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argocd-apps/apps/base/logging/job_clickhouse-schema.yaml
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unkinben f45cb6989f Add ClickHouse + Vector + NATS JetStream centralized logging (with S3 raw archive) (#296)
## Why

Metrics already land in VictoriaMetrics, but there is no centralized log store. This stands up the logs pillar: capture **all** logs from (a) k8s pods and (b) puppet-managed VMs into ClickHouse, with a **durable NATS JetStream bus** in the middle so logs survive a ClickHouse outage, can be **replayed** after a bad transform, and **fan out** to independent consumers. A third consumer archives selected raw logs to **S3 (Ceph RGW)** for long-horizon replay beyond the JetStream window. The puppet-side Vector rollout is a later task — this PR makes sure a reachable VM ingestion endpoint exists.

## Topology

`edge (publishers) → JetStream → consumers → sinks`

- **NATS JetStream** (dedicated, `logging` ns): 3-replica cluster, file storage on `cephrbd-fast-delete` (50Gi/node). Deliberately **separate from app messaging** (streamstack runs its own NATS in its own repo) for blast-radius isolation. Stream `LOGS` (subjects `logs.>`, `retention=limits`, S2-compressed, **3d / 130 GiB**). Durable consumers = independent offsets.
- **Edge publishers (thin)** — no parsing, just a routing subject:
  - `vector-agent` (DaemonSet): tails every node's pod logs (incl. control-plane) → JetStream `logs.k8s.<ns>.<container>`.
  - `vector-vm-ingest` (Deployment): HTTPS/NDJSON front door behind the `logs-ingest` Gateway → JetStream `logs.vm.<host>`. (Chosen over exposing NATS TCP to ~143 VMs: keeps VM shipping to a simple TLS POST while still gaining JetStream durability; direct-NATS-for-VMs noted as an alternative.)
- **Transform tier** `vector-aggregator` (StatefulSet): pulls the whole stream via durable consumer `transform`, routes by subject, normalises into `logs.raw`, and is the **sole ClickHouse writer**. Disk buffer shrunk to 2GiB/5Gi PVC (JetStream is the real outage buffer now).
- **Archiver** `vector-archiver` (Deployment): its **own** durable consumer `archiver` (independent offsets — archive lag can never stall ClickHouse) writes **raw, pre-transform** events to a Ceph RGW bucket as gzipped NDJSON, keyed `raw/<subject>/YYYY/MM/DD/`. Default subject filter **`logs.k8s.vault.>`** (Vault audit) — configurable via the bootstrap Job's `ARCHIVE_SUBJECTS`.
- **ClickHouse**: Altinity operator + single-shard `ClickHouseInstallation` (200Gi RBD), `logs.raw` MergeTree, 30d TTL, idempotent PostSync schema Job.

## Streams / consumers / auth

- Stream + both durable consumers provisioned by an **idempotent PostSync bootstrap Job** (`nats` CLI). Runbook lines for both replay directions are in the Job's header comment.
- **Distinct NATS users**: `log-producer` (publish `logs.>` only), `log-consumer` (pull + ack only), `log-admin` (bootstrap). Passwords from Vault (`nats-auth` Secret, env-var expansion in the server config). S3 creds from the `cephrgw-operator` `BucketAccess` Secret.

## S3 / retention

`ObjectStoreUser` + `Bucket` (`logs-archive`, retainOnDelete) + `BucketAccess` (read-write) via the in-estate cephrgw-operator. aws_s3 sink → `https://s3.ceph.unkin.net` (path-style, trusts the reflected `vault-ca-cert`). **Object retention is an RGW-side bucket lifecycle policy** (the operator doesn't manage lifecycle) — flagged as an operational knob, not invented here.

## Replay runbook

- **Within 3d (JetStream):** scale the transform tier to 0, `nats consumer rm LOGS transform`, re-run the bootstrap Job (recreates at DeliverAll) — or `nats consumer edit`/`--replay` from a seq/time.
- **Long-horizon (S3):** re-ingest archived objects through the transform tier (vector `aws_s3` source or a one-shot Job); the archive is the replay source beyond JetStream's window.

## Validation

- `kustomize build --enable-helm` clean; `kubeconform` (k8s 1.33.7) all valid — clickhouse-system **22**, logging **38** (incl. `ClickHouseInstallation` via datreeio and the `ceph.unkin.net` CRDs via **local schemas added under `schemas/`**), apps/base **10**.
- `pre-commit` (yamllint, check-json, no-plain-secrets) clean.
- **`vector test`** passes the transform-tier + VM-ingest unit tests; `vector validate` passes the agent + archiver configs.
- **End-to-end integration test (local docker):** ran nats-server (JetStream) with the exact auth block, created the stream + durable consumer, published via Vector (producer ACL), and consumed via Vector's JetStream durable consumer (consumer ACL) — all 3 events pulled, routed, shaped, and **acked** (Outstanding Acks: 0). Confirms the NATS ACLs, Vector JetStream publish, and durable-consumer pull+ack (at-least-once + durable offsets).

## Known upstream caveat

Vector's NATS JetStream source has an open reliability issue (vectordotdev/vector#24932: consumer can stall after a NATS "lame duck"/reconnect). Recovery is a pod restart of the affected consumer; noted for the runbook.

## Prerequisites (manual, one-time)

```
# ClickHouse
PW=$(openssl rand -base64 24); HASH=$(printf '%s' "$PW" | sha256sum | cut -d' ' -f1)
vault kv put kv/kubernetes/namespace/logging/default/clickhouse-credentials \
  username=vector password="$PW" password_sha256_hex="$HASH"
# NATS
vault kv put kv/kubernetes/namespace/logging/default/nats-auth \
  admin_password=$(openssl rand -base64 24) \
  producer_password=$(openssl rand -base64 24) \
  consumer_password=$(openssl rand -base64 24)
```
No terraform-vault change needed (templated `default` k8s auth policy already grants the `logging` namespace KV path). The `vault-ca-cert` Secret is reflected into `logging` by the existing reflector. RGW bucket + creds are provisioned by cephrgw-operator from the CRs in this PR.

## Open decisions (defaults chosen, flag to change)

- **Archive subject filter:** default `logs.k8s.vault.>` (Vault audit). Candidates to add: `logs.k8s.authentik.>`, `logs.k8s.kanidm.>`, VM auth roles — **please confirm the exact security set.**
- **Retention:** ClickHouse **3d** TTL; JetStream **3d** (130 GiB cap, 180Gi/node PVC, S2 compression); S3 lifecycle TBD (RGW-side).
- **Sizing:** NATS 50Gi/node; ClickHouse 200Gi; aggregator 5Gi/2GiB buffer.
- **HA:** ClickHouse single-replica (no Keeper) initially; NATS + transform tier are HA.
- **VM front door:** HTTPS/NDJSON → vm-ingest → JetStream (vs. direct NATS TCP to VMs).
- **CI image:** `timberio/vector:0.57.0-debian` + `natsio/nats-box:0.18.0` (Docker Hub) — mirror if runners restrict egress.

https://claude.ai/code/session_015ur3i7D2azsMAWTSVABApv

---

## Update: images via artifactapi, DHI, stateless transform tier

**Depends on unkin/terraform-artifactapi#16** (dockerhub allowlist patterns) — merge that first or images won't pull.

### Image table (all pulled through `artifactapi.k8s.syd1.au.unkin.net/dockerhub/…`)

| Image | Upstream | artifactapi path | DHI? |
|---|---|---|---|
| clickhouse/clickhouse-server:24.8 | Docker Hub | dockerhub/clickhouse/clickhouse-server | DHI exists — **not used**: subscription/private-namespace + shell-less breaks the bash schema Job |
| altinity/clickhouse-operator:0.27.2 | Docker Hub | dockerhub/altinity/clickhouse-operator | No DHI |
| altinity/metrics-exporter:0.27.2 | Docker Hub | dockerhub/altinity/metrics-exporter | No DHI |
| bitnami/kubectl:latest (crdHook) | Docker Hub | dockerhub/bitnami/kubectl | No DHI |
| nats:2.14.2-alpine | Docker Hub | dockerhub/library/nats | No DHI for nats |
| natsio/nats-server-config-reloader:0.23.0 | Docker Hub | dockerhub/natsio/nats-server-config-reloader | No DHI |
| natsio/nats-box:0.18.0 (bootstrap Job) | Docker Hub | dockerhub/natsio/nats-box | No DHI |
| timberio/vector:0.57.0-distroless-libc (runtime) | Docker Hub | dockerhub/timberio/vector | DHI exists — **not used** (subscription/private-namespace); distroless-libc is already near-hardened |
| timberio/vector:0.57.0-debian (CI only) | Docker Hub | dockerhub/timberio/vector | shell needed for the CI step |

**DHI decision:** Docker Hardened Images exist for clickhouse-server and vector, but they're **subscription-gated and served from a private Docker org namespace** (authenticated pull) — not reachable via the estate's anonymous artifactapi `dockerhub` proxy, and no DHI org/remote exists here. Their shell-less nature would also break the `bash` heredoc in the ClickHouse schema Job and the shell-based `vector-test` CI step. So: **upstream official through artifactapi**, using vector `distroless-libc` for runtime pods. Adopting DHI later would need a Docker Business subscription + an authenticated artifactapi remote for the DHI namespace.

### Transform tier is now a stateless Deployment

Was a StatefulSet with a disk buffer/PVC; now a **Deployment with no PVC and an in-memory buffer** — **JetStream is the sole durability layer**. Added a **CPU HPA (min 2 / max 8)**.

**Ack / backpressure design (important caveat):** Vector's NATS source has **`acknowledgements: no`** — it acks the JetStream message on receipt, *not* after the ClickHouse sink confirms. So end-to-end "sink-failure-must-not-ack" isn't achievable with the current source. What we get instead: the ClickHouse sink uses `buffer.when_full=block`, so on a ClickHouse outage the memory buffer fills, back-pressure stops the pull source, and **unpulled messages stay in JetStream and are redelivered**. The only at-risk window is the in-memory buffer (2000 events) of already-pulled events if a pod is killed *mid-outage*. This is the accepted trade for a stateless, autoscalable tier. HPA is safe because JetStream pull consumers distribute work across N replicas on the single durable consumer `transform`. (If stronger delivery is needed later: reintroduce a StatefulSet+disk buffer, or wait for upstream end-to-end-ack support on the nats source — vectordotdev/vector.)

---

## Update: 7d retention, tunable limits ConfigMap, honest sizing

- **Retention → 7 days** (`max_age=168h`), still `retention=limits` / `discard=old`: the transform tier and the archiver each have their own durable consumer and independently see every message — reading never deletes; only max_age/max_bytes evict.

- **Stream limits live in a ConfigMap** (`nats-stream-limits`: `max_age`, `max_bytes`, `dupe_window`). The `nats-bootstrap` PostSync Job reads them and does an idempotent **create-or-UPDATE** (`nats stream add` || `nats stream edit`). **How a change propagates:** the ConfigMap keeps its kustomize **content-hash suffix**, so editing a value renames the ConfigMap *and* rewrites the Job's `configMapKeyRef`s → the hook Job's spec changes → Argo re-runs it (on top of PostSync hooks running every sync with `hook-delete-policy=BeforeHookCreation`) → `nats stream edit` applies the new limits. No manual `nats` surgery. **Verified against a real nats-server:** create (7d), idempotent re-run, and a `max_age` change (168h→24h) all applied; all flags incl. `--compression=s2` accepted by nats CLI v0.2.3.

- **Honest 7d sizing (stated assumption — please sanity-check against real volume):**
  - Assume **~1,500 events/s** average @ **~1 KiB/event** stored JSON ⇒ **~130 GiB/day raw**, ~910 GiB/7d raw per replica.
  - Enable **JetStream S2 compression** (logs ~4× conservative) ⇒ **~33 GiB/day**, **~230 GiB/7d** compressed per replica.
  - **`max_bytes = 300 GiB`** (headroom over the 230 GiB estimate). **PVC = 400Gi/node** on `cephrbd-fast-delete` (max_bytes + file-store WAL/index/overhead, safely under). **3 replicas ⇒ 1.2 TiB provisioned.**
  - ⚠️ **This is a large, prominent number by design.** If real volume exceeds the assumption, `discard=old` truncates retention **below 7d** rather than silently overflowing. Raising retention/volume requires bumping **both** `max_bytes` (ConfigMap) **and** the file-store PVC (values-nats.yaml) together — the PVC is not a live-tunable knob.

- Replay window in the runbook is now **7d** (beyond that → the S3 archive).

---

## Update: retention cut to 3 days (both stores), PVCs shrunk

Ben: 1.2 TiB is too much. Both stores now retain **3 days**; long-term retention lives **exclusively in the encrypted S3 archive** (the archiver's configured subjects) — everything else is gone after 3d. That's the accepted design.

| Store | Retention | Byte cap | PVC/node | Replicas | Total |
|---|---|---|---|---|---|
| NATS JetStream `LOGS` | `max_age=72h` (3d) | `max_bytes=130 GiB` | 180Gi | 3 | **~0.5 TiB** (was 1.2 TiB) |
| ClickHouse `logs.raw` | `TTL 3 DAY` | — | 150Gi | 1 | 150Gi (was 200Gi) |

**NATS math:** ~33 GiB/day compressed (S2) × 3d ≈ 100 GiB → `max_bytes` 130 GiB (headroom) under a 180Gi PVC.
**ClickHouse math:** ~130 GiB/day raw, LZ4/ZSTD ~6× ⇒ ~20-25 GiB/day ⇒ ~60-75 GiB/3d; +merge headroom ⇒ 150Gi PVC. `logs.raw` is the only table.

The retention knobs remain in the `nats-stream-limits` ConfigMap (max_age/max_bytes/dupe_window) — tunable without redeploy; the ClickHouse TTL is in the bootstrap DDL.

⚠️ **PVC-shrink caveat:** this is a **plan-time** change — the stack **is not deployed yet**, so shrinking PVCs is clean. If it were already deployed, PVCs **cannot shrink in place** (a StatefulSet/CHI PVC resize-down needs a recreate/migration, not an edit).

Reviewed-on: #296
Co-authored-by: Ben Vincent <ben@unkin.net>
Co-committed-by: Ben Vincent <ben@unkin.net>
2026-07-28 19:54:27 +10:00

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YAML

---
# Declarative ClickHouse schema bootstrap. Runs as an ArgoCD PostSync hook so it
# executes after the ClickHouseInstallation is reconciled, and re-runs on every
# sync (idempotent CREATE ... IF NOT EXISTS). Edit the DDL here to evolve the
# schema; the Vector aggregator writes to logs.raw with skip_unknown_fields, so
# adding columns is backward-compatible.
apiVersion: batch/v1
kind: Job
metadata:
name: clickhouse-schema
namespace: logging
annotations:
argocd.argoproj.io/hook: PostSync
argocd.argoproj.io/hook-delete-policy: BeforeHookCreation
labels:
app.kubernetes.io/name: clickhouse-schema
app.kubernetes.io/component: bootstrap
spec:
backoffLimit: 20
activeDeadlineSeconds: 1800
ttlSecondsAfterFinished: 3600
template:
metadata:
labels:
app.kubernetes.io/name: clickhouse-schema
vector.dev/exclude: "true"
spec:
restartPolicy: OnFailure
securityContext:
runAsNonRoot: true
runAsUser: 101
runAsGroup: 101
containers:
- name: clickhouse-schema
image: artifactapi.k8s.syd1.au.unkin.net/dockerhub/clickhouse/clickhouse-server:24.8
securityContext:
allowPrivilegeEscalation: false
readOnlyRootFilesystem: true
capabilities:
drop:
- ALL
env:
- name: HOME
value: /tmp
- name: CLICKHOUSE_USER
valueFrom:
secretKeyRef:
name: clickhouse-credentials
key: username
- name: CLICKHOUSE_PASSWORD
valueFrom:
secretKeyRef:
name: clickhouse-credentials
key: password
command:
- /bin/bash
- -ec
- |
host=clickhouse-logs.logging.svc.cluster.local
echo "Waiting for ClickHouse at ${host}:9000 ..."
until clickhouse-client --host "$host" --port 9000 \
--user "$CLICKHOUSE_USER" --password "$CLICKHOUSE_PASSWORD" \
--query "SELECT 1" >/dev/null 2>&1; do
echo " not ready, retrying in 5s"; sleep 5
done
echo "Applying schema ..."
clickhouse-client --host "$host" --port 9000 \
--user "$CLICKHOUSE_USER" --password "$CLICKHOUSE_PASSWORD" \
--multiquery <<'EOSQL'
CREATE DATABASE IF NOT EXISTS logs;
CREATE TABLE IF NOT EXISTS logs.raw
(
timestamp DateTime64(3) DEFAULT now64(3),
host LowCardinality(String) DEFAULT '',
source LowCardinality(String) DEFAULT '',
namespace LowCardinality(String) DEFAULT '',
pod String DEFAULT '',
container LowCardinality(String) DEFAULT '',
stream LowCardinality(String) DEFAULT '',
severity LowCardinality(String) DEFAULT '',
message String DEFAULT '',
labels Map(LowCardinality(String), String),
fields Map(LowCardinality(String), String)
)
ENGINE = MergeTree
PARTITION BY toDate(timestamp)
ORDER BY (source, namespace, host, timestamp)
TTL toDateTime(timestamp) + INTERVAL 3 DAY
SETTINGS index_granularity = 8192;
EOSQL
echo "Schema applied."
resources:
requests:
cpu: 50m
memory: 128Mi
limits:
cpu: 500m
memory: 512Mi
volumeMounts:
- name: tmp
mountPath: /tmp
volumes:
- name: tmp
emptyDir: {}