A High Performance C++ Generic Benchmark for Computational Epidemiology

Simple item page
dc.contributor.authorPugaonkar, Aniket Narayanen
dc.contributor.committeechairMarathe, Madhav Vishnuen
dc.contributor.committeememberGupta, Sandeepen
dc.contributor.committeememberBisset, Keith R.en
dc.contributor.committeememberRibbens, Calvin J.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2015-02-01T09:00:53Zen
dc.date.available2015-02-01T09:00:53Zen
dc.date.issued2015-01-31en
dc.description.abstractAn effective tool used by planners and policy makers in public health, such as Center for Disease Control (CDC), to curtail spread of infectious diseases over a given population is contagion diffusion simulations. These simulations model the relevant characteristics of the population (age, gender, income etc.) and the disease (attack rate, etc.) and compute the spread under various configuration and plausible intervention strategies (such as vaccinations, school closure, etc.). Hence, the model and the computation form a complex agent based system and are highly compute and resource intensive. In this work, we design a benchmark consisting of several kernels which capture the essential compute, communication, and data access patterns for such applications. For each kernel, the benchmark provides different evaluation strategies. The goal is to (a) derive alternative implementations for computing the contagion by combining different implementation of the kernels, and (b) evaluate which combination of implementation, runtime, and hardware is most effective in running large scale contagion diffusion simulations. Our proposed benchmark is designed using C++ generic programming primitives and lifting sequential strategies for parallel computations. Together, these lead to a succinct description of the benchmark and significant code reuse when deriving strategies for new hardware. For the benchmark to be effective, this aspect is crucial, because the potential combination of hardware and runtime are growing rapidly thereby making infeasible to write optimized strategy for the complete contagion diffusion from ground up for each compute system.en
dc.description.degreeMaster of Scienceen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:4451en
dc.identifier.urihttp://hdl.handle.net/10919/51243en
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectBenchmarken
dc.subjectEpidemiologyen
dc.subjectEpiSimdemicsen
dc.subjectEpiFasten
dc.subjectC++11en
dc.subjectBOOST C++ librariesen
dc.subjectIntel TBBen
dc.subjectIntel Cilk Plusen
dc.subjectIntel MICen
dc.titleA High Performance C++ Generic Benchmark for Computational Epidemiologyen
dc.typeThesisen
thesis.degree.disciplineComputer Science and Applicationsen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Pugaonkar_AN_T_2015.pdf
Size:
1.63 MB
Format:
Adobe Portable Document Format
Download

Collections

Masters Theses