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GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Pooya Zandevakili, Ming Hu, Zhaohui Qin

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Tags: Algorithms, Biochemistry, Biology, Chemistry, Computational biology, Computer science, CUDA, Genetics, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

June 17, 2012 by hgpu

Implementing Molecular Dynamics on Hybrid High Performance Computers – Particle-Particle Particle-Mesh

W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington

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Tags: Algorithms, Chemistry, CUDA, Electrostatics, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, OpenCL, OpenMPI, Package, Physics, Tesla M2070

February 10, 2012 by hgpu

The Anatomy of High-Performance 2D Similarity Calculations

Imran S. Haque, Vijay S. Pande, W. Patrick Walters

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Tags: Algorithms, Biochemistry, Chemistry, Clustering, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

October 16, 2011 by hgpu

Coming Soon: Research in a Cloud

Pam Frost Gorder

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Tags: Chemistry, Cloud, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package

June 18, 2011 by hgpu

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

Tags: Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenMP, Package

June 16, 2011 by hgpu

Daubechies wavelets for high performance electronic structure calculations: The BigDFT project

Luigi Genovese, Brice Videau, Matthieu Ospici, Thierry Deutsch, Stefan Goedecker, Jean-Francois Mehaut

Tags: Chemistry, Molecular modeling, OpenCL, Package, Physics

January 16, 2011 by hgpu

OpenMM: A Hardware-Independent Framework for Molecular Simulations

Peter Eastman, Vijay Pande

Tags: Chemistry, Computational chemistry, Molecular modeling, Package

December 16, 2010 by hgpu

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

Imran S. Haque, Vijay S. Pande, W. Patrick Walters

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Tags: Chemistry, CUDA, nVidia, nVidia GeForce GTS 250, OpenMP, Package, Tesla T10

November 9, 2010 by hgpu

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada

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Tags: Chemistry, CUDA, GPU cluster, Molecular modeling, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Package, Python

November 6, 2010 by hgpu

PAPER – Accelerating parallel evaluations of ROCS

Imran S. Haque, Vijay S. Pande

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Tags: Chemistry, Computational chemistry, CUDA, Molecular overlay, nVidia, nVidia GeForce 8600 GT, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280, Package, ROCS, Shape comparison

November 3, 2010 by hgpu

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

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Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

Concurrent Scheduling of High-Level Parallel Programs on Multi-GPU Systems

wgpy: WebGL accelerated numpy-compatible array library for web browser

WgPy: GPU-accelerated NumPy-like array library for web browsers

Microbenchmarking OpenMP target offload with Catch2

A Microbenchmark Framework for Performance Evaluation of OpenMP Target Offloading

SUperman: Highly Efficient Permanent Computation Library

SUperman: Efficient Permanent Computation on GPUs

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

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