high performance computing on graphics processing units: hgpu.org

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

Petaflop biofluidics simulations on a two million-core system

Massimo Bernaschi, Satoshi Matsuoka, Mauro Bisson, Massimiliano Fatica, Toshio Endo, Simone Melchionna

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Tags: Algorithms, Biology, CUDA, GPU cluster, Medicine, nVidia, Optimization, Tesla M2050

January 11, 2012 by hgpu

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations

microSYCL: SYCL micro-benchmarks repository

Exploring SYCL as a Portability Layer for High-Performance Computing on CPUs

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high performance computing on graphics processing units: hgpu.org

Applications

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

Petaflop biofluidics simulations on a two million-core system

Recent source codes

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

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