Degree Type

Thesis

Date of Award

2011

Degree Name

Master of Science

Department

Computer Science

First Advisor

Masha Sosonkina

Second Advisor

Lu Ruan

Abstract

Modern quantum chemistry deals with electronic structure calculations of

unprecedented complexity and accuracy. They demand full power of

high-performance computing and must be in tune with the given architecture for

superior efficiency. To make such applications resource-aware, it is desirable

to enable their static and dynamic adaptations using some external software

(middleware), which may monitor both system availability and application needs,

rather than mix science with system-related calls inside the application.

The present work investigates scientific application interlinking

with middleware based on the example of the computational chemistry package GAMESS

and middleware NICAN. The existing synchronous model is limited by the possible delays

due to the middleware processing time under the sustainable runtime system conditions.

Proposed asynchronous and hybrid models aim at overcoming this limitation.

When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting

statically and dynamically its fragment scheduling policy based on the computing

platform conditions. Significant execution time and throughput gains have been

obtained due to such static adaptations when the compute nodes have very different core counts.

Dynamic adaptations are based on the main memory availability at run time.

NICAN prompts FMO to postpone scheduling certain fragments, if there is not

enough memory for their immediate execution. Hence, FMO may be able to complete

the calculations whereas without such adaptations it aborts.

Copyright Owner

Sai Kiran Talamudupula

Language

en

Date Available

2012-04-28

File Format

application/pdf

File Size

57 pages

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