high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Chemistry

Simulating Lattice Spin Models on Graphics Processing Units

Tal Levy, Guy Cohen, Eran Rabani

Tags: Chemistry, CUDA, Monte Carlo simulation, nVidia, Physics

January 13, 2011 by hgpu

Interactive Volume Rendering of Functional Representations in Quantum Chemistry

Yun Jang and Ugo Varetto

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Tags: Cg, Chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 260, Rendering

January 11, 2011 by hgpu

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

N. Sanna, I. Baccarelli, G. Morelli

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

January 11, 2011 by hgpu

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Muller-Wittig

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX

January 10, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

FPGA-based acceleration of CHARMM-potential minimization

Bharat Sukhwani, Martin C. Herbordt

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Tags: Chemistry, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

January 3, 2011 by hgpu

Accelerating S3D: A GPGPU Case Study

Kyle Spafford, Jeremy Meredith, Jeffrey Vetter, Jacqueline Chen, Ray Grout and Ramanan Sankaran

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Tags: Chemistry, Computational chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Tesla C1060

December 18, 2010 by hgpu

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

Mark Watson, Roberto Olivares-Amaya, Richard G. Edgar, Alan Aspuru-Guzik

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Tags: Chemistry, Computational chemistry, Molecular modeling, nVidia, Tesla C1060

December 17, 2010 by hgpu

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Nathan Schmid, Mathias Botschi, Wilfred F. Van Gunsteren

Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, nVidia Quadro FX 5800, Solvent effects

December 17, 2010 by hgpu

Molecular Dynamics on a Grand Scale

Matthew James Mawson Breeze

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Tags: ATI, ATI Radeon X1600, Chemistry, GLSL, Molecular dynamics, nVidia, nVidia GeForce 6200, nVidia GeForce 8800 GTS, OpenGL, Thesis

December 17, 2010 by hgpu

OpenMM: A Hardware-Independent Framework for Molecular Simulations

Peter Eastman, Vijay Pande

Source codes

Tags: Chemistry, Computational chemistry, Molecular modeling, Package

December 16, 2010 by hgpu

A massively multicore parallelization of the Kohn-Sham energy gradients

Philip Brown, Christopher J. Woods, Simon McIntosh-Smith, Frederick R. Manby

Tags: Chemistry, Computational chemistry, Molecular modeling

December 16, 2010 by hgpu

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Accelerating a Linear Programming Algorithm on AMD GPUs

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Towards Efficient and Practical GPU Multitasking in the Era of LLM

Bandicoot: C++ library for GPU accelerated linear algebra

Bandicoot: A Templated C++ Library for GPU Linear Algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

The Fused Kernel Library: A C++ API to Develop Highly-Efficient GPU Libraries

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

Block: Balancing Load in LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

SIGMo: High-Throughput Batched Subgraph Isomorphism on GPUs for Molecular Matching

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

DGEMM without FP64 Arithmetic – using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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high performance computing on graphics processing units: hgpu.org

Applications

Simulating Lattice Spin Models on Graphics Processing Units

Interactive Volume Rendering of Functional Representations in Quantum Chemistry

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

FPGA-based acceleration of CHARMM-potential minimization

Accelerating S3D: A GPGPU Case Study

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Molecular Dynamics on a Grand Scale

OpenMM: A Hardware-Independent Framework for Molecular Simulations

A massively multicore parallelization of the Kohn-Sham energy gradients

Recent source codes

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Bandicoot: C++ library for GPU accelerated linear algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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