high performance computing on graphics processing units: hgpu.org

Applications

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

David Dynerman, Erick Butzlaff, Julie C. Mitchell

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Tags: Bioinformatics, Biology, Biophysics, Chemistry, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Solvent effects

October 29, 2010 by hgpu

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger

Tags: ASIC, Chemistry, Computational chemistry, MDGRAPE, Poisson Boltzmann, Solvent effects

October 29, 2010 by hgpu

GPU acceleration of cutoff pair potentials for molecular modeling applications

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen Mei

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Tags: Algorithms, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, Tesla C870

October 28, 2010 by hgpu

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

M. J. Harvey, G. De Fabritiis

Tags: Chemistry, Computational chemistry, Molecular dynamics, nVidia

October 28, 2010 by hgpu

GPU acceleration of a production molecular docking code

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biophysics, Chemistry, FPGA, Molecular dynamics, nVidia, Tesla C1060

October 27, 2010 by hgpu

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

M. J. Harvey, G. Giupponi, G. De Fabritiis

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Tags: Biological Physics, Chemistry, Computational Physics, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Physics, Tesla C1060

October 27, 2010 by hgpu

NVPTX-SPIR-V Translator

Supporting CUDA for an extended RISC-V GPU architecture

Taichi Lattice Boltmann

Data-Oriented Language Implementation of Lattice-Boltzmann Method for Dense and Sparse Geometries

WarpDrive: Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning on a GPU

MLIR: Multi-Level Intermediate Representation

High Performance GPU Code Generation for Matrix-Matrix Multiplication using MLIR: Some Early Results

SeisSol: High Resolution Simulation os Seismic Wave Propagation in Realistic Media with Complex Geomerty

Performance Portability and Evaluation of Heterogeneous Components of SeisSol Targeted to Upcoming Intel HPC GPUs

perf4sight: A toolflow to model CNN training performance on Edge GPUs

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high performance computing on graphics processing units: hgpu.org

Applications

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

GPU acceleration of cutoff pair potentials for molecular modeling applications

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

GPU acceleration of a production molecular docking code

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Recent source codes

NVPTX-SPIR-V Translator

Taichi Lattice Boltmann

WarpDrive: Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning on a GPU

MLIR: Multi-Level Intermediate Representation

SeisSol: High Resolution Simulation os Seismic Wave Propagation in Realistic Media with Complex Geomerty

perf4sight: A toolflow to model CNN training performance on Edge GPUs

Parament: Parallelized Matrix Exponentiation for Numerical Time evolution

ndzip: A High-Throughput Parallel Lossless Compressor for Scientific Data

ScaleHLS Project

POCL: Portable Computing Language

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