distributed systems cs 15-440 programming models- part iv lecture 16, nov 4, 2013 mohammad hammoud 1

Distributed SystemsCS 15-440

Programming Models- Part IV

Lecture 16, Nov 4, 2013

Mohammad Hammoud

1

Today…

Last Session: Programming Models – Part III: MapReduce

Today’s Session: Programming Models – Part IV: Pregel & GraphLab

Announcements: Project 3 is due on Saturday Nov 9, 2013 by midnight PS3 is due on Wednesday Nov 13, 2013 by midnight Quiz 2 is on Nov 20, 2013 Final Exam is on Dec 8, 2013 at 9:00AM in room # 2051 Last day of classes will be Wednesday Dec 4, 2013 (we will hold

an overview session) 2

Objectives

Discussion on Programming Models

Why parallelizing our programs?

Parallel computer architectures

Traditional Models of parallel programming

Types of Parallel Programs

Message Passing Interface (MPI)

MapReduce, Pregel and GraphLab


Last 3 Sessions

Cont’d

The Pregel Analytics Engine

4

Pregel

Motivation & Definition

The Computation & Programming

Models

Input and Output

Architecture & Execution Flow

Fault-Tolerance

How to implement algorithms to process Big Graphs?

Create a custom distributed infrastructure for each new algorithm

Rely on existing distributed analytics engines like MapReduce

Use a single-computer graph algorithm library like BGL, LEDA, NetworkX etc.

Use a parallel graph processing system like Parallel BGL or CGMGraph

Motivation for Pregel

5

Difficult!

Inefficient and Cumbersome!

Usually Big Graphs are too large to fit on a single machine!

Not suited for Large-Scale Distributed Systems!

What is Pregel?

Pregel is a large-scale graph-parallel distributed analytics engine

Some Characteristics:• In-Memory (opposite to MapReduce)• High scalability• Automatic fault-tolerance• Flexibility in expressing graph algorithms• Message-Passing programming model• Tree-style, master-slave architecture• Synchronous

Pregel is inspired by Valiant’s Bulk Synchronous Parallel (BSP) model

6


7

Pregel



Models

Input and Output


Fault-Tolerance

The BSP Model

8

Data

Data

Data

Data

Data

Data

Data

Data

Data

Data

Data

Data

Data

Data

CPU 1CPU 1

CPU 2CPU 2

CPU 3CPU 3

CPU 1CPU 1

CPU 2CPU 2

CPU 3CPU 3

Data

Data

Data

Data

Data

Data

Data

CPU 1CPU 1

CPU 2CPU 2

CPU 3CPU 3

Iterations

Bar

rier

Bar

rier

Data

Data

Data

Data

Data

Data

Data

Bar

rier

Super-Step 1 Super-Step 2 Super-Step 3

Entities and Super-Steps

The computation is described in terms of vertices, edges and a sequence of super-steps

You give Pregel a directed graph consisting of vertices and edges Each vertex is associated with a modifiable

user-defined value Each edge is associated with a source vertex, value

and a destination vertex

During a super-step: A user-defined function F is executed at each vertex V F can read messages sent to V in superset S – 1 and send messages to other

vertices that will be received at superset S + 1 F can modify the state of V and its outgoing edges F can alter the topology of the graph 9

Topology Mutations The graph structure can be modified during any super-step

Vertices and edges can be added or deleted

Mutating graphs can create conflicting requests where multiple vertices at a super-step might try to alter the same edge/vertex

Conflicts are avoided using partial ordering and handlers Partial orderings:

Edges are removed before vertices Vertices are added before edges Mutations performed at super-step S are only effective at

super-step S + 1 All mutations precede calls to actual computations

Handlers: Among multiple conflicting requests, one request is selected arbitrarily

10

Algorithm Termination

Algorithm termination is based on every vertex voting to halt

In super-step 0, every vertex is active All active vertices participate in the computation of any given super-step A vertex deactivates itself by voting

to halt and enters an inactive state A vertex can return to active state

if it receives an external message

A Pregel program terminates when all vertices are simultaneously inactive and there are no messages in transit

11

Active InactiveInactive

Vote to Halt

Message Received

Vertex State Machine

Finding the Max Value in a Graph

3 6 2 1

3 6 2 16 2 66

6 6 2 66 6

6 6 6 66

Blue Arrows are messages

Blue vertices have voted to halt

6

S:

S + 1:

S + 2:

S + 3:

The Programming Model

Pregel adopts the message-passing programming model

Messages can be passed from any vertex to any other vertex in the graph Any number of messages can be passed The message order is not guaranteed Messages will not be duplicated

Combiners can be used to reduce

the number of messages passed

between super-steps

Aggregators are available for reduction operations (e.g., sum, min, and max)

13

The Pregel API in C++

A Pregel program is written by sub-classing the Vertex class:

14

template <typename VertexValue,typename EdgeValue,typename MessageValue>

class Vertex {public:

virtual void Compute(MessageIterator* msgs) = 0;

const string& vertex_id() const;int64 superstep() const;const VertexValue& GetValue();VertexValue* MutableValue();OutEdgeIterator GetOutEdgeIterator();

void SendMessageTo(const string& dest_vertex,const MessageValue& message);

void VoteToHalt();};

Override the compute function to

define the computation at each superstep

To pass messages to other

vertices

To define the types for vertices, edges and messages

To get the value of the current vertex

To modify the value of the vertex

Pregel Code for Finding the Max Value

Class MaxFindVertex: public Vertex<double, void, double> {

public:virtual void Compute(MessageIterator* msgs) {

int currMax = GetValue();SendMessageToAllNeighbors(currMax);for ( ; !msgs->Done(); msgs->Next()) {

if (msgs->Value() > currMax)currMax = msgs->Value();

}if (currMax > GetValue())

*MutableValue() = currMax;else VoteToHalt();

}};


16

Pregel



Models

Input and Output


Fault-Tolerance

Input, Graph Flow and Output

The input graph in Pregel is stored in a distributed storage layer (e.g., GFS or Bigtable)

The input graph is divided into partitions consisting of vertices and outgoing edges Default partitioning function is hash(ID) mod N, where N is the # of partitions

Partitions are stored at node memories for the duration of computations (hence, an in-memory model & not a disk-based one)

Outputs in Pregel are typically graphs isomorphic (or mutated) to input graphs Yet, outputs can be also aggregated statistics mined from input graphs

(depends on the graph algorithms)


18

Pregel



Models

Input and Output


Fault-Tolerance

The Architectural Model Pregel assumes a tree-style network topology and a

master-slave architecture

19

Core Switch

Rack Switch

Worker1 Worker2 Worker3

Rack Switch

Worker4 Worker5 Master

Push work (i.e., partitions) to all workers

Send Completion Signals

When the master receives the completion signal from every worker in super-step S, it starts super-step S + 1

The Execution Flow

Steps of Program Execution in Pregel:

1. Copies of the program code are distributed across all machines

1.1 One copy is designated as the master and every other copy is deemed as a worker/slave

2. The master partitions the graph and assigns workers partition(s), along with portions of input “graph data”

3. Every worker executes the user-defined function on each vertex

4. Workers can communicate among each others

20

The Execution Flow

Steps of Program Execution in Pregel:

5. The master coordinates the execution of super-steps

6. The master calculates the number of inactive vertices after each super-step and signals workers to terminate if all vertices are inactive (and no messages are in transit)

7. Each worker may be instructed to save its portion of the graph

21


22

Pregel



Models

Input and Output


Fault-Tolerance

Fault Tolerance in Pregel

Fault-tolerance is achieved through checkpointing At the start of every super-step the master may instruct the

workers to save the states of their partitions in a stable storage

Master uses “ping” messages to detect worker failures

If a worker fails, the master re-assigns corresponding vertices and input graph data to another available worker, and restarts the super-step The available worker re-loads the partition state of the failed

worker from the most recent available checkpoint

23

How Does Pregel Compare to MapReduce?

24

Pregel versus MapReduce

25

Aspect Hadoop MapReduce Pregel

Programming Model Shared-Memory (abstraction)

Message-Passing



Message-Passing

Computation Model Synchronous Synchronous



Message-Passing


Parallelism Model Data-Parallel Graph-Parallel



Message-Passing



Architectural Model Master-Slave Master-Slave



Message-Passing




Task/Vertex Scheduling Model

Pull-Based Push-Based



Message-Passing




Task/Vertex Scheduling Model

Pull-Based Push-Based

Application Suitability Loosely-Connected/Embarrassingly Parallel

Applications

Strongly-Connected Applications

Objectives

Discussion on Programming Models

Why parallelizing our programs?

Parallel computer architectures

Traditional Models of parallel programming

Types of Parallel Programs

Message Passing Interface (MPI)


The GraphLab Analytics Engine

27

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

Motivation for GraphLab

There is an exponential growth in the scale of Machine Learning and Data Mining (MLDM) algorithms

Designing, implementing and testing MLDM at large-scale are challenging due to: Synchronization Deadlocks Scheduling Distributed state management Fault-tolerance

The interest on analytics engines that can execute MLDM algorithms automatically and efficiently is increasing MapReduce is inefficient with iterative jobs (common in MLDM algorithms) Pregel cannot run asynchronous problems (common in MLDM algorithms)

28

What is GraphLab?

GraphLab is a large-scale graph-parallel distributed analytics engine

Some Characteristics:• In-Memory (opposite to MapReduce and similar to Pregel)• High scalability• Automatic fault-tolerance• Flexibility in expressing arbitrary graph algorithms (more flexible

than Pregel)• Shared-Memory abstraction (opposite to Pregel but similar to

MapReduce)• Peer-to-peer architecture (dissimilar to Pregel and MapReduce)• Asynchronous (dissimilar to Pregel and MapReduce)

29


30

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

GraphLab assumes problems modeled as graphs

It adopts two phases, the initialization and the execution phases

Input, Graph Flow and Output

31

Initialization PhaseInitialization Phase GraphLab Execution PhaseGraphLab Execution Phase

Distributed File system

(MapReduce) Graph Builder

Distributed File system

Raw Graph Data

Raw Graph Data

Raw Graph Data

Raw Graph Data

Parsing + PartitioningParsing +

Partitioning

Atom Collection

Atom Collection

Index Construction

Index Construction

Atom IndexAtom Index

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Cluster Distributed File system

TCP RPC Comms

TCP RPC Comms

Atom IndexAtom Index

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Atom File

Monitoring + Atom

Placement

Monitoring + Atom

Placement

GL EngineGL Engine

GL EngineGL Engine

GL EngineGL Engine

Components of the GraphLab Engine: The Data-Graph

The GraphLab engine incorporates three main parts:1. The data-graph, which represents the user program state at a cluster machine

32

Data-Graph

Vertex

Edge

The GraphLab engine incorporates three main parts:2. The update function, which involves two main functions:

2.1- Altering data within a scope of a vertex

2.2- Scheduling future update functions at neighboring vertices

vv

Sv

The scope of a vertex v (i.e., Sv) is the data stored in v and in all v’s adjacent edges and vertices

Components of the GraphLab Engine: The Update Function





The update function

Schedule v





CPU 1CPU 1

CPU 2CPU 2

ee ff gg

kkjjiihh

ddccbbaa bb

iihh

aa

ii

bb ee ff

jj

cc

Sch

edule

rSch

edule

r

The process repeats until the scheduler is emptyThe process repeats until the scheduler is empty

Components of the GraphLab Engine: The Sync Operation

The GraphLab engine incorporates three main parts:3. The sync operation, which maintains global statistics describing data

stored in the data-graph

Global values maintained by the sync operation can be written by all update functions across the cluster machines

The sync operation is similar to Pregel’s aggregators

A mutual exclusion mechanism is applied by the sync operation to avoid write-write conflicts

For scalability reasons, the sync operation is not enabled by default


37

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

The Architectural Model

GraphLab adopts a peer-to-peer architecture All engine instances are symmetric Engine instances communicate together using Remote Procedure Call

(RPC) protocol over TCP/IP The first triggered engine has an additional responsibility of being a

monitoring/master engine

Advantages: Highly scalable Precludes centralized bottlenecks and single point of failures

Main disadvantage: Complexity


39

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

The Programming Model

GraphLab offers a shared-memory programming model

It allows scopes to overlap and vertices to read/write from/to their scopes

Consistency Models in GraphLab

GraphLab guarantees sequential consistency Provides the same result as a sequential execution of the computational steps

User-defined consistency models Full Consistency Vertex Consistency Edge Consistency

41

Vertex v

Consistency Models in GraphLab

D1 D2 D3 D4 D5

D1↔2D1↔2 D2↔3

D2↔3 D3↔4D3↔4 D4↔5

D4↔5

1 2 3 4 5

D1 D2 D3 D4 D5

D1↔2D1↔2 D2↔3

D2↔3 D3↔4D3↔4 D4↔5

D4↔5

1 2 3 4 5

ReadWrite

ReadWrite

D1 D2 D3 D4 D5

D1↔2D1↔2 D2↔3

D2↔3 D3↔4D3↔4 D4↔5

D4↔5

1 2 3 4 5

ReadWrite


43

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

The Computation Model

GraphLab employs an asynchronous computation model

It suggests two asynchronous engines Chromatic Engine Locking Engine

The chromatic engine executes vertices partially asynchronous It applies vertex coloring (e.g., no adjacent vertices share the same color) All vertices with the same color are executed before proceeding to a different color

The locking engine executes vertices fully asynchronously Data on vertices and edges are susceptible to corruption It applies a permission-based distributed mutual exclusion mechanism to

avoid read-write and write-write hazards


45

GraphLab

Motivation &

Definition

The Programming

Model

Input, Output &

Components

The Architectural

Model

Fault-Tolerance

The Computation

Model

Fault-Tolerance in GraphLab

GraphLab uses distributed checkpointing to recover from machine failures

It suggests two checkpointing mechanisms Synchronous checkpointing (it suspends the entire execution of GraphLab) Asynchronous checkpointing

How Does GraphLab Compare to MapReduce and Pregel?

47

GraphLab vs. Pregel vs. MapReduceAspect Hadoop

MapReducePregel GraphLab

Programming Model

Shared-Memory Message-Passing Shared-Memory

Aspect Hadoop MapReduce

Pregel GraphLab

Programming Model


Computation Model

Synchronous Synchronous Asynchronous


Pregel GraphLab

Programming Model


Computation Model


Parallelism Model

Data-Parallel Graph-Parallel Graph-Parallel


Pregel GraphLab

Programming Model


Computation Model


Parallelism Model


Architectural Model

Master-Slave Master-Slave Peer-to-Peer


Pregel GraphLab

Programming Model


Computation Model


Parallelism Model


Architectural Model


Task/Vertex Scheduling

Model

Pull-Based Push-Based Push-Based


Pregel GraphLab

Programming Model


Computation Model


Parallelism Model


Architectural Model


Task/Vertex Scheduling

Model

Pull-Based Push-Based Push-Based

Application Suitability

Loosely-Connected/

Embarrassingly Parallel Applications

Strongly-Connected Applications

Strongly-Connected Applications (more

precisely MLDM apps)

Next Class

Fault-Tolerance

Back-up Slides

50

PageRank PageRank is a link analysis algorithm

The rank value indicates an importance of a particular web page

A hyperlink to a page counts as a vote of support

A page that is linked to by many pages with high PageRank receives a high rank itself

A PageRank of 0.5 means there is a 50% chance that a person clicking on a random link will be directed to the document with the 0.5 PageRank

PageRank (Cont’d) Iterate:

Where: α is the random reset probability L[j] is the number of links on page j

1 32

4 65

pagerank(i, scope){ // Get Neighborhood data (R[i], Wij, R[j]) scope;

// Update the vertex data

// Reschedule Neighbors if needed if R[i] changes then reschedule_neighbors_of(i); }

;][)1(][][

iNj

ji jRWiR

PageRank Example in GraphLab PageRank algorithm is defined as a per-vertex operation working on the scope

of the vertex

Dynamic computation

distributed systems cs 15-440 programming models- part iv lecture 16, nov 4, 2013 mohammad hammoud 1

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