Unable to get logs of Kubernetes cluster using EFK stack on ubuntu

10/12/2018

I am trying to do the log monitoring of my kubernetes cluster using Elasticsearch, Fluentd, and Kibana. Here is the link which I was followed in this task. I labeled the nodes with beta.kubernetes.io/fluentd-ds-ready: "true". Initially, I created the StatefulSet for Elasticsearch.

After that, I created the fluentd-es-configmap.yaml, fluentd-es-ds.yaml and checked the pods status using kubectl get pods -n kube-system. The Fluentd pods are showing status like container running. I checked the logs of the Fluentd container and it shows the error like:

2018-10-12 13:58:06 +0000 [warn]: [elasticsearch] bad chunk is moved to /tmp/fluentd-buffers/backup/worker0/elasticsearch/577e7f176a989a71a058275373e7f103.log 2018-10-12 13:58:51 +0000 [warn]: [elasticsearch] got unrecoverable error in primary and no secondary error_class=Fluent::Plugin::ElasticsearchOutput::ConnectionFailure error="Can not reach Elasticsearch cluster ({:host=>\"elasticsearch-logging\", :port=>9200, :scheme=>\"http\"})!"

2018-10-12 13:58:06 +0000 [warn]: [elasticsearch] bad chunk is moved to /tmp/fluentd-buffers/backup/worker0/elasticsearch/577e7f176a989a71a058275373e7f103.log 2018-10-12 13:58:51 +0000 [warn]: [elasticsearch] got unrecoverable error in primary and no secondary error_class=Fluent::Plugin::ElasticsearchOutput::ConnectionFailure error="Can not reach Elasticsearch cluster ({:host=>\"elasticsearch-logging\", :port=>9200, :scheme=>\"http\"})!"

My fluentd-configmap.yaml:

kind: ConfigMap
apiVersion: v1
metadata:
  name: fluentd-es-config-v0.1.0
  namespace: kube-system
  labels:
    addonmanager.kubernetes.io/mode: Reconcile
data:
  system.conf: |-
    <system>
      root_dir /tmp/fluentd-buffers/
    </system>
  containers.input.conf: |-
    # This configuration file for Fluentd / td-agent is used
    # to watch changes to Docker log files. The kubelet creates symlinks that
    # capture the pod name, namespace, container name & Docker container ID
    # to the docker logs for pods in the /var/log/containers directory on the host.
    # If running this fluentd configuration in a Docker container, the /var/log
    # directory should be mounted in the container.
    #
    # These logs are then submitted to Elasticsearch which assumes the
    # installation of the fluent-plugin-elasticsearch & the
    # fluent-plugin-kubernetes_metadata_filter plugins.
    # See https://github.com/uken/fluent-plugin-elasticsearch &
    # https://github.com/fabric8io/fluent-plugin-kubernetes_metadata_filter for
    # more information about the plugins.
    #
    # Example
    # =======
    # A line in the Docker log file might look like this JSON:
    #
    # {"log":"2014/09/25 21:15:03 Got request with path wombat\n",
    #  "stream":"stderr",
    #   "time":"2014-09-25T21:15:03.499185026Z"}
    #
    # The time_format specification below makes sure we properly
    # parse the time format produced by Docker. This will be
    # submitted to Elasticsearch and should appear like:
    # $ curl 'http://elasticsearch-logging:9200/_search?pretty'
    # ...
    # {
    #      "_index" : "logstash-2014.09.25",
    #      "_type" : "fluentd",
    #      "_id" : "VBrbor2QTuGpsQyTCdfzqA",
    #      "_score" : 1.0,
    #      "_source":{"log":"2014/09/25 22:45:50 Got request with path wombat\n",
    #                 "stream":"stderr","tag":"docker.container.all",
    #                 "@timestamp":"2014-09-25T22:45:50+00:00"}
    #    },
    # ...
    #
    # The Kubernetes fluentd plugin is used to write the Kubernetes metadata to the log
    # record & add labels to the log record if properly configured. This enables users
    # to filter & search logs on any metadata.
    # For example a Docker container's logs might be in the directory:
    #
    #  /var/lib/docker/containers/997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b
    #
    # and in the file:
    #
    #  997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b-json.log
    #
    # where 997599971ee6... is the Docker ID of the running container.
    # The Kubernetes kubelet makes a symbolic link to this file on the host machine
    # in the /var/log/containers directory which includes the pod name and the Kubernetes
    # container name:
    #
    #    synthetic-logger-0.25lps-pod_default_synth-lgr-997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b.log
    #    ->
    #    /var/lib/docker/containers/997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b/997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b-json.log
    #
    # The /var/log directory on the host is mapped to the /var/log directory in the container
    # running this instance of Fluentd and we end up collecting the file:
    #
    #   /var/log/containers/synthetic-logger-0.25lps-pod_default_synth-lgr-997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b.log
    #
    # This results in the tag:
    #
    #  var.log.containers.synthetic-logger-0.25lps-pod_default_synth-lgr-997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b.log
    #
    # The Kubernetes fluentd plugin is used to extract the namespace, pod name & container name
    # which are added to the log message as a kubernetes field object & the Docker container ID
    # is also added under the docker field object.
    # The final tag is:
    #
    #   kubernetes.var.log.containers.synthetic-logger-0.25lps-pod_default_synth-lgr-997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b.log
    #
    # And the final log record look like:
    #
    # {
    #   "log":"2014/09/25 21:15:03 Got request with path wombat\n",
    #   "stream":"stderr",
    #   "time":"2014-09-25T21:15:03.499185026Z",
    #   "kubernetes": {
    #     "namespace": "default",
    #     "pod_name": "synthetic-logger-0.25lps-pod",
    #     "container_name": "synth-lgr"
    #   },
    #   "docker": {
    #     "container_id": "997599971ee6366d4a5920d25b79286ad45ff37a74494f262e3bc98d909d0a7b"
    #   }
    # }
    #
    # This makes it easier for users to search for logs by pod name or by
    # the name of the Kubernetes container regardless of how many times the
    # Kubernetes pod has been restarted (resulting in a several Docker container IDs).
    # Json Log Example:
    # {"log":"[info:2016-02-16T16:04:05.930-08:00] Some log text here\n","stream":"stdout","time":"2016-02-17T00:04:05.931087621Z"}
    # CRI Log Example:
    # 2016-02-17T00:04:05.931087621Z stdout F [info:2016-02-16T16:04:05.930-08:00] Some log text here
    <source>
      @id fluentd-containers.log
      @type tail
      path /var/log/containers/*.log
      pos_file /var/log/es-containers.log.pos
      tag raw.kubernetes.*
      read_from_head true
      <parse>
        @type multi_format
        <pattern>
          format json
          time_key time
          time_format %Y-%m-%dT%H:%M:%S.%NZ
        </pattern>
        <pattern>
          format /^(?<time>.+) (?<stream>stdout|stderr) [^ ]* (?<log>.*)$/
          time_format %Y-%m-%dT%H:%M:%S.%N%:z
        </pattern>
      </parse>
    </source>
    # Detect exceptions in the log output and forward them as one log entry.
    <match raw.kubernetes.**>
      @id raw.kubernetes
      @type detect_exceptions
      remove_tag_prefix raw
      message log
      stream stream
      multiline_flush_interval 5
      max_bytes 500000
      max_lines 1000
    </match>
  system.input.conf: |-
    # Example:
    # 2015-12-21 23:17:22,066 [salt.state       ][INFO    ] Completed state [net.ipv4.ip_forward] at time 23:17:22.066081
    <source>
      @id minion
      @type tail
      format /^(?<time>[^ ]* [^ ,]*)[^\[]*\[[^\]]*\]\[(?<severity>[^ \]]*) *\] (?<message>.*)$/
      time_format %Y-%m-%d %H:%M:%S
      path /var/log/salt/minion
      pos_file /var/log/salt.pos
      tag salt
    </source>
    # Example:
    # Dec 21 23:17:22 gke-foo-1-1-4b5cbd14-node-4eoj startupscript: Finished running startup script /var/run/google.startup.script
    <source>
      @id startupscript.log
      @type tail
      format syslog
      path /var/log/startupscript.log
      pos_file /var/log/es-startupscript.log.pos
      tag startupscript
    </source>
    # Examples:
    # time="2016-02-04T06:51:03.053580605Z" level=info msg="GET /containers/json"
    # time="2016-02-04T07:53:57.505612354Z" level=error msg="HTTP Error" err="No such image: -f" statusCode=404
    # TODO(random-liu): Remove this after cri container runtime rolls out.
    <source>
      @id docker.log
      @type tail
      format /^time="(?<time>[^)]*)" level=(?<severity>[^ ]*) msg="(?<message>[^"]*)"( err="(?<error>[^"]*)")?( statusCode=($<status_code>\d+))?/
      path /var/log/docker.log
      pos_file /var/log/es-docker.log.pos
      tag docker
    </source>
    # Example:
    # 2016/02/04 06:52:38 filePurge: successfully removed file /var/etcd/data/member/wal/00000000000006d0-00000000010a23d1.wal
    <source>
      @id etcd.log
      @type tail
      # Not parsing this, because it doesn't have anything particularly useful to
      # parse out of it (like severities).
      format none
      path /var/log/etcd.log
      pos_file /var/log/es-etcd.log.pos
      tag etcd
    </source>
    # Multi-line parsing is required for all the kube logs because very large log
    # statements, such as those that include entire object bodies, get split into
    # multiple lines by glog.
    # Example:
    # I0204 07:32:30.020537    3368 server.go:1048] POST /stats/container/: (13.972191ms) 200 [[Go-http-client/1.1] 10.244.1.3:40537]
    <source>
      @id kubelet.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/kubelet.log
      pos_file /var/log/es-kubelet.log.pos
      tag kubelet
    </source>
    # Example:
    # I1118 21:26:53.975789       6 proxier.go:1096] Port "nodePort for kube-system/default-http-backend:http" (:31429/tcp) was open before and is still needed
    <source>
      @id kube-proxy.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/kube-proxy.log
      pos_file /var/log/es-kube-proxy.log.pos
      tag kube-proxy
    </source>
    # Example:
    # I0204 07:00:19.604280       5 handlers.go:131] GET /api/v1/nodes: (1.624207ms) 200 [[kube-controller-manager/v1.1.3 (linux/amd64) kubernetes/6a81b50] 127.0.0.1:38266]
    <source>
      @id kube-apiserver.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/kube-apiserver.log
      pos_file /var/log/es-kube-apiserver.log.pos
      tag kube-apiserver
    </source>
    # Example:
    # I0204 06:55:31.872680       5 servicecontroller.go:277] LB already exists and doesn't need update for service kube-system/kube-ui
    <source>
      @id kube-controller-manager.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/kube-controller-manager.log
      pos_file /var/log/es-kube-controller-manager.log.pos
      tag kube-controller-manager
    </source>
    # Example:
    # W0204 06:49:18.239674       7 reflector.go:245] pkg/scheduler/factory/factory.go:193: watch of *api.Service ended with: 401: The event in requested index is outdated and cleared (the requested history has been cleared [2578313/2577886]) [2579312]
    <source>
      @id kube-scheduler.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/kube-scheduler.log
      pos_file /var/log/es-kube-scheduler.log.pos
      tag kube-scheduler
    </source>
    # Example:
    # I0603 15:31:05.793605       6 cluster_manager.go:230] Reading config from path /etc/gce.conf
    <source>
      @id glbc.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/glbc.log
      pos_file /var/log/es-glbc.log.pos
      tag glbc
    </source>
    # Example:
    # I0603 15:31:05.793605       6 cluster_manager.go:230] Reading config from path /etc/gce.conf
    <source>
      @id cluster-autoscaler.log
      @type tail
      format multiline
      multiline_flush_interval 5s
      format_firstline /^\w\d{4}/
      format1 /^(?<severity>\w)(?<time>\d{4} [^\s]*)\s+(?<pid>\d+)\s+(?<source>[^ \]]+)\] (?<message>.*)/
      time_format %m%d %H:%M:%S.%N
      path /var/log/cluster-autoscaler.log
      pos_file /var/log/es-cluster-autoscaler.log.pos
      tag cluster-autoscaler
    </source>
    # Logs from systemd-journal for interesting services.
    # TODO(random-liu): Remove this after cri container runtime rolls out.
    <source>
      @id journald-docker
      @type systemd
      matches [{ "_SYSTEMD_UNIT": "docker.service" }]
      <storage>
        @type local
        persistent true
        path /var/log/journald-docker.pos
      </storage>
      read_from_head true
      tag docker
    </source>
    <source>
      @id journald-container-runtime
      @type systemd
      matches [{ "_SYSTEMD_UNIT": "{{ container_runtime }}.service" }]
      <storage>
        @type local
        persistent true
        path /var/log/journald-container-runtime.pos
      </storage>
      read_from_head true
      tag container-runtime
    </source>
    <source>
      @id journald-kubelet
      @type systemd
      matches [{ "_SYSTEMD_UNIT": "kubelet.service" }]
      <storage>
        @type local
        persistent true
        path /var/log/journald-kubelet.pos
      </storage>
      read_from_head true
      tag kubelet
    </source>
    <source>
      @id journald-node-problem-detector
      @type systemd
      matches [{ "_SYSTEMD_UNIT": "node-problem-detector.service" }]
      <storage>
        @type local
        persistent true
        path /var/log/journald-node-problem-detector.pos
      </storage>
      read_from_head true
      tag node-problem-detector
    </source>
    <source>
      @id kernel
      @type systemd
      matches [{ "_TRANSPORT": "kernel" }]
      <storage>
        @type local
        persistent true
        path /var/log/kernel.pos
      </storage>
      <entry>
        fields_strip_underscores true
        fields_lowercase true
      </entry>
      read_from_head true
      tag kernel
    </source>
  forward.input.conf: |-
    # Takes the messages sent over TCP
    <source>
      @type forward
    </source>
  monitoring.conf: |-
    # Prometheus Exporter Plugin
    # input plugin that exports metrics
    <source>
      @type prometheus
    </source>
    <source>
      @type monitor_agent
    </source>
    # input plugin that collects metrics from MonitorAgent
    <source>
      @type prometheus_monitor
      <labels>
        host ${hostname}
      </labels>
    </source>
    # input plugin that collects metrics for output plugin
    <source>
      @type prometheus_output_monitor
      <labels>
        host ${hostname}
      </labels>
    </source>
    # input plugin that collects metrics for in_tail plugin
    <source>
      @type prometheus_tail_monitor
      <labels>
        host ${hostname}
      </labels>
    </source>
  output.conf: |-
    # Enriches records with Kubernetes metadata
    <filter kubernetes.**>
      @type kubernetes_metadata
    </filter>
    <match **>
      @id elasticsearch
      @type elasticsearch
      @log_level info
      type_name fluentd
      include_tag_key true
      host elasticsearch-logging
      port 9200
      logstash_format true
      <buffer>
        @type file
        path /var/log/fluentd-buffers/kubernetes.system.buffer
        flush_mode interval
        retry_type exponential_backoff
        flush_thread_count 2
        flush_interval 5s
        retry_forever true
        retry_max_interval 30
        chunk_limit_size 10M
        total_limit_size 10G
        queue_limit_length 8
        overflow_action block
      </buffer>
    </match> 

I am trying to view the Kibana dashboard on the browser. But it shows as an empty response from the server.

Could anybody suggest me how to resolve this error?

Thanks in advance.

-- gayathri
docker
elasticsearch
fluentd
kubernetes

1 Answer

10/12/2018

The log message means that Fluentd cannot reach your ElasticSearch cluster. Based on the link that you shared.

You need to apply this service to expose your ElasticSearch cluster on port 9200 as elasticsearch-logging on the same namespace where your Fluentd pod is running. So it appears that elasticsearch-logging is missing. You can find out more details with:

kubectl -n kube-system get svc

and

kubectl -n kube-system describe svc elasticsearch-logging

Another issue could be that DNS is not resolvable within the namespace which could be coredns or kube-dns. You could try shelling into a pod in the same namespace:

kubectl -n kube-system exec -it <pod-in-kube-system> sh

Then inside

curl elasticsearch-logging:9200
-- Rico
Source: StackOverflow