Co-author(s) :

Astsatryan Hrachya ; Narsisian Wahi ; Mamasakhlisov Yevgeni

Abstract:

High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. The study aims to understand the scaling behavior of Gromacs (Groningen machine for chemical simulations) on various platforms, and the maximum performance in the prospect of energy consumption that can be accomplished by tuning the hardware and software parameters. Different system sizes (48K, 64K, and 272K) from scientific investigations have been studied show that the GPU (Graphics Processing Unit) scales rather beneficial than other resources, i.e., with GPU support. We track 2-3 times speedup compared to the latest multi-core CPUs. However, the so-called “threading effect” leads to the better results.

Date of publication:

16.01.2018

Identifier:

oai:noad.sci.am:135965

DOI:

10.1515/cait-2017-0056

ISSN:

1311-9702

Language:

English

Journal or Publication Title:

Cybernetics and Information Technologies

Volume:

17

Number:

5

URL:

click here to follow the link

Additional Information:

sicnas@sci.am ; hrach@sci.am ; wahi@sci.am ; y.mamasakhlisov@ysu.am

Affiliation:

The International Scientific – Educational Center ; Institute for Informatics and Automation Problems of NAS RA ; Yerevan State University

Country:

Armenia

Indexing:

WOS