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libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

Jocelyn Sunseri, David Ryan Koes

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Tags: Chemistry, Computer science, CUDA, Deep learning, Machine learning, Molecular modeling, Neural networks, nVidia, nVidia GeForce GTX Titan V, nVidia GeForce GTX Titan X, Package, PyTorch, TensorFlow

December 15, 2019 by hgpu

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel’s HPC Architectures: a Living Review [Article v1.0]

Luc-Henri Jolly, Alejandro Duran, Louis Lagardere, Jay W. Ponder, Pengyu Ren, Jean-Philip Piquemal

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Tags: Chemical Physics, Computational Physics, Computer science, Intel Xeon Phi, Mathematical Software, Molecular dynamics, Molecular modeling, OpenMP, Package

June 5, 2019 by hgpu

Acceleration of the MMFF94 routines within OpenBabel using Eigen and OpenCL

Omar Valerio Minero

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

February 28, 2013 by hgpu

Solving Molecular Distance Geometry Problems in OpenCL

Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos

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Tags: Chemistry, Computational chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560 Ti, OpenCL

June 27, 2012 by hgpu

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

Levente Fabry-Asztalos, Istvan Lorentz, Razvan Andonie

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Tags: Chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560, OpenCL, Optimization

May 23, 2012 by hgpu

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

Mayank Daga, Wu-chun Feng

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Tags: Algorithms, Biology, Biomolecules, Computational Complexity, CUDA, Electrostatics, Molecular modeling, nVidia, Optimization, Tesla C1060, Tesla C2050

May 12, 2012 by hgpu

Architecture-Aware Mapping and Optimization on a 1600-Core GPU

Mayank Daga, Thomas Scogland, Wu-chun Feng

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Tags: ATI, ATI Radeon HD 5870, Computer science, CUDA, Molecular modeling, nVidia, nVidia GeForce GTX 280, OpenCL, Optimization, Performance

January 3, 2012 by hgpu

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Yuki Furukawa, Ryota Koga, Koji Yasuda

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Molecular modeling, nVidia, nVidia GeForce GTX 580

November 30, 2011 by hgpu

Many-body quantum chemistry on graphics processing units

A. Eugene DePrince III, Jeff R. Hammond, Stephen K. Gray

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Matrix multiplication, Molecular modeling, nVidia, Tesla C2050

November 11, 2011 by hgpu

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Bharat Sukhwani

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Tags: Algorithms, Biology, Biomechanics, CUDA, FPGA, Molecular modeling, nVidia, Tesla C1060, Thesis

October 22, 2011 by hgpu

GPGPU-assisted prediction of ion binding sites in proteins

Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev

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Tags: Biology, Biophysics, CUDA, Molecular modeling, nVidia

October 7, 2011 by hgpu

Architecture-Aware Optimization on a 1600-core Graphics Processor

Mayank Daga, Thomas R.W. Scogland, Wu-chun Feng

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Tags: ATI, ATI Radeon HD 5870, Cluster computing, Computer science, CUDA, Molecular modeling, nVidia, nVidia GeForce GTX 280, OpenCL, Optimization, Tesla C2050

October 4, 2011 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

libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel’s HPC Architectures: a Living Review [Article v1.0]

Acceleration of the MMFF94 routines within OpenBabel using Eigen and OpenCL

Solving Molecular Distance Geometry Problems in OpenCL

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

Architecture-Aware Mapping and Optimization on a 1600-Core GPU

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Many-body quantum chemistry on graphics processing units

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

GPGPU-assisted prediction of ion binding sites in proteins

Architecture-Aware Optimization on a 1600-core Graphics Processor

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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