Harish created SPARK-17901:
------------------------------

             Summary: 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


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)



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

---------------------------------------------------------------------
To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org
For additional commands, e-mail: issues-h...@spark.apache.org

Reply via email to