Q: How to deploy elasticsearch with docker swarm? I create 3 virtual machine use docker-machine,there are:
NAME       ACTIVE   DRIVER       STATE     URL                         SWARM   DOCKER     ERRORS
cluster    -        virtualbox   Running   tcp://192.168.99.101:2376           v18.09.5   
cluster2   -        virtualbox   Running   tcp://192.168.99.102:2376           v18.09.5   
master     -        virtualbox   Running   tcp://192.168.99.100:2376           v18.09.5 

and then I create a docker swarm in master machine:
 docker-machine ssh master "docker swarm init ----advertise-addr 192.168.99.100"

and in cluster and cluster2 join master:
docker-machine ssh cluster "docker swarm join --advertise-addr 192.168.99.101 --token xxxx 192.168.99.100:2377"

docker-machine ssh cluster2 "docker swarm join --advertise-addr 192.168.99.102 --token xxxx 192.168.99.100:2377"

the docker node ls info:
ID                            HOSTNAME            STATUS              AVAILABILITY        MANAGER STATUS      ENGINE VERSION
r4a6y9wie4zp3pl4wi4e6wqp8     cluster             Ready               Active                                  18.09.5
sg9gq6s3k6vty7qap7co6eppn     cluster2            Ready               Active                                  18.09.5
xb6telu8cn3bfmume1kcektkt *   master              Ready               Active              Leader              18.09.5

there is deploy config swarm.yml:
version: "3.3"

services:
  elasticsearch:
    image: elasticsearch:7.0.0
    ports:
      - "9200:9200"
      - "9300:9300"
    environment:
      - cluster.name=elk
      - network.host=_eth1:ipv4_
      - network.bind_host=_eth1:ipv4_
      - network.publish_host=_eth1:ipv4_
      - discovery.seed_hosts=192.168.99.100,192.168.99.101
      - cluster.initial_master_nodes=192.168.99.100,192.168.99.101
      - bootstrap.memory_lock=false
      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
    networks:
      - backend
    deploy:
      mode: replicated
      replicas: 3
      #endpoint_mode: dnsrr
      restart_policy:
        condition: none
      resources:
        limits:
          cpus: "1.0"
          memory: "1024M"
        reservations:
          memory: 20M
networks:
  backend:
    # driver: overlay
    # attachable: true

i pull elasticsearch image to virtual machie:
docker-machine ssh master "docker image pull elasticsearch:7.0.0"
docker-machine ssh cluster "docker image pull elasticsearch:7.0.0"
docker-machine ssh cluster2 "docker image pull elasticsearch:7.0.0"

before run i run this command fix some elasticearch bootstrap error:
docker-machine ssh master "sudo sysctl -w vm.max_map_count=262144"
docker-machine ssh cluster "sudo sysctl -w vm.max_map_count=262144"
docker-machine ssh cluster2 "sudo sysctl -w vm.max_map_count=262144"

and then i run `docker stack deploy -c swarm.yml es, the elasticsearch cluster cannot work.
docker-machine ssh master
docker service logs es_elasticsearch -f 

show:
es_elasticsearch.1.uh1x0s9qr7mb@cluster    | {"type": "server", "timestamp": "2019-04-25T16:28:47,143+0000", "level": "WARN", "component": "o.e.c.c.ClusterFormationFailureHelper", "cluster.name": "elk", "node.name": "e8dba5562417",  "message": "master not discovered yet, this node has not previously joined a bootstrapped (v7+) cluster, and this node must discover master-eligible nodes [192.168.99.100, 192.168.99.101] to bootstrap a cluster: have discovered []; discovery will continue using [192.168.99.100:9300, 192.168.99.101:9300] from hosts providers and [{e8dba5562417}{Jy3t0AAkSW-jY-IygOCjOQ}{z7MYIf5wTfOhCX1r25wNPg}{10.255.0.46}{10.255.0.46:9300}{ml.machine_memory=1037410304, xpack.installed=true, ml.max_open_jobs=20}] from last-known cluster state; node term 0, last-accepted version 0 in term 0"  }
es_elasticsearch.2.swswlwmle9e9@cluster2    | {"type": "server", "timestamp": "2019-04-25T16:28:47,389+0000", "level": "WARN", "component": "o.e.c.c.ClusterFormationFailureHelper", "cluster.name": "elk", "node.name": "af5d88a04b42",  "message": "master not discovered yet, this node has not previously joined a bootstrapped (v7+) cluster, and this node must discover master-eligible nodes [192.168.99.100, 192.168.99.101] to bootstrap a cluster: have discovered []; discovery will continue using [192.168.99.100:9300, 192.168.99.101:9300] from hosts providers and [{af5d88a04b42}{zhxMeNMAQN2evKDlsA33qA}{fpYPTvJ6STmyqrgxlMkD_w}{10.255.0.47}{10.255.0.47:9300}{ml.machine_memory=1037410304, xpack.installed=true, ml.max_open_jobs=20}] from last-known cluster state; node term 0, last-accepted version 0 in term 0"  }
es_elasticsearch.3.x8ouukovhh80@master    | {"type": "server", "timestamp": "2019-04-25T16:28:48,818+0000", "level": "WARN", "component": "o.e.c.c.ClusterFormationFailureHelper", "cluster.name": "elk", "node.name": "0e7e4d96b31a",  "message": "master not discovered yet, this node has not previously joined a bootstrapped (v7+) cluster, and this node must discover master-eligible nodes [192.168.99.100, 192.168.99.101] to bootstrap a cluster: have discovered []; discovery will continue using [192.168.99.100:9300, 192.168.99.101:9300] from hosts providers and [{0e7e4d96b31a}{Xs9966RjTEWvEbuj4-ySYA}{-eV4lvavSHq6JhoW0qWu6A}{10.255.0.48}{10.255.0.48:9300}{ml.machine_memory=1037410304, xpack.installed=true, ml.max_open_jobs=20}] from last-known cluster state; node term 0, last-accepted version 0 in term 0"  }



I guess the cluster formation failed may be due to network configuration error. I don't know how to fix it, I try many times modify the config, fail and fail again. 

A: try, this is working :) docker-compose.yml
version: "3.7"
services:
  elasticsearch:
    image: docker.elastic.co/elasticsearch/elasticsearch:7.2.0
    hostname: "{{.Node.Hostname}}"
    environment:
      - node.name={{.Node.Hostname}}
      - cluster.name=my-cluster
      - "ES_JAVA_OPTS=-Xms2g -Xmx2g"
      - discovery.seed_hosts=elasticsearch
      - cluster.initial_master_nodes=node1,node2,node3
      - node.ml=false
      - xpack.ml.enabled=false
      - xpack.monitoring.enabled=false
      - xpack.security.enabled=false
      - xpack.watcher.enabled=false
      - bootstrap.memory_lock=false
    volumes:
      - elasticsearch-data:/usr/share/elasticsearch/data
    deploy:
      mode: global
      endpoint_mode: dnsrr
      resources:
        limits:
          memory: 4G
  nginx:
    image: nginx:1.17.1-alpine
    ports:
      - 9200:9200
    deploy:
      mode: global
    command: |
      /bin/sh -c "echo '
      user nobody nogroup;
      worker_processes auto;
      events {
        worker_connections 1024;
      }
      http {
        client_max_body_size 4g;
        resolver 127.0.0.11 ipv6=off;
        server {
          listen *:9200;
          location / {
            proxy_set_header Connection keep-alive;
            set $$url http://elasticsearch:9200;
            proxy_pass $$url;
            proxy_set_header  Host $$http_host;
            proxy_set_header  X-Real-IP $$remote_addr;
            proxy_set_header  X-Forwarded-For $$proxy_add_x_forwarded_for;
          }
        }
      }' | tee /etc/nginx/nginx.conf && nginx -t && nginx -g 'daemon off;'"

volumes:
  elasticsearch-data:


A: Trying to manually specify all the specific IP's and bindings is tricky because of the swarm overlaying network.
Instead, simply make your ES nodes discoverable and let Swarm take care of the node discovery and communication. To make them discoverable, we can use a predictable name like the Swarm node hostname.
Try change your environment settings in the swarm.yml file as follows:
    environment:
    - network.host=0.0.0.0
    - discovery.seed_hosts=elasticsearch #Service name, to let Swarm handle discovery
    - cluster.initial_master_nodes=master,cluster,cluster2 #Swarm nodes host names
    - node.name={{.Node.Hostname}} #To create a predictable node name

This of course assumes that we already known the swarm hostnames, which you pointed out in the screenshot above. Without knowing these values, we would have no way of having a predictable set of node names to look for. In that case, you could create 1 ES node entry with a particular node name, and then another entry which references the first entry's node name as the cluster.initial_master_nodes.

A: Use dnsrr mode without ports. Expose elasticsearch with nginx ;)
See my docker-compose.yml

A: In my experience https://github.com/shazChaudhry/docker-elastic works perfectly, and just one file from the entire repo is enough. I downloaded https://github.com/shazChaudhry/docker-elastic/blob/master/docker-compose.yml and removed the logstash bits, I didn't need that. Then added the following to .bashrc
export ELASTICSEARCH_HOST=$(hostname)
export ELASTICSEARCH_PASSWORD=foobar
export ELASTICSEARCH_USERNAME=elastic
export ELASTIC_VERSION=7.4.2
export INITIAL_MASTER_NODES=$ELASTICSEARCH_HOST

And docker stack deploy --compose-file docker-compose.yml elastic works.

A: Ideas I gleaned from Ahmet Vehbi Olgaç 's docker-compose.yml, which worked for me:


*

*Use deployment / mode: global. This will cause the swarm to deploy one replica to each swarm worker, for each node that is configured like this.

*Use deployment / endpoint_mode: dnsrr. This will let all containers in the swarm access the nodes by the service name.

*Use hostname: {{.Node.Hostname}} or a similar template-based expression. This ensures a unique name for each deployed container.

*Use environment / node.name={{.Node.Hostname}}. Again, you can vary the pattern. The point is that each es node should get a unique name.

*Use cluster.initial_master_nodes=*hostname1*,*hostname2*,.... Assuming you know the hostnames of your docker worker machines. Use whatever pattern you used in #3, but substitute out the whole hostname, and include all the hostnames.
If you don't know your hostnames, you can do what Andrew Cachia's answer suggests: set up one container (do not replicate it) to act solely as the master seed and give it a predictable hostname, then have all other nodes refer to that node as the master seed. However, this introduces a single point of failure.

A: Elasticsearch 8.5.0 answer.
For my needs, I didn't want to add a reverse-proxy/load balancer, but I do want to expose port 9200 on the swarm nodes where Elasticsearch replicas are running (using just swarm), so that external clients can access the Elasticsearch REST API. So I used endpoint mode dnsrr (ref) and exposed port 9200 on the hosts where the replicas run.
If you don't need to expose port 9200 (i.e., nothing will connect to the elasticsearch replicas outside of swarm), remove the ports: config from the elasticsearch service.
I also only want elasticsearch replicas to run on a subset of my swarm nodes (3 of them). I created docker node label elasticsearch on those three nodes. Then mode: global and constraint node.labels.elasticsearch==True will ensure 1 replica runs on each of those nodes.
I run kibana on one of those 3 nodes too: swarm can pick which one, since port 5601 is exposed on swarm's ingress overlay network.
Lines you'll likely need to edit are maked with ######.
# docker network create -d overlay --attachable elastic-net

# cat elastic-stack-env
#!/bin/bash
export STACK_VERSION=8.5.0   # Elasticsearch and Kibana version
export ES_PORT=9200          # port to expose Elasticsearch HTTP API to the host
export KIBANA_PORT=5601      # port to expose Kibana to the host

read -p "Enter elastic user password: " ELASTIC_PASSWORD
read -p "Enter kibana_system user password: " KIBANA_PASSWORD
export KIBANA_URL=https://kibana.my-domain.com:$KIBANA_PORT   #######
export SHARED_DIR=/some/nfs/or/shared/storage/elastic         #######
export KIBANA_SSL_KEY_PATH=config/certs/kibana.key
export KIBANA_SSL_CERT_PATH=config/certs/kibana.crt
export ELASTIC_NODES=swarm_node1,swarm_node2,swarm_node3      #######
  # ELASTIC_NODES must match what docker reports from {{.Node.Hostname}}
export KIBANA_SSL_CERT_AUTH_PATH=config/certs/My_Root_CA.crt  #######
export CLUSTER_NAME=docker-cluster
export MEM_LIMIT=4294967296  # 4 GB; increase or decrease based on the available host memory (in bytes)

# cat elastic-stack.yml
version: "3.8"
services:
  elasticsearch:
    image: localhost:5000/elasticsearch:${STACK_VERSION:?}  ####### I have a local registry
    deploy:
      endpoint_mode: dnsrr
      mode: global  # but note constraints below
      placement:
        constraints:
          - node.labels.elasticsearch==True
      resources:
        limits:
          memory:
            ${MEM_LIMIT}
    dns: 127.0.0.11  # use docker DNS only (may not be required)
    networks:
      - elastic-net
    volumes:
      - ${SHARED_DIR:?}/certs:/usr/share/elasticsearch/config/certs
      - /path/to/some/local/storage/elasticsearch:/usr/share/elasticsearch/data
    ports:  ##### remove if nothing outside of swarm needs to access port 9200
      - target: 9200
        published: ${ES_PORT}  # we publish this port so that external clients can access the ES REST API
        protocol: tcp
        mode: host  # required when using dnsrr
    environment:    # https://www.elastic.co/guide/en/elasticsearch/reference/master/settings.html
                    # https://www.elastic.co/guide/en/elasticsearch/reference/master/docker.html#docker-configuration-methods
      - node.name={{.Node.Hostname}}  # see Andrew Cachia's answer
      - cluster.name=${CLUSTER_NAME}
      - discovery.seed_hosts=elasticsearch             # use service name here, since (docker's) DNS is used:
        # https://www.elastic.co/guide/en/elasticsearch/reference/current/important-settings.html#unicast.hosts
      - cluster.initial_master_nodes=${ELASTIC_NODES}  # use node.names here
        # https://www.elastic.co/guide/en/elasticsearch/reference/current/important-settings.html#initial_master_nodes
      - ELASTIC_PASSWORD=${ELASTIC_PASSWORD}
      - xpack.security.enabled=true
      - xpack.security.http.ssl.enabled=true
      - xpack.security.http.ssl.key=certs/elasticsearch/elasticsearch.key
      - xpack.security.http.ssl.certificate=certs/elasticsearch/elasticsearch.crt
      - xpack.security.http.ssl.certificate_authorities=certs/ca/ca.crt
      - xpack.security.http.ssl.verification_mode=certificate
      - xpack.security.transport.ssl.enabled=true
      - xpack.security.transport.ssl.key=certs/elasticsearch/elasticsearch.key
      - xpack.security.transport.ssl.certificate=certs/elasticsearch/elasticsearch.crt
      - xpack.security.transport.ssl.certificate_authorities=certs/ca/ca.crt
      - xpack.security.transport.ssl.verification_mode=certificate
      - xpack.license.self_generated.type=basic
    healthcheck:
      test:
        [ "CMD-SHELL",
          "curl -s --cacert config/certs/ca/ca.crt https://localhost:9200 | grep -q 'missing authentication credentials'",
        ]
      interval: 10s
      timeout: 10s
      retries: 120
    logging:        # we use rsyslog
      driver: syslog
      options:
        syslog-facility: "local2"

  kibana:
    # this service depends on the setup service (defined below), but docker stack has no
    # way to specify dependencies, but more importantly, there's been a move away from this:
    # https://stackoverflow.com/a/47714157/215945
    image: localhost:5000/kibana:${STACK_VERSION:?}    ######
    hostname: kibana
    deploy:
      placement:
        constraints:
          - node.labels.elasticsearch==True  # run KB on any one of the ES nodes
      resources:
         limits:
          memory:
            ${MEM_LIMIT}
    dns: 127.0.0.11  # use docker DNS only (may not be required)
    networks:
      - elastic-net
    volumes:
      - ${SHARED_DIR:?}/kibana:/usr/share/kibana/data
      - ${SHARED_DIR:?}/certs:/usr/share/kibana/config/certs
    ports:
      - ${KIBANA_PORT}:5601
    environment:  # https://www.elastic.co/guide/en/kibana/master/settings.html
                  # https://www.elastic.co/guide/en/kibana/master/docker.html#environment-variable-config
                  # CAPS_WITH_UNDERSCORES must be used with Kibana
      - SERVER_NAME=kibana
      - ELASTICSEARCH_HOSTS=["https://elasticsearch:9200"]
      - ELASTICSEARCH_USERNAME=kibana_system
      - ELASTICSEARCH_PASSWORD=${KIBANA_PASSWORD}
      - ELASTICSEARCH_SSL_CERTIFICATEAUTHORITIES=config/certs/ca/ca.crt
      - SERVER_PUBLICBASEURL=${KIBANA_URL}
      # if you don't want to use https/TLS with Kibana, comment-out
      # the next four lines
      - SERVER_SSL_ENABLED=true
      - SERVER_SSL_KEY=${KIBANA_SSL_KEY_PATH}
      - SERVER_SSL_CERTIFICATE=${KIBANA_SSL_CERT_PATH}
      - SERVER_SSL_CERTIFICATEAUTHORITIES=${KIBANA_SSL_CERT_AUTH_PATH}
      - TELEMETRY_OPTIN=false
    healthcheck:
      test:
        [
          "CMD-SHELL",
          "curl -sIk https://localhost:5601 | grep -q 'HTTP/1.1 302 Found'",
        ]
      interval: 10s
      timeout: 10s
      retries: 120
    logging:
      driver: syslog
      options:
        syslog-facility: "local2"

  setup:
    image: localhost:5000/elasticsearch:${STACK_VERSION:?}   #######
    deploy:
      placement:
        constraints:
          - node.labels.elasticsearch==True
      restart_policy:  # https://docs.docker.com/compose/compose-file/compose-file-v3/#restart_policy
        condition: none
    volumes:
      - ${SHARED_DIR:?}/certs:/usr/share/elasticsearch/config/certs
    dns: 127.0.0.11  # use docker DNS only (may not be required)
    networks:
      - elastic-net
    command: >
      bash -c '
        until curl -s --cacert config/certs/ca/ca.crt https://elasticsearch:9200 | grep -q "missing authentication credentials"
        do
          echo "waiting 30 secs for Elasticsearch availability..."
          sleep 30
        done
        echo "setting kibana_system password"
        until curl -s -X POST --cacert config/certs/ca/ca.crt -u elastic:${ELASTIC_PASSWORD} -H "Content-Type: application/json" https://elasticsearch:9200/_security/user/kibana_system/_password -d "{\"password\":\"${KIBANA_PASSWORD}\"}" | grep -q "^{}"
        do
          echo "waiting 10 secs before trying to set password again..."
          sleep 10
        done
        echo "done"
      '
    logging:
      driver: syslog
      options:
        syslog-facility: "local2"

networks:
  elastic-net:
    external: true

Deploy:
# . ./elastic-stack-env
# docker stack deploy -c elastic-stack.yml elastic
# # ... after Kibana comes up, you can remove the setup service if you want:
# docker service rm elastic_setup

Here's how I created the Elasticsearch CA and cert:
# cat elastic-certs.yml
version: "3.8"
services:
  setup:
    image: localhost:5000/elasticsearch:${STACK_VERSION:?}   #######
    volumes:
      - ${SHARED_DIR:?}/certs:/usr/share/elasticsearch/config/certs
    user: "0:0"
    command: >
      bash -c '
        if [ ! -f certs/ca.zip ]; then
          echo "Creating CA";
          bin/elasticsearch-certutil ca --silent --pem -out config/certs/ca.zip;
          unzip config/certs/ca.zip -d config/certs;
        fi;
        if [ ! -f certs/certs.zip ]; then
          echo "Creating certs";
          echo -ne \
          "instances:\n"\
          "  - name: elasticsearch\n"\
          "    dns:\n"\
          "      - elasticsearch\n"\
          "      - localhost\n"\
          "    ip:\n"\
          "      - 127.0.0.1\n"\
          > config/certs/instances.yml;
          bin/elasticsearch-certutil cert --silent --pem -out config/certs/certs.zip --in config/certs/instances.yml --ca-cert config/certs/ca/ca.crt --ca-key config/certs/ca/ca.key;
          unzip config/certs/certs.zip -d config/certs;
          echo "Setting file permissions"
          chown -R root:root config/certs;
          find . -type d -exec chmod 750 \{\} \;;
          find . -type f -exec chmod 640 \{\} \;;
        fi;
        sleep infinity
      '
    healthcheck:
      test: ["CMD-SHELL", "[ -f config/certs/elasticsearch/elasticsearch.crt ]"]
      interval: 1s
      timeout: 5s
      retries: 120

# . ./elastic-stack-env
# docker stack deploy -c elastic-certs.yml elastic-certs
# # ... ensure files are created under $SHARED_DIR/certs, then
# docker stack rm elastic-certs

How I created the Kibana cert is outside the scope of this question.
I run a Fluent Bit swarm service (mode: global, docker network elastic-net) to send logs to the elasticsearch service.  Although outside the scope of this question, here's the salient config:
[OUTPUT]
    name          es
    match         <whatever is appropriate for you here>
    host          elasticsearch
    port          9200
    index         my-index-default
    http_user     fluentbit
    http_passwd   ${FLUENTBIT_PASSWORD}
    tls           on
    tls.ca_file   /certs/ca/ca.crt
    tls.crt_file  /certs/elasticsearch/elasticsearch.crt
    tls.key_file  /certs/elasticsearch/elasticsearch.key
    retry_limit   false
    suppress_type_name on
#   trace_output  on

Host elasticsearch will be resolved by docker's DNS server to the three IP addresses of the elasticsearch replicas, so there is no single point of failure.
