Achieving Strong Scaling with NAMD on Blue Gene/L

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.

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.

@INPROCEEDINGS{NAMDIPDPS06,
        author="Sameer Kumar and Chao Huang and Gheorghe Almasi and Laxmikant V. Kal\'{e}",
        title="Achieving Strong Scaling with {NAMD} on {Blue Gene/L}",
	booktitle = "Proceedings of IEEE International Parallel and Distributed Processing Symposium 2006",
	month = "April",
	year = "2006",
}