Flink slot removed exception

Question

I am getting the following exception

org.apache.flink.util.FlinkException: The assigned slot container_1546939492951_0001_01_003659_0 was removed.
at org.apache.flink.runtime.resourcemanager.slotmanager.SlotManager.removeSlot(SlotManager.java:789)
at org.apache.flink.runtime.resourcemanager.slotmanager.SlotManager.removeSlots(SlotManager.java:759)
at org.apache.flink.runtime.resourcemanager.slotmanager.SlotManager.internalUnregisterTaskManager(SlotManager.java:951)
at org.apache.flink.runtime.resourcemanager.slotmanager.SlotManager.unregisterTaskManager(SlotManager.java:372)
at org.apache.flink.runtime.resourcemanager.ResourceManager.closeTaskManagerConnection(ResourceManager.java:823)
at org.apache.flink.yarn.YarnResourceManager.lambda$onContainersCompleted$0(YarnResourceManager.java:346)
at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.handleRunAsync(AkkaRpcActor.java:332)
at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.handleRpcMessage(AkkaRpcActor.java:158)
at org.apache.flink.runtime.rpc.akka.FencedAkkaRpcActor.handleRpcMessage(FencedAkkaRpcActor.java:70)
at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.onReceive(AkkaRpcActor.java:142)
at org.apache.flink.runtime.rpc.akka.FencedAkkaRpcActor.onReceive(FencedAkkaRpcActor.java:40)
at akka.actor.UntypedActor$$anonfun$receive$1.applyOrElse(UntypedActor.scala:165)
at akka.actor.Actor$class.aroundReceive(Actor.scala:502)
at akka.actor.UntypedActor.aroundReceive(UntypedActor.scala:95)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:526)
at akka.actor.ActorCell.invoke(ActorCell.scala:495)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

when running a batch process involving joining two very large datasets.

Here is what I can see in the overview. The failure happened on a task manager which did not get any inputs. Weirdly the previous set (partition -> flat map -> map) did not send anything to that task manager despite having a rebalance in front.

Am running it on EMR. I see that there is a slot.idle.timeout, would that have an effect and if so how do I specify it for that job? Can it be done on the command line?

Answer 1

it's possible that this is a timeout issue, but usually when this happens to me it's because there's a failure (e.g. YARN kills the container because it's running beyond pmem or vmem limits). I'd recommend carefully checking the JobManager and all TaskManager log files.

Answer 2

You can add the following line in java code.

env.getCheckpointConfig().enableExternalizedCheckpoints(ExternalizedCheckpointCleanup.RETAIN_ON_CANCELLATION);

then your job will start on cancellation automatically.