infra-observability/README.md

Infra Observability (Kubernetes / declarative)

Grafana 13.2 / Prometheus 3.14 / Loki 3.7 / Tempo 3.0 plus Alloy 1.19, deployed fully declaratively (Kustomize) into the observability namespace of the local orbstack cluster.

Nothing is imperative: no helm install, no dashboard hand-created in the UI. The entire desired state lives in this repository and make deploy reconciles it.

Repository layout

Makefile                              # Every command (make = help)
k8s/
├── kustomization.yaml                # Root Kustomize manifest
├── namespace.yaml                    # observability namespace
├── secret.yaml                       # Grafana admin credentials (GITIGNORED)
├── secret.example.yaml               # Secret template
├── prometheus/
│   ├── prometheus.yaml               # Scrape config (Kubernetes SD)
│   ├── rbac.yaml                     # SA + discovery ClusterRole
│   ├── secret.yaml                   # LibreChat scrape token (GITIGNORED)
│   ├── secret.example.yaml           # Token template
│   ├── pvc.yaml                      # Persistent TSDB (10Gi)
│   ├── deployment.yaml               # Prometheus v3.14.0
│   └── service.yaml                  # :9090
├── loki/
│   ├── loki.yaml                     # Monolithic config, filesystem storage
│   ├── pvc.yaml                      # Chunks + index (10Gi)
│   ├── deployment.yaml               # Loki 3.7.6 (-target=all)
│   └── service.yaml                  # :3100 (HTTP) / :9096 (gRPC)
├── tempo/
│   ├── tempo.yaml                    # Monolithic config + metrics-generator
│   ├── pvc.yaml                      # WAL + trace blocks (10Gi)
│   ├── deployment.yaml               # Tempo 3.0.3 (-target=all)
│   └── service.yaml                  # :3200, OTLP :4317/:4318, Zipkin :9411
├── alloy/
│   ├── config.alloy                  # Pod logs -> Loki pipeline
│   ├── rbac.yaml                     # SA + ClusterRole (including pods/log)
│   ├── daemonset.yaml                # Alloy v1.19.0 (one pod per node)
│   └── service.yaml                  # :12345 (UI + /metrics)
├── grafana/
│   ├── provisioning/
│   │   ├── datasources.yaml          # Datasources with stable UIDs
│   │   └── dashboard-providers.yaml  # File provider
│   ├── dashboards/
│   │   ├── kustomization.yaml        # ConfigMap WITHOUT hash (hot reload)
│   │   ├── obs-stack-health.json     # uid: obs-stack-health
│   │   ├── obs-keycloak.json         # uid: obs-keycloak
│   │   ├── obs-librechat.json        # uid: obs-librechat
│   │   └── obs-classic-models-api.json
│   ├── pvc.yaml                      # Grafana SQLite database (5Gi)
│   ├── deployment.yaml               # Grafana 13.2.0
│   └── service.yaml                  # :3000
└── ingress/
    ├── certificate.yaml              # cert-manager Certificate (sttlab-local-ca)
    └── ingress.yaml                  # Three NGINX Ingresses

Getting started

make                     # Help: every available target
make deploy              # Deploy the whole stack
make hosts               # /etc/hosts entries to add
make grafana-password    # Admin credentials
make smoke               # End-to-end verification

URL	Purpose
https://grafana.sttlab.local	Grafana UI
https://prometheus.sttlab.local	Prometheus UI (targets, expression browser)
https://alloy.sttlab.local	Alloy UI (log pipeline state)

Sending traces from an in-cluster application: tempo.observability.svc.cluster.local:4317 (OTLP gRPC) or :4318 (OTLP HTTP).

Declarative dashboards with stable UIDs

This is the centrepiece of the repository: a dashboard only ever exists as a versioned JSON file, never as an object created through the UI.

Rules

1. One .json file per dashboard, under k8s/grafana/dashboards/.
2. The uid field is stable and never changes. It is what keeps URLs (/d/<uid>/…), cross-dashboard links, annotations and alerts alive across every redeployment. By convention the filename equals the UID (obs-keycloak.json -> uid: obs-keycloak).
3. The id field must stay null (or absent): it is an identifier internal to a Grafana instance and is not portable.
4. Datasources are referenced by stable UID, never by name: "datasource": { "type": "prometheus", "uid": "prometheus" }. Available UIDs: prometheus, loki, tempo.
5. allowUiUpdates: false: any change made in the UI is overwritten on the next reload. The file is the source of truth.

Adding a dashboard

cp my-dashboard.json k8s/grafana/dashboards/obs-my-topic.json
# edit the JSON: "uid": "obs-my-topic", "id": null
make dashboards-sync     # update the list in dashboards/kustomization.yaml
make dashboards          # apply (without restarting Grafana)

make dashboards-check (run automatically by dashboards and validate) verifies: valid JSON, uid present, uid unique, id null, file referenced in the kustomization, filename/UID consistency.

How the hot reload works

The grafana-dashboards ConfigMap is generated without a name-suffix hash (disableNameSuffixHash: true), so make dashboards updates it in place: the Grafana pod is not recreated and the file provider re-reads the directory (updateIntervalSeconds: 10).

Measured end-to-end delay: about 70 seconds (kubelet ConfigMap volume sync ~60s + provider poll 10s). For immediate effect: make restart-grafana.

Conversely, the provisioning ConfigMaps (datasources, providers) keep their hash suffix: those files are only read at startup, so the hash deliberately forces a pod restart when they change.

Persistence

PVC	Component	Size	Contents	Retention
prometheus-data	Prometheus	10Gi	TSDB	15 d / 8 GB
loki-data	Loki	10Gi	chunks + TSDB index	168 h (compactor)
tempo-data	Tempo	10Gi	WAL + trace blocks	168 h
grafana-data	Grafana	5Gi	SQLite database (users, prefs)	—

StorageClass local-path (the cluster default), ReadWriteOnce. The Deployments use strategy: Recreate: with an RWO volume the old pod must release it before the new one can start.

Alloy's read positions live on a hostPath (/var/lib/alloy), so restarting the DaemonSet does not re-ingest every log.

Wiping data

make pvc                             # PVC state
make flush-loki       CONFIRM=yes    # wipe the logs only
make flush-prometheus CONFIRM=yes    # wipe the TSDB only
make flush-pvc        CONFIRM=yes    # wipe EVERYTHING

The cycle is: scale 0 -> wait for pod deletion -> delete pvc -> reapply the kustomization (which recreates the PVC) -> scale 1. Every destructive target requires CONFIRM=yes.

Dashboards are not affected by flush-grafana: they are reprovisioned from the ConfigMaps at startup.

Wiring the three signals

• Prometheus discovers its targets through the Kubernetes API: apiserver, kubelet, container resource metrics, plus any Service or Pod carrying the prometheus.io/scrape: "true" annotation (prometheus.io/port, prometheus.io/path).
• Alloy reads every pod's logs through the Kubernetes API (no /var/log mount) and pushes them to Loki with namespace, pod, container, node, app, component and job labels.
• Tempo receives OTLP, and its metrics_generator pushes span metrics and service graphs to Prometheus through its remote-write receiver (--web.enable-remote-write-receiver).
• Grafana correlations: Loki -> Tempo (TraceID derived field), Tempo -> Loki (tracesToLogsV2), Tempo -> Prometheus (serviceMap, tracesToMetrics), Prometheus exemplars -> Tempo.

Container resource metrics

Prometheus scrapes the kubelet's /metrics/resource endpoint, not /metrics/cadvisor. On this cluster the cadvisor endpoint answers with machine_* series only and exposes no container_* at all, so CPU and memory panels would stay empty. /metrics/resource — the source metrics-server itself reads — provides container_cpu_usage_seconds_total and container_memory_working_set_bytes with namespace/pod/container labels.

kube-state-metrics is not deployed, so container restarts are derived from changes in container_start_time_seconds.

Connected applications

Application	Traces	Metrics	Logs	Dashboard
keycloak	OTel Java agent → tempo:4318	native /metrics (management port 9000)	JSON + MDC trace_id	obs-keycloak
librechat	OTel SDK → tempo:4318	built-in /metrics, Bearer token	stdout	obs-librechat
classic-models-api	opentelemetry-instrument → tempo:4318	django-prometheus /metrics	JSON + otelTraceID	obs-classic-models-api

The six Kong gateways share a single dashboard, obs-kong-gateways, with a gateway selector at the top (one, several, or all). Its variable resolves a subtlety of this setup: the metrics label is the full gateway name (catalog-dev) while the audit-log label is the short domain (catalog). The variable holds the short form, PromQL re-adds the -dev suffix, and LogQL uses it as-is — so one control drives both signals. The capture group in its regex also drops the unrelated kong gateway, which carries no -dev suffix.

Their manifests live in the infra-keycloak, infra-librechat and classic-models-api repositories; this repository only holds the platform.

Each application dashboard carries the same four sections: an overview of RED indicators, HTTP traffic, a runtime section specific to the stack in use, and a Logs row, followed by container resources.

The Logs row leans on Loki's detected_level, which is inferred at ingestion time, so a single query works across all three log formats — Keycloak emits JSON, LibreChat colour-coded text, and the Django API plain gunicorn access lines. No per-application parser is needed. The volume panel is scoped to the application container, while the two error panels cover the whole namespace so the datastore's own failures surface alongside the application's. Where a log line carries a trace_id, the Loki datasource's derived field turns it into a link straight to the matching trace in Tempo.

Connecting an application

1. Traces — point OTLP at Tempo: OTEL_EXPORTER_OTLP_ENDPOINT=http://tempo.observability.svc.cluster.local:4318 (:4317 for gRPC). RED span metrics and the service graph are then derived automatically by Tempo's metrics_generator, with no extra instrumentation.
2. Metrics — annotate the pod (not the Service):

   annotations:
     prometheus.io/scrape: "true"
     prometheus.io/port: "9000"
     prometheus.io/path: "/metrics"
   

3. Logs — nothing to do: Alloy collects every pod in the cluster. For Grafana to jump from a log line to its trace, the line only needs to contain a trace_id (the Loki datasource's derived field).

Token-protected endpoints

Annotation-based discovery cannot carry credentials, so an authenticated target gets its own scrape_config in k8s/prometheus/prometheus.yaml, with the token mounted from a Secret — see the librechat job, which reads /etc/prometheus/secrets/librechat/token.

That token must be identical on both sides: METRICS_SECRET in the librechat-secrets secret (namespace librechat) and the token key of the librechat-metrics secret (namespace observability, file k8s/prometheus/secret.yaml, gitignored).

A Kubernetes Secret is namespaced and a pod can only mount ones from its own namespace, so the same value has to exist twice — once for LibreChat, which verifies the token, once for Prometheus, which presents it. The risk is silent drift: regenerating one side without the other sends the scrape back to 401 without breaking anything else. make check-metrics-token (included in make diag) compares both copies.

Diagnostics

make status              # pods, services, PVCs, ingresses
make diag                # + endpoints, certificate, failing containers, events
make smoke               # health of all five components, datasources, dashboards, targets
make targets             # Prometheus targets and their last scrape error
make logs-loki           # follow one component's logs
make top                 # CPU/memory usage
make pf-grafana          # port-forward when the ingress is unavailable
make diff                # difference between the repository and the cluster
make validate            # kustomize build + server dry-run + dashboard checks

Secrets

k8s/secret.yaml and k8s/prometheus/secret.yaml are gitignored. make secret generates the first from secret.example.yaml with a random admin password if it does not exist (and is called automatically by make deploy).

The TLS certificate is not versioned either: it is issued by the existing sttlab-local-ca cert-manager ClusterIssuer (k8s/ingress/certificate.yaml).

Coexisting with what was already there

The observability namespace already hosts two deployments not managed by this repository, left untouched:

• jaeger (installed by Helm) — it also exposes OTLP on 4317/4318, but on its own Service, so there is no conflict with Tempo. Since all three applications now point at Tempo, Jaeger no longer receives anything; uninstall the Helm release whenever you want a single trace backend.
• audit-log-collector (Fluent Bit) — writes to its own PVC.

make undeploy and make destroy only run kubectl delete -k k8s/, so they touch nothing but the resources described here.