GraphX: Graph Processing in a Distributed Dataflow Framework

GraphX: Graph Processing in a Distributed Dataflow Framework
Joseph Gonzalez Postdoc, UC-Berkeley AMPLab Co-founder, GraphLab Inc. Joint work with Reynold Xin, Ankur Dave, Daniel Crankshaw, Michael Franklin, and Ion Stoica OSDI 2014 The goal of this project was to distill the essential advances developed in the context of specialized graph processing systems and lift those advances into general purpose distributed dataflow systems unifying graphs and tables and enabling a single system to easily and efficiently support both types of data and span the entire analytics pipeline. To motivate the need for this unified approach to analytics let me begin by illustrating modern analytics pipelines. UC BERKELEY

Modern Analytics Link Table Hyperlinks PageRank Top 20 Pages Raw
Title Link Hyperlinks PageRank Top 20 Pages Title PR Raw Wikipedia < / > XML Top Communities Com. PR.. Discussion Table User Disc. Community Detection User Community Com. Editor Graph

Tables Link Table Hyperlinks PageRank Top 20 Pages Raw Wikipedia
Title Link Hyperlinks PageRank Top 20 Pages Title PR Raw Wikipedia < / > XML Top Communities Com. PR.. Modern analytics involves many stages and many views of data. <Make animation auto + practice shortened versions of second and third path> Build community topic table separtely Discussion Table User Disc. Community Detection User Community Com. Editor Graph

Graphs Link Table Hyperlinks PageRank Top 20 Pages Raw Wikipedia
Title Link Hyperlinks PageRank Top 20 Pages Title PR Raw Wikipedia < / > XML Top Communities Com. PR.. Modern analytics involves many stages and many views of data. <Make animation auto + practice shortened versions of second and third path> Build community topic table separtely Discussion Table User Disc. Community Detection User Community Com. Editor Graph

Separate Systems Tables Graphs

Separate Systems Dataflow Systems Graphs Table Result Row

Separate Systems Dataflow Systems Graph Systems Table Dependency Graph
Result Row Dependency Graph Pregel Add list of papers to bottom of slide

Difficult to Use Users must Learn, Deploy, and Manage multiple systems Leads to brittle and often complex interfaces

Limited reuse internal data-structures across stages
Inefficient Extensive data movement and duplication across the network and file system < / > XML HDFS Limited reuse internal data-structures across stages

GraphX Unifies Computation on Tables and Graphs
Table View Graph View GraphX Spark Dataflow Framework Enabling a single system to easily and efficiently support the entire pipeline

? Separate Systems Dataflow Systems Graph Systems Dependency Graph
Pregel Table Row Row Result Row Row

Separate Systems Dataflow Systems Graph Systems Pregel Table
Dependency Graph Row Row Result Row Row

PageRank on the Live-Journal Graph
? Graphlab vs hadoop speedup Build spark second ----- Meeting Notes (3/21/14 15:09) ----- How many vertices is LJ, Wiki, Twitter? ----- Meeting Notes (3/24/14 20:39) ----- Animate, build in spark x faster than hadoop graphlab x faster than spark ----- Meeting Notes (10/3/14 09:56) ----- Try putting this before these optimizations Hadoop is 60x slower than GraphLab Spark is 16x slower than GraphLab

Distill the lessons learned from specialized graph systems
Key Question How can we naturally express and efficiently execute graph computation in a general purpose dataflow framework? Distill the lessons learned from specialized graph systems

Key Question Representation Optimizations
How can we naturally express and efficiently execute graph computation in a general purpose dataflow framework? Representation Optimizations

Raw Wikipedia Hyperlinks PageRank Top 20 Pages Link Table Editor Graph
< / > XML Hyperlinks PageRank Top 20 Pages Title PR Link Table Link Editor Graph Community Detection User Com. Discussion Table Disc. Top Communities PR..

Example Computation: PageRank
Express computation locally: Iterate until convergence Rank of Page i Weighted sum of neighbors’ ranks Random Reset Prob.

“Think like a Vertex.” - Malewicz et al., SIGMOD’10

Graph-Parallel Pattern
Gonzalez et al. [OSDI’12] Gather information from neighboring vertices

Gonzalez et al. [OSDI’12] Apply an update the vertex property

Gonzalez et al. [OSDI’12] Scatter information to neighboring vertices

Many Graph-Parallel Algorithms
MACHINE LEARNING NETWORK ANALYSIS Collaborative Filtering Community Detection Alternating Least Squares Triangle-Counting Stochastic Gradient Descent K-core Decomposition Tensor Factorization K-Truss Structured Prediction Graph Analytics Loopy Belief Propagation PageRank Max-Product Linear Programs Personalized PageRank Shortest Path Gibbs Sampling Graph Coloring Semi-supervised ML Graph SSL CoEM

Specialized Computational Pattern Specialized Graph Optimizations

Graph System Optimizations
Specialized Data-Structures Vertex-Cuts Partitioning Remote Caching / Mirroring Message Combiners Active Set Tracking ----- Meeting Notes (10/3/14 09:56) ----- Graph System Optimizations Make more crisp vertex-cut to mirror transition The Price we paid to do this was a specialized system. The question is how to make these optimizations work in a generalized.

Representation Optimizations Distributed Join Optimization
Graphs Horizontally Partitioned Tables Join Vertex Programs Dataflow Operators Optimizations Advances in Graph Processing Systems Distributed Join Optimization Materialized View Maintenance

Property Graph Data Model
B C A D F E Property Graph Vertex Property: User Profile Current PageRank Value ----- Meeting Notes (10/3/14 10:02) ----- Add legend for vertex and edge properties. ----- Meeting Notes (10/3/14 10:16) ----- separate structure from properties in our table representation enabling us to reuse structural information while transforming properties. Edge Property: Weights Timestamps

Encoding Property Graphs as Tables
Vertex Table (RDD) Routing Table (RDD) B C D E A F 1 2 Edge Table (RDD) A B C D E F Property Graph Part. 1 Machine 1 Machine 2 B C D E A F B C A D B C A A D D Vertex Cut F E A D ----- Meeting Notes (10/3/14 10:02) ----- Add legend for vertex and edge properties. ----- Meeting Notes (10/3/14 10:16) ----- separate structure from properties in our table representation enabling us to reuse structural information while transforming properties. Part. 2 F E

Separate Properties and Structure
Reuse structural information across multiple graphs Input Graph Transformed Graph Vertex Table Routing Table Edge Routing Table Edge Table Vertex Table Transform Vertex Properties The normalized representation is crucial to being able to support iterative computation as well as having multiple graphs and sub-graphs derived from the same base data.

Table Operators Table operators are inherited from Spark: map filter
groupBy sort union join leftOuterJoin rightOuterJoin reduce count fold reduceByKey groupByKey cogroup cross zip sample take first partitionBy mapWith pipe save ...

Graph Operators (Scala)
class Graph [ V, E ] { def Graph(vertices: Table[ (Id, V) ], edges: Table[ (Id, Id, E) ]) // Table Views def vertices: Table[ (Id, V) ] def edges: Table[ (Id, Id, E) ] def triplets: Table [ ((Id, V), (Id, V), E) ] // Transformations def reverse: Graph[V, E] def subgraph(pV: (Id, V) => Boolean, pE: Edge[V,E] => Boolean): Graph[V,E] def mapV(m: (Id, V) => T ): Graph[T,E] def mapE(m: Edge[V,E] => T ): Graph[V,T] // Joins def joinV(tbl: Table [(Id, T)]): Graph[(V, T), E ] def joinE(tbl: Table [(Id, Id, T)]): Graph[V, (E, T)] // Computation def mrTriplets(mapF: (Edge[V,E]) => List[(Id, T)], reduceF: (T, T) => T): Graph[T, E] } Make mrTriplets more visible. Emphasize how this API blurs distinction between graphs and tables

Graph Operators (Scala)
class Graph [ V, E ] { def Graph(vertices: Table[ (Id, V) ], edges: Table[ (Id, Id, E) ]) // Table Views def vertices: Table[ (Id, V) ] def edges: Table[ (Id, Id, E) ] def triplets: Table [ ((Id, V), (Id, V), E) ] // Transformations def reverse: Graph[V, E] def subgraph(pV: (Id, V) => Boolean, pE: Edge[V,E] => Boolean): Graph[V,E] def mapV(m: (Id, V) => T ): Graph[T,E] def mapE(m: Edge[V,E] => T ): Graph[V,T] // Joins def joinV(tbl: Table [(Id, T)]): Graph[(V, T), E ] def joinE(tbl: Table [(Id, Id, T)]): Graph[V, (E, T)] // Computation def mrTriplets(mapF: (Edge[V,E]) => List[(Id, T)], reduceF: (T, T) => T): Graph[T, E] } capture the Gather-Scatter pattern from specialized graph-processing systems . def mrTriplets(mapF: (Edge[V,E]) => List[(Id, T)], reduceF: (T, T) => T): Graph[T, E]

Triplets Join Vertices and Edges
The triplets operator joins vertices and edges: Vertices B A C D Triplets Edges A B C D A A B B A C B D

Map-Reduce Triplets Map-Reduce triplets collects information about the neighborhood of each vertex: Src. or Dst. MapFunction( )  (B, ) Reduce (B, ) (C, ) (D, ) A B MapFunction( )  (C, ) A C MapFunction( )  (C, ) B C MapFunction( )  (D, ) C D Message Combiners

Using these basic GraphX operators we implemented Pregel and GraphLab in under 50 lines of code!

The GraphX Stack (Lines of Code)
Spark (30,000) Pregel API (34) PageRank (20) Connected Comp. (20) K-core (60) Triangle Count (50) LDA (220) SVD++ (110) The simple set of GraphX operators are capable of expressing not only existing graph processing systems but can also be more convenient to express certain graph algorithms directly. Some algorithms are more naturally expressed using the GraphX primitive operators

Representation Optimizations Distributed Join Optimization
Graphs Horizontally Partitioned Tables Join Vertex Programs Dataflow Operators Optimizations Advances in Graph Processing Systems Distributed Join Optimization Materialized View Maintenance

Join Site Selection using Routing Tables
(RDD) B C D E A F 1 2 Vertex Table (RDD) Edge Table (RDD) Never Shuffle Edges! A B C D E F B C D E A F The routing table is one of the essential ideas GraphX introduces to optimize distributed joins. It is important to note that we never shuffle edges and this can be a big win since the edge table is often orders of magnitude larger than the vertex table.

Caching for Iterative mrTriplets
Vertex Table (RDD) Edge Table (RDD) Mirror Cache A B C D E F A B C D E A F A B C D A Reusable Hash Index Scan B C Mirror Cache D D D E F A E Reusable Hash Index Scan F

Incremental Updates for Triplets View
Vertex Table (RDD) Edge Table (RDD) Mirror Cache A B C D E F Change A A B C D E A F B C D A Change title Mirror Cache D E F A Change E Scan

Aggregation for Iterative mrTriplets
Vertex Table (RDD) Edge Table (RDD) Mirror Cache A B C D E F Change B C D E A F A Local Aggregate B B Change C C D Change Mirror Cache Change A Local Aggregate Change D Scan D E Change F F

Reduction in Communication Due to Cached Updates
Most vertices are within 8 hops of all vertices in their comp.

Benefit of Indexing Active Vertices
Without Active Tracking Active Vertex Tracking

Without Join Elimination
Identify and bypass joins for unused triplet fields Java bytecode inspection Without Join Elimination Join Elimination Better Factor of 2 reduction in communication

Additional Optimizations
Indexing and Bitmaps: To accelerate joins across graphs To efficiently construct sub-graphs Lineage based fault-tolerance Exploits Spark lineage to recover in parallel Eliminates need for costly check-points Substantial Index and Data Reuse: Reuse routing tables across graphs and sub-graphs Reuse edge adjacency information and indices Split Hash Table: reuse key sets across hash tables

System Comparison Goal: Demonstrate that GraphX achieves performance parity with specialized graph- processing systems. Setup: 16 node EC2 Cluster (m2.4xLarge) + 1GigE Compare against GraphLab/PowerGraph (C++), Giraph (Java), & Spark (Java/Scala) 8 GB RAM, 8 Virtual Cores

PageRank Benchmark EC2 Cluster of 16 x m2.4xLarge (8 cores) + 1GigE Twitter Graph (42M Vertices,1.5B Edges) UK-Graph (106M Vertices, 3.7B Edges) 18x 7x Runtime (Seconds) ----- Meeting Notes (10/3/14 10:02) ----- Make GraphX first. GraphX performs comparably to state-of-the-art graph processing systems.

Connected Comp. Benchmark
EC2 Cluster of 16 x m2.4xLarge (8 cores) + 1GigE Twitter Graph (42M Vertices,1.5B Edges) UK-Graph (106M Vertices, 3.7B Edges) 10x 8x Runtime (Seconds) Out-of-Memory GraphX performs comparably to state-of-the-art graph processing systems.

Graphs are just one stage…. What about a pipeline?

A Small Pipeline in GraphX
Raw Wikipedia < / > XML Hyperlinks PageRank Top 20 Pages HDFS Compute Spark Preprocess Spark Post. 1492 605 Also faster in human time but it is hard to measure. 375 342 Timed end-to-end GraphX is the fastest

Adoption and Impact GraphX is now part of Apache Spark
Part of Cloudera Hadoop Distribution In production at Alibaba Taobao Order of magnitude gains over Spark Inspired GraphLab Inc. SFrame technology Unifies Tables & Graphs on Disk

GraphX  Unified Tables and Graphs
New API Blurs the distinction between Tables and Graphs New System Unifies Data-Parallel Graph-Parallel Systems Enabling users to easily and efficiently express the entire analytics pipeline

Integrated Frameworks
What did we Learn? Specialized Systems Integrated Frameworks Graph Systems GraphX

Future Work Specialized Systems Integrated Frameworks Graph Systems GraphX Parameter Server ?

Future Work Specialized Systems Integrated Frameworks Graph Systems GraphX Parameter Server Asynchrony Non-deterministic Shared-State

Thank You http://amplab.cs.berkeley.edu/projects/graphx/
Reynold Xin Ankur Dave Daniel Crankshaw Michael Franklin Ion Stoica

Related Work Specialized Graph-Processing Systems: GraphLab [UAI’10], Pregel [SIGMOD’10], Signal- Collect [ISWC’10], Combinatorial BLAS [IJHPCA’11], GraphChi [OSDI’12], PowerGraph [OSDI’12], Ligra [PPoPP’13], X-Stream [SOSP’13] Alternative to Dataflow framework: Naiad [SOSP’13]: GraphLINQ Hyracks: Pregelix [VLDB’15] Distributed Join Optimization: Multicast Join [Afrati et al., EDBT’10] Semi-Join in MapReduce [Blanas et al., SIGMOD’10] Semi-Join in MapReduce

Edge Files Have Locality
UK-Graph (106M Vertices, 3.7B Edges) GraphLab rebalances the edge-files on-load. Runtime (Seconds) GraphX preserves the on-disk layout through Spark.  Better Vertex-Cut ----- Meeting Notes (10/3/14 10:05) ----- Skip

Scalability Scales slightly better than PowerGraph/GraphLab Runtime
Twitter Graph (42M Vertices,1.5B Edges) Scales slightly better than PowerGraph/GraphLab Runtime GraphX Each node has 8 virtual cores. (Runtime is in 10 iterations) Linear Scaling EC2-Nodes

Apache Spark Dataflow Platform
Zaharia et al., NSDI’12 Resilient Distributed Datasets (RDD): RDD Load Map RDD RDD Reduce HDFS HDFS ----- Meeting Notes (10/3/14 09:56) ----- Replace with standard spark slide

Zaharia et al., NSDI’12 Resilient Distributed Datasets (RDD): Persist in Memory RDD Load Map RDD RDD Reduce HDFS HDFS ----- Meeting Notes (10/3/14 09:56) ----- Switch to standard spark slide. .cache() Optimized for iterative access to data.

PageRank Benchmark EC2 Cluster of 16 x m2.4xLarge Nodes + 1GigE Twitter Graph (42M Vertices,1.5B Edges) UK-Graph (106M Vertices, 3.7B Edges) Runtime (Seconds) ✓ ? ? GraphX performs comparably to state-of-the-art graph processing systems.

Shared Memory Advantage
Spark Shared Nothing Model Core Core Core Core Shuffle Files GraphLab Shared Memory Core Shared De-serialized In-Memory Graph ----- Meeting Notes (10/3/14 10:02) ----- Skip

Shared Memory Advantage
Spark Shared Nothing Model Twitter Graph (42M Vertices,1.5B Edges) Core Core Core Core Shuffle Files Runtime (Seconds) GraphLab No SHM. TCP/IP Core

PageRank Benchmark Twitter Graph (42M Vertices,1.5B Edges) UK-Graph (106M Vertices, 3.7B Edges) GraphX performs comparably to state-of-the-art graph processing systems.

Connected Comp. Benchmark
EC2 Cluster of 16 x m2.4xLarge Nodes + 1GigE Twitter Graph (42M Vertices,1.5B Edges) UK-Graph (106M Vertices, 3.7B Edges) 10x 8x Runtime (Seconds) Out-of-Memory Out-of-Memory GraphX performs comparably to state-of-the-art graph processing systems.

Fault-Tolerance Leverage Spark Fault-Tolerance Mechanism

Graph-Processing Systems
Pregel oogle CombBLAS Kineograph X-Stream GraphChi Ligra GPS Representation Expose specialized API to simplify graph programming.

Vertex-Program Abstraction
Pregel_PageRank(i, messages) : // Receive all the messages total = 0 foreach( msg in messages) : total = total + msg // Update the rank of this vertex R[i] = total // Send new messages to neighbors foreach(j in out_neighbors[i]) : Send msg(R[i]) to vertex j i ----- Meeting Notes (10/3/14 09:56) ----- Might cut this.

The Vertex-Program Abstraction
R[4] * w41 R[3] * w31 R[2] * w21 + GraphLab_PageRank(i) // Compute sum over neighbors total = 0 foreach( j in neighbors(i)): total += R[j] * wji // Update the PageRank R[i] = total 4 1 3 2 Low, Gonzalez, et al. [UAI’10]

Example: Oldest Follower
23 42 Calculate the number of older followers for each user? val olderFollowerAge = graph .mrTriplets( e => // Map if(e.src.age > e.dst.age) { (e.srcId, 1) else { Empty } , (a,b) => a + b // Reduce ) .vertices B C 30 A Cut this slide ----- Meeting Notes (10/3/14 10:02) ----- Polish this slide and go through faster. D E 19 75 F 16

Enhanced Pregel in GraphX
Require Message Combiners pregelPR(i, messageList ): messageSum // Receive all the messages total = 0 foreach( msg in messageList) : total = total + msg messageSum // Update the rank of this vertex R[i] = total combineMsg(a, b): // Compute sum of two messages return a + b Remove Message Computation from the Vertex Program // Send new messages to neighbors foreach(j in out_neighbors[i]) : Send msg(R[i]/E[i,j]) to vertex sendMsg(ij, R[i], R[j], E[i,j]): // Compute single message return msg(R[i]/E[i,j])

PageRank in GraphX // Load and initialize the graph
val graph = GraphBuilder.text(“hdfs://web.txt”) val prGraph = graph.joinVertices(graph.outDegrees) // Implement and Run PageRank val pageRank = prGraph.pregel(initialMessage = 0.0, iter = 10)( (oldV, msgSum) => * msgSum, triplet => triplet.src.pr / triplet.src.deg, (msgA, msgB) => msgA + msgB)

Example Analytics Pipeline
// Load raw data tables val articles = sc.textFile(“hdfs://wiki.xml”).map(xmlParser) val links = articles.flatMap(article => article.outLinks) // Build the graph from tables val graph = new Graph(articles, links) // Run PageRank Algorithm val pr = graph.PageRank(tol = 1.0e-5) // Extract and print the top 20 articles val topArticles = articles.join(pr).top(20).collect for ((article, pageRank) <- topArticles) { println(article.title + ‘\t’ + pageRank) }

Zaharia et al., NSDI’12 Resilient Distributed Datasets (RDD): Persist in Memory RDD Load Map RDD RDD Reduce HDFS HDFS .cache() Lineage: HDFS RDD Reduce Map Load

GraphX: Graph Processing in a Distributed Dataflow Framework

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