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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

CuPBoP-AMD: Extending CUDA to AMD Platforms

CuPBoP-AMD: Extending CUDA to AMD Platforms

Kernel Tuner

Testing and Mutation Testing for GPU Kernels

GT4Py: GridTools for Python

GT4Py: High Performance Stencils for Weather and Climate Applications using Python

miniBUDE: A BUDE virtual-screening benchmark, in many programming models

Evaluation of FPGA-based high performance computing platforms

gossip: Efficient Communication Primitives for Multi-GPU Systems

Accelerating bioinformatics applications on CUDA-enabled multi-GPU systems

AUCMEDI: a framework for Automated Classification of Medical Images

Frameworks in Medical Image Analysis with Deep Neural Networks

Creating a Dataset for High-Performance Computing Code Translation using LLMs: A Bridge Between OpenMP Fortran and C+

Creating a Dataset for High-Performance Computing Code Translation using LLMs: A Bridge Between OpenMP Fortran and C+

AFOCL: Portable OpenCL Programming of FPGAs via Automated Built-in Kernel Management

AFOCL: Portable OpenCL Programming of FPGAs via Automated Built-in Kernel Management

CHARM-SYCL: New Unified Programming Environment for Multiple Accelerator Types

CHARM-SYCL: New Unified Programming Environment for Multiple Accelerator Types

pp-template: Template for Performance-Portable code development, targeting HOST-DEVICE computer architectures

An approach to performance portability through generic programming

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