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Cell Charge Approximation for Accelerating Molecular Simulation on CUDA-Enabled GPU

Shyam Mohan K T, Jayaraj P B

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Tags: Chemistry, CUDA, Electrostatics, Molecular dynamics, Molecular simulation, nVidia, Programming techniques

August 7, 2014 by hgpu

Molecular dynamics simulations through GPU video games technologies

Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida

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Tags: Bioinformatics, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, OpenCL, Physics

July 4, 2014 by hgpu

Evaluating CP2K on Exascale Hardware: Intel Xeon Phi

Fiona Reid, Iain Bethune

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Tags: Chemistry, Intel Xeon Phi, Molecular dynamics, MPI, OpenMP

June 15, 2014 by hgpu

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

David R. Glowacki, Michael O'Connor, Gaetano Calabró, James Price, Philip Tew, Thomas Mitchell, Joseph Hyde, David P. Tew, David J. Coughtrie and Simon McIntosh-Smith

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Tags: GPU, Molecular dynamics, OpenCL, Visualization

June 12, 2014 by simonmcs

A Performance Model for the Communication in Fast Multipole Methods on HPC Platforms

Huda Ibeid, Rio Yokota, David Keyes

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Tags: Algorithms, Astrophysics, Computer science, CUDA, Fast multipole method, Molecular dynamics, N-body simulation, nVidia, Physics, Tesla K20

June 1, 2014 by hgpu

GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis

Ivan Teo, Juan Perilla, Rezvan Shahoei, Ryan McGreevy, Chris Harrison

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Tags: Computer science, CUDA, Molecular dynamics, nVidia, Tutorial, Visualization

May 24, 2014 by hgpu

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Robert T. McGibbon, Bharath Ramsundar, Mohammad M. Sultan, Gert Kiss, Vijay S. Pande

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Tags: Algorithms, Biology, Biophysics, CUDA, Distributed computing, Machine learning, Molecular dynamics, nVidia, nVidia GeForce GTX Titan

May 9, 2014 by hgpu

On the Use of Remote GPUs and Low-Power Processors for the Acceleration of Scientific Applications

A. Castello, J. Duato, R. Mayo, A. J. Pena, E. S. Quintana-Orti, V. Roca, F. Silla

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Tags: Bioinformatics, Computer science, CUDA, Energy-efficient computing, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Virtualization

April 27, 2014 by hgpu

Parallelization of the Algorithm WHAM with NVIDIA CUDA

Nicolo' Savioli

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9500 GT, nVidia GeForce GT 320 M, Physics, Thesis

February 2, 2014 by hgpu

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

Lorenzo Rovigatti, Petr Sulc, Istvan Z. Reguly, Flavio Romano

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, Package, Physics, Soft Condensed Matter, Tesla C2070, Tesla K10, Tesla K20

January 23, 2014 by hgpu

Experiences Porting a Molecular Dynamics Code to GPUs on a Cray XK7

Donald K. Berry, Joseph Schuchart, Robert Henschel

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Tags: CUDA, Fortran, Molecular dynamics, MPI, nVidia, OpenACC, Physics, Tesla K20

December 19, 2013 by hgpu

GPU Accelerated Semiclassical Initial Value Representation Molecular Dynamics

Dario Tamascelli, Francesco S. Dambrosio, Riccardo Conte, Michele Ceotto

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, Physics, Tesla C2075, Tesla K20

December 18, 2013 by hgpu

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

Kokkidio: Fast, expressive, portable code, based on Kokkos and Eigen

LLaMA-Inference-Bench

LLM-Inference-Bench: Inference Benchmarking of Large Language Models on AI Accelerators

MATAR

On a Simplified Approach to Achieve Parallel Performance and Portability Across CPU and GPU Architectures

Over-synchronization in GPU Programs

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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