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https://issues.apache.org/jira/browse/KAFKA-3693?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15313441#comment-15313441
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Jun Rao commented on KAFKA-3693:
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[~maysamyabandeh], yes, I agree it would be better if the broker can be more 
defensive. However, the current logic is a bit subtle. Now only do we require 
the first LeaderAndIsrRequest to contain all the partitions on this broker, but 
also that before the first LeaderAndIsrRequest, the controller sends an 
UpdateMetadataRequest to the newly started broker. This is needed since if 
security is enabled, the newly started broker needs to know all the secure 
ports and that information is currently only propagated through 
UpdateMetadataRequest.

Now, for the situation that you described, when did broker 16 join the cluster? 
Currently, there is synchronization on the controller lock between handling new 
brokers and doing controlled shutdown. So, controller shouldn't be able to see 
broker 16 after the logic of handling new broker has been completed (after 
which point, the newly started broker would have received a LeaderAndIsrRequest 
with all partitions).

> Race condition between highwatermark-checkpoint thread and 
> handleLeaderAndIsrRequest at broker start-up
> -------------------------------------------------------------------------------------------------------
>
>                 Key: KAFKA-3693
>                 URL: https://issues.apache.org/jira/browse/KAFKA-3693
>             Project: Kafka
>          Issue Type: Bug
>          Components: core
>    Affects Versions: 0.9.0.1
>            Reporter: Maysam Yabandeh
>
> Upon broker start-up, a race between highwatermark-checkpoint thread to write 
> replication-offset-checkpoint file and handleLeaderAndIsrRequest thread 
> reading from it causes the highwatermark for some partitions to be reset to 
> 0. In the good case, this results the replica to truncate its entire log to 0 
> and hence initiates fetching of terabytes of data from the lead broker, which 
> sometimes leads to hours of downtime. We observed the bad cases that the 
> reset offset can propagate to recovery-point-offset-checkpoint file, making a 
> lead broker to truncate the file. This seems to have the potential to lead to 
> data loss if the truncation happens at both follower and leader brokers.
> This is the particular faulty scenario manifested in our tests:
> # The broker restarts and receive LeaderAndIsr from the controller
> # LeaderAndIsr message however does not contain all the partitions (probably 
> because other brokers were churning at the same time)
> # becomeLeaderOrFollower calls getOrCreatePartition and updates the 
> allPartitions with the partitions included in the LeaderAndIsr message {code}
>   def getOrCreatePartition(topic: String, partitionId: Int): Partition = {
>     var partition = allPartitions.get((topic, partitionId))
>     if (partition == null) {
>       allPartitions.putIfNotExists((topic, partitionId), new Partition(topic, 
> partitionId, time, this))
> {code}
> # replication-offset-checkpoint jumps in taking a snapshot of (the partial) 
> allReplicas' high watermark into replication-offset-checkpoint file {code}  
> def checkpointHighWatermarks() {
>     val replicas = 
> allPartitions.values.map(_.getReplica(config.brokerId)).collect{case 
> Some(replica) => replica}{code} hence rewriting the previous highwatermarks.
> # Later becomeLeaderOrFollower calls makeLeaders and makeFollowers which read 
> the (now partial) file through Partition::getOrCreateReplica {code}
>           val checkpoint = 
> replicaManager.highWatermarkCheckpoints(log.dir.getParentFile.getAbsolutePath)
>           val offsetMap = checkpoint.read
>           if (!offsetMap.contains(TopicAndPartition(topic, partitionId)))
>             info("No checkpointed highwatermark is found for partition 
> [%s,%d]".format(topic, partitionId))
> {code}
> We are not entirely sure whether the initial LeaderAndIsr message including a 
> subset of partitions is critical in making this race condition manifest or 
> not. But it is an important detail since it clarifies that a solution based 
> on not letting the highwatermark-checkpoint thread jumping in the middle of 
> processing a LeaderAndIsr message would not suffice.
> The solution we are thinking of is to force initializing allPartitions by the 
> partitions listed in the replication-offset-checkpoint (and perhaps 
> recovery-point-offset-checkpoint file too) when a server starts.
> Thoughts?



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