high performance computing on graphics processing units: hgpu.org

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LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

Christian Robert Trott

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Tags: Biology, Computational Physics, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 470, Package, Physics, Polymer Systems, Tesla C1060, Thesis

February 13, 2012 by hgpu

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Luis E. Ramirez-Chavez, Carlos A. Coello Coello, Eduardo Rodriguez-Tello

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Tags: Bioinformatics, Biology, CUDA, Differential equations, Differential evolution, nVidia, nVidia GeForce GTX 460, Optimization

January 23, 2012 by hgpu

Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Package, Sequence alignment

January 19, 2012 by hgpu

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

Nicolas Bonnel, Pierre-Francois Marteau

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Tags: Algorithms, Benchmarking, Biology, Databases, nVidia, OpenCL, Tesla M2050

January 18, 2012 by hgpu

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Hybrid computing, nVidia, nVidia GeForce GTX 580, RNA

January 15, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Algorithms, Biology, Computational biology, CUDA, Image processing, Machine learning, nVidia, Package, Tesla C2050

January 13, 2012 by hgpu

Implementation of Virtual Embryology using the Thrust library for CUDA

Anna Aichmayr Markus Dauschan

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Tags: Biology, CUDA, Neural networks, nVidia, Python

January 13, 2012 by hgpu

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Peng Jia, Liming Xuan, Lei Liu, Chaochun Wei

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Tags: Biology, Computational biology, CUDA, Genetics, nVidia, Package, Tesla C1060

January 11, 2012 by hgpu

Petaflop biofluidics simulations on a two million-core system

Massimo Bernaschi, Satoshi Matsuoka, Mauro Bisson, Massimiliano Fatica, Toshio Endo, Simone Melchionna

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Tags: Algorithms, Biology, CUDA, GPU cluster, Medicine, nVidia, Optimization, Tesla M2050

January 11, 2012 by hgpu

A Parallel Supercomputer Implementation of a Biological Inspired Neural Network and its use for Pattern Recognition

Vincent de Ladurantaye, Jean Lavoie, Jocelyn Bergeron, Maxime Parenteau, Huizhong Lu, Ramin Pichevar, Jean Rouat

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Tags: Biology, CUDA, MPI, Neural networks, nVidia, nVidia GeForce GTX 285, Pattern recognition

January 5, 2012 by hgpu

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Susumu Takekoshi, Naoya Nakamura, Yoshio Suzuki

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Tags: Biology, CUDA, Image reconstruction, Medicine, nVidia, nVidia GeForce GTX 470, Package, Tomography

December 30, 2011 by hgpu

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Clava: C/C++ Source-to-Source Tool based on Clang

Challenges and Opportunities in C/C++ Source-To-Source Compilation

gpuLik

Statistical Computing With Graphics Processing Units

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Accelerated Large-Scale Multiple Sequence Alignment

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

BarraCUDA – a fast short read sequence aligner using graphics processing units

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Implementation of Virtual Embryology using the Thrust library for CUDA

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Petaflop biofluidics simulations on a two million-core system

A Parallel Supercomputer Implementation of a Biological Inspired Neural Network and its use for Pattern Recognition

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Recent source codes

Clava: C/C++ Source-to-Source Tool based on Clang

gpuLik

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

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