Set Up Distributed ClickHouse for SigNoz

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info

In v0.12, SigNoz introduces support for distributed clickhouse. Only multiple shards are supported until v0.42.

In v0.42, support for multiple replicas in distributed clickhouse is added.

Prerequisites

SigNoz version >= 0.42
SigNoz OtelCollector and Schema Migrator >= 0.88.19
SigNoz Chart >= 0.38.1
Zookeeper (or ClickHouse Keeper) is mandatory for running a distributed ClickHouse cluster
3 nodes Zookeeper cluster recommended for distributed ClickHouse cluster with production environment, while single instance of Zookeeper should suffice for development environment

Distributed ClickHouse Setup for SigNoz

Basically, distributed ClickHouse cluster consists of the following:

More than one clickhouse shard/replica instances
All clickhouse server information included in remote_servers clickhouse config as shards
Zookeeper cluster with 1 or 3 nodes, and including it in zookeeper clickhouse config

Follow the instructions in the respective sections below to set up distributed clickhouse with multiple shards/replicas for your SigNoz cluster.

Using Docker

For ClickHouse cluster with 3 shards, you will need to include additional clickhouse services in docker-compose.yaml. You will also need to update clickhouse-cluster.xml to include those additional clickhouse services as multiple shards.

That can be done in the by un-commenting the following in docker-compose.yaml:

x-clickhouse-depend: &clickhouse-depend
  depends_on:
    clickhouse:
      condition: service_healthy
    clickhouse-2:
      condition: service_healthy
    clickhouse-3:
      condition: service_healthy

services:
  ...

  clickhouse-2:
    <<: *clickhouse-defaults
    container_name: signoz-clickhouse-2
    hostname: clickhouse-2
    ports:
      - "9001:9000"
      - "8124:8123"
      - "9182:9181"
    volumes:
      - ./clickhouse-config.xml:/etc/clickhouse-server/config.xml
      - ./clickhouse-users.xml:/etc/clickhouse-server/users.xml
      - ./clickhouse-cluster.xml:/etc/clickhouse-server/config.d/cluster.xml
      # - ./clickhouse-storage.xml:/etc/clickhouse-server/config.d/storage.xml
      - ./data/clickhouse-2/:/var/lib/clickhouse/

  clickhouse-3:
    <<: *clickhouse-defaults
    container_name: signoz-clickhouse-3
    hostname: clickhouse-3
    ports:
      - "9002:9000"
      - "8125:8123"
      - "9183:9181"
    volumes:
      - ./clickhouse-config.xml:/etc/clickhouse-server/config.xml
      - ./clickhouse-users.xml:/etc/clickhouse-server/users.xml
      - ./clickhouse-cluster.xml:/etc/clickhouse-server/config.d/cluster.xml
      # - ./clickhouse-storage.xml:/etc/clickhouse-server/config.d/storage.xml
      - ./data/clickhouse-3/:/var/lib/clickhouse/

To switch to 3 nodes Zookeepers cluster from default 1 node Zookeeper, un-comment the following in docker-compose.yaml:

x-clickhouse-defaults: &clickhouse-defaults
  ...
  depends_on:
    - zookeeper-1
    - zookeeper-2
    - zookeeper-3

services:
  zookeeper-1:
    ...
    environment:
      - ZOO_SERVER_ID=1
      - ZOO_SERVERS=0.0.0.0:2888:3888,zookeeper-2:2888:3888,zookeeper-3:2888:3888
      ...

  zookeeper-2:
    image: bitnami/zookeeper:3.7.0
    container_name: signoz-zookeeper-2
    hostname: zookeeper-2
    user: root
    ports:
      - "2182:2181"
      - "2889:2888"
      - "3889:3888"
    volumes:
      - ./data/zookeeper-2:/bitnami/zookeeper
    environment:
      - ZOO_SERVER_ID=2
      - ZOO_SERVERS=zookeeper-1:2888:3888,0.0.0.0:2888:3888,zookeeper-3:2888:3888
      - ALLOW_ANONYMOUS_LOGIN=yes
      - ZOO_AUTOPURGE_INTERVAL=1

  zookeeper-3:
    image: bitnami/zookeeper:3.7.0
    container_name: signoz-zookeeper-3
    hostname: zookeeper-3
    user: root
    ports:
      - "2183:2181"
      - "2890:2888"
      - "3890:3888"
    volumes:
      - ./data/zookeeper-3:/bitnami/zookeeper
    environment:
      - ZOO_SERVER_ID=3
      - ZOO_SERVERS=zookeeper-1:2888:3888,zookeeper-2:2888:3888,0.0.0.0:2888:3888
      - ALLOW_ANONYMOUS_LOGIN=yes
      - ZOO_AUTOPURGE_INTERVAL=1

Next, you will have to un-comment the following from clickhouse-cluster.xml:

<clickhouse>
    <zookeeper>
        ...
        <node index="2">
            <host>zookeeper-2</host>
            <port>2181</port>
        </node>
        <node index="3">
            <host>zookeeper-3</host>
            <port>2181</port>
        </node>
    </zookeeper>

    <remote_servers>
        <cluster>
            ...
            <shard>
                <replica>
                    <host>clickhouse-2</host>
                    <port>9000</port>
                </replica>
            </shard>
            <shard>
                <replica>
                    <host>clickhouse-3</host>
                    <port>9000</port>
                </replica>
            </shard>
        </cluster>
    </remote_servers>
</clickhouse>

Next, you will have to toggle DOCKER_MULTI_NODE_CLUSTER environment variable to true to ensure migrations are run on new instances (shards) of clickhouse.

services:  
  otel-collector:
    environment:
      - DOCKER_MULTI_NODE_CLUSTER=true

Finally, we execute the following to apply updated docker-compose.yaml:

cd deploy

./install.sh

(Optional) After the migration files run once in all clickhouse instances and healthy SigNoz cluster is verified, you need to make sure migration files do not run for every otel-collector container restart.

You can do that by toggling back DOCKER_MULTI_NODE_CLUSTER environment variable back to false.

services:  
  otel-collector:
    environment:
      - DOCKER_MULTI_NODE_CLUSTER=false

Followed by executing the commands below to apply updated docker-compose.yaml:

cd deploy

./install.sh

Using Docker Swarm

To set up ClickHouse cluster with 3 shards in Docker Swarm, you will need to include additional clickhouse services in docker-compose.yaml. You will also need to update clickhouse-cluster.xml to include those additional clickhouse services as multiple shards.

That can be done in the by un-commenting the following in docker-compose.yaml:

x-clickhouse-depend: &clickhouse-depend
  depends_on:
    clickhouse:
      condition: service_healthy
    clickhouse-2:
      condition: service_healthy
    clickhouse-3:
      condition: service_healthy

services:
  ...

  clickhouse-2:
    <<: *clickhouse-defaults
    hostname: clickhouse-2
    ports:
      - "9001:9000"
      - "8124:8123"
      - "9182:9181"
    volumes:
      - ./clickhouse-config.xml:/etc/clickhouse-server/config.xml
      - ./clickhouse-users.xml:/etc/clickhouse-server/users.xml
      - ./clickhouse-cluster.xml:/etc/clickhouse-server/config.d/cluster.xml
      # - ./clickhouse-storage.xml:/etc/clickhouse-server/config.d/storage.xml
      - ./data/clickhouse-2/:/var/lib/clickhouse/

  clickhouse-3:
    <<: *clickhouse-defaults
    hostname: clickhouse-3
    ports:
      - "9002:9000"
      - "8125:8123"
      - "9183:9181"
    volumes:
      - ./clickhouse-config.xml:/etc/clickhouse-server/config.xml
      - ./clickhouse-users.xml:/etc/clickhouse-server/users.xml
      - ./clickhouse-cluster.xml:/etc/clickhouse-server/config.d/cluster.xml
      # - ./clickhouse-storage.xml:/etc/clickhouse-server/config.d/storage.xml
      - ./data/clickhouse-3/:/var/lib/clickhouse/

To switch to 3 nodes Zookeepers cluster from default 1 node Zookeeper, un-comment the following in docker-compose.yaml:

x-clickhouse-defaults: &clickhouse-defaults
  ...
  depends_on:
    - zookeeper-1
    - zookeeper-2
    - zookeeper-3

services:
  zookeeper-1:
    ...
    environment:
      - ZOO_SERVER_ID=1
      - ZOO_SERVERS=0.0.0.0:2888:3888,zookeeper-2:2888:3888,zookeeper-3:2888:3888
      ...

  zookeeper-2:
    image: bitnami/zookeeper:3.7.0
    hostname: zookeeper-2
    user: root
    ports:
      - "2182:2181"
      - "2889:2888"
      - "3889:3888"
    volumes:
      - ./data/zookeeper-2:/bitnami/zookeeper
    environment:
      - ZOO_SERVER_ID=2
      - ZOO_SERVERS=zookeeper-1:2888:3888,0.0.0.0:2888:3888,zookeeper-3:2888:3888
      - ALLOW_ANONYMOUS_LOGIN=yes
      - ZOO_AUTOPURGE_INTERVAL=1

  zookeeper-3:
    image: bitnami/zookeeper:3.7.0
    hostname: zookeeper-3
    user: root
    ports:
      - "2183:2181"
      - "2890:2888"
      - "3890:3888"
    volumes:
      - ./data/zookeeper-3:/bitnami/zookeeper
    environment:
      - ZOO_SERVER_ID=3
      - ZOO_SERVERS=zookeeper-1:2888:3888,zookeeper-2:2888:3888,0.0.0.0:2888:3888
      - ALLOW_ANONYMOUS_LOGIN=yes
      - ZOO_AUTOPURGE_INTERVAL=1

Next, you will have to un-comment the following from clickhouse-cluster.xml:

<clickhouse>
    <zookeeper>
        ...
        <node index="2">
            <host>zookeeper-2</host>
            <port>2181</port>
        </node>
        <node index="3">
            <host>zookeeper-3</host>
            <port>2181</port>
        </node>
    </zookeeper>

    <remote_servers>
        <cluster>
            ...
            <shard>
                <replica>
                    <host>clickhouse-2</host>
                    <port>9000</port>
                </replica>
            </shard>
            <shard>
                <replica>
                    <host>clickhouse-3</host>
                    <port>9000</port>
                </replica>
            </shard>
        </cluster>
    </remote_servers>
</clickhouse>

Next, you will have to toggle DOCKER_MULTI_NODE_CLUSTER environment variable to true to ensure migrations are run on new instances (shards) of clickhouse.

services:  
  otel-collector:
    environment:
      - DOCKER_MULTI_NODE_CLUSTER=true

Finally, we execute the following to apply updated docker-compose.yaml:

cd deploy

docker stack deploy -c docker-swarm/clickhouse-setup/docker-compose.yaml signoz

You can do that by toggling back DOCKER_MULTI_NODE_CLUSTER environment variable back to false.

services:  
  otel-collector:
    environment:
      - DOCKER_MULTI_NODE_CLUSTER=false

Followed by executing the commands below to apply updated docker-compose.yaml:

cd deploy

docker stack deploy -c docker-swarm/clickhouse-setup/docker-compose.yaml signoz

Kubernetes Installation

To set up ClickHouse cluster of 2 shards with 2 replicas each and 3 nodes Zookeeper cluster, include the following in override-values.yaml:

clickhouse:
  layout:
    shardsCount: 2
    replicasCount: 2
  zookeeper:
    replicaCount: 3
schemaMigrator:
  enableReplication: true

info

In case of single replica in distributed ClickHouse cluster, you can use replicasCount: 1 and disable replication by either removing enableReplication or setting enableReplication: false in schemaMigrator.

Followed by helm upgrade command:

helm --namespace platform upgrade my-release signoz/signoz -f override-values.yaml

To spread ClickHouse instances across multiple nodes in desired order, update clickhouse.podDistribution in values.yaml.

Examples:

All instances in unique nodes:

clickhouse:
  podDistribution:
    - type: ClickHouseAntiAffinity
      topologyKey: kubernetes.io/hostname

Distribute shards of replicas across nodes:

clickhouse:
  podDistribution:
    - type: ReplicaAntiAffinity
      topologyKey: kubernetes.io/hostname

Distribute replicas of shards across nodes:

clickhouse:
  podDistribution:
    - type: ShardAntiAffinity
      topologyKey: kubernetes.io/hostname

For detailed instructions on the Pod Distribution, see here.

info

Replace my-release and platform from above with appropriate release name and SigNoz namespace respectively.

Prerequisites​

Distributed ClickHouse Setup for SigNoz​

Using Docker​

Using Docker Swarm​

Kubernetes Installation​

Prerequisites

Distributed ClickHouse Setup for SigNoz

Using Docker

Using Docker Swarm

Kubernetes Installation