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Declarative Grafana / Prometheus / Loki / Tempo observability stack

Browse Source 
Deploys the whole stack into the observability namespace of the local
cluster with Kustomize alone — no helm install, no dashboard created by
hand in the UI. The Makefile carries every command: deploy, dashboards,
diagnostics, PVC flush, teardown.

Dashboards are files, never UI objects. Each carries a stable uid, which
is what keeps URLs, cross-links and alerts alive across redeployments, and
references datasources by stable uid rather than by name. The dashboard
ConfigMap is generated without a name-suffix hash so applying it updates
it in place and Grafana reloads without a restart, while the provisioning
ConfigMaps keep their hash precisely so that a change there does force one.

Prometheus scrapes the kubelet /metrics/resource endpoint rather than
/metrics/cadvisor: on this cluster cadvisor exposes machine_* series only
and no container_* at all, which would leave every CPU and memory panel
empty.

Alloy ships every pod's logs to Loki through the Kubernetes API, so no
/var/log mount is needed. Tempo's metrics_generator feeds span metrics and
the service graph back into Prometheus, and the datasources are wired so a
log line's trace_id opens the matching trace.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This commit is contained in:
Stéphane Tailland
2026-08-25 07:27:38 +02:00
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# 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
```text
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
```bash
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
```bash
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
```bash
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` |
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):
```yaml
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
```bash
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.