high performance computing on graphics processing units: hgpu.org

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The accelerating implementation of BLAST with stream processor

Gang Wei, Chao Ma, Songwen Pei, Baifeng Wu

Tags: ATI, ATI Radeon HD 4850, Bioinformatics, Biology, BLAST, Brook, Sequence alignment

June 15, 2011 by hgpu

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

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

The accelerating implementation of BLAST with stream processor

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

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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