high performance computing on graphics processing units: hgpu.org

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 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

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

SW#db: GPU-accelerated exact sequence similarity database search

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

G-SNPM – A GPU-based SNP mapping tool

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

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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