high performance computing on graphics processing units: hgpu.org

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Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 2011 by hgpu

GPU acceleration for statistical gene classification

Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia

May 5, 2011 by hgpu

Accelerating scientific applications using GPU’s

M. Taher

Tags: Bioinformatics, Biology, Computer science, CUDA, FFT, nVidia, Security, Sequence alignment

May 3, 2011 by hgpu

Accelerating DNA analysis applications on GPU clusters

A. Tumeo, O. Villa

Tags: Bioinformatics, Biology, GPU cluster, MPI, nVidia, Tesla C1060

April 28, 2011 by hgpu

Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Umit Catalyurek, Joel Saltz, Metin Gurcan

Tags: Algorithms, Bioinformatics, Image processing, Medicine

April 26, 2011 by hgpu

Parallel Approaches for SWAMP Sequence Alignment

Shannon Steinfadt, Kevin Schaffer

Tags: Bioinformatics, Biology, Cell processor, FPGA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 19, 2011 by hgpu

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig

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Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, nVidia GeForce GTX 295, Package, Sequence alignment

April 18, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

Accelerating global sequence alignment using CUDA compatible multi-core GPU

T.R.P. Siriwardena, D.N. Ranasinghe

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

April 10, 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

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high performance computing on graphics processing units: hgpu.org

Fast network centrality analysis using GPUs

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

GPU Based Parallel Computing on Blast Program

GPU acceleration for statistical gene classification

Accelerating scientific applications using GPU’s

Accelerating DNA analysis applications on GPU clusters

Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

Parallel Approaches for SWAMP Sequence Alignment

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Accelerating global sequence alignment using CUDA compatible multi-core GPU

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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