diff options
12 files changed, 49 insertions, 26 deletions
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 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") ++ |