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NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions,(More)
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoffelectrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an(More)
NAMD † is a portable parallel application for biomolec-ular 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(More)
—Large-scale GPU clusters are gaining popularity in the scientific computing community. However, their deployment and production use are associated with a number of new challenges. In this paper, we present our efforts to address some of the challenges with building and running GPU clusters in HPC environments. We touch upon such issues as balanced cluster(More)
Achieving good scaling for fine-grained communication intensive applications on modern supercomputers remains challenging. In our previous work, we have shown that such an application --- NAMD --- scales well on the full Jaguar XT5 without long-range interactions; Yet, with them, the speedup falters beyond 64K cores. Although the new Gemini interconnect on(More)
Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational(More)
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load-balancing framework, we have attained speeds and(More)
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.(More)
A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this large molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling results. In this paper, we present parallel I/O(More)