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- Herausgeber: Packt Publishing
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Author Carlos R. Morrison (Staff Scientist, NASA) will empower the uninitiated reader to quickly assemble and operate a Pi3 supercomputer in the shortest possible time. The lifeblood of a supercomputer, the MPI code, is introduced early, and sample MPI code provides additional practice opportunities for you to test the effectiveness of your creation. You will learn how to configure various nodes and switches so that they can effectively communicate with each other. By the end of this book, you will have successfully built a supercomputer and the various applications related to it.
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Veröffentlichungsjahr: 2017
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Table of Contents
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.
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ISBN 978-1-78728-258-2
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Credits
Author
Carlos R. Morrison
Copy Editor
Safis Editing
Reviewer
Dr. Isaiah M. Blankson
Project Coordinator
Kinjal Bari
Commissioning Editor
Vijin Boricha
Proofreader
Safis Editing
Acquisition Editor
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Indexer
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Graphics
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Technical Editor
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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:
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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 cores to work on a given problem.
Chapter 7, Configuring the Eight Nodes, discusses how to configure the eight or 16-node Pi supercomputer. You will be shown how to edit the fstab file on the slave1 node to set up an automatic mount command, the rc.local file on the slave1 node to automatically mount the export drive containing the MPI test code folder, the hosts files on the master and slave1 nodes to reflect the temporary IP address, and host names on the remaining six or fourteen slave nodes. You will then be shown how to use the SD formatter for Windows to format the remaining slave SD cards, and win32 Disk Imager to copy the slave1 SD card image to the remaining slave nodes in the cluster. You will then edit/update, once again, the hosts file on the master and slaves to reflect their actual IP addresses, edit the interfaces file on the super cluster nodes, and finally, update the MAC and IP address on the network switch for the remaining slave nodes.
Chapter 8, Testing the Super Cluster, discusses how to use the shutdown -h now command to shut down your Pi computer, the -H command to solve the MPI π function in record time, and create convenience bash files to enhance the user experience while operating the supercomputer.
Chapter 9, Real-World Math Application, discusses how to write and run serial and MPI Taylor series, sine, cosine, tangent, and the natural log functions.
Chapter 10, Real-World Physics Application, discusses how to write and run the MPI code for a vibrating string.
Chapter 11, Real-World Engineering Application, discusses how to write and run a serial and MPI sawtooth Fourier series code.
What you need for this book
You will need Linux/Ubuntu OS installed on your PC with the option to access the Windows OS, and a basic working knowledge of the C language.
Who this book is for
This book targets hobbyists and enthusiasts who want to explore building supercomputers with microcomputers. Researchers will also find this book useful. Prior programming knowledge is necessary; knowledge of supercomputers is not.
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alpha@Mst0:/beta/gamma $ time mpiexec -H Mst0,Mst0,Mst0,Mst0,Slv1,Slv1,Slv1,Slv1,Slv2,Slv2 MPI_08_bNew terms and important words are shown in bold. Words that you see on the screen, for example, in menus or dialog boxes, appear in the text like this: "On a Windows 7 machine, click on Systems & Security, then click on System, then DeviceManager, and click on Processor."
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Chapter 1. Getting Started with Supercomputing
The prefix super in the moniker supercomputer may, to the ill-informed, conjure up images of the electronic supervillain HAL 9000 in Arthur C. Clarke's classic movie 2001: A Space Odyssey or the benevolent superhero Clark Kent, aka Superman, who inhabits the DC comic universe. However, the tag supercomputer is, in fact, associated with a non-fictional entity that has no ill-will towards humans - at least not at this moment in time. Supercomputing and supercomputers are the subject matter of this book.
In this chapter, we introduce the reader to the basics of supercomputing, or more precisely, parallel processing. Parallel processing is a computational technique that is currently enjoying widespread usage at many research institutions, including universities and government laboratories, where machines routinely carry out computation in the teraflops (1 billion floating point operations per second) and petaflops (1,000 teraflops) domain. Parallel processing significantly reduces the time needed to analyze and/or solve complex and difficult mathematical and scientific problems, such as weather prediction, where a daunting myriad of physical atmospheric conditions must be considered and processed simultaneously in order to obtain generally accurate weather forecasting.
Supercomputing is also employed in analyzing the extreme physical conditions extant at the origin of the much-discussed Big Bang event, in studying the dynamics of galaxy formation, and in simulating and analyzing the complex physics of atomic and thermonuclear explosions - data that is crucial to the military for maintaining and designing even more powerful weapons of mass destruction - holy crap!! This doesn't bode well for humanity. Anyway, these are just a few examples of tasks germane to parallel processing. Following are images of events that are being studied/simulated by scientist employing supercomputers:
The enhanced processing speed, so central to parallel computing, is achieved by assigning chunks of data to different processors in a computer network, where the processors then concurrently execute similar, specifically designed code logic on their share of the data. The partial solution from each processor is then gathered to produce a final result. You will indeed be exploring this technique later when you run example codes on your PC, and then on your Pi2 or Pi3 supercomputer.
The computational time compression associated with parallel computing is typically on the order of a few minutes or hours, rather than weeks, months, or years. The sharing of tasks among processors is facilitated by a communication protocol for programming parallel computers called Message Passing Interface (MPI). The MPI standard, which came to fruition between the 1980s and early 1990s, was finally ratified in 2012 by the MPI Forum, which has over 40 participating organizations.
You can visit https://computing.llnl.gov/tutorials/mpi/ for a brief history and tutorial on MPI, and https://computing.llnl.gov/tutorials/parallel_comp/ for parallel computing. You can also visit http://mpitutorial.com/tutorials/ for additional information and a tutorial on MPI programming.
In this chapter, you will learn about the following topics:
Von Neumann architecture
Dr. John von Neumann:
John von Neumann circa the 1940s
Any discussion concerning computers must include the contributions of the famed Hungarian mathematician/genius Dr. John von Neumann. He was the first to stipulate, in his famous 1945 paper, the general requirements for an electronic computer. This device was called a stored-program computer
