SPARK-1786: Edge Partition Serialization

This appears to address the issue with edge partition serialization.  The solution appears to be just registering the `PrimitiveKeyOpenHashMap`.  However I noticed that we appear to have forked that code in GraphX but retained the same name (which is confusing).  I also renamed our local copy to `GraphXPrimitiveKeyOpenHashMap`.  We should consider dropping that and using the one in Spark if possible.

Author: Ankur Dave <ankurdave@gmail.com>
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #724 from jegonzal/edge_partition_serialization and squashes the following commits:

b0a525a [Ankur Dave] Disable reference tracking to fix serialization test
bb7f548 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
67dac22 [Joseph E. Gonzalez] Making EdgePartition serializable.

graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala

@@ -24,6 +24,9 @@ import org.apache.spark.util.BoundedPriorityQueue
 import org.apache.spark.util.collection.BitSet
 
 import org.apache.spark.graphx.impl._
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
+import org.apache.spark.util.collection.OpenHashSet
+
 
 /**
  * Registers GraphX classes with Kryo for improved performance.
@@ -43,8 +46,8 @@ class GraphKryoRegistrator extends KryoRegistrator {
     kryo.register(classOf[PartitionStrategy])
     kryo.register(classOf[BoundedPriorityQueue[Object]])
     kryo.register(classOf[EdgeDirection])
-
-    // This avoids a large number of hash table lookups.
-    kryo.setReferences(false)
+    kryo.register(classOf[GraphXPrimitiveKeyOpenHashMap[VertexId, Int]])
+    kryo.register(classOf[OpenHashSet[Int]])
+    kryo.register(classOf[OpenHashSet[Long]])
   }
 }

graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartition.scala

@@ -20,7 +20,7 @@ package org.apache.spark.graphx.impl
 import scala.reflect.{classTag, ClassTag}
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 /**
  * A collection of edges stored in columnar format, along with any vertex attributes referenced. The
@@ -42,12 +42,12 @@ import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
 private[graphx]
 class EdgePartition[
     @specialized(Char, Int, Boolean, Byte, Long, Float, Double) ED: ClassTag, VD: ClassTag](
-    @transient val srcIds: Array[VertexId],
-    @transient val dstIds: Array[VertexId],
-    @transient val data: Array[ED],
-    @transient val index: PrimitiveKeyOpenHashMap[VertexId, Int],
-    @transient val vertices: VertexPartition[VD],
-    @transient val activeSet: Option[VertexSet] = None
+    val srcIds: Array[VertexId] = null,
+    val dstIds: Array[VertexId] = null,
+    val data: Array[ED] = null,
+    val index: GraphXPrimitiveKeyOpenHashMap[VertexId, Int] = null,
+    val vertices: VertexPartition[VD] = null,
+    val activeSet: Option[VertexSet] = None
   ) extends Serializable {
 
   /** Return a new `EdgePartition` with the specified edge data. */

graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartitionBuilder.scala

@@ -23,7 +23,7 @@ import scala.util.Sorting
 import org.apache.spark.util.collection.{BitSet, OpenHashSet, PrimitiveVector}
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 private[graphx]
 class EdgePartitionBuilder[@specialized(Long, Int, Double) ED: ClassTag, VD: ClassTag](
@@ -41,7 +41,7 @@ class EdgePartitionBuilder[@specialized(Long, Int, Double) ED: ClassTag, VD: Cla
     val srcIds = new Array[VertexId](edgeArray.size)
     val dstIds = new Array[VertexId](edgeArray.size)
     val data = new Array[ED](edgeArray.size)
-    val index = new PrimitiveKeyOpenHashMap[VertexId, Int]
+    val index = new GraphXPrimitiveKeyOpenHashMap[VertexId, Int]
     // Copy edges into columnar structures, tracking the beginnings of source vertex id clusters and
     // adding them to the index
     if (edgeArray.length > 0) {

graphx/src/main/scala/org/apache/spark/graphx/impl/EdgeTripletIterator.scala

@@ -20,7 +20,7 @@ package org.apache.spark.graphx.impl
 import scala.reflect.ClassTag
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 /**
  * The Iterator type returned when constructing edge triplets. This could be an anonymous class in

graphx/src/main/scala/org/apache/spark/graphx/impl/RoutingTablePartition.scala

@@ -25,7 +25,7 @@ import org.apache.spark.rdd.ShuffledRDD
 import org.apache.spark.util.collection.{BitSet, PrimitiveVector}
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 /**
  * A message from the edge partition `pid` to the vertex partition containing `vid` specifying that
@@ -69,7 +69,7 @@ object RoutingTablePartition {
     : Iterator[RoutingTableMessage] = {
     // Determine which positions each vertex id appears in using a map where the low 2 bits
     // represent src and dst
-    val map = new PrimitiveKeyOpenHashMap[VertexId, Byte]
+    val map = new GraphXPrimitiveKeyOpenHashMap[VertexId, Byte]
     edgePartition.srcIds.iterator.foreach { srcId =>
       map.changeValue(srcId, 0x1, (b: Byte) => (b | 0x1).toByte)
     }

graphx/src/main/scala/org/apache/spark/graphx/impl/ShippableVertexPartition.scala

@@ -22,7 +22,7 @@ import scala.reflect.ClassTag
 import org.apache.spark.util.collection.{BitSet, PrimitiveVector}
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 /** Stores vertex attributes to ship to an edge partition. */
 private[graphx]

graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartition.scala

@@ -22,7 +22,7 @@ import scala.reflect.ClassTag
 import org.apache.spark.util.collection.BitSet
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 private[graphx] object VertexPartition {
   /** Construct a `VertexPartition` from the given vertices. */

graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBase.scala

@@ -23,7 +23,7 @@ import scala.reflect.ClassTag
 import org.apache.spark.util.collection.BitSet
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 private[graphx] object VertexPartitionBase {
   /**
@@ -32,7 +32,7 @@ private[graphx] object VertexPartitionBase {
    */
   def initFrom[VD: ClassTag](iter: Iterator[(VertexId, VD)])
     : (VertexIdToIndexMap, Array[VD], BitSet) = {
-    val map = new PrimitiveKeyOpenHashMap[VertexId, VD]
+    val map = new GraphXPrimitiveKeyOpenHashMap[VertexId, VD]
     iter.foreach { pair =>
       map(pair._1) = pair._2
     }
@@ -45,7 +45,7 @@ private[graphx] object VertexPartitionBase {
    */
   def initFrom[VD: ClassTag](iter: Iterator[(VertexId, VD)], mergeFunc: (VD, VD) => VD)
     : (VertexIdToIndexMap, Array[VD], BitSet) = {
-    val map = new PrimitiveKeyOpenHashMap[VertexId, VD]
+    val map = new GraphXPrimitiveKeyOpenHashMap[VertexId, VD]
     iter.foreach { pair =>
       map.setMerge(pair._1, pair._2, mergeFunc)
     }

graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBaseOps.scala

@@ -25,7 +25,7 @@ import org.apache.spark.Logging
 import org.apache.spark.util.collection.BitSet
 
 import org.apache.spark.graphx._
-import org.apache.spark.graphx.util.collection.PrimitiveKeyOpenHashMap
+import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
 
 /**
  * An class containing additional operations for subclasses of VertexPartitionBase that provide
@@ -224,7 +224,7 @@ private[graphx] abstract class VertexPartitionBaseOps
    * Construct a new VertexPartition whose index contains only the vertices in the mask.
    */
   def reindex(): Self[VD] = {
-    val hashMap = new PrimitiveKeyOpenHashMap[VertexId, VD]
+    val hashMap = new GraphXPrimitiveKeyOpenHashMap[VertexId, VD]
     val arbitraryMerge = (a: VD, b: VD) => a
     for ((k, v) <- self.iterator) {
       hashMap.setMerge(k, v, arbitraryMerge)

graphx/src/main/scala/org/apache/spark/graphx/util/collection/PrimitiveKeyOpenHashMap.scala → graphx/src/main/scala/org/apache/spark/graphx/util/collection/GraphXPrimitiveKeyOpenHashMap.scala

@@ -29,7 +29,7 @@ import scala.reflect._
  * Under the hood, it uses our OpenHashSet implementation.
  */
 private[graphx]
-class PrimitiveKeyOpenHashMap[@specialized(Long, Int) K: ClassTag,
+class GraphXPrimitiveKeyOpenHashMap[@specialized(Long, Int) K: ClassTag,
                               @specialized(Long, Int, Double) V: ClassTag](
     val keySet: OpenHashSet[K], var _values: Array[V])
   extends Iterable[(K, V)]

graphx/src/test/scala/org/apache/spark/graphx/impl/EdgePartitionSuite.scala

@@ -22,6 +22,9 @@ import scala.util.Random
 
 import org.scalatest.FunSuite
 
+import org.apache.spark.SparkConf
+import org.apache.spark.serializer.KryoSerializer
+
 import org.apache.spark.graphx._
 
 class EdgePartitionSuite extends FunSuite {
@@ -120,4 +123,19 @@ class EdgePartitionSuite extends FunSuite {
     assert(!ep.isActive(-1))
     assert(ep.numActives == Some(2))
   }
+
+  test("Kryo serialization") {
+    val aList = List((0, 1, 0), (1, 0, 0), (1, 2, 0), (5, 4, 0), (5, 5, 0))
+    val a: EdgePartition[Int, Int] = makeEdgePartition(aList)
+    val conf = new SparkConf()
+      .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
+      .set("spark.kryo.registrator", "org.apache.spark.graphx.GraphKryoRegistrator")
+    val s = new KryoSerializer(conf).newInstance()
+    val aSer: EdgePartition[Int, Int] = s.deserialize(s.serialize(a))
+    assert(aSer.srcIds.toList === a.srcIds.toList)
+    assert(aSer.dstIds.toList === a.dstIds.toList)
+    assert(aSer.data.toList === a.data.toList)
+    assert(aSer.index != null)
+    assert(aSer.vertices.iterator.toSet === a.vertices.iterator.toSet)
+  }
 }