differentiated graph computation and partitioning on skewed graphs rong chen, jiaxin shi, yanzhe...

Differentiated Graph Computation and Partitioning on Skewed Graphs

Rong Chen, JiaXin Shi, Yanzhe Chen, and Haibo Chen

Institute of Parallel and Distributed SystemsShanghai Jiao Tong University

http://ipads.se.sjtu.edu.cn/projects/powerlyra.html

2014

PowerLyra

J

R Y

HB

H


Big Data Everywhere100 Hrs of

Video every minute

1.11 Billion Users

6 Billion Photos400 Million

Tweets/day

How do we understand and use Big Data?

Big Data Big Learning100 Hrs of

Video every minute

1.11 Billion Users

6 Billion Photos400 Million

Tweets/day

NLP

Big Learning: machine learning and data mining on

Big Data

It’s all about the graphs …

Example Algorithms

PageRank (Centrality Measures)

α is the random reset probabilityL[j] is the number of links on page j

𝑹 [𝟏 ]=0.15+0.85(𝑹 [𝟑 ]+ 13𝑹 [𝟒 ]+ 1

2𝑹[𝟓])

2 4

3 1 5

iterate until convergence

example:

http://ilpubs.stanford.edu:8090/422/1/1999-66.pdf

http://ilpubs.stanford.edu:8090/422/1/1999-66.pdf

Background: Graph Algorithms

IterativeComputation

DependentData

LocalAccesses

2 4

3 1 5

2 4

3 1 5

2 4

3 1 5

Coding graph algorithms as vertex-centric programs to process vertices in parallel and communicate along edges

"Think as a Vertex" philosophy

Think as a Vertex

1. aggregate value of neighbors2. update itself value3. activate neighbors

compute(v): double sum = 0 double value, last = v.get () foreach (n in v.in_nbrs) sum += n.value / n.nedges; value = 0.15 + 0.85 * sum;

v.set (value);

activate (v.out_nbrs);

Example: PageRank

1

2

3

AlgorithmImpl. compute() for vertex

Graph in Real World

Hallmark Property : Skewed power-law degree distributions

“most vertices have relatively few neighbors while a few have many neighbors”

cou

nt

degree

Low Degree Vertex

High Degree Vertex

Twitter Following Graph:1% of the vertices are adjacent to nearly half of the edges

star-like motif

Existing Graph Modelssampl

e graph

Graph Placement Comp. Pattern

Comm. CostDynamic Comp.

Load Balance

edge-cuts local

≤ #edge-cutsnono

edge-cuts local≤ 2 x

#mirrorsyesno

vertex-cuts distributed

≤ 5 x #mirrors

yesyes

Computation Model Pregel GraphLab PowerGraph

A B

A B

Pregel GraphLab

PowerGraph

A

B

A

B

x5

A

B

A

B

x2mirrormaste

r

Existing Graph Cuts

14 2

3

6

5

1 2

6

5

14 2

3

6

14 2

3 5 14 2

65 1 2

3

6

5

14 2

6

1

26

5

14

36

Edge-cut

Vertex-cut

master

mirror

dup.edge

flying maste

r

randomgreedy

imbalance

partition λ ingress runtimeRandom 16.0 263 94.2

Coordinated 5.5 391 33.7

Oblivious 12.8 289 75.3

Grid 8.9 138 43.6

Issues of Graph Partitioning

Edge-cut: Imbalance & replicated edges

Vertex-cut: do not exploit locality□ Random: high replication factor*□ Greedy: long ingress time, unfair to low-degree

vertex□ Constrained: imbalance, poor placement of low-

vertex

∗𝑟𝑒𝑝𝑙𝑖𝑐𝑎𝑡𝑖𝑜𝑛 𝑓𝑎𝑐𝑡𝑜𝑟：𝜆=

¿𝑟𝑒𝑝𝑙𝑖𝑐𝑎𝑡𝑖𝑜𝑛𝑠¿ 𝑣𝑒𝑟𝑡𝑖𝑐𝑒𝑠

Twitter Follower Graph 48 machines, |V|=42M |E|=1.47B

Principle of PowerLyra

Differentiated Graph Computation and Partitioning

The vitally important challenges associated to

the performance of distributed computation system

1. How to make resource locally accessible?2. How to evenly parallelize workloads?

Conflict

High-degree vertex Parallelism

Low-degree vertex LocalityOne

Size fit

All

Computation Model

High-degree vertex□ Goal: exploit parallelism□ Follow GAS model [PowerGraph OSDI’12]

“Gather Apply Scatter”compute (v) double sum = 0 double value, last = v.get () foreach (n in v.in_nbrs) sum += n.value / n.nedges; value = 0.15 + 0.85 * sum;

v.set (value);

activate (v.out_nbrs);

gather (n): return n.value / n.nedges;

scatter (v) activate (v.out_nbrs);

apply (v, acc): value = 0.15 + 0.85 * acc; v.set (value);

Computation Model

High-degree vertex□ Goal: exploit parallelism□ Follow GAS model [PowerGraph OSDI’12]

H HGather

master mirrorscall gather()master mirrors

1

2

Scattermaster mirrorscall scatter()master mirrors

4

5

Applycall apply()

master mirrors

3

1

2

3

4

5

Gather

Scatter

Apply

Gather

Scatter

Computation Model

Low-degree vertex□ Goal: exploit locality□ One direction locality (avoid replicated

edges)□ Local gather + distributed scatter□ Comm. Cost : ≤ 1 x #mirrors

L L

Gather call gather()

Scatter call scatter()

Applycall apply()

master mirrors

11

Gather

Scatter

Apply

Scatter

Observation: most algorithms only gather or scatter in one

direction(e.g., PageRank: G/IN and

S/OUT)

All of in-edges

e.g., PageRank: Gather/IN & Scatter/OUT

Computation Model

Generality□ Algorithm gather or scatter in two directions□ Adaptive degradation for gathering or scattering□ Easily check in runtime without overhead

(user has explicitly defined access direction in code)

L L1

Gather

Scatter

Apply

Gather

Scatter

e.g., Gather/IN & Scatter/ALL Type Gather Scatter Ex.

InIN/NONE

OUT/NONE PR

OutOUT/ NONE

IN/NONE DIA

Other ANY ANY LBP

2

1. Lower replication factor2. One direction locality3. Efficiency

(ingress/runtime)4. Balance (#edge)5. Fewer flying master

partition λ ingress runtime

Random 11.7 35.5 14.71

Coordinated 4.8 32.0 6.85

Oblivious 8.3 36.4 11.70

Grid 8.4 21.4 7.30

Low-cut 3.9 15.0 2.26

Synthetic Regular Graph*48 machines, |V|=10M |E|=93M

Graph Partitioning

Low-degree vertex□ Place one direction edges (e.g., in-edges) of a

vertex to its hash-based machine

□ Simple, but Best !

*https://github.com/graphlab-code/graphlab/blob/master/src/graphlab/graph/distributed_graph.hpp

https://github.com/graphlab-code/graphlab/blob/master/src/graphlab/graph/distributed_graph.hpp





Graph Partitioning

High-degree vertex□ Distribute edges (e.g., in-edges) according to

another endpoint vertex (e.g., source)□ The upper bound of replications imported by

placing all edges belonged to high-degree vertex is #machines

low-masterlow-mirror

high-masterhigh-mirror

Existing Vertex-cut

Low-degree mirror

Graph Partitioning

High-degree vertex□ Distribute edges (e.g., in-edges) according to

another endpoint vertex (e.g., source)□ The upper bound of replications imported by

placing all edges belonged to high-degree vertex is #machines

low-masterlow-mirror

high-masterhigh-mirror

High-cut

Graph Partitioning

Hybrid vertex-cut□ User defined threshold (θ) and the direction of

locality□ Group edges in hash-based machine of vertex□ Low-cut: done! / High-cut: re-assignment

14 25 3

6

14 15

2 13

14

3

1 2

5 1 23

6

group

reassign

construct

e.g., θ =3 ， IN

Heuristic for Hybrid-cut

Inspired by heuristic for edge-cut□ choose best master location of vertex

according to neighboring has located□ Consider one direction neighbors is enough□ Only apply to low-degree vertices□ Parallel ingress: periodically synchronize

private mapping-table (global vertex-id machine)

Optimization

Challenge: graph computation usually exhibits poor data access (cache) locality*□ irregular traversal of neighboring vertices along

edges

How about (cache) locality in communication?□ Problem: a mismatch of orders btw. sender &

receiver

*LUMSDAINE et al. Challenges in parallel graph processing. 2007

4

1 7

2 53

Locality-conscious Layout

General Idea: match orders by hybrid vertex-cut□ Tradeoff: ingress time vs. runtime□ Decentralized matching global vertex-id

9 86 2Low-master

high-mirrorHigh-master

low-mirror

4

35 4

5

72 6 1 8

2 6 1 8 3 9 7

4 9 8 6 2 5 1 9Zoning

M1

M2

M3

M1

M2

M3

H2 L2 h-mrr l-mrr

H3 L3 h-mrr l-mrr

H1 L1 h-mrr l-mrrZ1 Z2 Z3 Z4

8

15

52

8

4 371 6 8

2 6 4 3 9 7

9 3 1 2 5 46


General Idea: match orders by hybrid vertex-cut□ Tradeoff: ingress time vs. runtime□ Decentralized algorithm global vertex-id

9 86 2Low-master


low-mirror

Grouping

M1

M2

M3

M1

M2

M3 8

15

52

8

4 371 6 8

2 6 4 3 9 7

9 3 1 2 5 46

8

65

82

8

4 371 6 5

2 1 4 7 9 3

9 3 1 2 4 56

H2 L2 h1 h3 l1 l3

H3 L3 h1 h2 l1 l2

H1 L1 h2 h3 l2 l3

H2 L2 h-mrr l-mrr

H3 L3 h-mrr l-mrr

H1 L1 h-mrr l-mrrZ1 Z2 Z3 Z4



9 86 2Low-master


low-mirror

Sorting

M1

M2

M3

M1

M2

M3 5

65

52

8

7 341 6 8

2 1 4 7 3 9

3 9 1 2 4 86

8

65

82

8

4 371 6 5

2 1 4 7 9 3

9 3 1 2 4 56

H2 L2 h1 h3 l1 l3

H3 L3 h1 h2 l1 l2

H1 L1 h2 h3 l2 l3

H2 L2 h1 h3 l1 l3

H3 L3 h1 h2 l1 l2

H1 L1 h2 h3 l2 l3



9 86 2Low-master


low-mirror

Rolling

M1

M2

M3

M1

M2

M3 5

65

52

8

7 341 6 8

2 1 4 7 3 9

3 9 1 2 4 86

5

15

52

8

7 341 6 8

2 6 3 9 4 7

3 9 1 2 4 86

H2 L2 h3 h1 l3 l1

H3 L3 h1 h2 l1 l2

H1 L1 h2 h3 l2 l3

H2 L2 h1 h3 l1 l3

H3 L3 h1 h2 l1 l2

H1 L1 h2 h3 l2 l3

Evaluation

Experiment Setup□ 48-node EC2-like cluster (4-core 12G RAM 1GigE

NIC)□ Graph Algorithms

− PageRank− Approximate Diameter− Connected Components

□ Data Set: − 5 real-world graphs− 5 synthetic power-law graphs*

*Varying α and fixed 10 million vertices (smaller α produces denser graphs)

Runtime Speedup

48 machines and baseline: PowerGraph + Grid (default)

Real-world GraphsPower-law Graphs

Hybrid: 2.02X ~ 2.96X

Ginger: 2.17X ~ 3.26X

Hybrid: 1.40X ~ 2.05X

Ginger: 1.97X ~ 5.53X

PageRank Gather: IN / Scatter: OUT

better

Runtime Speedup

48 machines and baseline: PowerGraph + Grid (default)

Connected ComponentGather: NONE / Scatter: ALL

Approximate DiameterGather: OUT / Scatter:

NONE

Hybrid: 1.93X ~ 2.48X

Ginger: 1.97X ~ 3.15X

Hybrid: 1.44X ~ 1.88X

Ginger: 1.50X ~ 2.07X

better

Communication Cost

1.8 1.9 2 2.1 2.20%

20%

40%

60%

80%

100%

120%grid coor hybrid ginger

power-law constant (α)

% C

om

m.

Da

ta S

ize

Twit-ter

UK Wiki LJ Gweb

datasets

Power-law Graphs Real-world Graphs

394MB 170MB188MB

79.4

%

better

Effectiveness of Hybrid

Power-law (48)

Real-world (48)

Ingress Time

Scalability (Twitter)

Hybrid Graph Partitioning

better

Effectiveness of HybridHybrid Graph Computation

1.8 1.9 2 2.1 2.20

10

20

30

40

50

60


On

e I

tera

tio

n C

om

ms

(MB

)

1.8 1.9 2 2.1 2.20

2

4

6

8

10

12PG+HybridPG+GingerPL+Hybrid


Exe

cuti

on

Tim

e (

Se

c)

better

Scalability

Increasing of machines Increasing of data size

0.01

0.1

1 2 3 4 5 6 7 8 9 100

2

4

6

8

10

12

14 gridobliviouscoor-di-natedhybridginger

#Vertices (Millions)

Execu

tion T

ime (

Sec)

8 16 24 480

2

4

6

8

10

12

14

16gridobliviouscoor-di-natedhybridginger

#Machines

Execu

tion T

Ime (

Sec)

better

Conclusion

PowerLyra□ a new hybrid graph analytics engine that

embraces the best of both worlds of existing frameworks

□ an efficient hybrid graph partitioning algorithm that adopts different heuristics for different vertices.

□ outperforms PowerGraph with default partition by up to 5.53X and 3.26X for real-world and synthetic graphs accordingly



Questions

Thanks

PowerLyra

http://ipads.se.sjtu.edu.cn

Institute of Parallel And Distributed Systems


http://ipads.se.sjtu.edu.cn/

http://ipads.se.sjtu.edu.cn/




differentiated graph computation and partitioning on skewed graphs rong chen, jiaxin shi, yanzhe...

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