high performance computing on graphics processing units: hgpu.org

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High performance transcription factor-DNA docking with GPU computing

Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo

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Tags: Algorithms, Benchmarking, Bioinformatics, Biology, CUDA, Genetics, GPU cluster, nVidia, Tesla M2070

August 20, 2012 by hgpu

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Search, Sequence alignment

August 17, 2012 by hgpu

Algorithms for the mapping of genome sequences in GPGPU

David Seide

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Sequence alignment, Thesis

August 5, 2012 by hgpu

Computational modeling of synthetic microbial biofilms

Timothy J Rudge, Paul J Steiner, Andrew Phillips, Jim Haseloff

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Tags: Biology, Biophysics, nVidia, nVidia Quadro FX 5800, OpenCL, Pharmaceuticals

July 28, 2012 by hgpu

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Bhardwaj Aditi, Bhardwaj Rohatash K., Shishir K. Gangwar

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Tags: Algorithms, Biology, CUDA, nVidia, RNA

July 26, 2012 by hgpu

Parallel-META: efficient metagenomic data analysis based on high-performance computation

Xiaoquan Su, Jian Xu, Kang Ning

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Tags: Biology, Computational biology, CUDA, nVidia, Package, Tesla C2070

July 22, 2012 by hgpu

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

Lin Ma, Roger D. Chamberlain

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Tags: Biology, BLAST, Computational biology, CUDA, Hashing, nVidia, nVidia GeForce GTX 480, Performance

July 15, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

Accelerating large-scale protein structure alignments with graphics processing units

Bin Pang, Nan Zhao, Michela Becchi, Dmitry Korkin, Chi-Ren Shyu

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Tags: Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla C2050

June 30, 2012 by hgpu

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

Matthias Leinweber, Lars Baumgartner, Marco Mernberger, Thomas Fober, Eyke Hullermeier, Gerhard Klebe, Bernd Freisleben

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Tags: Biology, Java, Macromolecule, nVidia, nVidia GeForce GTX 580, OpenCL, Tesla M2050

June 26, 2012 by hgpu

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

June 21, 2012 by hgpu

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis

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Tags: Algorithms, Biology, Computational biology, Databases, nVidia, nVidia GeForce GTX 280, OpenCL, Pattern Search, Sequence matching

June 20, 2012 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

Applications

High performance transcription factor-DNA docking with GPU computing

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Algorithms for the mapping of genome sequences in GPGPU

Computational modeling of synthetic microbial biofilms

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Parallel-META: efficient metagenomic data analysis based on high-performance computation

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

GPU-Optimized Molecular Dynamics Simulations

Accelerating large-scale protein structure alignments with graphics processing units

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

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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