high performance computing on graphics processing units: hgpu.org

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Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

GPU Acceleration of the Generalized Interpolation Material Point Method

Wei-Fan Chiang, Michael DeLisi, Todd Hummel, Tyler Prete, Kevin Tew, Mary Hall, Phil Wallstedt, James Guilkey

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Tags: CUDA, nVidia, nVidia GeForce 9600 GT, Particle-in-cell methods, Physics

February 22, 2011 by hgpu

Accelerating Energy Minimization using Graphics Processors

Bharat Sukhwani, Martin C. Herbordt

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Tags: Chemistry, CUDA, Molecular modeling, nVidia, Tesla C1060

February 22, 2011 by hgpu

Accelerating the ANSYS Direct Sparse Solver with GPUs

Geraud P. Krawezik, Gene Poole

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Tags: Computer science, CUDA, Linear Algebra, Mixed precision, nVidia, Sparse direct solvers, Tesla C1060

February 22, 2011 by hgpu

Production Floating Point Applications on FPGAs

Martin C. Herbordt, Bharat Sukhwani, Matt Chiu, Md. Ashfaq Khan

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Tags: Chemistry, Computer science, CUDA, FPGA, Molecular dynamics, Molecular modeling, nVidia, Tesla C1060

February 22, 2011 by hgpu

Performance analysis and optimization of three-dimensional FDTD on GPU using roofline model

Ki-Hwan Kim, KyoungHo Kim, Q-Han Park

Tags: Computer science, CUDA, FDTD, Finite-difference time-domain, nVidia, nVidia GeForce GTX 480

February 22, 2011 by hgpu

Data Structures and Transformations for Physically Based Simulation on a GPU

Perhaad Mistry, Dana Schaa, Byunghyun Jang, David Kaeli, Albert Dvornik, Dwight Meglan

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Tags: Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 285, Physics-based simulation

February 22, 2011 by hgpu

GPU Acceleration of Runge-Kutta Integrators

Lawrence Murray

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Tags: Algorithms, CUDA, Mathematics, nVidia, ODEs, Ordinary differential equations

February 22, 2011 by hgpu

Software-Based ECC for GPUs

Naoya Maruyama, Akira Nukada, Satoshi Matsuoka

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Tags: Computer science, CUDA, Error recovery, FFT, N-body simulation, nVidia, nVidia GeForce 8800 GTS, nVidia GeForce GTX 285, Tesla S1070

February 21, 2011 by hgpu

Accelerated Root Finding for Computational Finance

Mark J. Bennett

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Tags: Algorithms, Computational finance, Differential equations, Finance, Stochastic simulation

February 21, 2011 by hgpu

An Automated Approach for SIMD Kernel Generation for GPU based Software Acceleration

Kanupriya Gulati and Sunil P Khatri

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Tags: Code generation, Compilers, Computer science, CUDA, nVidia, nVidia GeForce GTX 280

February 21, 2011 by hgpu

Assembling large mosaics of electron microscope images using GPU

Kannan Umadevi Venkataraju, Mark Kim, Dan Gerszewski, James R. Anderson, Mary Hall

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Tags: CUDA, Electron microscopy, Image processing, nVidia, nVidia GeForce GTX 280

February 21, 2011 by hgpu

bioagent-bench: Benchmark for evaluating LLM agents in bioinformatics

BioAgent Bench: An AI Agent Evaluation Suite for Bioinformatics

Benchmark suite for LLM inference on NVIDIA consumer GPUs

Private LLM Inference on Consumer Blackwell GPUs: A Practical Guide for Cost-Effective Local Deployment in SMEs

Theorizer: from the paper Generating Literature-Driven Scientific Discoveries at Scale

Generating Literature-Driven Scientific Theories at Scale

Nsight Python: a Python kernel profiling interface based on NVIDIA Nsight Tools

Nsight Python: A Python-First Profiling Toolkit for Seamless GPU Kernel Analysis (Tool)

Awesome LLM-Driven Kernel Generation

Towards Automated Kernel Generation in the Era of LLMs

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

See all packages

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high performance computing on graphics processing units: hgpu.org

Programming

Probing biomolecular machines with graphics processors

GPU Acceleration of the Generalized Interpolation Material Point Method

Accelerating Energy Minimization using Graphics Processors

Accelerating the ANSYS Direct Sparse Solver with GPUs

Production Floating Point Applications on FPGAs

Performance analysis and optimization of three-dimensional FDTD on GPU using roofline model

Data Structures and Transformations for Physically Based Simulation on a GPU

GPU Acceleration of Runge-Kutta Integrators

Software-Based ECC for GPUs

Accelerated Root Finding for Computational Finance

An Automated Approach for SIMD Kernel Generation for GPU based Software Acceleration

Assembling large mosaics of electron microscope images using GPU

Recent source codes

bioagent-bench: Benchmark for evaluating LLM agents in bioinformatics

Benchmark suite for LLM inference on NVIDIA consumer GPUs

Theorizer: from the paper Generating Literature-Driven Scientific Discoveries at Scale

Nsight Python: a Python kernel profiling interface based on NVIDIA Nsight Tools

Awesome LLM-Driven Kernel Generation

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

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