high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

William McDoniel, Markus Hohnerbach, Rodrigo Canales, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computer science, Intel Xeon Phi, Molecular dynamics, Performance

February 18, 2017 by hgpu

Deep Learning for Computational Chemistry

Garrett B. Goh, Nathan O. Hodas, Abhinav Vishnu

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Tags: Algorithms, Chemistry, Computational chemistry, Computer science, Deep learning, Machine learning, Neural networks, Review

January 19, 2017 by hgpu

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL, Performance, Physics

January 10, 2017 by hgpu

Molecular Activity Prediction using Deep Learning Software Library

Yoshiki Kato, Shinji Hamada, Hitoshi Goto

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Tags: Bioinformatics, Chemistry, Computer science, CUDA, Deep learning, nVidia, Package, Python, Tesla K20

November 5, 2016 by hgpu

Efficient and portable acceleration of quantum chemical many-body methods in mixed floating point precision using OpenACC compiler directives

Janus Juul Eriksen

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Tags: Chemical Physics, Chemistry, Mixed precision, nVidia, OpenACC, Physics, Tesla K40

September 27, 2016 by hgpu

Implementation and Performance Analysis of Many-body Quantum Chemical Methods on the Intel Xeon Phi Coprocessor and NVIDIA GPU Accelerator

Bobo Shi

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Intel Xeon Phi, nVidia, OpenMP, Tesla K40, Thesis

September 5, 2016 by hgpu

An investigation of GPU-based stiff chemical kinetics integration methods

Nicholas J. Curtis, Kyle E. Niemeyer, Chih-Jen Sung

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Tags: Algorithms, Chemistry, Computational Physics, CUDA, nVidia, Physics, Tesla C2075

July 16, 2016 by hgpu

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

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Tags: Algorithms, Chemistry, CUDA, Heterogeneous systems, Intel Xeon Phi, Medicine, Molecular dynamics, nVidia, nVidia GeForce GTX 980, OpenMP, Package

July 16, 2016 by hgpu

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Markus Hohnerbach, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computational chemistry, Computer science, CUDA, Intel Xeon Phi, Materials Science, Molecular dynamics, MPI, nVidia, Package, performance portability, Tesla K20, Tesla K40

July 13, 2016 by hgpu

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman

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Tags: Biochemistry, Biomolecules, Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenCL, OpenMP, Thesis

March 1, 2016 by hgpu

Scalable Metropolis Monte Carlo for simulation of hard shapes

Joshua A. Anderson, M. Eric Irrgang, Sharon C. Glotzer

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Tags: Benchmarking, Chemistry, Condensed matter, CUDA, Monte Carlo simulation, nVidia, Physics, Soft Condensed Matter, Tesla K20

September 17, 2015 by hgpu

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Mark James Abraham, Teemu Murtola, Roland Schulz, Szilard Pall, Jeremy C. Smith, Berk Hess, Erik Lindahl

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Tags: Algorithms, Biomolecules, Chemistry, CUDA, Heterogeneous systems, Molecular simulation, nVidia, nVidia GeForce GTX 980, OpenCL, Package, Tesla K40

July 20, 2015 by hgpu

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

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

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

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

Deep Learning for Computational Chemistry

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Molecular Activity Prediction using Deep Learning Software Library

Efficient and portable acceleration of quantum chemical many-body methods in mixed floating point precision using OpenACC compiler directives

Implementation and Performance Analysis of Many-body Quantum Chemical Methods on the Intel Xeon Phi Coprocessor and NVIDIA GPU Accelerator

An investigation of GPU-based stiff chemical kinetics integration methods

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

Scalable Metropolis Monte Carlo for simulation of hard shapes

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Recent source codes

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

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

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