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Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

Heru Suhartanto, Arry Yanuar, Ari Wibisono

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Tags: Cluster computing, Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTS 250, nVidia GeForce GTX 465, nVidia GeForce GTX 470, nVidia Quadro FX 4000

October 17, 2012 by hgpu

Kinetics of liquid-solid phase transition in large nickel clusters

Alexander V. Yakubovich, Gennady Sushko, Stefan Schramm, Andrey V. Solov'yov

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Tags: ATI, ATI Radeon HD 5870, Computational Physics, Mesoscale and Nanoscale Physics, Molecular dynamics, OpenCL, Phase transition, Physics, Solidification

October 15, 2012 by hgpu

Towards accelerating Smoothed Particle Hydrodynamics simulations for free-surface flows on multi-GPU clusters

Daniel Valdez-Balderas, Jose M. Dominguez, Benedict D. Rogers, Alejandro J.C. Crespo

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Tags: Algorithms, Computational Physics, Condensed matter, CUDA, Fluid dynamics, GPU cluster, Instrumentation and Methods for Astrophysics, Molecular dynamics, MPI, nVidia, nVidia GeForce GTX 480, Physics, Sorting, Tesla M2050

October 4, 2012 by hgpu

Path Integral Approaches and Graphics Processing Unit Tools for Quantum Molecular Dynamics Simulations

Stephen Joel Constable

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, OpenCL, Thesis

August 30, 2012 by hgpu

Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors

Ashfaquzzaman Khan

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Tags: Chemistry, FPGA, Molecular dynamics, nVidia, Review, Thesis

July 17, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

High-precision molecular dynamics simulation of UO2-PuO2: Anion self-diffusion in UO2

S.I. Potashnikov, A.S. Boyarchenkov, K.A. Nekrasov, A.Ya. Kupryazhkin

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Tags: Condensed matter, CUDA, DirectCompute, HLSL, Materials Science, Molecular dynamics, nVidia, Package

June 21, 2012 by hgpu

Relativistic Hydrodynamics on Graphic Cards

Jochen Gerhard, Volker Lindenstruth, Marcus Bleicher

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Tags: Algorithms, ATI, ATI Radeon HD 5870, Cluster computing, High Energy Physics - Phenomenology, High Energy Physics - Theory, Molecular dynamics, OpenCL, Performance, Physics, QCD

June 6, 2012 by hgpu

GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions

Michael Kopp, Felix Hofling

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, nVidia, Package, Physics, Tesla C2050, Tesla S1070

May 30, 2012 by hgpu

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Gotz, Mark J. Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C. Walker

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, Tesla C1060, Tesla C2070, Tesla M2090

May 26, 2012 by hgpu

Random number generators for massively parallel simulations on GPU

Markus Manssen, Martin Weigel, Alexander K. Hartmann

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Tags: Algorithms, Computational Physics, CUDA, High Energy Physics - Lattice, Molecular dynamics, Monte Carlo simulation, nVidia, nVidia GeForce GTX 480, Physics, Pseudo-random number generators, Review, Statistical Mechanics

May 1, 2012 by hgpu

Reuse and Refactoring of GPU Kernels to Design Complex Applications

Santonu Sarkar, Sayantan Mitra, Ashok Srinivasan

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Tags: Computer science, CUDA, FFT, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Optimization, Software Engineering, Tesla S1050

February 24, 2012 by hgpu

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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high performance computing on graphics processing units: hgpu.org

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

Kinetics of liquid-solid phase transition in large nickel clusters

Towards accelerating Smoothed Particle Hydrodynamics simulations for free-surface flows on multi-GPU clusters

Path Integral Approaches and Graphics Processing Unit Tools for Quantum Molecular Dynamics Simulations

Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors

GPU-Optimized Molecular Dynamics Simulations

High-precision molecular dynamics simulation of UO2-PuO2: Anion self-diffusion in UO2

Relativistic Hydrodynamics on Graphic Cards

GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Random number generators for massively parallel simulations on GPU

Reuse and Refactoring of GPU Kernels to Design Complex Applications

Recent source codes

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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