24 papers · ranked by Valyu relevance
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…
Tiago Perez, Márcio M. Gonçalves, José Rodrigo Azambuja, Leonardo Gobatto + 2 more
'Leonardo Gobatto' 'Marcelo Brandalero' 'Samuel Pagliarini'] Abstract—Modern Systems on Chip (SoC), almost as a rule, require accelerators for achieving energy efficiency and high performance for specific tasks that are not necessarily well suited for execution in standard processing units. Considering the broad range…
Ming Li, Ziqian Bi, Tianyang Wang, Yizhu Wen + 11 more
Power of Parallel Computing Authors: ['Ming Li' 'Ziqian Bi' 'Tianyang Wang' 'Yizhu Wen' 'Qian Niu' 'Junyu Liu' 'Benji Peng' 'Sen Zhang' 'Xiaoyong Pan' 'Jiawei Xu' 'Jinlang Wang' 'Keyu Chen' 'Caitlyn Heqi Yin' 'Pohsun Feng' 'Ming Liu'] | V Mastering GPGPU with CUDA: Unlocking the Power of Parallel Computing | 9 | | ---…
Maksudul Alam, Kalyan Perumalla
Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation…
Quim Aguado-Puig, Max Doblas, Christos Matzoros, Antonio Espinosa + 3 more
Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like…
Anirudh Srikanth, Carlotta Trigila, Emilie Roncali
The demand for specialized hardware to train AI models has increased in tandem with the increase in the model complexity over the recent years. Graphics processing unit (GPU) is one such hardware that is capable of parallelizing operations performed on a large chunk of data. Companies like Nvidia, AMD, and Google have…
Erik D. Huckvale, Hunter Moseley
in both desktop and high-performance computing environments Authors: ['Erik D. Huckvale' 'Hunter Moseley'] Over the lifetime of a computing task, determining the maximum usage of random-access memory (RAM) on both the motherboard and on a graphical processing unit (GPU), as well as the utilization percentage of the…
Yujie Chi, Keith Schubert, Andreu Badal, Emilie Roncali
Objectives. Monte Carlo (MC) simulation remains the gold standard for modeling complex physical interactions in transmission and emission tomography, with graphic processing unit (GPU) parallel computing offering unmatched computational performance and enabling practical, large-scale MC applications. In recent years…
Jiayi Du, Yu Zhou, Lihua Jin, Ke Sheng
As a powerful but computationally intensive method, hybrid computational models study the dynamics of multicellular systems by evolving discrete cells in reacting and diffusing extracellular microenvironments. As the scale and complexity of studied biological systems continuously increase, the exploding computational…
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…
Maximilian Zimmermann, Elke Pilat-Lohinger
We present a GPU accelerated N-body integrator using the Bulirsch-Stoer method, called GANBISS (GPU accelerated n-body code for binary star systems). It is designed to simulate the dynamical evolution of planetesimal disks in binary star systems which contain some thousand disk objects. However, it can also be used for…
Ke Yue, Nicholas Schwarz, Tischler Jonathan Z.
—The Laue diffraction microscopy uses the polychromatic Laue micro-diffraction technique to examine the structure of materials with sub-micron spatial resolution in all three dimensions. Properties that can be measured include local crystallographic orientations, orientation gradients and strains. All those data is…
M. Suvarna, O. Tehrani
GigaAPI is a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential. The API offers a comprehensive set of functionalities, including fundamental GPU operations, image processing, and complex…
Ayca Kirimtat, Ondrej Krejcar, Fow-Sen Choa
The approach of using more than one processor to compute in order to overcome the complexity of different medical imaging methods that make up an overall job is known as GPU (graphic processing unit)-based parallel processing. It is extremely important for several medical imaging techniques such as image…
Qin Li, Xin Zhu, Wenxi Chen, Anand Prakash Singh
Background: The simulation of electrophysiological cardiac models plays an important role in facilitating the investigation of cardiac behavior under various conditions. However, these simulations often require a lot of computational resources. Methods: To address this challenge, this study introduced a method for…
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…
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…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Zhuobin Huang, Xingda Wei, Yingyi Hao, Rong Chen + 3 more
using Validated Speculation Authors: ['Zhuobin Huang' 'Xingda Wei' 'Yingyi Hao' 'Rong Chen' 'Mingcong Han' 'Jinyu Gu' 'Haibo Chen'] Checkpointing (C) and restoring (R) are key components for GPU tasks. POS is an OS-level GPU C/R system: It can transparently checkpoint or restore processes that use the GPU, without…
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…
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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…