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
- ATLAS ARM
- 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)
- 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
- 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
- configuration, SLEPc / Downloading and configuring SLEPc
- Conjugate Gradients (CG)
- conjugate gradients (CG)
- Conjugate Gradients Squared (CGS)
- 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)
- gid parameter
- about / The external network storage
- Grand Unified Bootloader (GRUB)
- 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
- IP numbering in local networks
- reference link / Configuring the network interface
- iterative solvers
- versus direct solvers / Direct solvers versus iterative solvers
K
- Krylov subspace
L
- LAPACK
- 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
- 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)
- Metis
- mmcblk0p1 partition
- mmcblk0p2 partition
- 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
- partition table
- 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
- 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
- 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
- Transpose-Free Quasi-Minimal Residual (TFQMR)
- triangulation
- about / The triangulation of a body mesh
- tridiagonal matrix equation / Solving a positive symmetric tridiagonal system with ScaLAPACK
- Trusted Region
U
- U-Boot
- 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
- 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)
W
- WinSCP
- about / File transfer with WinSCP
- used, for file transfer / File transfer with WinSCP
X
- x-flag / First test program