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JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

Samuel S. Schoenholz, Ekin D. Cubuk

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Tags: Biochemistry, Chemistry, Computational Physics, CUDA, Fortran, Machine learning, Materials Science, Molecular dynamics, Neural networks, nVidia, Package, Physics, Python

December 15, 2019 by hgpu

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman

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Tags: Biochemistry, Biomolecules, Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenCL, OpenMP, Thesis

March 1, 2016 by hgpu

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

J.D. Tyzack, H.Y. Mussa, M.J. Williamson,J. Kirchmair, R.C. Glen.

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Tags: Biochemistry, CUDA, Machine learning, nVidia, nVidia GeForce GT 640, nVidia Tesla C2075

May 31, 2014 by hgpu

Accelerating Population Balance Model-based particulate process simulations via parallel computing

Anuj Varghese Prakash

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Tags: Biochemistry, Chemistry, Computer science, CUDA, Distributed computing, nVidia, nVidia GeForce GTX 280, Thesis

April 26, 2013 by hgpu

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

GPU Accelerated Molecular Surface Computing

Byungjoo Kim, Ku-Jin Kim, Joon-Kyung Seong

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Tags: Biochemistry, Chemistry, CUDA, KD-tree, Molecular surface, nVidia, nVidia GeForce GTX 590

February 26, 2012 by hgpu

High-throughput protein crystallization on the World Community Grid and the GPU

Yulia Kotseruba, Christian A Cumbaa, Igor Jurisica

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Tags: ATI, ATI Radeon HD 5770, Biochemistry, Image processing, nVidia, nVidia GeForce GT 330 M, nVidia Quadro FX 3800, OpenCL, Tesla C2050

February 11, 2012 by hgpu

Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs

Denis V. Gladkov, Samuel Alberts, Roshan M. D'Souza, Steven Andrews

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Tags: Algorithms, Biochemistry, Computational Complexity, Computer science, CUDA, nVidia, Tesla C2050

November 11, 2011 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

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Cristian Dittamo, Davide Cangelos

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Tags: Algorithms, Biochemistry, Biology, nVidia, nVidia GeForce 8600 M GS, Stochastic simulation

August 12, 2011 by hgpu

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

Lorenzo Dematte

Tags: Algorithms, Biochemistry, Biology, CUDA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260, nVidia Quadro FX 570 M

May 17, 2011 by hgpu

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, G. De Fabritiis

Tags: Biochemistry, Chemistry, Molecular dynamics, Thermodynamics

November 6, 2010 by hgpu

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

EnergyUCB-Bandit

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

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high performance computing on graphics processing units: hgpu.org

JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

Accelerating Population Balance Model-based particulate process simulations via parallel computing

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

GPU Accelerated Molecular Surface Computing

High-throughput protein crystallization on the World Community Grid and the GPU

Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs

The Anatomy of High-Performance 2D Similarity Calculations

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

Recent source codes

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

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

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

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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

EnergyUCB-Bandit

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