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gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs

Bertil Schmidt, Felix Kallenborn, Alexander Wichmann, Alejandro Chacon, Christian Hundt

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Tags: Bioinformatics, Biology, Computer science, CUDA, FPGA, Genomics, nVidia, nVidia A100, nVidia H100, nVidia L4, nVidia L40s, nVidia V100, Package

November 24, 2024 by hgpu

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

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

GSParLib: A multi-level programming interface unifying OpenCL and CUDA for expressing stream and data parallelism

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

A User’s Guide to KSig: GPU-Accelerated Computation of the Signature Kernel

IterApp: Iterative Application Skeleton

Boosting Performance of Iterative Applications on GPUs: Kernel Batching with CUDA Graphs

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

See all packages

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high performance computing on graphics processing units: hgpu.org

gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs

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

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

IterApp: Iterative Application Skeleton

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

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