high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

D. Akgün, Ü. Sakoğlu, M. Mete, J. Esquivel, B. Adinoff

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Tags: Biology, Magnetic resonance imaging, Medicine, MRI, Neuroscience, nVidia, nVidia GeForce GTX 660, OpenCL

June 9, 2014 by hgpu

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri

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Tags: Bioinformatics, Biology, Computational biology, CUDA, Differential equations, nVidia, ODEs, Ordinary differential equations, Tesla K20

May 30, 2014 by hgpu

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

Roberto Pinto Souto, Carla Osthoff, Douglas Augusto, Oswaldo Trelles, Ana Tereza Ribeiro de Vasconcelos

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sorting, Tesla K20

May 29, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

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

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

Ana M. Mihut, Graham Morgan, Marcus Kaiser

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Tags: Biology, CUDA, GLSL, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia Quadro 600, OpenGL, Programming techniques, Tesla K20

May 24, 2014 by hgpu

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

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

Gines David Guerrero Hernandez, Baldomero Imbernon, Horacio Perez-Sanchez, Francisco Sanz, Jose M. Garcia, Jose M. Cecilia

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Tags: Bioinformatics, Biology, CUDA, Medicine, nVidia, nVidia GeForce 7300 GT, nVidia GeForce GTX 465, nVidia GeForce GTX 480, nVidia GeForce GTX 590, Tesla C2070, Tesla K20

May 21, 2014 by hgpu

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

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Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Carlos Riveros, Manuel Ujaldon, Moscato Pablo

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Tesla C1060, Tesla C2050

May 12, 2014 by hgpu

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

You Li, Hao Chi, Leihao Xia, Xiaowen Chu

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, nVidia GeForce GTX 580, Spectrometry

May 12, 2014 by hgpu

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Shuang Wang, Jihoon Kim, Xiaoqian Jiang, Stefan F Brunner, Lucila Ohno-Machado

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Smith-Waterman algorithm, Tesla M2090

May 10, 2014 by hgpu

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Robert T. McGibbon, Bharath Ramsundar, Mohammad M. Sultan, Gert Kiss, Vijay S. Pande

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Tags: Algorithms, Biology, Biophysics, CUDA, Distributed computing, Machine learning, Molecular dynamics, nVidia, nVidia GeForce GTX Titan

May 9, 2014 by hgpu

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

GSParLib

GSParLib: A multi-level programming interface unifying OpenCL and CUDA for expressing stream and data parallelism

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

A User’s Guide to KSig: GPU-Accelerated Computation of the Signature Kernel

IterApp: Iterative Application Skeleton

Boosting Performance of Iterative Applications on GPUs: Kernel Batching with CUDA Graphs

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

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

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Recent source codes

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

GSParLib

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

IterApp: Iterative Application Skeleton

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

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