24 papers · ranked by Valyu relevance
Daniel A. Reed, Dennis Gannon, Jack Dongarra
The world of computing is in rapid transition, now dominated by a world of smartphones and cloud services, with profound implications for the future of advanced scientific computing. Simply put, highperformance computing (HPC) is at an important inflection point. For the last 60 years, the world's fastest…
Konstantinos Rallis, Ioannis Liliopoulos, Georgios D. Varsamis, Evangelos Tsipas + 3 more
The connection and eventual integration of High-Performance Computing (HPC) with Quantum Computing (QC) represents a transformative advancement in computational technology, promising significant enhancements in solving complex, previously intractable problems. This manuscript provides a comprehensive overview of the…
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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…
John Kruper, Ariel Rokem
Tractography based on diffusion-weighted MRI (dMRI) is the predominant in vivo method for mapping the brain’s white matter. However, it is also one of the most computationally demanding steps in neuroimaging data analysis-requiring the generation and filtering of millions of streamlines per subject. Over the past…
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…
Xinyao Yi
SIMD Architecture Authors: ['Xinyao Yi'] Abstract—Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2) incorporating powerful parallel…
Torsten Hoefler, Marcin Copik, Pete Beckman, Andrew Jones + 7 more
'Ian Foster' 'Manish Parashar' 'Daniel A. Reed' 'Matthias Troyer' 'T. C. Schulthess' 'Daniel Ernst' 'Jack Dongarra'] HPC and Cloud have evolved independently, specializing their innovations into performance or productivity. Acceleration as a Service (XaaS) is a recipe to empower both fields with a shared execution…
Xuzhen He, Viacheslav Kovtun
The recent dramatic progress in machine learning is partially attributed to the availability of high-performant computers and development tools. The accelerated linear algebra (XLA) compiler is one such tool that automatically optimises array operations (mostly fusion to reduce memory operations) and compiles the…
János Végh, Ádám József Berki
In all kinds of implementations of computing, whether technological or biological, some material carrier for the information exists, so in real-world implementations, the propagation speed of information cannot exceed the speed of its carrier. Because of this limitation, one must also consider the transfer time between…
Marissa E. Powers, Keith Mannthey, Priyanka Sebastian, Snehal Adsule + 6 more
Next Generation Sequencing (NGS) workloads largely consist of pipelines of tasks with heterogeneous compute, memory, and storage requirements. Identifying the optimal system configuration has historically required expertise in both system architecture and bioinformatics. This paper outlines infrastructure…
Benedikt Feldotto, Jochen Martin Eppler, Cristian Jimenez-Romero, Christopher Bignamini + 18 more
'Christopher Bignamini' 'Carlos Enrique Gutierrez' 'Ugo Albanese' 'Eloy Retamino' 'Viktor Vorobev' 'Vahid Zolfaghari' 'Alex Upton' 'Zhe Sun' 'Hiroshi Yamaura' 'Morteza Heidarinejad' 'Wouter Klijn' 'Abigail Morrison' 'Felipe Cruz' 'Colin McMurtrie' 'Alois C. Knoll' 'Jun Igarashi' 'Tadashi Yamazaki' 'Kenji Doya' 'Fabrice…
Tong Zhu, Pankaj Vats, Seth Onken, Al Dunstan + 13 more
Next-generation sequencing (NGS) has transformed genomics, enabling breakthroughs in biotechnology, healthcare, and pharmaceuticals. However, exponential data growth-outpacing Moore’s Law-presents critical computational challenges for secondary analysis. We introduce Parabricks, a freely accessible, GPU-accelerated…
Rene Miedema, Christos Strydis
Introduction In-silico simulations are a powerful tool in modern neuroscience for enhancing our understanding of complex brain systems at various physiological levels. To model biologically realistic and detailed systems, an ideal simulation platform must possess: (1) high performance and performance scalability, (2)…
Hammad Ather, Sophie Berkman, Giuseppe Cerati, Matti J. Kortelainen + 9 more
Traditionally, high energy physics (HEP) experiments have relied on x86 CPUs for the majority of their significant computing needs. As the field looks ahead to the next generation of experiments such as DUNE and the High-Luminosity LHC, the computing demands are expected to increase dramatically. To cope with this…
Chaoming Wang, Sichao He, Shouwei Luo, Yuxiang Huan + 1 more
Artificial intelligence (AI) is revolutionizing scientific research across various disciplines. The foundation of scientific research lies in rigorous scientific computing based on standardized physical units. However, current mainstream high-performance numerical computing libraries for AI generally lack native…
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…
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…
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…
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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…
Felix Johannes Schmitt, Vahid Rostami, Martin Paul Nawrot
Spiking neural networks (SNN) represent the state-of-the-art approach to the biologically realistic modeling of nervous system function. The systematic calibration for multiple free model parameters is necessary to achieve robust network function and demands high computing power and large memory resources. Special…
Yingqi Tian, Zhaoxuan Xie, Zhen Luo, Haibo Ma
Using the mixed precision strategy to optimize quantum chemistry codes has been proved promising in saving computational cost and maintaining chemical accuracy. Here, an efficient mixed-precision density matrix renormalization group (DMRG) scheme, containing a two-level mixed-precision hierarchy, is developed and…
Maxim Lippeveld, Daniel Peralta, Andrew Filby, Yvan Saeys
Due to high resolution and throughput of modern image cytometry platforms, morphologically profiling generated datasets poses a significant computational challenge. Here, we present Scalable Cytometry Image Processing (SCIP), an image processing software aimed at running on distributed high performance computing…
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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…
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We describe a collaborative research project spanning the disciplines of quantum hardware, quantum algorithms, conventional computational chemistry, synthetic medicinal chemistry and life sciences. Our project seeks to demonstrate an impact of quantum computing on human health. It is one of several funded by Wellcome…