high performance computing on graphics processing units: hgpu.org

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High-Throughput parallel blind Virtual Screening using BINDSURF

Irene Sanchez-Linares, Horacio Perez-Sanchez, Jose M Cecilia, Jose M Garcia

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Tesla C2050

September 15, 2012 by hgpu

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

Fahian Ahmed, Saddam Quirem, Gak Min, Byeong Kil Lee

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Tesla C1060

September 12, 2012 by hgpu

GPU accelerated QTL detection

G. Chapuis, O. Filangi, J.M. Elsen, D. Lavenier, P. Le Roy

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Tesla C2050

September 11, 2012 by hgpu

CUDA-Accelerated Data-Mining for Putative Heteromeric Transcription Factors and Target Genes Using Microarray Gene Expression Profiles

Edward A. Salinas, Amitava Karmaker

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Tags: Algorithms, Biology, Computer science, CUDA, Data mining, nVidia, nVidia GeForce GTX 590

August 31, 2012 by hgpu

High performance transcription factor-DNA docking with GPU computing

Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo

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Tags: Algorithms, Benchmarking, Bioinformatics, Biology, CUDA, Genetics, GPU cluster, nVidia, Tesla M2070

August 20, 2012 by hgpu

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Search, Sequence alignment

August 17, 2012 by hgpu

Algorithms for the mapping of genome sequences in GPGPU

David Seide

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Sequence alignment, Thesis

August 5, 2012 by hgpu

Computational modeling of synthetic microbial biofilms

Timothy J Rudge, Paul J Steiner, Andrew Phillips, Jim Haseloff

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Tags: Biology, Biophysics, nVidia, nVidia Quadro FX 5800, OpenCL, Pharmaceuticals

July 28, 2012 by hgpu

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Bhardwaj Aditi, Bhardwaj Rohatash K., Shishir K. Gangwar

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Tags: Algorithms, Biology, CUDA, nVidia, RNA

July 26, 2012 by hgpu

Parallel-META: efficient metagenomic data analysis based on high-performance computation

Xiaoquan Su, Jian Xu, Kang Ning

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Tags: Biology, Computational biology, CUDA, nVidia, Package, Tesla C2070

July 22, 2012 by hgpu

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

Lin Ma, Roger D. Chamberlain

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Tags: Biology, BLAST, Computational biology, CUDA, Hashing, nVidia, nVidia GeForce GTX 480, Performance

July 15, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

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

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

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high performance computing on graphics processing units: hgpu.org

Applications

High-Throughput parallel blind Virtual Screening using BINDSURF

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

GPU accelerated QTL detection

CUDA-Accelerated Data-Mining for Putative Heteromeric Transcription Factors and Target Genes Using Microarray Gene Expression Profiles

High performance transcription factor-DNA docking with GPU computing

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Algorithms for the mapping of genome sequences in GPGPU

Computational modeling of synthetic microbial biofilms

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Parallel-META: efficient metagenomic data analysis based on high-performance computation

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

GPU-Optimized Molecular Dynamics Simulations

Recent source codes

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

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

SUperman: Highly Efficient Permanent Computation Library

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

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