ef58 fix(monitoring): cap Prometheus TSDB by size to stop false absent()/==0 alerts
The 7 falsely-firing platform alerts (KeycloakDown, KeycloakDatabaseDown,
KubeAPIDown, KubeletDown, VPNTunnelDown, KubeVirtControlPlaneDown,
CDINoDefaultStorageClass) share ONE root cause, not per-rule label mismatches:
the Prometheus PVC is 100% full ("no space left on device" on every WAL commit).

Evidence from the live dev cluster:
- /prometheus is 4.8G/5Gi, 0 bytes free; every scrape logs "Scrape commit
  failed ... write to WAL: no space left on device". Scrapes still return 200
  (targets show healthy, lastScrape=now) but samples are never stored, so the
  TSDB head froze at 2026-08-28 13:45 UTC while the pod clock reads ~19:33 UTC.
- Instant queries at "now" therefore return an EMPTY vector, so every
  absent()/==0 platform rule trips. Evaluated at the last-good-sample time each
  expr is correctly FALSE (keycloak-0/keycloak-db-1 ready=1, apiserver+kubelet
  up=1 x3, tun0 series present, kubevirt control-plane expr empty, CDI default
  present) — the rules are correct; the monitor was simply blind.

`retention` alone prunes only by AGE: this cluster is 3d2h old with 3d dev
retention, so time-pruning has NEVER run and 3d of block churn (~1.2Gi/day) plus
a WAL that ballooned past 1Gi overran the 5Gi disk. Fix adds a size-based
retention cap (new MONITORING_PROMETHEUS_RETENTION_SIZE knob) kept below each
env's PVC so Prometheus drops oldest blocks before the disk fills, and bumps the
dev PVC 5Gi->8Gi for real WAL/head/compaction headroom.

- platform/monitoring/kube-prometheus-stack.yaml: retentionSize: ${knob}
- clusters/base/cluster-vars.yaml: knob default 8GiB (base 10Gi PVC)
- clusters/dev/kustomization.yaml: PVC 5Gi->8Gi, retentionSize 5GiB
- clusters/prod/kustomization.yaml: retentionSize 45GiB (50Gi PVC)
- platform/monitoring/README.md: knob table + rationale

Deploy note (PM): the PVC is already 100% full, so Prometheus cannot self-prune
until it can write. The 5Gi->8Gi bump must land as a Longhorn online expansion
(operator PVC expansion / manual patch); once free space returns, retentionSize
keeps it healthy. Watchdog left untouched.

Co-Authored-By: Claude Opus 4.8 <[email protected]>
2026-08-28 14:38:12 -05:00

222 lines
10 KiB
YAML

---
# kube-prometheus-stack — Prometheus + Alertmanager + Grafana + kube-state-metrics +
# node-exporter + the standard Kubernetes exporters/rules (docs/10). Serves R-OBS-01/02/03.
#
# Retention/PVC sizes are overlay knobs (R-ENV-02) resolved from cluster-vars via Flux
# postBuild.substituteFrom. Everything else is DEV-SCOPED for the ~22 GiB workstation ceiling:
# single replicas, modest requests/limits, ephemeral (emptyDir) Alertmanager/Grafana state, and
# the k3s-embedded control-plane scrape jobs disabled (they are not separately reachable on k3s and
# would otherwise show as permanently-down targets and burn RAM/alert noise).
apiVersion: helm.toolkit.fluxcd.io/v2
kind: HelmRelease
metadata:
name: kube-prometheus-stack
namespace: monitoring
spec:
interval: 30m
chart:
spec:
chart: kube-prometheus-stack
version: ">=65.0.0 <66.0.0" # TODO(WS-OBS): pin at bring-up; Renovate maintains
sourceRef:
kind: HelmRepository
name: prometheus-community
namespace: monitoring
install:
remediation:
retries: 3
upgrade:
remediation:
retries: 3
values:
# --- k3s trim: control-plane components are embedded in the k3s server process and are not
# scrapable as discrete endpoints. Disabling avoids permanently-firing "target down" noise.
kubeControllerManager:
enabled: false
kubeScheduler:
enabled: false
kubeEtcd:
enabled: false
kubeProxy:
enabled: false
# --- Prometheus ---
prometheus:
prometheusSpec:
replicas: 1
retention: ${MONITORING_PROMETHEUS_RETENTION} # overlay knob (dev 3d / prod long)
# SIZE-based retention cap (docs/10, R-OBS). `retention` alone prunes only by AGE — on a young
# cluster (< retention window) NOTHING is pruned yet, so a busy TSDB fills the PVC before the
# time window elapses. A full /prometheus wedges ALL WAL commits ("no space left on device"):
# scrapes still 200 but samples are never stored, the head freezes, and every absent()/==0
# platform alert (Keycloak/KubeAPI/Kubelet/VPN/KubeVirt/CDI…) fires falsely because instant
# queries at "now" return empty. retentionSize makes Prometheus drop the OLDEST blocks once the
# block set approaches this cap, so the disk never fills regardless of cluster age or churn.
# Kept BELOW the PVC size (leaves headroom for the WAL + head + compaction scratch, which are
# NOT counted by retentionSize). Prometheus size units are *iB (GiB), distinct from the K8s PVC
# `Gi`, so it is a separate overlay knob rather than a reuse of the PVC-size knob.
retentionSize: ${MONITORING_PROMETHEUS_RETENTION_SIZE} # overlay knob (dev 5GiB / base 8GiB / prod 45GiB)
# Discover ServiceMonitors/PodMonitors/Rules from ALL namespaces (flux, cert-manager,
# longhorn, velero, keycloak, cilium/hubble ship their own) — not just this release's.
ruleSelectorNilUsesHelmValues: false
serviceMonitorSelectorNilUsesHelmValues: false
podMonitorSelectorNilUsesHelmValues: false
probeSelectorNilUsesHelmValues: false
# Modest footprint for a home dev cluster (few hundred series). Limit gives headroom for
# WAL replay / compaction spikes without letting Prometheus eat the node.
resources:
requests:
cpu: 100m
memory: 512Mi
limits:
memory: 2Gi # 1Gi OOMKilled (exit 137) during TSDB compaction/checkpoint
# spikes; 2Gi holds. Nodes have headroom (~2Gi free each).
storageSpec:
volumeClaimTemplate:
spec:
storageClassName: longhorn # replicated tier (ADR-0003)
accessModes: ["ReadWriteOnce"]
resources:
requests:
storage: ${MONITORING_PROMETHEUS_PVC_SIZE} # overlay knob (dev 5Gi / prod large)
# --- Alertmanager: routes by severity to email (R-OBS-02) ---
alertmanager:
alertmanagerSpec:
replicas: 1
# DEV TRIM: no PVC — silences/notification-log live in emptyDir. Acceptable in dev (a
# restart re-fires active alerts). Prod overlay can add a small storage block.
resources:
requests:
cpu: 10m
memory: 32Mi
limits:
memory: 96Mi
# SMTP credentials are an OPERATOR HAND-OFF: a SOPS-encrypted Secret, referenced BY NAME
# only (docs/07). Mounted at /etc/alertmanager/secrets/<name>/ so the config below can read
# the password from a file (never inline plaintext).
secrets:
- alertmanager-smtp
# Routing/receivers. Non-secret SMTP endpoint fields (smarthost/from/to/username) are
# operator-supplied placeholders (REPLACE-ME, same convention as velero); the PASSWORD is
# read from the mounted SOPS secret via *_file. Both severities email; subject/route differ.
config:
global:
resolve_timeout: 5m
smtp_smarthost: "smtp.gmail.com:587" # operator hand-off (e.g. smtp.gmail.com:587)
smtp_from: "[email protected]" # operator hand-off (From: address)
smtp_auth_username: "[email protected]" # operator hand-off (SMTP login)
smtp_auth_password_file: /etc/alertmanager/secrets/alertmanager-smtp/smtp-password
smtp_require_tls: true
route:
group_by: ["alertname", "namespace"]
group_wait: 30s
group_interval: 5m
repeat_interval: 12h
receiver: email-warning
routes:
- matchers: ['severity = "critical"']
receiver: email-critical
# page-worthy — notify fast, remind often
group_wait: 10s
repeat_interval: 1h
receivers:
- name: email-warning
email_configs:
- to: "[email protected]" # alert inbox (operator: change if a different inbox is wanted)
send_resolved: true
headers:
subject: '[WARNING] {{ .CommonLabels.alertname }} ({{ .CommonLabels.namespace }})'
- name: email-critical
email_configs:
- to: "[email protected]" # alert inbox (operator: change if a different inbox is wanted)
send_resolved: true
headers:
subject: '[CRITICAL] {{ .CommonLabels.alertname }} ({{ .CommonLabels.namespace }})'
# --- Grafana: dashboards (R-OBS-03), surfaced in the C2 UI (docs/12) behind Keycloak SSO ---
grafana:
enabled: true
# Force a pod roll when the OIDC wiring changes so Grafana loads the grafana-oidc-credentials
# client-secret (env valueFrom is resolved at pod start; the secret was added after first boot, so
# generic_oauth started disabled). Bump this value to re-roll Grafana on future OIDC secret changes.
podAnnotations:
homelab.keithjackson.dev/oidc-rollout: "1"
# Admin bootstrap + (later) OIDC client are SOPS secrets referenced BY NAME (WS-SEC/ADR-0014).
admin:
existingSecret: grafana-admin-credentials
userKey: admin-user
passwordKey: admin-password
# DEV TRIM: emptyDir (default). Dashboards are provisioned from ConfigMaps (sidecar), so no
# durable Grafana DB is needed to iterate. Prod can enable persistence.
persistence:
enabled: false
# Auto-discover dashboard ConfigMaps labeled grafana_dashboard across namespaces (per-service
# dashboards rendered from ServiceDefinitions land here — docs/10 onboarding output).
sidecar:
dashboards:
enabled: true
searchNamespace: ALL
label: grafana_dashboard
datasources:
enabled: true
resources:
requests:
cpu: 50m
memory: 128Mi
limits:
memory: 256Mi
# --- Keycloak native-OIDC SSO (ADR-0014, deliverable #4 SSO proof) ---
# Grafana is a confidential OIDC client of the Keycloak `homelab` realm. The client SECRET comes
# from the SOPS-encrypted grafana-oidc-credentials Secret via env (referenced by name only,
# R-IDP-04). optional:true so the RUNNING Grafana keeps starting before the operator fills the
# secret — local admin login (below) stays available as the fallback until SSO is proven.
envValueFrom:
GF_AUTH_GENERIC_OAUTH_CLIENT_SECRET:
secretKeyRef:
name: grafana-oidc-credentials
key: client-secret
optional: true
grafana.ini:
server:
root_url: https://grafana.home.keithjackson.dev
auth.generic_oauth:
enabled: true
name: Keycloak
client_id: grafana
scopes: "openid email profile"
auth_url: https://keycloak.home.keithjackson.dev/realms/homelab/protocol/openid-connect/auth
token_url: https://keycloak.home.keithjackson.dev/realms/homelab/protocol/openid-connect/token
api_url: https://keycloak.home.keithjackson.dev/realms/homelab/protocol/openid-connect/userinfo
login_attribute_path: preferred_username
email_attribute_path: email
# Map Keycloak groups (the `groups` claim) to Grafana roles (R-IDP-06): platform-admins ->
# Admin, media-users -> Editor, everyone else -> Viewer.
role_attribute_path: "contains(groups[*], 'platform-admins') && 'Admin' || contains(groups[*], 'media-users') && 'Editor' || 'Viewer'"
# Keep local admin login enabled as break-glass until SSO is proven end-to-end; flip to
# disable_login_form:true afterwards (docs/15 break-glass, R-IDP-05).
# TODO(WS-SEC, post-proof): set auth.disable_login_form=true once SSO login is verified.
# --- Bundled exporters / operator: keep small ---
prometheusOperator:
resources:
requests:
cpu: 50m
memory: 96Mi
limits:
memory: 256Mi
kube-state-metrics:
resources:
requests:
cpu: 20m
memory: 64Mi
limits:
memory: 128Mi
prometheus-node-exporter:
resources:
requests:
cpu: 20m
memory: 32Mi
limits:
memory: 64Mi