Abhinav Bhatelé[1] , Sameer Kumar[3] , Chao Mei[1] , James C. Phillips[4] , Gengbin Zheng[1] ,
Laxmikant V. Kalé[1]
[1] Department of Computer Science
NAMD[2]NAMD stands for NAnoscale Molecular Dynamics
is a portable parallel application for biomolecular simulations.
NAMD pioneered the use of hybrid spatial and force decomposition, a
technique now used by most scalable programs for biomolecular simulations,
including Blue Matter and Desmond developed by IBM and D. E. Shaw respectively.
NAMD has been developed using Charm++ and benefits
from its adaptive communication-computation overlap and dynamic load
balancing. This paper focuses on new scalability challenges in
biomolecular simulations: using much larger machines and simulating
molecular systems with millions of atoms. We describe new techniques
developed to overcome these challenges. Since our approach
involves automatic adaptive runtime optimizations, one interesting
issue involves dealing with harmful interaction between multiple adaptive
strategies. NAMD runs on
a wide variety of platforms, ranging from commodity clusters to
supercomputers. It also scales to large machines: we
present results for up to 65,536 processors on IBM's Blue Gene/L
and 8,192 processors on Cray XT3/XT4. In addition, we
present performance results on NCSA's Abe,
SDSC's DataStar and TACC's LoneStar cluster, to demonstrate efficient
portability. We also compare NAMD with Desmond and Blue Matter.
