apache spark - FetchFailedException or MetadataFetchFailedException when processing big data set

Question

When I run the parsing code with 1 GB dataset it completes without any error. But, when I attempt 25 gb of data at a time I get below errors. I'm trying to understand how can I avoid below failures. Happy to hear any suggestions or ideas.

Differnt errors,

org.apache.spark.shuffle.MetadataFetchFailedException: Missing an output location for shuffle 0

org.apache.spark.shuffle.FetchFailedException: Failed to connect to ip-xxxxxxxx

org.apache.spark.shuffle.FetchFailedException: Error in opening FileSegmentManagedBuffer{file=/mnt/yarn/nm/usercache/xxxx/appcache/application_1450751731124_8446/blockmgr-8a7b17b8-f4c3-45e7-aea8-8b0a7481be55/08/shuffle_0_224_0.data, offset=12329181, length=2104094}

Cluster Details:

Yarn: 8 Nodes
Total cores: 64
Memory: 500 GB
Spark Version: 1.5

Spark submit statement:

spark-submit --master yarn-cluster 
                        --conf spark.dynamicAllocation.enabled=true 
                        --conf spark.shuffle.service.enabled=true 
                        --executor-memory 4g 
                        --driver-memory 16g 
                        --num-executors 50 
                        --deploy-mode cluster 
                        --executor-cores 1 
                        --class my.parser 
                        myparser.jar 
                        -input xxx 
                        -output xxxx 

One of stack trace:

at org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:460)
at org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:456)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
at org.apache.spark.MapOutputTracker$.org$apache$spark$MapOutputTracker$$convertMapStatuses(MapOutputTracker.scala:456)
at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:183)
at org.apache.spark.shuffle.hash.HashShuffleReader.read(HashShuffleReader.scala:47)
at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:90)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

Answer 1

This error is almost guaranteed to be caused by memory issues on your executors. I can think of a couple of ways to address these types of problems.

1) You could try to run with more partitions (do a repartition on your dataframe). Memory issues typically arise when one or more partitions contain more data than will fit in memory.

2) I'm noticing that you have not explicitly set spark.yarn.executor.memoryOverhead, so it will default to max(386, 0.10* executorMemory) which in your case will be 400MB. That sounds low to me. I would try to increase it to say 1GB (note that if you increase memoryOverhead to 1GB, you need to lower --executor-memory to 3GB)

3) Look in the log files on the failing nodes. You want to look for the text "Killing container". If you see the text "running beyond physical memory limits", increasing memoryOverhead will - in my experience - solve the problem.