high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Parallel accelerators for GlimmerHMM bioinformatics algorithm

Nafsika Chrysanthou, Grigorios Chrysos, Euripides Sotiriades, Ioannis Papaefstathiou

Tags: Algorithms, Bioinformatics, Biology, FPGA, Genetics

June 8, 2011 by hgpu

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

Satish Chikkagoudar, Kai Wang, Mingyao Li

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Tags: Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 1800, Package, Tesla C1060

June 7, 2011 by hgpu

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

M.N. Osman, R. Abdullah, N. AbdulRashid

Tags: Biology, Macromolecule, Molecular simulation, Pharmaceuticals

June 2, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 2011 by hgpu

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

K. Dohi, K. Benkridt, C. Ling, T. Hamada, Y. Shibata

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

May 31, 2011 by hgpu

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Alhadi Bustamam, Kevin Burrage, Nicholas A. Hamilton

Tags: Bioinformatics, Biology, CUDA, MPI, nVidia, Sparse matrix

May 30, 2011 by hgpu

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

Mohammad A. Bhuiyan, Vivek K. Pallipuram, Melissa C. Smith

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Tesla C870

May 28, 2011 by hgpu

GPU implementation of map-MRF for microscopy imagery segmentation

Danny Crookes, Paul Miller, Hugh Gribben, Charles Gillan, Damian McCaughey

Tags: Algorithms, Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX

May 25, 2011 by hgpu

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

Lorenzo Dematte

Tags: Algorithms, Biochemistry, Biology, CUDA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260, nVidia Quadro FX 570 M

May 17, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Fast short exact repeats finding on GPU

Weidong Sun, Weiwei Wang, Zongmin Ma

Tags: Algorithms, Biology, CUDA, Genetics, nVidia, Pattern Search

May 13, 2011 by hgpu

Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

tritonBLAS: Triton-based Analytical Approach for GEMM Kernel Parameter Selection

hls4ml: Machine learning on FPGAs using HLS

hls4ml: A Flexible, Open-Source Platform for Deep Learning Acceleration on Reconfigurable Hardware

NVIDIA Nemotron Parse 1.1

ThunderKittens: Tile primitives for speedy kernels

ParallelKittens: Systematic and Practical Simplification of Multi-GPU AI Kernels

Iris: AMD RAD's multi-GPU Triton-based framework for seamless multi-GPU programming

Iris: First-Class Multi-GPU Programming Experience in Triton

HipKittens: Fast and Furious AMD Kernels

Fortran xDSL dialects

An MLIR pipeline for offloading Fortran to FPGAs via OpenMP

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Parallel accelerators for GlimmerHMM bioinformatics algorithm

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

GPU implementation of map-MRF for microscopy imagery segmentation

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

GPU-based triangulation of the van der Waals surface

Fast short exact repeats finding on GPU

Fast network centrality analysis using GPUs

Recent source codes

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

hls4ml: Machine learning on FPGAs using HLS

NVIDIA Nemotron Parse 1.1

ThunderKittens: Tile primitives for speedy kernels

Iris: AMD RAD's multi-GPU Triton-based framework for seamless multi-GPU programming

HipKittens: Fast and Furious AMD Kernels

Fortran xDSL dialects

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