SQL query in Spark/scala Size exceeds Integer.MAX_VALUE

Question

I am trying to create a simple sql query on S3 events using Spark. I am loading ~30GB of JSON files as following:

val d2 = spark.read.json("s3n://myData/2017/02/01/1234");
d2.persist(org.apache.spark.storage.StorageLevel.MEMORY_AND_DISK);
d2.registerTempTable("d2");

Then I am trying to write to file the result of my query:

val users_count = sql("select count(distinct data.user_id) from d2");
users_count.write.format("com.databricks.spark.csv").option("header", "true").save("s3n://myfolder/UsersCount.csv");

But Spark is throwing the following exception:

java.lang.IllegalArgumentException: Size exceeds Integer.MAX_VALUE
at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:869)
at org.apache.spark.storage.DiskStore$$anonfun$getBytes$2.apply(DiskStore.scala:103)
at org.apache.spark.storage.DiskStore$$anonfun$getBytes$2.apply(DiskStore.scala:91)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1287)
at org.apache.spark.storage.DiskStore.getBytes(DiskStore.scala:105)
at org.apache.spark.storage.BlockManager.getLocalValues(BlockManager.scala:439)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:672)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:330)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:281)
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.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.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.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
at org.apache.spark.scheduler.Task.run(Task.scala:85)
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)

Note that the same query works for smaller amounts of data. What's the problem here?

Answer 1

No Spark shuffle block can be larger than 2GB (Integer.MAX_VALUE bytes) so you need more / smaller partitions.

You should adjust spark.default.parallelism and spark.sql.shuffle.partitions (default 200) such that the number of partitions can accommodate your data without reaching the 2GB limit (you could try aiming for 256MB / partition so for 200GB you get 800 partitions). Thousands of partitions is very common so don't be afraid to repartition to 1000 as suggested.

FYI, you may check the number of partitions for an RDD with something like rdd.getNumPartitions (ie d2.rdd.getNumPartitions)

There's a story to track the effort of addressing the various 2GB limits (been open for a while now): https://issues.apache.org/jira/browse/SPARK-6235

See http://www.slideshare.net/cloudera/top-5-mistakes-to-avoid-when-writing-apache-spark-applications/25 for more info on this error.

Answer 2

When I use the Spark core processing 200G of data, set up --conf spark.default.parallelism = 2000 and .repartition(100) , but the error will appear, finally, I use the following Settings to solve:

val conf = new SparkConf()
         .setAppName(appName)
         .set("spark.rdd.compress", "true")

Description of spark.rdd.compress

I hope it helps you