high performance computing on graphics processing units: hgpu.org

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A Massively Parallel Architecture for Bioinformatics

Gerd Pfeiffer, Stefan Baumgart, Jan Schroder, Manfred Schimmler

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Tags: Algorithms, Bioinformatics, Biology, FPGA, MapReduce

November 27, 2010 by hgpu

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

November 27, 2010 by hgpu

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Cell processor, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

November 27, 2010 by hgpu

Many-core algorithms for statistical phylogenetics

Marc A. Suchard, Andrew Rambaut

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

November 23, 2010 by hgpu

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment

November 21, 2010 by hgpu

Ultra-fast FFT protein docking on graphics processors

David W. Ritchie, Vishwesh Venkatraman

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Tags: Bioinformatics, Biology, CUDA, FFT, nVidia, nVidia GeForce GTX 285

November 19, 2010 by hgpu

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Ali Khajeh-Saeed, Stephen Poole, J. Blair Perot

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GT, nVidia GeForce 9800 GTX, nVidia GeForce GTX 295, Sequence matching, Smith-Waterman algorithm

November 18, 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

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

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Tags: Bioinformatics, Biomolecular assemblies, Chemistry, CUDA, Dynamic force spectroscopy, Langevin dynamics, Molecular dynamics, nVidia, nVidia GeForce GTX 295

November 9, 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

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

A Massively Parallel Architecture for Bioinformatics

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Many-core algorithms for statistical phylogenetics

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Ultra-fast FFT protein docking on graphics processors

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

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

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

A molecular docking system using CUDA

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

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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