Spark - convert string IDs to unique integer IDs - apache-spark

I have a dataset which looks like this, where each user and product ID is a string:
userA, productX
userA, productX
userB, productY
with ~2.8 million products and 300 million users; about 2.1 billion user-product associations.
My end goal is to run Spark collaborative filtering (ALS) on this dataset. Since it takes int keys for users and products, my first step is to assign a unique int to each user and product, and transform the dataset above so that users and products are represented by ints.
Here's what I've tried so far:
val rawInputData = sc.textFile(params.inputPath)
.filter { line => !(line contains "\\N") }
.map { line =>
val parts = line.split("\t")
(parts(0), parts(1)) // user, product
}
// find all unique users and assign them IDs
val idx1map = rawInputData.map(_._1).distinct().zipWithUniqueId().cache()
// find all unique products and assign IDs
val idx2map = rawInputData.map(_._2).distinct().zipWithUniqueId().cache()
idx1map.map{ case (id, idx) => id + "\t" + idx.toString
}.saveAsTextFile(params.idx1Out)
idx2map.map{ case (id, idx) => id + "\t" + idx.toString
}.saveAsTextFile(params.idx2Out)
// join with user ID map:
// convert from (userStr, productStr) to (productStr, userIntId)
val rev = rawInputData.cogroup(idx1map).flatMap{
case (id1, (id2s, idx1s)) =>
val idx1 = idx1s.head
id2s.map { (_, idx1)
}
}
// join with product ID map:
// convert from (productStr, userIntId) to (userIntId, productIntId)
val converted = rev.cogroup(idx2map).flatMap{
case (id2, (idx1s, idx2s)) =>
val idx2 = idx2s.head
idx1s.map{ (_, idx2)
}
}
// save output
val convertedInts = converted.map{
case (a,b) => a.toInt.toString + "\t" + b.toInt.toString
}
convertedInts.saveAsTextFile(params.outputPath)
When I try to run this on my cluster (40 executors with 5 GB RAM each), it's able to produce the idx1map and idx2map files fine, but it fails with out of memory errors and fetch failures at the first flatMap after cogroup. I haven't done much with Spark before so I'm wondering if there is a better way to accomplish this; I don't have a good idea of what steps in this job would be expensive. Certainly cogroup would require shuffling the whole data set across the network; but what does something like this mean?
FetchFailed(BlockManagerId(25, ip-***.ec2.internal, 48690), shuffleId=2, mapId=87, reduceId=25)
The reason I'm not just using a hashing function is that I'd eventually like to run this on a much larger dataset (on the order of 1 billion products, 1 billion users, 35 billion associations), and number of Int key collisions would become quite large. Is running ALS on a dataset of that scale even close to feasible?

I looks like you are essentially collecting all lists of users, just to split them up again. Try just using join instead of cogroup, which seems to me to do more like what you want. For example:
import org.apache.spark.SparkContext._
// Create some fake data
val data = sc.parallelize(Seq(("userA", "productA"),("userA", "productB"),("userB", "productB")))
val userId = sc.parallelize(Seq(("userA",1),("userB",2)))
val productId = sc.parallelize(Seq(("productA",1),("productB",2)))
// Replace userName with ID's
val userReplaced = data.join(userId).map{case (_,(prod,user)) => (prod,user)}
// Replace product names with ID's
val bothReplaced = userReplaced.join(productId).map{case (_,(user,prod)) => (user,prod)}
// Check results:
bothReplaced.collect()) // Array((1,1), (1,2), (2,2))
Please drop a comments on how well it performs.
(I have no idea what FetchFailed(...) means)

My platform version : CDH :5.7, Spark :1.6.0/StandAlone;
My Test Data Sizeļ¼š31815167 all data; 31562704 distinct user strings, 4140276 distinct product strings .
First idea:
My first idea is to use collectAsMap action and then use the map idea to change the user/product string to int . With driver memory up to 12G , i got OOM or GC overhead exception (the exception is limited by driver memory).
But this idea can only use on a small data size, with bigger data size , you need a bigger driver memory .
Second idea :
Second idea is to use join method, as Tobber proposaled. Here is some test result:
Job setup:
driver: 2G , 2 cpu;
executor : (8G , 4 cpu) * 7;
I follow the steps:
1) find unique user strings and zipWithIndexes;
2) join the original data;
3) save the encoded data;
The job take about 10 minutes to finish.

Related

how to efficiently parse dataframe object into a map of key-value pairs

i'm working with a dataframe with the columns basketID and itemID. is there a way to efficiently parse through the dataset and generate a map where the keys are basketID and the value is a set of all the itemID contained within each basket?
my current implementation uses a for loop over the data frame which isn't very scalable. is it possible to do this more efficiently? any help would be appreciated thanks!
screen shot of sample data
the goal is to obtain basket = Map("b1" -> Set("i1", "i2", "i3"), "b2" -> Set("i2", "i4"), "b3" -> Set("i3", "i5"), "b4" -> Set("i6")). heres the implementation I have using a for loop
// create empty container
val basket = scala.collection.mutable.Map[String, Set[String]]()
// loop over all numerical indexes for baskets (b<i>)
for (i <- 1 to 4) {
basket("b" + i.toString) = Set();
}
// loop over every row in df and store the items to the set
df.collect().foreach(row =>
basket(row(0).toString) += row(1).toString
)
You can simply do aggregateByKey operation then collectItAsMap will directly give you the desired result. It is much more efficient than simple groupBy.
import scala.collection.mutable
case class Items(basketID: String,itemID: String)
import spark.implicits._
val result = output.as[Items].rdd.map(x => (x.basketID,x.itemID))
.aggregateByKey[mutable.Buffer[String]](new mutable.ArrayBuffer[String]())
((l: mutable.Buffer[String], p: String) => l += p ,
(l1: mutable.Buffer[String], l2: mutable.Buffer[String]) => (l1 ++ l2).distinct)
.collectAsMap();
you can check other aggregation api's like reduceBy and groupBy over here.
please also check aggregateByKey vs groupByKey vs ReduceByKey differences.
This is efficient assuming your dataset is small enough to fit into the driver's memory. .collect will give you an array of rows on which you are iterating which is fine. If you want scalability then instead of Map[String, Set[String]] (this will reside in driver memory) you can use PairRDD[String, Set[String]] (this will be distributed).
//NOT TESTED
//Assuming df is dataframe with 2 columns, first is your basketId and second is itemId
df.rdd.map(row => (row.getAs[String](0), row.getAs[String](1)).groupByKey().mapValues(x => x.toSet)

How would you limit the number of records to process per grouped key in spark? (for skewed data)

I have two large datasets. There are multiple groupings of the same ids. Each group has a score. I'm trying to broadcast the score to each id in each group. But I have a nice constraint that I don't care about groups with more than 1000 ids.
Unfortunately, Spark keeps reading the full grouping. I can't seem to figure out a way to push down the limit so that Spark only reads up to 1000 records, and if there are any more gives up.
So far I've tried this:
def run: Unit = {
// ...
val scores: RDD[(GroupId, Score)] = readScores(...)
val data: RDD[(GroupId, Id)] = readData(...)
val idToScore: RDD[(Id, Score)] = scores.cogroup(data)
.flatMap(maxIdsPerGroupFilter(1000))
// ...
}
def maxIdsPerGroupFilter(maxIds: Int)(t: (GroupId, (Iterable[Score], Iterable[Id]))): Iterator[(Id, Score)] = {
t match {
case (groupId: GroupId, (scores: Iterable[Score], ids: Iterable[Id])) =>
if (!scores.iterator.hasNext) {
return Iterator.empty
}
val score: Score = scores.iterator.next()
val iter = ids.iterator
val uniqueIds: mutable.HashSet[Id] = new mutable.HashSet[Id]
while (iter.hasNext) {
uniqueIds.add(iter.next())
if (uniqueIds.size > maxIds) {
return Iterator.empty
}
}
uniqueIds.map((_, score)).iterator
}
}
(Even with variants where the filter function just returns empty iterators, Spark still is insistent on reading all the data)
The side effect of this is that because some groups have too many ids, I have a lot of skew in the data and the job can never finish when processing the full scale of data.
I want the reduce-side to only read in the data it needs, and not crap out because of data skew.
I have a feeling that somehow I need to create a transform that is able to push down a limit or take clause, but I can't figure out how.
Can't we just filter out those groups which have records more than 1k using count() in grouped data?
or if you want to have those groups also which have more than 1k records but only to pick upto 1k records then in spark sql query you can use ROW_NUMBER() OVER (PARTITION BY id ORDER BY someColumn DESC) AS rn and then put condition rn<=1000.

How can you get around the 2GB buffer limit when using Dataset.groupByKey?

When using Dataset.groupByKey(_.key).mapGroups or Dataset.groupByKey(_.key).cogroup in Spark, I've run into a problem when one of the groupings results in more than 2GB of data.
I need to normalize the data by group before I can start to reduce it, and I would like to split up the groups into smaller subgroups so they distribute better. For example, here's one way I've attempted to split the groups:
val groupedInputs = inputData.groupByKey(_.key).mapGroups {
case(key, inputSeries) => inputSeries.grouped(maxGroupSize).map(group => (key, group))
}
But unfortunately however I try to work around it, my jobs always die with an error like this: java.lang.UnsupportedOperationException: Cannot grow BufferHolder by size 23816 because the size after growing exceeds size limitation 2147483632. When using Kryo serialization I get a different Kryo serialization failed: Buffer overflow error recommending I increase spark.kryoserializer.buffer.max, but I've already increased it to the 2GB limit.
One solution that occurs to me is to add a random value to the keys before grouping them. This isn't ideal since it'll split up every group (not just the large ones), but I'm willing to sacrifice "ideal" for the sake of "working". That code would look something like this:
val splitInputs = inputData.map( record => (record, ThreadLocalRandom.current.nextInt(splitFactor)))
val groupedInputs = splitInputs.groupByKey{ case(record, split) => (record.key, split)).mapGroups {
case((key, _), inputSeries) => inputSeries.grouped(maxGroupSize).map(group => (key, group.map(_._1)))
}
Add a salt key and do groupBy on your key and the salt key and later
import scala.util.Random
val start = 1
val end = 5
val randUdf = udf({() => start + Random.nextInt((end - start) + 1)})
val saltGroupBy=skewDF.withColumn("salt_key", randUdf())
.groupBy(col("name"), col("salt_key"))
So your all the skew data doesn't go into one executor and cause the 2GB Limit.
But you have to develop a logic to aggregate the above result and finally remove the salt key at the end.
When you use groupBy all the records with the same key will reach one executor and bottle neck occur.
The above is one of the method to mitigate it.
For this case, where the dataset had a lot of skew and it was important to group the records into regularly-sized groups, I decided to process the dataset in two passes. First I used a window function to number the rows by key, and converted that to a "group index," based on a configurable "maxGroupSize":
// The "orderBy" doesn't seem necessary here,
// but the row_number function requires it.
val partitionByKey = Window.partitionBy(key).orderBy(key)
val indexedData = inputData.withColumn("groupIndex",
(row_number.over(partitionByKey) / maxGroupSize).cast(IntegerType))
.as[(Record, Int)]
Then I can group by key and index, and produce groups that are consistently sized--the keys with a lot of records get split up more, and the keys with few records may not be split up at all.
indexedData.groupByKey{ case (record, groupIndex) => (record.key, groupIndex) }
.mapGroups{ case((key, _), recordGroup) =>
// Remove the index values before returning the groups
(key, recordGroup.map(_._1))
}

avoid partitions unbalancing Spark

I have a performance problem with a code I'm revisioning, everytime will give an OOM while performing a count.
I think I found the problem, basically after keyBy tranformation, being executed aggregateByKey.
The problem lies to the fact that almost 98% of the RDD elements has the same key, so aggregationByKey, generate shuffle, putting nearly all records into the same partition, bottom line: just few executors works, and has to much memory pressure.
This is the code:
val rddAnomaliesByProcess : RDD[AnomalyPO] = rddAnomalies
.keyBy(po => po.getProcessCreator.name)
.aggregateByKey(List[AnomalyPO]())((list,value) => value +: list,_++_)
.map {case(name,list) =>
val groupByKeys = list.groupBy(po => (po.getPodId, po.getAnomalyCode, po.getAnomalyReason, po.getAnomalyDate, po.getMeasureUUID))
val lastOfGroupByKeys = groupByKeys.map{po => (po._1, List(po._2.sortBy { po => po.getProcessDate.getMillis }.last))}
lastOfGroupByKeys.flatMap(f => f._2)
}
.flatMap(f => f)
log.info("not duplicated Anomalies: " + rddAnomaliesByProcess.count)
I would a way to perform operation in a more parallel way, allowing all executors to work nearly equally. How can I do that?
Should I have to use a custom partitioner?
If your observation is correct and
98% of the RDD elements has the same key
then change of partitioner won't help you at all. By the definition of the partitioner 98% of the data will have to be processed by a single executor.
Luckily bad code is probably the bigger problem here than the skew. Skipping over:
.aggregateByKey(List[AnomalyPO]())((list,value) => value +: list,_++_)
which is just a folk magic it looks like the whole pipeline can be rewritten as a simple reuceByKey. Pseudocode:
Combine name and local keys into a single key:
def key(po: AnomalyPO) = (
// "major" key
po.getProcessCreator.name,
// "minor" key
po.getPodId, po.getAnomalyCode,
po.getAnomalyReason, po.getAnomalyDate, po.getMeasureUUID
)
Key containing name, date and additional fields should have much higher cardinality than the name alone.
Map to pairs and reduce by key:
rddAnomalies
.map(po => (key(po), po))
.reduceByKey((x, y) =>
if(x.getProcessDate.getMillis > y.getProcessDate.getMillis) x else y
)

What is an efficient way to partition by column but maintain a fixed partition count?

What is the best way to partition the data by a field into predefined partition count?
I am currently partitioning the data by specifying the partionCount=600. The count 600 is found to give best query performance for my dataset/cluster setup.
val rawJson = sqlContext.read.json(filename).coalesce(600)
rawJson.write.parquet(filenameParquet)
Now I want to partition this data by the column 'eventName' but still keep the count 600. The data currently has around 2000 unique eventNames, plus the number of rows in each eventName is not uniform. Around 10 eventNames have more than 50% of the data causing data skew. Hence if I do the partitioning like below, its not very performant. The write is taking 5x more time than without.
val rawJson = sqlContext.read.json(filename)
rawJson.write.partitionBy("eventName").parquet(filenameParquet)
What is a good way to partition the data for these scenarios? Is there a way to partition by eventName but spread this into 600 partitions?
My schema looks like this:
{
"eventName": "name1",
"time": "2016-06-20T11:57:19.4941368-04:00",
"data": {
"type": "EventData",
"dataDetails": {
"name": "detailed1",
"id": "1234",
...
...
}
}
}
Thanks!
This is a common problem with skewed data and there are several approaches you can take.
List bucketing works if the skew remains stable over time, which may or may not be the case, especially if new values of the partitioning variable are introduced. I have not researched how easy it is to adjust list bucketing over time and, as your comment states, you can't use that anyway because it is a Spark 2.0 feature.
If you are on 1.6.x, the key observation is that you can create your own function that maps each event name into one of 600 unique values. You can do this as a UDF or as a case expression. Then, you simply create a column using that function and then partition by that column using repartition(600, 'myPartitionCol) as opposed to coalesce(600).
Because we deal with very skewed data at Swoop, I've found the following workhorse data structure to be quite useful for building partitioning-related tools.
/** Given a key, returns a random number in the range [x, y) where
* x and y are the numbers in the tuple associated with a key.
*/
class RandomRangeMap[A](private val m: Map[A, (Int, Int)]) extends Serializable {
private val r = new java.util.Random() // Scala Random is not serializable in 2.10
def apply(key: A): Int = {
val (start, end) = m(key)
start + r.nextInt(end - start)
}
override def toString = s"RandomRangeMap($r, $m)"
}
For example, here is how we build a partitioner for a slightly different case: one where the data is skewed and the number of keys is small so we have to increase the number of partitions for the skewed keys while sticking with 1 as the minimum number of partitions per key:
/** Partitions data such that each unique key ends in P(key) partitions.
* Must be instantiated with a sequence of unique keys and their Ps.
* Partition sizes can be highly-skewed by the data, which is where the
* multiples come in.
*
* #param keyMap maps key values to their partition multiples
*/
class ByKeyPartitionerWithMultiples(val keyMap: Map[Any, Int]) extends Partitioner {
private val rrm = new RandomRangeMap(
keyMap.keys
.zip(
keyMap.values
.scanLeft(0)(_+_)
.zip(keyMap.values)
.map {
case (start, count) => (start, start + count)
}
)
.toMap
)
override val numPartitions =
keyMap.values.sum
override def getPartition(key: Any): Int =
rrm(key)
}
object ByKeyPartitionerWithMultiples {
/** Builds a UDF with a ByKeyPartitionerWithMultiples in a closure.
*
* #param keyMap maps key values to their partition multiples
*/
def udf(keyMap: Map[String, Int]) = {
val partitioner = new ByKeyPartitionerWithMultiples(keyMap.asInstanceOf[Map[Any, Int]])
(key:String) => partitioner.getPartition(key)
}
}
In your case, you have to merge several event names into a single partition, which would require changes but I hope the code above gives you an idea how to approach the problem.
One final observation is that if the distribution of event names values a lot in your data over time, you can perform a statistics gathering pass over some part of the data to compute a mapping table. You don't have to do this all the time, just when it is needed. To determine that, you can look at the number of rows and/or size of output files in each partition. In other words, the entire process can be automated as part of your Spark jobs.

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