INTRODUCTION TO

PARALLEL
COMPUTING
Prepared by
Dr M.MANIMARAN
Senior Associate Professor (Grade-1)
School of Computing Science and Engineering
VIT Bhopal University
OBJECTIVES:
To introduce you to the basic concepts and
ideas in parallel computing
To familiarize you with the major
programming models in parallel computing
To provide you with with guidance for
designing efficient parallel programs

2
 OUTLINE:

❑ Introduction to Parallel Computing / High

Performance Computing (HPC)

❑ Concepts and terminology

❑ Parallel programming models

❑ Parallelizing your programs

❑ Parallel examples

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What is High Performance Computing?

Pravetz 82 and 8M, Bulgarian Apple

clones Image credit: flickr 4
What is High Performance Computing?

Pravetz 82 and 8M, Bulgarian Apple

clones Image credit: flickr 4
What is High Performance Computing?

Odyssey supercomputer is the major

computational resource of FAS RC:
• 2,140 nodes / 60,000 cores
• 14 petabytes of storage

5
What is High Performance Computing?

Odyssey supercomputer is the major

computational resource of FAS RC:
• 2,140 nodes / 60,000 cores
• 14 petabytes of storage

Using the world’s fastest and largest computers to solve large

and complex problems.
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Serial Computation:
Traditionally software has been written for serial computations:

❑ To be run on a single computer having a single Central Processing Unit

(CPU)
❑ A problem is broken into a discrete set of instructions
❑ Instructions are executed one after another
❑ Only one instruction can be executed at any moment in time

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 Parallel Computing:
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

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 Parallel
Computers:
Virtually all stand-alone computers today are parallel from a
hardware perspective:

❑ Multiple functional units (floating point, integer, GPU, etc.)

❑ Multiple execution units / cores
❑ Multiple hardware threads

Intel Core i7 CPU and its

major components

Image Credit: Intel

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Parallel
Computers:
Networks connect multiple stand-alone computers (nodes) to create
larger parallel computer clusters

❑ 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

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Why Use HPC?
Major 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.

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Why Use HPC?
Major 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.

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Why Use HPC?
Major 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.

Provide concurrency: A single compute resource can only do one

thing at a time. Multiple computing resources can be doing many
things simultaneously.

10
Why Use HPC?
Major 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.

Provide concurrency: A single compute resource can only do one

thing at a time. Multiple computing resources can be doing many
things simultaneously.

Use of non-local resources: Using compute resources on a

wide area network, or even the Internet when local
compute resources are scarce. 10
Future
Trends:

Source:
Top500.org

1
Future
Trends:

Source:
Top500.org

The race is already on for Exascale

Computing! 1
HPC
Terminology:
❑ Supercomputing / High-Performance Computing (HPC)
❑ Flop(s) – Floating point operation(s)
❑ Node – a stand alone computer
❑ CPU / Core – a modern CPU usually has several cores (individual processing
units )
❑ Task – a logically discrete section from the computational work
❑ Communication – data exchange between parallel tasks
❑ Speedup – time of serial execution / time of parallel execution
❑ Massively Parallel – refer to hardware of parallel systems with many
processors (“many” = hundreds of thousands)
❑ Pleasantly Parallel – solving many similar but independent
tasks simultaneously. Requires very little communication
❑ Scalability - a proportionate increase in parallel speedup with the addition of
more processors

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Parallel Computer Memory
Architectures:
Shared Memory:
❑ Multiple processors can operate
independently, but share the same memory
resources
❑ Changes in a memory location caused by one
CPU are visible to all processors

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 Parallel Computer Memory
Architectures:
Shared Memory:
❑ Multiple processors can operate
independently, but share the same memory
resources
❑ Changes in a memory location caused by one
CPU are visible to all processors

Advantages:
❑ Global address space provides a user-friendly programming perspective to memory
❑ Fast and uniform data sharing due to proximity of memory to CPUs

Disadvantages:
❑ Lack of scalability between memory and CPUs. Adding more CPUs increases
traffic on the shared memory-CPU path
❑ Programmer responsibility for “correct” access to global memory

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Parallel Computer Memory
Architectures:
Distributed Memory:
❑ Requires a communication network to
connect inter-processor memory
❑ Processors have their own local memory.
Changes made by one CPU have no effect on
others
❑ Requires communication to exchange data
among processors

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 Parallel Computer Memory
Architectures:
Distributed Memory:
❑ Requires a communication network to
connect inter-processor memory
❑ Processors have their own local memory.
Changes made by one CPU have no effect on
others
❑ Requires communication to exchange data
among processors

Advantages:
❑ Memory is scalable with the number of CPUs
❑ Each CPU can rapidly access its own memory without overhead incurred with trying to
maintain global cache coherency

Disadvantages:
❑ Programmer is responsible for many of the details associated with data communication
between processors
❑ It is usually difficult to map existing data structures to this memory organization,
based on global memory 14
Parallel Computer Memory
Architectures:
Hybrid Distributed-Shared Memory:

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

❑ Shared memory component can be a shared memory machine and/or GPU

❑ Processors on a compute node share same memory space
❑ Requires communication to exchange data between compute nodes

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Parallel Computer Memory
Architectures:
Hybrid Distributed-Shared Memory:

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

❑ Shared memory component can be a shared memory machine and/or GPU

❑ Processors on a compute node share same memory space
❑ Requires communication to exchange data between compute nodes

Advantages and Disadvantages:

❑ Whatever is common to both shared and distributed memory
architectures
❑ Increased scalability is an important advantage
❑ Increased programming complexity is a major disadvantage
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Parallel Programming
Models:
Parallel Programming Models exist as an abstraction above hardware and
memory architectures

❑ Shared Memory (without threads)

❑ Shared Threads Models (Pthreads, OpenMP)

❑ Distributed Memory / Message Passing (MPI)

❑ Data Parallel

❑ Hybrid

❑ Single Program Multiple Data (SPMD)

❑ Multiple Program Multiple Data (MPMD)

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 Shared Threads Models:

POSIX Threads

❑ Library based; requires parallel coding

❑ C Language only; Interfaces for Perl, Python and others exist
❑ 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
❑ 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"

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 Distributed Memory / Message Passing
Models:
❑ 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

❑ Message Passing Interface (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

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Data Parallel
Model:
❑ May also referred to as the Partitioned Global Address Space (PGAS)
model
❑ It displays these characteristics:
▪ Address space is treated globally
▪ Parallel work focuses on performing operations on a data set
▪ Tasks work on different portions from the same data structure
▪ Tasks perform the same operation

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 Data Parallel
Model:
❑ May also referred to as the Partitioned Global Address Space (PGAS) model
❑ It displays these characteristics:
▪ Address space is treated globally
▪ Parallel work focuses on performing operations on a data set
▪ Tasks work on different portions from the same data structure
▪ Tasks perform the same operation

Example Implementations:

❑ Coarray Fortran: A small set of extension to Fortran 95. Compiler dependent

❑ Unified Parallel C (UPC): An extension to the C programming language.

Compiler dependent

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 Hybrid Parallel Programming
Models:

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 increasingly common hardware environment
of clustered multi/many-core machines

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 Hybrid Parallel Programming
Models:

Another similar and increasingly popular example of a hybrid model is using MPI with GPU
(Graphics Processing Unit) programming

❑ GPUs perform computationally intensive kernels using local, on-node data

❑ Communications between processes on different nodes occurs over the network using
MPI

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 Languages using parallel
❑computing:
C/C++

❑ Fortran

❑ MATLAB

❑ Python

❑ R

❑ Perl

❑ Julia

❑ And others
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Can my code be
parallelized?
❑ Does it have large loops that repeat the same
operations?

❑ Does your code do multiple tasks that are not dependent

on one another? If so is the dependency weak?

❑ Can any dependencies or information sharing be

overlapped with computation? If not, is the amount of
communications small?

❑ Do multiple tasks depend on the same data?

❑ Does the order of operations matter? If so how strict does

it have to be?
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Basic guidance for efficient
parallelization:
❑ Is it even worth parallelizing my code?

▪ Does your code take an intractably long amount of time to complete?

▪ Do you run a single large model or do statistics on multiple small runs?

▪ Would the amount of time it take to parallelize your code be worth the
gain in speed?

❑ Parallelizing established code vs. starting from scratch

▪ Established code: Maybe easier / faster to parallelize, but my not give

good performance or scaling

▪ Start from scratch: Takes longer, but will give better performance,
accuracy, and gives the opportunity to turn a “black box” into a code
you understand

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Basic guidance for efficient
parallelization:
❑ Increase the fraction of your program that can be parallelized. Identify
the most time consuming parts of your program and parallelize them.
This could require modifying your intrinsic algorithm and code’s
organization

❑ Balance parallel workload

❑ Minimize time spent in communication

❑ Use simple arrays instead of user defined derived types

❑ Partition data. Distribute arrays and matrices – allocate specific memory

for each MPI process

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Considerations about parallelization:
You parallelize your program to run faster, and to solve larger and
more complex problems.

How much faster will the program run?

Speedup:
Time to complete the
job on one process
T
S(n) =
T(1) Time to complete the job
on n process
Efficiency: (n)

Tells you how efficiently you

S(n) parallelize
E(n) = n your code

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Oversimplified
example:
p fraction of program that can be parallelized
1 - p fraction of program that cannot be parallelized
n number of processors

Then the time of running the parallel program will be

1 – p + p/n of the time for running the serial program

80% can be parallelized

20 % cannot be parallelized
n=4
1 - 0.8 + 0.8 / 4 = 0.4 i.e., 40% of the time for running the serial code
You get 2.5 speed up although you run on 4 cores since only 80% of
your code can be parallelized (assuming that all parts in the code can
complete in equal time)

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Oversimplified example,
cont’d: 80%
20%
Serial

20% 20%
Parallel
Process 1
parallelized

Process 2
Not parallelized

Process 3

Process 4
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More realistic
example: 80%
20%
Serial

20% 20%
Parallel
Process 1
parallelized

Process 2
Not parallelized

Communication
Process 3
overhead

Process 4
Load unbalance 29
Realistic example: Speedup of matrix vector multiplication
in large scale shell-model calculations

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Designing parallel programs -
partitioning:
One of the first steps in designing a parallel program is to break the problem into
discrete “chunks” that can be distributed to multiple parallel tasks.

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Designing parallel programs -
partitioning:
One of the first steps in designing a parallel program is to break the problem into
discrete “chunks” that can be distributed to multiple parallel tasks.

Domain Decomposition:
Data associate with a problem is
partitioned – each parallel task works
on a portion of the data

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Designing parallel programs -
partitioning:
One of the first steps in designing a parallel program is to break the problem into
discrete “chunks” that can be distributed to multiple parallel tasks.

Domain Decomposition:
Data associate with a problem is
partitioned – each parallel task works
on a portion of the data

There are different

ways to partition the
data

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Designing parallel programs -
partitioning:
One of the first steps in designing a parallel program is to break the problem into
discrete “chunks” that can be distributed to multiple parallel tasks.

Functional Decomposition:
Problem is decomposed according to the work that must be done. Each parallel
task performs a fraction of the total computation.

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each
other.

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each other.

Cost of communication: Computational resources are used to package and transmit

data. Requires frequently synchronization – some tasks will wait instead of doing work.
Could saturate network bandwidth.

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each other.

Cost of communication: Computational resources are used to package and transmit

data. Requires frequently synchronization – some tasks will wait instead of doing work.
Could saturate network bandwidth.

Latency vs. Bandwidth: Latency is the time it takes to send a minimal message between
two tasks. Bandwidth is the amount of data that can be communicated per unit of time.
Sending many small messages can cause latency to dominate communication overhead.

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each other.

Cost of communication: Computational resources are used to package and transmit

data. Requires frequently synchronization – some tasks will wait instead of doing work.
Could saturate network bandwidth.

Latency vs. Bandwidth: Latency is the time it takes to send a minimal message between
two tasks. Bandwidth is the amount of data that can be communicated per unit of time.
Sending many small messages can cause latency to dominate communication overhead.

Synchronous vs. Asynchronous communication: Synchronous communication is referred

to as blocking communication – other work stops until the communication is completed.
Asynchronous communication is referred to as non-blocking since other work can be done
while communication is taking place.

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each other.

Cost of communication: Computational resources are used to package and transmit

data. Requires frequently synchronization – some tasks will wait instead of doing work.
Could saturate network bandwidth.

Latency vs. Bandwidth: Latency is the time it takes to send a minimal message between
two tasks. Bandwidth is the amount of data that can be communicated per unit of time.
Sending many small messages can cause latency to dominate communication overhead.

Synchronous vs. Asynchronous communication: Synchronous communication is referred

to as blocking communication – other work stops until the communication is completed.
Asynchronous communication is referred to as non-blocking since other work can be done
while communication is taking place.

Scope of communication: Point-to-point communication – data transmission between

tasks.
Collective communication – involves all tasks (in a communication group)

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Designing parallel programs -
communication:
Most parallel applications require tasks to share data with each other.

Cost of communication: Computational resources are used to package and transmit

data. Requires frequently synchronization – some tasks will wait instead of doing work.
Could saturate network bandwidth.

Latency vs. Bandwidth: Latency is the time it takes to send a minimal message between
two tasks. Bandwidth is the amount of data that can be communicated per unit of time.
Sending many small messages can cause latency to dominate communication overhead.

Synchronous vs. Asynchronous communication: Synchronous communication is referred

to as blocking communication – other work stops until the communication is completed.
Asynchronous communication is referred to as non-blocking since other work can be done
while communication is taking place.

Scope of communication: Point-to-point communication – data transmission between

tasks.
Collective communication – involves all tasks (in a communication group)

This is only partial list of things to consider!

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Designing parallel programs – load
balancing:
Load balancing is the practice of distributing approximately equal amount of work so that
all tasks are kept busy all the time.

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Designing parallel programs – load
balancing:
Load balancing is the practice of distributing approximately equal amount of work so that
all tasks are kept busy all the time.

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Designing parallel programs – load
balancing:
Load balancing is the practice of distributing approximately equal amount of work so that
all tasks are kept busy all the time.

How to Achieve Load Balance?

Equally partition the work given to each task: For array/matrix operations equally
distribute the data set among parallel tasks. For loop iterations where the work done
for each iteration is equal, evenly distribute iterations among tasks.

Use dynamic work assignment: Certain class problems result in load imbalance even if
data is distributed evenly among tasks (sparse matrices, adaptive grid methods, many
body simulations, etc.). Use scheduler – task pool approach. As each task finishes, it
queues to get a new piece of work. Modify your algorithm to handle imbalances
dynamically.
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Designing parallel programs –
I/O:
The Bad News:
❑ I/O operations are inhibitors of parallelism
❑ I/O operations are orders of magnitude slower than memory
operations
❑ Parallel file systems may be immature or not available on all systems
❑ I/O that must be conducted over network can cause severe bottlenecks

35
Designing parallel programs –
I/O:
The Bad News:
❑ I/O operations are inhibitors of parallelism
❑ I/O operations are orders of magnitude slower than memory operations
❑ Parallel file systems may be immature or not available on all systems
❑ I/O that must be conducted over network can cause severe bottlenecks

The Good News:

❑ Parallel file systems are available (e.g., Lustre)
❑ MPI parallel I/O interface has been available since 1996 as a part of MPI-2

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Designing parallel programs –
I/O:
The Bad News:
❑ I/O operations are inhibitors of parallelism
❑ I/O operations are orders of magnitude slower than memory operations
❑ Parallel file systems may be immature or not available on all systems
❑ I/O that must be conducted over network can cause severe bottlenecks

The Good News:

❑ Parallel file systems are available (e.g., Lustre)
❑ MPI parallel I/O interface has been available since 1996 as a part of MPI-2

I/O Tips:
❑ Reduce overall I/O as much as possible
❑ If you have access to parallel file system, use it
❑ Writing large chunks of data rather than small ones is significantly more efficient
❑ Fewer, larger files perform much better than many small files
❑ Have a subset of parallel tasks to perform the I/O instead of using all tasks, or
❑ Confine I/O to a single tasks and then broadcast (gather) data to (from) other
tasks

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Example – array
processing:

task 1 task 2 … task N

Parallel code
Find out if I am MASTER or
WORKER if I am MASTER

Serial code initiate the array

send each WORKER info on part of array it
do i = 1, N owns send each WORKER its portion of initial
array receive results from each WORKER
a( i ) = fcn( i )
end do else if I am WORKER
receive from MASTER info on part of array I
own receive from MASTER my part of array

# process my portion of
array do i = mystart, myend
a( i ) = fcn( i )
end do
send MASTER

results end if
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