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Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

A Memory Model for Scientific Algorithms on Graphics Processors

Naga K. Govindaraju, Scott Larsen, Jim Gray, Dinesh Manocha

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Tags: Algorithms, Computer science, FFT, Memory model, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, nVidia GeForce 7900 GTX, Sorting

October 30, 2010 by hgpu

Accelerating Density Functional Calculations with Graphics Processing Unit

Koji Yasuda

Tags: Chemistry, Computational chemistry, Molecular modeling

October 30, 2010 by hgpu

A hardware redundancy and recovery mechanism for reliable scientific computation on graphics processors

Jeremy W. Sheaffer, David P. Luebke, Kevin Skadron

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Tags: Computer science, Error recovery

October 30, 2010 by hgpu

Performance enhancement of MAGIC FDTD-PIC plasma-wave simulations using GPU processing

Andrew J. Woods, Lars D. Ludeking

Tags: Physics, Plasma physics

October 30, 2010 by hgpu

Optimizing data intensive GPGPU computations for DNA sequence alignment

Cole Trapnell, Michael C. Schatz

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

October 30, 2010 by hgpu

Accelerating molecular modeling applications with graphics processors

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten

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Tags: Chemistry, Computational chemistry, CUDA, Electrostatic potential, Molecular dynamics, Molecular modeling, Multilevel summation, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

Mars: a MapReduce framework on graphics processors

Bingsheng He, Wenbin Fang, Qiong Luo, Naga K. Govindaraju, Tuyong Wang

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Tags: Computer science, CUDA, Data parallelism, MapReduce, nVidia, nVidia GeForce 8800 GTX, Package, Programming techniques, Web Analysis

October 30, 2010 by hgpu

Exploiting graphics processing units for computational biology and bioinformatics

Joshua L. Payne, Nicholas A. Sinnott-Armstrong, Jason H. Moore

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Tags: All-Pairs Distance, Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 9600 M, Package

October 30, 2010 by hgpu

High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA

Robert G. Belleman, Jeroen Bedorf, Simon F. Portegies Zwart

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Tags: Astrophysics, CUDA, Gravitation, N-body simulation, nVidia, nVidia GeForce 8800 GTX, Stellar dynamics

October 30, 2010 by hgpu

A performance study of general-purpose applications on graphics processors using CUDA

S. Che, M. Boyer, J. Meng, D. Tarjan, J. Sheaffer, K. Skadron

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Tags: Computer science, CUDA, nVidia, nVidia GeForce GTX 260, OpenMP, Package, Performance

October 30, 2010 by hgpu

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

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Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

Code examples for paper on SYCL backend of Kokkos - IWOCL 2024

Experiences with implementing Kokkos’ SYCL backend

ROCm's implementation of Gromacs

GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

GPU plugin for PySCF

Python-Based Quantum Chemistry Calculations with GPU Acceleration

QArray

QArray: a GPU-accelerated constant capacitance model simulator for large quantum dot arrays

Celerity: High-level C++ for Accelerator Clusters

Balancing Tracking Granularity and Parallelism in Many-Task Systems: The Horizons Approach

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

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