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Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Particle swarm optimization, Sequence alignment, Tesla C1060

July 24, 2015 by hgpu

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla K20

June 30, 2015 by hgpu

Concurrent Task Execution on the Intel Xeon Phi

Yucheng Zhu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Intel Xeon Phi, nVidia, OpenMP, Sequence alignment, Smith-Waterman algorithm, Tesla K20, Thesis

June 22, 2015 by hgpu

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

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

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

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah Wheelan, Steven L. Salzberg, Alex Szalay

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

August 10, 2014 by hgpu

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

Rahul Shirude, Valmik B. Nikam, B.B. Meshram

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX Titan, RNA, Sequence alignment, String matching, Tesla K20

July 26, 2014 by hgpu

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Kedhar M, DR. M. Rajasekhara Babu, Mayank G, Abhinivesh M

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Tags: Bioinformatics, Biology, CUDA, nVidia, Programming techniques, RNA, Sequence alignment, Tesla C2070

July 12, 2014 by hgpu

Fast Sequence Alignment Method Using CUDA-enabled GPU

Yeim-Kuan Chang, De-Yu Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 19, 2014 by hgpu

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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

See all packages

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high performance computing on graphics processing units: hgpu.org

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Concurrent Task Execution on the Intel Xeon Phi

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

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

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Fast Sequence Alignment Method Using CUDA-enabled GPU

Recent source codes

E2C-Sim: a simulator and workload generator for Edge-to-Cloud environments

Kernel Tuner

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

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