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