Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC

被引：13

作者：

Kutzner, Carsten ^{[1
]}

Apostolov, Rossen ^{[2
,3
]}

Hess, Berk ^{[2
]}

Grubmueller, Helmut ^{[1
]}

机构：

[1] Max Planck Inst Biophys Chem, Theoret & Computat Biophys Dept, Fassberg 11, D-37073 Gottingen, Germany

[2] KTH Royal Inst Technol, Theoret & Computat Biophys, Dept Theoret Phys, S-10691 Stockholm, Sweden

[3] KTH Royal Inst Technol, PDC Ctr High Performance Comp, S-10044 Stockholm, Sweden

来源：

PARALLEL COMPUTING: ACCELERATING COMPUTATIONAL SCIENCE AND ENGINEERING (CSE) | 2014年 / 25卷

基金：

欧洲研究理事会;

关键词：

GROMACS; molecular dynamics; SuperMUC; benchmark; biomolecular simulation;

D O I：

10.3233/978-1-61499-381-0-722

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Here we report on the performance of GROMACS 4.6 on the SuperMUC cluster at the Leibniz Rechenzentrum in Garching. We carried out benchmarks with three biomolecular systems consisting of eighty thousand to twelve million atoms in a strong scaling test each. The twelve million atom simulation system reached a performance of 49 nanoseconds per day on 32,768 cores.

引用

页码：722 / 727

页数：6

共 50 条

[1] Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster
Kutzner, Carsten
Miletic, Vedran
Rodriguez, Karen Palacio
Rampp, Markus
Hummer, Gerhard
de Groot, Bert L.
Grubmueller, Helmut
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2025, 46 (05)
[2] Multiscaling Algorithms for Molecular Dynamics Simulations with GROMACS
Goga, Nicolae
Marrink, Siewert
Costache, Stefania Victoria
Moldoveanu, Florica
2009 IEEE INTERNATIONAL SYSTEMS CONFERENCE, PROCEEDINGS, 2009, : 350 - +
[3] Scalable Constant pH Molecular Dynamics in GROMACS
Aho, Noora
Buslaev, Pavel
Jansen, Anton
Bauer, Paul
Groenhof, Gerrit
Hess, Berk
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, : 6148 - 6160
[4] Application of the molecular dynamics simulation GROMACS in food science
Yu, Dongping
Li, Haiping
Liu, Yuzi
Yang, Xingqun
Yang, Wei
Fu, Yiran
Zuo, Yi-ao
Huang, Xianya
FOOD RESEARCH INTERNATIONAL, 2024, 190
[5] Flooding in GROMACS:: Accelerated barrier crossings in molecular dynamics
Lange, Oliver E.
Schaefer, Lars V.
Grubmueller, Helmut
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2006, 27 (14) : 1693 - 1702
[6] Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
Pall, Szilard
Zhmurov, Artem
Bauer, Paul
Abraham, Mark
Lundborg, Magnus
Gray, Alan
Hess, Berk
Lindahl, Erik
JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (13):
[7] Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Vieira, Ivo Henrique Provensi
Botelho, Eduardo Buganemi
Gomes, Thales Junior de Souza
Kist, Roger
Caceres, Rafael Andrade
Zanchi, Fernando Berton
BMC BIOINFORMATICS, 2023, 24 (01)
[8] Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Ivo Henrique Provensi Vieira
Eduardo Buganemi Botelho
Thales Junior de Souza Gomes
Roger Kist
Rafael Andrade Caceres
Fernando Berton Zanchi
BMC Bioinformatics, 24
[9] Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
Pall, Szilard
Abraham, Mark James
Kutzner, Carsten
Hess, Berk
Lindahl, Erik
SOLVING SOFTWARE CHALLENGES FOR EXASCALE, 2015, 8759 : 3 - 27
[10] GROMACS - A SOFTWARE PACKAGE AND A PARALLEL COMPUTER FOR MOLECULAR-DYNAMICS
VANDRUNEN, R
VANDERSPOEL, D
BERENDSEN, HJC
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 1995, 209 : 49 - COMP

← 1 2 3 4 5 →