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From Spico Florin <spicoflo...@gmail.com>
Subject Re: Driver OutOfMemoryError in MapOutputTracker$.serializeMapStatuses for 40 TB shuffle.
Date Fri, 08 Nov 2019 09:01:38 GMT
Hi!
What file system are you using: EMRFS or HDFS?
Also what memory are you using for the reducer ?

On Thu, Nov 7, 2019 at 8:37 PM abeboparebop <abeboparebop@gmail.com> wrote:

> 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
> >>
>
>
>
>
>
> --
> Sent from: http://apache-spark-user-list.1001560.n3.nabble.com/
>
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