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From Vadim Semenov <va...@datadoghq.com>
Subject Re: Driver OutOfMemoryError in MapOutputTracker$.serializeMapStatuses for 40 TB shuffle.
Date Fri, 07 Sep 2018 15:28:11 GMT
You have too many partitions, so when the driver is trying to gather
the status of all map outputs and send back to executors it chokes on
the size of the structure that needs to be GZipped, and since it's
bigger than 2GiB, it produces OOM.
On Fri, Sep 7, 2018 at 10:35 AM Harel Gliksman <harelglik@gmail.com> wrote:
>
> Hi,
>
> We are running a Spark (2.3.1) job on an EMR cluster with 500 r3.2xlarge (60 GB, 8 vcores,
160 GB SSD ). Driver memory is set to 25GB.
>
> It processes ~40 TB of data using aggregateByKey in which we specify numPartitions =
300,000.
> Map side tasks succeed, but reduce side tasks all fail.
>
> We notice the following driver error:
>
> 18/09/07 13:35:03 WARN Utils: Suppressing exception in finally: null
>
>  java.lang.OutOfMemoryError
>
> at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
> at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
> at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
> at java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:253)
> at java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:211)
> at java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:145)
> at java.io.ObjectOutputStream$BlockDataOutputStream.writeBlockHeader(ObjectOutputStream.java:1894)
> at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1875)
> at java.io.ObjectOutputStream$BlockDataOutputStream.flush(ObjectOutputStream.java:1822)
> at java.io.ObjectOutputStream.flush(ObjectOutputStream.java:719)
> at java.io.ObjectOutputStream.close(ObjectOutputStream.java:740)
> at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$2.apply$mcV$sp(MapOutputTracker.scala:790)
> at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1389)
> at org.apache.spark.MapOutputTracker$.serializeMapStatuses(MapOutputTracker.scala:789)
> at org.apache.spark.ShuffleStatus.serializedMapStatus(MapOutputTracker.scala:174)
> at org.apache.spark.MapOutputTrackerMaster$MessageLoop.run(MapOutputTracker.scala:397)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
> Exception in thread "map-output-dispatcher-0" java.lang.OutOfMemoryError
> at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
> at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
> at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
> at java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:253)
> at java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:211)
> at java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:145)
> at java.io.ObjectOutputStream$BlockDataOutputStream.writeBlockHeader(ObjectOutputStream.java:1894)
> at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1875)
> at java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1786)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1189)
> at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174)
> at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348)
> at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply$mcV$sp(MapOutputTracker.scala:787)
> at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply(MapOutputTracker.scala:786)
> at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply(MapOutputTracker.scala:786)
> at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1380)
> at org.apache.spark.MapOutputTracker$.serializeMapStatuses(MapOutputTracker.scala:789)
> at org.apache.spark.ShuffleStatus.serializedMapStatus(MapOutputTracker.scala:174)
> at org.apache.spark.MapOutputTrackerMaster$MessageLoop.run(MapOutputTracker.scala:397)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
> Suppressed: java.lang.OutOfMemoryError
> at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
> at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
> at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
> at java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:253)
> at java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:211)
> at java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:145)
> at java.io.ObjectOutputStream$BlockDataOutputStream.writeBlockHeader(ObjectOutputStream.java:1894)
> at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1875)
> at java.io.ObjectOutputStream$BlockDataOutputStream.flush(ObjectOutputStream.java:1822)
> at java.io.ObjectOutputStream.flush(ObjectOutputStream.java:719)
> at java.io.ObjectOutputStream.close(ObjectOutputStream.java:740)
> at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$2.apply$mcV$sp(MapOutputTracker.scala:790)
> at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1389)
> ... 6 more
>
> We found this reference (https://issues.apache.org/jira/browse/SPARK-1239) to a similar
issue that was closed in 2016.
>
> Please advise,
>
> Harel.
>
>


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