Elasticsearch not coming up after restart

After deleting elasticsearch pod, it is not able to come up. (Ready state 0/1)
Cluster health is yellow.
fluentd is not able to connect to ES.

elasticsearch@elasticsearch-master-0:~$ curl -XGET 'http://localhost:9200/_cluster/health?pretty=true'
{
  "cluster_name" : "elasticsearch",
  "status" : "yellow",
  "timed_out" : false,
  "number_of_nodes" : 1,
  "number_of_data_nodes" : 1,
  "active_primary_shards" : 15,
  "active_shards" : 15,
  "relocating_shards" : 0,
  "initializing_shards" : 0,
  "unassigned_shards" : 7,
  "delayed_unassigned_shards" : 0,
  "number_of_pending_tasks" : 0,
  "number_of_in_flight_fetch" : 0,
  "task_max_waiting_in_queue_millis" : 0,
  "active_shards_percent_as_number" : 68.18181818181817
}
elasticsearch@elasticsearch-master-0:~$

elasticsearch-master-0            0/1     Running   0                40m
fluentd-lbzgp                     1/1     Running   0                56m
kibana-kibana-5988749c45-cwmwc    0/1     Running   0                70m
<elastic.yaml>
apiVersion: apps/v1
kind: StatefulSet
metadata:
  annotations:
    meta.helm.sh/release-name: efk
    meta.helm.sh/release-namespace: default
  creationTimestamp: "2022-07-27T05:53:38Z"
  generation: 1
  labels:
    app: elasticsearch-master
    app.kubernetes.io/managed-by: Helm
  name: elasticsearch-master
  namespace: default
  resourceVersion: "17974675"
  uid: ef543fee-faf2-4516-8695-4e330438268a
spec:
  podManagementPolicy: OrderedReady
  replicas: 1
  revisionHistoryLimit: 10
  selector:
    matchLabels:
      app: elasticsearch-master
  serviceName: elasticsearch-master-headless
  template:
    metadata:
      creationTimestamp: null
      labels:
        app: elasticsearch-master
    spec:
      containers:
      - env:
        - name: node.name
          valueFrom:
            fieldRef:
              apiVersion: v1
              fieldPath: metadata.name
        - name: discovery.seed_hosts
          value: elasticsearch-master-headless
        - name: cluster.name
          value: elasticsearch
        - name: network.host
          value: 0.0.0.0
        - name: cluster.deprecation_indexing.enabled
          value: "false"
        - name: ES_JAVA_OPTS
          value: -Xmx512m -Xms512m
        - name: node.roles
          value: master,data,data_content,data_hot,data_warm,data_cold,ingest,ml,remote_cluster_client,transform,
        - name: discovery.type
          value: single-node
        - name: ELASTIC_PASSWORD
          valueFrom:
            secretKeyRef:
              key: password
              name: elasticsearch-credentials
        - name: xpack.security.enabled
          value: "false"
        image: artifactory.radisys.com:8093/vdu.rsys/efk/elasticsearch:7.17.3
        imagePullPolicy: IfNotPresent
        name: elasticsearch
        ports:
        - containerPort: 9200
          name: http
          protocol: TCP
        - containerPort: 9300
          name: transport
          protocol: TCP
        readinessProbe:
          exec:
            command:
            - bash
            - -c
            - |
              set -e
              # If the node is starting up wait for the cluster to be ready (request params: "wait_for_status=green&timeout=1s" )
              # Once it has started only check that the node itself is responding
              START_FILE=/tmp/.es_start_file

              # Disable nss cache to avoid filling dentry cache when calling curl
              # This is required with Elasticsearch Docker using nss < 3.52
              export NSS_SDB_USE_CACHE=no

              http () {
                local path="${1}"
                local args="${2}"
                set -- -XGET -s

                if [ "$args" != "" ]; then
                  set -- "$@" $args
                fi

                if [ -n "${ELASTIC_PASSWORD}" ]; then
                  set -- "$@" -u "elastic:${ELASTIC_PASSWORD}"
                fi

                curl --output /dev/null -k "$@" "http://127.0.0.1:9200${path}"
              }

              if [ -f "${START_FILE}" ]; then
                echo 'Elasticsearch is already running, lets check the node is healthy'
                HTTP_CODE=$(http "/" "-w %{http_code}")
                RC=$?
                if [[ ${RC} -ne 0 ]]; then
                  echo "curl --output /dev/null -k -XGET -s -w '%{http_code}' \${BASIC_AUTH} http://127.0.0.1:9200/ failed with RC ${RC}"
                  exit ${RC}
                fi
                # ready if HTTP code 200, 503 is tolerable if ES version is 6.x
                if [[ ${HTTP_CODE} == "200" ]]; then
                  exit 0
                elif [[ ${HTTP_CODE} == "503" && "7" == "6" ]]; then
                  exit 0
                else
                  echo "curl --output /dev/null -k -XGET -s -w '%{http_code}' \${BASIC_AUTH} http://127.0.0.1:9200/ failed with HTTP code ${HTTP_CODE}"
                  exit 1
                fi

              else
                echo 'Waiting for elasticsearch cluster to become ready (request params: "wait_for_status=green&timeout=1s" )'
                if http "/_cluster/health?wait_for_status=green&timeout=1s" "--fail" ; then
                  touch ${START_FILE}
                  exit 0
                else
                  echo 'Cluster is not yet ready (request params: "wait_for_status=green&timeout=1s" )'
                  exit 1
                fi
              fi
          failureThreshold: 3
          initialDelaySeconds: 10
          periodSeconds: 10
          successThreshold: 3
          timeoutSeconds: 5
        resources:
          limits:
            cpu: "8"
            memory: 8Gi
          requests:
            cpu: "1"
            memory: 5Gi
        securityContext:
          runAsNonRoot: true
          runAsUser: 1000
        terminationMessagePath: /dev/termination-log
        terminationMessagePolicy: File
        volumeMounts:
        - mountPath: /usr/share/elasticsearch/data
          name: elasticsearch-storage
      dnsPolicy: ClusterFirst
      initContainers:
      - command:
        - chown
        - -R
        - 1000:1000
        - /usr/share/elasticsearch/
        image: artifactory.radisys.com:8093/vdu.rsys/efk/busybox:1.34.1
        imagePullPolicy: IfNotPresent
        name: init-volume-permission
        resources: {}
        securityContext:
          privileged: true
          runAsUser: 0
        terminationMessagePath: /dev/termination-log
        terminationMessagePolicy: File
        volumeMounts:
        - mountPath: /usr/share/elasticsearch/data
          name: elasticsearch-storage
      restartPolicy: Always
      schedulerName: default-scheduler
      securityContext: {}
      terminationGracePeriodSeconds: 30
      volumes:
      - name: elasticsearch-storage
        persistentVolumeClaim:
          claimName: elasticsearch-pvc
  updateStrategy:
    rollingUpdate:
      partition: 0
    type: RollingUpdate
status:
  collisionCount: 0
  currentReplicas: 1
  currentRevision: elasticsearch-master-5cf649ffb6
  observedGeneration: 1
  replicas: 1
  updateRevision: elasticsearch-master-5cf649ffb6
  updatedReplicas: 1

</elastic.yaml>
[root@node1 containers]# kubectl get sc
NAME              PROVISIONER                    RECLAIMPOLICY   VOLUMEBINDINGMODE      ALLOWVOLUMEEXPANSION   AGE
elastic-storage   kubernetes.io/no-provisioner   Retain          WaitForFirstConsumer   false                  59m
[root@node1 containers]# kubectl get pv
NAME               CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                       STORAGECLASS      REASON   AGE
du-log-volume-pv   10Gi       RWO            Retain           Bound    default/du-log-volume-pvc                              41m
elasticsearch-pv   30Gi       RWO            Retain           Bound    default/elasticsearch-pvc   elastic-storage            59m
[root@node1 containers]# kubectl get pvc
NAME                STATUS   VOLUME             CAPACITY   ACCESS MODES   STORAGECLASS      AGE
du-log-volume-pvc   Bound    du-log-volume-pv   10Gi       RWO                              41m
elasticsearch-pvc   Bound    elasticsearch-pv   30Gi       RWO            elastic-storage   59m
[root@node1 containers]#

This is PV hostpath: 
[root@node1 data]# cd /mnt/elastic/data
[root@node1 data]# ls -lrt
total 0
drwxrwxr-x 3 labadmin labadmin 15 Jul 27 05:53 nodes
[root@node1 data]# cd nodes/0/
[root@node1 0]# ls -lrt
total 8
-rw-rw-r--  1 labadmin labadmin    0 Jul 27 05:53 node.lock
drwxrwxr-x 17 labadmin labadmin 4096 Jul 27 06:06 indices
drwxrwxr-x  2 labadmin labadmin   42 Jul 27 06:24 snapshot_cache
drwxrwxr-x  2 labadmin labadmin 4096 Jul 27 06:24 _state
[root@node1 0]#

I can see some data here.

Final ovservation:

  1. If ES cluster health is green and I restart ES (by deleting pod), it is able to come up.
  2. If ES cluster health is yellow (using single node, so health turns yellow as soon as fluentd starts pushing data) and I restart ES (by deleting pod), it is NOT able to come up.

what can I do to ensure ES comes up after restart?

What does the Elasticsearch logs say when it does not come up?

Not much information available. On elasticsearch pod console logs, it is stuck here.

{"type": "server", "timestamp": "2022-07-27T06:24:42,865Z", "level": "INFO", "component": "o.e.c.r.a.AllocationService", "cluster.name": "elasticsearch", "node.name": "elasticsearch-master-0", "message": "Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[du-oam-server-app-logs][0], [.kibana-event-log-7.17.3-000001][0], [.ds-ilm-history-5-2022.07.27-000001][0]]]).", "cluster.uuid": "2qXzWEoVSIOtO118d8a6Qg", "node.id": "Ak16eLnrSry3aYWQjO1tyQ"  }
{"type": "server", "timestamp": "2022-07-27T06:24:43,667Z", "level": "INFO", "component": "o.e.i.g.DatabaseNodeService", "cluster.name": "elasticsearch", "node.name": "elasticsearch-master-0", "message": "successfully reloaded changed geoip database file [/tmp/elasticsearch-1182559791185354524/geoip-databases/Ak16eLnrSry3aYWQjO1tyQ/GeoLite2-City.mmdb]", "cluster.uuid": "2qXzWEoVSIOtO118d8a6Qg", "node.id": "Ak16eLnrSry3aYWQjO1tyQ"  }
{"type": "server", "timestamp": "2022-07-27T06:24:48,615Z", "level": "INFO", "component": "o.e.i.g.GeoIpDownloader", "cluster.name": "elasticsearch", "node.name": "elasticsearch-master-0", "message": "geoip database [GeoLite2-ASN.mmdb] is up to date, updated timestamp", "cluster.uuid": "2qXzWEoVSIOtO118d8a6Qg", "node.id": "Ak16eLnrSry3aYWQjO1tyQ"  }
{"type": "server", "timestamp": "2022-07-27T06:24:48,666Z", "level": "INFO", "component": "o.e.i.g.GeoIpDownloader", "cluster.name": "elasticsearch", "node.name": "elasticsearch-master-0", "message": "geoip database [GeoLite2-City.mmdb] is up to date, updated timestamp", "cluster.uuid": "2qXzWEoVSIOtO118d8a6Qg", "node.id": "Ak16eLnrSry3aYWQjO1tyQ"  }
{"type": "server", "timestamp": "2022-07-27T06:24:48,704Z", "level": "INFO", "component": "o.e.i.g.GeoIpDownloader", "cluster.name": "elasticsearch", "node.name": "elasticsearch-master-0", "message": "geoip database [GeoLite2-Country.mmdb] is up to date, updated timestamp", "cluster.uuid": "2qXzWEoVSIOtO118d8a6Qg", "node.id": "Ak16eLnrSry3aYWQjO1tyQ"  }

Kibana also lost connection with ES.

{"type":"log","@timestamp":"2022-07-27T08:24:56+00:00","tags":["warning","plugins","alerting"],"pid":8,"message":"Alerting framework is degraded due to the error: ConnectionError: connect ECONNREFUSED 10.233.17.119:9200"}
{"type":"log","@timestamp":"2022-07-27T08:24:58+00:00","tags":["error","plugins","security","authentication"],"pid":8,"message":"License is not available, authentication is not possible."}
{"type":"log","@timestamp":"2022-07-27T08:25:00+00:00","tags":["warning","plugins","licensing"],"pid":8,"message":"License information could not be obtained from Elasticsearch due to ConnectionError: connect ECONNREFUSED 10.233.17.119:9200 error"}
{"type":"response","@timestamp":"2022-07-27T08:24:48+00:00","tags":[],"pid":8,"method":"get","statusCode":200,"req":{"url":"/app/kibana","method":"get","headers":{"host":"localhost:5601","user-agent":"curl/7.68.0","accept":"*/*"},"remoteAddress":"127.0.0.1","userAgent":"curl/7.68.0"},"res":{"statusCode":200,"responseTime":12255},"message":"GET /app/kibana 200 12255ms"}
{"type":"response","@timestamp":"2022-07-27T08:24:58+00:00","tags":[],"pid":8,"method":"get","statusCode":503,"req":{"url":"/app/kibana","method":"get","headers":{"host":"localhost:5601","user-agent":"curl/7.68.0","accept":"*/*"},"remoteAddress":"127.0.0.1","userAgent":"curl/7.68.0"},"res":{"statusCode":503,"responseTime":2216,"contentLength":86},"message":"GET /app/kibana 503 2216ms - 86.0B"}
{"type":"log","@timestamp":"2022-07-27T08:25:00+00:00","tags":["error","plugins","security","authentication"],"pid":8,"message":"License is not available, authentication is not possible."}
{"type":"log","@timestamp":"2022-07-27T08:25:01+00:00","tags":["warning","plugins","licensing"],"pid":8,"message":"License information could not be obtained from Elasticsearch due to ConnectionError: connect ECONNREFUSED 10.233.17.119:9200 error"}

ES is working fine.
Readiness had issue, which was waiting for cluster health to be green, but ES health is generally yellow in case of single node.

So because readiness was not successful, the ready state was 0/1 and due to this the ES service clusterIP was not accessible by kibana and fluentd.

Fixing the readiness to look for both green and yellow health worked for me

2 Likes

Thank you very much @samee_alam for the solution.

The steps:

$ kubectl edit statefulset -n logging elasticsearch-master

Add these 3 lines with elif in this code snippet:

  echo 'Waiting for elasticsearch cluster to become ready (request params: "wait_for_status=green&timeout=1s" )'
  if http "/_cluster/health?wait_for_status=green&timeout=1s" "--fail" ; then
    touch ${START_FILE}
    exit 0
  elif http "/_cluster/health?wait_for_status=yellow&timeout=1s" "--fail" ; then
    touch ${START_FILE}
    exit 0
  else
    echo 'Cluster is not yet ready (request params: "wait_for_status=green&timeout=1s" )'
    exit 1
1 Like

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