cleanUp

Addressed reviewer comments and added better documentation of code.
Added commons-math3 as a dependency of spark (okay’ed by Matei). “mvm
clean install” compiled. Recovered files that were reverted by accident
in the merge.
TODOs: figure out API for sampleByKeyExact and update Java, Python, and
the markdown file accordingly.

Author: dorx

core/pom.xml

@@ -70,8 +70,6 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-math3</artifactId>
-      <version>3.3</version>
-      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>com.google.code.findbugs</groupId>

core/src/main/scala/org/apache/spark/rdd/RDD.scala

@@ -874,6 +874,27 @@ abstract class RDD[T: ClassTag](
     jobResult
   }
 
+  /**
+   * A version of {@link #aggregate()} that passes the TaskContext to the function that does
+   * aggregation for each partition.
+   */
+  def aggregateWithContext[U: ClassTag](zeroValue: U)(seqOp: ((TaskContext, U), T) => U,
+      combOp: (U, U) => U): U = {
+    // Clone the zero value since we will also be serializing it as part of tasks
+    var jobResult = Utils.clone(zeroValue, sc.env.closureSerializer.newInstance())
+    // pad seqOp and combOp with taskContext to conform to aggregate's signature in TraversableOnce
+    val paddedSeqOp = (arg1: (TaskContext, U), item: T) => (arg1._1, seqOp(arg1, item))
+    val paddedcombOp = (arg1: (TaskContext, U), arg2: (TaskContext, U)) =>
+      (arg1._1, combOp(arg1._2, arg1._2))
+    val cleanSeqOp = sc.clean(paddedSeqOp)
+    val cleanCombOp = sc.clean(paddedcombOp)
+    val aggregatePartition = (tc: TaskContext, it: Iterator[T]) =>
+      (it.aggregate(tc, zeroValue)(cleanSeqOp, cleanCombOp))._2
+    val mergeResult = (index: Int, taskResult: U) => jobResult = combOp(jobResult, taskResult)
+    sc.runJob(this, aggregatePartition, mergeResult)
+    jobResult
+  }
+
   /**
    * Return the number of elements in the RDD.
    */

core/src/main/scala/org/apache/spark/util/random/SamplingUtils.scala

@@ -17,7 +17,7 @@
 
 package org.apache.spark.util.random
 
-import org.apache.commons.math3.distribution.{PoissonDistribution, NormalDistribution}
+import org.apache.commons.math3.distribution.PoissonDistribution
 
 private[spark] object SamplingUtils {
 
@@ -43,7 +43,7 @@ private[spark] object SamplingUtils {
    * @return a sampling rate that guarantees sufficient sample size with 99.99% success rate
    */
   def computeFractionForSampleSize(sampleSizeLowerBound: Int, total: Long,
-                                   withReplacement: Boolean): Double = {
+      withReplacement: Boolean): Double = {
     val fraction = sampleSizeLowerBound.toDouble / total
     if (withReplacement) {
       val numStDev = if (sampleSizeLowerBound < 12) 9 else 5
@@ -56,12 +56,29 @@ private[spark] object SamplingUtils {
   }
 }
 
+/**
+ * Utility functions that help us determine bounds on adjusted sampling rate to guarantee exact
+ * sample sizes with high confidence when sampling with replacement.
+ *
+ * The algorithm for guaranteeing sample size instantly accepts items whose associated value drawn
+ * from Pois(s) is less than the lower bound and puts items whose value is between the lower and
+ * upper bound in a waitlist. The final sample is consisted of all items accepted on the fly and a
+ * portion of the waitlist needed to make the exact sample size.
+ */
 private[spark] object PoissonBounds {
 
   val delta = 1e-4 / 3.0
-  val phi = new NormalDistribution().cumulativeProbability(1.0 - delta)
 
-  def getLambda1(s: Double): Double = {
+  /**
+   * Compute the threshold for accepting items on the fly. The threshold value is a fairly small
+   * number, which means if the item has an associated value < threshold, it is highly likely to
+   * be in the final sample. Hence we accept items with values less than the returned value of this
+   * function instantly.
+   *
+   * @param s sample size
+   * @return threshold for accepting items on the fly
+   */
+  def getLowerBound(s: Double): Double = {
     var lb = math.max(0.0, s - math.sqrt(s / delta)) // Chebyshev's inequality
     var ub = s
     while (lb < ub - 1.0) {
@@ -79,7 +96,16 @@ private[spark] object PoissonBounds {
     poisson.inverseCumulativeProbability(delta)
   }
 
-  def getLambda2(s: Double): Double = {
+  /**
+   * Compute the threshold for waitlisting items. An item is waitlisted if its associated value is
+   * greater than the lower bound determined above but below the upper bound computed here.
+   * The value is computed such that we only need to keep log(s) items in the waitlist and still be
+   * able to guarantee sample size with high confidence.
+   *
+   * @param s sample size
+   * @return threshold for waitlisting the item
+   */
+  def getUpperBound(s: Double): Double = {
     var lb = s
     var ub = s + math.sqrt(s / delta) // Chebyshev's inequality
     while (lb < ub - 1.0) {

core/src/main/scala/org/apache/spark/util/random/StratifiedSampler.scala

@@ -26,6 +26,9 @@ import scala.Some
 import org.apache.spark.rdd.RDD
 
 private[spark] object StratifiedSampler extends Logging {
+  /**
+   * Returns the function used by aggregate to collect sampling statistics for each partition.
+   */
   def getSeqOp[K, V](withReplacement: Boolean,
       fractionByKey: (K => Double),
       counts: Option[Map[K, Long]]): ((TaskContext, Result[K]),(K, V)) => Result[K] = {
@@ -43,9 +46,9 @@ private[spark] object StratifiedSampler extends Logging {
         if (stratum.q1.isEmpty || stratum.q2.isEmpty) {
           val n = counts.get(item._1)
           val s = math.ceil(n * fraction).toLong
-          val lmbd1 = PB.getLambda1(s)
+          val lmbd1 = PB.getLowerBound(s)
           val minCount = PB.getMinCount(lmbd1)
-          val lmbd2 = if (lmbd1 == 0) PB.getLambda2(s) else PB.getLambda2(s - minCount)
+          val lmbd2 = if (lmbd1 == 0) PB.getUpperBound(s) else PB.getUpperBound(s - minCount)
           val q1 = lmbd1 / n
           val q2 = lmbd2 / n
           stratum.q1 = Some(q1)
@@ -60,6 +63,8 @@ private[spark] object StratifiedSampler extends Logging {
           stratum.addToWaitList(ArrayBuffer.fill(x2)(rng.nextUniform(0.0, 1.0)))
         }
       } else {
+        // We use the streaming version of the algorithm for sampling without replacement.
+        // Hence, q1 and q2 change on every iteration.
         val g1 = - math.log(delta) / stratum.numItems
         val g2 = (2.0 / 3.0) * g1
         val q1 = math.max(0, fraction + g2 - math.sqrt((g2 * g2 + 3 * g2 * fraction)))
@@ -79,7 +84,11 @@ private[spark] object StratifiedSampler extends Logging {
     }
   }
 
-  def getCombOp[K](): (Result[K], Result[K])  => Result[K] = {
+  /**
+   * Returns the function used by aggregate to combine results from different partitions, as
+   * returned by seqOp.
+   */
+  def getCombOp[K](): (Result[K], Result[K]) => Result[K] = {
     (r1: Result[K], r2: Result[K]) => {
       // take union of both key sets in case one partition doesn't contain all keys
       val keyUnion = r1.resultMap.keys.toSet.union(r2.resultMap.keys.toSet)
@@ -100,6 +109,10 @@ private[spark] object StratifiedSampler extends Logging {
     }
   }
 
+  /**
+   * Given the result returned by the aggregate function, we need to determine the threshold used
+   * to accept items to generate the exact sample size.
+   */
   def computeThresholdByKey[K](finalResult: Map[K, Stratum], fractionByKey: (K => Double)):
     (K => Double) = {
     val thresholdByKey = new mutable.HashMap[K, Double]()
@@ -122,11 +135,15 @@ private[spark] object StratifiedSampler extends Logging {
     thresholdByKey
   }
 
-  def computeThresholdByKey[K](finalResult: Map[K, String]): (K => String) = {
-    finalResult
-  }
-
-  def getBernoulliSamplingFunction[K, V](rdd:RDD[(K,  V)],
+  /**
+   * Return the per partition sampling function used for sampling without replacement.
+   *
+   * When exact sample size is required, we make an additional pass over the RDD to determine the
+   * exact sampling rate that guarantees sample size with high confidence.
+   *
+   * The sampling function has a unique seed per partition.
+   */
+  def getBernoulliSamplingFunction[K, V](rdd: RDD[(K,  V)],
       fractionByKey: K => Double,
       exact: Boolean,
       seed: Long): (Int, Iterator[(K, V)]) => Iterator[(K, V)] = {
@@ -146,6 +163,16 @@ private[spark] object StratifiedSampler extends Logging {
     }
   }
 
+  /**
+   * Return the per partition sampling function used for sampling with replacement.
+   *
+   * When exact sample size is required, we make two additional passed over the RDD to determine
+   * the exact sampling rate that guarantees sample size with high confidence. The first pass
+   * counts the number of items in each stratum (group of items with the same key) in the RDD, and
+   * the second pass uses the counts to determine exact sampling rates.
+   *
+   * The sampling function has a unique seed per partition.
+   */
   def getPoissonSamplingFunction[K, V](rdd:RDD[(K,  V)],
       fractionByKey: K => Double,
       exact: Boolean,
@@ -191,6 +218,10 @@ private[spark] object StratifiedSampler extends Logging {
   }
 }
 
+/**
+ * Object used by seqOp to keep track of the number of items accepted and items waitlisted per
+ * stratum, as well as the bounds for accepting and waitlisting items.
+ */
 private[random] class Stratum(var numItems: Long = 0L, var numAccepted: Long = 0L)
   extends Serializable {
 
@@ -205,13 +236,14 @@ private[random] class Stratum(var numItems: Long = 0L, var numAccepted: Long = 0
   def addToWaitList(elem: Double) = waitList += elem
 
   def addToWaitList(elems: ArrayBuffer[Double]) = waitList ++= elems
-
-  override def toString() = {
-    "numItems: " + numItems + " numAccepted: " + numAccepted + " q1: " + q1 + " q2: " + q2 +
-      " waitListSize:" + waitList.size
-  }
 }
 
+/**
+ * Object used by seqOp and combOp to keep track of the sampling statistics for all strata.
+ *
+ * When used by seqOp for each partition, we also keep track of the partition ID in this object
+ * to make sure a single random number generator with a unique seed is used for each partition.
+ */
 private[random] class Result[K](var resultMap: Map[K, Stratum],
                 var cachedPartitionId: Option[Int] = None,
                 val seed: Long)

core/src/test/scala/org/apache/spark/rdd/RDDSuite.scala

@@ -141,6 +141,38 @@ class RDDSuite extends FunSuite with SharedSparkContext {
     assert(result.toSet === Set(("a", 6), ("b", 2), ("c", 5)))
   }
 
+  test("aggregateWithContext") {
+    val data = Array(("a", 1), ("b", 2), ("a", 2), ("c", 5), ("a", 3))
+    val numPartitions = 2
+    val pairs = sc.makeRDD(data, numPartitions)
+    //determine the partitionId for each pair
+    type StringMap = HashMap[String, Int]
+    val partitions = pairs.collectPartitions()
+    val offSets = new StringMap
+    for (i <- 0 to numPartitions - 1) {
+      partitions(i).foreach({ case (k, v) => offSets.put(k, offSets.getOrElse(k, 0) + i)})
+    }
+    val emptyMap = new StringMap {
+      override def default(key: String): Int = 0
+    }
+    val mergeElement: ((TaskContext, StringMap), (String, Int)) => StringMap = (arg1, pair) => {
+      val stringMap = arg1._2
+      val tc = arg1._1
+      stringMap(pair._1) += pair._2 + tc.partitionId
+      stringMap
+    }
+    val mergeMaps: (StringMap, StringMap) => StringMap = (map1, map2) => {
+      for ((key, value) <- map2) {
+        map1(key) += value
+      }
+      map1
+    }
+    val result = pairs.aggregateWithContext(emptyMap)(mergeElement, mergeMaps)
+    val expected = Set(("a", 6), ("b", 2), ("c", 5))
+      .map({ case (k, v) => (k -> (offSets.getOrElse(k, 0) + v))})
+    assert(result.toSet === expected)
+  }
+
   test("basic caching") {
     val rdd = sc.makeRDD(Array(1, 2, 3, 4), 2).cache()
     assert(rdd.collect().toList === List(1, 2, 3, 4))