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Introduction to Parallel Computing

Blaise Barney, Lawrence Livermore National Laboratory UCRL-MI-133316

Table of Contents
1. Abstract
2. Overview
1. What is Parallel Computing?
2. Why Use Parallel Computing?
3. Concepts and Terminology
1. von Neumann Computer Architecture
2. Flynn's Classical Taxonomy
3. Some General Parallel Terminology
4. Parallel Computer Memory Architectures
1. Shared Memory
2. Distributed Memory
3. Hybrid Distributed-Shared Memory
5. Parallel Programming Models
1. Overview
2. Shared Memory Model
3. Threads Model
4. Message Passing Model
5. Data Parallel Model
6. Other Models
6. Designing Parallel Programs
1. Automatic vs. Manual Parallelization
2. Understand the Problem and the Program
3. Partitioning
4. Communications
5. Synchronization
6. Data Dependencies
7. Load Balancing
8. Granularity
9. I/O
10. Limits and Costs of Parallel Programming
11. Performance Analysis and Tuning
7. Parallel Examples
1. Array Processing
2. PI Calculation
3. Simple Heat Equation
4. 1-D Wave Equation
8. References and More Information

Abstract

This tutorial covers the very basics of parallel computing, and is intended for someone who is just becoming acquainted with the
subject. It begins with a brief overview, including concepts and terminology associated with parallel computing. The topics of
parallel memory architectures and programming models are then explored. These topics are followed by a discussion on a number
of issues related to designing parallel programs. The tutorial concludes with several examples of how to parallelize simple serial

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programs.

Level/Prerequisites: None

Overview

What is Parallel Computing?

Traditionally, software has been written for serial computation:

To be run on a single computer having a single Central Processing Unit (CPU);
A problem is broken into a discrete series of instructions.
Instructions are executed one after another.
Only one instruction may execute at any moment in time.

In the simplest sense, parallel computing is the simultaneous use of multiple compute resources to solve a computational
problem:
To be run using multiple CPUs
A problem is broken into discrete parts that can be solved concurrently
Each part is further broken down to a series of instructions
Instructions from each part execute simultaneously on different CPUs

The compute resources can include:

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A single computer with multiple processors;

An arbitrary number of computers connected by a network;
A combination of both.

The computational problem usually demonstrates characteristics such as the ability to be:
Broken apart into discrete pieces of work that can be solved simultaneously;
Execute multiple program instructions at any moment in time;
Solved in less time with multiple compute resources than with a single compute resource.

The Universe is Parallel:

Parallel computing is an evolution of serial computing that attempts to emulate what has always been the state of affairs in
the natural world: many complex, interrelated events happening at the same time, yet within a sequence. For example:
Galaxy formation Rush hour traffic
Planetary movement Automobile assembly line
Weather and ocean patterns Building a space shuttle
Tectonic plate drift Ordering a hamburger at the drive through.
The Real World is Massively Parallel

Uses for Parallel Computing:

Historically, parallel computing has been considered to be "the high end of computing", and has been used to model
difficult scientific and engineering problems found in the real world. Some examples:
Atmosphere, Earth, Environment
Physics - applied, nuclear, particle, condensed matter, high pressure, fusion, photonics
Bioscience, Biotechnology, Genetics
Chemistry, Molecular Sciences
Geology, Seismology

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Mechanical Engineering - from prosthetics to spacecraft

Electrical Engineering, Circuit Design, Microelectronics
Computer Science, Mathematics

Today, commercial applications provide an equal or greater driving force in the development of faster computers. These
applications require the processing of large amounts of data in sophisticated ways. For example:
Databases, data mining
Oil exploration
Web search engines, web based business services
Medical imaging and diagnosis
Pharmaceutical design
Management of national and multi-national corporations
Financial and economic modeling
Advanced graphics and virtual reality, particularly in the entertainment industry
Networked video and multi-media technologies
Collaborative work environments

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Overview

Why Use Parallel Computing?

Main Reasons:

Save time and/or money: In theory, throwing more resources at a task will shorten its time to completion, with potential
cost savings. Parallel clusters can be built from cheap, commodity components.

Solve larger problems: Many problems are so large and/or complex that it is impractical or impossible to solve them on a
single computer, especially given limited computer memory. For example:
"Grand Challenge" (en.wikipedia.org/wiki/Grand_Challenge) problems requiring PetaFLOPS and PetaBytes of
computing resources.
Web search engines/databases processing millions of transactions per second

Provide concurrency: A single compute resource can only do one thing at a time. Multiple computing resources can be
doing many things simultaneously. For example, the Access Grid (www.accessgrid.org) provides a global collaboration
network where people from around the world can meet and conduct work "virtually".

Use of non-local resources: Using compute resources on a wide area network, or even the Internet when local compute
resources are scarce. For example:
SETI@home (setiathome.berkeley.edu) uses over 330,000 computers for a compute power over 528 TeraFLOPS (as
of August 04, 2008)
Folding@home (folding.stanford.edu) uses over 340,000 computers for a compute power of 4.2 PetaFLOPS (as of
November 4, 2008)

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Limits to serial computing: Both physical and practical reasons pose significant constraints to simply building ever faster
serial computers:
Transmission speeds - the speed of a serial computer is directly dependent upon how fast data can move through
hardware. Absolute limits are the speed of light (30 cm/nanosecond) and the transmission limit of copper wire (9
cm/nanosecond). Increasing speeds necessitate increasing proximity of processing elements.
Limits to miniaturization - processor technology is allowing an increasing number of transistors to be placed on a
chip. However, even with molecular or atomic-level components, a limit will be reached on how small components
can be.
Economic limitations - it is increasingly expensive to make a single processor faster. Using a larger number of
moderately fast commodity processors to achieve the same (or better) performance is less expensive.

Current computer architectures are increasingly relying upon hardware level parallelism to improve performance:

Multiple execution units

Pipelined instructions
Multi-core

Who and What?

Top500.org provides statistics on parallel computing users - the charts below are just a sample. Some things to note:
Sectors may overlap - for example, research may be classified research. Respondents have to choose between the
two.
"Not Specified" is by far the largest application - probably means multiple applications.

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The Future:

During the past 20 years, the trends indicated by ever faster networks, distributed systems, and multi-processor computer
architectures (even at the desktop level) clearly show that parallelism is the future of computing.

Concepts and Terminology

von Neumann Architecture

Named after the Hungarian mathematician John von Neumann who first authored the general requirements for an
electronic computer in his 1945 papers.
Since then, virtually all computers have followed this basic design, which differed from earlier computers programmed

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through "hard wiring".

Comprised of four main components:

Memory
Control Unit
Arithmetic Logic Unit
Input/Output
Read/write, random access memory is used to store both program
instructions and data
Program instructions are coded data which tell the computer to
do something
Data is simply information to be used by the program
Control unit fetches instructions/data from memory, decodes the
instructions and then sequentially coordinates operations to
accomplish the programmed task.
Aritmetic Unit performs basic arithmetic operations
Input/Output is the interface to the human operator

Concepts and Terminology

Flynn's Classical Taxonomy

There are different ways to classify parallel computers. One of the more widely used classifications, in use since 1966, is
called Flynn's Taxonomy.

Flynn's taxonomy distinguishes multi-processor computer architectures according to how they can be classified along the
two independent dimensions of Instruction and Data. Each of these dimensions can have only one of two possible states:
Single or Multiple.

The matrix below defines the 4 possible classifications according to Flynn:

SISD SIMD

Single Instruction, Single Data Single Instruction, Multiple Data

MISD MIMD

Multiple Instruction, Single Data Multiple Instruction, Multiple Data

Single Instruction, Single Data (SISD):

A serial (non-parallel) computer

Single instruction: only one instruction stream is being acted on by the CPU during any
one clock cycle
Single data: only one data stream is being used as input during any one clock cycle
Deterministic execution
This is the oldest and even today, the most common type of computer
Examples: older generation mainframes, minicomputers and workstations; most modern
day PCs.

UNIVAC1 IBM 360 CRAY1

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CDC 7600 PDP1 Dell Laptop

Single Instruction, Multiple Data (SIMD):

A type of parallel computer

Single instruction: All processing units execute the
same instruction at any given clock cycle
Multiple data: Each processing unit can operate on
a different data element
Best suited for specialized problems characterized
by a high degree of regularity, such as
graphics/image processing.
Synchronous (lockstep) and deterministic execution
Two varieties: Processor Arrays and Vector
Pipelines
Examples:
Processor Arrays: Connection Machine
CM-2, MasPar MP-1 & MP-2, ILLIAC IV
Vector Pipelines: IBM 9000, Cray X-MP,
Y-MP & C90, Fujitsu VP, NEC SX-2,
Hitachi S820, ETA10
Most modern computers, particularly those with
graphics processor units (GPUs) employ SIMD
instructions and execution units.

ILLIAC IV MasPar

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Cray X-MP Cray Y-MP Thinking Machines CM-2 Cell Processor

Multiple Instruction, Single Data (MISD):

A single data stream is fed into multiple processing

units.
Each processing unit operates on the data
independently via independent instruction streams.
Few actual examples of this class of parallel
computer have ever existed. One is the
experimental Carnegie-Mellon C.mmp computer
(1971).
Some conceivable uses might be:
multiple frequency filters operating on a
single signal stream
multiple cryptography algorithms attempting
to crack a single coded message.

Multiple Instruction, Multiple Data (MIMD):

Currently, the most common type of parallel

computer. Most modern computers fall into this
category.
Multiple Instruction: every processor may be
executing a different instruction stream
Multiple Data: every processor may be working
with a different data stream
Execution can be synchronous or asynchronous,
deterministic or non-deterministic
Examples: most current supercomputers,
networked parallel computer clusters and "grids",
multi-processor SMP computers, multi-core PCs.
Note: many MIMD architectures also include
SIMD execution sub-components

IBM POWER5 HP/Compaq Alphaserver Intel IA32

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AMD Opteron Cray XT3 IBM BG/L

Concepts and Terminology

Some General Parallel Terminology

Like everything else, parallel computing has its own "jargon". Some of the more commonly used terms associated with parallel
computing are listed below. Most of these will be discussed in more detail later.

Task
A logically discrete section of computational work. A task is typically a program or program-like set of instructions that is
executed by a processor.

Parallel Task
A task that can be executed by multiple processors safely (yields correct results)

Serial Execution
Execution of a program sequentially, one statement at a time. In the simplest sense, this is what happens on a one processor
machine. However, virtually all parallel tasks will have sections of a parallel program that must be executed serially.

Parallel Execution
Execution of a program by more than one task, with each task being able to execute the same or different statement at the
same moment in time.

Pipelining
Breaking a task into steps performed by different processor units, with inputs streaming through, much like an assembly
line; a type of parallel computing.

Shared Memory
From a strictly hardware point of view, describes a computer architecture where all processors have direct (usually bus
based) access to common physical memory. In a programming sense, it describes a model where parallel tasks all have the
same "picture" of memory and can directly address and access the same logical memory locations regardless of where the
physical memory actually exists.

Symmetric Multi-Processor (SMP)

Hardware architecture where multiple processors share a single address space and access to all resources; shared memory
computing.

Distributed Memory
In hardware, refers to network based memory access for physical memory that is not common. As a programming model,
tasks can only logically "see" local machine memory and must use communications to access memory on other machines
where other tasks are executing.

Communications
Parallel tasks typically need to exchange data. There are several ways this can be accomplished, such as through a shared
memory bus or over a network, however the actual event of data exchange is commonly referred to as communications
regardless of the method employed.

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Synchronization
The coordination of parallel tasks in real time, very often associated with communications. Often implemented by
establishing a synchronization point within an application where a task may not proceed further until another task(s)
reaches the same or logically equivalent point.

Synchronization usually involves waiting by at least one task, and can therefore cause a parallel application's wall clock
execution time to increase.

Granularity
In parallel computing, granularity is a qualitative measure of the ratio of computation to communication.
Coarse: relatively large amounts of computational work are done between communication events
Fine: relatively small amounts of computational work are done between communication events

Observed Speedup
Observed speedup of a code which has been parallelized, defined as:

wall-clock time of serial execution

-----------------------------------
wall-clock time of parallel execution

One of the simplest and most widely used indicators for a parallel program's performance.

Parallel Overhead
The amount of time required to coordinate parallel tasks, as opposed to doing useful work. Parallel overhead can include
factors such as:
Task start-up time
Synchronizations
Data communications
Software overhead imposed by parallel compilers, libraries, tools, operating system, etc.
Task termination time

Massively Parallel
Refers to the hardware that comprises a given parallel system - having many processors. The meaning of "many" keeps
increasing, but currently, the largest parallel computers can be comprised of processors numbering in the hundreds of
thousands.

Embarrassingly Parallel
Solving many similar, but independent tasks simultaneously; little to no need for coordination between the tasks.

Scalability
Refers to a parallel system's (hardware and/or software) ability to demonstrate a proportionate increase in parallel speedup
with the addition of more processors. Factors that contribute to scalability include:
Hardware - particularly memory-cpu bandwidths and network communications
Application algorithm
Parallel overhead related
Characteristics of your specific application and coding

Multi-core Processors
Multiple processors (cores) on a single chip.

Cluster Computing
Use of a combination of commodity units (processors, networks or SMPs) to build a parallel system.

Supercomputing / High Performance Computing

Use of the world's fastest, largest machines to solve large problems.

Parallel Computer Memory Architectures

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Shared Memory
General Characteristics:

Shared memory parallel computers vary

widely, but generally have in common the
ability for all processors to access all memory
as global address space.

Multiple processors can operate independently

but share the same memory resources.

Changes in a memory location effected by one

processor are visible to all other processors.

Shared memory machines can be divided into

two main classes based upon memory access
times: UMA and NUMA.

Uniform Memory Access (UMA): Shared Memory (UMA)

Most commonly represented today by

Symmetric Multiprocessor (SMP) machines
Identical processors
Equal access and access times to memory
Sometimes called CC-UMA - Cache Coherent
UMA. Cache coherent means if one processor
updates a location in shared memory, all the
other processors know about the update. Cache
coherency is accomplished at the hardware
level.

Non-Uniform Memory Access (NUMA):

Shared Memory (NUMA)
Often made by physically linking two or more
SMPs
One SMP can directly access memory of
another SMP
Not all processors have equal access time to all
memories
Memory access across link is slower
If cache coherency is maintained, then may
also be called CC-NUMA - Cache Coherent
NUMA

Advantages:

Global address space provides a user-friendly programming perspective to memory

Data sharing between tasks is both fast and uniform due to the proximity of memory to CPUs

Disadvantages:

Primary disadvantage is the lack of scalability between memory and CPUs. Adding more CPUs can geometrically increases
traffic on the shared memory-CPU path, and for cache coherent systems, geometrically increase traffic associated with
cache/memory management.
Programmer responsibility for synchronization constructs that ensure "correct" access of global memory.
Expense: it becomes increasingly difficult and expensive to design and produce shared memory machines with ever
increasing numbers of processors.

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Parallel Computer Memory Architectures

Distributed Memory
General Characteristics:

Like shared memory systems, distributed memory systems vary widely but share a common characteristic. Distributed
memory systems require a communication network to connect inter-processor memory.

Processors have their own local memory. Memory addresses in one processor do not map to another processor, so there is
no concept of global address space across all processors.

Because each processor has its own local memory, it operates independently. Changes it makes to its local memory have
no effect on the memory of other processors. Hence, the concept of cache coherency does not apply.

When a processor needs access to data in another processor, it is usually the task of the programmer to explicitly define
how and when data is communicated. Synchronization between tasks is likewise the programmer's responsibility.

The network "fabric" used for data transfer varies widely, though it can can be as simple as Ethernet.

Advantages:

Memory is scalable with number of processors. Increase the number of processors and the size of memory increases
proportionately.
Each processor can rapidly access its own memory without interference and without the overhead incurred with trying to
maintain cache coherency.
Cost effectiveness: can use commodity, off-the-shelf processors and networking.

Disadvantages:

The programmer is responsible for many of the details associated with data communication between processors.
It may be difficult to map existing data structures, based on global memory, to this memory organization.
Non-uniform memory access (NUMA) times

Parallel Computer Memory Architectures

Hybrid Distributed-Shared Memory

The largest and fastest computers in the world today employ both shared and distributed memory architectures.

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The shared memory component is usually a cache coherent SMP machine. Processors on a given SMP can address that
machine's memory as global.

The distributed memory component is the networking of multiple SMPs. SMPs know only about their own memory - not
the memory on another SMP. Therefore, network communications are required to move data from one SMP to another.

Current trends seem to indicate that this type of memory architecture will continue to prevail and increase at the high end
of computing for the foreseeable future.

Advantages and Disadvantages: whatever is common to both shared and distributed memory architectures.

Parallel Programming Models

Overview
There are several parallel programming models in common use:
Shared Memory
Threads
Message Passing
Data Parallel
Hybrid

Parallel programming models exist as an abstraction above hardware and memory architectures.

Although it might not seem apparent, these models are NOT specific to a particular type of machine or memory
architecture. In fact, any of these models can (theoretically) be implemented on any underlying hardware. Two examples:

1. Shared memory model on a distributed memory machine: Kendall Square Research (KSR) ALLCACHE approach.

Machine memory was physically distributed, but appeared to the user as a single shared memory (global address
space). Generically, this approach is referred to as "virtual shared memory". Note: although KSR is no longer in
business, there is no reason to suggest that a similar implementation will not be made available by another vendor in
the future.

2. Message passing model on a shared memory machine: MPI on SGI Origin.

The SGI Origin employed the CC-NUMA type of shared memory architecture, where every task has direct access to
global memory. However, the ability to send and receive messages with MPI, as is commonly done over a network
of distributed memory machines, is not only implemented but is very commonly used.

Which model to use is often a combination of what is available and personal choice. There is no "best" model, although
there certainly are better implementations of some models over others.

The following sections describe each of the models mentioned above, and also discuss some of their actual
implementations.

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Parallel Programming Models

Shared Memory Model

In the shared-memory programming model, tasks share a common address space, which they read and write
asynchronously.

Various mechanisms such as locks / semaphores may be used to control access to the shared memory.

An advantage of this model from the programmer's point of view is that the notion of data "ownership" is lacking, so there
is no need to specify explicitly the communication of data between tasks. Program development can often be simplified.

An important disadvantage in terms of performance is that it becomes more difficult to understand and manage data
locality.
Keeping data local to the processor that works on it conserves memory accesses, cache refreshes and bus traffic that
occurs when multiple processors use the same data.
Unfortunately, controlling data locality is hard to understand and beyond the control of the average user.

Implementations:

On shared memory platforms, the native compilers translate user program variables into actual memory addresses, which
are global.

No common distributed memory platform implementations currently exist. However, as mentioned previously in the
Overview section, the KSR ALLCACHE approach provided a shared memory view of data even though the physical
memory of the machine was distributed.

Parallel Programming Models

Threads Model
In the threads model of parallel programming, a single process can have multiple, concurrent execution paths.

Perhaps the most simple analogy that can be used to describe threads is the concept of a single program that includes a
number of subroutines:

The main program a.out is scheduled to run by the native

operating system. a.out loads and acquires all of the
necessary system and user resources to run.

a.out performs some serial work, and then creates a

number of tasks (threads) that can be scheduled and run by
the operating system concurrently.

Each thread has local data, but also, shares the entire
resources of a.out. This saves the overhead associated
with replicating a program's resources for each thread.
Each thread also benefits from a global memory view
because it shares the memory space of a.out.

A thread's work may best be described as a subroutine within the main program. Any thread can execute any
subroutine at the same time as other threads.

Threads communicate with each other through global memory (updating address locations). This requires
synchronization constructs to ensure that more than one thread is not updating the same global address at any time.

Threads can come and go, but a.out remains present to provide the necessary shared resources until the application
has completed.

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Threads are commonly associated with shared memory architectures and operating systems.

Implementations:

From a programming perspective, threads implementations commonly comprise:

A library of subroutines that are called from within parallel source code
A set of compiler directives imbedded in either serial or parallel source code

In both cases, the programmer is responsible for determining all parallelism.

Threaded implementations are not new in computing. Historically, hardware vendors have implemented their own
proprietary versions of threads. These implementations differed substantially from each other making it difficult for
programmers to develop portable threaded applications.

Unrelated standardization efforts have resulted in two very different implementations of threads: POSIX Threads and
OpenMP.

POSIX Threads
Library based; requires parallel coding
Specified by the IEEE POSIX 1003.1c standard (1995).
C Language only
Commonly referred to as Pthreads.
Most hardware vendors now offer Pthreads in addition to their proprietary threads implementations.
Very explicit parallelism; requires significant programmer attention to detail.

OpenMP
Compiler directive based; can use serial code
Jointly defined and endorsed by a group of major computer hardware and software vendors. The OpenMP Fortran
API was released October 28, 1997. The C/C++ API was released in late 1998.
Portable / multi-platform, including Unix and Windows NT platforms
Available in C/C++ and Fortran implementations
Can be very easy and simple to use - provides for "incremental parallelism"

Microsoft has its own implementation for threads, which is not related to the UNIX POSIX standard or OpenMP.

More Information:

POSIX Threads tutorial: computing.llnl.gov/tutorials/pthreads

OpenMP tutorial: computing.llnl.gov/tutorials/openMP

Parallel Programming Models

Message Passing Model

The message passing model demonstrates the following characteristics:

A set of tasks that use their own local

memory during computation. Multiple tasks
can reside on the same physical machine
and/or across an arbitrary number of
machines.

Tasks exchange data through

communications by sending and receiving
messages.

Data transfer usually requires cooperative

operations to be performed by each process.
For example, a send operation must have a

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matching receive operation.

Implementations:

From a programming perspective, message passing implementations commonly comprise a library of subroutines that are
imbedded in source code. The programmer is responsible for determining all parallelism.

Historically, a variety of message passing libraries have been available since the 1980s. These implementations differed
substantially from each other making it difficult for programmers to develop portable applications.

In 1992, the MPI Forum was formed with the primary goal of establishing a standard interface for message passing
implementations.

Part 1 of the Message Passing Interface (MPI) was released in 1994. Part 2 (MPI-2) was released in 1996. Both MPI
specifications are available on the web at http://www-unix.mcs.anl.gov/mpi/.

MPI is now the "de facto" industry standard for message passing, replacing virtually all other message passing
implementations used for production work. Most, if not all of the popular parallel computing platforms offer at least one
implementation of MPI. A few offer a full implementation of MPI-2.

For shared memory architectures, MPI implementations usually don't use a network for task communications. Instead, they
use shared memory (memory copies) for performance reasons.

More Information:

MPI tutorial: computing.llnl.gov/tutorials/mpi

Parallel Programming Models

Data Parallel Model

The data parallel model demonstrates the following characteristics:

Most of the parallel work focuses on performing

operations on a data set. The data set is typically
organized into a common structure, such as an
array or cube.

A set of tasks work collectively on the same data

structure, however, each task works on a
different partition of the same data structure.

Tasks perform the same operation on their

partition of work, for example, "add 4 to every
array element".

On shared memory architectures, all tasks may have

access to the data structure through global memory. On
distributed memory architectures the data structure is
split up and resides as "chunks" in the local memory of
each task.

Implementations:

Programming with the data parallel model is usually accomplished by writing a program with data parallel constructs. The
constructs can be calls to a data parallel subroutine library or, compiler directives recognized by a data parallel compiler.

Fortran 90 and 95 (F90, F95): ISO/ANSI standard extensions to Fortran 77.

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Contains everything that is in Fortran 77

New source code format; additions to character set
Additions to program structure and commands
Variable additions - methods and arguments
Pointers and dynamic memory allocation added
Array processing (arrays treated as objects) added
Recursive and new intrinsic functions added
Many other new features

Implementations are available for most common parallel platforms.

High Performance Fortran (HPF): Extensions to Fortran 90 to support data parallel programming.
Contains everything in Fortran 90
Directives to tell compiler how to distribute data added
Assertions that can improve optimization of generated code added
Data parallel constructs added (now part of Fortran 95)

HPF compilers were common in the 1990s, but are no longer commonly implemented.

Compiler Directives: Allow the programmer to specify the distribution and alignment of data. Fortran implementations
are available for most common parallel platforms.

Distributed memory implementations of this model usually have the compiler convert the program into standard code with
calls to a message passing library (MPI usually) to distribute the data to all the processes. All message passing is done
invisibly to the programmer.

Parallel Programming Models

Other Models
Other parallel programming models besides those previously mentioned certainly exist, and will continue to evolve along
with the ever changing world of computer hardware and software. Only three of the more common ones are mentioned
here.

Hybrid:

In this model, any two or more parallel programming models are combined.

Currently, a common example of a hybrid model is the combination of the message passing model (MPI) with either the
threads model (POSIX threads) or the shared memory model (OpenMP). This hybrid model lends itself well to the
increasingly common hardware environment of networked SMP machines.

Another common example of a hybrid model is combining data parallel with message passing. As mentioned in the data
parallel model section previously, data parallel implementations (F90, HPF) on distributed memory architectures actually
use message passing to transmit data between tasks, transparently to the programmer.

Single Program Multiple Data (SPMD):

SPMD is actually a "high level" programming model that can be built upon any combination of the previously mentioned
parallel programming models.

A single program is executed by all tasks simultaneously.

At any moment in time, tasks can be executing the same

or different instructions within the same program.

SPMD programs usually have the necessary logic

programmed into them to allow different tasks to branch or conditionally execute only those parts of the program they are
designed to execute. That is, tasks do not necessarily have to execute the entire program - perhaps only a portion of it.

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All tasks may use different data

Multiple Program Multiple Data (MPMD):

Like SPMD, MPMD is actually a "high level" programming model that can be built upon any combination of the
previously mentioned parallel programming models.

MPMD applications typically have multiple executable

object files (programs). While the application is being run
in parallel, each task can be executing the same or
different program as other tasks.

All tasks may use different data

Designing Parallel Programs

Automatic vs. Manual Parallelization

Designing and developing parallel programs has characteristically been a very manual process. The programmer is typically
responsible for both identifying and actually implementing parallelism.

Very often, manually developing parallel codes is a time consuming, complex, error-prone and iterative process.

For a number of years now, various tools have been available to assist the programmer with converting serial programs into
parallel programs. The most common type of tool used to automatically parallelize a serial program is a parallelizing
compiler or pre-processor.

A parallelizing compiler generally works in two different ways:

Fully Automatic
The compiler analyzes the source code and identifies opportunities for parallelism.
The analysis includes identifying inhibitors to parallelism and possibly a cost weighting on whether or not the
parallelism would actually improve performance.
Loops (do, for) loops are the most frequent target for automatic parallelization.

Programmer Directed
Using "compiler directives" or possibly compiler flags, the programmer explicitly tells the compiler how to
parallelize the code.
May be able to be used in conjunction with some degree of automatic parallelization also.

If you are beginning with an existing serial code and have time or budget constraints, then automatic parallelization may be
the answer. However, there are several important caveats that apply to automatic parallelization:
Wrong results may be produced
Performance may actually degrade
Much less flexible than manual parallelization
Limited to a subset (mostly loops) of code
May actually not parallelize code if the analysis suggests there are inhibitors or the code is too complex

The remainder of this section applies to the manual method of developing parallel codes.

Designing Parallel Programs

Understand the Problem and the Program

Undoubtedly, the first step in developing parallel software is to first understand the problem that you wish to solve in
parallel. If you are starting with a serial program, this necessitates understanding the existing code also.

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Before spending time in an attempt to develop a parallel solution for a problem, determine whether or not the problem is
one that can actually be parallelized.

Example of Parallelizable Problem:

Calculate the potential energy for each of several thousand independent

conformations of a molecule. When done, find the minimum energy
conformation.

This problem is able to be solved in parallel. Each of the molecular conformations is independently determinable.
The calculation of the minimum energy conformation is also a parallelizable problem.

Example of a Non-parallelizable Problem:

Calculation of the Fibonacci series (1,1,2,3,5,8,13,21,...) by use of the formula:

F(n) = F(n-1) + F(n-2)

This is a non-parallelizable problem because the calculation of the Fibonacci sequence as shown would entail
dependent calculations rather than independent ones. The calculation of the F(n) value uses those of both F(n-1) and
F(n-2). These three terms cannot be calculated independently and therefore, not in parallel.

Identify the program's hotspots:

Know where most of the real work is being done. The majority of scientific and technical programs usually
accomplish most of their work in a few places.
Profilers and performance analysis tools can help here
Focus on parallelizing the hotspots and ignore those sections of the program that account for little CPU usage.

Identify bottlenecks in the program

Are there areas that are disproportionately slow, or cause parallelizable work to halt or be deferred? For example,
I/O is usually something that slows a program down.
May be possible to restructure the program or use a different algorithm to reduce or eliminate unnecessary slow
areas

Identify inhibitors to parallelism. One common class of inhibitor is data dependence, as demonstrated by the Fibonacci
sequence above.

Investigate other algorithms if possible. This may be the single most important consideration when designing a parallel
application.

Designing Parallel Programs

Partitioning
One of the first steps in designing a parallel program is to break the problem into discrete "chunks" of work that can be
distributed to multiple tasks. This is known as decomposition or partitioning.

There are two basic ways to partition computational work among parallel tasks: domain decomposition and functional
decomposition.

Domain Decomposition:

In this type of partitioning, the data associated with a problem is decomposed. Each parallel task then works on a portion of
of the data.

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There are different ways to partition data:

Functional Decomposition:

In this approach, the focus is on the computation that is to be performed rather than on the data manipulated by the
computation. The problem is decomposed according to the work that must be done. Each task then performs a portion of
the overall work.

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Functional decomposition lends itself well to problems that can be split into different tasks. For example:

Ecosystem Modeling
Each program calculates the population of a given group, where each group's growth depends on that of its neighbors. As
time progresses, each process calculates its current state, then exchanges information with the neighbor populations. All
tasks then progress to calculate the state at the next time step.

Signal Processing
An audio signal data set is passed through four distinct computational filters. Each filter is a separate process. The first
segment of data must pass through the first filter before progressing to the second. When it does, the second segment of
data passes through the first filter. By the time the fourth segment of data is in the first filter, all four tasks are busy.

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Climate Modeling
Each model component can be thought of as a separate task. Arrows represent exchanges of data between components
during computation: the atmosphere model generates wind velocity data that are used by the ocean model, the ocean model
generates sea surface temperature data that are used by the atmosphere model, and so on.

Combining these two types of problem decomposition is common and natural.

Designing Parallel Programs

Communications
Who Needs Communications?

The need for communications between tasks depends upon your problem:

You DON'T need communications

Some types of problems can be decomposed and executed in parallel with virtually no need for tasks to share data.
For example, imagine an image processing operation where every pixel in a black and white image needs to have its
color reversed. The image data can easily be distributed to multiple tasks that then act independently of each other to
do their portion of the work.
These types of problems are often called embarrassingly parallel because they are so straight-forward. Very little
inter-task communication is required.

You DO need communications

Most parallel applications are not quite so simple, and do require tasks to share data with each other. For example, a
3-D heat diffusion problem requires a task to know the temperatures calculated by the tasks that have neighboring
data. Changes to neighboring data has a direct effect on that task's data.

Factors to Consider:

There are a number of important factors to consider when designing your program's inter-task communications:

Cost of communications
Inter-task communication virtually always implies overhead.
Machine cycles and resources that could be used for computation are instead used to package and transmit data.
Communications frequently require some type of synchronization between tasks, which can result in tasks spending
time "waiting" instead of doing work.
Competing communication traffic can saturate the available network bandwidth, further aggravating performance
problems.

Latency vs. Bandwidth

latency is the time it takes to send a minimal (0 byte) message from point A to point B. Commonly expressed as
microseconds.
bandwidth is the amount of data that can be communicated per unit of time. Commonly expressed as megabytes/sec

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or gigabytes/sec.
Sending many small messages can cause latency to dominate communication overheads. Often it is more efficient to
package small messages into a larger message, thus increasing the effective communications bandwidth.

Visibility of communications
With the Message Passing Model, communications are explicit and generally quite visible and under the control of
the programmer.
With the Data Parallel Model, communications often occur transparently to the programmer, particularly on
distributed memory architectures. The programmer may not even be able to know exactly how inter-task
communications are being accomplished.

Synchronous vs. asynchronous communications

Synchronous communications require some type of "handshaking" between tasks that are sharing data. This can be
explicitly structured in code by the programmer, or it may happen at a lower level unknown to the programmer.
Synchronous communications are often referred to as blocking communications since other work must wait until the
communications have completed.
Asynchronous communications allow tasks to transfer data independently from one another. For example, task 1 can
prepare and send a message to task 2, and then immediately begin doing other work. When task 2 actually receives
the data doesn't matter.
Asynchronous communications are often referred to as non-blocking communications since other work can be done
while the communications are taking place.
Interleaving computation with communication is the single greatest benefit for using asynchronous communications.

Scope of communications
Knowing which tasks must communicate with each other is critical during the design stage of a parallel code. Both of
the two scopings described below can be implemented synchronously or asynchronously.
Point-to-point - involves two tasks with one task acting as the sender/producer of data, and the other acting as the
receiver/consumer.
Collective - involves data sharing between more than two tasks, which are often specified as being members in a
common group, or collective. Some common variations (there are more):

Efficiency of communications
Very often, the programmer will have a choice with regard to factors that can affect communications performance.
Only a few are mentioned here.
Which implementation for a given model should be used? Using the Message Passing Model as an example, one MPI
implementation may be faster on a given hardware platform than another.
What type of communication operations should be used? As mentioned previously, asynchronous communication
operations can improve overall program performance.
Network media - some platforms may offer more than one network for communications. Which one is best?

Overhead and Complexity

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Finally, realize that this is only a partial list of things to consider!!!

Designing Parallel Programs

Synchronization
Types of Synchronization:

Barrier
Usually implies that all tasks are involved
Each task performs its work until it reaches the barrier. It then stops, or "blocks".
When the last task reaches the barrier, all tasks are synchronized.
What happens from here varies. Often, a serial section of work must be done. In other cases, the tasks are
automatically released to continue their work.

Lock / semaphore
Can involve any number of tasks
Typically used to serialize (protect) access to global data or a section of code. Only one task at a time may use (own)
the lock / semaphore / flag.
The first task to acquire the lock "sets" it. This task can then safely (serially) access the protected data or code.
Other tasks can attempt to acquire the lock but must wait until the task that owns the lock releases it.
Can be blocking or non-blocking

Synchronous communication operations

Involves only those tasks executing a communication operation
When a task performs a communication operation, some form of coordination is required with the other task(s)
participating in the communication. For example, before a task can perform a send operation, it must first receive an
acknowledgment from the receiving task that it is OK to send.
Discussed previously in the Communications section.

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Designing Parallel Programs

Data Dependencies
Definition:

A dependence exists between program statements when the order of statement execution affects the results of the
program.

A data dependence results from multiple use of the same location(s) in storage by different tasks.

Dependencies are important to parallel programming because they are one of the primary inhibitors to parallelism.

Examples:

Loop carried data dependence

DO 500 J = MYSTART,MYEND
A(J) = A(J-1) * 2.0
500 CONTINUE

The value of A(J-1) must be computed before the value of A(J), therefore A(J) exhibits a data dependency on A(J-1).
Parallelism is inhibited.

If Task 2 has A(J) and task 1 has A(J-1), computing the correct value of A(J) necessitates:

Distributed memory architecture - task 2 must obtain the value of A(J-1) from task 1 after task 1 finishes its
computation
Shared memory architecture - task 2 must read A(J-1) after task 1 updates it

Loop independent data dependence

task 1 task 2
------ ------

X = 2 X = 4
. .
. .
Y = X**2 Y = X**3

As with the previous example, parallelism is inhibited. The value of Y is dependent on:

Distributed memory architecture - if or when the value of X is communicated between the tasks.
Shared memory architecture - which task last stores the value of X.

Although all data dependencies are important to identify when designing parallel programs, loop carried dependencies are
particularly important since loops are possibly the most common target of parallelization efforts.

How to Handle Data Dependencies:

Distributed memory architectures - communicate required data at synchronization points.

Shared memory architectures -synchronize read/write operations between tasks.

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Designing Parallel Programs

Load Balancing
Load balancing refers to the practice of distributing work among tasks so that all tasks are kept busy all of the time. It can
be considered a minimization of task idle time.

Load balancing is important to parallel programs for performance reasons. For example, if all tasks are subject to a barrier
synchronization point, the slowest task will determine the overall performance.

How to Achieve Load Balance:

Equally partition the work each task receives

For array/matrix operations where each task performs similar work, evenly distribute the data set among the tasks.
For loop iterations where the work done in each iteration is similar, evenly distribute the iterations across the tasks.
If a heterogeneous mix of machines with varying performance characteristics are being used, be sure to use some
type of performance analysis tool to detect any load imbalances. Adjust work accordingly.

Use dynamic work assignment

Certain classes of problems result in load imbalances even if data is evenly distributed among tasks:
Sparse arrays - some tasks will have actual data to work on while others have mostly "zeros".
Adaptive grid methods - some tasks may need to refine their mesh while others don't.
N-body simulations - where some particles may migrate to/from their original task domain to another task's;
where the particles owned by some tasks require more work than those owned by other tasks.
When the amount of work each task will perform is intentionally variable, or is unable to be predicted, it may be
helpful to use a scheduler - task pool approach. As each task finishes its work, it queues to get a new piece of work.
It may become necessary to design an algorithm which detects and handles load imbalances as they occur
dynamically within the code.

Designing Parallel Programs

Granularity
Computation / Communication Ratio:

In parallel computing, granularity is a qualitative measure of the ratio of computation to communication.

Periods of computation are typically separated from periods of communication by synchronization events.

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Fine-grain Parallelism:

Relatively small amounts of computational work are done between communication events

Low computation to communication ratio

Facilitates load balancing

Implies high communication overhead and less opportunity for performance enhancement

If granularity is too fine it is possible that the overhead required for communications and
synchronization between tasks takes longer than the computation.

Coarse-grain Parallelism:

Relatively large amounts of computational work are done between

communication/synchronization events

High computation to communication ratio

Implies more opportunity for performance increase

Harder to load balance efficiently

Which is Best?

The most efficient granularity is dependent on the algorithm and the hardware environment in
which it runs.

In most cases the overhead associated with communications and synchronization is high relative
to execution speed so it is advantageous to have coarse granularity.

Fine-grain parallelism can help reduce overheads due to load imbalance.

Designing Parallel Programs

I/O
The Bad News:

I/O operations are generally regarded as inhibitors to parallelism

Parallel I/O systems may be immature or not available for all platforms

In an environment where all tasks see the same file space, write operations can result in file overwriting

Read operations can be affected by the file server's ability to handle multiple read requests at the same time

I/O that must be conducted over the network (NFS, non-local) can cause severe bottlenecks and even crash file servers.

The Good News:

Parallel file systems are available. For example:

GPFS: General Parallel File System for AIX (IBM)
Lustre: for Linux clusters (SUN Microsystems)
PVFS/PVFS2: Parallel Virtual File System for Linux clusters (Clemson/Argonne/Ohio State/others)
PanFS: Panasas ActiveScale File System for Linux clusters (Panasas, Inc.)
HP SFS: HP StorageWorks Scalable File Share. Lustre based parallel file system (Global File System for Linux)
product from HP

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The parallel I/O programming interface specification for MPI has been available since 1996 as part of MPI-2. Vendor and
"free" implementations are now commonly available.

Some options:

If you have access to a parallel file system, investigate using it. If you don't, keep reading...

Rule #1: Reduce overall I/O as much as possible

Confine I/O to specific serial portions of the job, and then use parallel communications to distribute data to parallel
tasks. For example, Task 1 could read an input file and then communicate required data to other tasks. Likewise,
Task 1 could perform write operation after receiving required data from all other tasks.

For distributed memory systems with shared filespace, perform I/O in local, non-shared filespace. For example, each
processor may have /tmp filespace which can used. This is usually much more efficient than performing I/O over the
network to one's home directory.

Create unique filenames for each task's input/output file(s)

Designing Parallel Programs

Limits and Costs of Parallel Programming

Amdahl's Law:

Amdahl's Law states that potential program speedup is defined

by the fraction of code (P) that can be parallelized:

1
speedup = --------
1 - P

If none of the code can be parallelized, P = 0 and the speedup =

1 (no speedup).

If all of the code is parallelized, P = 1 and the speedup is infinite

(in theory).

If 50% of the code can be parallelized, maximum speedup = 2,

meaning the code will run twice as fast.

Introducing the number of processors performing the parallel

fraction of work, the relationship can be modeled by:

1
speedup = ------------
P + S
---
N

where P = parallel fraction, N = number of processors and S =

serial fraction.

It soon becomes obvious that there are limits to the scalability of

parallelism. For example:

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speedup
--------------------------------
N P = .50 P = .90 P = .99
----- ------- ------- -------
10 1.82 5.26 9.17
100 1.98 9.17 50.25
1000 1.99 9.91 90.99
10000 1.99 9.91 99.02
100000 1.99 9.99 99.90

However, certain problems demonstrate increased performance by increasing the problem size. For example:

2D Grid Calculations 85 seconds 85%

Serial fraction 15 seconds 15%

We can increase the problem size by doubling the grid dimensions and halving the time step. This results in four times the
number of grid points and twice the number of time steps. The timings then look like:

2D Grid Calculations 680 seconds 97.84%

Serial fraction 15 seconds 2.16%

Problems that increase the percentage of parallel time with their size are more scalable than problems with a fixed
percentage of parallel time.

Complexity:

In general, parallel applications are much more complex than corresponding serial applications, perhaps an order of
magnitude. Not only do you have multiple instruction streams executing at the same time, but you also have data flowing
between them.

The costs of complexity are measured in programmer time in virtually every aspect of the software development cycle:
Design
Coding
Debugging
Tuning
Maintenance

Adhering to "good" software development practices is essential when when working with parallel applications - especially
if somebody besides you will have to work with the software.

Portability:

Thanks to standardization in several APIs, such as MPI, POSIX threads, HPF and OpenMP, portability issues with parallel
programs are not as serious as in years past. However...

All of the usual portability issues associated with serial programs apply to parallel programs. For example, if you use
vendor "enhancements" to Fortran, C or C++, portability will be a problem.

Even though standards exist for several APIs, implementations will differ in a number of details, sometimes to the point of

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requiring code modifications in order to effect portability.

Operating systems can play a key role in code portability issues.

Hardware architectures are characteristically highly variable and can affect portability.

Resource Requirements:

The primary intent of parallel programming is to decrease execution wall clock time, however in order to accomplish this,
more CPU time is required. For example, a parallel code that runs in 1 hour on 8 processors actually uses 8 hours of CPU
time.

The amount of memory required can be greater for parallel codes than serial codes, due to the need to replicate data and
for overheads associated with parallel support libraries and subsystems.

For short running parallel programs, there can actually be a decrease in performance compared to a similar serial
implementation. The overhead costs associated with setting up the parallel environment, task creation, communications and
task termination can comprise a significant portion of the total execution time for short runs.

Scalability:

The ability of a parallel program's performance to scale is a result of a number of interrelated factors. Simply adding more
machines is rarely the answer.

The algorithm may have inherent limits to scalability. At some point, adding more resources causes performance to
decrease. Most parallel solutions demonstrate this characteristic at some point.

Hardware factors play a significant role in scalability. Examples:

Memory-cpu bus bandwidth on an SMP machine
Communications network bandwidth
Amount of memory available on any given machine or set of machines
Processor clock speed

Parallel support libraries and subsystems software can limit scalability independent of your application.

Designing Parallel Programs

Performance Analysis and Tuning

As with debugging, monitoring and analyzing parallel program execution is significantly more of a challenge than for serial
programs.

A number of parallel tools for execution monitoring and program analysis are available.

Some are quite useful; some are cross-platform also.

Some starting points:

LC's "Supported Software and Computing Tools" web pages at: computing.llnl.gov/code/content/software_tools.php
A dated, but potentially useful LC whitepaper on the subject of "High Performance Tools and Technologies"
describes a large number of tools, and a number of performance related topics applicable to code developers. Find it
at: computing.llnl.gov/tutorials/performance_tools/HighPerformanceToolsTechnologiesLC.pdf.
Performance Analysis Tools Tutorial

Work remains to be done, particularly in the area of scalability.

Parallel Examples

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Array Processing

This example demonstrates calculations on 2-dimensional array

elements, with the computation on each array element being
independent from other array elements.

The serial program calculates one element at a time in sequential

order.

Serial code could be of the form:

do j = 1,n
do i = 1,n
a(i,j) = fcn(i,j)
end do
end do

The calculation of elements is independent of one another - leads to

an embarrassingly parallel situation.

The problem should be computationally intensive.

Array Processing
Parallel Solution 1

Arrays elements are distributed so that each processor owns a portion

of an array (subarray).

Independent calculation of array elements ensures there is no need for

communication between tasks.

Distribution scheme is chosen by other criteria, e.g. unit stride (stride

of 1) through the subarrays. Unit stride maximizes cache/memory
usage.

Since it is desirable to have unit stride through the subarrays, the

choice of a distribution scheme depends on the programming
language. See the Block - Cyclic Distributions Diagram for the
options.

After the array is distributed, each task executes the portion of the
loop corresponding to the data it owns. For example, with Fortran
block distribution:

do j = mystart, myend
do i = 1,n
a(i,j) = fcn(i,j)
end do
end do

Notice that only the outer loop variables are different from the serial
solution.

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One Possible Solution:

Implement as a Single Program Multiple Data (SPMD) model.

Master process initializes array, sends info to worker processes and receives results.

Worker process receives info, performs its share of computation and sends results to master.

Using the Fortran storage scheme, perform block distribution of the array.

Pseudo code solution: red highlights changes for parallelism.

find out if I am MASTER or WORKER

if I am MASTER

initialize the array

send each WORKER info on part of array it owns
send each WORKER its portion of initial array

receive from each WORKER results

else if I am WORKER
receive from MASTER info on part of array I own
receive from MASTER my portion of initial array

# calculate my portion of array

do j = my first column,my last column
do i = 1,n
a(i,j) = fcn(i,j)
end do
end do

send MASTER results

endif

Example: MPI Program in C

Example: MPI Program in Fortran

Array Processing
Parallel Solution 2: Pool of Tasks
The previous array solution demonstrated static load balancing:
Each task has a fixed amount of work to do
May be significant idle time for faster or more lightly loaded processors - slowest tasks determines overall
performance.

Static load balancing is not usually a major concern if all tasks are performing the same amount of work on identical
machines.

If you have a load balance problem (some tasks work faster than others), you may benefit by using a "pool of tasks"
scheme.

Pool of Tasks Scheme:

Two processes are employed

Master Process:

Holds pool of tasks for worker processes to do

Sends worker a task when requested

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Collects results from workers

Worker Process: repeatedly does the following

Gets task from master process

Performs computation
Sends results to master

Worker processes do not know before runtime which portion of array they will handle or how many tasks they will
perform.

Dynamic load balancing occurs at run time: the faster tasks will get more work to do.

Pseudo code solution: red highlights changes for parallelism.

find out if I am MASTER or WORKER

if I am MASTER

do until no more jobs

send to WORKER next job
receive results from WORKER
end do

tell WORKER no more jobs

else if I am WORKER

do until no more jobs

receive from MASTER next job

calculate array element: a(i,j) = fcn(i,j)

send results to MASTER

end do

endif

Discussion:

In the above pool of tasks example, each task calculated an individual array element as a job. The computation to
communication ratio is finely granular.

Finely granular solutions incur more communication overhead in order to reduce task idle time.

A more optimal solution might be to distribute more work with each job. The "right" amount of work is problem dependent.

Parallel Examples

PI Calculation

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The value of PI can be calculated in a number of ways.

Consider the following method of approximating PI
1. Inscribe a circle in a square
2. Randomly generate points in the square
3. Determine the number of points in the square that
are also in the circle
4. Let r be the number of points in the circle divided
by the number of points in the square
5. PI ~ 4 r
6. Note that the more points generated, the better the
approximation

Serial pseudo code for this procedure:

npoints = 10000
circle_count = 0

do j = 1,npoints
generate 2 random numbers between 0 and 1
xcoordinate = random1
ycoordinate = random2
if (xcoordinate, ycoordinate) inside circle
then circle_count = circle_count + 1
end do

PI = 4.0*circle_count/npoints

Note that most of the time in running this program would

be spent executing the loop

Leads to an embarrassingly parallel solution

Computationally intensive
Minimal communication
Minimal I/O

PI Calculation
Parallel Solution

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Parallel strategy: break the loop into portions that can be

executed by the tasks.

For the task of approximating PI:

Each task executes its portion of the loop a number of
times.
Each task can do its work without requiring any
information from the other tasks (there are no data
dependencies).
Uses the SPMD model. One task acts as master and
collects the results.

Pseudo code solution: red highlights changes for parallelism.

npoints = 10000
circle_count = 0

p = number of tasks
num = npoints/p

find out if I am MASTER or WORKER

do j = 1,num
generate 2 random numbers between 0 and 1
xcoordinate = random1
ycoordinate = random2
if (xcoordinate, ycoordinate) inside circle
then circle_count = circle_count + 1
end do

if I am MASTER

receive from WORKERS their circle_counts

compute PI (use MASTER and WORKER calculations)

else if I am WORKER

send to MASTER circle_count

endif

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Example: MPI Program in C

Example: MPI Program in Fortran

Parallel Examples

Simple Heat Equation

Most problems in parallel computing require communication among

the tasks. A number of common problems require communication with
"neighbor" tasks.

The heat equation describes the temperature change over time, given
initial temperature distribution and boundary conditions.

A finite differencing scheme is employed to solve the heat equation

numerically on a square region.

The initial temperature is zero on the boundaries and high in the

middle.

The boundary temperature is held at zero.

For the fully explicit problem, a time stepping algorithm is used. The
elements of a 2-dimensional array represent the temperature at points
on the square.

The calculation of an element is dependent upon neighbor element

values.

A serial program would contain code like:

do iy = 2, ny - 1
do ix = 2, nx - 1
u2(ix, iy) =
u1(ix, iy) +
cx * (u1(ix+1,iy) + u1(ix-1,iy) - 2.*u1(ix,iy)) +
cy * (u1(ix,iy+1) + u1(ix,iy-1) - 2.*u1(ix,iy))
end do
end do

Simple Heat Equation

Parallel Solution 1
Implement as an SPMD model

The entire array is partitioned and distributed as subarrays to all tasks.

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Each task owns a portion of the total array.

Determine data dependencies

interior elements belonging to a task are independent of other
tasks
border elements are dependent upon a neighbor task's data,
necessitating communication.

Master process sends initial info to workers, checks for convergence

and collects results

Worker process calculates solution, communicating as necessary with

neighbor processes

Pseudo code solution: red highlights changes for parallelism.

find out if I am MASTER or WORKER

if I am MASTER
initialize array
send each WORKER starting info and subarray

do until all WORKERS converge

gather from all WORKERS convergence data
broadcast to all WORKERS convergence signal
end do

receive results from each WORKER

else if I am WORKER
receive from MASTER starting info and subarray

do until solution converged

update time
send neighbors my border info
receive from neighbors their border info

update my portion of solution array

determine if my solution has converged

send MASTER convergence data
receive from MASTER convergence signal
end do

send MASTER results

endif

Example: MPI Program in C

Example: MPI Program in Fortran

Simple Heat Equation

Parallel Solution 2: Overlapping Communication and Computation
In the previous solution, it was assumed that blocking communications were used by the worker tasks. Blocking
communications wait for the communication process to complete before continuing to the next program instruction.

In the previous solution, neighbor tasks communicated border data, then each process updated its portion of the array.

Computing times can often be reduced by using non-blocking communication. Non-blocking communications allow work
to be performed while communication is in progress.

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Each task could update the interior of its part of the solution array while the communication of border data is occurring,
and update its border after communication has completed.

Pseudo code for the second solution: red highlights changes for non-blocking communications.

find out if I am MASTER or WORKER

if I am MASTER
initialize array
send each WORKER starting info and subarray

do until all WORKERS converge

gather from all WORKERS convergence data
broadcast to all WORKERS convergence signal
end do

receive results from each WORKER

else if I am WORKER
receive from MASTER starting info and subarray

do until solution converged

update time

non-blocking send neighbors my border info

non-blocking receive neighbors border info

update interior of my portion of solution array

wait for non-blocking communication complete
update border of my portion of solution array

determine if my solution has converged

send MASTER convergence data
receive from MASTER convergence signal
end do

send MASTER results

endif

Parallel Examples

1-D Wave Equation

In this example, the amplitude along a uniform, vibrating string is calculated after a specified amount of time has elapsed.

The calculation involves:

the amplitude on the y axis
i as the position index along the x axis
node points imposed along the string
update of the amplitude at discrete time steps.

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The equation to be solved is the one-dimensional wave equation:

A(i,t+1) = (2.0 * A(i,t)) - A(i,t-1) + (c * (A(i-1,t) - (2.0 * A(i,t)) + A(i+1,t)))

where c is a constant

Note that amplitude will depend on previous timesteps (t, t-1) and neighboring points (i-1, i+1). Data dependence will mean
that a parallel solution will involve communications.

1-D Wave Equation

Parallel Solution
Implement as an SPMD model

The entire amplitude array is partitioned and distributed as subarrays to all tasks. Each task owns a portion of the total
array.

Load balancing: all points require equal work, so the points should be divided equally

A block decomposition would have the work partitioned into the number of tasks as chunks, allowing each task to own
mostly contiguous data points.

Communication need only occur on data borders. The larger the block size the less the communication.

Pseudo code solution:

find out number of tasks and task identities

#Identify left and right neighbors

left_neighbor = mytaskid - 1
right_neighbor = mytaskid +1
if mytaskid = first then left_neigbor = last
if mytaskid = last then right_neighbor = first

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find out if I am MASTER or WORKER

if I am MASTER
initialize array
send each WORKER starting info and subarray
else if I am WORKER
receive starting info and subarray from MASTER
endif

#Update values for each point along string

#In this example the master participates in calculations
do t = 1, nsteps
send left endpoint to left neighbor
receive left endpoint from right neighbor
send right endpoint to right neighbor
receive right endpoint from left neighbor

#Update points along line

do i = 1, npoints
newval(i) = (2.0 * values(i)) - oldval(i)
+ (sqtau * (values(i-1) - (2.0 * values(i)) + values(i+1)))
end do

end do

#Collect results and write to file

if I am MASTER
receive results from each WORKER
write results to file
else if I am WORKER
send results to MASTER
endif

Example: MPI Program in C

Example: MPI Program in Fortran

This completes the tutorial.

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References and More Information

Author: Blaise Barney, Livermore Computing.

A search on the WWW for "parallel programming" or "parallel computing" will yield a wide variety of information.

Recommended reading:
"Designing and Building Parallel Programs". Ian Foster.
http://www-unix.mcs.anl.gov/dbpp/
"Introduction to Parallel Computing". Ananth Grama, Anshul Gupta, George Karypis, Vipin Kumar.

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http://www-users.cs.umn.edu/~karypis/parbook/
"Overview of Recent Supercomputers". A.J. van der Steen, Jack Dongarra.
www.phys.uu.nl/~steen/web03/overview.html

Photos/Graphics have been created by the author, created by other LLNL employees, obtained from non-copyrighted,
government or public domain (such as http://commons.wikimedia.org/) sources, or used with the permission of authors
from other presentations and web pages.

History: These materials have evolved from the following sources, which are no longer maintained or available.
Tutorials located in the Maui High Performance Computing Center's "SP Parallel Programming Workshop".
Tutorials located at the Cornell Theory Center's "Education and Training" web page.

https://computing.llnl.gov/tutorials/parallel_comp/
Last Modified: 10/12/2010 10:58:47 [email protected]
UCRL-MI-133316

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