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A Pattern Language for Parallel Programming. Beverly Sanders University of Florida. Overview of talk. History of pattern languages Motivation for a pattern language for parallel programming Pattern example: Reengineering for Parallelism

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a pattern language for parallel programming

A Pattern Language for Parallel Programming

Beverly Sanders

University of Florida

overview of talk
Overview of talk
  • History of pattern languages
  • Motivation for a pattern language for parallel programming
  • Pattern example: Reengineering for Parallelism
  • Tour through the entire pattern language via a programming example
history 60s and 70s
History ‘60s and ‘70s
  • Berkeley architecture professor Christopher Alexander
  • 253 patterns for city planning, landscaping, and architecture
  • Attempted to capture principles for “living” design.
example six foot balcony
Example: Six Foot Balcony
  • Balconies less than six feet deep are hardly ever used
  • Discussion of what makes a good balcony
  • Therefore: Whenever you build a balcony or a porch, always make it at least six feet deep. If possible, recess at least a part of it into the building so that it is not cantilevered out and separated from the building by a simple line, and enclose it partially
a new approach to design
A new approach to design

Not just a collection of patterns, but a pattern language

  • Patterns lead to other patterns
  • Patterns are hierarchical and compositional
  • Embodies design methodology and vocabulary

Small impact on architectural practice

patterns in object oriented programming
Patterns in Object-oriented Programming
  • OOPSLA’87 Kent Beck and Ward Cunningham
  • 1995 Design Patterns: Elements of Reusable Object-Oriented SoftwareGang of Four (GOF): Gamma, Helm, Johnson, Vlissides,
    • catalog of patterns
    • Creation, structural, behavioral
  • PLoP Conferences
gof pattern example
GOF Pattern Example
  • Behavioral Pattern: Visitor
    • Separate the structure of an object collection from the operations performed on that collection.
    • Example: Abstract syntax tree in a compiler
      • Multiple node types (declaration, command, expression, etc.)
      • Action during traversal depends on both type of node and compiler pass (type checking, code generation)
      • Can add new functionality by implementing new visitor without modifying AST code.
impact of gof book
Impact of GOF book
  • Good solutions to frequently recurring problems
  • New vocabulary
  • Pattern catalog
  • Significant influence on object-oriented programming!
design pattern
Design Pattern
  • High quality solution to frequently recurring problem in some domain
  • Each pattern has a name, providing a vocabulary for discussing the solutions
  • Written in prescribed format to allow the reader to quickly understand the solution and its context
a pattern format
A pattern format
  • Name
  • Also known as
  • Problem
  • Context
  • Forces
  • Solution
  • Examples and known uses
  • Related patterns

pattern language
Pattern Language
  • Carefully structured collection of patterns
  • Structure embodies a design methodology and leads user through the language so that complex designs can be developed using patterns
  • Provides domain specific advice to the designer
  • Not a programming language
parallel programming
Parallel Programming
  • Parallel hardware becoming increasingly mainstream and inexpensive
    • Multicore CPUs in desktop PCs and servers
    • Clusters
  • Software to fully exploit the hardware currently rare (except specialized area of high performance computing)
  • Can a pattern language providing guidance for the entire development process make parallel programming easier?
structure of the pattern language
Structure of the pattern language
    • Reengineering for Parallelism pattern for dealing with legacy sequential code
  • 4 Design spaces
    • Finding Concurrency
      • Help designer expose exploitable concurrency—find high level task and data decomposition
    • Algorithm Structure
      • Help designer map tasks to processes or threads to best take advantage of the potential concurrency
structure of the pattern language continued
Structure of the pattern language, continued
  • Supporting Structures
    • Code structuring patterns
    • Distributed and thread-safe data structures
  • Implementation Mechanisms
    • Low level mechanisms used to write parallel programs
    • 3 categories of mechanisms
      • UE (process/thread) Management
      • Synchronization
      • Communication
starting with legacy sequential application
Starting with legacy sequential application?
  • Reengineering for Parallelism pattern provides guidance to
    • Manage the process
    • Determine what to change
  • We’ll look at this as an example pattern
reengineering for parallelism
Reengineering for Parallelism
  • Problem:

How can existing applications be parallelized using PLPP to improve performance by making use of parallel hardware?

  • Context:

We have legacy code that cannot be rewritten from scratch, need to improve performance…

  • Forces:
    • User base has expectations for behavior
    • Existing application may not be fully understood
    • Amdahl’s law pushes programmer to avoid sequential bottlenecks at any cost, which may imply wholesale restructuring of the program
    • Starting point is working code that embodies significant programming work, bug fixes, and knowledge. Minimizing changes is desirable. It is rarely feasible to make sweeping rewrites.
    • Concurrency introduces new classes of errors that are hard to detect and make software difficult to validate.
solution preparation
Solution:Preparation
  • Survey the landscape
    • Pattern provides a list of questions to help assess existing code
    • Many are the same as in any reengineering project
    • Is program numerically well-behaved?
  • Define the scope and get users’ buy-in
    • Required precision of results
    • Input range
    • Performance
    • Feasibility (back of envelope calculations)
  • Define a testing protocol
solution continued
Solution: Continued
  • Identify hot spots—where is most of the time spent?
    • Look at code
    • Use profiling tools
  • Parallelization
    • Start with hot spots first
    • As much as possible, make sequence of small changes, each followed by testing
    • Use PLPP patterns (pattern provides guidance)
reengineering for parallelism pattern continued
Reengineering for Parallelism Pattern, continued
  • Extended example
  • Discussion of related patterns
    • Patterns for legacy code
    • Patterns for parallel programming
example molecular dynamics
Example: Molecular dynamics
  • Simulate motion in large molecular system
  • Example application: how protein interacts with drug
  • Forces
    • Bonded forces within a molecule
    • Long-range forces between molecules
      • Not tractable N2
      • Use cutoff method—only consider forces from neighbors that are “close enough”
sequential molecular dynamics simulation
Sequential Molecular dynamics simulation

real atoms(3,N)

real force(3,N)

int neighbors(2,M)

loop over time steps

Compute bonded forces

Compute neighbors

Compute long-range forces

Update position …

end loop

starting with legacy sequential code
Starting with legacy sequential code?
  • If so start with the

Reengineering for Parallelism pattern

  • Next: Finding Concurrency Design Space
finding concurrency design space
Finding Concurrency Design Space

DecompositionPatterns

Dependency Analysis

Patterns

Design Evaluation

finding concurrency design space25
Finding Concurrency Design Space

Decomposition Patterns

Task Decomposition

Data Decomposition

Dependency Analysis

Patterns

Design Evaluation

molecular dynamics decomposition
Molecular dynamics decomposition
  • Each function is a loop over atoms
  • Suggests task decomposition with each task corresponding to a loop iteration (update of an atom)
    • tasks for bonded forces
    • tasks for long -range forces
    • tasks to update positions
    • tasks to compute neighbor list
  • Data shared between the tasks
finding concurrency design space27
Finding Concurrency Design Space

Decomposition Patterns

Dependency Analysis

Patterns

Group tasks

Order tasks

Data Sharing

Design Evaluation

molecular dynamics dependency analysis
Molecular dynamics dependency analysis

Neighbor list

Bonded forces

Long-range forces

Update position

next time step

molecular dynamics dependency analysis29
Molecular dynamics dependency analysis

Neighbor list

Bonded forces

neighbors

Long-range forces

atoms(3,N)

forces(3,N)

Update position

Read

Write

Accumulate

next time step

finding concurrency design space30
Finding Concurrency Design Space

Decomposition Patterns

Dependency Analysis

Patterns

Suitability for target platform

Design Quality (flexibility, efficiency, simplicity)

Preparation for the next phase

Design Evaluation

design evaluation for molecular dynamics
Design evaluation for molecular dynamics
  • Target architecture for example: distributed memory cluster, message passing
  • Data sharing has enough special properties (read only, accumulate, temporal constraints) that we should be able to make it work in a distributed memory environment.
  • Design seems OK, move to next design space
algorithm structure design space
Algorithm structure design space
  • Map tasks to Units of Execution (threads or processes)
  • Target platform properties
    • number of UEs
    • communication between UEs
  • Major organizing principle
organize by tasks

Recursive?

Divide and Conquer

yes

no

Task

Parallelism

Organize by tasks?
organize by data

Recursive?

Recursive Data

yes

no

Geometric

Decomposition

Organize by data?
organize by ordering

Regular?

Pipeline

Event-based

Coordination

Organize by ordering?

yes

no

algorithm structure for molecular dynamics
Algorithm structure for molecular dynamics
  • Organized by task
  • Task decomposition pattern
    • Granularity: decide bonded forces not worth parallelizing now.
    • Load balancing: static OK, partition iterations of original loop (over atoms) to UEs
    • Termination: easy since number of UEs can be determined in advance
separable dependencies
Separable dependencies
  • Multiple tasks update force array concurrently by adding to its value.
  • This type of update is called accumulation
  • Allows dependencies to be separated from concurrent part of computation
    • Each UE gets a local copy of data
    • Updates local copy
    • After local updates completed, reduce (combine results using associative operator)
supporting structures design space
Supporting Structures Design Space

A intermediate stage between algorithm structures and implementation mechanisms (Similar level to GOF)

  • Program structuring patterns
    • SPMD, Fork/Join, Loop Parallelism, Master/Worker
  • Data structures
    • Shared queue, Distributed array, Shared data
choose spmd pattern
Choose SPMD Pattern
  • Single program multiple data.
    • Each UE executes exactly the same program
    • Uses process ID to determine behavior
    • Issues: replicate or partition data, computation?
slide40
Replicate or partition data in MD?
    • Replicate atoms, force.
    • Partition neighbor list
  • Duplicate non-parallelized parts of computation, or designate one process to compute?
    • Duplicate all computation except I/O.
parallel simulation
Parallel Simulation

real atoms(3,N)

real force(3,N)

int neighbors(2,M)

myID = getProcessID

nprocs = getNumberProcesses

loop over time steps

Compute bonded forces //replicate computation

Compute neighbors

//only for atoms assigned to myID

Compute long range forces

globalSum(N,&forces)

//reduction to combine all force arrays

Update position …

end loop

if (myid == printID) printResults

implementation mechanisms
Implementation Mechanisms
  • Describes low level mechanisms used to write parallel programs
  • 3 categories of mechanisms
    • UE (process/thread) Management
    • Synchronization
    • Communication
  • Not in pattern format
  • We discuss OpenMP, MPI, and Java
implement simulation
Implement Simulation
  • For our target platform, MPI is the best choice
  • Need to add standard code for initialization and MPI specific reduction operator to previous solution
pattern languages evolve
Pattern languages evolve
  • A pattern language should not be considered a static document:
    • Evaluate and revise
    • Extend with new patterns: new parallel programming models, specific application domains
    • We added the Reengineering for Parallelism pattern as a result of feedback from readers
for more information
For more information
  • Mattson, Sanders, and Massingill. Patterns for Parallel Programming. Addison-Wesley Software Patterns Series. 2005
  • Reengineering for Parallelism, PLoP05

www.cise.ufl.edu/research/ParallelPatterns

acknowledgements and collaborators
Acknowledgements and collaborators
  • The pattern language is joint work with:
    • Tim Mattson, Intel
    • Berna Massingill, Trinity University
  • Supported by NSF and Intel