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At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…

Genomics · Quantitative Biology 2024-07-04 Zülal Bingöl , Mohammed Alser , Onur Mutlu , Ozcan Ozturk , Can Alkan

The matrix-free gather-batched-GEMM-scatter pattern eliminates global stiffness assembly for three-dimensional SIMP topology optimization, but the conventional three-stage implementation forces avoidable DRAM traffic between stages. We…

Computational Engineering, Finance, and Science · Computer Science 2026-04-21 Shaoliang Yang , Jun Wang , Yunsheng Wang

Utilizing GPUs is critical for high performance on heterogeneous systems. However, leveraging the full potential of GPUs for accelerating legacy CPU applications can be a challenging task for developers. The porting process requires…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-06-27 Shilei Tian , Tom Scogland , Barbara Chapman , Johannes Doerfert

Over the past decade, GPUs have demonstrated significant potential in accelerating Online Analytical Processing (OLAP) operations. However, there remains a substantial gap in their application to Online Transaction Processing (OLTP), as…

Databases · Computer Science 2026-05-26 Zihan Sun , Yuyu Luo , Yong Zhang , Chao Li , Chunxiao Xing

The numerical integration of stochastic trajectories to estimate the time to pass a threshold is an interesting physical quantity, for instance in Josephson junctions and atomic force microscopy, where the full trajectory is not accessible.…

Computational Physics · Physics 2018-02-15 Vincenzo Pierro , Luigi Troiano , Elena Mejuto , Giovannni Filatrella

The Random Phase Approximation (RPA) for correlation energy in the grid-based projector augmented wave (gpaw) code is accelerated by porting to the Graphics Processing Unit (GPU) architecture. The acceleration is achieved by grouping…

Computational Physics · Physics 2013-07-31 Jun Yan , Lin Li , Christopher O'Grady

It is commonly agreed that highly parallel software on Exascale computers will suffer from many more runtime failures due to the decreasing trend in the mean time to failures (MTTF). Therefore, it is not surprising that a lot of research is…

Distributed, Parallel, and Cluster Computing · Computer Science 2015-05-19 Faisal Shahzad , Moritz Kreutzer , Thomas Zeiser , Rui Machado , Andreas Pieper , Georg Hager , Gerhard Wellein

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-10-19 I. Zacharoudiou , J. W. S. McCullough , P. V. Coveney

We propose Booster, a novel accelerator for gradient boosting trees based on the unique characteristics of gradient boosting models. We observe that the dominant steps of gradient boosting training (accounting for 90-98% of training time)…

Hardware Architecture · Computer Science 2020-11-06 Mingxuan He , T. N. Vijaykumar , Mithuna Thottethodi

Stochastic simulations need multiple replications in order to build confidence intervals for their results. Even if we do not need a large amount of replications, it is a good practice to speed-up the whole simulation time using the…

Distributed, Parallel, and Cluster Computing · Computer Science 2015-01-08 Jonathan Passerat-Palmbach , Jonathan Caux , Pridi Siregar , Claude Mazel , David Hill

Recently, tensor algebra have witnessed significant applications across various domains. Each operator in tensor algebra features different computational workload and precision. However, current general accelerators, such as VPU, GPGPU, and…

Hardware Architecture · Computer Science 2024-05-06 Chenyang Ai , Lechuan Zhao , Zhijie Huang , Cangyuan Li , Xinan Wang , Ying Wang

In recent years the computational capacity of single Field Programmable Gate Arrays (FPGA) devices as well as their versatility has increased significantly. Adding to that the High Level Synthesis frameworks allowing to program such…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-07-22 G. Korcyl , P. Korcyl

The Coherent Accelerator Processor Interface (CAPI) is a general term for the infrastructure that provides high throughput and low latency path to the flash storage connected to the IBM POWER 8+ System. CAPI accelerator card is attached…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-09-17 Kaushik Velusamy , Smriti Prathapan , Milton Halem

Nowadays, GPU accelerators are commonly used to speed up general-purpose computing tasks on a variety of hardware. However, due to the diversity of GPU architectures and processed data, optimization of codes for a particular type of…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-09-20 Jiří Filipovič , Jana Hozzová , Amin Nezarat , Jaroslav Oľha , Filip Petrovič

We describe ASAGA, an asynchronous parallel version of the incremental gradient algorithm SAGA that enjoys fast linear convergence rates. Through a novel perspective, we revisit and clarify a subtle but important technical issue present in…

Optimization and Control · Mathematics 2017-11-09 Rémi Leblond , Fabian Pedregosa , Simon Lacoste-Julien

Stencil codes are performance-critical in many compute-intensive applications, but suffer from significant address calculation and irregular memory access overheads. This work presents SARIS, a general and highly flexible methodology for…

Mathematical Software · Computer Science 2024-04-09 Paul Scheffler , Luca Colagrande , Luca Benini

Large language models (LLMs) have revolutionized AI applications, yet their enormous computational demands severely limit deployment and real-time performance. Quantization methods can help reduce computational costs, however, attaining the…

Machine Learning · Computer Science 2025-09-03 Shaobo Ma , Chao Fang , Haikuo Shao , Zhongfeng Wang

Modern Graphics Processing Units (GPUs) are well provisioned to support the concurrent execution of thousands of threads. Unfortunately, different bottlenecks during execution and heterogeneous application requirements create imbalances in…

Neural network (NN) accelerators have been integrated into a wide-spectrum of computer systems to accommodate the rapidly growing demands for artificial intelligence (AI) and machine learning (ML) applications. NN accelerators share the…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-07-14 Kuan-Chieh Hsu , Hung-Wei Tseng

Recent advances in multi and many-core processors have led to significant improvements in the performance of scientific computing applications. However, the addition of a large number of complex cores have also increased the overall power…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-02-23 Akash Dutta , Jee Choi , Ali Jannesari
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