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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)

1 Answer

0 votes
by (31.4k points)
edited by

This error is almost guaranteed to be caused because of memory issues on your executors.

Here are some ways to address these types of problems:

1) 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 the capacity.

2) Here, 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, which is very low according 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)

Also, org.apache.spark.shuffle.FetchFailedException can occur due to timeout retrieving shuffle partitions. To fix this problem, you can set the following:

  • SET spark.reducer.maxReqsInFlight=1;  -- Only pull one file at a time to use full network bandwidth.

  • SET spark.shuffle.io.retryWait=60s;  -- Increase the time to wait while retrieving shuffle partitions before retrying. Longer times are necessary for larger files.

  • SET spark.shuffle.io.maxRetries=10;

If you want to know more about Spark, then do check out this awesome video tutorial:

 

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