Achieving strong scaling with NAMD on Blue Gene/L

Author

Kumar, Sameer ; Huang, Chao ; Almasi, Gheorghe ; Kalé, Laxmikant V.

Author_Institution

IBM T.J. Watson Res. Center, Yorktown Heights, NY, USA

fYear

2006

fDate

25-29 April 2006

Abstract

NAMD is a scalable molecular dynamics application, which has demonstrated its performance on several parallel computer architectures. Strong scaling is necessary for molecular dynamics as problem size is fixed, and a large number of iterations need to be executed to understand interesting biological phenomenon. The Blue Gene/L machine is a massive source of compute power. It consists of tens of thousands of embedded Power PC 440 processors. In this paper, we present several techniques to scale NAMD to 8192 processors of Blue Gene/L. These include topology specific optimizations, new messaging protocols, load-balancing, and overlap of computation and communication. We were able to achieve 1.2 TF of peak performance for cutoff simulations and 0.99 TF with PME.

Keywords

biological techniques; embedded systems; molecular dynamics method; multiprocessing systems; parallel architectures; protocols; resource allocation; Blue Gene/L; C++ lanuage; NAMD; biological phenomenon; load-balancing; molecular dynamics; parallel computer architectures; protocols; topology specific optimizations; Application software; Biology computing; Chaotic communication; Computational modeling; Computer architecture; Concurrent computing; Molecular biophysics; Parallel processing; Proteins; Scalability;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International

Print_ISBN

1-4244-0054-6

Type

conf

DOI

10.1109/IPDPS.2006.1639298

Filename

1639298