Achieving Strong Scaling with NAMD on Blue Gene/L
IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2006
Publication Type: Paper
Repository URL: NAMDIPDPS06
Abstract
NAMD is a scalable molecular dynamics application, which has proven
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.
TextRef
Sameer Kumar and Chao Huang and Gheorghe Almasi and Laxmikant V. Kale,
"Achieving Strong Scaling with NAMD on Blue Gene/L", Proceedings of IEEE
International Parallel and Distributed Processing Symposium 2006, April 2006.
People
- Sameer Kumar
- Chao Huang
- Gheorghe Almasi
- Laxmikant Kale
Research Areas