Configure Zipkin with Mysql in Docker

If you are here, you know what Zipkin is and what it's good at, but if needed, check out its homepage OpenZipkin · A distributed tracing system.

 It was a bit of a challenge for me to persist the data with mysql, otherwise every time the docker containers exits, everything is cleared ( after all it has an in memory persistence by default ).

First of all we need the yml files to get the containers up and running. I will paste their content here

 1. docker-compose-mysql.yml

#
# Copyright 2015-2020 The OpenZipkin Authors
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License
# is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
# or implied. See the License for the specific language governing permissions and limitations under
# the License.
#

# This file uses the version 2 docker-compose file format, described here:
# https://docs.docker.com/compose/compose-file/#version-2
#
# This runs the zipkin and zipkin-mysql containers, using docker-compose's
# default networking to wire the containers together.
#
# Note that this file is meant for learning Zipkin, not production deployments.

version: '2.4'

services:
  storage:
    image: ghcr.io/openzipkin/zipkin-mysql:${TAG:-latest}
    container_name: mysql
    # Uncomment to expose the storage port for testing
    ports:
       - 3306:3306

  # Use MySQL instead of in-memory storage
  zipkin:
    extends:
      file: docker-compose.yml
      service: zipkin
    # slim doesn't include MySQL support, so switch to the larger image
    image: ghcr.io/openzipkin/zipkin:${TAG:-latest}
    environment:
      - STORAGE_TYPE=mysql
      - MYSQL_HOST=storage
      # Add the baked-in username and password for the zipkin-mysql image
      - MYSQL_USER=zipkin
      - MYSQL_PASS=zipkin
    depends_on:
      - storage

  dependencies:
    extends:
      file: docker-compose-dependencies.yml
      service: dependencies
    environment:
      - STORAGE_TYPE=mysql
      - MYSQL_HOST=storage
      # Add the baked-in username and password for the zipkin-mysql image
      - MYSQL_USER=zipkin
      - MYSQL_PASS=zipkin
    depends_on:
      - storage

2. docker-compose.yml

#
# Copyright 2015-2020 The OpenZipkin Authors
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License
# is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
# or implied. See the License for the specific language governing permissions and limitations under
# the License.
#

# This file uses the version 2 docker-compose file format, described here:
# https://docs.docker.com/compose/compose-file/#version-2
#
# This runs the zipkin slim container, using docker-compose's default networking
# to wire other containers together.
#
# Note that this file is meant for learning Zipkin, not production deployments.

version: '2.4'

services:
  # The zipkin process services the UI, and also exposes a POST endpoint that
  # instrumentation can send trace data to.
  zipkin:
    image: ghcr.io/openzipkin/zipkin-slim:${TAG:-latest}
    container_name: zipkin
    # Environment settings are defined here https://github.com/openzipkin/zipkin/blob/master/zipkin-server/README.md#environment-variables
    environment:
      - STORAGE_TYPE=mem
      # Point the zipkin at the storage backend
      - MYSQL_HOST=mysql
      # Uncomment to enable self-tracing
      # - SELF_TRACING_ENABLED=true
      # Uncomment to increase heap size
      # - JAVA_OPTS=-Xms128m -Xmx128m -XX:+ExitOnOutOfMemoryError
    ports:
      # Port used for the Zipkin UI and HTTP Api
      - 9412:9411
    # Uncomment to enable debug logging
    # command: --logging.level.zipkin2=DEBUG
 

Note: for some reason port 9411 was taken on my machine. I tried to kill the process using it but eventually it didn't work. That is why 9412 is present here. 

3. docker-compose-dependencies.yml

#
# Copyright 2015-2020 The OpenZipkin Authors
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License
# is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
# or implied. See the License for the specific language governing permissions and limitations under
# the License.
#

version: '2.4'

services:
  # Adds a cron to process spans since midnight every hour, and all spans each day
  # This data is served by http://192.168.99.100:8080/dependency
  #
  # For more details, see https://github.com/openzipkin/docker-zipkin-dependencies
  dependencies:
    image: ghcr.io/openzipkin/zipkin-dependencies
    container_name: dependencies
    entrypoint: crond -f
    # environment:
      # Uncomment to see dependency processing logs
      # - ZIPKIN_LOG_LEVEL=DEBUG
      # Uncomment to adjust memory used by the dependencies job
      # - JAVA_OPTS=-verbose:gc -Xms1G -Xmx1G
 

While having all this files in the same folder, use docker-compose to bring them up.

docker-compose -f docker-compose-mysql.yml up

We are not yet ready. The tables which will hold the data regarding our spans are not ready.

Establish a connection to the db using MySql Workbench. As noted above, user zipkin and password zipkin.

Create a new query and create the tables:

CREATE TABLE IF NOT EXISTS zipkin_spans (
`trace_id_high` BIGINT NOT NULL DEFAULT 0 COMMENT 'If non zero, this means the trace uses 128 bit traceIds instead of 64 bit',
`trace_id` BIGINT NOT NULL,
`id` BIGINT NOT NULL,
`name` VARCHAR(255) NOT NULL,
`parent_id` BIGINT,
`debug` BIT(1),
`start_ts` BIGINT COMMENT 'Span.timestamp(): epoch micros used for endTs query and to implement TTL',
`duration` BIGINT COMMENT 'Span.duration(): micros used for minDuration and maxDuration query'
) ENGINE=InnoDB CHARACTER SET=utf8 COLLATE utf8_general_ci;
ALTER TABLE zipkin_spans ADD UNIQUE KEY(trace_id_high, trace_id, id) COMMENT 'ignore insert on duplicate';

ALTER TABLE zipkin_spans ADD INDEX(trace_id_high, trace_id, id) COMMENT 'for joining with zipkin_annotations';
ALTER TABLE zipkin_spans ADD INDEX(trace_id_high, trace_id) COMMENT 'for getTracesByIds';
ALTER TABLE zipkin_spans ADD INDEX(name) COMMENT 'for getTraces and getSpanNames';
ALTER TABLE zipkin_spans ADD INDEX(start_ts) COMMENT 'for getTraces ordering and range';

CREATE TABLE IF NOT EXISTS zipkin_annotations (
trace_id_high BIGINT NOT NULL DEFAULT 0 COMMENT 'If non zero, this means the trace uses 128 bit traceIds instead of 64 bit',
trace_id BIGINT NOT NULL COMMENT 'coincides with zipkin_spans.trace_id',
span_id BIGINT NOT NULL COMMENT 'coincides with zipkin_spans.id',
a_key VARCHAR(255) NOT NULL COMMENT 'BinaryAnnotation.key or Annotation.value if type == -1',
a_value BLOB COMMENT 'BinaryAnnotation.value(), which must be smaller than 64KB',
a_type INT NOT NULL COMMENT 'BinaryAnnotation.type() or -1 if Annotation',
a_timestamp BIGINT COMMENT 'Used to implement TTL; Annotation.timestamp or zipkin_spans.timestamp',
endpoint_ipv4 INT COMMENT 'Null when Binary/Annotation.endpoint is null',
endpoint_ipv6 BINARY(16) COMMENT 'Null when Binary/Annotation.endpoint is null, or no IPv6 address',
endpoint_port SMALLINT COMMENT 'Null when Binary/Annotation.endpoint is null',
endpoint_service_name VARCHAR(255) COMMENT 'Null when Binary/Annotation.endpoint is null'
) ENGINE=InnoDB CHARACTER SET=utf8 COLLATE utf8_general_ci;


ALTER TABLE zipkin_annotations ADD UNIQUE KEY(trace_id_high, trace_id, span_id, a_key, a_timestamp) COMMENT 'Ignore insert on duplicate';
ALTER TABLE zipkin_annotations ADD INDEX(trace_id_high, trace_id, span_id) COMMENT 'for joining with zipkin_spans';
ALTER TABLE zipkin_annotations ADD INDEX(trace_id_high, trace_id) COMMENT 'for getTraces/ByIds';
ALTER TABLE zipkin_annotations ADD INDEX(endpoint_service_name) COMMENT 'for getTraces and getServiceNames';
ALTER TABLE zipkin_annotations ADD INDEX(a_type) COMMENT 'for getTraces';
ALTER TABLE zipkin_annotations ADD INDEX(a_key) COMMENT 'for getTraces';
ALTER TABLE zipkin_annotations ADD INDEX(trace_id, span_id, a_key) COMMENT 'for dependencies job';


CREATE TABLE IF NOT EXISTS zipkin_dependencies (
day DATE NOT NULL,
parent VARCHAR(255) NOT NULL,
child VARCHAR(255) NOT NULL,
call_count BIGINT
) ENGINE=InnoDB CHARACTER SET=utf8 COLLATE utf8_general_ci;

ALTER TABLE zipkin_dependencies ADD UNIQUE KEY(day, parent, child);

ALTER TABLE zipkin_dependencies add `error_count` BIGINT
ALTER TABLE zipkin_spans ADD `remote_service_name` VARCHAR(255);

Having all this, Zipkin started to work and maintain its state after restarts.