NDLI: Blue matter on blue gene/L: massively parallel computation for biomolecular simulation

Content Provider	IEEE Xplore Digital Library
Author	Suits, F. Eleftheriou, M. Giampapa, M. Rayshubskiy, A. Fitch, B. Pitman, M.C. Ward, T.J.C. Germain, R.S.
Copyright Year	2005
Description	Author affiliation: IBM Thomas J. Watson Research Center, Yorktown Heights, NY (Suits, F.; Eleftheriou, M.; Giampapa, M.; Rayshubskiy, A.; Fitch, B.; Pitman, M.C.; Germain, R.S.) \|\| IBM Hursley Park, Hursley, UK (Ward, T.J.C.)
Abstract	This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of protein folding and membrane-protein systems. The design philosophy of the Blue Gene/L architecture relies on large numbers of power efficient nodes (whose technology is derived from the world of embedded microprocessors) to enable packing of many such nodes into a small volume to achieve high performance. In order for an application to exploit the potential of this architecture, the application must scale well to large node counts. Because the scientific goals of the project entail simulating very long time-scales, up to microseconds, strong scaling of a fixed size problem to these large node counts is a requirement. In pursuit of this objective we have considered a variety of parallel decompositions and explored ways to exploit and map algorithms onto the two primary high performance interconnects provided by the Blue Gene architecture, the 3D-torus network and the collective network. Our current version of the application continues to speed up through 4096 nodes and is being used for studies of a protein/lipid system (for which some results have already been published) and for protein folding/unfolding simulations.
Starting Page	207
Ending Page	212
File Size	432069
Page Count	6
File Format	PDF
ISBN	1595931619
DOI	10.1145/1084834.1084888
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-09-19
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Association for Computing Machinery, Inc. (ACM)
Subject Keyword	Concurrent computing Computational modeling Biological system modeling Proteins Hardware Bonding forces Boundary conditions Microprocessors Permission Supercomputers synthesis biochip microfluidics physical design
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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