11/20/23, 1:41 PM Introduction to Parallel Computing Tutorial | HPC @ LLNL

Introduction to Parallel Computing Tutorial

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Table of Contents
1. Abstract
A. Parallel Computing Overview
i. What Is Parallel Computing?
ii. Why Use Parallel Computing?
iii. Who Is Using Parallel Computing?
B. Concepts and Terminology
i. von Neumann Computer Architecture
ii. Flynn’s Taxonomy
iii. Parallel Computing Terminology
iv. Potential Benefits, Limits and Costs of Parallel Programming
C. Parallel Computer Memory Architectures
i. Shared Memory
ii. Distributed Memory
iii. Hybrid Distributed-Shared Memory
D. Parallel Programming Models
i. Shared Memory Model
ii. Threads Model
iii. Distributed Memory / Message Passing Model
iv. Data Parallel Model
v. Hybrid Model
vi. SPMD and MPMP
E. Designing Parallel Programs
i. Automatic vs. Manual Parallelization
ii. Understand the Problem and the Program
iii. Partitioning
iv. Communications
v. Synchronization
vi. Data Dependencies
vii. Load Balancing
viii. Granularity
ix. I/O
x. Debugging
xi. Performance Analysis and Tuning
F. Parallel Examples
i. Array Processing
ii. PI Calculation
iii. Simple Heat Equation
iv. 1-D Wave Equation
G. References and More Information

Abstract
This is the first tutorial in the "Livermore Computing Getting Started" workshop. It is intended to provide only a brief overview
of the extensive and broad topic of Parallel Computing, as a lead-in for the tutorials that follow it. As such, it covers just the
very basics of parallel computing, and is intended for someone who is just becoming acquainted with the subject and who is
planning to attend one or more of the other tutorials in this workshop. It is not intended to cover Parallel Programming in
depth, as this would require significantly more time. The tutorial begins with a discussion on parallel computing - what it is
and how it's used, followed by a discussion on concepts and terminology associated with parallel computing. The topics of

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parallel memory architectures and programming models are then explored. These topics are followed by a series of practical
discussions on a number of the complex issues related to designing and running parallel programs. The tutorial concludes
with several examples of how to parallelize several simple problems. References are included for further self-study.

Overview
What Is Parallel Computing?
Serial Computing
Traditionally, software has been written for serial computation:

A problem is broken into a discrete series of instructions

Instructions are executed sequentially one after another
Executed on a single processor
Only one instruction may execute at any moment in time

Serial computing generic example

For example:

Serial computing example of processing payroll

Parallel Computing
In the simplest sense, parallel computing is the simultaneous use of multiple compute resources to solve a computational
problem:
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 processors
An overall control/coordination mechanism is employed

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Parallel computing generic example

For example:

Parallel computing example of processing payroll

The computational problem should be able to:

Be broken apart into discrete pieces of work that can be solved simultaneously;
Execute multiple program instructions at any moment in time;
Be solved in less time with multiple compute resources than with a single compute resource.
The compute resources are typically:
A single computer with multiple processors/cores
An arbitrary number of such computers connected by a network

Parallel Computers
Virtually all stand-alone computers today are parallel from a hardware perspective:
Multiple functional units (L1 cache, L2 cache, branch, prefetch, decode, floating-point, graphics processing (GPU),
integer, etc.)
Multiple execution units/cores
Multiple hardware threads

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IBM BG/Q Compute Chip with 18 cores (PU) and 16 L2 Cache units (L2)

Networks connect multiple stand-alone computers (nodes) to make larger parallel computer clusters.

Network connections

For example, the schematic below shows a typical LLNL parallel computer cluster:
Each compute node is a multi-processor parallel computer in itself
Multiple compute nodes are networked together with an Infiniband network
Special purpose nodes, also multi-processor, are used for other purposes

Example of typical parallel computer cluster

The majority of the world's large parallel computers (supercomputers) are clusters of hardware produced by a handful
of (mostly) well known vendors.

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Source: Top500.org

Why Use Parallel Computing?

The Real World Is Massively Complex
In the natural world, many complex, interrelated events are happening at the same time, yet within a temporal
sequence.
Compared to serial computing, parallel computing is much better suited for modeling, simulating and understanding
complex, real world phenomena.
For example, imagine modeling these serially:

Real world phenomena can be simulated with parallel computing

Real world phenomena can be simulated with parallel computing

Main Reasons for Using Parallel Programming

SAVE TIME AND/OR MONEY
In theory, throwing more resources at a task will shorten its time to completion, with potential cost savings.
Parallel computers can be built from cheap, commodity components.

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Working in parallel shortens completion time

SOLVE LARGER / MORE COMPLEX PROBLEMS

Many problems are so large and/or complex that it is impractical or impossible to solve them using a serial program,
especially given limited computer memory.
Example: "Grand Challenge Problems" (en.wikipedia.org/wiki/Grand_Challenge) requiring petaflops and petabytes of
computing resources.
Example: Web search engines/databases processing millions of transactions every second

Parallel computing can solve increasingly complex problems

PROVIDE CONCURRENCY
A single compute resource can only do one thing at a time. Multiple compute resources can do many things
simultaneously.
Example: Collaborative Networks provide a global venue where people from around the world can meet and conduct
work "virtually."

Collaborative networks

TAKE ADVANTAGE OF NON-LOCAL RESOURCES

Using compute resources on a wide area network, or even the Internet when local compute resources are scarce or
insufficient.
Example: SETI@home (setiathome.berkeley.edu) has over 1.7 million users in nearly every country in the world (May,
2018).

SETI has a large worldwide user base

MAKE BETTER USE OF UNDERLYING PARALLEL HARDWARE

Modern computers, even laptops, are parallel in architecture with multiple processors/cores.
Parallel software is specifically intended for parallel hardware with multiple cores, threads, etc.
In most cases, serial programs run on modern computers "waste" potential computing power.

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Parallel computing cores

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.
In this same time period, there has been a greater than 500,000x increase in supercomputer performance, with no end
currently in sight.
The race is already on for Exascale Computing - we are entering Exascale era
Exaflop = 1018 calculations per second
US DOE Exascale Computing Project: https://www.exascaleproject.org

Source: Top500.org

Who Is Using Parallel Computing?

Science and Engineering
Historically, parallel computing has been considered to be "the high end of computing," and has been used to model difficult
problems in many areas of science and engineering:
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
Defense, Weapons

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Parallel computing is key to simulating a range of complex physical phenomena

Industrial and Commercial

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:

"Big Data," databases, data mining

Artificial Intelligence (AI)
Oil exploration
Web search engines, web based business services
Medical imaging and diagnosis
Pharmaceutical design
Financial and economic modeling
Management of national and multi-national corporations
Advanced graphics and virtual reality, particularly in the entertainment industry
Networked video and multi-media technologies
Collaborative work environments

Parallel computing is used in many commercial applications

Global Applications
Parallel computing is now being used extensively around the world, in a wide variety of applications.

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Source: Top500.org

Source: Top500.org

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Source: Top500.org

Concepts and Terminology

von Neumann Computer Architecture
Named after the Hungarian mathematician John von Neumann who first
authored the general requirements for an electronic computer in his 1945
papers.
Also known as "stored-program computer" - both program instructions and
data are kept in electronic memory. Differs from earlier computers which were
programmed through "hard wiring".
Since then, virtually all computers have followed this basic design:

Comprised of four main components:

1. Memory
2. Control Unit
3. Arithmetic Logic Unit
4. Input/Output

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Read/write, random access memory is used John von Neumann circa 1940s
to store both program instructions and data (Source: LANL archives)
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.
Arithmetic Unit performs basic arithmetic operations
Input/Output is the interface to the human operator
Parallel computers still follow this basic design, just multiplied in units. The basic,
fundamental architecture remains the same. More info on his other remarkable
Basic computing architecture accomplishments: http://en.wikipedia.org/wiki/John_von_Neumann

Flynn's Classical Taxonomy

There are a number of different ways to classify parallel computers. Examples are available in the references.
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 Stream and Data Stream. 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:

Flynn's taxonomy

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 type of computer
Examples: older generation mainframes, minicomputers, workstations and single processor/core PCs.

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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: Thinking Machines 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.

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Multiple Instruction, Single Data (MISD)

A type of parallel computer
Multiple Instruction: Each processing unit operates on the data independently via separate instruction streams.
Single Data: A single data stream is fed into multiple processing units.
Few (if any) actual examples of this class of parallel computer have ever existed.
Some conceivable uses might be:
multiple frequency filters operating on a single signal stream
multiple cryptography algorithms attempting to crack a single coded message.

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Multiple Instruction, Multiple Data (MIMD)

A type of parallel computer
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
Currently, the most common type of parallel computer - most modern supercomputers fall into this category.
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

General Parallel Computing 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.

CPU
Contemporary CPUs consist of one or more cores - a distinct execution unit with its own instruction stream. Cores with a CPU
may be organized into one or more sockets - each socket with its own distinct memory . When a CPU consists of two or more
sockets, usually hardware infrastructure supports memory sharing across sockets.

Node
A standalone "computer in a box." Usually comprised of multiple CPUs/processors/cores, memory, network interfaces, etc.
Nodes are networked together to comprise a supercomputer.

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Nodes in a supercomputer

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. A parallel program consists of multiple tasks running on multiple processors.
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
Describes a computer architecture where all processors have direct 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)

Shared memory hardware architecture where multiple processors share a single address space and have equal access to all
resources - memory, disk, etc.
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.

Synchronization
The coordination of parallel tasks in real time, very often associated with communications.

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

Computational Granularity
In parallel computing, granularity is a quantitative or 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

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Required execution time that is unique to parallel tasks, as opposed to that for doing useful work. Parallel overhead can
include factors such as:
Task start-up time
Synchronizations
Data communications
Software overhead imposed by parallel languages, libraries, operating system, etc.
Task termination time

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

Embarrassingly (IDEALY) 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 resources. Factors that contribute to scalability include:

Hardware - particularly memory-cpu bandwidths and network communication properties

Application algorithm
Parallel overhead related
Characteristics of your specific application

Potential Benefits, 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:

Speedup when introducing more processors Amdahl's law

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

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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 = .95 P = .99
----- ------- ------- ------- -------
10 1.82 5.26 6.89 9.17
100 1.98 9.17 16.80 50.25
1,000 1.99 9.91 19.62 90.99
10,000 1.99 9.91 19.96 99.02
100,000 1.99 9.99 19.99 99.90

"Famous" quote: You can spend a lifetime getting 95% of your code to be parallel, and never achieve better than 20x
speedup no matter how many processors you throw at it!

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

2D Grid Calculations
Parallel fraction 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
Parallel fraction 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 more complex than corresponding serial applications. 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 developing parallel applications.

Portability
Thanks to standardization in several APIs, such as MPI, OpenMP and POSIX threads, 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.

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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
Two types of scaling based on time to solution: strong scaling and
weak scaling.
Strong scaling (Amdahl):
The total problem size stays fixed as more processors are
added.
Goal is to run the same problem size faster
Perfect scaling means problem is solved in 1/P time
(compared to serial)
Weak scaling (Gustafson):
The problem size per processor stays fixed as more processors
are added. The total problem size is proportional to the
number of processors used.
Goal is to run larger problem in same amount of time
Perfect scaling means problem Px runs in same time as single
processor run
The ability of a parallel program's performance to scale is a result of
a number of interrelated factors. Simply adding more processors is
rarely the answer.
The algorithm may have inherent limits to scalability. At some point,
adding more resources causes performance to decrease. This is a
common situation with many parallel applications. Strong and weak scaling
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.

Parallel Computer Memory Architectures

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.
Historically, shared memory machines have been classified as UMA and NUMA, based upon memory access times.

Uniform Memory Access (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.

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Uniform memory access

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

Non-uniform memory access

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.

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 be as simple as Ethernet.

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Distributed memory

Advantages
Memory is scalable with the 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 global 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 times - data residing on a remote node takes longer to access than node local data.

Hybrid Distributed-Shared Memory

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

The shared memory component can be a shared memory machine and/or graphics processing units (GPU).
The distributed memory component is the networking of multiple shared memory/GPU machines, which know only
about their own memory - not the memory on another machine. Therefore, network communications are required to
move data from one machine 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.
Increased scalability is an important advantage
Increased programmer complexity is an important disadvantage

Parallel Programming Models

There are several parallel programming models in common use:
Shared Memory (without threads)
Threads
Distributed Memory / Message Passing
Data Parallel
Hybrid
Single Program Multiple Data (SPMD)
Multiple Program Multiple Data (MPMD)
Parallel programming models exist as an abstraction above hardware and memory architectures.
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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
from the past are discussed below.

SHARED memory model on a DISTRIBUTED memory machine

Kendall Square Research (KSR) ALLCACHE approach. Machine memory was physically distributed across networked
machines, but appeared to the user as a single shared memory global address space. Generically, this approach is referred
to as "virtual shared memory".

DISTRIBUTED memory model on a SHARED memory machine

Message Passing Interface (MPI) on SGI Origin 2000. The SGI Origin 2000 employed the CC-NUMA type of shared memory
architecture, where every task has direct access to global address space spread across all machines. However, the ability to
send and receive messages using MPI, as is commonly done over a network of distributed memory machines, was
implemented and commonly used.

Which model to use? This 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.

Shared Memory Model (without threads)

In this programming model, processes/tasks share a common
address space, which they read and write to asynchronously.
Various mechanisms such as locks / semaphores are used to
control access to the shared memory, resolve contentions and to
prevent race conditions and deadlocks.
This is perhaps the simplest parallel programming model.
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. All
processes see and have equal access to shared memory. 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 process that works on it conserves
Shared memory model
memory accesses, cache refreshes and bus traffic that occurs
when multiple processes use the same data.
Unfortunately, controlling data locality is hard to understand and may be beyond the control of the average user.

Implementations

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On stand-alone shared memory machines, native operating systems, compilers and/or hardware provide support for
shared memory programming. For example, the POSIX standard provides an API for using shared memory, and UNIX
provides shared memory segments (shmget, shmat, shmctl, etc.).
On distributed memory machines, memory is physically distributed across a network of machines, but made global
through specialized hardware and software. A variety of SHMEM implementations are available:
http://en.wikipedia.org/wiki/SHMEM.

Threads Model
This programming model is a type of shared memory programming.
In the threads model of parallel programming, a single "heavy
weight" process can have multiple "light weight", concurrent
execution paths.
For example:
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. This is the "heavy
weight" process.
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 ("light
weight"). 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 Threads model
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.

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 the parallelism (although compilers can sometimes help).

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
Specified by the IEEE POSIX 1003.1c standard (1995). C Language only.
Part of Unix/Linux operating systems
Library based
Commonly referred to as Pthreads.
Very explicit parallelism; requires significant programmer attention to detail.

OpenMP
Industry standard, jointly defined and endorsed by a group of major computer hardware and software vendors,
organizations and individuals.
Compiler directive based
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Portable / multi-platform, including Unix and Windows platforms

Available in C/C++ and Fortran implementations
Can be very easy and simple to use - provides for "incremental parallelism". Can begin with serial code.
Other threaded implementations are common, but not discussed here:
Microsoft threads
Java, Python threads
CUDA threads for GPUs

More Information
POSIX Threads tutorial: hpc.llnl.gov/sites/default/files/2019.08.21.TAU_.pdf
OpenMP tutorial: hpc-tutorials.llnl.gov/openmp/

Distributed Memory / Message Passing Model

This 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 matching receive operation.

Implementations:
Distributed memory model
From a programming perspective, message passing
implementations usually comprise a library of subroutines. Calls to these subroutines 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 and MPI-3 in
2012. All MPI specifications are available on the web at http://www.mpi-forum.org/docs/.
MPI is the "de facto" industry standard for message passing, replacing virtually all other message passing
implementations used for production work. MPI implementations exist for virtually all popular parallel computing
platforms. Not all implementations include everything in MPI-1, MPI-2 or MPI-3.

More Information
MPI tutorial: hpc-tutorials.llnl.gov/mpi/

Data Parallel Model

May also be referred to as the Partitioned Global Address Space
(PGAS) model.
The data parallel model demonstrates the following characteristics:
Address space is treated globally
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. Data parallel model
On distributed memory architectures, the global data structure can
be split up logically and/or physically across tasks.

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Implementations:

Currently, there are several parallel programming implementations in various stages of developments, based on the
Data Parallel / PGAS model.
Coarray Fortran: a small set of extensions to Fortran 95 for SPMD parallel programming. Compiler dependent. More
information: https://en.wikipedia.org/wiki/Coarray_Fortran
Unified Parallel C (UPC): an extension to the C programming language for SPMD parallel programming. Compiler
dependent. More information: https://upc.lbl.gov/
Global Arrays: provides a shared memory style programming environment in the context of distributed array data
structures. Public domain library with C and Fortran77 bindings. More information:
https://en.wikipedia.org/wiki/Global_Arrays
X10: a PGAS based parallel programming language being developed by IBM at the Thomas J. Watson Research Center.
More information: http://x10-lang.org/
Chapel: an open source parallel programming language project being led by Cray. More information:
http://chapel.cray.com/

Hybrid Model
A hybrid model
combines
more than one
of the
previously
described
programming
models. Hybrid model with MPI and CUDA
Hybrid model with MPI and OpenMP
Currently, a
common example of a hybrid model is the combination of the
message passing model (MPI) with the threads model (OpenMP).
Threads perform computationally intensive kernels using local, on-node data
Communications between processes on different nodes occurs over the network using MPI
This hybrid model lends itself well to the most popular (currently) hardware environment of clustered multi/many-core
machines.
Another similar and increasingly popular example of a hybrid model is using MPI with CPU-GPU (graphics processing
unit) programming.
MPI tasks run on CPUs using local memory and communicating with each other over a network.
Computationally intensive kernels are off-loaded to GPUs on-node.
Data exchange between node-local memory and GPUs uses CUDA (or something equivalent).
Other hybrid models are common:
MPI with Pthreads
MPI with non-GPU accelerators

SPMD and MPMD

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.
SINGLE PROGRAM: All tasks execute their copy of the same
program simultaneously. This program can be threads, message
SPMD model
passing, data parallel or hybrid.
MULTIPLE DATA: All tasks may use different data
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.
The SPMD model, using message passing or hybrid programming, is probably the most commonly used parallel
programming model for multi-node clusters.

Multiple Program Multiple Data (MPMD)

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Like SPMD, MPMD is actually a "high level" programming model that

can be built upon any combination of the previously mentioned
parallel programming models.
MULTIPLE PROGRAM: Tasks may execute different programs
simultaneously. The programs can be threads, message passing,
MPMD model
data parallel or hybrid.
MULTIPLE DATA: All tasks may use different data
MPMD applications are not as common as SPMD applications, but may be better suited for certain types of problems,
particularly those that lend themselves better to functional decomposition than domain decomposition (discussed later
under Partitioning).

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) 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.
The most common compiler generated parallelization is done using on-node shared memory and threads (such as
OpenMP).
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 compiler 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.

Understand the Problem and the Program

Programs = algorithms + data + (hardware)

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Determine whether the problem can actually be parallelized

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 means 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 an easy-to-parallelize 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 problem and algorithm with little-to-no parallelism:

Calculation of the first 10,000 members of the Fibonacci series (0,1,1,2,3,5,8,13,21,...) by use of the formula:
F(n) = F(n-1) + F(n-2)
The calculation of the F(n) value uses those of both F(n-1) and F(n-2), which must be computed first.

An example of a parallel algorithm for solving this problem (using Binet's formula):

where

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:

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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.
Take advantage of optimized third party parallel software and highly optimized math libraries available from leading
vendors (IBM's ESSL, Intel's MKL, AMD's AMCL, etc.).

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
the data.

Domain decomposition

There are different ways to partition data:

Partitioning examples

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

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.

Ecosystem modeling

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.

Signal processing

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.

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Climate modeling

Complex relationships between climate and atmospheric modeling components

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

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.
These types of problems are often called embarrassingly parallel - little or no communications are required.
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.

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Parallel processing without need for much

communication

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 2-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.

Parallel processing that needs a lot of

communication

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

Communication is complex

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.
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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):

Different types of communication scope

Efficiency of communications

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Oftentimes, the programmer has choices 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 fabric—different platforms use different networks. Some networks perform better than others. Choosing a
platform with a faster network may be an option.

Overhead and complexity

Example of parallel communications overhead and complexity

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

Synchronization
Managing the sequence of work and the tasks performing it is a critical design consideration for most parallel programs.
Can be a significant factor in program performance (or lack of it)
Often requires "serialization" of segments of the program.

Synchronization of tasks in parallel processing is an important design

consideration

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
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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.

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.

Visualization of dependencies

Examples
Loop carried data dependence
DO J = MYSTART,MYEND
A(J) = A(J-1) * 2.0
END DO

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

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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.

Load Balancing
Load balancing refers to the practice of distributing approximately equal amounts of 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:

Adaptive grid methods - some tasks may

need to refine their mesh while others
don't.
Sparse arrays - some tasks will have actual data to
work on while others have mostly "zeros."

N-body simulations - particles may migrate across task domains

requiring more work for some tasks.

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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 receives a new piece from the work queue.

Scheduler-task pool

Ultimately, it may become necessary to design an algorithm which detects and handles load imbalances as they occur
dynamically within the code.

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.
Fine-grain parallelism
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 Coarse-grain parallelism
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.

I/O
The Bad News

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I/O operations

I/O operations are generally regarded as inhibitors to parallelism.

I/O operations require orders of magnitude more time than memory operations.
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 (IBM). Now called IBM Spectrum Scale.
Lustre: for Linux clusters (Intel)
HDFS: Hadoop Distributed File System (Apache)
PanFS: Panasas ActiveScale File System for Linux clusters (Panasas, Inc.)
And more - see http://en.wikipedia.org/wiki/List_of_file_systems#Distributed_parallel_file_systems
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.
A few pointers:
Rule #1: Reduce overall I/O as much as possible.
If you have access to a parallel file system, use it.
Writing large chunks of data rather than small chunks is usually significantly more efficient.
Fewer, larger files performs better than many small files.
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.
Aggregate I/O operations across tasks - rather than having many tasks perform I/O, have a subset of tasks perform
it.

Debugging
Debugging parallel codes can be incredibly difficult, particularly as codes scale upwards.
The good news is that there are some excellent debuggers available to assist:
Threaded - pthreads and OpenMP
MPI
GPU / accelerator
Hybrid
Livermore Computing users have access to several parallel debugging tools installed on LC's clusters:
TotalView from RogueWave Software
DDT from Allinea
Inspector from Intel
Stack Trace Analysis Tool (STAT) - locally developed at LLNL
All of these tools have a learning curve associated with them.
For details and getting started information, see:
LC's web pages at hpc.llnl.gov/software/development-environment-software
TotalView tutorial: hpc.llnl.gov/documentation/tutorials/totalview-tutorial

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Using debugging tools

Performance Analysis and Tuning

As with debugging, analyzing and tuning parallel program performance can be much more challenging than for serial
programs.
Fortunately, there are a number of excellent tools for parallel program performance analysis and tuning.
Livermore Computing users have access to several such tools, most of which are available on all production clusters.
Some starting points for tools installed on LC systems:
LC's web pages at https://hpc.llnl.gov/software/development-environment-software
TAU: http://www.cs.uoregon.edu/research/tau/docs.php
HPCToolkit: http://hpctoolkit.org/documentation.html
Open|Speedshop: https://www.openspeedshop.org/
Vampir / Vampirtrace: http://vampir.eu/
Valgrind: http://valgrind.org/
PAPI: http://icl.cs.utk.edu/papi/
mpiP: http://mpip.sourceforge.net/
memP: http://memp.sourceforge.net/

Using performance analysis and tuning tools

Parallel Examples
Array Processing
This example demonstrates calculations on 2-dimensional array elements;
a function is evaluated on each array element.
The computation on each array element is independent from other array
elements.
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The problem is computationally intensive.

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

Questions to ask:
Is this problem able to be parallelized?
How would the problem be partitioned?
Are communications needed?
Are there any data dependencies?
Are there synchronization needs? 2-D array
Will load balancing be a concern?

Parallel Solution 1
The calculation of elements is independent of one another - leads to an
embarrassingly parallel solution.
Arrays elements are evenly distributed so that each process owns a
portion of the array (subarray).
Distribution scheme is chosen for efficient memory access; 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. Parallel solution 1
Independent calculation of array elements ensures there is no need for
communication or synchronization between tasks.
Since the amount of work is evenly distributed across processes, there should not be load balance concerns.
After the array is distributed, each task executes the portion of the loop corresponding to the data it owns.
For example, both Fortran (column-major) and C (row-major) block distributions are shown:

Column-major:

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

Row-major:

for i (i = mystart; i < myend; i++) {

for j (j = 0; j < n; j++) {
a(i,j) = fcn(i,j);
}
}

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

One possible solution:

Implement as a Single Program Multiple Data (SPMD) model - every task executes the same program.
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.
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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 programs
MPI Array Program in C
MPI Array Program in Fortran

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
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.
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find out if I am MASTER or WORKER

if I am MASTER

do until no more jobs

if request send to WORKER next job
else receive results from WORKER
end do

else if I am WORKER

do until no more jobs

request job from MASTER
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.

PI Calculation
The value of PI can be calculated in various ways. Consider the
Monte Carlo method of approximating PI:
Inscribe a circle with radius r in a square with side length of 2r
The area of the circle is Πr2 and the area of the square is 4r2
The ratio of the area of the circle to the area of the square is:
Πr2 / 4r2 = Π / 4
If you randomly generate N points inside the square,
approximately
N * Π / 4 of those points (M) should fall inside the circle.
Π is then approximated as:
N*Π/4=M
Π/4=M/N
Π=4*M/N
Note that increasing the number of points generated
improves the approximation.
Serial pseudo code for this procedure:

Calculating pi in serial

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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

The problem is computationally intensive—most of the time is spent executing the loop
Questions to ask:
Is this problem able to be parallelized?
How would the problem be partitioned?
Are communications needed?
Are there any data dependencies?
Are there synchronization needs?
Will load balancing be a concern?

Parallel Solution
Another problem that's easy to parallelize:
All point calculations are independent; no data dependencies
Work can be evenly divided; no load balance concerns
No need for communication or synchronization between tasks
Parallel strategy:
Divide the loop into equal portions that can be executed by
the pool of tasks
Each task independently performs its work
A SPMD model is used
One task acts as the master to collect results and compute the
value of PI
Pseudo code solution: red highlights changes for parallelism.

Calculating pi in parallel

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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

Example Programs
MPI Pi Calculation Program in C
MPI Pi Calculation Program in Fortran

Simple Heat Equation

Most problems in parallel
computing require
communication among the tasks.
A number of common problems
require communication with
"neighbor" tasks.
The 2-D heat equation describes
the temperature change over
time, given initial temperature
distribution and boundary
conditions.
A finite differencing scheme is Finite differencing scheme
employed to solve the heat
2-D heat problem
equation numerically on a square region.
The elements of a 2-dimensional array represent the temperature at
points on the square.
The initial temperature is zero on the boundaries and high in the middle.
The boundary temperature is held at zero.
A time stepping algorithm is used.
The calculation of an element is dependent upon neighbor element values:

Calculation of the above

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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

Questions to ask:
Is this problem able to be parallelized?
How would the problem be partitioned?
Are communications needed?
Are there any data dependencies?
Are there synchronization needs?
Will load balancing be a concern?

Parallel Solution
This problem is more challenging, since there are data dependencies,
which require communications and synchronization.
The entire array is partitioned and distributed as subarrays to all tasks.
Each task owns an equal portion of the total array.
Because the amount of work is equal, load balancing should not be a
concern
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.
Implement as an SPMD model:
Master process sends initial info to workers, and then waits to collect
results from all workers
Parallel solution to 2-D heat problem
Worker processes calculate solution within specified number of time
steps, 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
receive results from each WORKER

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

# Perform time steps

do t = 1, nsteps
update time
send neighbors my border info
receive from neighbors their border info
update my portion of solution array

end do

send MASTER results

endif

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Example Programs
MPI Heat Equation Program in C
MPI Heat Equation Program in Fortran

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.

1-D wave problem

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).
Questions to ask:
Is this problem able to be parallelized?
How would the problem be partitioned?
Are communications needed?
Are there any data dependencies?
Are there synchronization needs?
Will load balancing be a concern?

1-D Wave Equation Parallel Solution

This is another example of a problem involving data dependencies. A parallel solution will involve communications and
synchronization.
The entire amplitude array is partitioned and distributed as subarrays to all tasks. Each task owns an equal 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.

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Parallel solution to 1-D wave problem

Implement as an SPMD model:

Master process sends initial info to workers, and then waits to collect results from all workers
Worker processes calculate solution within specified number of time steps, communicating as necessary with
neighbor processes
Pseudo code solution: red highlights changes for parallelism.

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

#Perform time steps

#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 Programs
MPI Concurrent Wave Equation Program in C
MPI Concurrent Wave Equation Program in Fortran

This completes the tutorial.

Evaluation Form

Please complete the online evaluation form.

References and More Information

Author: Blaise Barney, Livermore Computing (retired), Donald Frederick, LLNL
Contact: [email protected]
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A search on the Web for "parallel programming" or "parallel computing" will yield a wide variety of information.
Recommended reading - Parallel Programming:
"Designing and Building Parallel Programs", Ian Foster - from the early days of parallel computing, but still
illuminating.
http://www.mcs.anl.gov/~itf/dbpp/
"Introduction to Parallel Computing", Ananth Grama, Anshul Gupta, George Karypis, Vipin Kumar.
University of Oregon - Intel Parallel Computing Curriculum
https://ipcc.cs.uoregon.edu/curriculum.html
UC Berkeley CS267, Applications of Parallel Computing, Prof. Jim Demmel, UCB --
https://sites.google.com/lbl.gov/cs267-spr2020
Udacity CS344: Intro to Parallel Programming - https://developer.nvidia.com/udacity-cs344-intro-parallel-
programming
"Programming on Parallel Machines", Norm Matloff, UC Davis:
http://heather.cs.ucdavis.edu/~matloff/158/PLN/ParProcBookS2011.pdf
Cornell Virtual Workshop: Parallel Programming Concepts and High-Performance Computing -
https://cvw.cac.cornell.edu/Parallel/
CS267, Applications of Parallel Computers, Spring 2021, Prof. Jim Demmel, UCB -
https://sites.google.com/lbl.gov/cs267-spr2021
Introduction to High Performance Scientific Computing", Victor Eijkhout, TACC
COMP 705: Advanced Parallel Computing (Fall, 2017), SDSU, Prof. Mary Thomas -
https://edoras.sdsu.edu/~mthomas/f17.705
Georg Hager's SC '20 Tutorial on Node-Level Performance Tuning - https://blogs.fau.de/hager/tutorials/sc20
Recommended reading - Linux
An Introduction to Linux - https://cvw.cac.cornell.edu/Linux/
Linux Tutorial for Beginners: Introduction to Linux Operating System - https://www.youtube.com/watch?v=V1y-
mbWM3B8
"Introduction to Linux" - Boston University - https://www.bu.edu/tech/files/2018/05/2018-Summer-Tutorial-
Intro-to-Lin…
Photos/Graphics have been created by the authors, 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 evolved from the following sources:

Tutorials developed by the Cornell University Center for Advanced Computing (CAC) available
at https://cvw.cac.cornell.edu/.
Tutorials developed by the Maui High Performance Computing Center’s “SP Parallel Programming Workshop” (no
longer available).

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