NDLI: Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics

Content Provider	IEEE Xplore Digital Library
Author	Fitch, B.G. Rayshubskiy, A. Eleftheriou, M. Ward, T.J.C. Giampapa, M. Pitman, M.C. Germain, R.S.
Copyright Year	2006
Description	Author affiliation: IBM Res. Div., IBM Thomas J. Watson Res. Center, Yorktown Heights, NY (Fitch, B.G.; Rayshubskiy, A.; Eleftheriou, M.; Ward, T.J.C.; Giampapa, M.; Pitman, M.C.; Germain, R.S.)
Abstract	This paper describes a novel spatial-force decomposition for N-body simulations for which we observe O(sqrt(p)) communication scaling. This has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for handling electrostatic interactions. Using this decomposition, Blue Matter running on Blue Gene/L has achieved simulation rates in excess of 1000 time steps per second and demonstrated significant speed-ups to O(1) atom per node. Blue Matter employs a communicating sequential process (CSP) style model with application communication state machines compiled to hardware interfaces. The scalability achieved has enabled methodologically rigorous biomolecular simulations on biologically interesting systems, such as membrane-bound proteins, whose time scales dwarf previous work on those systems. Major scaling improvements require exploration of alternative algorithms for treating the long range electrostatics
Sponsorship	IEEE Comput. Soc. ACM Sigarch
Starting Page	44
Ending Page	44
File Size	334026
Page Count	1
File Format	PDF
ISBN	0769527000
DOI	10.1109/SC.2006.16
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-11-11
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Concurrent computing Biological system modeling Computational modeling Electrostatics Scalability Hardware Parallel programming Permission Nanobioscience Biomembranes
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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