PPL: Molecular Dynamics

Molecular Dynamics - NAMD

NAMD is the result of an interdisciplinary collaboration between Prof. Kale, computer science Prof. Robert D. Skeel, and physics Prof. Klaus J. Schulten at the Theoretical and Computational Biophysics Group (TCBG) of Beckman Institute. Find the most recent scaling performance results for NAMD in this publication:

Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale, Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms, Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. Charm++, developed by Prof. Kale and co-workers, simplifies parallel programming and provides automatic load balancing, which was crucial to the performance of NAMD.

    In SC2002, Prof. Kale and co-authors James C. Phillips, Gengbin Zheng and Sameer Kumar, won a Gordon Bell Award for special accomplishment for their paper NAMD: Biomolecular Simulation on Thousands of Processors.
    NAMD is implemented using the Converse runtime system, and the major components of NAMD are written in Charm++.
    Converse provides machine-independent interface to all popular parallel computers as well as workstation clusters. Converse also implements a data-driven execution model, allowing parallel languages such as Charm++ to support the dynamic behavior of NAMD's chunk-based decomposition scheme.
    The dynamic components of NAMD are implemented in the Charm++ parallel language. It is composed of collections of C++ objects, which communicate by remotely invoking methods on other objects. This supports the multi-partition decompositions in NAMD. Also data-driven execution adaptively overlaps communication and computation. Finally, NAMD benefits from Charm++'s load balancing framework to achieve unsurpassed parallel performance.
    NAMD developers also extensively use the Projections, a performance visualization tool in Charm++, to diagnose and optimize the performance of NAMD.
    The official NAMD home page is located at TCBG NAMD Research.

Outside of NAMD, we are experimenting with alternative ways to parallelize molecular dynamics computations.

Software

Please click here to download NAMD.

People

Papers

10-25 Laxmikant V. Kale, Abhinav Bhatele, Eric J. Bohm, James C. Phillips, NAnoscale Molecular Dynamics (NAMD), Encyclopedia of Parallel Computing, David Padua, Ed., 2011 (to appear)
10-20 Gengbin Zheng, Abhinav Bhatele, Esteban Meneses and Laxmikant V. Kale, Periodic Hierarchical Load Balancing for Large Supercomputers, accepted for publication in International Journal for High Performance Computing Applications (IJHPCA), 2010
10-15 Gengbin Zheng, Gagan Gupta, Eric Bohm, Isaac Dooley, and Laxmikant V. Kale, Simulating Large Scale Parallel Applications using Statistical Models for Sequential Execution Blocks, To Appear in the Proceedings of the 16th International Conference on Parallel and Distributed Systems (ICPADS 2010)
10-08 Gengbin Zheng, Esteban Meneses, Abhinav Bhatele and Laxmikant V. Kale, Hierarchical Load Balancing for Charm++ Applications on Large Supercomputers, Proceedings of the International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), 2010
09-02 Abhinav Bhatele, Laxmikant V. Kale and Sameer Kumar, Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications, Proceedings of 23rd ACM International Conference on Supercomputing (ICS), 2009.
08-01 Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale, Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms, Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008
07-10 Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale, NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations, Department of Computer Science Tech Report UIUCDCS-R-2009-3034, February 2009.
07-05 Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele, Biomolecular modeling in the era of petascale computing, Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008
07-02 Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, Laxmikant V. Kale, Scalable Molecular Dynamics with NAMD on Blue Gene/L, IBM Journal of Research and Development, Volume 52, No. 1/2, 2007
05-13 Sameer Kumar, Chao Huang, Gheorghe Almasi, Laxmikant V. Kale, Achieving Strong Scaling with NAMD on Blue Gene/L, Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006
03-03 Laxmikant V. Kale, Sameer Kumar, Gengbin Zheng, Chee Wai Lee, Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study, Terascale Performance Analysis Workshop, International Conference on Computational Science(ICCS), 2003
02-07 James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kale, NAMD: Biomolecular Simulation on Thousands of Processors, Proceedings of SC 2002
02-04 James Phillips, Gengbin Zheng, Laxmikant V. Kale, NAMD: Biomolecular Simulation on Thousands of Processors, Workshop: Scaling to New Heights
98-10 Tamar Schlick and Robert Skeel and Axel Brunger and Laxmikant Kale and John A. Board Jr. and Jan Jermans and Klaus Schulten , Algorithmic Challenges in Computational Molecular Biophysics , Journal of Computational Physics, Vol. 151, pp. 9-48, 1999.
98-05 James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kale, Robert D. Skeel and Klaus Schulten, Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code, In book "Computational Molecular Dynamics: Challenges, Methods, Ideas"
98-04 Robert Brunner, Laxmikant Kale and James Phillips, Flexibility and Interoperability in a Parallel Molecular Dynamics Code, In book, "Object Oriented Methods for Inter-operable Scientific and Engineering Computing"
98-03 Laxmikant Kale, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten, NAMD2: Greater Scalability for Parallel Molecular Dynamics, Journal of Computational Physics
98-02 L. V. Kale, Milind Bhandarkar and Robert Brunner , Load Balancing in Parallel Molecular Dynamics, Fifth International Symposium on Solving Irregularly Structured Problems in Parallel
96-04 Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten , NAMD - a Parallel, Object-Oriented Molecular Dynamics Program, International Journal Supercomputing Applications and High Performance Computing, Winter 1996, Volume 10, number 4. Also, Beckman Institute Technical Report TB-95-17.