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Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Zhuren Liu, Shouzhe Zhang, Justin Garrigus, Hui Zhao

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, CUDA, Genomics, nVidia, nVidia GeForce RTX 3070, Package

May 28, 2023 by hgpu

Understanding Performance Portability of Bioinformatics Applications in SYCL on an NVIDIA GPU

Zheming Jin, Jeffrey S. Vetter

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Tags: Benchmarking, Bioinformatics, Computer science, CUDA, Heterogeneous systems, nVidia, Package, performance portability, SYCL, Tesla V100

April 16, 2023 by hgpu

Improving Performance of Hardware Accelerators by Optimizing Data Movement: A Bioinformatics Case Study

Peter Knoben, Nikolaos Alachiotis

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Tags: Bioinformatics, Biology, Computer science, FPGA, OpenCL, Package

February 12, 2023 by hgpu

SaLoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs

Seongyeon Park, Hajin Kim, Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee, Youngsok Kim, Jinho Lee

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 1650, nVidia GeForce RTX 3090, Sequence alignment, Smith-Waterman algorithm, String matching

January 29, 2023 by hgpu

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

Understanding the Power of Evolutionary Computation for GPU Code Optimization

Jhe-Yu Liou, Muaaz Awan, Steven Hofmeyr, Stephanie Forrest, Carole-Jean Wu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Evolutionary Computations, Neural and Evolutionary Computing, nVidia, nVidia GeForce GTX 1080 Ti, Package, performance portability, Sequence alignment, Tesla P100, Tesla V100

September 4, 2022 by hgpu

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack

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Tags: AMD Radeon Instinct MI100, ATI, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce RTX 3090, OpenCL, Package, Sequence alignment, Tesla A100

May 22, 2022 by hgpu

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

Manuel Costanzo, Enzo Rucci, Carlos Garcia Sanchez, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX Titan X, nVidia GeForce RTX 2070, Sequence alignment, Smith-Waterman algorithm, SYCL

March 27, 2022 by hgpu

WarpCore: A Library for fast Hash Tables on GPUs

Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt

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Tags: Bioinformatics, Computer science, CUDA, Hashing, nVidia, nVidia Quadro GV100, Tesla V100

September 20, 2020 by hgpu

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Tesla V100

February 16, 2020 by hgpu

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

Huihui Zou, Shanjiang Tang, Ce Yu, Hao Fu, Yusen Li, Wenjie Tang

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Tags: Algorithms, APU, Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 750, OpenCL, Sequence alignment, Smith-Waterman algorithm

December 9, 2018 by hgpu

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J. Andrew McCammon, Ross C. Walker

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 1080 Ti, nVidia GeForce GTX Titan X

January 20, 2018 by hgpu

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Dragon-Alpha&cu32: A Java-based Tensor Computing Framework With its High-Performance CUDA Library

Beehive SPIR-V Toolkit

Experiences in Building a Composable and Functional API for Runtime SPIR-V Code Generation

TorchBench: a collection of open source benchmarks used to evaluate PyTorch performance

TorchBench: Benchmarking PyTorch with High API Surface Coverage

Prediction of Performance and Power Consumption of GPGPU Applications

Descend: an attempt at safe imperative GPU programming

Descend: A Safe GPU Systems Programming Language

Redwood heterogeneous framework

Redwood: Flexible and Portable Heterogeneous Tree Traversal Workloads

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high performance computing on graphics processing units: hgpu.org

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Understanding Performance Portability of Bioinformatics Applications in SYCL on an NVIDIA GPU

Improving Performance of Hardware Accelerators by Optimizing Data Movement: A Bioinformatics Case Study

SaLoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs

Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment

Understanding the Power of Evolutionary Computation for GPU Code Optimization

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

WarpCore: A Library for fast Hash Tables on GPUs

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Recent source codes

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

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Dragon-Alpha&cu32: A Java-based Tensor Computing Framework With its High-Performance CUDA Library

Beehive SPIR-V Toolkit

TorchBench: a collection of open source benchmarks used to evaluate PyTorch performance

Prediction of Performance and Power Consumption of GPGPU Applications

Descend: an attempt at safe imperative GPU programming

Redwood heterogeneous framework

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