26 papers · ranked by Valyu relevance
Paul Cardosi, Bérenger Bramas, Bilal Alatas
Parallelization is needed everywhere, from laptops and mobile phones to supercomputers. Among parallel programming models, task-based programming has demonstrated a powerful potential and is widely used in high-performance scientific computing. Not only does it allow efficient parallelization across distributed…
Daniele D’Agostino, Daniele Cesini
Heterogeneous computing denotes a scenario where different computing platforms are exploited for specific applications ([5]). While the demand for computational resources continues to grow with increasing need for querying and analyzing the volumes and rates of Big Data, energy efficiency is limiting the traditional…
Andreas Kurth, Björn Forsberg, Luca Benini
—Heterogeneous computers integrate general-purpose host processors with domain-specific accelerators to combine versatility with efficiency and high performance. To realize the full potential of heterogeneous computers, however, many hardware and software design challenges have to be overcome. While architectural and…
Ali Mokhtari, Mohsen Amini Salehi
—Heterogeneity has been an indispensable aspect of distributed computing throughout the history of these systems. In particular, with the increasing prevalence of accelerator technologies (e.g., GPUs and TPUs) and the emergence of domain-specific computing via ASICs and FPGA, the matter of heterogeneity and harnessing…
Jalal Abdulbaqi
Supercomputers become faster as hardware and software technologies continue to evolve. Current supercomputers are capable of 1015 floating point operations per second (FLOPS) that called Petascale system. The High Performance Computer (HPC) community is Looking forward to the system with capability of 1018 (FLOPS) that…
Ahmed Hadi Ali AL-Jumaili, Ravie Chandren Muniyandi, Mohammad Kamrul Hasan, Johnny Koh Siaw Paw + 2 more
Traditional parallel computing for power management systems has prime challenges such as execution time, computational complexity, and efficiency like process time and delays in power system condition monitoring, particularly consumer power consumption, weather data, and power generation for detecting and predicting…
Clément Flint, Ludovic Paillat, Bérenger Bramas, Muhammad Aleem
High-performance computing (HPC) relies increasingly on heterogeneous hardware and especially on the combination of central and graphical processing units. The task-based method has demonstrated promising potential for parallelizing applications on such computing nodes. With this approach, the scheduling strategy…
Ali Mokhtari, Saeid Ghafouri, Pooyan Jamshidi, Mohsen Amini Salehi
Although system heterogeneity has been extensively studied in the past, there is yet to be a study on measuring the impact of heterogeneity on system performance. For this purpose, we propose a heterogeneity measure that can characterize the impact of the heterogeneity of a system on its performance behavior in terms…
Davor Sluga, Tomaz Curk, Blaz Zupan, Uros Lotric
Background The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks…
Hugo Andrade, Ivica Crnković
—The increasing demands for computing performance have been a reality regardless of the requirements for smaller and more energy efficient devices. Throughout the years, the strategy adopted by industry was to increase the robustness of a single processor by increasing its clock frequency and mounting more transistors…
Estela Suarez, Jorge Amaya, Martin Frank, Oliver Freyermuth + 3 more
'Maria Girone' 'Bartosz Kostrzewa' 'Susanne Pfalzner'] 1Julich Supercomputing Centre, Forschungszentrum Juelich GmbH, J ¨ ulich, ¨ Germany 2 SiPEARL, Maisons-Laffitte, France 3 Institute of Computer Science, Rheinische Friedrich-Wilhelms-Universitat Bonn, ¨ Bonn, Germany 4European Space Agency, Space Weather Office…
Hugo Andrade, Ivica Crnković, Jan Bosch
—The most important way to achieve higher performance in computer systems is through heterogeneous computing, i.e., by adopting hardware platforms containing more than one type of processor, such as CPUs, GPUs, and FPGAs. Several types of algorithms can be executed significantly faster on a heterogeneous platform.…
Yanyan Dai, Xiangli Zhang
Aiming at the static task scheduling problems in heterogeneous environment, a heuristic task scheduling algorithm named HCPPEFT is proposed. In task prioritizing phase, there are three levels of priority in the algorithm to choose task. First, the critical tasks have the highest priority, secondly the tasks with longer…
Guoqing Lei, Yong Dou, Wen Wan, Fei Xia + 3 more
'Dan Zou'] Background Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the…
Ali M Elsawwaf, Gamal M Aly, Hossam M Faheem, Mahmoud Fayez
Rapid development realms of parallel architectures and its heterogeneity have inspired researchers to invent new scheduling strategies to efficiently distribute workloads among these architectures in a way that may lead to better performance. This paper presents a comprehensive study on optimizing resource utilization…
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…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Shengdun Wu, Haiping Huang, Shengjun Wang, Guozhang Chen + 2 more
Cortical neuronal activity varies over time and across repeated stimulation trials, yet consistently represents stimulus features. The dynamical mechanism underlying this reliable representation and computation remains elusive. This study uncovers a mechanism that achieves reliable neural information processing…
Anik Chaudhuri, Shabnam Choudhury, Anwoy Kumar Mohanty, Manoranjan Satpathy + 2 more
Studying the heterogeneity in cancerous tissue is challenging in cancer research. It is vital to process the real-world data efficiently to understand the heterogeneous nature of cancer tissue. GPU compatible models, which can estimate the subpopulation of cancerous tissue, are fast if the size of input data, i.e., the…
Marco Savioli, Paolo Calligari, Ugo Locatelli, Gianfranco Bocchinfuso
We introduce GROMODEX, a novel tool designed to optimise GROMACS molecular dynamics (MD) simulations using a structured Design of Experiments (DoE) approach. GROMACS, though efficient, requires extensive tuning of parameters to perform optimally on different hardware and molecular systems. Manual tuning is tedious and…
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…
Anjana Santhosh, Rishikesh Narayanan
Artificial recurrent networks are widely used as models to study the complex dynamics underlying biological neural networks during execution of cognitive tasks. However, most studies assume individual units in the recurrent network to be homogeneous repeating units, whereas real neurons exhibit several forms of…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
Authors not listed
Imagine a computer capable of solving currently unsolvable problems. Quantum computing leverages the principles of quantum mechanics to tackle complex challenges that would take classical computers centuries to complete. In this Commentary, we explore the current state of quantum computing development and how it will…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…