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Displaying 1-4 out of 4 total
Efficient SDS Simulations on Multi-GPU Nodes of XSEDE High-End Clusters
Found in: 2013 IEEE 9th International Conference on eScience (eScience)
By Samuel Schlachter,Stephen Herbein,Michela Taufer, Shuching Ou,Sandeep Patel,Jeremy S. Logan
Issue Date:October 2013
pp. 116-123
Efficiently studying Sodium Dodecyl Sulfate (SDS) molecules' formations in the presence of different molar concentrations on high-end GPU clusters whose nodes share accelerators exposes us to several challenges, including the need to dynamically adapt the ...
Performance Dissection of a Molecular Dynamics Code across CUDA and GPU Generations
Found in: 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW)
By Matthew Wezowicz,Trilce Estrada,Sandeep Patel,Michela Taufer
Issue Date:May 2013
pp. 1355-1364
The first release of CUDA was in 2007. Since then, we have experienced frequent new releases. CUDA reached its maximum performance with CUDA 4.0. Since its release, NVIDIA has started a re-design of the CUDA framework driven by software engineering princip...
GPU-Enabled Macromolecular Simulation: Challenges and Opportunities
Found in: Computing in Science & Engineering
By Michela Taufer,Narayan Ganesan,Sandeep Patel
Issue Date:January 2013
pp. 56-57
GPU-enabled simulation of fully atomistic macromolecular systems is rapidly gaining momentum, enabled by massive parallelism and the parallelizability of various components of the underlying algorithms and methodologies. Here, we consider key aspects requi...
FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME
Found in: Parallel and Distributed Processing Workshops and PhD Forum, 2011 IEEE International Symposium on
By Narayan Ganesan,Michela Taufer,Brad Bauer,Sandeep Patel
Issue Date:May 2011
pp. 472-480
When studying membrane-bound protein receptors, it is necessary to move beyond the current state-of-the-art simulations that only consider small membrane patches and implicit solvent. Limits of traditional computer platforms negatively impact the model's l...