NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Demonstrating the scalability of a molecular dynamics application on a Petaflop computer
ICS '01 Proceedings of the 15th international conference on Supercomputing
Isoefficiency: Measuring the Scalability of Parallel Algorithms and Architectures
IEEE Parallel & Distributed Technology: Systems & Technology
Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines
IEEE Computational Science & Engineering
Achieving high performance on extremely large parallel machines: performance prediction and load balancing
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue Gene/L torus interconnection network
IBM Journal of Research and Development
Design and exploitation of a high-performance SIMD floating-point unit for Blue Gene/L
IBM Journal of Research and Development
Design and implementation of message-passing services for the Blue Gene/L supercomputer
IBM Journal of Research and Development
Achieving strong scaling with NAMD on blue Gene/L
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Performance measurements of the 3D FFT on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
IBM Journal of Research and Development
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Proceedings of the 23rd international conference on Supercomputing
Beyond homogeneous decomposition: scaling long-range forces on Massively Parallel Systems
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Modeling mutations of influenza virus with IBM Blue Gene
IBM Journal of Research and Development
Ownership passing: efficient distributed memory programming on multi-core systems
Proceedings of the 18th ACM SIGPLAN symposium on Principles and practice of parallel programming
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NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the problem size is fixed and a large number of iterations must be executed in order to understand interesting biological phenomena. Hence, we need MD applications to scale to thousands of processors, even though the individual timestep on one processor is quite small. NAMD has demonstrated its performance on several parallel computer architectures. In this paper, we present various compiler optimization techniques that use single-instruction, multiple-data (SIMD) instructions to obtain good sequential performance with NAMD on the embedded IBM PowerPC® 440 processor core. We also present several techniques to scale the NAMD application to 20,480 nodes of the IBM Blue Gene/L™ (BG/L) system. These techniques include topology-specific optimizations to localize communication, new messaging protocols that are optimized for the BG/L torus, topology-aware load balancing, and overlap of computation and communication. We also present performance results of various molecular systems with sizes ranging from 5,570 to 327,506 atoms.