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home-network-k3s-impl/platform/monitoring/kube-prometheus-stack.yaml
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jakman85andClaude Opus 5 aae63c97a3 fix(monitoring): node-exporter extraArgs REPLACES the chart default, so restate it
Verified against the chart (helm show values prometheus-community/prometheus-node-exporter)
and against the live DaemonSet's argv on prod: the subchart's extraArgs default is
NOT empty — it ships the two filesystem excludes
(mount-points-exclude for /dev,/proc,/sys,containerd,docker,kubelet and the
fs-types-exclude list). Setting extraArgs to just --collector.mountstats would have
silently dropped both, so the filesystem collector would have begun reporting every
container overlay and every kubelet bind mount: a large cardinality jump, and a
behaviour change in NodeDiskFillingUp, which alerts per mountpoint. Both defaults
are now restated verbatim alongside the new collector, with a note to re-reconcile
them on a chart upgrade.

Co-Authored-By: Claude Opus 5 <[email protected]>
2026-09-13 22:42:08 -05:00

422 lines
25 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
# The 65->88 catch-up is a large multi-major jump (operator + KSM + node-exporter roll, plus the
# Prometheus/Alertmanager StatefulSets). The default 5m Helm timeout is too short for the full rollout
# to reach Ready, so Flux logged "context deadline exceeded" and rolled back to 65.8.1 four times.
# A generous timeout lets one attempt finish; remediateLastFailure:false keeps partial progress instead
# of yo-yoing back to the old chart (a re-reconcile then drives it forward). CRDs are pre-applied
# server-side (Helm never updates crds/ on upgrade), so schema is already at operator v0.93.1.
timeout: 20m0s
chart:
spec:
chart: kube-prometheus-stack
version: ">=88.0.0 <89.0.0" # k8s-1.36 catch-up (po v0.93; CRDs pre-applied server-side, Helm won't update them). Renovate maintains
sourceRef:
kind: HelmRepository
name: prometheus-community
namespace: monitoring
install:
remediation:
retries: 3
upgrade:
remediation:
retries: 2
remediateLastFailure: false
cleanupOnFail: true
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: 3Gi # 1Gi OOMKilled (exit 137) during TSDB compaction/checkpoint;
# 2Gi ran pinned at ~98% (2002Mi) with no room for compaction/WAL-replay
# spikes (the classic Prometheus OOM). Nodes are 24Gi at 38-44% used
# (~14Gi free each), so 3Gi gives real headroom.
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: 384Mi # Grafana 13.x (image 13.2.0, kps 88) baseline is well above Grafana 11.x (kps 65)
limits:
memory: 768Mi # 256Mi OOMKilled (exit 137) Grafana 13.x during apiserver/unified-storage
# startup — the silent SIGKILL that made the whole 65->88 Helm upgrade
# time out (the new Grafana pod never went Ready). 512Mi then ran pinned at
# ~98% (499Mi) with no headroom — one render/GC spike from OOM. 768Mi holds
# with real headroom (nodes 24Gi, ~14Gi free each).
# --- 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.${BASE_DOMAIN}
auth.generic_oauth:
enabled: true
name: Keycloak
client_id: grafana
scopes: "openid email profile"
auth_url: https://keycloak.${BASE_DOMAIN}/realms/homelab/protocol/openid-connect/auth
token_url: https://keycloak.${BASE_DOMAIN}/realms/homelab/protocol/openid-connect/token
api_url: https://keycloak.${BASE_DOMAIN}/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:
# Expose the egress-gateway NODE LABEL as a metric label so alerts can ask "does this cluster
# have a VPN egress gateway at all?". KSM exposes NO custom labels by default, so without this
# `kube_node_labels` does not exist and any join against it silently matches nothing.
# Consumed by `VPNTunnelDown` (platform/monitoring/alerts.yaml): the alert is armed only on a
# cluster that actually has a labelled gateway node, and ARMS ITSELF the moment one is labelled
# — which is how prod (no gateway today) stops emailing a permanently-firing critical alert
# without anyone having to remember to re-enable it later. Scoped to one label on one resource:
# 3 extra series, no cardinality concern. Label name is sanitized by KSM to
# `label_homelab_keithjackson_dev_egress_gateway` (`label_` + non-alphanumerics -> `_`).
metricLabelsAllowlist:
- "nodes=[homelab.keithjackson.dev/egress-gateway]"
# --- VELERO SCHEDULE OBJECTS AS METRICS (added 2026-09-13) ---------------------------------
# Velero exports NOTHING that enumerates Schedule objects and nothing that exposes
# `spec.paused`. Verified on prod against velero v1.18.1: all 35 velero_* metric names that
# carry a `schedule` label are created by a backup ATTEMPT, so a Schedule that has never run
# has NO series at all — a throwaway `paused: true` Schedule produced zero lines in
# `curl velero:8085/metrics`. Consequence: `VeleroNoRecentBackup`
# (`time() - velero_backup_last_successful_timestamp{schedule!=""}`) was structurally INERT for
# a never-successful schedule, because `time() - <absent series>` yields no series. prod sat
# with `velero-daily` (the VOLUME-DATA schedule) paused and unbacked-up, and nothing alerted.
#
# No PromQL can fix that — the fact is not in the TSDB — so the Schedule CRs themselves are
# exported here. KSM's custom-resource-state collector is the right mechanism precisely
# because it is ALREADY the platform's CRD-to-metrics path (this same block exports
# kube_node_labels for VPNTunnelDown); it needs no new exporter, image, ServiceMonitor or
# scrape job, and the series land on the existing kube-state-metrics target.
#
# Consumed by VeleroScheduleNeverBackedUp / VeleroSchedulePaused / VeleroNoVolumeDataBackup
# (platform/monitoring/alerts.yaml). Cost: 4 series per Schedule — 8 on prod today.
#
# Chart mechanics, verified by rendering kube-prometheus-stack 88.6.5 (KSM subchart 8.4.1,
# KSM v2.20.0) and by running that exact KSM image against prod's API:
# * `customResourceState.enabled` mounts this `config` as a ConfigMap at
# /etc/customresourcestate/config.yaml and adds --custom-resource-state-config-file.
# `--custom-resource-state-only` is NOT set, so the standard kube_* metrics keep flowing.
# * the chart auto-adds the apiextensions.k8s.io/customresourcedefinitions list+watch rule
# (rbac.customResourceState.createClusterRoleRules, default true). That rule is MANDATORY,
# not cosmetic: without it KSM logs "customresourcedefinitions ... is forbidden" and emits
# the CRS metrics as an EMPTY SET — silent, exactly the inert-alert failure mode again.
# Measured: the first probe run, with velero.io access but no CRD access, produced 0 series.
# * `rbac.extraRules` below is the only RBAC this repo must supply (read-only, one CRD).
# * `metricNamePrefix` deliberately yields `kube_velero_schedule_*`, NOT `velero_*`: these are
# kube-state-metrics series about Kubernetes objects, and must not be mistaken for
# something Velero itself exports.
# * `nilIsZero` matters — a Schedule that simply omits `spec.paused` (the chart renders
# `velero-daily-resources-only` that way) must still publish paused=0 rather than nothing,
# or `== 1` would be evaluated against a missing series.
# * the KSM Deployment carries NO checksum annotation over this ConfigMap, so a change to
# `config` alone does not restart the pod: after editing it, `kubectl -n monitoring rollout
# restart deploy/kube-prometheus-stack-kube-state-metrics`. Enabling it the first time
# changes the pod spec (new arg + volume), so the initial rollout is automatic.
rbac:
extraRules:
- apiGroups: ["velero.io"]
resources: ["schedules"]
verbs: ["get", "list", "watch"]
customResourceState:
enabled: true
config:
spec:
resources:
- groupVersionKind:
group: velero.io
version: v1
kind: Schedule
metricNamePrefix: kube_velero_schedule
labelsFromPath:
# `schedule` (not `name`) so these join 1:1 with Velero's own `schedule` label.
schedule: [metadata, name]
namespace: [metadata, namespace]
metrics:
- name: created
help: "Unix creation time of the Velero Schedule object."
each:
type: Gauge
gauge:
# KSM parses the RFC3339 timestamp to a unix float (verified live).
# This is what gives VeleroScheduleNeverBackedUp a grace period, so a
# newly added schedule is not alerted before its first run is even due.
path: [metadata, creationTimestamp]
- name: paused
help: "1 if the Velero Schedule is paused and creating no backups."
each:
type: Gauge
gauge:
path: [spec, paused]
nilIsZero: true
- name: protects_volume_data
help: "1 if the Schedule captures pod volume DATA, not just Kubernetes objects."
each:
type: Gauge
gauge:
# THE anti-masking signal: read from the field that defines it, so a
# resources-only schedule can never stand in for a volume-data one.
path: [spec, template, defaultVolumesToFsBackup]
nilIsZero: true
- name: info
help: "Descriptive metadata for the Velero Schedule (cron, phase)."
each:
type: Info
info:
# NOTE: KSM OMITS a label whose path is absent (a Schedule with no
# status.phase yet yields no `phase` label at all), so label sets differ
# between series here. Context for dashboards — never join on this metric.
labelsFromPath:
cron: [spec, schedule]
phase: [status, phase]
# MEMORY RAISED 2026-09-13 after 91 OOMKills. Measured, not guessed: working set 111 MiB
# with a 6h peak of 123.3 MiB against the old 128Mi limit — KSM was dying on every spike,
# roughly every 11 minutes (exit 137). That matters beyond the restarts: THIRTEEN alert
# rules read kube_* series, so each kill made them intermittently inert, and an alert that
# is only sometimes able to fire is the quiet version of the inert-alert class this repo
# keeps getting bitten by (KubePodNotReady and KubeDeploymentReplicasMismatch were both
# stuck pending on it). The trigger was enabling customResourceState below for the Velero
# Schedule metrics — it adds a CRD informer plus the mandatory CRD list/watch, and that
# marginal cost crossed a limit already sitting ~4 MiB above the working set.
# 384Mi is ~3x the observed peak and costs nothing here: the nodes report 18.7-22.3 GiB
# available. Re-measure with
# max_over_time(container_memory_working_set_bytes{container="kube-state-metrics"}[6h])
# before trimming it back.
resources:
requests:
cpu: 20m
memory: 192Mi
limits:
memory: 384Mi
prometheus-node-exporter:
# --- NFS OBSERVABILITY (added 2026-09-14) -------------------------------------------------
# WHY. Five in-tree NFS PVs on 192.168.2.102 carry the whole media library and the legacy
# Nextcloud dataset, and I/O PSI counts an NFS stall as an I/O stall. That is why prod-1's
# 20.98% PSI spike at 02:40Z on 2026-09-14 looked inexplicable from the block layer: devices
# at 0.09-0.21 utilisation, 1.4-4.8 ms per write, zero NFS retransmissions. The one signal
# that moved was 114 NFS reads/s on prod-1 against 0 on the other two nodes.
#
# WHAT IS ALREADY THERE, SO NOBODY "ENABLES" IT TWICE. The `nfs` collector is ON BY DEFAULT
# and its series are confirmed present on prod (node_nfs_rpcs_total, node_nfs_requests_total
# by method/proto, node_nfs_rpc_retransmissions_total — all three nodes, 2026-09-14). It is
# host-wide, read from /proc/net/rpc/nfs, which works because this DaemonSet is hostNetwork.
# It gives op COUNTS and retransmissions. It gives NO LATENCY and no per-mount breakdown, so
# it can say "the server dropped requests" but not "the export is slow".
#
# WHAT THIS ARGUMENT ADDS. `mountstats` reads /proc/.../mountstats and emits per-mount,
# per-operation counters including cumulative RPC queue time and round-trip time, which
# divided by the request count is the per-operation NFS latency this platform has never had.
# That is the missing half of the I/O-cause question: with it, "PSI is high and the export is
# answering slowly" and "PSI is high because WE are asking for a lot" become distinguishable,
# and so does the case where neither holds and the load is coming from the Proxmox media
# stack that still has operational control of the same files.
#
# COST, MEASURED-ADJACENT NOT ASSUMED. mountstats is per-mount and per-operation, so it is
# the highest-cardinality collector in node-exporter. NFSv4.1 exposes ~70 operations and the
# collector emits ~8 counters per operation plus ~15 mount-level series, so roughly 575
# series per mounted export, and the mounts are per POD (kubelet mounts an in-tree NFS PV
# once per pod), so they churn on every restart. With five exports that is ~2.9k series
# against a head of 451,650 measured on prod 2026-09-14 — about 0.6%, inside the 3Gi
# Prometheus limit and the 45GiB retentionSize. Re-measure after rollout with
# count({__name__=~"node_mountstats_.*"})
# and if it lands materially above ~5k series, drop the collector rather than growing the PVC.
#
# VERIFY BEFORE TRUSTING — THIS MAY LAND INERT, AND THAT MUST BE CHECKED NOT ASSUMED.
# node-exporter runs with --path.procfs=/host/proc and hostPID, so it reads ITS OWN mount
# namespace, not the host's. The kubelet-created NFS mounts should still be visible because
# the `root` volume is a hostPath of / with mountPropagation: HostToContainer, which
# propagates them in — they will appear with mount points prefixed /host/root/var/lib/kubelet/
# (the `export` label, e.g. 192.168.2.102:/mnt/Storage/plex, is the stable thing to aggregate
# by). The node-exporter image is distroless with no shell, so this could not be tested from
# outside the collector; note that node_filesystem_* currently reports only ext4 and tmpfs,
# which is explained by the kubelet mount-point exclusion above but is NOT proof either way.
# AFTER THIS ROLLS OUT, RUN:
# count({__name__=~"node_mountstats_.*"}) -> must be non-zero
# count(node_mountstats_nfs_operations_requests_total) by (export)
# If it is empty, REVERT this argument — a collector that is on and produces nothing is the
# same lie as an alert rule on a metric nobody scrapes. No alert rule references
# node_mountstats_* yet, deliberately, for exactly that reason; the per-export latency rule
# is the follow-up once the series are confirmed, and runbooks/node-io.md records the gap.
#
# extraArgs REPLACES, IT DOES NOT APPEND — and the chart's DEFAULT for this key is not empty.
# prometheus-node-exporter's own values.yaml ships two filesystem excludes in `extraArgs`
# (confirmed against the chart, and against the live DaemonSet's argv on prod). Listing only
# `--collector.mountstats` here would silently DROP both, so the filesystem collector would
# start reporting every container overlay and every kubelet bind mount: a large cardinality
# jump and a behaviour change in NodeDiskFillingUp, which alerts per mountpoint. Both
# defaults are therefore restated verbatim below. If the chart's defaults change on an
# upgrade, this list must be re-reconciled against
# helm show values prometheus-community/prometheus-node-exporter | grep -A3 '^extraArgs:'
extraArgs:
- --collector.filesystem.mount-points-exclude=^/(dev|proc|sys|run/containerd/.+|var/lib/docker/.+|var/lib/kubelet/.+)($|/)
- --collector.filesystem.fs-types-exclude=^(autofs|binfmt_misc|bpf|cgroup2?|configfs|debugfs|devpts|devtmpfs|fusectl|hugetlbfs|iso9660|mqueue|nsfs|overlay|proc|procfs|pstore|rpc_pipefs|securityfs|selinuxfs|squashfs|sysfs|tracefs|erofs)$
- --collector.mountstats
resources:
requests:
cpu: 20m
memory: 32Mi
limits:
# mountstats parses a per-mount, per-operation table on every scrape. 64Mi was sized for
# the default collector set; raised with headroom for that parse rather than discovering
# the ceiling as an OOMKill on the exporter that every node alert depends on.
memory: 96Mi