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 <abebopare...@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 < > > > 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: http://apache-spark-user-list.1001560.n3.nabble.com/ > > --------------------------------------------------------------------- > To unsubscribe e-mail: user-unsubscr...@spark.apache.org > >
