high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Parallelizing Peptide-Spectrum scoring using modern graphics processing units

Jian Zhang, I. McQuillan, FangXiang Wu

Tags: Biology, CUDA, Macromolecule, nVidia, Spectrometry

June 14, 2011 by hgpu

Cellular Level Agent Based Modelling on the Graphics Processing Unit

Paul Richmond, Simon Coakley, Daniela Romano

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Tags: Biology, Cellular modelling, CUDA, nVidia, Real-time graphics, Visualization

June 14, 2011 by hgpu

Single molecule detection of tuberculosis nucleic acid using dark field Tethered Particle Motion

Sanneke Brinkers, Heidelinde R.C. Dietrich, Sjoerd Stallinga, Jurriaan J. Mes, Ian T. Young, Bernd Rieger

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Tags: Algorithms, Biology, Biophysics, RNA

June 9, 2011 by hgpu

cuGWAM: Genome-wide association multifactor dimensionality reduction using CUDA-enabled high-performance graphics processing unit

Min-Seok Kwon, Kyunga Kim, Sungyoung Lee, Taesung Park

Source codes

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, Package

June 9, 2011 by hgpu

Parallelism of Clonal Selection for PSP on CUDA

Hongbing Zhu, Heng Xiao, JinGuang Gu

Tags: Biology, CUDA, Macromolecule, nVidia

June 9, 2011 by hgpu

Parallel accelerators for GlimmerHMM bioinformatics algorithm

Nafsika Chrysanthou, Grigorios Chrysos, Euripides Sotiriades, Ioannis Papaefstathiou

Tags: Algorithms, Bioinformatics, Biology, FPGA, Genetics

June 8, 2011 by hgpu

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

Satish Chikkagoudar, Kai Wang, Mingyao Li

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Tags: Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 1800, Package, Tesla C1060

June 7, 2011 by hgpu

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

M.N. Osman, R. Abdullah, N. AbdulRashid

Tags: Biology, Macromolecule, Molecular simulation, Pharmaceuticals

June 2, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 2011 by hgpu

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

K. Dohi, K. Benkridt, C. Ling, T. Hamada, Y. Shibata

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

May 31, 2011 by hgpu

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Alhadi Bustamam, Kevin Burrage, Nicholas A. Hamilton

Tags: Bioinformatics, Biology, CUDA, MPI, nVidia, Sparse matrix

May 30, 2011 by hgpu

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

Mohammad A. Bhuiyan, Vivek K. Pallipuram, Melissa C. Smith

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Tesla C870

May 28, 2011 by hgpu

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Parallelizing Peptide-Spectrum scoring using modern graphics processing units

Cellular Level Agent Based Modelling on the Graphics Processing Unit

Single molecule detection of tuberculosis nucleic acid using dark field Tethered Particle Motion

cuGWAM: Genome-wide association multifactor dimensionality reduction using CUDA-enabled high-performance graphics processing unit

Parallelism of Clonal Selection for PSP on CUDA

Parallel accelerators for GlimmerHMM bioinformatics algorithm

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

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