ClickHouse Operator configuration guide

This guide covers how to configure ClickHouse and Keeper clusters using the operator.

ClickHouseCluster configuration

Basic configuration

apiVersion: clickhouse.com/v1alpha1
kind: ClickHouseCluster
metadata:
  name: my-cluster
spec:
  replicas: 3           # Number of replicas per shard
  shards: 2             # Number of shards
  keeperClusterRef:
    name: my-keeper     # Reference to KeeperCluster
  dataVolumeClaimSpec:
    resources:
      requests:
        storage: 10Gi

Replicas and shards

• Replicas: Number of ClickHouse instances per shard (for high availability)
• Shards: Number of horizontal partitions (for scaling)

spec:
  replicas: 3  # Default: 3
  shards: 2    # Default: 1

A cluster with replicas: 3 and shards: 2 will create 6 ClickHouse pods total.

Keeper integration

Every ClickHouse cluster must reference a KeeperCluster for coordination:

spec:
  keeperClusterRef:
    name: my-keeper
    # namespace: keeper-system  # Optional, defaults to the ClickHouseCluster namespace

When keeperClusterRef.namespace is set, the operator must watch both namespaces. If WATCH_NAMESPACE is configured, include the ClickHouse and Keeper namespaces in that list.

KeeperCluster configuration

apiVersion: clickhouse.com/v1alpha1
kind: KeeperCluster
metadata:
  name: my-keeper
spec:
  replicas: 3  # Must be odd: 1, 3, 5, 7, 9, 11, 13, or 15
  dataVolumeClaimSpec:
    resources:
      requests:
        storage: 5Gi

Storage configuration

Configure persistent storage with dataVolumeClaimSpec, a standard Kubernetes PersistentVolumeClaimSpec. The operator turns it into a per-replica PersistentVolumeClaim mounted at the data path /var/lib/clickhouse:

spec:
  dataVolumeClaimSpec:
    storageClassName: fast-ssd  # Optional: consider your storage class based on the installed CSI
    resources:
      requests:
        storage: 100Gi

Attaching extra disks in a multi-disk (JBOD) layout, running without a persistent volume, expanding capacity, custom storage policies, at-rest encryption, and the rules for what cannot change after creation are covered in the dedicated Storage and volumes guide.

Cluster domain

spec.clusterDomain sets the Kubernetes DNS suffix the operator uses when it builds the fully-qualified pod host names it writes into the ClickHouse server configuration. It defaults to cluster.local and exists on both ClickHouseCluster and KeeperCluster.

spec:
  clusterDomain: cluster.local   # default; override only for a custom domain

For ClickHouse replicas the operator creates a governing headless Service <cluster-name>-clickhouse-headless that serves client traffic. And per-replica services <cluster-name>-clickhouse-internal-<shard>-<index> that publish unready Pods for internal traffic and management requests from the operator. This can be used for replica recovery if it cannot become ready itself.

Keeper nodes use pod names through their headless Service: <pod>.<headless-service>.<namespace>.svc.<clusterDomain>.

Pod configuration

Automatic topology spread and affinity

Distribute pods across availability zones:

spec:
  podTemplate:
    topologyZoneKey: topology.kubernetes.io/zone
    nodeHostnameKey: kubernetes.io/hostname

Manual configuration

Arbitrary pod affinity/anti-affinity rules and topology spread constraints can be specified.

spec:
  podTemplate:
    affinity:
      <your-affinity-rules-here>
    topologySpreadConstraints:
      <your-topology-spread-constraints-here>

See API Reference for all supported Pod template options.

Pod disruption budgets

The operator creates a PodDisruptionBudget (PDB) for each cluster so that voluntary disruptions — node drains, rolling upgrades, autoscaler evictions — cannot take down enough pods to lose quorum or break availability.

For ClickHouse clusters with more than one shard, one PDB is created per shard so a disruption in one shard cannot count against another.

Defaults

The operator picks safe defaults based on the cluster size so that a fresh apply already protects against accidental quorum loss.

For a 3-shard ClickHouseCluster with replicas: 3, the operator creates three PDBs, one per shard, each with minAvailable: 1.

Overriding the defaults

Use spec.podDisruptionBudget to override either minAvailable or maxUnavailable (exactly one):

spec:
  replicas: 3
  shards: 2
  podDisruptionBudget:
    minAvailable: 2   # keep at least 2 of 3 replicas in every shard up during a disruption

Or the maxUnavailable form, with a percentage:

spec:
  replicas: 5
  podDisruptionBudget:
    maxUnavailable: 40%

You can also pass the unhealthyPodEvictionPolicy field through to the generated PDB — useful when you need to allow eviction of pods that are still in NotReady:

spec:
  podDisruptionBudget:
    minAvailable: 2
    unhealthyPodEvictionPolicy: AlwaysAllow

Policies

spec.podDisruptionBudget.policy lets you choose how aggressively the operator manages PDBs:

Example — disable PDB management completely on a development cluster:

spec:
  podDisruptionBudget:
    policy: Disabled

Example — keep your hand-crafted PDB next to the cluster and stop the operator from touching it:

spec:
  podDisruptionBudget:
    policy: Ignored

Cluster-wide opt-out

PDB management can also be disabled cluster-wide via the operator’s ENABLE_PDB environment variable. With ENABLE_PDB=false, the operator skips the PDB reconcile step for every ClickHouseCluster and KeeperCluster regardless of their spec.podDisruptionBudget.policy, and does not watch PodDisruptionBudget resources at all. The operator’s ServiceAccount therefore does not need RBAC permissions on poddisruptionbudgets.policy/v1, which is useful when running the operator under a restricted ServiceAccount that intentionally omits those permissions.

# in the operator Deployment spec
env:
- name: ENABLE_PDB
  value: "false"

This is intended for environments that ship their own disruption policies (e.g. through Gatekeeper / Kyverno) and want the operator out of the loop entirely.

Container configuration

Custom image

Use a specific ClickHouse image:

spec:
  containerTemplate:
    image:
      repository: clickhouse/clickhouse-server
      tag: "25.12"
    imagePullPolicy: IfNotPresent

Container resources

Configure CPU and memory for ClickHouse containers:

# default values
spec:
  containerTemplate:
    resources:
      requests:
        cpu: "250m"
        memory: "512Mi"
      limits:
        cpu: "1"
        memory: "512Mi"

Environment variables

Add custom environment variables:

spec:
  containerTemplate:
    env:
    - name: CUSTOM_ENV_VAR
      value: "1"

Volume mounts

Add additional volume mounts:

spec:
  containerTemplate:
    volumeMounts:
    - name: custom-config
      mountPath: /etc/clickhouse-server/config.d/custom.xml
      subPath: custom.xml

See API Reference for all supported Container template options.

TLS/SSL configuration

Configure secure endpoints

Pass a reference to a Kubernetes Secret containing TLS certificates to enable secure endpoints

spec:
  settings:
    tls:
      enabled: true
      required: true # Insecure ports are disabled if set
      serverCertSecret:
        name: <certificate-secret-name>

SSL certificate secret format

It is expected that the Secret contains the server keypair:

• tls.crt - PEM encoded server certificate
• tls.key - PEM encoded private key

ClickHouse-Keeper communication over TLS

If KeeperCluster has TLS enabled, ClickHouseCluster would use secure connection to Keeper nodes automatically.

ClickHouseCluster verifies Keeper node certificates against the system trust store, plus any caBundle you configure.

To trust a private CA (for example, a self-signed or internal CA), provide a custom CA bundle reference:

spec:
    settings:
        tls:
          caBundle:
            name: <ca-certificate-secret-name>
            key: <ca-certificate-key>

External Secret

By default the operator creates and owns a Secret containing the cluster’s internal credentials (interserver password, management password, keeper identity, cluster secret, named-collections key). The Secret is named after the cluster and lives in the cluster’s namespace.

If you want to manage these credentials yourself — for example, sourcing them from HashiCorp Vault, AWS Secrets Manager, or External Secrets Operator — point the operator at a pre-existing Secret using spec.externalSecret:

apiVersion: clickhouse.com/v1alpha1
kind: ClickHouseCluster
metadata:
  name: sample
spec:
  replicas: 2
  keeperClusterRef:
    name: sample
  dataVolumeClaimSpec:
    resources:
      requests:
        storage: 10Gi
  externalSecret:
    name: my-clickhouse-credentials
    policy: Observe

Required keys

The Secret must contain the following keys:

A complete Secret looks like this:

apiVersion: v1
kind: Secret
metadata:
  name: my-clickhouse-credentials
  namespace: sample
type: Opaque
stringData:
  interserver-password: "a-strong-random-password"
  management-password: "another-strong-password"
  keeper-identity: "clickhouse:keeper-auth-password"
  cluster-secret: "cluster-internal-secret"
  named-collections-key: "0123456789abcdef0123456789abcdef"   # 32 hex chars = 16 bytes
  disk-encryption-key: "00112233445566778899aabbccddeeff"     # only when settings.encryption is set

Policy: Observe vs Manage

spec.externalSecret.policy controls how the operator handles missing required keys:

Pick Observe when an external system (Vault, ESO, sealed-secrets, GitOps) is the source of truth and you want the operator to fail loudly on misconfiguration. Pick Manage when you want self-sufficient bootstrapping but still want to retain ownership of the Secret object itself (for example, to back it up).

Status condition and troubleshooting

The operator exposes a ExternalSecretValid condition on ClickHouseCluster.status.conditions. Inspect it when reconciliation looks stuck:

# Plain kubectl — works out of the box
kubectl describe clickhousecluster sample | sed -n '/Conditions:/,$p'

# Same data as YAML
kubectl get clickhousecluster sample -o yaml | sed -n '/conditions:/,/^[^ ]/p'

# Pretty-printed JSON (requires jq)
kubectl get clickhousecluster sample -o jsonpath='{.status.conditions}' | jq

Possible reasons:

The operator requeues reconciliation while the Secret is invalid, so once you add the missing keys the next reconcile picks them up automatically — no need to bounce pods.

Additional ports

The operator exposes a fixed set of ports on every ClickHouse Pod and its public headless Service: 8123 HTTP, 9000 native, 9009 interserver, 9001/9002 management, 9363 Prometheus metrics, and the TLS variants 8443/9440 when TLS is enabled. The interserver and management ports are additionally exposed through the per-replica internal Services so replicas and the operator can communicate before a replica becomes ready. To make ClickHouse listen on additional protocols — MySQL, PostgreSQL, gRPC, or any custom port — declare them in spec.additionalPorts:

spec:
  additionalPorts:
    - name: mysql
      port: 9004
    - name: postgres
      port: 9005
    - name: grpc
      port: 9100

The operator adds those ports to the Pod’s containerPorts and the public headless Service. The complete example lives at examples/custom_protocols.yaml.

End-to-end example: MySQL wire protocol

To expose ClickHouse over the MySQL wire protocol on port 9004:

apiVersion: clickhouse.com/v1alpha1
kind: ClickHouseCluster
metadata:
  name: sample
spec:
  replicas: 1
  keeperClusterRef:
    name: sample
  dataVolumeClaimSpec:
    resources:
      requests:
        storage: 2Gi

  # 1) Open the port on the Pod and the public headless Service.
  additionalPorts:
    - name: mysql
      port: 9004

  # 2) Tell ClickHouse server to actually listen on it.
  settings:
    extraConfig:
      protocols:
        mysql:
          type: mysql
          port: 9004
          description: "MySQL wire protocol"

After applying, verify from inside the cluster:

kubectl exec sample-clickhouse-0-0-0 -- \
  clickhouse-client --port 9004 --query "SELECT 1"

Field constraints

Reserved ports and names

The validating webhook rejects additionalPorts entries that would collide with ports the operator binds itself. All TLS-related ports are reserved unconditionally so that flipping spec.settings.tls.enabled later cannot break a previously valid cluster.

The following names are also rejected — they are the operator’s internal protocol-type identifiers (not the human-readable aliases):

A rejected request produces an error such as:

spec.additionalPorts[0].port: 8123 is reserved for the operator-managed HTTP port
spec.additionalPorts[0].name: "http" is reserved by the operator

Version probe and upgrade channel

The operator does two independent things with cluster versions:

1. Version reporting — for ClickHouseCluster, a Kubernetes Job runs the container image once to detect the running ClickHouse version; for KeeperCluster, the operator reads the server-reported version from running replicas. The detected version is recorded in .status.version and used by other reconciliation steps (e.g. the External Secret named-collections key is only required from ClickHouse 25.12).
2. Upgrade channel — a periodic check against the public ClickHouse release feed (https://clickhouse.com/data/version_date.tsv). The operator reports whether a newer version is available via the VersionUpgraded status condition. It never upgrades the cluster on its own — the user is in control of the image tag.

Choosing a release channel

spec.upgradeChannel selects which set of upstream releases the operator compares against. Same field exists on both ClickHouseCluster and KeeperCluster.

spec:
  upgradeChannel: lts   # or "stable", or "25.8", or omitted

Allowed values (validated by the CRD with the pattern ^(lts|stable|\d+\.\d+)?$):

For production, pinning the channel to an explicit <major>.<minor> (e.g. 25.8) is generally preferred. It locks the cluster to the intended major release line and lets the operator surface a WrongReleaseChannel warning if any replica somehow drifts onto a different major — which matters especially when the image is referenced by a digest (@sha256:...) rather than by a human-readable tag. The empty default is fine for development clusters where major-version jumps are not a concern.

Status conditions

Two conditions surface the result of the probe and the upgrade check:

Inspect them with:

kubectl get clickhousecluster sample -o yaml | sed -n '/conditions:/,/^[^ ]/p'

Overriding the version probe Job

This applies to ClickHouseCluster only. KeeperCluster no longer runs a version-probe Job — its version is read directly from the running Keeper replicas — so spec.versionProbeTemplate is deprecated and has no effect there.

The probe is implemented as a regular Kubernetes Job. If your cluster has admission policies that require specific Tolerations, node selectors, security contexts, or you want to limit how long completed probe Jobs linger, override the template via spec.versionProbeTemplate:

spec:
  versionProbeTemplate:
    spec:
      ttlSecondsAfterFinished: 600   # delete completed probe Jobs 10 minutes after completion
      template:
        spec:
          nodeSelector:
            kubernetes.io/arch: amd64
          tolerations:
            - key: dedicated
              operator: Equal
              value: clickhouse
              effect: NoSchedule
          containers:
            - name: version-probe
              resources:
                requests:
                  cpu: 50m
                  memory: 64Mi

The container name version-probe is the operator’s default — the entry under containers: matches it by name, so the operator deep-merges the user-provided fields on top of the defaults.

Operator-wide controls

Two flags on the operator manager control the upgrade-check loop globally:

Set --disable-version-update-checks=true in air-gapped environments or when egress to clickhouse.com is not allowed.

ClickHouse settings

Default user password

spec.settings.defaultUserPassword sets the password for the built-in default user. Provide the value from a key in a Secret (recommended) or a ConfigMap that you create, rather than inline in the CR:

spec:
  settings:
    defaultUserPassword:
      passwordType: password   # default; see "Password types" below
      secret:                  # exactly one of secret or configMap
        name: clickhouse-password   # name of the Secret/ConfigMap
        key: password               # the key inside it, not the password value

Provide exactly one of secret or configMap, each with both name (the object) and key (the entry that holds the password).

Password types

passwordType tells ClickHouse how to interpret the value. It defaults to password (plaintext); the alternatives are hashed forms such as password_sha256_hex and password_double_sha1_hex. Prefer a hashed type so the plaintext is never stored. See the ClickHouse user settings for the full list.

Full example with a Secret

Create the Secret, then reference its key:

kubectl create secret generic clickhouse-password \
  --from-literal=password='your-secure-password'

apiVersion: clickhouse.com/v1alpha1
kind: ClickHouseCluster
metadata:
  name: my-cluster
spec:
  settings:
    defaultUserPassword:
      passwordType: password
      secret:
        name: clickhouse-password
        key: password

For a hashed password, store the hash instead of the plaintext:

echo -n 'your-secure-password' | sha256sum   # use the hex digest as the value
kubectl create secret generic clickhouse-password \
  --from-literal=password='<sha256-hex-digest>'

spec:
  settings:
    defaultUserPassword:
      passwordType: password_sha256_hex
      secret:
        name: clickhouse-password
        key: password

Using a ConfigMap

A ConfigMap works the same way, but its contents are not protected like a Secret. Use it only for non-sensitive or already-hashed values, such as a password_sha256_hex digest:

spec:
  settings:
    defaultUserPassword:
      passwordType: password_sha256_hex
      configMap:
        name: clickhouse-config
        key: default_password

Custom users in configuration

Configure additional users in configuration files.

Create a ConfigMap and Secret for user:

apiVersion: v1
kind: ConfigMap
metadata:
  name: user-config
data:
  reader.yaml: |
    users:
      reader:
        password:
          - '@from_env': READER_PASSWORD
        profile: default
        grants:
          query:
            - "GRANT SELECT ON *.*"
---
apiVersion: v1
kind: Secret
metadata:
  name: reader-password
data:
  password: "c2VjcmV0LXBhc3N3b3Jk"  # base64("secret-password")

Add custom configuration to ClickHouseCluster:

spec:
  podTemplate:
    volumes:
      - name: reader-user
        configMap:
          name: user-config
  containerTemplate:
    env:
      - name: READER_PASSWORD
        valueFrom:
          secretKeyRef:
            name: reader-password
            key: password
    volumeMounts:
      - mountPath: /etc/clickhouse-server/users.d/
        name: reader-user
        readOnly: true

Database sync

Enable automatic database synchronization for new replicas:

spec:
  settings:
    enableDatabaseSync: true  # Default: true

When enabled, the operator synchronizes Replicated and integration tables to new replicas.

Every replica Pod carries the clickhouse.com/ReplicaInitialized readiness gate, so a new replica is published through the public headless Service only after the operator completes its initialization: the default database is converted to the Replicated engine and the schema is synchronized. Until then, the operator and the other replicas reach it through its internal Service. With enableDatabaseSync: false, the operator marks replicas initialized immediately, so readiness follows the container probes alone.

The operator never drops a populated non-Replicated default database. Such a replica still starts serving client traffic after schema preparation, but the cluster reports SchemaInSync=False with reason DefaultDatabaseNotReplicated until you resolve that database yourself.

Before a replica is removed on scale-down, the operator first unloads client traffic from it, waits until it stops being published, replicates its remaining data to the surviving replicas, and only then deletes it.

Server logging

Configure the ClickHouse server log through spec.settings.logger. Every field is optional with a safe default, so a cluster you never touch already logs at trace to both the container console and a rotated file on disk.

spec:
  settings:
    logger:
      logToFile: true   # Default: true. Set false to log only to the console
      jsonLogs: false   # Default: false. Set true for structured JSON log lines
      level: trace      # Default: trace
      size: 1000M       # Default: 1000M. Rotate a log file once it reaches this size
      count: 50         # Default: 50. Number of rotated files to keep

The operator always keeps console logging on so that kubectl logs works, and layers file logging on top when logToFile is true. A cluster with the defaults renders this logger block:

logger:
  console: true
  level: trace
  log: /var/log/clickhouse-server/clickhouse-server.log
  errorlog: /var/log/clickhouse-server/clickhouse-server.err.log
  size: 1000M
  count: 50

The same spec.settings.logger block applies to a KeeperCluster; the operator writes its files under /var/log/clickhouse-keeper/ instead.

Custom configuration

Embedded extra configuration

Instead of mounting custom configuration files, you can directly specify additional ClickHouse configuration options.

Add custom ClickHouse configuration using extraConfig:

spec:
  settings:
    extraConfig:
      background_pool_size: 20

Useful links:

• YAML configuration examples
• All server settings

Embedded extra users configuration

You can also specify additional ClickHouse users configuration using extraUsersConfig. This is useful for defining users, profiles, quotas, and grants directly in the cluster specification.

spec:
  settings:
    extraUsersConfig:
      users:
        analyst:
          password:
            - '@from_env': ANALYST_PASSWORD
          profile: "readonly"
          quota: "default"
      profiles:
        readonly:
          readonly: 1
          max_memory_usage: 10000000000
      quotas:
        default:
          interval:
            duration: 3600
            queries: 1000
            errors: 100

See documentation for all supported ClickHouse users configuration options.

Configuration example

Complete configuration example:

apiVersion: clickhouse.com/v1alpha1
kind: KeeperCluster
metadata:
  name: sample
spec:
  replicas: 3
  dataVolumeClaimSpec:
    storageClassName: <storage-class-name>
    resources:
      requests:
        storage: 10Gi
  podTemplate:
    topologyZoneKey: topology.kubernetes.io/zone
    nodeHostnameKey: kubernetes.io/hostname
  containerTemplate:
    resources:
      requests:
        cpu: "2"
        memory: "4Gi"
      limits:
        cpu: "4"
        memory: "8Gi"
  settings:
    tls:
      enabled: true
      required: true
      serverCertSecret:
        name: <keeper-certificate-secret>
---
apiVersion: v1
kind: ConfigMap
metadata:
  name: default-user-password
data:
  # secret-password
  password: "..." # sha256 hex of the password
---
apiVersion: clickhouse.com/v1alpha1
kind: ClickHouseCluster
metadata:
  name: sample
spec:
  replicas: 2
  dataVolumeClaimSpec:
    storageClassName: <storage-class-name>
    resources:
      requests:
        storage: 200Gi
  keeperClusterRef:
    name: sample
  podTemplate:
    topologyZoneKey: topology.kubernetes.io/zone
    nodeHostnameKey: kubernetes.io/hostname
  settings:
    tls:
      enabled: true
      required: true
      serverCertSecret:
        name: clickhouse-cert
    defaultUserPassword:
      passwordType: password_sha256_hex
      configMap:
        key: password
        name: default-password