Building a Beaglebone Black Super Cluster电子书

Building a BeagleBone Black Super Cluster

Table of Contents

Building a BeagleBone Black Super Cluster

Credits

About the Author

About the Reviewers

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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

Errata

Piracy

Questions

1. BeagleBone Black System Board

Introducing the hardware

The central processing unit

I/O interfaces and control buttons

The onboard memory and flash storage

The storage memory partition structure

The boot-selection button

Recovering a boot failure

Operating systems

ARMhf images

The Ubuntu 12.04 ARMhf Linux system

Software programming

The open source philosophy

Software modularity and dependencies

The source code and programming languages

Low-level programming

High-level programming

The compiler toolchain

Summary

2. Building a Beowulf Cluster

Minimal configuration and optional equipment

Minimal configuration

Using a USB keyboard

Using the HDMI adapter and monitor

Building a scalable board-mounting system

Board-holding rods

Board spacers

Cooling system

Using a low-cost power source

Power requirements

Power cables

Modifying the ATX power supply

Setting up the network backbone

The network topology

The RJ45 network cables

The Ethernet multiport switch

The storage memory

Installing images on microSD cards

The swap space on an SD card

The external network storage

Summary

3. Operating System Setup and Configuration

The Linux host environment

Creating the master node's installation image

Bootable SD cards and partition tables

Downloading Ubuntu for ARM

Writing the installation image to the microSD card

Adapting the image size to the card space

Installing the operating system on the master node

Configuring the network interface

Flashing the internal eMMC

The external network storage

Installing and configuring the slave nodes

Creating the slave node's installation image

Configuring the slave node's network interface

Flashing the internal eMMC

Creating SSH login keys

A crash course in developing applications

Installing development tools

First test program

Transferring files from and to the BeagleBone master node

The FTP server

File transfer with WinSCP

Summary

4. Parallel Computing with OpenMPI and ScaLAPACK

MPI – Message Passing Interface

The process control

The software structure

Installing and configuring OpenMPI

Downloading and installing OpenMPI packages

Configuring the default hostfile

Creating a test application

Simple node synchronization

Passing values between nodes

ScaLAPACK and linear mathematical problems

Installing and configuring ScaLAPACK

Solving a positive symmetric tridiagonal system with ScaLAPACK

Understanding the code

Understanding the mathematics behind the code

Summary

5. Advanced Solving of General Equation Systems

PETSc – a toolkit for scientific computation

Installing graphical libraries

Downloading and configuring PETSc

Compiling PETSc

Installing PETSc on your cluster nodes

PETSc example programs

Compiling and running PETSc programs

Simple vector math

Solving linear equations with SuperLU_DIST

Direct solvers versus iterative solvers

Solving nonlinear equations with SNES

SLEPc – a library for Eigenvalue problems

Downloading and configuring SLEPc

Compiling SLEPc

A SLEPc example program

Compiling a SLEPc program

Demonstrating the cluster's scaling ability

Summary

6. Scientific and Technological Examples of Parallel Computing

Calculations on cloud-distributed mesh grids

The triangulation of a body mesh

Finite elements

A practical example – the temperature gradient

deal.II – a powerful Physics calculation library

Obtaining deal.II

Configuring deal.II

Building deal.II

Example programs

Using makefiles

First deal.II example – triangulation

Explaining the code

Dimensional independent code

Iterative triangulation refinement

Parallel solution of elastic equations

The visualization of calculated data

Summary

A. References

Index