Spark map inside flatmap to replicate cartesian join - scala

I'm trying to fuzzy join two datasets, one of the quotes and one of the sales. For arguments sake, the joining attributes are first name, surname, dob and email.
I have 26m+ quotes and 1m+ sales. Customers may not have used the accurate information for one or more of the attributes, so I'm giving them a score for each match (1,1,1,1) where all match (0,0,0,0) where none match.
So I end up with something similar to
q1, s1, (0,0,1,0)
q1, s2, (0,1,0,1)
q1, s3, (1,1,1,1)
q2, s1, (1,0,0,1)
...
q26000000 s1 (0,1,0,0)
So I think this is equivalent to a cartesian product that I'm managing my making a large number of partitions for the quotes
val quotesRaw = sc.textfile(....)
val quotes = quotesRaw.repartition(quotesRaw.count().toInt() / 100000)
val sales = sc.textfile(...)
val sb = sc.broadcast(sales.collect())
quotes.mapPartitions(p=> (
p.flatMap(q => (
sb.value.map(s =>
q._1, s._1, ( if q._2 == s._2 1 else 0, etc)
)
)
This all works if I keep the numbers low, like 26m quotes but only 1000 sales but if I run it will all the sales it just stops responding when running
I'm running it with the following config.
spark-submit --conf spark.akka.frameSize=1024 \
--conf spark.executor.memory=3g --num-executors=30 \
--driver-memory 6g --class SalesMatch --deploy-mode client \
--master yarn SalesMatching-0.0.1-SNAPSHOT.jar \
hdfs://cluster:8020/data_import/Sales/SourceSales/2014/09/01/SourceSales_20140901.txt \
hdfs://cluster:8020/data_import/CDS/Enquiry/2014/01/01/EnquiryBackFill_20140101.txt \
hdfs://cluster:8020/tmp/_salesdata_matches_new
Is there anything that jumps out as obviously incorrect here?

Assuming 100k quotes per partition and 11M sales of total size 40MB your code generates roughly 4TB data per partition so it is rather unlikely your workers can handle this and it definitely cannot be done in memory.
I assume you're interested only in close matches so it makes sense to filter early. Simplifying your code a little (as far as I can tell there is no reason to use mapPartitions) :
// Check if match is close enough, where T is type of (q._1, s._1, (...))
def isCloseMatch(match: T): Boolean = ???
quotes.flatMap(q => sb.value
.map(s => (q._1, s._1, (....))) // Map as before
.filter(isCloseMatch) // yield only close matches
)
General remarks:
Creating broadcast from a RDD is an expensive process. First you have to transfer all data to the driver and then distribute among workers. It means repeated serialization/deserialization, network traffic and cost of storing data
For relatively simple operations like this it could be a good idea to use high level Spark SQL API:
import org.apache.spark.sql.DataFrame
val salesDF: DataFrame = ???
val salesDF: DataFrame = ???
val featureCols: Seq[String] = ???
val threshold: Int = ???
val inds = featureCols // Boolean columns
.map(col => (quotesDF(col) === salesDF(col)).alias(s"${col}_ind"))
val isSimilar = inds // sum(q == s) > threshold
.map(c => c.cast("integer").alias(c.toString))
.reduce(_ + _)
.geq(threshold)
val combined = quotesDF
.join(salesDF, isSimilar, "left")

Related

How to optimize below spark code (scala)?

I have some huge files (of 19GB, 40GB etc.). I need to execute following algorithm on these files:
Read the file
Sort it on the basis of 1 column
Take 1st 70% of the data:
a) Take all the distinct records of the subset of the columns
b) write it to train file
Take the last 30% of the data:
a) Take all the distinct records of the subset of the columns
b) write it to test file
I tried running following code in spark (using Scala).
import scala.collection.mutable.ListBuffer
import java.io.FileWriter
import org.apache.spark.sql.functions.year
val offers = sqlContext.read
.format("com.databricks.spark.csv")
.option("header", "true") // Use first line of all files as header
.option("inferSchema", "true") // Automatically infer data types
.option("delimiter", ",")
.load("input.txt")
val csvOuterJoin = offers.orderBy("utcDate")
val trainDF = csvOuterJoin.limit((csvOuterJoin.count*.7).toInt)
val maxTimeTrain = trainDF.agg(max("utcDate"))
val maxtimeStamp = maxTimeTrain.collect()(0).getTimestamp(0)
val testDF = csvOuterJoin.filter(csvOuterJoin("utcDate") > maxtimeStamp)
val inputTrain = trainDF.select("offerIdClicks","userIdClicks","userIdOffers","offerIdOffers").distinct
val inputTest = testDF.select("offerIdClicks","userIdClicks","userIdOffers","offerIdOffers").distinct
inputTrain.rdd.coalesce(1,false).saveAsTextFile("train.csv")
inputTest.rdd.coalesce(1,false).saveAsTextFile("test.csv")
This is how I initiate spark-shell:
./bin/spark-shell --packages com.databricks:spark-csv_2.11:1.4.0 --total-executor-cores 70 --executor-memory 10G --driver-memory 20G
I execute this code on a distributed cluster with 1 master and many slaves each having sufficient amount of RAM. As of now, this code ends up taking a lot of memory and I get java heap space issues.
Is there a way to optimize the above code (preferably in spark)? I appreciate any kind of minimal help in optimizing the above code.
The problem is you don't distribute at all. And the source is here:
val csvOuterJoin = offers.orderBy("utcDate")
val trainDF = csvOuterJoin.limit((csvOuterJoin.count*.7).toInt)
limit operation is not designed for large scale operations and it moves all records to a single partition:
val df = spark.range(0, 10000, 1, 1000)
df.rdd.partitions.size
Int = 1000
// Take all records by limit
df.orderBy($"id").limit(10000).rdd.partitions.size
Int = 1
You can use RDD API:
val ordered = df.orderBy($"utcDate")
val cnt = df.count * 0.7
val train = spark.createDataFrame(ordered.rdd.zipWithIndex.filter {
case (_, i) => i <= cnt
}.map(_._1), ordered.schema)
val test = spark.createDataFrame(ordered.rdd.zipWithIndex.filter {
case (_, i) => i > cnt
}.map(_._1), ordered.schema)
coalesce(1,false) means merging all data into one partition, aka keeping 40GB data in memory of one node.
Never try to get all data in one file by coalesce(1,false).
Instead, you should just call saveAsTextFile(so the output looks like part-00001, part00002, etc.) and then merge these partition files outside.
The merge operation depends on your file system. In case of HDFS, you can use http://hadoop.apache.org/docs/r2.7.3/hadoop-project-dist/hadoop-common/FileSystemShell.html#getmerge

Get all possible combinations of 3 values from n possible elements

I'm trying to get the list of all the possible combinations of 3 elements from a list of 30 items. I tried to use the following code, but it fails throwing an OutOfMemoryError. Is there any alternative approach which is more efficient than this?
val items = sqlContext.table(SOURCE_DB + "." + SOURCE_TABLE).
select("item_id").distinct.cache
val items.take(1) // Compute cache before join
val itemCombinations = items.select($"item_id".alias("id_A")).
join(
items.select($"item_id".alias("id_B")), $"id_A".lt($"id_B")).
join(
items.select($"item_id".alias("id_C")), $"id_B".lt($"id_C"))
The approach seems OK but might generate quite some overhead at the query execution level. Give that n is a fairly small number, we could do it using the Scala implementation directly:
val localItems = items.collect
val combinations = localItems.combinations(3)
The result is an iterator that can be consumed one element at the time, without significant memory overhead.
Spark Version (edit)
Given the desire to make a Spark version of this, it could be possible to avoid the query planner (assuming that the issue is there), by dropping to RDD level. This is basically the same expression as the join in the question:
val items = sqlContext.table(SOURCE_DB + "." + SOURCE_TABLE).select("item_id").rdd
val combinations = items.cartesian(items).filter{case(x,y) => x<y}.cartesian(items).filter{case ((x,y),z) => y<z}
Running an equivalent code in my local machine:
val data = List.fill(1000)(scala.util.Random.nextInt(999))
val rdd = sparkContext.parallelize(data)
val combinations = rdd.cartesian(rdd).filter{case(x,y) => x<y}.cartesian(rdd).filter{case ((x,y),z) => y<z}
combinations.count
// res5: Long = 165623528

Spark program performance - GC & Task Deserialization & Concurrent execution

I have a cluster of 4 machines, 1 master and three workers, each with 128G memory and 64 cores. I'm using Spark 1.5.0 in stand alone mode. My program reads data from Oracle tables using JDBC, then does ETL, manipulating data, and does machine learning tasks like k-means.
I have a DataFrame (myDF.cache()) which is join results with two other DataFrames, and cached. The DataFrame contains 27 million rows and the size of data is around 1.5G. I need to filter the data and calculate 24 histogram as follows:
val h1 = myDF.filter("pmod(idx, 24) = 0").select("col1").histogram(arrBucket)
val h2 = myDF.filter("pmod(idx, 24) = 1").select("col1").histogram(arrBucket)
// ......
val h24 = myDF.filter("pmod(idx, 24) = 23").select("col1").histogram(arrBucket)
Problems:
Since my DataFrame is cached, I expect the filter, select, and histogram is very fast. However, the actual time is about 7 seconds for each calculation, which is not acceptable. From UI, it show the GC time takes 5 seconds and Task Deserialization Time 4 seconds. I've tried different JVM parameters but cannot improve further. Right now I'm using
-Xms25G -Xmx25G -XX:MaxPermSize=512m -XX:+UseG1GC -XX:MaxGCPauseMillis=200 \
-XX:ParallelGCThreads=32 \
-XX:ConcGCThreads=8 -XX:InitiatingHeapOccupancyPercent=70
What puzzles me is that the size of data is nothing compared with available memory. Why does GC kick in every time filter/select/histogram running? Is there any way to reduce the GC time and Task Deserialization Time?
I have to do parallel computing for h[1-24], instead of sequential. I tried Future, something like:
import scala.concurrent.{Await, Future, blocking}
import scala.concurrent.ExecutionContext.Implicits.global
val f1 = Future{myDF.filter("pmod(idx, 24) = 1").count}
val f2 = Future{myDF.filter("pmod(idx, 24) = 2").count}
val f3 = Future{myDF.filter("pmod(idx, 24) = 3").count}
val future = for {c1 <- f1; c2 <- f2; c3 <- f3} yield {
c1 + c2 + c3
}
val summ = Await.result(future, 180 second)
The problem is that here Future only means jobs are submitted to the scheduler near-simultaneously, not that they end up being scheduled and run simultaneously. Future used here doesn't improve performance at all.
How to make the 24 computation jobs run simultaneously?
A couple of things you can try:
Don't compute pmod(idx, 24) all over again. Instead you can simply compute it once:
import org.apache.spark.sql.functions.{pmod, lit}
val myDfWithBuckets = myDF.withColumn("bucket", pmod($"idx", lit(24)))
Use SQLContext.cacheTable instead of cache. It stores table using compressed columnar storage which can be used to access only required columns and as stated in the Spark SQL and DataFrame Guide "will automatically tune compression to minimize memory usage and GC pressure".
myDfWithBuckets.registerTempTable("myDfWithBuckets")
sqlContext.cacheTable("myDfWithBuckets")
If you can, cache only the columns you actually need instead of projecting each time.
It is not clear for me what is the source of a histogram method (do you convert to RDD[Double] and use DoubleRDDFunctions.histogram?) and what is the argument but if you want to compute all histograms at the same time you can try to groupBy bucket and apply histogram once for example using histogram_numeric UDF:
import org.apache.spark.sql.functions.callUDF
val n: Int = ???
myDfWithBuckets
.groupBy($"bucket")
.agg(callUDF("histogram_numeric", $"col1", lit(n)))
If you use predefined ranges you can obtain a similar effect using custom UDF.
Notes
how to extract values computed by histogram_numeric? First lets create a small helper
import org.apache.spark.sql.Row
def extractBuckets(xs: Seq[Row]): Seq[(Double, Double)] =
xs.map(x => (x.getDouble(0), x.getDouble(1)))
now we can map using pattern matching as follows:
import org.apache.spark.rdd.RDD
val histogramsRDD: RDD[(Int, Seq[(Double, Double)])] = histograms.map{
case Row(k: Int, hs: Seq[Row #unchecked]) => (k, extractBuckets(hs)) }

Joining process with broadcast variable ends up endless spilling

I am joining two RDDs from text files in standalone mode. One has 400 million (9 GB) rows, and the other has 4 million (110 KB).
3-grams doc1 3-grams doc2
ion - 100772C111 ion - 200772C222
on - 100772C111 gon - 200772C222
n - 100772C111 n - 200772C222
... - .... ... - ....
ion - 3332145654 on - 58898874
mju - 3332145654 mju - 58898874
... - .... ... - ....
In each file, doc numbers (doc1 or doc2) appear one under the other. And as a result of join I would like to get a number of common 3-grams between the docs.e.g.
(100772C111-200772C222,2) --> There two common 3-grams which are 'ion' and ' n'
The server on which I run my code has 128 GB RAM and 24 cores. I set my IntelliJ configurations - VM options part with -Xmx64G
Here is my code for this:
val conf = new SparkConf().setAppName("abdulhay").setMaster("local[4]").set("spark.shuffle.spill", "true")
.set("spark.shuffle.memoryFraction", "0.6").set("spark.storage.memoryFraction", "0.4")
.set("spark.executor.memory","40g")
.set("spark.driver.memory","40g")
val sc = new SparkContext(conf)
val emp = sc.textFile("\\doc1.txt").map(line => (line.split("\t")(3),line.split("\t")(1))).distinct()
val emp_new = sc.textFile("\\doc2.txt").map(line => (line.split("\t")(3),line.split("\t")(1))).distinct()
val emp_newBC = sc.broadcast(emp_new.groupByKey.collectAsMap)
val joined = emp.mapPartitions(iter => for {
(k, v1) <- iter
v2 <- emp_newBC.value.getOrElse(k, Iterable())
} yield (s"$v1-$v2", 1))
val olsun = joined.reduceByKey((a,b) => a+b)
olsun.map(x => x._1 + "\t" + x._2).saveAsTextFile("...\\out.txt")
So as seen, during join process using broadcast variable my key values change. So it seems I need to repartition the joined values? And it is highly expensive. As a result, i ended up too much spilling issue, and it never ended. I think 128 GB memory must be sufficient. As far as I understood, when broadcast variable is used shuffling is being decreased significantly? So what is wrong with my application?
Thanks in advance.
EDIT:
I have also tried spark's join function as below:
var joinRDD = emp.join(emp_new);
val kkk = joinRDD.map(line => (line._2,1)).reduceByKey((a, b) => a + b)
again ending up too much spilling.
EDIT2:
val conf = new SparkConf().setAppName("abdulhay").setMaster("local[12]").set("spark.shuffle.spill", "true")
.set("spark.shuffle.memoryFraction", "0.4").set("spark.storage.memoryFraction", "0.6")
.set("spark.executor.memory","50g")
.set("spark.driver.memory","50g")
val sc = new SparkContext(conf)
val emp = sc.textFile("S:\\Staff_files\\Mehmet\\Projects\\SPARK - scala\\wos14.txt").map{line => val s = line.split("\t"); (s(5),s(0))}//.distinct()
val emp_new = sc.textFile("S:\\Staff_files\\Mehmet\\Projects\\SPARK - scala\\fwo_word.txt").map{line => val s = line.split("\t"); (s(3),s(1))}//.distinct()
val cog = emp_new.cogroup(emp)
val skk = cog.flatMap {
case (key: String, (l1: Iterable[String], l2: Iterable[String])) =>
(l1.toSeq ++ l2.toSeq).combinations(2).map { case Seq(x, y) => if (x < y) ((x, y),1) else ((y, x),1) }.toList
}
val com = skk.countByKey()
I would not use broadcast variables. When you say:
val emp_newBC = sc.broadcast(emp_new.groupByKey.collectAsMap)
Spark is first moving the ENTIRE dataset into the master node, a huge bottleneck and prone to produce memory errors on the master node. Then this piece of memory is shuffled back to ALL nodes (lots of network overhead), bound to produce memory issues there too.
Instead, join the RDDs themselves using join (see description here)
Figure out also if you have too few keys. For joining Spark basically needs to load the entire key into memory, and if your keys are too few that might still be too big a partition for any given executor.
A separate note: reduceByKey will repartition anyway.
EDIT: ---------------------
Ok, given the clarifications, and assuming that the number of 3-grams per doc# is not too big, this is what I would do:
Key both files by 3-gram to get (3-gram, doc#) tuples.
cogroup both RDDs, that gets you the 3gram key and 2 lists of doc#
Process those in a single scala function, output a set of all unique permutations of (doc-pairs).
then do coutByKey or countByKeyAprox to get a count of the number of distinct 3-grams for each doc pair.
Note: you can skip the .distinct() calls with this one. Also, you should not split every line twice. Change line => (line.split("\t")(3),line.split("\t")(1))) for line => { val s = line.split("\t"); (s(3),s(1)))
EDIT 2:
You also seem to be tuning your memory badly. For instance, using .set("spark.shuffle.memoryFraction", "0.4").set("spark.storage.memoryFraction", "0.6") leaves basically no memory for task execution (since they add up to 1.0). I should have seen that sooner but was focused on the problem itself.
Check the tunning guides here and here.
Also, if you are running it on a single machine, you might try with a single, huge executor (or even ditch Spark completely), as you don't need overhead of a distributed processing platform (and distributed hardware failure tolerance, etc).

Scala distributed execution of function objects

Given the following function objects,
val f : Int => Double = (i:Int) => i + 0.1
val g1 : Double => Double = (x:Double) => x*10
val g2 : Double => Double = (x:Double) => x/10
val h : (Double,Double) => Double = (x:Double,y:Double) => x+y
and for instance 3 remote servers or nodes (IP xxx.xxx.xxx.1, IP 2 and IP 3), how to distribute the execution of this program,
val fx = f(1)
val g1x = g1( fx )
val g2x = g2( fx )
val res = h ( g1x, g2x )
so that
fx is computed in IP 1,
g1x is computed in IP 2,
g2x is computed in IP 3,
res is computed in IP 1
May Scala Akka or Apache Spark provide a simple approach to this ?
Update
RPC (Remote Procedure Call) Finagle as suggested by #pkinsky may be a feasible choice.
Consider load-balancing policies as a mechanism for selecting a node for execution, at least any free available node policy.
I can speak for Apache Spark. It can do what you are looking for with the code below. But it's not designed for this kind of parallel computation. It is designed for parallel computation where you also have a large amount of parallel data distributed on many machines. So the solution looks a bit silly, as we distribute a single integer across a single machine for example (for f(1)).
Also, Spark is designed to run the same computation on all the data. So running g1() and g2() in parallel goes a bit against the design. (It's possible, but not elegant, as you see.)
// Distribute the input (1) across 1 machine.
val rdd1 = sc.parallelize(Seq(1), numSlices = 1)
// Run f() on the input, collect the results and take the first (and only) result.
val fx = rdd1.map(f(_)).collect.head
// The next stage's input will be (1, fx), (2, fx) distributed across 2 machines.
val rdd2 = sc.parallelize(Seq((1, fx), (2, fx)), numSlices = 2)
// Run g1() on one machine, g2() on the other.
val gxs = rdd2.map {
case (1, x) => g1(x)
case (2, x) => g2(x)
}.collect
val g1x = gxs(0)
val g2x = gxs(1)
// Same deal for h() as for f(). The input is (g1x, g2x), distributed to 1 machine.
val rdd3 = sc.parallelize(Seq((g1x, g2x)), numSlices = 1)
val res = rdd3.map { case (g1x, g2x) => h(g1x, g2x) }.collect.head
You can see that Spark code is based around the concept of RDDs. An RDD is like an array, except it's partitioned across multiple machines. sc.parallelize() creates such a parallel collection from a local collection. For example rdd2 in the above code will be created from the local collection Seq((1, fx), (2, fx)) and split across two machines. One machine will have Seq((1, fx)), the other will have Seq((2, fx)).
Next we do a transformation on the RDD. map is a common transformation that creates a new RDD of the same length by applying a function to each element. (Same as Scala's map.) The map we run on rdd2 will replace (1, x) with g1(x) and (2, x) with g2(x). So on one machine it will cause g1() to run, while on the other g2() will run.
Transformations run lazily, only when you want to access the results. The methods that access the results are called actions. The most straightforward example is collect, which downloads the contents of the entire RDD from the cluster to the local machine. (It is exactly the opposite of sc.parallelize().)
You can try and see all this if you download Spark, start bin/spark-shell, and copy your function definitions and the above code into the shell.