Merge branch 'master' of github.com:amplab/graphx
This commit is contained in:
commit
b3bcfc09c7
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@ -273,9 +273,9 @@ object Analytics extends Logging {
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logInfo("GRAPHX: Number of vertices " + graph.vertices.count)
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logInfo("GRAPHX: Number of edges " + graph.edges.count)
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val pr = Analytics.pagerank(graph, numIter)
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// val pr = if(isDynamic) Analytics.dynamicPagerank(graph, tol, numIter)
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// else Analytics.pagerank(graph, numIter)
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//val pr = Analytics.pagerank(graph, numIter)
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val pr = if(isDynamic) Analytics.deltaPagerank(graph, tol, numIter)
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else Analytics.pagerank(graph, numIter)
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logInfo("GRAPHX: Total rank: " + pr.vertices.map{ case (id,r) => r }.reduce(_+_) )
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if (!outFname.isEmpty) {
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println("Saving pageranks of pages to " + outFname)
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@ -5,6 +5,7 @@ import com.esotericsoftware.kryo.Kryo
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import org.apache.spark.graph.impl.MessageToPartition
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import org.apache.spark.serializer.KryoRegistrator
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import org.apache.spark.graph.impl._
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import scala.collection.mutable.BitSet
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class GraphKryoRegistrator extends KryoRegistrator {
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@ -14,6 +15,7 @@ class GraphKryoRegistrator extends KryoRegistrator {
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kryo.register(classOf[MessageToPartition[Object]])
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kryo.register(classOf[(Vid, Object)])
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kryo.register(classOf[EdgePartition[Object]])
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kryo.register(classOf[BitSet])
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// This avoids a large number of hash table lookups.
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kryo.setReferences(false)
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@ -55,7 +55,6 @@ object GraphLoader {
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private def fromEdges[ED: ClassManifest](edges: RDD[Edge[ED]]): GraphImpl[Int, ED] = {
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val vertices = edges.flatMap { edge => List((edge.srcId, 1), (edge.dstId, 1)) }
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.reduceByKey(_ + _)
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.map{ case (vid, degree) => (vid, degree) }
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GraphImpl(vertices, edges, 0)
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}
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}
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@ -190,7 +190,8 @@ class VertexSetRDD[@specialized V: ClassManifest](
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override def filter(pred: Tuple2[Vid,V] => Boolean): VertexSetRDD[V] = {
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val cleanF = index.rdd.context.clean(pred)
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val newValues = index.rdd.zipPartitions(valuesRDD){
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(keysIter, valuesIter) =>
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(keysIter: Iterator[VertexIdToIndexMap],
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valuesIter: Iterator[(IndexedSeq[V], BitSet)]) =>
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val index = keysIter.next()
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assert(keysIter.hasNext() == false)
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val (oldValues, bs) = valuesIter.next()
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@ -222,7 +223,7 @@ class VertexSetRDD[@specialized V: ClassManifest](
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val cleanF = index.rdd.context.clean(f)
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val newValuesRDD: RDD[ (IndexedSeq[U], BitSet) ] =
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valuesRDD.mapPartitions(iter => iter.map{
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case (values, bs) =>
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case (values, bs: BitSet) =>
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/**
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* @todo Consider using a view rather than creating a new
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* array. This is already being done for join operations.
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@ -255,10 +256,11 @@ class VertexSetRDD[@specialized V: ClassManifest](
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val cleanF = index.rdd.context.clean(f)
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val newValues: RDD[ (IndexedSeq[U], BitSet) ] =
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index.rdd.zipPartitions(valuesRDD){
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(keysIter, valuesIter) =>
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(keysIter: Iterator[VertexIdToIndexMap],
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valuesIter: Iterator[(IndexedSeq[V], BitSet)]) =>
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val index = keysIter.next()
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assert(keysIter.hasNext() == false)
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val (oldValues, bs) = valuesIter.next()
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val (oldValues, bs: BitSet) = valuesIter.next()
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assert(valuesIter.hasNext() == false)
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/**
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* @todo Consider using a view rather than creating a new array.
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@ -296,10 +298,11 @@ class VertexSetRDD[@specialized V: ClassManifest](
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}
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val newValuesRDD: RDD[ (IndexedSeq[(V,W)], BitSet) ] =
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valuesRDD.zipPartitions(other.valuesRDD){
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(thisIter, otherIter) =>
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val (thisValues, thisBS) = thisIter.next()
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(thisIter: Iterator[(IndexedSeq[V], BitSet)],
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otherIter: Iterator[(IndexedSeq[W], BitSet)]) =>
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val (thisValues, thisBS: BitSet) = thisIter.next()
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assert(!thisIter.hasNext)
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val (otherValues, otherBS) = otherIter.next()
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val (otherValues, otherBS: BitSet) = otherIter.next()
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assert(!otherIter.hasNext)
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val newBS = thisBS & otherBS
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val newValues = thisValues.view.zip(otherValues)
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@ -328,11 +331,13 @@ class VertexSetRDD[@specialized V: ClassManifest](
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if(index != other.index) {
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throw new SparkException("A zipJoin can only be applied to RDDs with the same index!")
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}
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val newValuesRDD: RDD[ (IndexedSeq[(V,Option[W])], BitSet) ] = valuesRDD.zipPartitions(other.valuesRDD){
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(thisIter, otherIter) =>
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val (thisValues, thisBS) = thisIter.next()
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val newValuesRDD: RDD[ (IndexedSeq[(V,Option[W])], BitSet) ] =
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valuesRDD.zipPartitions(other.valuesRDD){
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(thisIter: Iterator[(IndexedSeq[V], BitSet)],
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otherIter: Iterator[(IndexedSeq[W], BitSet)]) =>
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val (thisValues, thisBS: BitSet) = thisIter.next()
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assert(!thisIter.hasNext)
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val (otherValues, otherBS) = otherIter.next()
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val (otherValues, otherBS: BitSet) = otherIter.next()
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assert(!otherIter.hasNext)
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val otherOption = otherValues.view.zipWithIndex
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.map{ (x: (W, Int)) => if(otherBS(x._2)) Option(x._1) else None }
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@ -384,7 +389,9 @@ class VertexSetRDD[@specialized V: ClassManifest](
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// Compute the new values RDD
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val newValues: RDD[ (IndexedSeq[(V,Option[W])], BitSet) ] =
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index.rdd.zipPartitions(valuesRDD, otherShuffled) {
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(thisIndexIter, thisIter, tuplesIter) =>
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(thisIndexIter: Iterator[VertexIdToIndexMap],
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thisIter: Iterator[(IndexedSeq[V], BitSet)],
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tuplesIter: Iterator[(Vid,W)]) =>
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// Get the Index and values for this RDD
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val index = thisIndexIter.next()
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assert(!thisIndexIter.hasNext)
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@ -618,10 +625,14 @@ object VertexSetRDD {
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def apply[V: ClassManifest](
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rdd: RDD[(Vid,V)], reduceFunc: (V, V) => V): VertexSetRDD[V] = {
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// Preaggregate and shuffle if necessary
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// Preaggregation.
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val aggregator = new Aggregator[Vid, V, V](v => v, reduceFunc, reduceFunc)
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val partitioner = new HashPartitioner(rdd.partitions.size)
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val preAgg = rdd.mapPartitions(aggregator.combineValuesByKey).partitionBy(partitioner)
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val preAgg = rdd.partitioner match {
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case Some(p) => rdd
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case None =>
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val partitioner = new HashPartitioner(rdd.partitions.size)
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// Preaggregation.
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val aggregator = new Aggregator[Vid, V, V](v => v, reduceFunc, reduceFunc)
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rdd.mapPartitions(aggregator.combineValuesByKey, true).partitionBy(partitioner)
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}
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val groups = preAgg.mapPartitions( iter => {
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val indexMap = new VertexIdToIndexMap()
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@ -80,21 +80,6 @@ object EdgeTripletBuilder {
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}
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// {
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// val iterFun = (iter: Iterator[(Pid, ((VertexIdToIndexMap, Array[VD]), EdgePartition[ED]))]) => {
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// val (pid, ((vidToIndex, vertexArray), edgePartition)) = iter.next()
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// assert(iter.hasNext == false)
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// // Return an iterator that looks up the hash map to find matching
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// // vertices for each edge.
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// new EdgeTripletIterator(vidToIndex, vertexArray, edgePartition)
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// }
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// ClosureCleaner.clean(iterFun)
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// localVidMap.zipJoin(vTableReplicatedValues).zipJoinRDD(eTable)
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// .mapPartitions( iterFun ) // end of map partition
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// }
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// }
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/**
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* A Graph RDD that supports computation on graphs.
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*/
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@ -105,9 +90,6 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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@transient val eTable: RDD[(Pid, EdgePartition[ED])] )
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extends Graph[VD, ED] {
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// def this() = this(null,null,null)
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/**
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* (localVidMap: VertexSetRDD[Pid, VertexIdToIndexMap]) is a version of the
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* vertex data after it is replicated. Within each partition, it holds a map
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@ -127,7 +109,7 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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/** Return a RDD of edges. */
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@transient override val edges: RDD[Edge[ED]] = {
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eTable.mapPartitions { iter => iter.next()._2.iterator }
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eTable.mapPartitions( iter => iter.next()._2.iterator , true )
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}
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@ -136,21 +118,6 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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EdgeTripletBuilder.makeTriplets(localVidMap, vTableReplicatedValues, eTable)
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// {
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// val iterFun = (iter: Iterator[(Pid, (VertexHashMap[VD], EdgePartition[ED]))]) => {
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// val (pid, (vmap, edgePartition)) = iter.next()
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// //assert(iter.hasNext == false)
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// // Return an iterator that looks up the hash map to find matching
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// // vertices for each edge.
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// new EdgeTripletIterator(vmap, edgePartition)
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// }
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// ClosureCleaner.clean(iterFun)
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// vTableReplicated.join(eTable).mapPartitions( iterFun ) // end of map partition
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// }
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override def cache(): Graph[VD, ED] = {
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eTable.cache()
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vid2pid.cache()
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@ -175,6 +142,64 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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}
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/**
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* Display the lineage information for this graph.
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*/
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def printLineage() = {
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def traverseLineage(rdd: RDD[_], indent: String = "", visited: Map[Int, String] = Map.empty[Int, String]) {
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if(visited.contains(rdd.id)) {
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println(indent + visited(rdd.id))
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println(indent)
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} else {
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val locs = rdd.partitions.map( p => rdd.preferredLocations(p) )
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val cacheLevel = rdd.getStorageLevel
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val name = rdd.id
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val deps = rdd.dependencies
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val partitioner = rdd.partitioner
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val numparts = partitioner match { case Some(p) => p.numPartitions; case None => 0}
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println(indent + name + ": " + cacheLevel.description + " (partitioner: " + partitioner + ", " + numparts +")")
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println(indent + " |---> Deps: " + deps.map(d => (d, d.rdd.id) ).toString)
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println(indent + " |---> PrefLoc: " + locs.map(x=> x.toString).mkString(", "))
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deps.foreach(d => traverseLineage(d.rdd, indent + " | ", visited))
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}
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}
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println("eTable ------------------------------------------")
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traverseLineage(eTable, " ")
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var visited = Map(eTable.id -> "eTable")
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println("\n\nvTable.index ------------------------------------")
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traverseLineage(vTable.index.rdd, " ", visited)
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visited += (vTable.index.rdd.id -> "vTable.index")
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println("\n\nvTable.values ------------------------------------")
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traverseLineage(vTable.valuesRDD, " ", visited)
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visited += (vTable.valuesRDD.id -> "vTable.values")
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println("\n\nvTable ------------------------------------------")
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traverseLineage(vTable, " ", visited)
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visited += (vTable.id -> "vTable")
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println("\n\nvid2pid -----------------------------------------")
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traverseLineage(vid2pid, " ", visited)
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visited += (vid2pid.id -> "vid2pid")
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visited += (vid2pid.valuesRDD.id -> "vid2pid.values")
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println("\n\nlocalVidMap -------------------------------------")
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traverseLineage(localVidMap, " ", visited)
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visited += (localVidMap.id -> "localVidMap")
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println("\n\nvTableReplicatedValues --------------------------")
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traverseLineage(vTableReplicatedValues, " ", visited)
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visited += (vTableReplicatedValues.id -> "vTableReplicatedValues")
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println("\n\ntriplets ----------------------------------------")
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traverseLineage(triplets, " ", visited)
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println(visited)
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} // end of print lineage
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override def reverse: Graph[VD, ED] = {
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val newEtable = eTable.mapPartitions( _.map{ case (pid, epart) => (pid, epart.reverse) },
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preservesPartitioning = true)
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@ -213,13 +238,6 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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new GraphImpl(vTable, vid2pid, localVidMap, newETable)
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}
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// override def correctEdges(): Graph[VD, ED] = {
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// val sc = vertices.context
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// val vset = sc.broadcast(vertices.map(_.id).collect().toSet)
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// val newEdges = edges.filter(e => vset.value.contains(e.src) && vset.value.contains(e.dst))
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// Graph(vertices, newEdges)
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// }
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override def subgraph(epred: EdgeTriplet[VD,ED] => Boolean = (x => true),
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vpred: (Vid, VD) => Boolean = ((a,b) => true) ): Graph[VD, ED] = {
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@ -382,16 +400,6 @@ class GraphImpl[VD: ClassManifest, ED: ClassManifest] protected (
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object GraphImpl {
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def apply[VD: ClassManifest, ED: ClassManifest](
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@ -528,28 +536,6 @@ object GraphImpl {
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}.cache()
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// @todo assert edge table has partitioner
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// val localVidMap: VertexSetRDD[Pid, VertexIdToIndexMap] =
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// msgsByPartition.mapPartitionsWithIndex( (pid, iter) => {
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// val vidToIndex = new VertexIdToIndexMap
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// var i = 0
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// for (msg <- iter) {
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// vidToIndex.put(msg.data._1, i)
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// i += 1
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// }
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// Array((pid, vidToIndex)).iterator
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// }, preservesPartitioning = true).indexed(eTable.index)
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// val vTableReplicatedValues: VertexSetRDD[Pid, Array[VD]] =
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// msgsByPartition.mapPartitionsWithIndex( (pid, iter) => {
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// val vertexArray = ArrayBuilder.make[VD]
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// for (msg <- iter) {
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// vertexArray += msg.data._2
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// }
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// Array((pid, vertexArray.result)).iterator
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// }, preservesPartitioning = true).indexed(eTable.index)
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// (localVidMap, vTableReplicatedValues)
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}
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