High Performance Computing

Modules presented in Chapter 13 on modeling with matrices include sections that discuss the utility of high performance computing (HPC) in computational science. Moreover, Chapter 12 provides an introduction to some of the hardware and algorithms for HPC, which is becoming increasingly important with the advent of “Big Data” and massive computational problems.

The text’s Modules 10.5, 11.4, 13.2, 13.3, 13.4, 14.14, and 13.5 were based on six modules, developed with encouragement and funding by The National Computational Science Institute Undergraduate Petascale Education Program (UPEP). UPEP, which is an NCSA Blue Waters project in collaboration with the National Computational Science Institute (NCSI) and national HPC programs, supported three initiatives:

• Professional Development Workshops for undergraduate faculty
• Research Experiences for undergraduates
• Materials Development by undergraduate faculty for undergraduates

The Materials Development initiative had the goal “to support undergraduate faculty in preparing a diverse community of students for petascale computing.” Angela Shiflet and George Shiflet wrote six UPEP modules, and various Wofford College students (Shay Ellison, Whitney E. Sanders, Jesse A. Hanley), who were UPEP interns, implemented the module’s HPC programs in C with MPI. In 2014-2015, Blue Waters Intern Matt Beasley (Wofford College), under the direction of Angela Shiflet, is developing additional materials, including tutorials and programs in C and MPI, that will appear on this website. These materials can be used in a high-performance computing or a computational science course or as components of computer science courses to introduce various concepts of HPC with applications. The text’s modules with links to the original UPEP modules and HPC programs along with HPC tutorials follow:

• Module 10.5 Biofilms: United They Stand, Divided They Colonize
• Module 11.4 Modeling an “Able” Invader – the “Cane” Toad
• Module 13.2 Living Links: Applications of Matrix Operations to Population Studies
• Module 13.3 Time after Time: Age- and Stage-Structured Models – includes one parallel version (C/MPI) for parameter sweeping and another version (C/MPI) for a parallel matrix implementation
  • Parameter Sweeping for Age-Structure Model Tutorial by Matt Beasley
  • Leslie Matrix Parallelization Tutorial by Matt Beasley
• Modules 13.4 and 14.14 Probable Cause: Modeling with Markov Chains
• Module 13.5 Getting the “Edge” on the Next Flu Pandemic: We Should’a “Node” Better – includes MATLAB scripts implementing a parallel version of the social network model

Educational Modules on High Performance Computing Bioinformatics Algorithms

with NCSI Blue Waters Interns

(Programs available in Instructor's Manual section)

Aligning Sequences--Sequentially and Concurrently

by

Angela B. Shiflet¹, George W. Shiflet¹, Daniel S. Couch¹,
Pietro Hiram Guzzi², Mario Cannataro^2
1Wofford College, Spartanburg, SC, USA
²University “Magna Græcia” of Catanzaro, Catanzaro, Italy

Copyright © 2016

Please check this site periodically for additional HPC materials.