research-article

20 petaflops simulation of proteins suspensions in crowding conditions

Authors:

Massimo Bernaschi,

Massimiliano Fatica,

Simone MelchionnaAuthors Info & Claims

SC '13: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis

Article No.: 2, Pages 1 - 11

https://doi.org/10.1145/2503210.2504563

Published: 17 November 2013 Publication History

Abstract

We present performance results for the simulation of proteins suspensions in crowding conditions obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. Previous versions of MUPHY have been used in the past for the simulation of blood flow through the human coronary arteries and DNA translocation across nanopores. The simulation exhibits excellent scalability up to 18, 000 K20X Nvidia GPUs and achieves almost 20 Petaflops of aggregate sustained performance with a peak performance of 27.5 Petaflops for the most intensive computing component. Those figures demonstrate once again the flexibility of MUPHY in simulating biofluidic phenomena, exploiting at their best the features of the architecture in use. Preliminary results were obtained in the present case on a completely different platform, the IBM Blue Gene/Q. The combination of novel mathematical models, computational algorithms, hardware technology, code tuning and parallelization techniques required to achieve these results are presented.

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Cited By

Succi S(2023)Lattice Fluid Dynamics: Thirty-five Years Down the RoadComptes Rendus. Mécanique10.5802/crmeca.161350:S1(1-12)Online publication date: 11-Apr-2023
https://doi.org/10.5802/crmeca.161
Zacharoudiou IMcCullough JCoveney P(2022)Development and performance of a HemeLB GPU code for human-scale blood flow simulationComputer Physics Communications10.1016/j.cpc.2022.108548(108548)Online publication date: Sep-2022
https://doi.org/10.1016/j.cpc.2022.108548
Shealy BYousefi MSrinath ASmith MSchiller U(2021)GPU Acceleration of the HemeLB Code for Lattice Boltzmann Simulations in Sparse Complex GeometriesIEEE Access10.1109/ACCESS.2021.30736679(61224-61236)Online publication date: 2021
https://doi.org/10.1109/ACCESS.2021.3073667
Show More Cited By

20 petaflops simulation of proteins suspensions in crowding conditions
1. Applied computing
  1. Life and medical sciences
  2. Physical sciences and engineering

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Published In

cover image ACM Conferences

SC '13: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis

November 2013

1123 pages

ISBN:9781450323789

DOI:10.1145/2503210

General Chair:
William Gropp
University of Illinois at Urbana-Champaign, Urbana, Illinois
,
Program Chair:
Satoshi Matsuoka
Tokyo Institute of Technology, Tokyo, Japan

Copyright © 2013 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 17 November 2013

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IEEE-CS

SC13: International Conference for High Performance Computing, Networking, Storage and Analysis

November 17 - 21, 2013

Colorado, Denver

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SC '13 Paper Acceptance Rate 91 of 449 submissions, 20%;

Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Cited By

Succi S(2023)Lattice Fluid Dynamics: Thirty-five Years Down the RoadComptes Rendus. Mécanique10.5802/crmeca.161350:S1(1-12)Online publication date: 11-Apr-2023
https://doi.org/10.5802/crmeca.161
Zacharoudiou IMcCullough JCoveney P(2022)Development and performance of a HemeLB GPU code for human-scale blood flow simulationComputer Physics Communications10.1016/j.cpc.2022.108548(108548)Online publication date: Sep-2022
https://doi.org/10.1016/j.cpc.2022.108548
Shealy BYousefi MSrinath ASmith MSchiller U(2021)GPU Acceleration of the HemeLB Code for Lattice Boltzmann Simulations in Sparse Complex GeometriesIEEE Access10.1109/ACCESS.2021.30736679(61224-61236)Online publication date: 2021
https://doi.org/10.1109/ACCESS.2021.3073667
Tomczak T(2018)Lattice Boltzmann Method for Sparse GeometriesAnalysis and Applications of Lattice Boltzmann Simulations10.4018/978-1-5225-4760-0.ch005(152-187)Online publication date: 2018
https://doi.org/10.4018/978-1-5225-4760-0.ch005
Tomczak TSzafran R(2018)Sparse Geometries Handling in Lattice Boltzmann Method Implementation for Graphic ProcessorsIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2018.281023729:8(1865-1878)Online publication date: 1-Aug-2018
https://doi.org/10.1109/TPDS.2018.2810237
Chiricotto MSterpone FDerreumaux PMelchionna S(2016)Multiscale simulation of molecular processes in cellular environmentsPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences10.1098/rsta.2016.0225374:2080(20160225)Online publication date: 3-Oct-2016
https://doi.org/10.1098/rsta.2016.0225
Rossinelli DTang YLykov KAlexeev DBernaschi MHadjidoukas PBisson MJoubert WConti CKarniadakis GFatica MPivkin IKoumoutsakos PKern JVetter J(2015)The in-silico lab-on-a-chipProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/2807591.2807677(1-12)Online publication date: 15-Nov-2015
https://dl.acm.org/doi/10.1145/2807591.2807677
Joubert WArchibald RBerrill MMichael Brown WEisenbach MGrout RLarkin JLevesque JMesser BNorman MPhilip BSankaran RTharrington ATurner J(2015)Accelerated application developmentComputers and Electrical Engineering10.1016/j.compeleceng.2015.04.00846:C(123-138)Online publication date: 1-Aug-2015
https://dl.acm.org/doi/10.1016/j.compeleceng.2015.04.008
Moreland KOldfield R(2015)Formal Metrics for Large-Scale Parallel PerformanceHigh Performance Computing10.1007/978-3-319-20119-1_34(488-496)Online publication date: 20-Jun-2015
https://doi.org/10.1007/978-3-319-20119-1_34

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