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

GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs

Ahmed Shamsul Arefin, Carlos Riveros, Regina Berretta, Pablo Moscato

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Tags: Bioinformatics, Computer science, CUDA, Machine learning, Nearest neighbour, nVidia, Package, Pattern recognition, Tesla C2050

September 5, 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

Ensemble K-Means on Modern Many Core Hardware

Girish Ravunnikutty

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Tags: Bioinformatics, Clustering, Computer science, Data mining, Machine learning, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Pattern recognition, Thesis

July 28, 2012 by hgpu

Accelerating large-scale protein structure alignments with graphics processing units

Bin Pang, Nan Zhao, Michela Becchi, Dmitry Korkin, Chi-Ren Shyu

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Tags: Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla C2050

June 30, 2012 by hgpu

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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

June 21, 2012 by hgpu

Design of high-performance parallelized gene predictors in MATLAB

Sylvain Robert Rivard, Jean-Gabriel Mailloux, Rachid Beguenane, Hung Tien Bui,

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Tags: Algorithms, Bioinformatics, Biology, CUDA, FFT, Genetics, nVidia, nVidia GeForce GTX 560

April 13, 2012 by hgpu

An Algorithm for Fast Edit Distance Computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 275, Security, Sequence alignment

March 11, 2012 by hgpu

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Luis E. Ramirez-Chavez, Carlos A. Coello Coello, Eduardo Rodriguez-Tello

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Tags: Bioinformatics, Biology, CUDA, Differential equations, Differential evolution, nVidia, nVidia GeForce GTX 460, Optimization

January 23, 2012 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

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high performance computing on graphics processing units: hgpu.org

High-Throughput parallel blind Virtual Screening using BINDSURF

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

GPU accelerated QTL detection

GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs

High performance transcription factor-DNA docking with GPU computing

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

Ensemble K-Means on Modern Many Core Hardware

Accelerating large-scale protein structure alignments with graphics processing units

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Design of high-performance parallelized gene predictors in MATLAB

An Algorithm for Fast Edit Distance Computation on GPUs

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

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

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