high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Ashwin M. Aji, Liqing Zhang, Wu C. Feng

Tags: Bioinformatics, Biology, Next-Generation sequencing, nVidia

March 9, 2011 by hgpu

Application-guided tool development for architecturally diverse computation

Roger D. Chamberlain, Jeremy Buhler, Mark A. Franklin, James H. Buckley

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Tags: Algorithms, Astrophysics, Biology, Computer science, CUDA, Finance, FPGA, Heterogeneous systems, Monte Carlo simulation, nVidia, nVidia GeForce GTX 260, Search, Security

March 7, 2011 by hgpu

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Zhihui Du, Zhaoming Yin, David A. Bader

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

March 7, 2011 by hgpu

Efficient parallel algorithms for maximum-density segment problem

Xue Wang, Fasheng Qiu, S.K. Prasad, Guantao Chen

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

March 7, 2011 by hgpu

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

Cory W. Quammen, Alvin C. Richardson, Julian Haase, Benjamin D. Harrison, Russell M. Taylor, Kerry S. Bloom

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Tags: Algorithms, Biology, CUDA, Image generation, Microscopy, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package

March 2, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

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

February 27, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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

February 27, 2011 by hgpu

HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie

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Tags: Bioinformatics, Biology, CUDA, FFT, Molecular simulation, nVidia, Tesla C1060

February 25, 2011 by hgpu

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Yaohang Li, Douglas Wardell, Vincent Freeh

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Tags: Algorithms, Biology, Molecular dynamics

February 24, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

Accelerating the Stochastic Simulation Algorithm

David Jenkins, Gregory D. Peterson

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Tags: Biology, CUDA, Monte Carlo simulation, MPI, nVidia, Stochastic simulation, Tesla C870

February 21, 2011 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

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Application-guided tool development for architecturally diverse computation

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Efficient parallel algorithms for maximum-density segment problem

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

HexServer: an FFT-based protein docking server powered by graphics processors

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Probing biomolecular machines with graphics processors

Accelerating the Stochastic Simulation Algorithm

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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