FYI, I posted this to user@ and have followed up with a bug report: https://issues.apache.org/jira/browse/SPARK-17204 <https://issues.apache.org/jira/browse/SPARK-17204>
Michael > Begin forwarded message: > > From: Michael Allman <mich...@videoamp.com> > Subject: Anyone else having trouble with replicated off heap RDD persistence? > Date: August 16, 2016 at 3:45:14 PM PDT > To: user <u...@spark.apache.org> > > Hello, > > A coworker was having a problem with a big Spark job failing after several > hours when one of the executors would segfault. That problem aside, I > speculated that her job would be more robust against these kinds of executor > crashes if she used replicated RDD storage. She's using off heap storage (for > good reason), so I asked her to try running her job with the following > storage level: `StorageLevel(useDisk = true, useMemory = true, useOffHeap = > true, deserialized = false, replication = 2)`. The job would immediately fail > with a rather suspicious looking exception. For example: > > com.esotericsoftware.kryo.KryoException: Encountered unregistered class ID: > 9086 > at > com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:137) > at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:670) > at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:781) > at > org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:229) > at > org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:169) > at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73) > at > org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32) > at > org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) > at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:461) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificColumnarIterator.hasNext(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown > Source) > at > org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) > at > org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47) > at org.apache.spark.scheduler.Task.run(Task.scala:85) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) > 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) > > or > > java.lang.IndexOutOfBoundsException: Index: 6, Size: 0 > at java.util.ArrayList.rangeCheck(ArrayList.java:653) > at java.util.ArrayList.get(ArrayList.java:429) > at > com.esotericsoftware.kryo.util.MapReferenceResolver.getReadObject(MapReferenceResolver.java:60) > at com.esotericsoftware.kryo.Kryo.readReferenceOrNull(Kryo.java:834) > at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:788) > at > org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:229) > at > org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:169) > at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73) > at > org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32) > at > org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) > at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:461) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificColumnarIterator.hasNext(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown > Source) > at > org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) > at > org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47) > at org.apache.spark.scheduler.Task.run(Task.scala:85) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) > 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) > > or > > java.lang.NullPointerException > at > org.apache.spark.sql.execution.columnar.InMemoryTableScanExec$$anonfun$doExecute$1$$anonfun$6.apply(InMemoryTableScanExec.scala:141) > at > org.apache.spark.sql.execution.columnar.InMemoryTableScanExec$$anonfun$doExecute$1$$anonfun$6.apply(InMemoryTableScanExec.scala:140) > at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:463) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificColumnarIterator.hasNext(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificColumnarIterator.hasNext(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown > Source) > at > org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) > at > org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47) > at org.apache.spark.scheduler.Task.run(Task.scala:85) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) > at java.lang.Thread.run(Thread.java:745) > > I tried switching to Java serialization. I got a different exception: > > java.io.StreamCorruptedException: invalid stream header: 780000D0 > at > java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:808) > at java.io.ObjectInputStream.<init>(ObjectInputStream.java:301) > at > org.apache.spark.serializer.JavaDeserializationStream$$anon$1.<init>(JavaSerializer.scala:63) > at > org.apache.spark.serializer.JavaDeserializationStream.<init>(JavaSerializer.scala:63) > at > org.apache.spark.serializer.JavaSerializerInstance.deserializeStream(JavaSerializer.scala:122) > at > org.apache.spark.serializer.SerializerManager.dataDeserializeStream(SerializerManager.scala:146) > at > org.apache.spark.storage.BlockManager.getLocalValues(BlockManager.scala:433) > at > org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:672) > at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:330) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:281) > at > org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:283) > at > org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:283) > at > org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:283) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47) > at org.apache.spark.scheduler.Task.run(Task.scala:85) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) > 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) > > All of this suggests some kind of memory corruption. Has anyone else had a > problem like this using off heap storage with replication factor 2? > > Thanks, > > Michael
