Hi,
I am having a hard time running outer join operation on two parquet
datasets. The dataset size is large ~500GB with a lot of culumns in tune of
1000.
As per YARN administer imposed limits in the queue, I can have a total of 20
vcores and 8GB memory per executor.
I specified meory overhead and increased number of shuffle partitions to no
avail. This is how I submitted the job with pyspark,
spark-submit --master yarn-cluster --executor-memory 5500m --num-executors
19 --executor-cores 1 --conf spark.yarn.executor.memoryOverhead=2000 --conf
spark.sql.shuffle.partitions=2048 --driver-memory 7g --queue
<queue_name>./<python_script>
The relevant code is,
cm_go.registerTempTable("x")
ko.registerTempTable("y")
joined_df = sqlCtx.sql("select * from x FULL OUTER JOIN y ON field1=field2")
joined_df.write.save("/user/data/output")
I am getting errors like these:
ExecutorLostFailure (executor 5 exited caused by one of the running tasks)
Reason: Container marked as failed:
container_e36_1487531133522_0058_01_000006 on host: dn2.bigdatalab.org. Exit
status: 52. Diagnostics: Exception from container-launch.
Container id: container_e36_1487531133522_0058_01_000006
Exit code: 52
Stack trace: ExitCodeException exitCode=52:
at org.apache.hadoop.util.Shell.runCommand(Shell.java:933)
at org.apache.hadoop.util.Shell.run(Shell.java:844)
at
org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:1123)
at
org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:225)
at
org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:317)
at
org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:83)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Container exited with a non-zero exit code 52
----------------------------------------------------------------------------------------------------------
FetchFailed(null, shuffleId=0, mapId=-1, reduceId=508, message=
org.apache.spark.shuffle.MetadataFetchFailedException: Missing an output
location for shuffle 0
at
org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:695)
at
org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:691)
at
scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
at
scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
at
scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732)
at
org.apache.spark.MapOutputTracker$.org$apache$spark$MapOutputTracker$$convertMapStatuses(MapOutputTracker.scala:691)
at
org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:145)
at
org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:49)
at
org.apache.spark.sql.execution.ShuffledRowRDD.compute(ShuffledRowRDD.scala:169)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at
org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
)
I would appreciate if someone can help me out on this.
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