12067
Mariusz Uchronski, Agnieszka Kwiecien, Marcin Gebarowski
CP2K is an application for atomistic and molecular simulation and, with its excellent scalability, is particularly important with regards to use on future exascale systems. The code is well parallelized using MPI and hybrid MPI/OpenMP, typically scaling well to ~1 core per atom in the system. The research on CP2K done within PRACE-1IP stated that […]
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Brendan M McLaughlin, Connor P Ballance
Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC […]
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Gerhard Burger
Computer simulations play a vital role in understanding the phase behavior of colloidal dispersions, however, most simulation results suffer from finite-size effects. These finite-size effects can be eliminated by finite-size scaling or by simulating large system sizes. In this thesis we show how to simulate large system sizes efficiently on Graphical Processing Units (GPUs). Whereas […]
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You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano, Zhong-Yuan Lu
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the computational power of GPUs. In addition, the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can […]
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Imre Pechan, Bela Feher
Hardware acceleration is the general concept of applying a specialized hardware for a given problem instead of an ordinary CPU in order to get lower processing time. General purpose CPUs can be considered as a totally general platform suitable for executing virtually any software or algorithm. Application specific accelerators have a custom architecture that fits […]
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Claus Braun, Stefan Holst, Hans-Joachim Wunderlich, Juan Manuel Castillo, Joachim Gross
Markov-Chain Monte-Carlo (MCMC) methods are an important class of simulation techniques, which execute a sequence of simulation steps, where each new step depends on the previous ones. Due to this fundamental dependency, MCMC methods are inherently hard to parallelize on any architecture. The upcoming generations of hybrid CPU/GPGPU architectures with their multi-core CPUs and tightly […]
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John A. Stratton, Christopher Rodrigues, I-Jui Sung, Nady Obeid, Li-Wen Chang, Nasser Anssari, Geng Daniel Liu, Wen-mei W. Hwu
The Parboil benchmarks are a set of throughput computing applications useful for studying the performance of throughput computing architecture and compilers. The name comes from the culinary term for a partial cooking process, which represents our belief that useful throughput computing benchmarks must be "cooked", or preselected to implement a scalable algorithm with fine-grained parallel […]
M.N. Osman, R. Abdullah, N. AbdulRashid
Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical […]
Quan Liao, Jibo Wang, Ian A. Watson
Compound selection procedures based on molecular similarity and diversity are widely used in drug discovery. Current algorithms are often time consuming when applied to very large compound sets. This paper describes the acceleration of two selection algorithms (the leader and the spread algorithms) on graphical processing units (GPUs). We first parallelized the molecular similarity calculation […]
John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz
Molecular dynamics simulations are known to run for many days or weeks before completion. In this paper we explore the use of GPUs to accelerate a Lennard-Jones-based molecular dynamics simulation of up to 27000 atoms. We demonstrate speedups that exceed 100x on commodity Nvidia GPUs and discuss the strategies that allow for such exceptional speedups. […]
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Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie
HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ~15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein […]
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James C. Phillips, John E. Stone
GPU acceleration and other computer performance increases will offer critical benefits to biomedical science. Computer simulation has become an integral part of the study of the structure and function of biological molecules. For years, parallel computers have been used to conduct these computationally demanding simulations and to analyze their results. These simulations function as a […]
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