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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

Performance portability study of epistasis detection using SYCL on NVIDIA GPU

Zheming Jin, Jeffrey S. Vetter

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Tags: Computer science, CUDA, Genomics, nVidia, performance portability, SYCL, Tesla V100

October 9, 2022 by hgpu

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

Accelerating Genomics Research with OpenCL and FPGAs

Chris Rauer, George S. Powley, Mir Ahsan, Nicholas Finamore

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Tags: Algorithms, Biology, Computer science, FPGA, Genomics, OpenCL

October 15, 2017 by hgpu

A Linear Algebra Approach to Fast DNA Mixture Analysis Using GPUs

Siddharth Samsi, Brian Helfer, Jeremy Kepner, Albert Reuther, Darrell O. Ricke

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Tags: Algorithms, Computer science, CUDA, Genomics, Linear Algebra, Matrix multiplication, nVidia, Performance, Tesla K80

July 5, 2017 by hgpu

Genetically Improved BarraCUDA

W. B. Langdon, Brian Yee Hong Lam

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Tags: Algorithms, Benchmarking, Biology, CUDA, Genomics, nVidia, nVidia GeForce GT 730, Package, Tesla K20, Tesla K40, Tesla K80

June 1, 2015 by hgpu

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam

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Tags: Biology, CUDA, Genomics, nVidia, Package, Tesla K40

September 29, 2014 by hgpu

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Gary K. Chen, Eric Chi, John Ranola, Kenneth Lange

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Tags: Algorithms, Bioinformatics, Biology, Cluster analysis, Clustering, Genomics, Hierarchical clustering, nVidia, OpenCL, Package, Tesla C2050

September 9, 2014 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

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

Performance portability study of epistasis detection using SYCL on NVIDIA GPU

Molecular dynamics recipes for genome research

Accelerating Genomics Research with OpenCL and FPGAs

A Linear Algebra Approach to Fast DNA Mixture Analysis Using GPUs

Genetically Improved BarraCUDA

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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