Build Supercomputers with Raspberry Pi 3

Table of Contents

Build Supercomputers with Raspberry Pi 3

Credits

About the Author

About the Reviewer

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Why subscribe?

Customer Feedback

Dedication

Preface

What this book covers

What you need for this book

Who this book is for

Conventions

Reader feedback

Customer support

Downloading the example code

Downloading the color images of this book

Errata

Piracy

Questions

1. Getting Started with Supercomputing

Von Neumann architecture

Flynn's classical taxonomy

Historical perspective

Serial computing technique

Parallel computing technique

The need for greater processing speed

Additional analytical perspective

Sources for reference

Summary

2. One Node Supercomputing

Linux installation

PC processor

Accessing processor technical details

Write/run serial π code

Message passing interface

Basic MPI code

MPI π code

Critical MPI for loop structure

MPI Euler code

MPI Leibniz code

MPI Nilakantha code

Summary

3. Preparing the Initial Two Nodes

Listing of parts

The Pi2/Pi3 computer

Project overview

Super stack assembly

Preparing the master node

Transferring the code

Preparing the slave node

Summary

4. Static IP Address and Hosts File Setup

Configuring static IP address of the master Pi

Configuring a network switch static IP address

Hosts file setup

Summary

5. Creating a Common User for All Nodes

Adding a new user for all nodes

ID key generation

ID key transfer

Summary

6. Creating a Mountable Drive on the Master Node

Summary

7. Configuring the Eight Nodes

Automating mounting of drives

Setting up the host file for all nodes

Formatting the remaining slave SD cards

Copying the slave1 SD card image to the main computer drive

Copying the slave1 image to the remaining slave SD cards

Summary

8. Testing the Super Cluster

Wielding the -H command

Pi2 supercomputing

Pi3 supercomputing

Creating bash files

Using unrestrained MPI code logic

Summary

9. Real-World Math Application

MPI Taylor series sine(x) function

MPI Taylor series cosine(x) function

MPI Taylor series tan(x) function

MPI Taylor series ln(x) function

Summary

10. Real-World Physics Application

MPI concurrent wave equation and code

Drawing graphs

Summary

11. Real-World Engineering Application

MPI Fourier series sawtooth signal

Summary

A. Appendix

Definitions 

Build Supercomputers with Raspberry Pi 3

Build Supercomputers with Raspberry Pi 3

Copyright © 2017 Packt Publishing 

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without the prior written permission of the publisher, except in the case of brief quotations embedded in critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy of the information presented. However, the information contained in this book is sold without warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers and distributors will be held liable for any damages caused or alleged to be caused directly or indirectly by this book.

Packt Publishing has endeavored to provide trademark information about all of the companies and products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot guarantee the accuracy of this information.

First published: March 2017

Production reference: 1210317

Published by Packt Publishing Ltd.

Livery Place

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ISBN 978-1-78728-258-2

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Credits

About the Author

Carlos R. Morrison was born in Kingston, Jamaica, West Indies. He received a B.S. (Hons) degree in physics with a mathematics minor in 1986 from Hofstra University, Hempstead, NY, and an M.S. degree in physics in 1989 from Polytechnic University, Brooklyn, NY.

In 1989, he joined the NASA Glenn Research Center, Cleveland, OH, as a staff scientist in the solid-state physics branch and, in 1999, he transferred to the structures and dynamics branch. He has authored and coauthored several journal and technical articles associated with aerospace and electromagnetic devices. He holds several patents, including one on the Morrison Motor for which he won the 2004 R&D 100 Award, and software technologies used to control magnetic bearings. He is currently engaged in research associated with room temperature and superconducting reluctance motors, and Simulink Simulation of said motors.

Mr. Morrison is a member of the American Physical Society and the National Technical Association.

I would like to thank Dr. Isaiah Blankson for reading the manuscript, and for building and testing the Pi cluster.

About the Reviewer

Dr. Isaiah M. Blankson received his PhD in Aeronautics and Astronautics from the Massachusetts Institute of Technology, Cambridge, MA, USA. He is a specialist in hypersonic aerodynamics and propulsion. His current research involves the use of computational (CFD) and experimental methods for Magneto Hydrodynamic (MHD) energy bypass engine concepts for space-access vehicles, and non-equilibrium plasma for applications in hypersonic aerodynamics and propulsion. Previously, he was an aerospace scientist at the General Electric Global Research Center (CRD) in Niskayuna, NY. He has several US patents, including one on an MHD-controlled turbojet engine for space access, and another on an exoskeletal gas-turbine engine. He is the author of numerous technical publications, and an associate fellow of the American Institute of Aeronautics and Astronautics (AIAA). Over the years, he has received many awards, including the distinguished presidential rank award for sustained superior accomplishment in 2012. As chief scientist at IMB and associates LLC, he develops and tests small-platform supercomputers for solving complex engineering problems. 

Here are some of the other books he has worked on:

Reviewer of selected chapters: Book to be published (2017) by Cambridge University Press, UK

Plasma Physics for Engineering, by Dr. Joseph J. S. Shang and Dr. Sergey T. Surzhikov

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Dedication

This book is dedicated to the memory of my mother, Volda O. Morrison, who, in my formative years, provided encouragement, and support buttressing my interest in physics. Also, to my wife, Peta-Gaye, and daughters Camille, and Brittany who encouraged me to keep writing, and finally, to my younger brother Ramong who endured many of my antics throughout our earlier years.

Preface

This book explains how to build and operate a powerful eight or 16-node Pi2 or Pi3 supercomputer. You will be provided detailed systematic instructions on installing the Linux/Ubuntu operating system on your PC, and its use in configuring, communicating with, and ultimately operating your Pi supercomputer.

Initially, you will learn how to write and run a serial and a Message Passing Interface (MPI) π code on your PC, which is then used as a one-node supercomputer. Armed with this knowledge, you will then configure a Pi one-node, 4-core supercomputer on which you subsequently run the previous mentioned MPI π code. Next, you will assemble a two-node, 8-core Pi supercomputer on which, again, you will execute said MPI π code, and finally, you will construct an eight or 16-node Pi supercomputer, which you will employ to solve complex calculations incorporating the MPI construct.

What this book covers

Chapter 1, Getting Started with Supercomputing, provides an overall perspective on the concept of supercomputing. The chapter discusses Von Neumann’s architecture, Flynn’s classical taxonomy, a historical perspective on supercomputing, serial and parallel computing techniques, and justifications – including an analytical perspective – for greater processing speeds.

Chapter 2, One Node Supercomputing, discusses how to do supercomputing on one node, in this instance, your PC. You will be instructed how to install Linux/Ubuntu on your PC, which you will then use to run a serial and MPI π code. Next, you will learn about the critical for loop construct that is used to assign tasks among the cores/processes. Finally, you will write/copy, and run/generate π from the MPI Euler, Leibniz, and Nilakantha infinite series.

Chapter 3, Preparing the Initial Two Nodes, discusses how to build a two-node Pi supercomputer. Initially, you will be presented with a list of parts. You will then learn about the origin of the Pi microcomputer, and its technical specs. Next, you will be shown how to configure the master node in preparation for transferring the requisite MPI test codes from your PC to the master node. Finally, you will configure the first slave node in preparation for the creation a two-node (master and slave1) supercomputer.

Chapter 4, Static IP Address and Hosts File Setup, discusses how to configure the static IP address of the master, slave1, and network switch. Next, you will learn how to set up the hosts file.

Chapter 5, Creating a Common User for All Nodes, discusses how to create a new user for the master node, how to create a password for the new user on the master node, how to create a new user for the slave1 node, and how to create a password for the new user on the slave1 node. In addition, you will learn how to generate a special key on the master node, which is required for seamless transitioning between the nodes without using a password. You will then learn how to copy the special key from the master node to the slave1 node. Next, you will edit the .bashrc file on the master node to facilitate seamless special key access to all the nodes. Finally, you will learn how to use the which command.

Chapter 6, Creating a Mountable Drive on the Master Node, discusses how to use the mkdir command to make a directory/folder, the chown command for changing ownership of the export drive from the root user to a new user, and the rpcbind command, which allows the master Pi to export the export drive on the master to slave nodes. You will learn how to edit the exports file, which at facilitates exporting the export drive on the master node to the slave nodes, use the nfs-kernel-server command; edit the bootup script rc.local, which will make the export drive on the master node mountable for use by the slave nodes; use the mount command to manually mount the export drive containing the MPI codes; use the cat command to display the content of a file; use the cp -a command to copy files/codes to the export drive; and use the -H command to task any or all nodes; and