26 papers · ranked by Valyu relevance
Nauman Ahmed, Tong Dong Qiu, Koen Bertels, Zaid Al-Ars
Background In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can…
Marcel Stimberg, Dan F. M. Goodman, Thomas Nowotny
“Brian” is a popular Python-based simulator for spiking neural networks, commonly used in computational neuroscience. GeNN is a C++-based meta-compiler for accelerating spiking neural network simulations using consumer or high performance grade graphics processing units (GPUs). Here we introduce a new software package…
Xin Wang, Bin Zhang, Xu Cao, Fei Liu + 2 more
Fluorescence molecular tomography (FMT) with early-photons can improve the spatial resolution and fidelity of the reconstructed results. However, its computing scale is always large which limits its applications. In this paper, we introduced an acceleration strategy for the early-photon FMT with graphics processing…
Matthew Leach, Peter Heywood, Alexander G. Fletcher, Paul Richmond
Chaste is an open-source C++ library providing a general-purpose framework for cell-based simulations of biological tissues. It has been applied to a wider range of biological processes, including morphogenesis, carcinogenesis, and wound healing. Such simulations often involve numerous mechanical interactions between…
Yongfei Wang, Junping Wang, Jiarui Tian, Lin Li + 4 more
'Fang Peng' 'Hu Ke' 'Alberto Marchisio'] Early warning of geological hazards requires monitoring extreme weather conditions, such as heavy rainfall. Atmospheric circulation models are used for weather forecasting and climate simulation. As a critical physical process in atmospheric circulation models, the…
Ronald M. Caplan, J. A. Linker, Z. Mikić, Cooper Downs + 2 more
'V. S. Titov'] Abstract. GPU accelerators have had a notable impact on high-performance computing across many disciplines. They provide high performance with low cost/power, and therefore have become a primary compute resource on many of the largest supercomputers. Here, we implement multi-GPU acceleration into our…
Jørgen Wictor Henriksen, Knut Dagestad Rand, Geir Kjetil Sandve, Ivar Grytten
As decreasing DNA sequencing costs leads to a steadily increasing rate of generated data, the development of efficient algorithms for processing of the sequence data is increasingly important to reduce costs and energy consumption. Recent work have shown that genotyping can be done efficiently and accurately using…
Abouzied M. A. Nasar, Benedict D. Rogers, Georgios Fourtakas, Scott T. Kay + 1 more
'Scott T. Kay' 'Matthieu Schaller'] School of Engineering. The University of Manchester, Nancy Rothwell Building, Manchester M13 9QS, UK. Department of Physics and Astronomy, The University of Manchester, Schuster Building, Manchester, M139PL, UK. Lorentz Institute for theoretical physics, Leiden University, PO Box…
Kyle A. O’Connell, Zelaikha B. Yosufzai, Ross A. Campbell, Collin J. Lobb + 7 more
As genome sequencing becomes a more integral part of scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of…
Eric Wright, Mauricio Ferrato, Alex Bryer, Robert Searles + 2 more
Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging…
Jingcheng Shen, Jie Mei, Marcus Walldén, Fumihiko Ino
FreeSurfer is among the most widely used suites of software for the study of cortical and subcortical brain anatomy. However, analysis using FreeSurfer can be time-consuming and it lacks support for the graphics processing units (GPUs) after the core development team stopped maintaining GPU-accelerated versions due to…
Guillermo Vigueras, Ishani Roy, Andrew Cookson, Jack Lee + 2 more
'Nicolas Smith' 'David Nordsletten'] In this paper, we look at the acceleration of weakly coupled electromechanics using the graphics processing unit (GPU). Specifically, we port to the GPU a number of components of Heart-a CPU-based finite element code developed for simulating multi-physics problems. On the basis of a…
Sheng Zhang, Lishu Duan, Hanbo Jiang
graphics processing units Authors: ['Sheng Zhang' 'Lishu Duan' 'Hanbo Jiang'] This study presents a reconstruction of the Gaussian Beam Tracing solution using CUDA, with a particular focus on the utilisation of GPU acceleration as a means of overcoming the performance limitations of traditional CPU algorithms in…
Matt Stack, Paul Macklin, Robert Searles, Sunita Chandrasekaran
Computational biology has increasingly turned to agent-based modeling—which represents individual biological cells as discrete software agents—to explore complex biological systems where many cells interact through exchange of mechanical forces, exchange of diffusing chemical factors, and other biomechanical feedback…
Wei Wang, Lifan Xu, John Cavazos, Howie H. Huang + 2 more
'Tobias Preis'] Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires…
Shidi Tang, Ji Ding, Xiangyu Zhu, Zheng Wang + 2 more
AutoDock Vina and its derivatives have established themselves as a prevailing pipeline for virtual screening in contemporary drug discovery. Our Vina-GPU method leverages the parallel computing power of GPUs to accelerate AutoDock Vina, and Vina-GPU 2.0 further enhances the speed of AutoDock Vina and its derivatives.…
Kyle E. Niemeyer, Chih‐Jen Sung
The progress made in accelerating simulations of fluid flow using GPUs, and the challenges that remain, are surveyed. The review first provides an introduction to GPU computing and programming, and discusses various considerations for improved performance. Case studies comparing the performance of CPU- and GPU-based…
Bernd Amann, Youry Khmelevsky, Gaétan Hains
The vast amount of processing power and memory bandwidth provided by modern Graphics Processing Units (GPUs) make them a platform for data-intensive applications. The database community identified GPUs as effective co-processors for data processing. In the past years, there were many approaches to make use of GPUs at…
Authors not listed
The imperative to screen ultra-large chemical libraries necessitates high-throughput computational tools capable of efficiently leveraging all available structural and chemical information. We introduce UniDock-Pro, a unified platform built upon the GPU-accelerated Uni-Dock architecture, which integrates…
Gaogao Liu, Wenbo Yang, Peng Li, Guodong Qin + 6 more
'Youming Wang' 'Shuai Wang' 'Ning Yue' 'Dongjie Huang' 'Luís Castedo Ribas'] The data volume and computation task of MIMO radar is huge; a very high-speed computation is necessary for its real-time processing. In this paper, we mainly study the time division MIMO radar signal processing flow, propose an improved MIMO…
Stefan Westerlund, Chris Harris
Searching for sources of electromagnetic emission in spectral-line radio astronomy interferometric data is a computationally intensive process. Parallel programming techniques and High Performance Computing hardware may be used to improve the computational performance of a source finding program. However, it is…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Authors not listed
Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and design of new materials. This work describes an initial implementation for performing multireference wave function method localized active space self-consistent field (LASSCF) calculations through the use of…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs -accelerated implementation within Tinker-HP. For the specific use with the flexible AMOEBA polarizable force field (PFF), we introduce the new "dual–water" GaMD…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA…