<p>From time to time we find that some logs are missing in the ES, while we are able to see them in Kubernetes.</p>
<p>Only problems in logs I was able to find, point out to a problem with the kubernetes parser with things like these in the fluent-bit logs:
<code>[2020/11/22 09:53:18] [debug] [filter:kubernetes:kubernetes.1] could not merge JSON log as requested</code></p>
<p>Problems seem to go away (at least no more &quot;warn/errors&quot; in fluent-bit logs) once we configure the kubernetes filter with the &quot;Merge_Log&quot; option to &quot;Off&quot;. But then of course we loss a big functionality such as actually having fields/values other than &quot;message&quot; itself.</p>
<p>There is no other error/warn message in either fluent-bit or elasticsearch other than this, that's why is my main suspect. Log (log_level in info) is filled with:</p>
<pre><code>k --context contexto09 -n logging-system logs -f -l app=fluent-bit --max-log-requests 31 | grep -iv &quot;\[ info\]&quot;
[2020/11/22 19:45:02] [ warn] [engine] failed to flush chunk '1-1606074289.692844263.flb', retry in 25 seconds: task_id=31, input=appstream &gt; output=es.0
[2020/11/22 19:45:02] [ warn] [engine] failed to flush chunk '1-1606074208.938295842.flb', retry in 25 seconds: task_id=67, input=appstream &gt; output=es.0
[2020/11/22 19:45:08] [ warn] [engine] failed to flush chunk '1-1606074298.662911160.flb', retry in 10 seconds: task_id=76, input=appstream &gt; output=es.0
[2020/11/22 19:45:13] [ warn] [engine] failed to flush chunk '1-1606074310.619565119.flb', retry in 9 seconds: task_id=77, input=appstream &gt; output=es.0
[2020/11/22 19:45:13] [ warn] [engine] failed to flush chunk '1-1606073869.655178524.flb', retry in 1164 seconds: task_id=33, input=appstream &gt; output=es.0
[2020/11/22 19:45:18] [ warn] [engine] failed to flush chunk '1-1606074298.662911160.flb', retry in 282 seconds: task_id=76, input=appstream &gt; output=es.0
[2020/11/22 19:45:21] [ warn] [engine] failed to flush chunk '1-1606073620.626120246.flb', retry in 1974 seconds: task_id=8, input=appstream &gt; output=es.0
[2020/11/22 19:45:21] [ warn] [engine] failed to flush chunk '1-1606074050.441691966.flb', retry in 1191 seconds: task_id=51, input=appstream &gt; output=es.0
[2020/11/22 19:45:22] [ warn] [engine] failed to flush chunk '1-1606074310.619565119.flb', retry in 79 seconds: task_id=77, input=appstream &gt; output=es.0
[2020/11/22 19:45:22] [ warn] [engine] failed to flush chunk '1-1606074319.600878876.flb', retry in 6 seconds: task_id=78, input=appstream &gt; output=es.0
[2020/11/22 19:45:09] [ warn] [engine] failed to flush chunk '1-1606073576.849876665.flb', retry in 1091 seconds: task_id=4, input=appstream &gt; output=es.0
[2020/11/22 19:45:12] [ warn] [engine] failed to flush chunk '1-1606074292.958592278.flb', retry in 898 seconds: task_id=141, input=appstream &gt; output=es.0
[2020/11/22 19:45:14] [ warn] [engine] failed to flush chunk '1-1606074302.347198351.flb', retry in 32 seconds: task_id=143, input=appstream &gt; output=es.0
[2020/11/22 19:45:14] [ warn] [engine] failed to flush chunk '1-1606074253.953778140.flb', retry in 933 seconds: task_id=133, input=appstream &gt; output=es.0
[2020/11/22 19:45:16] [ warn] [engine] failed to flush chunk '1-1606074313.923004098.flb', retry in 6 seconds: task_id=144, input=appstream &gt; output=es.0
[2020/11/22 19:45:18] [ warn] [engine] failed to flush chunk '1-1606074022.933436366.flb', retry in 73 seconds: task_id=89, input=appstream &gt; output=es.0
[2020/11/22 19:45:18] [ warn] [engine] failed to flush chunk '1-1606074304.968844730.flb', retry in 82 seconds: task_id=145, input=appstream &gt; output=es.0
[2020/11/22 19:45:19] [ warn] [engine] failed to flush chunk '1-1606074316.958207701.flb', retry in 10 seconds: task_id=146, input=appstream &gt; output=es.0
[2020/11/22 19:45:19] [ warn] [engine] failed to flush chunk '1-1606074283.907428020.flb', retry in 207 seconds: task_id=139, input=appstream &gt; output=es.0
[2020/11/22 19:45:22] [ warn] [engine] failed to flush chunk '1-1606074313.923004098.flb', retry in 49 seconds: task_id=144, input=appstream &gt; output=es.0
[2020/11/22 19:45:24] [ warn] [engine] failed to flush chunk '1-1606074232.931522416.flb', retry in 109 seconds: task_id=129, input=appstream &gt; output=es.0
...
...
[2020/11/22 19:46:31] [ warn] [engine] chunk '1-1606074022.933436366.flb' cannot be retried: task_id=89, input=appstream &gt; output=es.0

</code></pre>
<p>If I enable &quot;debug&quot; for log_level, then I do see these <code>1. [2020/11/22 09:53:18] [debug] [filter:kubernetes:kubernetes.1] could not merge JSON log as requested</code> which I assume are the reason why the chunks are failing to flush as I don't have the fialed to flush chunk errors when all &quot;merge_log&quot; are off.</p>
<p>My current fluent-bit config is like this:</p>
<pre><code>kind: ConfigMap
metadata:
  labels:
    app: fluent-bit
    app.kubernetes.io/instance: cluster-logging
    chart: fluent-bit-2.8.6
    heritage: Tiller
    release: cluster-logging
  name: config
  namespace: logging-system
apiVersion: v1
data:
  fluent-bit-input.conf: |
    [INPUT]
        Name             tail
        Path             /var/log/containers/*.log
        Exclude_Path     /var/log/containers/cluster-logging-*.log,/var/log/containers/elasticsearch-data-*.log,/var/log/containers/kube-apiserver-*.log
        Parser           docker
        Tag              kube.*
        Refresh_Interval 5
        Mem_Buf_Limit    15MB
        Skip_Long_Lines  On
        Ignore_Older     7d
        DB               /tail-db/tail-containers-state.db
        DB.Sync          Normal
    [INPUT]
        Name            systemd
        Path            /var/log/journal/
        Tag             host.*
        Max_Entries     1000
        Read_From_Tail  true
        Strip_Underscores  true
    [INPUT]
        Name             tail
        Path             /var/log/containers/kube-apiserver-*.log
        Parser           docker
        Tag              kube-apiserver.*
        Refresh_Interval 5 
        Mem_Buf_Limit    5MB
        Skip_Long_Lines  On
        Ignore_Older     7d
        DB               /tail-db/tail-kube-apiserver-containers-state.db
        DB.Sync          Normal

  fluent-bit-filter.conf: |
    [FILTER]
        Name                kubernetes
        Match               kube.*
        Kube_Tag_Prefix     kube.var.log.containers.
        Kube_URL            https://kubernetes.default.svc:443
        Kube_CA_File        /var/run/secrets/kubernetes.io/serviceaccount/ca.crt
        Kube_Token_File     /var/run/secrets/kubernetes.io/serviceaccount/token
        K8S-Logging.Parser  On
        K8S-Logging.Exclude On
        Merge_Log           On
        Keep_Log            Off
        Annotations         Off
    [FILTER]
        Name                kubernetes
        Match               kube-apiserver.*
        Kube_Tag_Prefix     kube-apiserver.var.log.containers.
        Kube_URL            https://kubernetes.default.svc:443
        Kube_CA_File        /var/run/secrets/kubernetes.io/serviceaccount/ca.crt
        Kube_Token_File     /var/run/secrets/kubernetes.io/serviceaccount/token
        K8S-Logging.Parser  Off
        K8S-Logging.Exclude Off
        Merge_Log           Off
        Keep_Log            On
        Annotations         Off

  fluent-bit-output.conf: |
    [OUTPUT]
        Name  es
        Match logs
        Host  elasticsearch-data
        Port  9200
        Logstash_Format On
        Retry_Limit 5
        Type  flb_type
        Time_Key @timestamp
        Replace_Dots On
        Logstash_Prefix logs
        Logstash_Prefix_Key index
        Generate_ID On
        Buffer_Size 2MB
        Trace_Output Off
    [OUTPUT]
        Name  es
        Match sys
        Host  elasticsearch-data
        Port  9200
        Logstash_Format On
        Retry_Limit 5
        Type  flb_type
        Time_Key @timestamp
        Replace_Dots On
        Logstash_Prefix sys-logs
        Generate_ID On
        Buffer_Size 2MB
        Trace_Output Off
    [OUTPUT]
        Name  es
        Match host.*
        Host  elasticsearch-data
        Port  9200
        Logstash_Format On
        Retry_Limit 10
        Type  flb_type
        Time_Key @timestamp
        Replace_Dots On
        Logstash_Prefix host-logs
        Generate_ID On
        Buffer_Size 2MB
        Trace_Output Off
    [OUTPUT]
        Name  es
        Match kube-apiserver.*
        Host  elasticsearch-data
        Port  9200
        Logstash_Format On
        Retry_Limit 10
        Type _doc 
        Time_Key @timestamp
        Replace_Dots On
        Logstash_Prefix kube-apiserver
        Generate_ID On
        Buffer_Size 2MB
        Trace_Output Off

  fluent-bit-stream-processor.conf: |
    [STREAM_TASK]
        Name   appstream
        Exec   CREATE STREAM appstream WITH (tag='logs') AS SELECT * from TAG:'kube.*' WHERE NOT (kubernetes['namespace_name']='ambassador-system' OR kubernetes['namespace_name']='argocd' OR kubernetes['namespace_name']='istio-system' OR kubernetes['namespace_name']='kube-system' OR kubernetes['namespace_name']='logging-system' OR kubernetes['namespace_name']='monitoring-system' OR kubernetes['namespace_name']='storage-system') ;
    [STREAM_TASK]
        Name   sysstream
        Exec   CREATE STREAM sysstream WITH (tag='sys') AS SELECT * from TAG:'kube.*' WHERE (kubernetes['namespace_name']='ambassador-system' OR kubernetes['namespace_name']='argocd' OR kubernetes['namespace_name']='istio-system' OR kubernetes['namespace_name']='kube-system' OR kubernetes['namespace_name']='logging-system' OR kubernetes['namespace_name']='monitoring-system' OR kubernetes['namespace_name']='storage-system') ;

  fluent-bit-service.conf: |
    [SERVICE]
        Flush        3
        Daemon       Off
        Log_Level    info
        Parsers_File parsers.conf
        Streams_File /fluent-bit/etc/fluent-bit-stream-processor.conf

  fluent-bit.conf: |
    @INCLUDE fluent-bit-service.conf
    @INCLUDE fluent-bit-input.conf
    @INCLUDE fluent-bit-filter.conf
    @INCLUDE fluent-bit-output.conf
    
  parsers.conf: |
    [PARSER]
        Name         docker
        Format       json
        Time_Key     time
        Time_Format  %Y-%m-%dT%H:%M:%S.%L
        Time_Keep    On
</code></pre>
<p>Merge_Log is off for &quot;kube-apiserver.<em>&quot; and so far is working ok, although the end behaviour is not desirable (no field mapping being done). Merge_Log for &quot;kube.</em>&quot; is on and is generating the fields in ES as expected...but we are losing logs.</p>
<p>I found the relevant code in kubernetes parser that lead to this error, but I lack the knowledge to understand how to &quot;fix&quot; the error that leads to this message <a href="https://github.com/fluent/fluent-bit/blob/master/plugins/filter_kubernetes/kubernetes.c#L162" rel="noreferrer">https://github.com/fluent/fluent-bit/blob/master/plugins/filter_kubernetes/kubernetes.c#L162</a></p>
<p>This is starting to be really frustrating and I can't figure out why this happens or better, how to fix it. Any help please?</p>

<hr />
<ol>
<li>May be I'm missing smth, but I can't find any output for <code>kube.*</code></li>
</ol>
<hr />
<ol start="2">
<li></li>
</ol>
<p>I've got same error and after enabling</p>
<pre><code>[OUTPUT]
  ....
  Trace_Error on
</code></pre>
<p>Elastic returns to Fluentbit conflict in fields mapping.</p>
<pre><code>stderr F {&quot;took&quot;:0,&quot;errors&quot;:true,&quot;items&quot;:[{&quot;index&quot;:{&quot;_index&quot;:&quot;app-2022.01.02&quot;,&quot;_type&quot;:&quot;_doc&quot;,&quot;_id&quot;:&quot;H8keHX4BFLcmSeMefxLq&quot;,&quot;status&quot;:400,&quot;error&quot;:{&quot;type&quot;:&quot;mapper_parsing_exception&quot;,&quot;reason&quot;:&quot;failed to parse field [log_processed.pid] of type [long] in document with id 'H8keHX4BFLcmSeMefxLq'. Preview of field's value: '18:tid 140607188051712'&quot;,&quot;caused_by&quot;:{&quot;type&quot;:&quot;illegal_argument_exception&quot;,&quot;reason&quot;:&quot;For input string: \&quot;18:tid 140607188051712\&quot;&quot;}}}}]}
</code></pre>
<p>Index mapping in my Elastic has field <code>pid</code> with type long, but I tried to push text value from another <code>[PARSER]</code>, once it has been fixed, issue has gone.</p>
<p><a href="https://i.stack.imgur.com/mYWom.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/mYWom.png" alt="enter image description here" /></a></p>
