Apache Flink & Graph Processing

Batch & Stream Graph Processing
with Apache Flink
Vasia Kalavri
vasia@apache.org
@vkalavri
Apache Flink Meetup London
October 5th, 2016

2
Graphs capture relationships
between data items
connections, interactions, purchases,
dependencies, friendships, etc.
Recommenders
Social networks
Bioinformatics
Web search

Outline
• Distributed Graph Processing 101
• Gelly: Batch Graph Processing with Apache Flink
• BREAK!
• Gelly-Stream: Continuous Graph Processing with
Apache Flink

Apache Flink
• An open-source, distributed data analysis framework
• True streaming at its core
• Streaming & Batch API
4
Historic data
Kafka, RabbitMQ, ...
HDFS, JDBC, ...
Event logs
ETL, Graphs, 
Machine Learning 
Relational, …
Low latency, 
windowing,
aggregations, ...

WHEN DO YOU NEED
DISTRIBUTED GRAPH
PROCESSING?

MY GRAPH IS SO BIG,
IT DOESN’T FIT IN A
SINGLE MACHINE
Big Data Ninja
MISCONCEPTION #1

NAIVE WHO(M)-T0-FOLLOW
▸ Naive Who(m) to Follow:
▸ compute a friends-of-friends
list per user
▸ exclude existing friends
▸ rank by common
connections

DON’T JUST
CONSIDER YOUR
INPUT GRAPH SIZE.
INTERMEDIATE DATA
MATTERS TOO!

DISTRIBUTED PROCESSING
IS ALWAYS FASTER THAN
SINGLE-NODE
Data Science Rockstar
MISCONCEPTION #2

Apache Flink & Graph Processing

GRAPHS DON’T APPEAR OUT OF THIN AIR
Expectation…

GRAPHS DON’T APPEAR OUT OF THIN AIR
Reality!

WHEN DO YOU NEED DISTRIBUTED GRAPH PROCESSING?
▸ When you do have really big graphs
▸ When the intermediate data is big
▸ When your data is already distributed
▸ When you want to build end-to-end graph pipelines

HOW DO WE EXPRESS A
DISTRIBUTED GRAPH
ANALYSIS TASK?

RECENT DISTRIBUTED GRAPH PROCESSING HISTORY
2004
MapReduce
Pegasus
2009
Pregel
2010
Signal-Collect
PowerGraph
2012
Iterative value propagation
Giraph++
2013
Graph Traversals
NScale
2014
Ego-network analysis
Arabesque
2015
Pattern Matching
Tinkerpop

PREGEL: THINK LIKE A VERTEX
1
5
4
3
2
1 3, 4
2 1, 4
5 3
...

PREGEL: SUPERSTEPS
(Vi+1, outbox) <— compute(Vi, inbox)
1 3, 4
2 1, 4
5 3
..
1 3, 4
2 1, 4
5 3
..
Superstep i Superstep i+1

PAGERANK: THE WORD COUNT OF GRAPH PROCESSING
VertexID Out-degree
Transition
Probability
1 2 1/2
2 2 1/2
3 0 -
4 3 1/3
5 1 1
1
5
4
3
2

VertexID Out-degree
Transition
Probability
1 2 1/2
2 2 1/2
3 0 -
4 3 1/3
5 1 1
PR(3) = 0.5*PR(1) + 0.33*PR(4) + PR(5)
1
5
4
3
2

1
5
4
3
2
VertexID Out-degree
Transition
Probability
1 2 1/2
2 2 1/2
3 0 -
4 3 1/3
5 1 1
PR(3) = 0.5*PR(1) + 0.33*PR(4) + PR(5)

PREGEL EXAMPLE: PAGERANK
void compute(messages):
sum = 0.0
for (m <- messages) do
sum = sum + m
end for
setValue(0.15/numVertices() + 0.85*sum)
for (edge <- getOutEdges()) do
sendMessageTo(
edge.target(), getValue()/numEdges)
end for
sum up received
messages
update vertex rank
distribute rank
to neighbors

SIGNAL-COLLECT
outbox <— signal(Vi)
1 3, 4
2 1, 4
5 3
..
1 3, 4
2 1, 4
5 3
..
Superstep i
Vi+1 <— collect(inbox)
1 3, 4
2 1, 4
5 3
..
Signal Collect
Superstep i+1

SIGNAL-COLLECT EXAMPLE: PAGERANK
void signal():
for (edge <- getOutEdges()) do
sendMessageTo(
edge.target(), getValue()/numEdges)
end for
void collect(messages):
sum = 0.0
for (m <- messages) do
sum = sum + m
end for
setValue(0.15/numVertices() + 0.85*sum)
distribute rank
to neighbors
sum up
messages
update vertex
rank

GATHER-SUM-APPLY (POWERGRAPH)
1
...
...
Gather Sum
1
2
5
...
Apply
3
1 5
5 3
1
...
Gather
3
1 5
5 3
Superstep i Superstep i+1

GSA EXAMPLE: PAGERANK
double gather(source, edge, target):
return target.value() / target.numEdges()
double sum(rank1, rank2):
return rank1 + rank2
double apply(sum, currentRank):
return 0.15 + 0.85*sum
compute
partial rank
combine
partial ranks
update rank

PREGEL VS. SIGNAL-COLLECT VS. GSA
Update Function
Properties
Update Function
Logic
Communication
Scope
Communication
Logic
Pregel arbitrary arbitrary any vertex arbitrary
Signal-Collect arbitrary
based on
received
messages
any vertex
based on vertex
state
GSA
associative &
commutative
based on
neighbors’
values
neighborhood
based on vertex
state

CAN WE HAVE IT ALL?
▸ Data pipeline integration: built on top of an
efﬁcient distributed processing engine
▸ Graph ETL: high-level API with abstractions and
methods to transform graphs
▸ Familiar programming model: support popular
programming abstractions

Gelly
the Apache Flink Graph API

Apache Flink Stack
Gelly
Table/SQL
ML
SAMOA
DataSet (Java/Scala) DataStream (Java/Scala)
HadoopM/R
Local Remote Yarn Embedded
Dataflow
Dataflow
Table/SQL
Cascading
Streaming dataflow runtime
CEP

Meet Gelly
• Java & Scala Graph APIs on top of Flink’s DataSet API
Flink Core
Scala API
(batch and streaming)
Java API
(batch and streaming)
FlinkML GellyTable API ...
Transformations
and Utilities
Iterative Graph
Processing
Graph Library
34

Gelly is NOT
• a graph database
• a specialized graph processor
35

Hello, Gelly!
ExecutionEnvironment env = ExecutionEnvironment.getExecutionEnvironment();
DataSet<Edge<Long, NullValue>> edges = getEdgesDataSet(env);
Graph<Long, Long, NullValue> graph = Graph.fromDataSet(edges, env);
DataSet<Vertex<Long, Long>> verticesWithMinIds = graph.run(
new ConnectedComponents(maxIterations));
val env = ExecutionEnvironment.getExecutionEnvironment
val edges: DataSet[Edge[Long, NullValue]] = getEdgesDataSet(env)
val graph = Graph.fromDataSet(edges, env)
val components = graph.run(new ConnectedComponents(maxIterations))
Java
Scala

Graph Methods
Graph Properties
getVertexIds
getEdgeIds
numberOfVertices
numberOfEdges
getDegrees
Mutations
add vertex/edge
remove vertex/edge
Transformations
map, filter, join
subgraph, union,
difference
reverse, undirected
getTriplets
Generators
R-Mat (power-law)
Grid
Star
Complete
…

Example: mapVertices
// increment each vertex value by one 
val graph = Graph.fromDataSet(...) 
 
// increment each vertex value by one 
val updatedGraph = graph.mapVertices(v => v.getValue + 1)
4
2
8
5
5
3
1
7
4
5

Example: subGraph
val graph: Graph[Long, Long, Long] = ... 
 
// keep only vertices with positive values 
// and only edges with negative values 
val subGraph = graph.subgraph(
vertex => vertex.getValue > 0,
edge => edge.getValue < 0
)

Neighborhood Methods
Apply a reduce function to the 1st-hop neighborhood
of each vertex in parallel
graph.reduceOnNeighbors(
new MinValue, EdgeDirection.OUT)

What makes Gelly unique?
• Batch graph processing on top of a streaming
dataﬂow engine
• Built for end-to-end analytics
• Support for multiple iteration abstractions
• Graph algorithm building blocks
• A large open-source library of graph algorithms

Why streaming dataﬂow?
• Batch engines materialize data… even if they don’t
have to
• the graph is always loaded and materialized in memory,
even if not needed, e.g. mapping, ﬁltering, transformation
• Communication and computation overlap
• We can do continuous graph processing (more
after the break!)

End-to-end analytics
• Graphs don’t appear out of thin air…
• We need to support pre- and post-processing
• Gelly can be easily mixed with the DataSet API:
pre-processing, graph analysis, and post-
processing in the same Flink program

Iterative Graph Processing
• Gelly offers iterative graph processing abstractions
on top of Flink’s Delta iterations
• vertex-centric
• scatter-gather
• gather-sum-apply
• partition-centric*

Flink Iteration Operators
Input
Iterative
Update Function
Result
Replace
Workset
Iterative
Update Function
Result
Solution Set
State

Optimization
• the runtime is aware of the iterative execution
• no scheduling overhead between iterations
• caching and state maintenance are handled automatically
Push work 
“out of the loop”
Maintain state as indexCache Loop-invariant Data

Vertex-Centric SSSP
final class SSSPComputeFunction extends ComputeFunction {
override def compute(vertex: Vertex, messages: MessageIterator) = {
var minDistance = if (vertex.getId == srcId) 0 else Double.MaxValue
while (messages.hasNext) {
val msg = messages.next
if (msg < minDistance)
minDistance = msg
}
if (vertex.getValue > minDistance) {
setNewVertexValue(minDistance)
for (edge: Edge <- getEdges)
sendMessageTo(edge.getTarget, vertex.getValue + edge.getValue)
}

Algorithms building blocks
• Allow operator re-use across graph algorithms
when processing the same input with a similar
conﬁguration

Library of Algorithms
• PageRank
• Single Source Shortest Paths
• Label Propagation
• Weakly Connected Components
• Community Detection
• Triangle Count & Enumeration
• Local and Global Clustering Coefﬁcient
• HITS
• Jaccard & Adamic-Adar Similarity
• Graph Summarization
• val ranks = inputGraph.run(new PageRank(0.85, 20))

Tracker
Tracker
Ad Server
display
relevant ads
cookie
exchange
proﬁling
Web Tracking

Can’t we block them?
proxy
Tracker
Tracker
Ad Server
Legitimate site

• not frequently updated
• not sure who or based on what criteria URLs are
blacklisted
• miss “hidden” trackers or dual-role nodes
• blocking requires manual matching against the list
• can you buy your way into the whitelist?
Available Solutions
Crowd-sourced “black lists” of tracker URLs:
- AdBlock, DoNotTrack, EasyPrivacy

DataSet
• 6 months (Nov 2014 - April 2015) of augmented
Apache logs from a web proxy
• 80m requests, 2m distinct URLs, 3k users

h2
h3 h4
h5 h6
h8
h7
h1
h3
h4
h5
h6
h1
h2
h7
h8
r1
r2
r3
r5
r6
r7
NT
NT
T
T
?
T
NT
NT
r4
r1
r2
r3
r3
r3
r4
r5r6
r7
hosts-projection graph
: referer
: non-tracker host
: tracker host
: unlabeled host
The Hosts-Projection Graph
U: Referers
referer-hosts graph
V: hosts

Classiﬁcation via Label Propagation
non-tracker tracker unlabeled
55

Data Pipeline
raw logs
cleaned
logs
1: logs pre-
processing
2: bipartite graph
creation
3: largest
connected
component
extraction
4: hosts-
projection
graph creation
5: community
detection
google-analytics.com: T
bscored-research.com: T
facebook.com: NT
github.com: NT
cdn.cxense.com: NT
...
6: results
DataSet API
Gelly
DataSet API

Feeling Gelly?
• Gelly Guide
https://ci.apache.org/projects/flink/flink-docs-master/libs/
gelly_guide.html
• To Petascale and Beyond @Flink Forward ‘16
http://flink-forward.org/kb_sessions/to-petascale-and-beyond-apache-
flink-in-the-clouds/
• Web Tracker Detection @Flink Forward ’15
https://www.youtube.com/watch?v=ZBCXXiDr3TU
paper: Kalavri, Vasiliki, et al. "Like a pack of wolves: Community
structure of web trackers." International Conference on Passive and
Active Network Measurement, 2016.

Gelly-Stream
single-pass stream graph
processing with Flink

Real Graphs are dynamic
Graphs are created from events happening in real-time

How we’ve done graph processing so far
1. Load: read the graph
from disk and partition it in
memory

2. Compute: read and
mutate the graph state
memory

3. Store: write the ﬁnal
graph state back to disk
2. Compute: read and
mutate the graph state
memory

What’s wrong with this model?
• It is slow
• wait until the computation is over before you see
any result
• pre-processing and partitioning
• It is expensive
• lots of memory and CPU required in order to
scale
• It requires re-computation for graph changes
• no efﬁcient way to deal with updates

Can we do graph processing
on streams?
• Maintain the
dynamic graph
structure
• Provide up-to-date
results with low
latency
• Compute on fresh
state only

Single-pass graph streaming
• Each event is an edge addition
• Maintain only a graph summary
• Recent events are grouped in graph
windows

Graph Summaries
• spanners for distance estimation
• sparsiﬁers for cut estimation
• sketches for homomorphic properties
graph summary
algorithm algorithm~R1 R2

1
43
2
5
i=0
Batch Connected
Components
6
7
8

1
43
2
5
6
7
8
i=0
Batch Connected
Components
1
4
3
4
5
2
3
5
2
4
7
8
6
7
6
8

1
21
2
2
i=1
Batch Connected
Components
6
6
6

1
21
1
2
6
6
6
i=1
Batch Connected
Components
2
1
2
2
1
1
2
1
2
7
6
6
6

1
11
1
1
i=2
Batch Connected
Components
6
6
6

54
76
86
42
31
52
Stream Connected
Components
Graph Summary: Disjoint
Set (Union-Find)
• Only store component IDs
and vertex IDs

54
76
86
42
43
31
52
1
3
Cid = 1

54
76
86
42
43
87
31
52
1
3
Cid = 1
2
5
Cid = 2

54
76
86
42
43
87
41
31
52
1
3
Cid = 1
2
5
Cid = 2
4

54
76
86
42
43
87
41
31
52
1
3
Cid = 1
2
5
Cid = 2
4
6
7
Cid = 6

54
76
86
42
43
87
41
31
52
1
3
Cid = 1
2
5
Cid = 2
4
6
7
Cid = 6
8

54
76
86
42
43
87
41
52
1
3
Cid = 1
2
5
Cid = 2
4
6
7
Cid = 6
8

54
76
86
42
43
87
41
6
7
Cid = 6
8
1
3
Cid = 1
2
5
Cid = 2
4

54
76
86
42
43
87
41
1
3
Cid = 1
2
5
4
6
7
Cid = 6
8

Distributed Stream Connected
Components

Stream Connected
Components with Flink
DataStream<DisjointSet> cc =
edgeStream 
.keyBy(0) 
.timeWindow(Time.of(100, TimeUnit.MILLISECONDS)) 
.fold(new DisjointSet(), new UpdateCC()) 
.flatMap(new Merger()) 
.setParallelism(1);

Stream Connected
edgeStream 
.keyBy(0) 
.setParallelism(1);
Partition the edge
stream

Stream Connected
edgeStream 
.keyBy(0) 
.setParallelism(1);
Define the merging
frequency

Stream Connected
edgeStream 
.keyBy(0) 
.setParallelism(1);
merge locally

Stream Connected
edgeStream 
.keyBy(0) 
.setParallelism(1); merge globally

Gelly on Streams
DataStreamDataSet
Distributed Dataﬂow
Deployment
Gelly Gelly-Stream
• Static Graphs
• Multi-Pass Algorithms
• Full Computations
• Dynamic Graphs
• Single-Pass Algorithms
• Approximate Computations
DataStream

Introducing Gelly-Stream
Gelly-Stream enriches the DataStream API with two new additional ADTs:
• GraphStream:
• A representation of a data stream of edges.
• Edges can have state (e.g. weights).
• Supports property streams, transformations and aggregations.
• GraphWindow:
• A “time-slice” of a graph stream.
• It enables neighborhood aggregations

GraphStream Operations
.getEdges()
.getVertices()
.numberOfVertices()
.numberOfEdges()
.getDegrees()
.inDegrees()
.outDegrees()
GraphStream -> DataStream
.mapEdges();
.distinct();
.filterVertices();
.filterEdges();
.reverse();
.undirected();
.union();
GraphStream -> GraphStream
Property Streams Transformations

Graph Stream Aggregations
result
aggregate
property streamgraph
stream
(window) fold
combine
fold
reduce
local
summaries
global
summary
edges
agg
global aggregates
can be persistent or transient
graphStream.aggregate(
new MyGraphAggregation(window, fold, combine, transform))

Slicing Graph Streams
graphStream.slice(Time.of(1, MINUTE));
11:40 11:41 11:42 11:43

Aggregating Slices
graphStream.slice(Time.of(1, MINUTE), direction)
.reduceOnEdges();
.foldNeighbors();
.applyOnNeighbors();
• Slicing collocates edges by vertex
information
• Neighborhood aggregations on sliced
graphs
source
target
Aggregations

Finding Matches Nearby
graphStream.filterVertices(GraphGeeks())
.slice(Time.of(15, MINUTE), EdgeDirection.IN)
.applyOnNeighbors(FindPairs())
slice
GraphStream :: graph geek check-ins
wendy checked_in soap_bar
steve checked_in soap_bar
tom checked_in joe’s_grill
sandra checked_in soap_bar
rafa checked_in joe’s_grill
wendy
steve
sandra
soap
bar
tom
rafa
joe’s
grill
FindPairs
{wendy, steve}
{steve, sandra}
{wendy, sandra}
{tom, rafa}
GraphWindow :: user-place

Feeling Gelly?
• Gelly Guide
https://ci.apache.org/projects/flink/flink-docs-master/libs/
gelly_guide.html
• Gelly-Stream Repository
https://github.com/vasia/gelly-streaming
• Gelly-Stream talk @FOSDEM16
https://fosdem.org/2016/schedule/event/graph_processing_apache_flink/
• Related Papers
http://www.citeulike.org/user/vasiakalavri/tag/graph-streaming

Apache Flink & Graph Processing

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