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Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment

Manuel Costanzo, Enzo Rucci, Carlos García Sánchez, Marcelo Naiouf, Manuel Prieto-Matías

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, Heterogeneous systems, Intel, Intel UHD 630, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980, nVidia GeForce RTX 2070, nVidia GeForce RTX 3090, OpenCL, Sequence alignment, SYCL, Tesla V100

November 27, 2022 by hgpu

Performance Assessment of using OpenCL on FPGA Systems for ODE Solvers

Patrick Tobias Haft

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Tags: Code generation, Computational biology, Computer science, Differential equations, FPGA, nVidia, nVidia GeForce GTX 980 Ti, ODEs, OpenCL, Optimization, Ordinary differential equations, Tesla K20, Thesis

May 16, 2021 by hgpu

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar Hernandez, Jeremy C. Smith, Ada Sedova

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Tags: Biology, Biomolecules, Computational biology, CUDA, molecular docking, nVidia, nVidia DGX-2, nVidia GeForce RTX 2080 Ti, OpenCL, supercomputer, Tesla V100

July 12, 2020 by hgpu

Parallel Tree Traversal for Nearest Neighbor Query on the GPU

Moohyeon Nam, Jinwoong Kim, Beomseok Nam

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Tags: Algorithms, Biology, Computational biology, Computer science, CUDA, Information Retrieval, Nearest neighbour, nVidia, Tesla K40

September 5, 2016 by hgpu

PROJECTION Algorithm for Motif Finding on GPUs

Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna

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Tags: Algorithms, Biology, Computational biology, CUDA, nVidia

May 26, 2016 by hgpu

On Longest Repeat Queries Using GPU

Yun Tian, Bojian Xu

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Tags: Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 660 Ti

January 28, 2015 by hgpu

Hybrid CPU-GPU Pipeline Framework

Fahad Khalid, Frank Feinbube, Andreas Polze

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Tags: Biology, Computational biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 680

November 18, 2014 by hgpu

High-accuracy Optimization by Parallel Iterative Discrete Approximation and Multi-GPU Computing

Di Zhao

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Tags: Biology, Computational biology, Computational finance, CUDA, Finance, nVidia, nVidia GeForce GTX 660, Thesis

November 13, 2014 by hgpu

Finding Longest Common Subsequences by GPU-Based Parallel Ant Colony Optimization

David Markvica

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Tags: Algorithms, Biology, Computational biology, Computer science, Heterogeneous systems, Metaheuristics, nVidia, nVidia GeForce GTX 560 Ti, OpenCL, Optimization, Pattern recognition, Thesis

October 27, 2014 by hgpu

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Nikolay Pydiura, Pavel Karpov, Yaroslav Blume

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Tags: AMD Radeon R9 280, ATI, Biology, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, OpenCL

October 25, 2014 by hgpu

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri

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Tags: Bioinformatics, Biology, Computational biology, CUDA, Differential equations, nVidia, ODEs, Ordinary differential equations, Tesla K20

May 30, 2014 by hgpu

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

Sampath Kumar, P. K. Baruah

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, nVidia, Sequence matching, Smith-Waterman algorithm, Tesla M2050

November 2, 2013 by hgpu

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Clava: C/C++ Source-to-Source Tool based on Clang

Challenges and Opportunities in C/C++ Source-To-Source Compilation

gpuLik

Statistical Computing With Graphics Processing Units

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

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