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

Published: 19 September 2005 Publication History

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.

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cover image ACM Conferences
CODES+ISSS '05: Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
September 2005
356 pages
ISBN:1595931619
DOI:10.1145/1084834
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: 19 September 2005

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Author Tags

  1. biochip
  2. microfluidics
  3. physical design
  4. synthesis

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CODES+ISSS '05 Paper Acceptance Rate 50 of 200 submissions, 25%;
Overall Acceptance Rate 280 of 864 submissions, 32%

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  • (2010)Simulating Biomolecules on the Petascale SupercomputersPetascale Computing10.1201/9781584889106.ch11(211-235)Online publication date: 31-Jan-2010
  • (2009)Millisecond-scale molecular dynamics simulations on AntonProceedings of the Conference on High Performance Computing Networking, Storage and Analysis10.1145/1654059.1654126(1-11)Online publication date: 14-Nov-2009
  • (2009)Millisecond-scale molecular dynamics simulations on AntonProceedings of the Conference on High Performance Computing Networking, Storage and Analysis10.1145/1654059.1654099(1-11)Online publication date: 14-Nov-2009
  • (2009)A performance model with a fixed point for a molecular dynamics kernelComputer Science - Research and Development10.1007/s00450-009-0086-423:3-4(195-201)Online publication date: 6-May-2009
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