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Posted to issues@spark.apache.org by "Harel Ben Attia (JIRA)" <ji...@apache.org> on 2018/07/11 14:20:00 UTC
[jira] [Commented] (SPARK-17901) NettyRpcEndpointRef: Error sending
message and Caused by: java.util.ConcurrentModificationException
[ https://issues.apache.org/jira/browse/SPARK-17901?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16540155#comment-16540155 ]
Harel Ben Attia commented on SPARK-17901:
-----------------------------------------
We're encountering the same issue, with spark spark-2.2.0-bin-hadoop2.7 . It is indeed a different stack trace than SPARK-17816. The stack trace itself it below.
{code:java}
org.apache.spark.SparkException: Exception thrown in awaitResult: at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:205) at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75) at org.apache.spark.rpc.RpcEndpointRef.askSync(RpcEndpointRef.scala:92) at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:726) at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply$mcV$sp(Executor.scala:755) at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply(Executor.scala:755) at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply(Executor.scala:755) at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1954) at org.apache.spark.executor.Executor$$anon$2.run(Executor.scala:755) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.util.ConcurrentModificationException at java.util.ArrayList.writeObject(ArrayList.java:770) at sun.reflect.GeneratedMethodAccessor35.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1128) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548) at java.io.ObjectOutputStream.defaultWriteObject(ObjectOutputStream.java:441) at java.util.Collections$SynchronizedCollection.writeObject(Collections.java:2081) at sun.reflect.GeneratedMethodAccessor34.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1128) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174) at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174) at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509) at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178) at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348) at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:43) at org.apache.spark.rpc.netty.RequestMessage.serialize(NettyRpcEnv.scala:554) at org.apache.spark.rpc.netty.NettyRpcEnv.ask(NettyRpcEnv.scala:227) at org.apache.spark.rpc.netty.NettyRpcEndpointRef.ask(NettyRpcEnv.scala:512) at org.apache.spark.rpc.RpcEndpointRef.askSync(RpcEndpointRef.scala:91) ... 13 more
{code}
> NettyRpcEndpointRef: Error sending message and Caused by: java.util.ConcurrentModificationException
> ---------------------------------------------------------------------------------------------------
>
> Key: SPARK-17901
> URL: https://issues.apache.org/jira/browse/SPARK-17901
> Project: Spark
> Issue Type: Bug
> Components: PySpark
> Affects Versions: 2.0.1
> Reporter: Harish
> Priority: Major
>
> I have 2 data frames one with 10K rows and 10,000 columns and another with 4M rows with 50 columns. I joined this and trying to find mean of merged data set,
> i calculated the mean using lamda using python mean() function. I cant write in pyspark due to 64KB code limit issue.
> After calculating the mean i did rdd.take(2). it works.But creating the DF from RDD and DF.show is progress for more than 2 hours (I stopped the process) with below message (102 GB , 6 cores per node -- total 10 nodes+ 1master)
> 16/10/13 04:36:31 WARN NettyRpcEndpointRef: Error sending message [message = Heartbeat(9,[Lscala.Tuple2;@68eedafb,BlockManagerId(9, 10.63.136.103, 35729))] in 1 attempts
> org.apache.spark.SparkException: Exception thrown in awaitResult
> at org.apache.spark.rpc.RpcTimeout$$anonfun$1.applyOrElse(RpcTimeout.scala:77)
> at org.apache.spark.rpc.RpcTimeout$$anonfun$1.applyOrElse(RpcTimeout.scala:75)
> at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
> at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
> at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
> at scala.PartialFunction$OrElse.apply(PartialFunction.scala:167)
> at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:83)
> at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:102)
> at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:518)
> at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply$mcV$sp(Executor.scala:547)
> at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:547)
> at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:547)
> at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1877)
> at org.apache.spark.executor.Executor$$anon$1.run(Executor.scala:547)
> at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
> at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
> at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
> at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.util.ConcurrentModificationException
> at java.util.ArrayList.writeObject(ArrayList.java:766)
> at sun.reflect.GeneratedMethodAccessor36.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1028)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.defaultWriteObject(ObjectOutputStream.java:441)
> at java.util.Collections$SynchronizedCollection.writeObject(Collections.java:2081)
> at sun.reflect.GeneratedMethodAccessor38.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1028)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174)
> at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348)
> at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:43)
> at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:100)
> at org.apache.spark.rpc.netty.NettyRpcEnv.serialize(NettyRpcEnv.scala:253)
> at org.apache.spark.rpc.netty.NettyRpcEnv.ask(NettyRpcEnv.scala:227)
> at org.apache.spark.rpc.netty.NettyRpcEndpointRef.ask(NettyRpcEnv.scala:508)
> at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:101)
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