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From Koert Kuipers <ko...@tresata.com>
Subject Re: NegativeArraySizeException / segfault
Date Wed, 08 Jun 2016 16:43:18 GMT
great!

we weren't able to reproduce it because the unit tests use a broadcast-join
while on the cluster it uses sort-merge-join. so the issue is in
sort-merge-join.

we are now able to reproduce it in tests using
spark.sql.autoBroadcastJoinThreshold=-1
it produces weird looking garbled results in the join.
hoping to get a minimal reproducible example soon.

On Wed, Jun 8, 2016 at 10:24 AM, Pete Robbins <robbinspg@gmail.com> wrote:

> 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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