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From Harel Gliksman <harelg...@gmail.com>
Subject Driver OutOfMemoryError in MapOutputTracker$.serializeMapStatuses for 40 TB shuffle.
Date Fri, 07 Sep 2018 14:34:49 GMT
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
<https://www.google.com/url?q=https://issues.apache.org/jira/browse/SPARK-1239&sa=D&source=hangouts&ust=1536416255076000&usg=AFQjCNF5KWUuXDr9ZWNn4Geos1sQlpKHwA>)
to a similar issue that was closed in 2016.

Please advise,

Harel.

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