25 papers · ranked by Valyu relevance
Jayshree Ghorpade-Aher
The future of computation is the Graphical Processing Unit, i.e. the GPU. The promise that the graphics cards have shown in the field of image processing and accelerated rendering of 3D scenes, and the computational capability that these GPUs possess, they are developing into great parallel computing units. It is quite…
Ari Harju, Topi Siro, Filippo Federici Canova, Samuli Hakala + 1 more
'Teemu Rantalaiho'] Abstract. The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics and quantum simulations for…
Ludovico Rella
This paper investigates the role of the materiality of computation in two domains: blockchain technologies and artificial intelligence (AI). Although historically designed as parallel computing accelerators for image rendering and videogames, graphics processing units (GPUs) have been instrumental in the explosion of…
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…
Heeseung Jo, Jinkyu Jeong, Myoungho Lee, Dong Hoon Choi
Recently, biological applications start to be reimplemented into the applications which exploit many cores of GPUs for better computation performance. Therefore, by providing virtualized GPUs to VMs in cloud computing environment, many biological applications will willingly move into cloud environment to enhance their…
D. Vom Bruch
As high energy physics experiments reach higher luminosities and intensities, the computing burden for real time data processing and reduction grows. Following the developments in the computing landscape, multi-core processors such as graphics processing units (GPUs) are increasingly used for such tasks. These…
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…
Jeyarajan Thiyagalingam, Daniel Goodman, Julia A. Schnabel, Anne Trefethen + 1 more
'Anne Trefethen' 'Vicente Grau'] Images are ubiquitous in biomedical applications from basic research to clinical practice. With the rapid increase in resolution, dimensionality of the images and the need for real-time performance in many applications, computational requirements demand proper exploitation of multicore…
Yehia Arafa, Ammar ElWazir, Abdelrahman Elkanishy, Youssef Aly + 5 more
'Ayatelrahman Elsayed' 'Abdel‐Hameed A. Badawy' 'Gopinath Chennupati' 'Stephan Eidenbenz' 'Nandakishore Santhi'] Abstract—GPUs are prevalent in modern computing systems at all scales. They consume a significant fraction of the energy in these systems. However, vendors do not publish the actual cost of the power/energy…
Moises Hernandez-Fernandez, Istvan Reguly, Saad Jbabdi, Mike Giles + 2 more
The great potential of computational diffusion MRI (dMRI) relies on indirect inference of tissue microstructure and brain connections, since modelling and tractography frameworks map diffusion measurements to neuroanatomical features. This mapping however can be computationally highly expensive, particularly given the…
Roy Ben-Shalom, Nikhil S. Artherya, Christopher Cross, Hersh Sanghevi + 2 more
Generating biologically detailed models of neurons is an important goal for modern neuroscience. Unfortunately, constraining parameters within biologically detailed models can be difficult, leading to poor model predictions, especially if such models are extended beyond the specific problems for which they were…
Sparsh Mittal, Jeffrey S. Vetter
Recent years have witnessed a phenomenal growth in the computational capabilities and applications of GPUs. However, this trend has also led to dramatic increase in their power consumption. This paper surveys research works on analyzing and improving energy efficiency of GPUs. It also provides a classification of these…
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…
Hao Li, Yi-Cheng Tu, Bo Zeng, Rashid Mehmood
The unrivaled computing capabilities of modern GPUs meet the demand of processing massive amounts of data seen in many application domains. While traditional HPC systems support applications as standalone entities that occupy entire GPUs, there are GPU-based DBMSs where multiple tasks are meant to be run at the same…
Adrian Przybylski, Björn Thiel, Jan Keller-Findeisen, Bernd Stock + 1 more
We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of…
Feifei Shen, Zhenjian Song, Congrui Wu, Jia-Qi Geng + 1 more
can improve the image processing capability of micro-computer system. This paper studies the parallelism of the different stages of decimation in time radix 2 FFT algorithm, designs the butterfly and scramble kernels and implements 2D FFT on GPU. The experiment result demonstrates the validity and advantage over…
N. Ávalos, Miguel Sofo Haro
We introduce a simulator of charge transport in fully-depleted, thick CCDs that include Coulomb repulsion between carriers. The calculation of this long-range interaction is highly intensive computationally, and only a few thousands of carriers can be simulated in reasonable times using regular CPUs. G-CoReCCD takes…
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…
Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab
Protein tertiary structure prediction (PSP) is one of the most challenging problems in bioinformatics. Different methods have been introduced to solve this problem so far, but PSP is computationally intensive and belongs to the NP-hard class. One of the best solutions to accelerate PSP is the use of a massively…
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…
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…
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…
Authors not listed
Machine learning interatomic potentials (MLIPs) have revolutionized molecular simulations, but as they evolve, so does the demand for advanced computing architectures, particularly graphics processing units (GPUs). However, the high cost of GPUs limits accessibility, making it crucial to compare GPU and central…
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…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…