NAMD2: Greater Scalability for Parallel Molecular Dynamics
Authors:
Laxmikant Kale, Robert Skeel, Milind Bhandarkar, Robert Brunner,
Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki,
Krishnan Varadarajan, and Klaus Schulten
Parallel Programming Laboratory, Department of Computer Science, University
of Illinois at Urbana-Champaign
Journal of Computational Physics
Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decomposition to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations. NAMD2 uses a portable run-time framework that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters. This paper also describes the performance obtained on some benchmark applications.