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Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Amadou Chaibou, Oumarou Sie

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 670, OpenMP, Sequence alignment, Smith-Waterman algorithm

June 22, 2015 by hgpu

Implementation of K-shortest Path Algorithm in GPU Using CUDA

Avadhesh Pratap Singh, Dhirendra Pratap Singh

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Sequence alignment, Tesla C2075

June 7, 2015 by hgpu

Improving CUDA DNA Analysis Software with Genetic Programming

William B. Langdon, Brian Yee Hong Lam, Justyna Petke, Mark Harman

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Tags: Algorithms, Artificial intelligence, Bioinformatics, Computer science, CUDA, Genetic programming, nVidia, Package, Tesla K20, Tesla K40

May 12, 2015 by hgpu

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 295, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

April 7, 2015 by hgpu

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla K20

March 28, 2015 by hgpu

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

Johannes Koster

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Tags: Algorithms, Bayesian, Bioinformatics, Biology, Filtering, Next-Generation sequencing, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Thesis

March 23, 2015 by hgpu

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Sequence alignment, Smith-Waterman algorithm

February 27, 2015 by azhar ali

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Factorization, GPU cluster, MPI, Nonnegative matrix factorization, nVidia, Package, Tesla C1060

February 19, 2015 by hgpu

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Johannes Koster, Sven Rahmann

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Tags: Algorithms, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 780, OpenCL

October 20, 2014 by hgpu

Mapping dynamic programming algorithms on graphics processing units

Muhammad Kashif Hanif

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, nVidia GeForce GTX 560 Ti, Thesis

October 11, 2014 by hgpu

Accelerating Protein Coordinate Conversion using GPUs

Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla C2075

October 10, 2014 by hgpu

A massively parallel algorithm for constructing the BWT of large string sets

Jacopo Pantaleoni

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, Tesla K40

October 4, 2014 by hgpu

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

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high performance computing on graphics processing units: hgpu.org

Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Implementation of K-shortest Path Algorithm in GPU Using CUDA

Improving CUDA DNA Analysis Software with Genetic Programming

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

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

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Mapping dynamic programming algorithms on graphics processing units

Accelerating Protein Coordinate Conversion using GPUs

A massively parallel algorithm for constructing the BWT of large string sets

Recent source codes

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Ginkgo: high-performance linear algebra library for manycore systems

AlphaFold2

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