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Accelerating Drug Discovery in AutoDock-GPU with Tensor Cores

Gabin Schieffer, Ivy Peng

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Tags: Chemistry, Computer science, CUDA, Macromolecule, molecular docking, nVidia, nVidia A100, nVidia V100, Physics, Tesla T4

October 20, 2024 by hgpu

Graphtoy: Fast Software Simulation of Applications for AMD’s AI Engines

Jonathan Strobl, Leonardo Solis-Vasquez, Yannick Lavan, Andreas Koch

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Tags: ATI, Computer science, FPGA, molecular docking, Package

February 18, 2024 by hgpu

Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs

Gianmarco Accordi, Davide Gadioli, Emanele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo

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Tags: Computer science, CUDA, HPC, molecular docking, nVidia, nVidia A100, oneAPI, Performance, SYCL

February 12, 2024 by hgpu

Experiences Migrating CUDA to SYCL: A Molecular Docking Case Study

Leonardo Solis-Vasquez, Edward Mascarenhas, Andreas Koch

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Tags: Chemistry, Computer science, CUDA, molecular docking, nVidia, nVidia A100, oneAPI, Package, SYCL

May 28, 2023 by hgpu

Accelerating AutoDock VINA with GPUs

Shidi Tang, Ruiqi Chen, Mengru Lin, Qingde Lin, Yanxiang Zhu, Jiansheng Wu, Haifeng Hu, Ming Ling

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Tags: Chemistry, Databases, Heterogeneous systems, molecular docking, nVidia, nVidia GeForce GTX 1060, nVidia GeForce RTX 2080 Ti, nVidia GeForce RTX 3090, OpenCL, Package

October 17, 2021 by hgpu

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, and Stefano Forli

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Tags: Algorithms, Chemistry, Macromolecule, molecular docking, OpenCL, Package, Physics

February 28, 2021 by hgpu

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar Hernandez, Jeremy C. Smith, Ada Sedova

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Tags: Biology, Biomolecules, Computational biology, CUDA, molecular docking, nVidia, nVidia DGX-2, nVidia GeForce RTX 2080 Ti, OpenCL, supercomputer, Tesla V100

July 12, 2020 by hgpu

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli

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Tags: AMD Radeon RX Vega 56, ATI, Biology, Chemistry, Energy-efficient computing, Heterogeneous systems, molecular docking, nVidia, OpenCL, Tesla V100

March 1, 2020 by hgpu

Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes

Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano

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Tags: Computer science, CUDA, Heterogeneous systems, HPC, molecular docking, MPI, nVidia, OpenACC, OpenMP, Tesla K80

January 27, 2019 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Mikhail A. Farkov

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Tags: Algorithms, Bioinformatics, Biology, CUDA, molecular docking, nVidia, nVidia GeForce GT 440, Tesla K20, Tesla M2090

September 24, 2014 by hgpu

High performance in silico virtual drug screening on many-core processors

Simon McIntosh-Smith, James Price, Richard B Sessions, Amaurys A Ibarra

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Tags: GPU, molecular docking, OpenCL, performance portability, virtual screening, Xeon Phi

April 11, 2014 by simonmcs

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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