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 < > vadim@ > > 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 < > harelglik@ > > >> 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: 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