I have an RDD of (String,String,Int).
I want to reduce it based on the first two strings
And Then based on the first String I want to group the (String,Int) and sort them
After sorting I need to group them into small groups each containing n elements.
I have done the code below. The problem is the number of elements in the step 2 is very large for a single key
and the reduceByKey(x++y) takes a lot of time.
//Input
val data = Array(
("c1","a1",1), ("c1","b1",1), ("c2","a1",1),("c1","a2",1), ("c1","b2",1),
("c2","a2",1), ("c1","a1",1), ("c1","b1",1), ("c2","a1",1))
val rdd = sc.parallelize(data)
val r1 = rdd.map(x => ((x._1, x._2), (x._3)))
val r2 = r1.reduceByKey((x, y) => x + y ).map(x => ((x._1._1), (x._1._2, x._2)))
// This is taking long time.
val r3 = r2.mapValues(x => ArrayBuffer(x)).reduceByKey((x, y) => x ++ y)
// from the list I will be doing grouping.
val r4 = r3.map(x => (x._1 , x._2.toList.sorted.grouped(2).toList))
Problem is the "c1" has lot of unique entries like b1 ,b2....million and reduceByKey is killing time because all the values are going to single node.
Is there a way to achieve this more efficiently?
// output
Array((c1,List(List((a1,2), (a2,1)), List((b1,2), (b2,1)))), (c2,List(List((a1,2), (a2,1)))))
There at least few problems with a way you group your data. The first problem is introduced by
mapValues(x => ArrayBuffer(x))
It creates a large amount of mutable objects which provide no additional value since you cannot leverage their mutability in the subsequent reduceByKey
reduceByKey((x, y) => x ++ y)
where each ++ creates a new collection and neither argument can be safely mutated. Since reduceByKey applies map side aggregation situation is even worse and pretty much creates GC hell.
Is there a way to achieve this more efficiently?
Unless you have some deeper knowledge about data distribution which can be used to define smarter partitioner the simplest improvement is to replace mapValues + reduceByKey with simple groupByKey:
val r3 = r2.groupByKey
It should be also possible to use a custom partitioner for both reduceByKey calls and mapPartitions with preservesPartitioning instead of map.
class FirsElementPartitioner(partitions: Int)
extends org.apache.spark.Partitioner {
def numPartitions = partitions
def getPartition(key: Any): Int = {
key.asInstanceOf[(Any, Any)]._1.## % numPartitions
}
}
val r2 = r1
.reduceByKey(new FirsElementPartitioner(8), (x, y) => x + y)
.mapPartitions(iter => iter.map(x => ((x._1._1), (x._1._2, x._2))), true)
// No shuffle required here.
val r3 = r2.groupByKey
It requires only a single shuffle and groupByKey is simply a local operations:
r3.toDebugString
// (8) MapPartitionsRDD[41] at groupByKey at <console>:37 []
// | MapPartitionsRDD[40] at mapPartitions at <console>:35 []
// | ShuffledRDD[39] at reduceByKey at <console>:34 []
// +-(8) MapPartitionsRDD[1] at map at <console>:28 []
// | ParallelCollectionRDD[0] at parallelize at <console>:26 []
Related
I would like to get the mode (the most common number) from an rdd using Spark + Scala.
I can get it doing the following but I think it could be a better way to calculate this. The most important thing is if more than one value has the same number of repetition, I need to return both of them.
Let's see my example code:
val l = List(3,4,4,3,3,7,7,7,9)
val rdd = spark.sparkContext.parallelize(l)
val grouped = rdd.map (e => (e, 1)).groupBy(_._1).map(e=> (e._1, e._2.size))
val maxRep = grouped.collect().maxBy(_._2)._2
val mode = grouped.filter(e => e._2 == maxRep).map(e => e._1).collect
And the result is right:
Array[Int] = Array(3, 7)
but is there a better way to do this? I mean considering the performance because the original RDD would be much bigger than this.
This should work and be a little bit more efficient.
(only if you are sure the total number of elements is small)
val counted = rdd.countByValue()
val max = counted.valuesIterator.max
val maxElements = count.collect { case (k, v) if (v == max) => k }
If there could be many elements, consider this alternative which is memory safe.
val counted = rdd.map(x => (x, 1L)).reduceByKey(_ + _).cache()
val max = counted.values.max
val maxElements = counted.map { case (k, v) => (v, k) }.lookup(max)
How about get the max key-value pair from a double groupBy? This works even better for bigger data size.
rdd.groupBy(identity).mapValues(_.size).groupBy(_._2).max
// res1: (Int, Iterable[(Int, Int)]) = (3,CompactBuffer((3,3), (7,3)))
To get the element
rdd.groupBy(identity).mapValues(_.size).groupBy(_._2).max._2.map(_._1)
// res4: Iterable[Int] = List(3, 7)
The first groupBy will get element into (element -> count) with type Map[Int, Long], the second groupBy will group (element -> count) by count, like (count -> Iterable((element, count)), then simply max to get the key-value pair with the maximum key value, which is the count.
I am using spark to read a csv file like this :
x, y, z
x, y
x
x, y, c, f
x, z
I want to make a map of items vs their count. This is the code I wrote :
private def genItemMap[Item: ClassTag](data: RDD[Array[Item]], partitioner: HashPartitioner): mutable.Map[Item, Long] = {
val immutableFreqItemsMap = data.flatMap(t => t)
.map(v => (v, 1L))
.reduceByKey(partitioner, _ + _)
.collectAsMap()
val freqItemsMap = mutable.Map(immutableFreqItemsMap.toSeq: _*)
freqItemsMap
}
When I run it, it is taking a lot of time and shuffle space. Is there a way to reduce the time?
I have a 2 node cluster with 2 cores each and 8 partitions. The number of lines in the csv file are 170000.
If you just want to do an unique item count thing, then I suppose you can take the following approach.
val data: RDD[Array[Item]] = ???
val itemFrequency = data
.flatMap(arr =>
arr.map(item => (item, 1))
)
.reduceByKey(_ + _)
Do not provide any partitioner while reducing, otherwise it will cause re-shuffling. Just keep it with the partitioning it already had.
Also... do not collect the distributed data into a local in-memory object like a Map.
I am using df.randomSplit() but it is not splitting into equal rows. Is there any other way I can achieve it?
In my case I needed balanced (equal sized) partitions in order to perform a specific cross validation experiment.
For that you usually:
Randomize the dataset
Apply modulus operation to assign each element to a fold (partition)
After this step you will have to extract each partition using filter, afaik there is still no transformation to separate a single RDD into many.
Here is some code in scala, it only uses standard spark operations so it should be easy to adapt to python:
val npartitions = 3
val foldedRDD =
// Map each instance with random number
.zipWithIndex
.map ( t => (t._1, t._2, new scala.util.Random(t._2*seed).nextInt()) )
// Random ordering
.sortBy( t => (t._1(m_classIndex), t._3) )
// Assign each instance to fold
.zipWithIndex
.map( t => (t._1, t._2 % npartitions) )
val balancedRDDList =
for (f <- 0 until npartitions)
yield foldedRDD.filter( _._2 == f )
I am joining a large number of rdd's and I was wondering whether there is a generic way of removing the parenthesis that are being created on each join.
Here is a small sample:
val rdd1 = sc.parallelize(Array((1,2),(2,4),(3,6)))
val rdd2 = sc.parallelize(Array((1,7),(2,8),(3,6)))
val rdd3 = sc.parallelize(Array((1,2),(2,4),(3,6)))
val result = rdd1.join(rdd2).join(rdd3)
res: result: org.apache.spark.rdd.RDD[(Int, ((Int, Int), Int))] = Array((1,((2,7),2)), (3,((4,8),4)), (3,((4,8),6)), (3,((4,6),4)), (3,((4,6),6)))
I know I can use map
result.map((x) => (x._1,(x._2._1._1,x._2._1._2,x._2._2))).collect
Array[(Int, (Int, Int, Int))] = Array((1,(2,7,2)), (2,(4,8,4)), (3,(6,6,6)))
but with a large number of rdd's each containing many elements it quite quickly becomes difficult to use this method
With a large number of rdd's each containing many elements this approach simply won't work because the largest built-in tuple is still Tuple22. If you join homogeneous RDD some type of sequence:
def joinAndMerge(rdd1: RDD[(Int, Seq[Int])], rdd2: RDD[(Int, Seq[Int])]) =
rdd1.join(rdd2).mapValues{ case (x, y) => x ++ y }
Seq(rdd1, rdd2, rdd3).map(_.mapValues(Seq(_))).reduce(joinAndMerge)
If you have only three RDDs it can be cleaner to use cogroup:
rdd1.cogroup(rdd2, rdd3)
.flatMapValues { case (xs, ys, zs) => for {
x <- xs; y <- ys; z <- zs
} yield (x, y, z) }
If values are heterogenous it makes more sense to use DataFrames:
def joinByKey(df1: DataFrame, df2: DataFrame) = df1.join(df2, Seq("k"))
Seq(rdd1, rdd2, rdd3).map(_.toDF("k", "v")).reduce(joinByKey)
In Apache Spark I have two RDD's. The first data : RDD[(K,V)] containing data in key-value form. The second pairs : RDD[(K,K)] contains a set of interesting key-pairs of this data.
How can I efficiently construct an RDD pairsWithData : RDD[((K,K)),(V,V))], such that it contains all the elements from pairs as the key-tuple and their corresponding values (from data) as the value-tuple?
Some properties of the data:
The keys in data are unique
All entries in pairs are unique
For all pairs (k1,k2) in pairs it is guaranteed that k1 <= k2
The size of 'pairs' is only a constant the size of data |pairs| = O(|data|)
Current data sizes (expected to grow): |data| ~ 10^8, |pairs| ~ 10^10
Current attempts
Here is some example code in Scala:
import org.apache.spark.rdd.RDD
import org.apache.spark.SparkContext._
// This kind of show the idea, but fails at runtime.
def massPairLookup1(keyPairs : RDD[(Int, Int)], data : RDD[(Int, String)]) = {
keyPairs map {case (k1,k2) =>
val v1 : String = data lookup k1 head;
val v2 : String = data lookup k2 head;
((k1, k2), (v1,v2))
}
}
// Works but is O(|data|^2)
def massPairLookup2(keyPairs : RDD[(Int, Int)], data : RDD[(Int, String)]) = {
// Construct all possible pairs of values
val cartesianData = data cartesian data map {case((k1,v1),(k2,v2)) => ((k1,k2),(v1,v2))}
// Select only the values who's keys are in keyPairs
keyPairs map {(_,0)} join cartesianData mapValues {_._2}
}
// Example function that find pairs of keys
// Runs in O(|data|) in real life, but cannot maintain the values
def relevantPairs(data : RDD[(Int, String)]) = {
val keys = data map (_._1)
keys cartesian keys filter {case (x,y) => x*y == 12 && x < y}
}
// Example run
val data = sc parallelize(1 to 12) map (x => (x, "Number " + x))
val pairs = relevantPairs(data)
val pairsWithData = massPairLookup2(pairs, data)
// Print:
// ((1,12),(Number1,Number12))
// ((2,6),(Number2,Number6))
// ((3,4),(Number3,Number4))
pairsWithData.foreach(println)
Attempt 1
First I tried just using the lookup function on data, but that throws an runtime error when executed. It seems like self is null in the PairRDDFunctions trait.
In addition I am not sure about the performance of lookup. The documentation says This operation is done efficiently if the RDD has a known partitioner by only searching the partition that the key maps to. This sounds like n lookups takes O(n*|partition|) time at best, which I suspect could be optimized.
Attempt 2
This attempt works, but I create |data|^2 pairs which will kill performance. I do not expect Spark to be able to optimize that away.
Your lookup 1 doesn't work because you cannot perform RDD transformations inside workers (inside another transformation).
In the lookup 2, I don't think it's necessary to perform full cartesian...
You can do it like this:
val firstjoin = pairs.map({case (k1,k2) => (k1, (k1,k2))})
.join(data)
.map({case (_, ((k1, k2), v1)) => ((k1, k2), v1)})
val result = firstjoin.map({case ((k1,k2),v1) => (k2, ((k1,k2),v1))})
.join(data)
.map({case(_, (((k1,k2), v1), v2))=>((k1, k2), (v1, v2))})
Or in a more dense form:
val firstjoin = pairs.map(x => (x._1, x)).join(data).map(_._2)
val result = firstjoin.map({case (x,y) => (x._2, (x,y))})
.join(data).map({case(x, (y, z))=>(y._1, (y._2, z))})
I don't think you can do it more efficiently, but I might be wrong...