Book Image

Building a BeagleBone Black Super Cluster

By : Andreas J Reichel
Book Image

Building a BeagleBone Black Super Cluster

By: Andreas J Reichel

Overview of this book

Table of Contents (14 chapters)
Building a BeagleBone Black Super Cluster
Credits
About the Author
About the Reviewers
www.PacktPub.com
Preface
References
Index

Index

A

  • Angstrom LINUX Distribution
    • about / Operating systems
  • applications, developing
    • crash course / A crash course in developing applications
    • development tools, installing / Installing development tools
    • test program, writing / First test program
  • ARMhf
    • about / ARMhf images
  • ARMhf platform
    • URL / The Ubuntu 12.04 ARMhf Linux system
  • ATLAS ARM
    • URL / ScaLAPACK and linear mathematical problems
  • ATX power supply
    • modifying / Modifying the ATX power supply

B

  • BeagleBone Black
    • hardware / Introducing the hardware
    • storage memory partition structure / The storage memory partition structure
    • boot-selection button / The boot-selection button
    • operating systems / Operating systems
    • software programming / Software programming
  • BeagleBone master node
    • files, transferring / Transferring files from and to the BeagleBone master node
  • Beowulf cluster
    • optional equipments / Minimal configuration and optional equipment
    • minimal configuration / Minimal configuration
    • USB keyboard, using / Using a USB keyboard
    • HDMI adapter / Using the HDMI adapter and monitor
    • monitor / Using the HDMI adapter and monitor
  • BiConjugate Gradient Stabilized (BiCGSTAB)
    • about / PETSc – a toolkit for scientific computation
  • bit / The source code and programming languages
  • board-holding rods
    • about / Board-holding rods
  • board spacers
    • about / Board spacers
  • boot-selection button
    • about / The boot-selection button
    • boot failure recovery / Recovering a boot failure
  • bootable SD cards
    • about / Bootable SD cards and partition tables
  • byte / The source code and programming languages
  • bytes
    • word / The source code and programming languages
    • double word / The source code and programming languages
    • quad word / The source code and programming languages

C

  • calculated data
    • visualizing, Visit used / The visualization of calculated data
  • compiler
    • about / The compiler toolchain
  • compiler toolchain
    • about / The compiler toolchain
  • configuration, deal.II
    • about / Configuring deal.II
  • configuration, PETSc
    • about / Downloading and configuring PETSc
  • configuration, SLEPc / Downloading and configuring SLEPc
  • Conjugate Gradients (CG)
    • about / PETSc – a toolkit for scientific computation
  • conjugate gradients (CG)
    • using / Iterative triangulation refinement
  • Conjugate Gradients Squared (CGS)
    • about / PETSc – a toolkit for scientific computation
  • cooling system
    • about / Cooling system

D

  • deal.II
    • about / deal.II – a powerful Physics calculation library
    • obtaining / Obtaining deal.II
    • configuring / Configuring deal.II
    • building / Building deal.II
    • example / Example programs
    • makefiles, using / Using makefiles
  • Delaunay criterion
    • about / The triangulation of a body mesh
  • direct solvers
    • versus iterative solvers / Direct solvers versus iterative solvers
  • domain name server (DNS) / Configuring the default hostfile
  • dynamic linking
    • about / The compiler toolchain

E

  • elastic equations
    • solution / Parallel solution of elastic equations
  • Ethernet multiport switch
    • about / The Ethernet multiport switch
  • example, deal.II
    • compiling / First deal.II example – triangulation
    • code / Explaining the code
    • dimensional independent code / Dimensional independent code
    • iterative triangulation refinement / Iterative triangulation refinement
    • elastic equations, solving / Parallel solution of elastic equations
  • example, PETSc
    • compiling / Compiling and running PETSc programs
    • executing / Compiling and running PETSc programs
    • simple vector math / Simple vector math
    • linear equations, solving with SuperLU_DIST / Solving linear equations with SuperLU_DIST
    • direct solvers, versus iterative solvers / Direct solvers versus iterative solvers
    • non-linear equations, solving with SNES / Solving nonlinear equations with SNES
  • example, SLEPc
    • URL, for downloading / A SLEPc example program
    • compiling / Compiling a SLEPc program
    • cluster's scaling ability, demonstrating / Demonstrating the cluster's scaling ability
  • Executable and Linking Format (ELF)
    • about / The compiler toolchain
  • executable format
    • about / The compiler toolchain
  • external network storage
    • about / The external network storage

F

  • file transfer, BeagleBone master node
    • about / Transferring files from and to the BeagleBone master node
    • FTP server, used / The FTP server
    • by WinSCP / File transfer with WinSCP
  • file transfer protocol (FTP) / Transferring files from and to the BeagleBone master node
  • finite elements
    • about / Finite elements
    • example / A practical example – the temperature gradient
  • Fortran library / Solving a positive symmetric tridiagonal system with ScaLAPACK
  • FTP server
    • about / The FTP server
    • used, for file transfer / The FTP server

G

  • general-purpose I/O (GPIO) / I/O interfaces and control buttons
  • Generalized Minimal Residual (GMRES)
    • about / PETSc – a toolkit for scientific computation
  • gid parameter
    • about / The external network storage
  • Grand Unified Bootloader (GRUB)
    • about / Bootable SD cards and partition tables
  • graphical libraries, PETSc
    • installing / Installing graphical libraries

H

  • hardware, BeagleBone Black
    • central processing unit / The central processing unit
    • I/O-interfaces / I/O interfaces and control buttons
    • control buttons / I/O interfaces and control buttons
    • onboard memory and flash storage / The onboard memory and flash storage
  • high-level programming
    • about / High-level programming
  • hub
    • about / Setting up the network backbone

I

  • installation, PETSc
    • on cluster nodes / Installing PETSc on your cluster nodes
  • installation image, master node
    • creating / Creating the master node's installation image
    • writing, to microSD card / Writing the installation image to the microSD card
    • image size, adapting to card space / Adapting the image size to the card space
  • installation process, Ubuntu
    • steps / Writing the installation image to the microSD card
  • IP numbering in local networks
    • reference link / Configuring the network interface
  • iterative solvers
    • versus direct solvers / Direct solvers versus iterative solvers

K

  • Krylov subspace
    • about / PETSc – a toolkit for scientific computation

L

  • LAPACK
    • about / ScaLAPACK and linear mathematical problems
  • library files, ScaLAPACK
    • librefblas.a / Installing and configuring ScaLAPACK
    • libreflapack.a / Installing and configuring ScaLAPACK
    • libscalapack.a / Installing and configuring ScaLAPACK
    • libtmg.a / Installing and configuring ScaLAPACK
  • linear equations
    • solving, with SuperLU_DIST / Solving linear equations with SuperLU_DIST
  • linear problem on four cluster nodes example
    • reference link / Solving a positive symmetric tridiagonal system with ScaLAPACK
  • linear solvers
    • Generalized Minimal Residual (GMRES) / PETSc – a toolkit for scientific computation
    • Conjugate Gradients (CG) / PETSc – a toolkit for scientific computation
    • Conjugate Gradients Squared (CGS) / PETSc – a toolkit for scientific computation
    • BiConjugate Gradient Stabilized (BiCGSTAB) / PETSc – a toolkit for scientific computation
    • Transpose-Free Quasi-Minimal Residual (TFQMR) / PETSc – a toolkit for scientific computation
  • Line Search
    • about / PETSc – a toolkit for scientific computation
  • Linux host environment
    • about / The Linux host environment
  • low-cost power source
    • using / Using a low-cost power source
    • power requirements / Power requirements
    • power cables / Power cables
    • ATX power supply, modifying / Modifying the ATX power supply
  • low-level programming
    • about / Low-level programming

M

  • makefiles
    • about / Example programs
    • using / Using makefiles
  • master boot record (MBR)
    • about / Bootable SD cards and partition tables
  • Metis
    • about / Downloading and configuring PETSc
  • mmcblk0p1 partition
    • about / The storage memory partition structure
  • mmcblk0p2 partition
    • about / The storage memory partition structure
  • MPI
    • about / MPI – Message Passing Interface
    • development / MPI – Message Passing Interface
    • features / MPI – Message Passing Interface
    • process control / The process control
    • software structure / The software structure
  • mpic++ / Creating a test application
  • mpiexec command / Passing values between nodes
  • mpirun command / Creating a test application
  • MPI_Barrier function / Simple node synchronization
  • MPI_COMM_WORLD / Creating a test application
  • MPI_Finalize command / Creating a test application

N

  • network backbone
    • setting up / Setting up the network backbone
  • network topology
    • about / The network topology
    • RJ45 network cables / The RJ45 network cables
    • Ethernet multiport switch / The Ethernet multiport switch
  • nibble / The source code and programming languages
  • non-linear equations
    • solving, with SNES / Solving nonlinear equations with SNES
  • nonlinear solvers
    • Line Search / PETSc – a toolkit for scientific computation
    • Trusted Region / PETSc – a toolkit for scientific computation

O

  • object files
    • about / The compiler toolchain
  • OpenMPI
    • configuring / Installing and configuring OpenMPI
    • about / Installing and configuring OpenMPI
    • packages / Downloading and installing OpenMPI packages
    • downloading / Downloading and installing OpenMPI packages
    • installing / Downloading and installing OpenMPI packages
    • default hostfile, configuring / Configuring the default hostfile
    • test application, creating / Creating a test application
    • simple node synchronization / Simple node synchronization
    • value, passing between nodes / Passing values between nodes
    • linear mathematical problems / ScaLAPACK and linear mathematical problems
    • ScaLAPACK, using / ScaLAPACK and linear mathematical problems
  • operating system installation, on master node
    • performing / Installing the operating system on the master node
    • network interface, configuring / Configuring the network interface
    • internal eMMC, flashing / Flashing the internal eMMC
  • operating systems
    • about / Operating systems
    • ARMhf images / ARMhf images
    • Ubuntu 12.04 ARMhf Linux system / The Ubuntu 12.04 ARMhf Linux system

P

  • PARMetis
    • about / Downloading and configuring PETSc
  • partition table
    • about / Bootable SD cards and partition tables
  • PETSc
    • about / PETSc – a toolkit for scientific computation
    • linear solvers / PETSc – a toolkit for scientific computation
    • nonlinear solvers / PETSc – a toolkit for scientific computation
    • graphical libraries, installing / Installing graphical libraries
    • downloading / Downloading and configuring PETSc
    • URL, for downloading / Downloading and configuring PETSc
    • configuring / Downloading and configuring PETSc
    • compiling / Compiling PETSc
    • installing, on cluster nodes / Installing PETSc on your cluster nodes
    • example / PETSc example programs
    • URL, for user manual / PETSc example programs, Solving nonlinear equations with SNES
  • positive symmetric tridiagonal system, solving
    • ScaLAPACK used / Solving a positive symmetric tridiagonal system with ScaLAPACK
    • code / Understanding the code
    • code mathematics / Understanding the mathematics behind the code
  • process control, MPI
    • about / The process control
  • programmable real time units (PRUs) / I/O interfaces and control buttons
  • putty
    • URL / Minimal configuration

R

  • RJ45 network cables
    • about / The RJ45 network cables

S

  • Samba
    • URL / The external network storage
  • scalable board mounting system
    • building / Building a scalable board-mounting system
    • board-holding rods / Board-holding rods
    • board spacers / Board spacers
    • cooling system / Cooling system
  • ScaLAPACK
    • about / ScaLAPACK and linear mathematical problems, Installing and configuring ScaLAPACK
    • using / ScaLAPACK and linear mathematical problems
    • BLAS library / ScaLAPACK and linear mathematical problems
    • diagrammatic representation / ScaLAPACK and linear mathematical problems
    • MPI library / ScaLAPACK and linear mathematical problems
    • PBLAS library / ScaLAPACK and linear mathematical problems
    • BLACS library / ScaLAPACK and linear mathematical problems
    • installing / Installing and configuring ScaLAPACK
    • download link / Installing and configuring ScaLAPACK
    • configuring / Installing and configuring ScaLAPACK
    • prefix option / Installing and configuring ScaLAPACK
    • positive symmetric tridiagonal system, solving / Solving a positive symmetric tridiagonal system with ScaLAPACK
  • Secure Copy Protocol (SCP) / File transfer with WinSCP
  • setup script, ScaLAPACK
    • download link / Installing and configuring ScaLAPACK
  • slave nodes
    • installing / Installing and configuring the slave nodes
    • configuring / Installing and configuring the slave nodes
    • installation image, creating / Creating the slave node's installation image
    • network interface, configuring / Configuring the slave node's network interface
    • internal eMMC, flashing / Flashing the internal eMMC
    • SSH login keys, creating / Creating SSH login keys
  • SLEPc
    • about / SLEPc – a library for Eigenvalue problems
    • downloading / Downloading and configuring SLEPc
    • configuring / Downloading and configuring SLEPc
    • URL, for downloading / Downloading and configuring SLEPc
    • compiling / Compiling SLEPc
    • example / A SLEPc example program
  • SNES
    • used, for solving non-linear equations / Solving nonlinear equations with SNES
    • about / Solving nonlinear equations with SNES
  • software programming
    • about / Software programming
    • open source philosophy / The open source philosophy
    • software modularity and dependencies / Software modularity and dependencies
    • source code / The source code and programming languages
    • programming languages / The source code and programming languages
    • machine language / The source code and programming languages
    • low-level programming / Low-level programming
    • high-level programming / High-level programming
    • compiler toolchain / The compiler toolchain
  • software structure, MPI
    • about / The software structure
  • static linking
    • about / The compiler toolchain
  • storage memory
    • about / The storage memory
    • installation images, on microSD cards / Installing images on microSD cards
    • swap space, on SD card / The swap space on an SD card
    • external network storage / The external network storage
  • storage memory partition structure
    • about / The storage memory partition structure
  • SuperLU_DIST
    • used, for solving linear equations / Solving linear equations with SuperLU_DIST
  • switch
    • about / Setting up the network backbone

T

  • technological/scientific calculations
    • performing, on cloud-distributed mesh grids / Calculations on cloud-distributed mesh grids
    • triangulation / The triangulation of a body mesh
    • finite elements / Finite elements
  • templates
    • about / Dimensional independent code
  • Time Steppers
    • about / PETSc – a toolkit for scientific computation
  • Transpose-Free Quasi-Minimal Residual (TFQMR)
    • about / PETSc – a toolkit for scientific computation
  • triangulation
    • about / The triangulation of a body mesh
  • tridiagonal matrix equation / Solving a positive symmetric tridiagonal system with ScaLAPACK
  • Trusted Region
    • about / PETSc – a toolkit for scientific computation

U

  • U-Boot
    • about / Bootable SD cards and partition tables
  • Ubuntu
    • downloading, for ARM / Downloading Ubuntu for ARM
    • download link / Downloading Ubuntu for ARM
    • installation process / Writing the installation image to the microSD card
  • Ubuntu 12.04 ARMhf Linux system
    • about / The Ubuntu 12.04 ARMhf Linux system
  • Ubuntu versions
    • root filesystem partition / Downloading Ubuntu for ARM
    • Linux header files / Downloading Ubuntu for ARM
    • boot loader partition / Downloading Ubuntu for ARM
  • uid parameter
    • about / The external network storage
  • Unsymmetric MultiFrontal sparse LU factorization (UMFPACK)
    • about / Obtaining deal.II

V

  • very secure ftp daemon
    • about / The FTP server
  • Visit
    • about / The visualization of calculated data
    • used, for visualizing calculated data / The visualization of calculated data
  • volume boot record (VBR)
    • about / Bootable SD cards and partition tables

W

  • WinSCP
    • about / File transfer with WinSCP
    • used, for file transfer / File transfer with WinSCP

X

  • x-flag / First test program