Elasticsearch passwords tool always returns "setting already set" error

I am following the official ES documentation here for configuring a basic dev 3 node cluster with TLS using docker compose but am stuck at the 5th step – creating user passwords using the elasticsearch-setup-passwords tool.

I have so far been able to get a 3 node cluster working without TLS. I have also torn it down and restarted with certs created and TLS enabled as the docs say and see that the various containers output looks fine. Any attempt to run

docker exec es01 /bin/bash -c "bin/elasticsearch-setup-passwords auto --batch -Expack.security.http.ssl.certificate=certificates/es01/es01.crt -Expack.security.http.ssl.certificate_authorities=certificates/ca/ca.crt -Expack.security.http.ssl.key=certificates/es01/es01.key --url https://es01:9200"

as mentioned in the docs always returns

Sets the passwords for reserved users

Non-option arguments:
command

Option             Description
------             -----------
-E <KeyValuePair>  Configure a setting
-h, --help         Show help
-s, --silent       Show minimal output
-v, --verbose      Show verbose output
ERROR: setting [xpack.security.http.ssl.certificate_authorities] already set, saw [certificates/ca/ca.crt] and [/usr/share/elasticsearch/config/certificates/ca/ca.crt]

Any one of the settings designated in the command above will throw this “already set” error, yet it is listed in the official documentation. If I run the command as just

docker exec es01 /bin/bash -c "bin/elasticsearch-setup-passwords auto --batch --url https://es01:9200"

It will generate the passwords as expected.

If I do not specify the xpack security settings will the proper certificated be used? There are some other default certificates that exist in the containers that I do not want to use for this, is there a way I can verify that the correct set was used? Is there a way to overwrite the “already set” settings?

The official documentation does not explain this clearly and I have not been able to find anything for this specifically on SO or the web.

I am using Docker Desktop version 2.2.0.5 for MacOS Catalina version 10.15.4 with Docker Compose version 1.25.4 and ES version 7.7.0

My docker compose file looks like:

version: '2.2'

services:
  es01:
    image: docker.elastic.co/elasticsearch/elasticsearch:${VERSION}
    container_name: es01
    environment:
      - node.name=es01
      - cluster.name=es-docker-cluster
      - discovery.seed_hosts=es02,es03
      - cluster.initial_master_nodes=es01,es02,es03
      - bootstrap.memory_lock=true
      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
      - xpack.license.self_generated.type=basic 
      - xpack.security.enabled=true
      - xpack.security.http.ssl.enabled=true 
      - xpack.security.http.ssl.key=$CERTS_DIR/es01/es01.key
      - xpack.security.http.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.http.ssl.certificate=$CERTS_DIR/es01/es01.crt
      - xpack.security.transport.ssl.enabled=true 
      - xpack.security.transport.ssl.verification_mode=certificate 
      - xpack.security.transport.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.transport.ssl.certificate=$CERTS_DIR/es01/es01.crt
      - xpack.security.transport.ssl.key=$CERTS_DIR/es01/es01.key
    ulimits:
      memlock:
        soft: -1
        hard: -1
    volumes:
      - data01:/usr/share/elasticsearch/data
      - certs:$CERTS_DIR
    ports:
      - 9200:9200
    networks:
      - elastic

    healthcheck:
      test: curl --cacert $CERTS_DIR/ca/ca.crt -s https://localhost:9200 >/dev/null; if [[ $$? == 52 ]]; then echo 0; else echo 1; fi
      interval: 30s
      timeout: 10s
      retries: 5

  es02:
    image: docker.elastic.co/elasticsearch/elasticsearch:${VERSION}
    container_name: es02
    environment:
      - node.name=es02
      - cluster.name=es-docker-cluster
      - discovery.seed_hosts=es01,es03
      - cluster.initial_master_nodes=es01,es02,es03
      - bootstrap.memory_lock=true
      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
      - xpack.license.self_generated.type=basic
      - xpack.security.enabled=true
      - xpack.security.http.ssl.enabled=true
      - xpack.security.http.ssl.key=$CERTS_DIR/es02/es02.key
      - xpack.security.http.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.http.ssl.certificate=$CERTS_DIR/es02/es02.crt
      - xpack.security.transport.ssl.enabled=true
      - xpack.security.transport.ssl.verification_mode=certificate
      - xpack.security.transport.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.transport.ssl.certificate=$CERTS_DIR/es02/es02.crt
      - xpack.security.transport.ssl.key=$CERTS_DIR/es02/es02.key
    ulimits:
      memlock:
        soft: -1
        hard: -1
    volumes:
      - data02:/usr/share/elasticsearch/data
      - certs:$CERTS_DIR
    networks:
      - elastic

  es03:
    image: docker.elastic.co/elasticsearch/elasticsearch:${VERSION}
    container_name: es03
    environment:
      - node.name=es03
      - cluster.name=es-docker-cluster
      - discovery.seed_hosts=es01,es02
      - cluster.initial_master_nodes=es01,es02,es03
      - bootstrap.memory_lock=true
      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
      - xpack.license.self_generated.type=basic
      - xpack.security.enabled=true
      - xpack.security.http.ssl.enabled=true
      - xpack.security.http.ssl.key=$CERTS_DIR/es03/es03.key
      - xpack.security.http.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.http.ssl.certificate=$CERTS_DIR/es02/es02.crt
      - xpack.security.transport.ssl.enabled=true
      - xpack.security.transport.ssl.verification_mode=certificate
      - xpack.security.transport.ssl.certificate_authorities=$CERTS_DIR/ca/ca.crt
      - xpack.security.transport.ssl.certificate=$CERTS_DIR/es03/es03.crt
      - xpack.security.transport.ssl.key=$CERTS_DIR/es03/es03.key
    ulimits:
      memlock:
        soft: -1
        hard: -1
    volumes:
      - data03:/usr/share/elasticsearch/data
      - certs:$CERTS_DIR
    networks:
      - elastic
  kib01:
    image: docker.elastic.co/kibana/kibana:${VERSION}
    container_name: kib01
    depends_on: {"es01": {"condition": "service_healthy"}}
    ports:
      - 5601:5601
    environment:
      SERVERNAME: localhost
      ELASTICSEARCH_URL: https://es01:9200
      ELASTICSEARCH_HOSTS: https://es01:9200
      ELASTICSEARCH_USERNAME: kibana
      ELASTICSEARCH_PASSWORD: CHANGEME
      ELASTICSEARCH_SSL_CERTIFICATEAUTHORITIES: $CERTS_DIR/ca/ca.crt
      SERVER_SSL_ENABLED: "true"
      SERVER_SSL_KEY: $CERTS_DIR/kib01/kib01.key
      SERVER_SSL_CERTIFICATE: $CERTS_DIR/kib01/kib01.crt
    volumes:
      - certs:$CERTS_DIR
    networks:
      - elastic
volumes:
  data01:
    driver: local
    name: data01
  data02:
    driver: local
    name: data02
  data03:
    driver: local
    name: data03
  certs:
    driver: local
    name: certs

networks:
  elastic:
    driver: bridge
    name: elastic

Source: StackOverflow