high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Design of high-performance parallelized gene predictors in MATLAB

Sylvain Robert Rivard, Jean-Gabriel Mailloux, Rachid Beguenane, Hung Tien Bui,

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Tags: Algorithms, Bioinformatics, Biology, CUDA, FFT, Genetics, nVidia, nVidia GeForce GTX 560

April 13, 2012 by hgpu

An Algorithm for Fast Edit Distance Computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 275, Security, Sequence alignment

March 11, 2012 by hgpu

Multiscale Hemodynamics Using GPU Clusters

Mauro Bisson, Massimo Bernaschi, Simone Melchionna, Sauro Succi, Efthimios Kaxiras

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Tags: Biology, CUDA, Fluid dynamics, GPU cluster, Lattice Boltzmann model, Medicine, nVidia, Tesla C1060

February 17, 2012 by hgpu

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

Christian Robert Trott

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Tags: Biology, Computational Physics, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 470, Package, Physics, Polymer Systems, Tesla C1060, Thesis

February 13, 2012 by hgpu

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Luis E. Ramirez-Chavez, Carlos A. Coello Coello, Eduardo Rodriguez-Tello

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Tags: Bioinformatics, Biology, CUDA, Differential equations, Differential evolution, nVidia, nVidia GeForce GTX 460, Optimization

January 23, 2012 by hgpu

Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Package, Sequence alignment

January 19, 2012 by hgpu

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

Nicolas Bonnel, Pierre-Francois Marteau

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Tags: Algorithms, Benchmarking, Biology, Databases, nVidia, OpenCL, Tesla M2050

January 18, 2012 by hgpu

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Hybrid computing, nVidia, nVidia GeForce GTX 580, RNA

January 15, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Algorithms, Biology, Computational biology, CUDA, Image processing, Machine learning, nVidia, Package, Tesla C2050

January 13, 2012 by hgpu

Implementation of Virtual Embryology using the Thrust library for CUDA

Anna Aichmayr Markus Dauschan

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Tags: Biology, CUDA, Neural networks, nVidia, Python

January 13, 2012 by hgpu

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Peng Jia, Liming Xuan, Lei Liu, Chaochun Wei

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Tags: Biology, Computational biology, CUDA, Genetics, nVidia, Package, Tesla C1060

January 11, 2012 by hgpu

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Accelerating a Linear Programming Algorithm on AMD GPUs

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Towards Efficient and Practical GPU Multitasking in the Era of LLM

Bandicoot: C++ library for GPU accelerated linear algebra

Bandicoot: A Templated C++ Library for GPU Linear Algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

The Fused Kernel Library: A C++ API to Develop Highly-Efficient GPU Libraries

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

Block: Balancing Load in LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

SIGMo: High-Throughput Batched Subgraph Isomorphism on GPUs for Molecular Matching

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

DGEMM without FP64 Arithmetic – using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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high performance computing on graphics processing units: hgpu.org

Applications

Design of high-performance parallelized gene predictors in MATLAB

An Algorithm for Fast Edit Distance Computation on GPUs

Multiscale Hemodynamics Using GPU Clusters

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Accelerated Large-Scale Multiple Sequence Alignment

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

BarraCUDA – a fast short read sequence aligner using graphics processing units

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Implementation of Virtual Embryology using the Thrust library for CUDA

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Recent source codes

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Bandicoot: C++ library for GPU accelerated linear algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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