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From Pete Robbins <robbin...@gmail.com>
Subject Re: NegativeArraySizeException / segfault
Date Wed, 08 Jun 2016 14:24:31 GMT
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 <koert@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
>

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