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From abeboparebop <abebopare...@gmail.com>
Subject Re: Driver OutOfMemoryError in MapOutputTracker$.serializeMapStatuses for 40 TB shuffle.
Date Thu, 07 Nov 2019 18:37:45 GMT
I ran into the same issue processing 20TB of data, with 200k tasks on both
the map and reduce sides. Reducing to 100k tasks each resolved the issue.
But this could/would be a major problem in cases where the data is bigger or
the computation is heavier, since reducing the number of partitions may not
be an option.


harelglik wrote
> I understand the error is because the number of partitions is very high,
> yet when processing 40 TB (and this number is expected to grow) this
> number
> seems reasonable:
> 40TB / 300,000 will result in partitions size of ~ 130MB (data should be
> evenly distributed).
> 
> On Fri, Sep 7, 2018 at 6:28 PM Vadim Semenov &lt;

> vadim@

> &gt; wrote:
> 
>> 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 &lt;

> harelglik@

> &gt;
>> 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.
>> >
>> >
>>
>>
>> --
>> Sent from my iPhone
>>





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