diff options
author | Ankur Dave <ankurdave@gmail.com> | 2014-11-10 19:31:52 -0800 |
---|---|---|
committer | Reynold Xin <rxin@databricks.com> | 2014-11-10 19:31:52 -0800 |
commit | 300887bd76c5018bfe396c5d47443be251368359 (patch) | |
tree | 1503e244c4f5b013bca02e6925eb923ec67695c1 /graphx/src/main | |
parent | c764d0ac1c6410ca2dd2558cb6bcbe8ad5f02481 (diff) | |
download | spark-300887bd76c5018bfe396c5d47443be251368359.tar.gz spark-300887bd76c5018bfe396c5d47443be251368359.tar.bz2 spark-300887bd76c5018bfe396c5d47443be251368359.zip |
[SPARK-3649] Remove GraphX custom serializers
As [reported][1] on the mailing list, GraphX throws
```
java.lang.ClassCastException: java.lang.Long cannot be cast to scala.Tuple2
at org.apache.spark.graphx.impl.RoutingTableMessageSerializer$$anon$1$$anon$2.writeObject(Serializers.scala:39)
at org.apache.spark.storage.DiskBlockObjectWriter.write(BlockObjectWriter.scala:195)
at org.apache.spark.util.collection.ExternalSorter.spillToMergeableFile(ExternalSorter.scala:329)
```
when sort-based shuffle attempts to spill to disk. This is because GraphX defines custom serializers for shuffling pair RDDs that assume Spark will always serialize the entire pair object rather than breaking it up into its components. However, the spill code path in sort-based shuffle [violates this assumption][2].
GraphX uses the custom serializers to compress vertex ID keys using variable-length integer encoding. However, since the serializer can no longer rely on the key and value being serialized and deserialized together, performing such encoding would either require writing a tag byte (costly) or maintaining state in the serializer and assuming that serialization calls will alternate between key and value (fragile).
Instead, this PR simply removes the custom serializers. This causes a **10% slowdown** (494 s to 543 s) and **16% increase in per-iteration communication** (2176 MB to 2518 MB) for PageRank (averages across 3 trials, 10 iterations per trial, uk-2007-05 graph, 16 r3.2xlarge nodes).
[1]: http://apache-spark-user-list.1001560.n3.nabble.com/java-lang-ClassCastException-java-lang-Long-cannot-be-cast-to-scala-Tuple2-td13926.html#a14501
[2]: https://github.com/apache/spark/blob/f9d6220c792b779be385f3022d146911a22c2130/core/src/main/scala/org/apache/spark/util/collection/ExternalSorter.scala#L329
Author: Ankur Dave <ankurdave@gmail.com>
Closes #2503 from ankurdave/SPARK-3649 and squashes the following commits:
a49c2ad [Ankur Dave] [SPARK-3649] Remove GraphX custom serializers
Diffstat (limited to 'graphx/src/main')
4 files changed, 6 insertions, 445 deletions
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/VertexRDD.scala b/graphx/src/main/scala/org/apache/spark/graphx/VertexRDD.scala index 2c8b245955..12216d9d33 100644 --- a/graphx/src/main/scala/org/apache/spark/graphx/VertexRDD.scala +++ b/graphx/src/main/scala/org/apache/spark/graphx/VertexRDD.scala @@ -27,8 +27,6 @@ import org.apache.spark.storage.StorageLevel import org.apache.spark.graphx.impl.RoutingTablePartition import org.apache.spark.graphx.impl.ShippableVertexPartition import org.apache.spark.graphx.impl.VertexAttributeBlock -import org.apache.spark.graphx.impl.RoutingTableMessageRDDFunctions._ -import org.apache.spark.graphx.impl.VertexRDDFunctions._ /** * Extends `RDD[(VertexId, VD)]` by ensuring that there is only one entry for each vertex and by @@ -233,7 +231,7 @@ class VertexRDD[@specialized VD: ClassTag]( case _ => this.withPartitionsRDD[VD3]( partitionsRDD.zipPartitions( - other.copartitionWithVertices(this.partitioner.get), preservesPartitioning = true) { + other.partitionBy(this.partitioner.get), preservesPartitioning = true) { (partIter, msgs) => partIter.map(_.leftJoin(msgs)(f)) } ) @@ -277,7 +275,7 @@ class VertexRDD[@specialized VD: ClassTag]( case _ => this.withPartitionsRDD( partitionsRDD.zipPartitions( - other.copartitionWithVertices(this.partitioner.get), preservesPartitioning = true) { + other.partitionBy(this.partitioner.get), preservesPartitioning = true) { (partIter, msgs) => partIter.map(_.innerJoin(msgs)(f)) } ) @@ -297,7 +295,7 @@ class VertexRDD[@specialized VD: ClassTag]( */ def aggregateUsingIndex[VD2: ClassTag]( messages: RDD[(VertexId, VD2)], reduceFunc: (VD2, VD2) => VD2): VertexRDD[VD2] = { - val shuffled = messages.copartitionWithVertices(this.partitioner.get) + val shuffled = messages.partitionBy(this.partitioner.get) val parts = partitionsRDD.zipPartitions(shuffled, true) { (thisIter, msgIter) => thisIter.map(_.aggregateUsingIndex(msgIter, reduceFunc)) } @@ -371,7 +369,7 @@ object VertexRDD { def apply[VD: ClassTag](vertices: RDD[(VertexId, VD)]): VertexRDD[VD] = { val vPartitioned: RDD[(VertexId, VD)] = vertices.partitioner match { case Some(p) => vertices - case None => vertices.copartitionWithVertices(new HashPartitioner(vertices.partitions.size)) + case None => vertices.partitionBy(new HashPartitioner(vertices.partitions.size)) } val vertexPartitions = vPartitioned.mapPartitions( iter => Iterator(ShippableVertexPartition(iter)), @@ -412,7 +410,7 @@ object VertexRDD { ): VertexRDD[VD] = { val vPartitioned: RDD[(VertexId, VD)] = vertices.partitioner match { case Some(p) => vertices - case None => vertices.copartitionWithVertices(new HashPartitioner(vertices.partitions.size)) + case None => vertices.partitionBy(new HashPartitioner(vertices.partitions.size)) } val routingTables = createRoutingTables(edges, vPartitioned.partitioner.get) val vertexPartitions = vPartitioned.zipPartitions(routingTables, preservesPartitioning = true) { @@ -454,7 +452,7 @@ object VertexRDD { .setName("VertexRDD.createRoutingTables - vid2pid (aggregation)") val numEdgePartitions = edges.partitions.size - vid2pid.copartitionWithVertices(vertexPartitioner).mapPartitions( + vid2pid.partitionBy(vertexPartitioner).mapPartitions( iter => Iterator(RoutingTablePartition.fromMsgs(numEdgePartitions, iter)), preservesPartitioning = true) } diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/MessageToPartition.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/MessageToPartition.scala deleted file mode 100644 index 714f3b81c9..0000000000 --- a/graphx/src/main/scala/org/apache/spark/graphx/impl/MessageToPartition.scala +++ /dev/null @@ -1,50 +0,0 @@ -/* - * Licensed to the Apache Software Foundation (ASF) under one or more - * contributor license agreements. See the NOTICE file distributed with - * this work for additional information regarding copyright ownership. - * The ASF licenses this file to You under the Apache License, Version 2.0 - * (the "License"); you may not use this file except in compliance with - * the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.apache.spark.graphx.impl - -import scala.language.implicitConversions -import scala.reflect.{classTag, ClassTag} - -import org.apache.spark.Partitioner -import org.apache.spark.graphx.{PartitionID, VertexId} -import org.apache.spark.rdd.{ShuffledRDD, RDD} - - -private[graphx] -class VertexRDDFunctions[VD: ClassTag](self: RDD[(VertexId, VD)]) { - def copartitionWithVertices(partitioner: Partitioner): RDD[(VertexId, VD)] = { - val rdd = new ShuffledRDD[VertexId, VD, VD](self, partitioner) - - // Set a custom serializer if the data is of int or double type. - if (classTag[VD] == ClassTag.Int) { - rdd.setSerializer(new IntAggMsgSerializer) - } else if (classTag[VD] == ClassTag.Long) { - rdd.setSerializer(new LongAggMsgSerializer) - } else if (classTag[VD] == ClassTag.Double) { - rdd.setSerializer(new DoubleAggMsgSerializer) - } - rdd - } -} - -private[graphx] -object VertexRDDFunctions { - implicit def rdd2VertexRDDFunctions[VD: ClassTag](rdd: RDD[(VertexId, VD)]) = { - new VertexRDDFunctions(rdd) - } -} 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 b27485953f..7a7fa91aad 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 @@ -30,24 +30,6 @@ import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap import org.apache.spark.graphx.impl.RoutingTablePartition.RoutingTableMessage private[graphx] -class RoutingTableMessageRDDFunctions(self: RDD[RoutingTableMessage]) { - /** Copartition an `RDD[RoutingTableMessage]` with the vertex RDD with the given `partitioner`. */ - def copartitionWithVertices(partitioner: Partitioner): RDD[RoutingTableMessage] = { - new ShuffledRDD[VertexId, Int, Int]( - self, partitioner).setSerializer(new RoutingTableMessageSerializer) - } -} - -private[graphx] -object RoutingTableMessageRDDFunctions { - import scala.language.implicitConversions - - implicit def rdd2RoutingTableMessageRDDFunctions(rdd: RDD[RoutingTableMessage]) = { - new RoutingTableMessageRDDFunctions(rdd) - } -} - -private[graphx] object RoutingTablePartition { /** * A message from an edge partition to a vertex specifying the position in which the edge diff --git a/graphx/src/main/scala/org/apache/spark/graphx/impl/Serializers.scala b/graphx/src/main/scala/org/apache/spark/graphx/impl/Serializers.scala deleted file mode 100644 index 3909efcdfc..0000000000 --- a/graphx/src/main/scala/org/apache/spark/graphx/impl/Serializers.scala +++ /dev/null @@ -1,369 +0,0 @@ -/* - * Licensed to the Apache Software Foundation (ASF) under one or more - * contributor license agreements. See the NOTICE file distributed with - * this work for additional information regarding copyright ownership. - * The ASF licenses this file to You under the Apache License, Version 2.0 - * (the "License"); you may not use this file except in compliance with - * the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.apache.spark.graphx.impl - -import scala.language.existentials - -import java.io.{EOFException, InputStream, OutputStream} -import java.nio.ByteBuffer - -import scala.reflect.ClassTag - -import org.apache.spark.serializer._ - -import org.apache.spark.graphx._ -import org.apache.spark.graphx.impl.RoutingTablePartition.RoutingTableMessage - -private[graphx] -class RoutingTableMessageSerializer extends Serializer with Serializable { - override def newInstance(): SerializerInstance = new ShuffleSerializerInstance { - - override def serializeStream(s: OutputStream): SerializationStream = - new ShuffleSerializationStream(s) { - def writeObject[T: ClassTag](t: T): SerializationStream = { - val msg = t.asInstanceOf[RoutingTableMessage] - writeVarLong(msg._1, optimizePositive = false) - writeInt(msg._2) - this - } - } - - override def deserializeStream(s: InputStream): DeserializationStream = - new ShuffleDeserializationStream(s) { - override def readObject[T: ClassTag](): T = { - val a = readVarLong(optimizePositive = false) - val b = readInt() - (a, b).asInstanceOf[T] - } - } - } -} - -private[graphx] -class VertexIdMsgSerializer extends Serializer with Serializable { - override def newInstance(): SerializerInstance = new ShuffleSerializerInstance { - - override def serializeStream(s: OutputStream) = new ShuffleSerializationStream(s) { - def writeObject[T: ClassTag](t: T) = { - val msg = t.asInstanceOf[(VertexId, _)] - writeVarLong(msg._1, optimizePositive = false) - this - } - } - - override def deserializeStream(s: InputStream) = new ShuffleDeserializationStream(s) { - override def readObject[T: ClassTag](): T = { - (readVarLong(optimizePositive = false), null).asInstanceOf[T] - } - } - } -} - -/** A special shuffle serializer for AggregationMessage[Int]. */ -private[graphx] -class IntAggMsgSerializer extends Serializer with Serializable { - override def newInstance(): SerializerInstance = new ShuffleSerializerInstance { - - override def serializeStream(s: OutputStream) = new ShuffleSerializationStream(s) { - def writeObject[T: ClassTag](t: T) = { - val msg = t.asInstanceOf[(VertexId, Int)] - writeVarLong(msg._1, optimizePositive = false) - writeUnsignedVarInt(msg._2) - this - } - } - - override def deserializeStream(s: InputStream) = new ShuffleDeserializationStream(s) { - override def readObject[T: ClassTag](): T = { - val a = readVarLong(optimizePositive = false) - val b = readUnsignedVarInt() - (a, b).asInstanceOf[T] - } - } - } -} - -/** A special shuffle serializer for AggregationMessage[Long]. */ -private[graphx] -class LongAggMsgSerializer extends Serializer with Serializable { - override def newInstance(): SerializerInstance = new ShuffleSerializerInstance { - - override def serializeStream(s: OutputStream) = new ShuffleSerializationStream(s) { - def writeObject[T: ClassTag](t: T) = { - val msg = t.asInstanceOf[(VertexId, Long)] - writeVarLong(msg._1, optimizePositive = false) - writeVarLong(msg._2, optimizePositive = true) - this - } - } - - override def deserializeStream(s: InputStream) = new ShuffleDeserializationStream(s) { - override def readObject[T: ClassTag](): T = { - val a = readVarLong(optimizePositive = false) - val b = readVarLong(optimizePositive = true) - (a, b).asInstanceOf[T] - } - } - } -} - -/** A special shuffle serializer for AggregationMessage[Double]. */ -private[graphx] -class DoubleAggMsgSerializer extends Serializer with Serializable { - override def newInstance(): SerializerInstance = new ShuffleSerializerInstance { - - override def serializeStream(s: OutputStream) = new ShuffleSerializationStream(s) { - def writeObject[T: ClassTag](t: T) = { - val msg = t.asInstanceOf[(VertexId, Double)] - writeVarLong(msg._1, optimizePositive = false) - writeDouble(msg._2) - this - } - } - - override def deserializeStream(s: InputStream) = new ShuffleDeserializationStream(s) { - def readObject[T: ClassTag](): T = { - val a = readVarLong(optimizePositive = false) - val b = readDouble() - (a, b).asInstanceOf[T] - } - } - } -} - -//////////////////////////////////////////////////////////////////////////////// -// Helper classes to shorten the implementation of those special serializers. -//////////////////////////////////////////////////////////////////////////////// - -private[graphx] -abstract class ShuffleSerializationStream(s: OutputStream) extends SerializationStream { - // The implementation should override this one. - def writeObject[T: ClassTag](t: T): SerializationStream - - def writeInt(v: Int) { - s.write(v >> 24) - s.write(v >> 16) - s.write(v >> 8) - s.write(v) - } - - def writeUnsignedVarInt(value: Int) { - if ((value >>> 7) == 0) { - s.write(value.toInt) - } else if ((value >>> 14) == 0) { - s.write((value & 0x7F) | 0x80) - s.write(value >>> 7) - } else if ((value >>> 21) == 0) { - s.write((value & 0x7F) | 0x80) - s.write(value >>> 7 | 0x80) - s.write(value >>> 14) - } else if ((value >>> 28) == 0) { - s.write((value & 0x7F) | 0x80) - s.write(value >>> 7 | 0x80) - s.write(value >>> 14 | 0x80) - s.write(value >>> 21) - } else { - s.write((value & 0x7F) | 0x80) - s.write(value >>> 7 | 0x80) - s.write(value >>> 14 | 0x80) - s.write(value >>> 21 | 0x80) - s.write(value >>> 28) - } - } - - def writeVarLong(value: Long, optimizePositive: Boolean) { - val v = if (!optimizePositive) (value << 1) ^ (value >> 63) else value - if ((v >>> 7) == 0) { - s.write(v.toInt) - } else if ((v >>> 14) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7).toInt) - } else if ((v >>> 21) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14).toInt) - } else if ((v >>> 28) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21).toInt) - } else if ((v >>> 35) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21 | 0x80).toInt) - s.write((v >>> 28).toInt) - } else if ((v >>> 42) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21 | 0x80).toInt) - s.write((v >>> 28 | 0x80).toInt) - s.write((v >>> 35).toInt) - } else if ((v >>> 49) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21 | 0x80).toInt) - s.write((v >>> 28 | 0x80).toInt) - s.write((v >>> 35 | 0x80).toInt) - s.write((v >>> 42).toInt) - } else if ((v >>> 56) == 0) { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21 | 0x80).toInt) - s.write((v >>> 28 | 0x80).toInt) - s.write((v >>> 35 | 0x80).toInt) - s.write((v >>> 42 | 0x80).toInt) - s.write((v >>> 49).toInt) - } else { - s.write(((v & 0x7F) | 0x80).toInt) - s.write((v >>> 7 | 0x80).toInt) - s.write((v >>> 14 | 0x80).toInt) - s.write((v >>> 21 | 0x80).toInt) - s.write((v >>> 28 | 0x80).toInt) - s.write((v >>> 35 | 0x80).toInt) - s.write((v >>> 42 | 0x80).toInt) - s.write((v >>> 49 | 0x80).toInt) - s.write((v >>> 56).toInt) - } - } - - def writeLong(v: Long) { - s.write((v >>> 56).toInt) - s.write((v >>> 48).toInt) - s.write((v >>> 40).toInt) - s.write((v >>> 32).toInt) - s.write((v >>> 24).toInt) - s.write((v >>> 16).toInt) - s.write((v >>> 8).toInt) - s.write(v.toInt) - } - - def writeDouble(v: Double): Unit = writeLong(java.lang.Double.doubleToLongBits(v)) - - override def flush(): Unit = s.flush() - - override def close(): Unit = s.close() -} - -private[graphx] -abstract class ShuffleDeserializationStream(s: InputStream) extends DeserializationStream { - // The implementation should override this one. - def readObject[T: ClassTag](): T - - def readInt(): Int = { - val first = s.read() - if (first < 0) throw new EOFException - (first & 0xFF) << 24 | (s.read() & 0xFF) << 16 | (s.read() & 0xFF) << 8 | (s.read() & 0xFF) - } - - def readUnsignedVarInt(): Int = { - var value: Int = 0 - var i: Int = 0 - def readOrThrow(): Int = { - val in = s.read() - if (in < 0) throw new EOFException - in & 0xFF - } - var b: Int = readOrThrow() - while ((b & 0x80) != 0) { - value |= (b & 0x7F) << i - i += 7 - if (i > 35) throw new IllegalArgumentException("Variable length quantity is too long") - b = readOrThrow() - } - value | (b << i) - } - - def readVarLong(optimizePositive: Boolean): Long = { - def readOrThrow(): Int = { - val in = s.read() - if (in < 0) throw new EOFException - in & 0xFF - } - var b = readOrThrow() - var ret: Long = b & 0x7F - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F) << 7 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F) << 14 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F) << 21 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F).toLong << 28 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F).toLong << 35 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F).toLong << 42 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= (b & 0x7F).toLong << 49 - if ((b & 0x80) != 0) { - b = readOrThrow() - ret |= b.toLong << 56 - } - } - } - } - } - } - } - } - if (!optimizePositive) (ret >>> 1) ^ -(ret & 1) else ret - } - - def readLong(): Long = { - val first = s.read() - if (first < 0) throw new EOFException() - (first.toLong << 56) | - (s.read() & 0xFF).toLong << 48 | - (s.read() & 0xFF).toLong << 40 | - (s.read() & 0xFF).toLong << 32 | - (s.read() & 0xFF).toLong << 24 | - (s.read() & 0xFF) << 16 | - (s.read() & 0xFF) << 8 | - (s.read() & 0xFF) - } - - def readDouble(): Double = java.lang.Double.longBitsToDouble(readLong()) - - override def close(): Unit = s.close() -} - -private[graphx] sealed trait ShuffleSerializerInstance extends SerializerInstance { - - override def serialize[T: ClassTag](t: T): ByteBuffer = throw new UnsupportedOperationException - - override def deserialize[T: ClassTag](bytes: ByteBuffer): T = - throw new UnsupportedOperationException - - override def deserialize[T: ClassTag](bytes: ByteBuffer, loader: ClassLoader): T = - throw new UnsupportedOperationException - - // The implementation should override the following two. - override def serializeStream(s: OutputStream): SerializationStream - override def deserializeStream(s: InputStream): DeserializationStream -} |