high performance computing on graphics processing units: hgpu.org

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Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

Xiaokang Zhang, Xing Zhang, Z. Hong Zhou

Tags: Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Hemant D. Tagare, Andrew Barthel, Fred J. Sigworth

Tags: Algorithms, Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

Fast free-form deformation using graphics processing units

Marc Modat, Gerard R. Ridgway, Zeike A. Taylor, Manja Lehmann, Josephine Barnes, David J. Hawkes, Nick C. Fox, Sebastien Ourselin

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX, Package

November 17, 2010 by hgpu

permGPU: Using graphics processing units in RNA microarray association studies

Ivo Shterev, Sin H. Jung, Stephen George, Kouros Owzar

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Package, RNA

November 17, 2010 by hgpu

SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk of genetic epistasis in bipolar disorder

Xiaohan Hu, Qiang Liu, Zhao Zhang, Zhiqiang Li, Shilin Wang, Lin He, Yongyong Shi

Tags: Bioinformatics, Biology, Genetics

November 17, 2010 by hgpu

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

Daniel Castano-Diez, Margot Scheffer, Ashraf Al-Amoudi, Achilleas S. Frangakis

Tags: Biology, Cryo-electron tomography, Image alignment, Image processing

November 17, 2010 by hgpu

Fast Bio-Inspired Computation using a GPU-based Systemic Computer

Marjan Rouhipour, Peter J. Bentley, Hooman Shayani

Tags: Biology

November 16, 2010 by hgpu

A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors

Jayram Moorkanikara M. Nageswaran, Nikil Dutt, Jeffrey L. Krichmar, Alex Nicolau, Alexander V. Veidenbaum

Tags: Biology, Computer science, CUDA, Neural networks, nVidia, nVidia GeForce GTX 280, STDP

November 13, 2010 by hgpu

Fast recursive filters for simulating nonlinear dynamic systems

J. H. van Hateren

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Tags: Algorithms, Biology, Neurons and Cognition

November 13, 2010 by hgpu

A molecular docking system using CUDA

Youngtae Roh, Jun Lee, Sungjun Park, Jee I. Kim

Tags: Bioinformatics, Biology, Biophysics, Chemistry, Molecular dynamics

November 9, 2010 by hgpu

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Juliane Liepe, Chris Barnes, Erika Cule, Kamil Erguler, Paul Kirk, Tina Toni, Michael P. H. Stumpf

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Python

November 9, 2010 by hgpu

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

John L. Van Hemert, Julie A. Dickerson

Tags: Bioinformatics, Biology, CUDA, Medicine, Metabolomics, Monte Carlo simulation, Next-Generation sequencing, nVidia

November 8, 2010 by hgpu

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

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

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Fast free-form deformation using graphics processing units

permGPU: Using graphics processing units in RNA microarray association studies

SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk of genetic epistasis in bipolar disorder

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

Fast Bio-Inspired Computation using a GPU-based Systemic Computer

A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors

Fast recursive filters for simulating nonlinear dynamic systems

A molecular docking system using CUDA

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

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