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Workshop/Tutorial Resources

Getting Started

Basic Information

Curriculum Modules

The BCCD comes with a number of parallel and distributed computing modules built-in, these are located in ~bccd. New modules are currently under development by LittleFe owners as part of the effort described here: http://littlefe.net/curriculum

Module name Author Pointer In the BCCD?
Area under a curve Aaron Weeden http://www.shodor.org/petascale/materials/UPModules/AreaUnderCurve/ Yes
GalaxSee David Joiner http://shodor.org/petascale/materials/UPModules/NBody/ Yes
GalaxSee-v2 David Joiner http://bccd.net/wiki/index.php/GalaxSee-v2 Yes
Hello World 2 Yes
Life David Joiner http://bccd.net/wiki/index.php/Game_of_Life Yes
Molecular Dynamics Charlie Peck http://bccd.net/wiki/index.php/Molecular-dynamics Yes
Pandemic Aaron Weeden http://www.shodor.org/petascale/materials/UPModules/InfectiousDisease/ Yes
Parameter Space David Joiner http://bccd.net/wiki/index.php/Parameter_Space Yes
StatKit Sam Leeman-Munk http://bccd.net/wiki/index.php/StatKit Yes
LittleFe CPU Load Monitor Zach Goodwyn http://cluster.earlham.edu/svn/bccd-ng/trunk/trees/etc/skel/Community-Modules/UMW/cpumon/README Yes
Numerical Quadrature MPI David John and Stan Thomas http://csweb.cs.wfu.edu/bigiron/LittleFE-MPI-TrapezoidalRule/_build/html/index.html Yes
Numerical Quadrature CUDA David John and Stan Thomas http://csweb.cs.wfu.edu/bigiron/LittleFE-CUDA-TrapezoidalRule/build/html/index.html Yes
Parallel Sort by Regular Sampling David John and Stan Thomas http://csweb.cs.wfu.edu/bigiron/LittleFE-PSRS/build/html/index.html Yes
Operating Systems Labs David Monismith http://monismith.info/cs550/hw.html Yes
mpiBLAST National Computational Biology Institute http://www.bccd.net/wiki/index.php/Running_mpiBLAST No
Simpson Rule Andrew Fitz Gibbon http://bccd.net/wiki/index.php/Simpson_Rule_MPI_Example No
Computer Essentials and Quiz Liviu Popa-Simil http://littlefe.net/files/CEQ.zip No
Dominating Set with GPUs Christian Trefftz http://www.cis.gvsu.edu/~trefftzc/dominatingSetWithGPUs/VersionOne/intro.html No
Biofilms Angela B. Shiflet, George W. Shiflet, Shay M. Ellison http://shodor.org/petascale/materials/UPModules/biofilms/ No
Getting the edge of the next Flue epidemic Angela B. Shiflet, George W. Shiflet http://shodor.org/petascale/materials/UPModules No
Multithreading and Multiprocessing Henry Neeman http://shodor.org/petascale/materials/UPModules/sipeMultithreadingMultiprocessModule2/ No
Techniques and Technologies Henry Neeman http://www.shodor.org/petascale/materials/UPModules/sipeTechniquesAndTechnologiesModule3/ No
A Beginner's Guide to High-Performance Computing Henry Neeman http://www.shodor.org/petascale/materials/UPModules/beginnersGuideHPC/ No
Order from Chaos:A sampling of Stochastic Optimization Algorithms David A. Joiner http://shodor.org/petascale/materials/UPModules/StochOpt/ No
Living Links:Applications of Matrix Operations to Population Studies Rubin H. Landau http://shodor.org/petascale/materials/UPModules/populationMatrices/ No
Time after Time:age and stage structured models Angela B. Shiflet, George W. Shiflet and Jesse A. Hanley http://www.shodor.org/petascale/materials/modules/?sr=0 No
Conway's Game of Life Aaron Weeden http://www.shodor.org/petascale/materials/UPModules/GameOfLife/ No
Modeling an "Able" Invader:the "Cane" toad Angela B. Shiflet, George W. Shiflet and Whitney Sanders http://www.shodor.org/petascale/materials/UPModules/ableInvader/ No
Dynamic Programming with CUDA Pt 1 Robert Hochberg http://www.shodor.org/petascale/materials/UPModules/dynamicProgrammingPartI/ No
Dynamic Programming with CUDA Pt 2 Robert Hochberg http://www.shodor.org/petascale/materials/UPModules/dynamicProgrammingCUDAPtII/ No
How Many People Does It Take To....A parallel Approach to the Party Problem David Toth http://www.shodor.org/petascale/materials/UPModules/howManyPeople/ No
Matrix Multiplication with CUDA Robert Hochberg http://www.shodor.org/petascale/materials/UPModules/matrixMultiplication/ No
BLAST-ing in Parallel:Enabling an Essential Computational Tool to Keep PEace with the Explosive Growth in Biological Sequence Data Jeffrey D. Krause,Michael Ly http://www.shodor.org/petascale/materials/UPModules/BLAST/ No
Sieve of Eratosthenes Aaron Weeden http://www.shodor.org/petascale/materials/UPModules/sieveOfEratosthenes/ Yes
Scaling in nature and in the machine Russell Manson http://shodor.org/petascale/materials/UPModules/scalingInNature/ No
Binary Tree Traversal Aaron Weeden and Patrick Royal www.shodor.org/petascale/materials/UPModules/Binary_Tree_Traversal/ Yes
Suffix Trees:How to do Google search in bioinformatics? Ananth Kalyanaraman http://www.shodor.org/petascale/materials/UPModules/suffixTrees/ No
Probable Cause:Modeling with Markov Chains Angela B. Shiflet, George W. Shiflet and Whitney Sanders http://www.shodor.org/petascale/materials/modules/?sr=20 No
Parallel Spectral Numerical Methods Gong Chen, Brandon Cloutier, Ning Li, Benson Muite and Paul Rigge http://shodor.org/petascale/materials/UPModules/Parallel_Spectral_Methods/ No
Scientific Visualisation with CUDA Robert Hochberg and John Riselvato http://shodor.org/petascale/materials/UPModules/scientificVisualizationCUDA/ No
Introduction to GPU Programming using CUDA Paul Gray http://www.shodor.org/petascale/materials/UPModules/IntroGPU/ No
Learning Automated Performance Analysis using PetaKit and the BCCD Ivan Babic, Mobeen Ludin, and Charlie Peck http://www.shodor.org/petascale/materials/UPModules/PetaKit_BCCD/ Yes
Multi-Threaded Programming Introduction using the Sum3 Problem Mark McKenney and Igor Crk http://www.cs.siue.edu/~marmcke/docs/introToParallelism/index.html No
Image Processing using PETSc (work in progress) John Chrispell https://bitbucket.org/jchrispe/imagepropetsc/ No
Heat Diffusion in MPI (work in progress) Louie Elliot No
Heat Diffusion in OpenCL (work in progress) Amalan Iyengar https://github.com/scrblnrd3/GPGPU-Diffusion No
GalaxSee OpenCL (work in progress) Amalan Iyengar https://github.com/scrblnrd3/GalaxCL No
OnRamp Interactive Learning Portal (work in progress) Samantha S. Foley No
Parallel Suffix Arrays (work in progress) Ana Carmen Gonzalez No
Visualizing LAMMPS (work in progress) Steve Harnish No
Parallel Matlab for Aerospace Engineering (work in progress) M. Javed Khan and Bruce Heath No
Random numbers, C++, and Erlang (work in progress) David Naugler No
Work-sharing TSP (work in progress) David Valentine No

Developer Information

Configuring and Customizing

Tools and Clustering

Articles

Feedback

Note: This is beta software, and should not even be interpreted as production-quality.

Miscellania

Licensing

The free stuff

BCCDv3, defined as the build, automation, and testing framework and other software contributed by the BCCD developers, is licensed under the GNU General Public License, version 3.

The core of BCCDv3 is based off Debian. All software packaged by Debian must meet the Debian Free Software Guidelines, which include licenses found here.

Some of the stacking filesystem support and hardware autodetection is based off KNOPPIX, which is licensed under the GNU General Public license, version 2.

The stacking filesystem the BCCD uses is AUFS, which is licensed under the GNU General Public license, version 2.

The non-free stuff

The basic software you need to use the BCCD is all freely available. Some of the software (all found in /bccd/software) is licensed solely for use inside the BCCD environment. The software in this category includes but is not limited to:

The authors of these software packages generously provide free licensing to the BCCD project to further our educational mission, so please be respectful and don't copy this software outside the BCCD.

Explanation

What does all this license legalese mean? In short, the BCCD is free and open-source for all, with the notable exceptions above. You may use it, modify, and redistribute yourself as long as all the license terms remain intact.

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