hammerlab / magic-rdds   4.3.0

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Miscellaneous functionality for manipulating Apache Spark RDDs.

Scala versions: 2.12 2.11

Magic RDDs

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Enrichment methods for Apache Spark RDDs:

$ spark-shell --packages org.hammerlab:magic-rdds_2.11:4.3.0
…
scala> import magic_rdds._
scala> sc.parallelize(List(1, 1, 1, 2, 2, 2, 2, 2, 2, 10)).runLengthEncode.collect()
res0: Array[(Int, Int)] = Array((1,3), (2,6), (10,1))

Using

Use these Maven coordinates to depend on magic-rdds' latest Scala 2.11 build:

<dependency>
  <groupId>org.hammerlab</groupId>
  <artifactId>magic-rdds_2.11</artifactId>
  <version>4.3.0</version>
</dependency>

In SBT, use:

"org.hammerlab" %% "magic-rdds" % "4.3.0"

Overview

Following are explanations of some of the RDDs provided by this repo and the functionality they provide:

RDDs

RDD-helpers found in the org.hammerlab.magic.rdd package.

Run-length encoding

Exposes a runLengthEncode method on RDDs, per the example above.

Scans

Basic .scanLeft / .scanRight
val rdd = sc.parallelize(1 to 10)

rdd.scanLeft(0)(_ + _).collect
// Array(0, 1, 3, 6, 10, 15, 21, 28, 36, 45)

rdd.scanRight(0)(_ + _).collect
// Array(54, 52, 49, 45, 40, 34, 27, 19, 10, 0)

Before the .collect, these each return a ScanRDD, which is a wrapper around the post-scan RDD, the total sum, and an array with the first element in each partition, and is automatically implicitly-convertible to its contained RDD.

Include each element in the partial-sum that replaces it
rdd.scanLeftInclusive(0)(_ + _).collect
// Array[Int] = Array(1, 3, 6, 10, 15, 21, 28, 36, 45, 55)

rdd.scanRightInclusive(0)(_ + _).collect
// Array(55, 54, 52, 49, 45, 40, 34, 27, 19, 10)
Use cats.Monoids
import cats.instances.int._

rdd.scanLeft
rdd.scanRight
rdd.scanLeftInclusive
rdd.scanRightInclusive
Operate on "value"s of key-values pairs
val pairRDD = sc.parallelize('a' to 'j' zip (1 to 10))

pairRDD.scanLeftValues.collect
// Array((a,0), (b,1), (c,3), (d,6), (e,10), (f,15), (g,21), (h,28), (i,36), (j,45))

pairRDD.scanLeftValuesInclusive.collect
// Array((a,1), (b,3), (c,6), (d,10), (e,15), (f,21), (g,28), (h,36), (i,45), (j,55))

pairRDD.scanRightValues.collect
// Array((a,54), (b,52), (c,49), (d,45), (e,40), (f,34), (g,27), (h,19), (i,10), (j,0))

pairRDD.scanRightValuesInclusive.collect
// Array((a,55), (b,54), (c,52), (d,49), (e,45), (f,40), (g,34), (h,27), (i,19), (j,10))

Additionally, .scanRight and .scanRightValues expose two implementations with performance tradeoffs:

  • the default implementation achieves a scanRight by sequencing the following operations:

    • reverse
    • scanLeft
    • reverse

  • an alternate implementation, enabled by setting useRDDReversal = false in the first parameter list, calls Iterator.scanRight on each partition at one point, which materializes the entire partition into memory:

    pairRDD.scanRightValues(useRDDReversal = false).collect
// Array((a,54), (b,52), (c,49), (d,45), (e,40), (f,34), (g,27), (h,19), (i,10), (j,0))

    This is generally dangerous with Spark RDDs, where the assumption is typically that a partition is larger than the available executor memory, meaning such an operation is likely to cause an OOM.

.reverse

Reverse the elements in an RDD, optionally preserving (though still inverting) their partitioning:

sc.parallelize(1 to 10).reverse().collect
res2: Array[Int] = Array(10, 9, 8, 7, 6, 5, 4, 3, 2, 1)

reduceByKey extensions

Self-explanatory: .maxByKey, .minByKey

RDD Comparisons / Diffs

Example setup:

val rdd1 = sc.parallelize(1 to 10)
val rdd2 = sc.parallelize((1 to 5) ++ (12 to 7 by -1))

import cmp._
unorderedCmp: compare, disregarding order/position of elements:
val Unordered.Stats(both, onlyA, onlyB) = rdd1.unorderedCmp(rdd2).stats
both = 9   (1 to 5, 7 to 10)
onlyA = 1  (6)
onlyB = 2  (11, 12)
orderedCmp: distinguish between common elements at the same vs. different indices:
val Ordered.Stats(eq, reordered, onlyA, onlyB) = rdd1.orderedCmp(rdd2).stats
// eq = 6        (1, 2, 3, 4, 5, 9)
// reordered = 3 (7, 8, 10)
// onlyA = 1     (6)
// onlyB = 2     (11, 12)
compareByKey: unordered comparison of values for each key of paired-RDDs:
import hammerlab.iterator._

val chars10  = ('a' to 'j') zipWithIndex
val chars4   = chars10.take(4)
val chars5_2 = chars10.mapValues(_ + 10).takeEager(5)

val rdd1 = sc.parallelize(chars10  ++ chars4)
val rdd2 = sc.parallelize(chars5_2 ++ chars4)

val Keyed.Stats(eq, extraA, extraB, onlyA, onlyB) = rdd1.compareByKey(rdd2).stats
// eq     = 4 (a →  1, b →  2, c →  3, d →  4)
// extraA = 4 (a →  1, b →  2, c →  3, d →  4; second copy of each)
// extraB = 0 
// onlyA  = 6 (e →  5, f →  6, g →  7, h →  8, i →  9, j →  10)
// onlyB  = 5 (a → 11, b → 12, c → 13, d → 14, e → 15)

collectParts

collect an RDD while keeping elements in their respective partitions:

sc.parallelize(1 to 12).collectParts
// Array(Array(1, 2, 3), Array(4, 5, 6), Array(7, 8, 9), Array(10, 11, 12))

.size

A smarter version of RDD.count:

  • results are cached; subsequent calls don't recompute

  • size of a UnionRDDs also computes and caches sizes of its constituent RDDs

  • .sizes, .total: compute sizes of sequences / tuples of RDDs in one Spark job. For example, instead of:

     val count1 = rdd1.count
 val count2 = rdd2.count

    which runs two Spark jobs, you can instead write:

     val (count1, count2) = (rdd1, rdd2).sizes

    and save a job.

.lazyZipWithIndex

Functionally equivalent to RDD.zipWithIndex, but runs the first of the two necessary jobs (computing per-partition sizes and cumulative offsets) lazily, in a manner truer to the spirit of the lazy-wherever-possible RDD API than the .zipWithIndex implementation.

  • .saveAsSequenceFile, .saveCompressed for non-paired RDDs.

Sliding / Windowed Traversals

Exposes several methods in the spirit of Scala collections' similar API.

Tuple2 / Tuple3:

sc.parallelize(1 to 6).sliding2.collect
// Array((1,2), (2,3), (3,4), (4,5), (5,6))

sc.parallelize(1 to 6).sliding3.collect
// Array((1,2,3), (2,3,4), (3,4,5), (4,5,6))

2- and 3-element windows with Option contexts; input and output RDDs have same number of eleemnts:

sc.parallelize(1 to 6).sliding2Next.collect
// Array((1,Some(2)), (2,Some(3)), (3,Some(4)), (4,Some(5)), (5,Some(6)), (6,None))

sc.parallelize(1 to 6).sliding2Prev.collect
// Array((None,1), (Some(1),2), (Some(2),3), (Some(3),4), (Some(4),5), (Some(5),6))

sc.parallelize(1 to 6).sliding3Opt.collect
// Array((None,1,Some(2)), (Some(1),2,Some(3)), (Some(2),3,Some(4)), (Some(3),4,Some(5)), (Some(4),5,Some(6)), (Some(5),6,None))

sc.parallelize(1 to 6).sliding3Next.collect
// Array((1,Some(2),Some(3)), (2,Some(3),Some(4)), (3,Some(4),Some(5)), (4,Some(5),Some(6)), (5,Some(6),None), (6,None,None))

Arbitrary number of elements in Seqs, optionally preserving total number of elements by keeping partial entries:

sc.parallelize(1 to 6).sliding(4).collect
// Array(List(1, 2, 3, 4), List(2, 3, 4, 5), List(3, 4, 5, 6))

scala> sc.parallelize(1 to 6).sliding(4, includePartial = true).collect
// Array(List(1, 2, 3, 4), List(2, 3, 4, 5), List(3, 4, 5, 6), List(4, 5, 6), List(5, 6), List(6))

.cappedGroupByKey

Like RDD.groupByKey but takes only the first maxPerKey elements for each key:

sc.parallelize(1 to 10).keyBy(_ % 2).cappedGroupByKey(3).collect
// Array((0,Vector(2, 4, 6)), (1,Vector(1, 3, 5)))

.sampleByKey

Similar to .cappedGroupByKey, but samples elements from each key in an unbiased manner:

sc.parallelize(1 to 100).keyBy(_ % 2).sampleByKey(3).collect
// Array((0,ArrayBuffer(24, 78, 98)), (1,ArrayBuffer(17, 47, 49)))

.splitByKey

Split an RDD[(K, V)] into a Map[K, RDD[V]], i.e. multiple RDDs each containing the values corresponding to one key.

This is generally a questionable thing to want to do, as subsequent operations on each RDD lose out on Spark's ability to parallelize things.

However, if you are going to do it, this implementation is much better than what you might do naively, i.e. using .filter N times on the original RDD.

Instead, this shuffles the full RDD once, into a partitioning where each key's pairs occupy a contiguous range of partitions; it then partition-slices views over those ranges and exposes them as standalone, per-key RDDs.

2-D prefix sum

Given an RDD of elements that each have a logical "row", "column", and "summable" value (an RDD[((Int, Int), V)]), generate an RDD that replaces each value with the sum of all values at greater (or equal) (row,col) positions:

val n = 4
val rdd = sc.parallelize(1 to n flatMap { r ⇒ 1 to n map { c ⇒ r -> c -> r*c } })
def printGrid(rdd: RDD[((Int, Int), Int)]) = {
  val map = rdd.collectAsMap.toMap
  for {
    r ← n to 1 by -1
    c ← 1 to n
  } {
    print("% 4d".format(map((r, c))))
    if (c == n) print("\n")
  }
}

printGrid(rdd)
//   4   8  12  16
//   3   6   9  12
//   2   4   6   8
//   1   2   3   4

val prefix_sum.Result(_, cdf, _, _) = rdd.prefixSum2D()

printGrid(cdf)
//  40  36  28  16
//  70  63  49  28
//  90  81  63  36
// 100  90  70  40

Examples from the tests may clarify further.

"Batch" execution

This feature exposes a coarse avenue for forcing fewer than spark.executor.cores tasks to run concurrently on each executor, during a given stage.

The stage in question is split up into multiple Spark stages, each comprised of a set number of partitions from the upstream RDD (the "batch size").

If this size is chosen to be ≤ the number of executors, then in general a maximum of one task will be assigned to each executor.

This can be useful when some stages in an app are very memory-expensive, while others are not: the memory-expensive ones can be "batched" in this way, each task availing itself of a full executor's-worth of memory.

The implementation splits the upstream partitions into (N/batch size) batches and executes each batch as a single stage before combining the results into single RDD:

scala> import org.hammerlab.magic.rdd.batch.implicits._
// create RDD of 10 partitions
val rdd = sc.parallelize(0 until 100, 10)
val res = rdd.batch(numPartitionsPerBatch = 4)

// print operations graph to see how many batches are selected
res.toDebugString
// (10) ReduceRDD[4] at RDD at ReduceRDD.scala:19 []
//  +-(2) MapRDD[3] at RDD at MapRDD.scala:21 []
//     +-(4) MapRDD[2] at RDD at MapRDD.scala:21 []
//        +-(4) MapRDD[1] at RDD at MapRDD.scala:21 []
//           |  ParallelCollectionRDD[0] at parallelize at <console>:27 []

See the package README for more info!

And more!

Browse the code and tests, file an issue, or drop by Gitter for more info.

Building

Typical SBT commands will build/test/package the project:

sbt test
sbt assembly

Releasing

While set to a -SNAPSHOT version:

sbt publish

To release a non--SNAPSHOT version:

sbt publishSigned sonatypeRelease

Statistics

14 Dependencies

6 Dependents