Introduction to Parallel Computing 2010/4/3 6:45p

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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 programs.

Level/Prerequisites: None

Overview

What is Parallel Computing?

Traditionally, software has been written for serial computation:

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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:

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

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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
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

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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

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

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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)

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 through "hard wiring".

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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

Cray X-MP Cray Y-MP Thinking Machines CM-2 Cell Processor (GPU)

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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

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exchange is commonly referred to as communications regardless of the method employed.

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

Shared Memory

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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 (UMA)
Shared memory
machines can be
divided into two main
classes based upon
memory access times:
UMA and NUMA.

Uniform Memory
Access (UMA):

Most commonly
represented today by
Symmetric
Shared Memory (NUMA)
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):

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

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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 insure "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.

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

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architectures.

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.

Parallel Programming Models

Shared Memory Model

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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 insure 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.

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

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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 as
well 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 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

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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.

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.

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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)

Implementations are available for most common parallel platforms.

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.

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

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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.

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:

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F(k + 2) = F(k + 1) + F(k)

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 k + 2 value uses those of both k + 1 and k. 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.

There are different ways to partition data:

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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.

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

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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.

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

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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 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.

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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

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.

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Discussed previously in the Communications section.

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.

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

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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.

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:

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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

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)

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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:

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.

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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 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

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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

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

insures 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

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Notice that only the outer loop variables are

different from the serial solution.

One Possible Solution:

Implement as 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
Collects results from workers

Worker Process: repeatedly does the following

Gets task from master process

Performs computation

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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
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)

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else if I am WORKER

send to MASTER circle_count

endif

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. 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

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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.

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

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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.

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,

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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

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.

Please complete the online evaluation form.

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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.
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: Mon, 01 Mar 2010 21:46:39 GMT blaiseb@llnl.gov
UCRL-MI-133316

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