From 0e2bde2030f8e455c5a269fc38d4ff05b395ca32 Mon Sep 17 00:00:00 2001
From: Ankur Dave <ankurdave@gmail.com>
Date: Mon, 12 May 2014 13:05:24 -0700
Subject: [PATCH] SPARK-1786: Reopening PR 724
Addressing issue in MimaBuild.scala.
Author: Ankur Dave <ankurdave@gmail.com>
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>
Closes #742 from jegonzal/edge_partition_serialization and squashes the following commits:
8ba6e0d [Ankur Dave] Add concatenation operators to MimaBuild.scala
cb2ed3a [Joseph E. Gonzalez] addressing missing exclusion in MimaBuild.scala
5d27824 [Ankur Dave] Disable reference tracking to fix serialization test
c0a9ae5 [Ankur Dave] Add failing test for EdgePartition Kryo serialization
a4a3faa [Joseph E. Gonzalez] Making EdgePartition serializable.
---
.../spark/graphx/GraphKryoRegistrator.scala | 9 ++++++---
.../spark/graphx/impl/EdgePartition.scala | 14 +++++++-------
.../graphx/impl/EdgePartitionBuilder.scala | 4 ++--
.../graphx/impl/EdgeTripletIterator.scala | 2 +-
.../graphx/impl/RoutingTablePartition.scala | 4 ++--
.../graphx/impl/ShippableVertexPartition.scala | 2 +-
.../spark/graphx/impl/VertexPartition.scala | 2 +-
.../graphx/impl/VertexPartitionBase.scala | 6 +++---
.../graphx/impl/VertexPartitionBaseOps.scala | 4 ++--
...ala => GraphXPrimitiveKeyOpenHashMap.scala} | 2 +-
.../spark/graphx/impl/EdgePartitionSuite.scala | 18 ++++++++++++++++++
project/MimaBuild.scala | 8 +++++---
12 files changed, 49 insertions(+), 26 deletions(-)
rename graphx/src/main/scala/org/apache/spark/graphx/util/collection/{PrimitiveKeyOpenHashMap.scala => GraphXPrimitiveKeyOpenHashMap.scala} (98%)
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala b/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala
index d295d0127a..f97f329c0e 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala
+++ b/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]])
}
}
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartition.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartition.scala
index 871e81f8d2..a5c9cd1f8b 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartition.scala
+++ b/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. */
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartitionBuilder.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartitionBuilder.scala
index ecb49bef42..4520beb991 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgePartitionBuilder.scala
+++ b/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) {
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgeTripletIterator.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgeTripletIterator.scala
index ebb0b9418d..56f79a7097 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/EdgeTripletIterator.scala
+++ b/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
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/RoutingTablePartition.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/RoutingTablePartition.scala
index 927e32ad0f..d02e9238ad 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/RoutingTablePartition.scala
+++ b/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)
}
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/ShippableVertexPartition.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/ShippableVertexPartition.scala
index f4e221d4e0..dca54b8a7d 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/ShippableVertexPartition.scala
+++ b/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]
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartition.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartition.scala
index f1d174720a..55c7a19d1b 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartition.scala
+++ b/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. */
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBase.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBase.scala
index 8d9e0204d2..34939b2444 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBase.scala
+++ b/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)
}
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBaseOps.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBaseOps.scala
index 21ff615fec..a4f769b294 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/impl/VertexPartitionBaseOps.scala
+++ b/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)
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/util/collection/PrimitiveKeyOpenHashMap.scala b/graphx/src/main/scala/org/apache/spark/graphx/util/collection/GraphXPrimitiveKeyOpenHashMap.scala
similarity index 98%
rename from graphx/src/main/scala/org/apache/spark/graphx/util/collection/PrimitiveKeyOpenHashMap.scala
rename to graphx/src/main/scala/org/apache/spark/graphx/util/collection/GraphXPrimitiveKeyOpenHashMap.scala
index 7b02e2ed1a..57b01b6f2e 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/util/collection/PrimitiveKeyOpenHashMap.scala
+++ b/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)]
diff --git a/graphx/src/test/scala/org/apache/spark/graphx/impl/EdgePartitionSuite.scala b/graphx/src/test/scala/org/apache/spark/graphx/impl/EdgePartitionSuite.scala
index d2e0c01bc3..28fd112f2b 100644
--- a/graphx/src/test/scala/org/apache/spark/graphx/impl/EdgePartitionSuite.scala
+++ b/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)
+ }
}
diff --git a/project/MimaBuild.scala b/project/MimaBuild.scala
index fafc9b36a7..e147be7dda 100644
--- a/project/MimaBuild.scala
+++ b/project/MimaBuild.scala
@@ -30,7 +30,7 @@ object MimaBuild {
// Read package-private excludes from file
val excludeFilePath = (base.getAbsolutePath + "/.mima-excludes")
- val excludeFile = file(excludeFilePath)
+ val excludeFile = file(excludeFilePath)
val packagePrivateList: Seq[String] =
if (!excludeFile.exists()) {
Seq()
@@ -41,10 +41,10 @@ object MimaBuild {
// Exclude a single class and its corresponding object
def excludeClass(className: String) = {
Seq(
- excludePackage(className),
+ excludePackage(className),
ProblemFilters.exclude[MissingClassProblem](className),
ProblemFilters.exclude[MissingTypesProblem](className),
- excludePackage(className + "$"),
+ excludePackage(className + "$"),
ProblemFilters.exclude[MissingClassProblem](className + "$"),
ProblemFilters.exclude[MissingTypesProblem](className + "$")
)
@@ -78,6 +78,8 @@ object MimaBuild {
excludeSparkClass("graphx.VertexRDD") ++
excludeSparkClass("graphx.impl.GraphImpl") ++
excludeSparkClass("graphx.impl.RoutingTable") ++
+ excludeSparkClass("graphx.util.collection.PrimitiveKeyOpenHashMap") ++
+ excludeSparkClass("graphx.util.collection.GraphXPrimitiveKeyOpenHashMap") ++
excludeSparkClass("mllib.recommendation.MFDataGenerator") ++
excludeSparkClass("mllib.optimization.SquaredGradient") ++
excludeSparkClass("mllib.regression.RidgeRegressionWithSGD") ++
--
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