high performance computing on graphics processing units: hgpu.org

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Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Matthias Vigelius, Aidan Lane, Bernd Meyer

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Rendering, Stochastic simulation

September 23, 2011 by hgpu

GPU Computation in Bioinspired Algorithms: A Review

M. G. Arenas, A. M. Mora, G. Romero and P. A. Castillo

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Tags: Algorithms, ATI, Bioinformatics, Biology, Computational biology, CUDA, nVidia, OpenCL, Overview, Review

September 8, 2011 by hgpu

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 2011 by hgpu

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain

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Tags: Algorithms, Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce GTX 280, RNA, Tesla C870

August 27, 2011 by hgpu

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

EpiGPU

Gibran Hemani, Athanasios Theocharidis, Wenhua Wei, Chris Haley

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Tags: ATI, Biology, Genetics, nVidia, OpenCL

August 21, 2011 by hgpu

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

Paolo Angelelli, Kim Nylund, Odd Helge Gilja, Helwig Hauser

Tags: Biology, Medicine, OpenCL, Ultrasound, Visualization

August 21, 2011 by hgpu

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

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Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 2011 by hgpu

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pratim Pande, Ananth Kalyanaraman

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment

August 12, 2011 by hgpu

High-performance biocomputing for simulating the spread of contagion over large contact networks

Keith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng

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Tags: Biology, CUDA, GPU cluster, nVidia, Tesla S2050

August 12, 2011 by hgpu

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Cristian Dittamo, Davide Cangelos

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Tags: Algorithms, Biochemistry, Biology, nVidia, nVidia GeForce 8600 M GS, Stochastic simulation

August 12, 2011 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_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

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Manycore high-performance computing in bioinformatics

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

GPU Computation in Bioinspired Algorithms: A Review

Two-Level Approach to Efficient Visualization of Protein Dynamics

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

EpiGPU

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

FPGA acceleration of rigid-molecule docking codes

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

High-performance biocomputing for simulating the spread of contagion over large contact networks

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Recent source codes

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

ROCm's implementation of Gromacs

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

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