[SPARK-1786] Kryo Serialization Error in GraphX - ASF JIRA

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Details

Type: Bug
Status: Resolved
Priority: Major
Resolution: Fixed
Affects Version/s: 1.0.0
Fix Version/s: 1.0.0
Component/s: GraphX
Labels:
None

Description

The following code block will generate a serialization error when run in the spark-shell with Kryo enabled:

import org.apache.spark.storage._
import org.apache.spark.graphx._
import org.apache.spark.graphx.util._

val g = GraphGenerators.gridGraph(sc, 100, 100)
val e = g.edges
e.persist(StorageLevel.MEMORY_ONLY_SER)
e.collect().foreach(println(_)) // <- Runs successfully the first time.

// The following line will fail:
e.collect().foreach(println(_))

The following error is generated:

scala> e.collect().foreach(println(_))
14/05/09 18:31:13 INFO SparkContext: Starting job: collect at EdgeRDD.scala:59
14/05/09 18:31:13 INFO DAGScheduler: Got job 1 (collect at EdgeRDD.scala:59) with 8 output partitions (allowLocal=false)
14/05/09 18:31:13 INFO DAGScheduler: Final stage: Stage 1(collect at EdgeRDD.scala:59)
14/05/09 18:31:13 INFO DAGScheduler: Parents of final stage: List()
14/05/09 18:31:13 INFO DAGScheduler: Missing parents: List()
14/05/09 18:31:13 INFO DAGScheduler: Submitting Stage 1 (MappedRDD[15] at map at EdgeRDD.scala:59), which has no missing parents
14/05/09 18:31:13 INFO DAGScheduler: Submitting 8 missing tasks from Stage 1 (MappedRDD[15] at map at EdgeRDD.scala:59)
14/05/09 18:31:13 INFO TaskSchedulerImpl: Adding task set 1.0 with 8 tasks
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:0 as TID 8 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:0 as 1779 bytes in 3 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:1 as TID 9 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:1 as 1779 bytes in 4 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:2 as TID 10 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:2 as 1779 bytes in 4 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:3 as TID 11 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:3 as 1779 bytes in 4 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:4 as TID 12 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:4 as 1779 bytes in 3 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:5 as TID 13 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:5 as 1782 bytes in 4 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:6 as TID 14 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:6 as 1783 bytes in 4 ms
14/05/09 18:31:13 INFO TaskSetManager: Starting task 1.0:7 as TID 15 on executor localhost: localhost (PROCESS_LOCAL)
14/05/09 18:31:13 INFO TaskSetManager: Serialized task 1.0:7 as 1783 bytes in 4 ms
14/05/09 18:31:13 INFO Executor: Running task ID 9
14/05/09 18:31:13 INFO Executor: Running task ID 8
14/05/09 18:31:13 INFO Executor: Running task ID 11
14/05/09 18:31:13 INFO Executor: Running task ID 14
14/05/09 18:31:13 INFO Executor: Running task ID 10
14/05/09 18:31:13 INFO Executor: Running task ID 13
14/05/09 18:31:13 INFO Executor: Running task ID 15
14/05/09 18:31:13 INFO Executor: Running task ID 12
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_6 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_4 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_2 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_7 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_1 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_3 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_0 locally
14/05/09 18:31:13 INFO BlockManager: Found block rdd_12_5 locally
14/05/09 18:31:13 ERROR Executor: Exception in task ID 13
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 10
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 11
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 12
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 15
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 8
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 9
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR Executor: Exception in task ID 14
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 WARN TaskSetManager: Lost TID 11 (task 1.0:3)
14/05/09 18:31:13 WARN TaskSetManager: Loss was due to java.lang.NullPointerException
java.lang.NullPointerException
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
	at org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
	at org.apache.spark.scheduler.Task.run(Task.scala:51)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
	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)
14/05/09 18:31:13 ERROR TaskSetManager: Task 1.0:3 failed 1 times; aborting job
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 1]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 2]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 3]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 4]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO DAGScheduler: Failed to run collect at EdgeRDD.scala:59
14/05/09 18:31:13 INFO TaskSchedulerImpl: Cancelling stage 1
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 5]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 6]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
14/05/09 18:31:13 INFO TaskSetManager: Loss was due to java.lang.NullPointerException [duplicate 7]
14/05/09 18:31:13 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
org.apache.spark.SparkException: Job aborted due to stage failure: Task 1.0:3 failed 1 times, most recent failure: Exception failure in TID 11 on host localhost: java.lang.NullPointerException
        org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:269)
        org.apache.spark.graphx.impl.EdgePartition$$anon$1.next(EdgePartition.scala:262)
        scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        scala.collection.Iterator$class.foreach(Iterator.scala:727)
        scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        scala.collection.AbstractIterator.to(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
        org.apache.spark.rdd.RDD$$anonfun$15.apply(RDD.scala:706)
        org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
        org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1071)
        org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
        org.apache.spark.scheduler.Task.run(Task.scala:51)
        org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:208)
        java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        java.lang.Thread.run(Thread.java:744)
Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1033)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1017)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1015)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1015)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:633)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:633)
	at scala.Option.foreach(Option.scala:236)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:633)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1207)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
	at akka.actor.ActorCell.invoke(ActorCell.scala:456)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
	at akka.dispatch.Mailbox.run(Mailbox.scala:219)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
	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

We believe the error is associated with serialization of the EdgePartition.

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Assignee:: Joseph E. Gonzalez

Reporter:: Joseph E. Gonzalez

Votes:: 0 Vote for this issue

Watchers:: 2 Start watching this issue

Dates

Created:: 10/May/14 01:29

Updated:: 12/May/14 02:22

Resolved:: 12/May/14 02:22