NAMD2

NAMD2: Greater scalability for parallel molecular dynamics. Molecular dynamics programs simulate the behavior of biomolecular systems, leading to 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 Charm++, 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. par NAMD2 uses a portable run-time framework called Converse 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 and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications.


References in zbMATH (referenced in 17 articles )

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  1. Bajaj, Chandrajit; Bauer, Benedikt; Bettadapura, Radhakrishna; Vollrath, Antje: Nonuniform Fourier transforms for rigid-body and multidimensional rotational correlations (2013)
  2. Chen, Zhiguo; Fu, Yi; Xu, Wenbo; Li, Ming: Molecular dynamics simulation of barnase: contribution of noncovalent intramolecular interaction to thermostability (2013)
  3. Heinke, Florian; Labudde, Dirk: Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus (2012)
  4. Spijker, Peter; Anciaux, Guillaume; Molinari, Jean-François: The effect of loading on surface roughness at the atomistic level (2012)
  5. Gonnet, Pedro: Using piecewise polynomials for faster potential function evaluation (2010)
  6. Coveney, P.V.; Saksena, R.S.; Zasada, S.J.; Mckeown, M.; Pickles, S.: The application hosting environment: lightweight middleware for grid-based computational science (2007)
  7. Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko: Long-range interactions and parallel scalability in molecular simulations (2007)
  8. Li, Aiqin; Dowell, Earl H.: Modal reduction of mathematical models of biological molecules (2006)
  9. Weinbach, Yael; Elber, Ron: Revisiting and parallelizing SHAKE (2005)
  10. Zheng, Gengbin; Wilmarth, Terry; Jagadishprasad, Praveen; Kalé, Laxmikant V.: Simulation-based performance prediction for large parallel machines (2005)
  11. Bishop, T. C.; Cortez, R.; Zhmudsky, O. O.: Investigation of bend and shear waves in a geometrically exact elastic rod model. (2004)
  12. Wypychowski, Jarosław; Pytliński, Jarosław; Skorwider, Łukasz; Nazaruk, Mirosław; Benedyczak, Krzysztof; Wroński, Michał; Bała, Piotr: Life sciences grid in EUROGRID and GRIP projects (2004)
  13. Mann, Geoff; Yun, R.H.; Nyland, Lars; Prins, Jan; Board, John; Hermans, Jan: The Sigma MD programm and a generic interface applicable to multi-functional programs with complex, hierarchical command structure (2002)
  14. Bhandarkar, Milind; Kalé, L.V.; de Sturler, Eric; Hoeflinger, Jay: Adaptive load balancing for MPI programs (2001)
  15. Kalé, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus: NAMD2: Greater scalability for parallel molecular dynamics (1999)
  16. Schlick, Tamar; Skeel, Robert D.; Brunger, Axel T.; Kalé, Laxmikant V.; Board, John A.jun.; Hermans, Jan; Schulten, Klaus: Algorithmic challenges in computational molecular biophysics (1999)
  17. Stern, Christian: A system architecture for parallel particle simulation in real-time: interactive scientific visualization in molecular dynamics (1998)