How to use COGROUP for large datasets - scala

Question

I have two rdd's namely val tab_a: RDD[(String, String)] and val tab_b: RDD[(String, String)] I'm using cogroup for those datasets like:
val tab_c = tab_a.cogroup(tab_b).collect.toArray
val updated = tab_c.map { x =>
{
//somecode
}
}
I'm using tab_c cogrouped values for map function and it works fine for small datasets but in case of huge datasets it throws Out Of Memory exception.
I have tried converting the final value to RDD but no luck same error
val newcos = spark.sparkContext.parallelize(tab_c)
1.How to use Cogroup for large datasets ?
2.Can we persist the cogrouped value ?
Code
val source_primary_key = source.map(rec => (rec.split(",")(0), rec))
source_primary_key.persist(StorageLevel.DISK_ONLY)
val destination_primary_key = destination.map(rec => (rec.split(",")(0), rec))
destination_primary_key.persist(StorageLevel.DISK_ONLY)
val cos = source_primary_key.cogroup(destination_primary_key).repartition(10).collect()
var srcmis: Array[String] = new Array[String](0)
var destmis: Array[String] = new Array[String](0)
var extrainsrc: Array[String] = new Array[String](0)
var extraindest: Array[String] = new Array[String](0)
var srcs: String = Seq("")(0)
var destt: String = Seq("")(0)
val updated = cos.map { x =>
{
val key = x._1
val value = x._2
srcs = value._1.mkString(",")
destt = value._2.mkString(",")
if (srcs.equalsIgnoreCase(destt) == false && destt != "") {
srcmis :+= srcs
destmis :+= destt
}
if (srcs == "") {
extraindest :+= destt.mkString("")
}
if (destt == "") {
extrainsrc :+= srcs.mkString("")
}
}
}
Code Updated:
val tab_c = tab_a.cogroup(tab_b).filter(x => x._2._1 =!= x => x._2._2)
// tab_c = {1,Compactbuffer(1,john,US),Compactbuffer(1,john,UK)}
{2,Compactbuffer(2,john,US),Compactbuffer(2,johnson,UK)}..
ERROR:
ERROR LiveListenerBus: SparkListenerBus has already stopped! Dropping event SparkListenerTaskEnd(4,3,ResultTask,FetchFailed(null,0,-1,27,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:697)
at org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:693)
ERROR YarnScheduler: Lost executor 8 on datanode1: Container killed by YARN for exceeding memory limits. 1.0 GB of 1020 MB physical memory used. Consider boosting spark.yarn.executor.memoryOverhead.
Thank you

Answer 1

When you use collect() you are basically telling spark to move all the resulting data back to the master node, which can easily produce a bottleneck. You are no longer using Spark at that point, just a plain array in a single machine.
To trigger computation just use something that requires the data at every node, that's why executors live on top of a distributed file system. For instance saveAsTextFile().
Here are some basic examples.
Remember, the entire objective here (that is, if you have big data) is to move the code to your data and compute there, not to bring all the data to the computation.

Answer 2

TL;DR Don't collect.
To run this code safely, without additional assumptions (on average requirements for worker nodes might be significantly smaller), every node (driver and each executor) would require memory significantly exceeding total memory requirements for all data.
If you were to run it outside Spark you would need only one node. Therefore Spark provides no benefits here.
However if you skip collect.toArray and make some assumptions about data distribution you might run it just fine.