Výsledky vyhledávání - "Iain Bethune"

Akademický článek

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Autor: Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton

Publikováno v: SoftwareX, Vol 5, Iss , Pp 44-50 (2016)

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and

Externí odkaz: https://doaj.org/article/20929ee567e54c2a96f600a073dedeab

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CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space

Autor: Charles A. Laughton, Conrado Pedebos, Iain Bethune, Ardita Shkurti, Vivek Balasubramanian, Shantenu Jha, Ioanna Danai Styliari

Publikováno v: Journal of Chemical Theory and Computation. 15:2587-2596

CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the investigation of NMR data. Here we investigate the potential of the CoCo method, in combination w

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f149cce6cdae7234020f80e95934e620
https://doi.org/10.1021/acs.jctc.8b00657

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pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Autor: Elena Breitmoser, Modesto Orozco, Charles A. Laughton, Pau Andrio, Ardita Shkurti, Iain Bethune, Ramon Goni

Publikováno v: SoftwareX
Shkurti, A, Goni, R, Andrio, P, Breitmoser, E, Bethune, I, Orozco, M & Laughton, C 2016, ' pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data ', SoftwareX . https://doi.org/10.1016/j.softx.2016.04.002
SoftwareX, Vol 5, Iss, Pp 44-50 (2016)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::189f26e98f63d95600180c0a52824bd0

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Evaluating Cp2K On Exascale Hardware: Intel Xeon Phi

Autor: Iain Bethune

CP2K, a popular open-source European atomistic simulation package has been ported to the Intel Xeon Phi architecture, requiring no code modifications except minor bug fixes. Benchmarking of a small molecular dynamics simulation has been carried out u

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::acf1bfd407b11d8717f6969b9f2ecfff

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Performance analysis of asynchronous Jacobi’s method implemented in MPI, SHMEM and OpenMP

Autor: Iain Bethune, Nicholas J. Dingle, Nicholas J. Higham, J. Mark Bull

Publikováno v: The International Journal of High Performance Computing Applications. 28:97-111

Ever-increasing core counts create the need to develop parallel algorithms that avoid closely coupled execution across all cores. We present performance analysis of several parallel asynchronous implementations of Jacobi’s method for solving system

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8443d60d685944d07cb4b5a5387fe1fd
https://doi.org/10.1177/1094342013493123

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ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques

Autor: Charles A. Laughton, Eugen Hruska, Vivekanandan Balasubramanian, Elena Breitmoser, Shantenu Jha, Cecilia Clementi, Ardita Shkurti, Iain Bethune

Publikováno v: eScience

For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient sampling. We

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18f7ac86aedc8671f5d160fa80acb41e
https://doi.org/10.1109/escience.2016.7870921

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Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot

Autor: Mark Santcroos, Ralph Castain, Andre Merzky, Iain Bethune, Shantenu Jha

Traditionally HPC systems such as Crays have been designed to support mostly monolithic workloads. However, the workload of many important scientific applications is constructed out of spatially and temporally heterogeneous tasks that are often dynam

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a07b2aa60b76f76cf20c71dd96b6627

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Mapping application performance to HPC architecture

Autor: A. R. Porter, Charles A. Laughton, L. Steenman-Clark, Christine Kitchen, Lorna Smith, Iain Bethune, Ilian T. Todorov, Eugene E Jones, M. Plummer, B. Ralston, Paul Calleja, Martyn F. Guest, S. Rankin, A. Korzynski, Richard Kenway, Mike Ashworth, Alan Gray

Publikováno v: Computer Physics Communications. 183:520-529

A suite of application benchmarks, designed to be broadly representative of UK HPC usage, has been developed to stress a broad range of architectural features of large scale parallel HPC resources. A generic methodology to investigate application per

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5b1ac19bd1a0516a785bbcd543a661e1
https://doi.org/10.1016/j.cpc.2011.11.013

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Genefer: Programs for Finding Large Probable Generalized Fermat Primes

Autor: Iain Bethune, Yves Gallot

Publikováno v: Journal of Open Research Software; Vol 3, No 1 (2015); e10
Bethune, I & Gallot, Y 2015, ' Genefer: Programs for finding large probable generalized Fermat primes ' vol. 3, no. 1 . DOI: 10.5334/jors.ca
Journal of Open Research Software, Vol 3, Iss 1, Pp e10-e10 (2015)

Genefer is a suite of programs for performing Probable Primality (PRP) tests of Generalised Fermat numbers 'b'2'n'+1 (GFNs) using a Fermat test. Optimised implementations are available for modern CPUs using single instruction, multiple data (SIMD) in

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ebc22c73a927e18f75b67c96934d722a
http://openresearchsoftware.metajnl.com/jms/article/view/jors.ca

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Linear instability, nonlinear instability, and ligament dynamics in three-dimensional laminar two-layer liquid/liquid flows

Autor: Iain Bethune, Peter D. M. Spelt, Lennon Ó Náraigh, David Scott, Prashant Valluri

Publikováno v: Journal of Fluid Mechanics
Journal of Fluid Mechanics, Cambridge University Press (CUP), 2014, 750, pp.464-506. ⟨10.1017/jfm.2014.274⟩

We consider the linear and nonlinear stability of two-phase density-matched but viscosity-contrasted fluids subject to laminar Poiseuille flow in a channel, paying particular attention to the formation of three-dimensional waves. A combination of Orr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f47c10b5b5a2869cca18470a0074cb6c
https://hal.archives-ouvertes.fr/hal-01044603/document

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