I just raised https://issues.apache.org/jira/browse/SPARK-15822 for a similar looking issue. Analyzing the core dump from the segv with Memory Analyzer it looks very much like a UTF8String is very corrupt.
Cheers, On Fri, 27 May 2016 at 21:00 Koert Kuipers <ko...@tresata.com> wrote: > hello all, > after getting our unit tests to pass on spark 2.0.0-SNAPSHOT we are now > trying to run some algorithms at scale on our cluster. > unfortunately this means that when i see errors i am having a harder time > boiling it down to a small reproducible example. > > today we are running an iterative algo using the dataset api and we are > seeing tasks fail with errors which seem to related to unsafe operations. > the same tasks succeed without issues in our unit tests. > > i see either: > > 16/05/27 12:54:46 ERROR executor.Executor: Exception in task 31.0 in stage > 21.0 (TID 1073) > java.lang.NegativeArraySizeException > at > org.apache.spark.unsafe.types.UTF8String.getBytes(UTF8String.java:229) > at > org.apache.spark.unsafe.types.UTF8String.toString(UTF8String.java:821) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificSafeProjection.apply(Unknown > Source) > at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) > at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) > at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) > at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434) > at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.sort_addToSorter$(Unknown > Source) > at > org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown > Source) > at > org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) > at > org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$7$$anon$1.hasNext(WholeStageCodegenExec.scala:359) > at > org.apache.spark.sql.execution.aggregate.SortBasedAggregateExec$$anonfun$doExecute$1$$anonfun$3.apply(SortBasedAggregateExec.scala:74) > at > org.apache.spark.sql.execution.aggregate.SortBasedAggregateExec$$anonfun$doExecute$1$$anonfun$3.apply(SortBasedAggregateExec.scala:71) > at > org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:775) > at > org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:775) > at > org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:318) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:282) > at > org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:318) > at org.apache.spark.rdd.RDD.iterator(RDD.scala:282) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79) > at > org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47) > at org.apache.spark.scheduler.Task.run(Task.scala:85) > at > org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) > > or alternatively: > > # A fatal error has been detected by the Java Runtime Environment: > # > # SIGSEGV (0xb) at pc=0x00007fe571041cba, pid=2450, tid=140622965913344 > # > # JRE version: Java(TM) SE Runtime Environment (7.0_75-b13) (build > 1.7.0_75-b13) > # Java VM: Java HotSpot(TM) 64-Bit Server VM (24.75-b04 mixed mode > linux-amd64 compressed oops) > # Problematic frame: > # v ~StubRoutines::jbyte_disjoint_arraycopy > > i assume the best thing would be to try to get it to print out the > generated code that is causing this? > what switch do i need to use again to do so? > thanks, > koert >
