<abstract xmlns="http://www.w3.org/1999/xhtml"><p> 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.</p></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.

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Cybernetics and Information Technologies

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire...

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Article Category: Special Issue With Selected Papers From The Workshop “Two Years Avitohol: Advanced High Performance Computing Applications 2017

Published Online: Jan 16, 2018

Page range: 68 - 80

DOI: https://doi.org/10.1515/cait-2017-0056

Keywords
Molecular dynamics simulations, protein, DNA, sodium dodecyl sulphate, energy consumption, Gromacs, benchmarking, HPC

© by Armen Poghosyan

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Article Category: Special Issue With Selected Papers From The Workshop “Two Years Avitohol: Advanced High Performance Computing Applications 2017

Published Online: Jan 16, 2018

Page range: 68 - 80

DOI: https://doi.org/10.1515/cait-2017-0056

KeywordsMolecular dynamics simulations, protein, DNA, sodium dodecyl sulphate, energy consumption, Gromacs, benchmarking, HPC

© by Armen Poghosyan

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Keywords
Molecular dynamics simulations, protein, DNA, sodium dodecyl sulphate, energy consumption, Gromacs, benchmarking, HPC