high performance computing on graphics processing units: hgpu.org

hgpu.org » Bioinformatics

Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, FPGA, Package, Sequence alignment

January 19, 2012 by hgpu

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, Hybrid computing, nVidia, nVidia GeForce GTX 580, RNA

January 15, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Reza Farivar, Shivaram Venkataraman, Yanen Li, Ellick Chan, Abhishek Verma, Roy H. Campbell

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Filtering, GPU cluster, nVidia, Sequence alignment, Tesla S1070

December 26, 2011 by hgpu

Achieving High Throughput Sequencing with Graphics Processing Units

Su Chen, Chaochao Zhang, Feng Shen, Ling Bai, Hai Jiang, Damir Herman

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, Sequence alignment, Tesla C2050

December 10, 2011 by hgpu

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Shucai Xiao, Heshan Lin, Wu-chun Feng

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, BLAST, Databases, Heterogeneous systems, nVidia, Optimization, Tesla C1060, Tesla C2050

November 23, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Andres Rodriguez, Oswaldo Trelles, Manuel Ujaldon

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GX2

November 22, 2011 by hgpu

Parallel Approach for Longest Common Subsequence problem on GPU

Raik Issaoui, Amine Draief, Abdelfettah Belghith

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 430, OpenCL, Sequence matching

November 16, 2011 by hgpu

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Gustavo Encarnacao, Nuno Sebastiao, Nuno Roma

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Suffix trees

November 13, 2011 by hgpu

Molecular Docking on FPGA and GPU Platforms

I. Pechan, B. Feher

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260

November 13, 2011 by hgpu

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Mian Lu, Jiuxin Zhao, Qiong Luo, Bingqiang Wang, Shaohua Fu, Zhe Lin

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Compression, nVidia, Package, Sorting, Tesla M2050

November 12, 2011 by hgpu

MSCCL++: A GPU-driven communication stack for scalable AI applications

MSCCL++: Rethinking GPU Communication Abstractions for Cutting-edge AI Applications

Benchmark compute shader of Unity against InteropUnityCUDA

InteropUnityCUDA: A Tool for Interoperability Between Unity and CUDA

Data-efficient LLM Fine-tuning for Code Generation

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

DeepCompile: A Compiler-Driven Approach to Optimizing Distributed Deep Learning Training

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

GigaAPI for GPU Parallelization

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

* * *

high performance computing on graphics processing units: hgpu.org

Accelerated Large-Scale Multiple Sequence Alignment

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

BarraCUDA – a fast short read sequence aligner using graphics processing units

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Achieving High Throughput Sequencing with Graphics Processing Units

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Parallel Approach for Longest Common Subsequence problem on GPU

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Molecular Docking on FPGA and GPU Platforms

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Recent source codes

MSCCL++: A GPU-driven communication stack for scalable AI applications

Benchmark compute shader of Unity against InteropUnityCUDA

Data-efficient LLM Fine-tuning for Code Generation

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

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Most viewed papers (last 30 days)