high performance computing on graphics processing units: hgpu.org

Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida

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Tags: Bioinformatics, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, OpenCL, Physics

July 4, 2014 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, Graph theory, nVidia, Path problems, Tesla C2050, Thesis

July 3, 2014 by hgpu

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Chao Yu, Bo Yang

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Tags: ATI, ATI Radeon HD 7870, Biology, Computer science, OpenCL

July 1, 2014 by hgpu

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

Nagaveni V, G T Raju

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, Medicine, nVidia, String matching, Tesla C2070

June 28, 2014 by hgpu

An efficient parallel algorithm for accelerating computational protein design

Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng

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Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla K20

June 23, 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

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

Yilan Liu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 770

June 13, 2014 by hgpu

Vortex: Overcoming Memory Capacity Limitations in GPU-Accelerated Large-Scale Data Analytics

HexGen: Generative Inference of Large Language Model over Heterogeneous Environment

Demystifying Cost-Efficiency in LLM Serving over Heterogeneous GPUs

Ilargi: a GPU Compatible Factorized ML Model Training Framework

MPI-CorrBench 2.0.0

Modernization and Optimization of MPI Codes

VFLog: vertical + gpu + free join + datalog

Column-Oriented Datalog on the GPU

ViVid Project

Exploring data flow design and vectorization with oneAPI for streaming applications on CPU+GPU

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

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high performance computing on graphics processing units: hgpu.org

Applications

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

A Multi-GPU Compute Solution for Optimized Genomic Selection Analysis

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Analysis of Surface Folding Patterns of DICCCOLS Using the GPU-Optimized Geodesic Field Estimate

Molecular dynamics simulations through GPU video games technologies

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

An efficient parallel algorithm for accelerating computational protein design

Fast Sequence Alignment Method Using CUDA-enabled GPU

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

Recent source codes

cuSZp: Fast GPU error-bounded lossy compressor for floating-point data

Kokkos C++ Performance Portability Programming EcoSystem

Training-free Post-training Efficient Sub-quadratic Complexity Attention

Vortex: Overcoming Memory Capacity Limitations in GPU-Accelerated Large-Scale Data Analytics

HexGen: Generative Inference of Large Language Model over Heterogeneous Environment

Ilargi: a GPU Compatible Factorized ML Model Training Framework

MPI-CorrBench 2.0.0

VFLog: vertical + gpu + free join + datalog

ViVid Project

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

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