high performance computing on graphics processing units: hgpu.org

Leonardo Bottolo, Marc Chadeau-Hyam, David I. Hastie, Tanja Zeller, Benoit Liquet, Paul Newcombe, Loic Yengo, Philipp S. Wild, Arne Schillert, Andreas Ziegler, Sune F. Nielsen, Adam S. Butterworth, Weang Kee Ho, Raphaele Castagne, Thomas Munzel, David Tregouet, Mario Falchi15, Francois Cambien, Borge G. Nordestgaard, Frederic Fumeron, Anne Tybjaerg-Hansen, Philippe Froguel, John Danesh, Enrico Petretto, Stefan Blankenberg, Laurence Tiret, Sylvia Richardson

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Tags: Algorithms, Bayesian, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C1060

August 16, 2013 by hgpu

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka Michailova, Andrew D. McCulloch, Michael Holst, J. Andrew McCammon

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Tags: Algorithms, Bioinformatics, Biology, Biomolecules, CUDA, KD-tree, Molecular surface, nVidia, nVidia GeForce GTX 680

August 9, 2013 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

high performance computing on graphics processing units: hgpu.org

Exploiting parallel features of modern computer architectures in bioinformatics

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Accelerating calculations of RNA secondary structure partition functions using GPUs

High-performance Dynamic Programming on FPGAs with OpenCL

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

Enabling the use of Heterogeneous Computing for Bioinformatics

Fast k-NNG construction with GPU-based quick multi-select

Expressed Sequence Tag Clustering using Commercial Gaming Hardware

GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

Recent source codes

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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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