Name
Title | ||
|---|---|---|
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation |
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. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1145/1084834.1084888 | CODES+ISSS |
Keywords | Field | DocType |
protein folding,blue gene,blue matter application development,parallel computation,blue gene project,l architecture,blue matter,blue gene architecture,large number,collective network,biomolecular simulation,large node count,high performance,microfluidics,concurrent computing,application development,computational modeling,membrane protein,proteins,hardware,power efficiency,biochip,physical design,boundary conditions | Permission,Architecture,Computer science,Parallel computing,Exploit,Concurrent computing,Physical design,Philosophy of design,Scaling,Speedup | Conference |
ISBN | Citations | PageRank |
1-59593-161-9 | 12 | 1.91 |
References | Authors | |
14 | 8 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Robert S. Germain | 1 | 234 | 30.97 |
| Blake G. Fitch | 2 | 252 | 32.82 |
| A. Rayshubskiy | 3 | 136 | 20.57 |
| Maria Eleftheriou | 4 | 244 | 34.04 |
| Michael C. Pitman | 5 | 51 | 7.08 |
| F. Suits | 6 | 201 | 29.82 |
| Mark Giampapa | 7 | 279 | 38.45 |
| T. J. Christopher Ward | 8 | 252 | 34.78 |