Accelerating molecular dynamic simulation on the cell processor and Playstation 3

@article{Luttmann2009AcceleratingMD,
  title={Accelerating molecular dynamic simulation on the cell processor and Playstation 3},
  author={Edgar Luttmann and Daniel L. Ensign and Vaidyanathan Vishal and Mike Houston and Noam Rimon and Jeppe {\O}land and Guha Jayachandran and Mark S. Friedrichs and Vijay S. Pande},
  journal={Journal of Computational Chemistry},
  year={2009},
  volume={30}
}
Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing… 
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29 Citations
Background Citations
5
Methods Citations
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Results Citations
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29 Citations

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A Heterogeneous, Purpose Built Computer Architecture for Accelerating Biomolecular Simulation
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
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The improved performance of modern simulation methods coupled with hardware advances is shifting the rate-limiting steps of common biomolecular simulations of small to moderately sized systems from the generation of data to the pre- and postprocessing phases of the workflow, namely, simulation setup and data processing, management, and analysis.
Long-timescale molecular dynamics simulations of protein structure and function.
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
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A GPLv2 implementation called AWE-WQ of a THE AUTHORS algorithm using the master/worker distributed computing WorkQueue (WQ) framework is provided, which is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage, seamless heterogeneous cluster usage, and support for arbitrary MD codes such as GROMACS.
A Memory Centric Kernel Framework for Accelerating Short-Range, Interactive Particle Simulation
  • Ian Stewart, Shujia Zhou
  • Computer Science
    2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing
  • 2010
To maximize the performance of emerging multi- and many-core accelerators such as the IBM Cell B.E. and the NVIDIA GPU, a Memory Centric Kernel Framework (MCKF) was developed. MCKF allows a user to…
An (almost) direct deployment of the Fast Multipole Method on the Cell processor
TLDR
This paper presents the first deployment of the Fast Multipole Method on the Cell processor (PowerXCell 8i) in single and double precisions, which scales linearly on several Cell blades and which is able to handle both uniform and non-uniform distributions of particles.
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
TLDR
This work introduces a new approach for learning a distance metric explicitly constructed to model kinetic similarity, which enables the construction of models, especially in the regime of high anisotropy in the diffusion constant, with fewer states than was previously possible.
Numerical characterization of nonlinear dynamical systems using parallel computing: The role of GPUs approach
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
  • R. Dror, J. P. Grossman, D. E. Shaw
  • Computer Science
    2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
  • 2010
TLDR
Key elements of Anton's approach, in addition to tightly integrated communication hardware, include formulating data transfer in terms of counted remote writes, leveraging fine-grained communication, and establishing fixed, optimized communication patterns.
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