Re: Spark 1.5.2 Shuffle Blocks - running out of memory

[Nirav Patel]

Is this a limit of spark shuffle block currently?

On Tue, May 3, 2016 at 11:18 AM, Nirav Patel  wrote:

> Hi,
>
> My spark application getting killed abruptly during a groupBy operation
> where shuffle happens. All shuffle happens with PROCESS_LOCAL locality. I
> see following in driver logs. Should not this logs be in executors? Anyhow
> looks like ByteBuffer is running out of memory. What will be workaround for
> this?
>
>
> 2016-05-02 22:38:53,595 INFO
> [sparkDriver-akka.actor.default-dispatcher-14]
> org.apache.spark.MapOutputTrackerMasterEndpoint: Asked to send map output
> locations for shuffle 3 to hdn2.mycorp:45993
> 2016-05-02 22:38:53,832 INFO
> [sparkDriver-akka.actor.default-dispatcher-14]
> org.apache.spark.storage.BlockManagerInfo: Removed broadcast_4_piece0 on
> 10.250.70.117:52328 in memory (size: 2.1 KB, free: 15.5 MB)
> 2016-05-02 22:39:03,704 WARN [New I/O worker #5]
> org.jboss.netty.channel.DefaultChannelPipeline: An exception was thrown by
> a user handler while handling an exception event ([id: 0xa8147f0c, /
> 10.250.70.110:48056 => /10.250.70.117:38300] EXCEPTION:
> java.lang.OutOfMemoryError: Java heap space)
> java.lang.OutOfMemoryError: Java heap space
> at java.nio.HeapByteBuffer.(HeapByteBuffer.java:57)
> at java.nio.ByteBuffer.allocate(ByteBuffer.java:331)
> at
> org.jboss.netty.buffer.CompositeChannelBuffer.toByteBuffer(CompositeChannelBuffer.java:649)
> at
> org.jboss.netty.buffer.AbstractChannelBuffer.toByteBuffer(AbstractChannelBuffer.java:530)
> at
> org.jboss.netty.channel.socket.nio.SocketSendBufferPool.acquire(SocketSendBufferPool.java:77)
> at
> org.jboss.netty.channel.socket.nio.SocketSendBufferPool.acquire(SocketSendBufferPool.java:46)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioWorker.write0(AbstractNioWorker.java:194)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioWorker.writeFromTaskLoop(AbstractNioWorker.java:152)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioChannel$WriteTask.run(AbstractNioChannel.java:335)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioSelector.processTaskQueue(AbstractNioSelector.java:366)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioSelector.run(AbstractNioSelector.java:290)
> at
> org.jboss.netty.channel.socket.nio.AbstractNioWorker.run(AbstractNioWorker.java:90)
> at
> org.jboss.netty.channel.socket.nio.NioWorker.run(NioWorker.java:178)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:744)
> 2016-05-02 22:39:05,783 ERROR
> [sparkDriver-akka.actor.default-dispatcher-14]
> org.apache.spark.rpc.akka.ErrorMonitor: Uncaught fatal error from thread
> [sparkDriver-akka.remote.default-remote-dispatcher-5] shutting down
> ActorSystem [sparkDriver]
> java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOf(Arrays.java:2271)
> at
> java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:113)
> at
> java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
> at
> java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:140)
> at
> java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1876)
> at
> java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1785)
> at
> java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1188)
> at
> java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:347)
> at
> akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply$mcV$sp(Serializer.scala:129)
> at
> akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply(Serializer.scala:129)
> at
> akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply(Serializer.scala:129)
> at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
> at akka.serialization.JavaSerializer.toBinary(Serializer.scala:129)
> at
> akka.remote.MessageSerializer$.serialize(MessageSerializer.scala:36)
> at
> akka.remote.EndpointWriter$$anonfun$serializeMessage$1.apply(Endpoint.scala:843)
> at
> akka.remote.EndpointWriter$$anonfun$serializeMessage$1.apply(Endpoint.scala:843)
> at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
> at akka.remote.EndpointWriter.serializeMessage(Endpoint.scala:842)
> at akka.remote.EndpointWriter.writeSend(Endpoint.scala:743)
> at
> akka.remote.EndpointWriter$$anonfun$2.applyOrElse(Endpoint.scala:718)
> at akka.actor.Actor$class.aroundReceive(Actor.scala:467)
> at akka.remote.EndpointActor.aroundReceive(Endpoint.scala:411)
> at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
> 

Spark 1.5.2 Shuffle Blocks - running out of memory

[Nirav Patel]

Hi,

My spark application getting killed abruptly during a groupBy operation
where shuffle happens. All shuffle happens with PROCESS_LOCAL locality. I
see following in driver logs. Should not this logs be in executors? Anyhow
looks like ByteBuffer is running out of memory. What will be workaround for
this?


2016-05-02 22:38:53,595 INFO [sparkDriver-akka.actor.default-dispatcher-14]
org.apache.spark.MapOutputTrackerMasterEndpoint: Asked to send map output
locations for shuffle 3 to hdn2.mycorp:45993
2016-05-02 22:38:53,832 INFO [sparkDriver-akka.actor.default-dispatcher-14]
org.apache.spark.storage.BlockManagerInfo: Removed broadcast_4_piece0 on
10.250.70.117:52328 in memory (size: 2.1 KB, free: 15.5 MB)
2016-05-02 22:39:03,704 WARN [New I/O worker #5]
org.jboss.netty.channel.DefaultChannelPipeline: An exception was thrown by
a user handler while handling an exception event ([id: 0xa8147f0c, /
10.250.70.110:48056 => /10.250.70.117:38300] EXCEPTION:
java.lang.OutOfMemoryError: Java heap space)
java.lang.OutOfMemoryError: Java heap space
at java.nio.HeapByteBuffer.(HeapByteBuffer.java:57)
at java.nio.ByteBuffer.allocate(ByteBuffer.java:331)
at
org.jboss.netty.buffer.CompositeChannelBuffer.toByteBuffer(CompositeChannelBuffer.java:649)
at
org.jboss.netty.buffer.AbstractChannelBuffer.toByteBuffer(AbstractChannelBuffer.java:530)
at
org.jboss.netty.channel.socket.nio.SocketSendBufferPool.acquire(SocketSendBufferPool.java:77)
at
org.jboss.netty.channel.socket.nio.SocketSendBufferPool.acquire(SocketSendBufferPool.java:46)
at
org.jboss.netty.channel.socket.nio.AbstractNioWorker.write0(AbstractNioWorker.java:194)
at
org.jboss.netty.channel.socket.nio.AbstractNioWorker.writeFromTaskLoop(AbstractNioWorker.java:152)
at
org.jboss.netty.channel.socket.nio.AbstractNioChannel$WriteTask.run(AbstractNioChannel.java:335)
at
org.jboss.netty.channel.socket.nio.AbstractNioSelector.processTaskQueue(AbstractNioSelector.java:366)
at
org.jboss.netty.channel.socket.nio.AbstractNioSelector.run(AbstractNioSelector.java:290)
at
org.jboss.netty.channel.socket.nio.AbstractNioWorker.run(AbstractNioWorker.java:90)
at
org.jboss.netty.channel.socket.nio.NioWorker.run(NioWorker.java:178)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
2016-05-02 22:39:05,783 ERROR
[sparkDriver-akka.actor.default-dispatcher-14]
org.apache.spark.rpc.akka.ErrorMonitor: Uncaught fatal error from thread
[sparkDriver-akka.remote.default-remote-dispatcher-5] shutting down
ActorSystem [sparkDriver]
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2271)
at
java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:113)
at
java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at
java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:140)
at
java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1876)
at
java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1785)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1188)
at
java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:347)
at
akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply$mcV$sp(Serializer.scala:129)
at
akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply(Serializer.scala:129)
at
akka.serialization.JavaSerializer$$anonfun$toBinary$1.apply(Serializer.scala:129)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
at akka.serialization.JavaSerializer.toBinary(Serializer.scala:129)
at
akka.remote.MessageSerializer$.serialize(MessageSerializer.scala:36)
at
akka.remote.EndpointWriter$$anonfun$serializeMessage$1.apply(Endpoint.scala:843)
at
akka.remote.EndpointWriter$$anonfun$serializeMessage$1.apply(Endpoint.scala:843)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
at akka.remote.EndpointWriter.serializeMessage(Endpoint.scala:842)
at akka.remote.EndpointWriter.writeSend(Endpoint.scala:743)
at
akka.remote.EndpointWriter$$anonfun$2.applyOrElse(Endpoint.scala:718)
at akka.actor.Actor$class.aroundReceive(Actor.scala:467)
at akka.remote.EndpointActor.aroundReceive(Endpoint.scala:411)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
at akka.actor.ActorCell.invoke(ActorCell.scala:487)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
at akka.dispatch.Mailbox.run(Mailbox.scala:220)
at
akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at