high performance computing on graphics processing units: hgpu.org

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Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pratim Pande, Ananth Kalyanaraman

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

August 12, 2011 by hgpu

High-performance biocomputing for simulating the spread of contagion over large contact networks

Keith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng

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Tags: Biology, CUDA, GPU cluster, nVidia, Tesla S2050

August 12, 2011 by hgpu

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Cristian Dittamo, Davide Cangelos

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Tags: Algorithms, Biochemistry, Biology, nVidia, nVidia GeForce 8600 M GS, Stochastic simulation

August 12, 2011 by hgpu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande

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Tags: Biology, Cell processor, CUDA, FPGA, Molecular dynamics, nVidia, nVidia GeForce 7800 GTX, Performance, Review, Sequence alignment

August 7, 2011 by hgpu

Accelerated simulation of spiking neural networks using GPUs

Andreas K. Fidjeland, Murray P. Shanahan

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Tags: Biology, CUDA, Neural networks, nVidia, Tesla C1060

August 6, 2011 by hgpu

Unifying stream based and reconfigurable computing to design application accelerators

Bruno Francisco, Frederico Pratas, Leonel Sousa

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Tags: Bioinformatics, Biology, Computer science, Data parallelism, FPGA, nVidia, nVidia GeForce GTX 285

August 2, 2011 by hgpu

Near-real-time simulations of biolelectric activity in small mammalian hearts using graphical processing units

E.J. Vigmond, P.M. Boyle, L.J. Leon, G. Plank

Tags: Biology, Heart, Medicine, ODEs, Ordinary differential equations, Partial differential equations, PDEs

July 27, 2011 by hgpu

High-Throughput Sequence Translation Using CUDA

Sun Wei-dong, Ma Zong-min

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

July 25, 2011 by hgpu

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

Pei Liu, A. Hemani

Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment, Smith-Waterman algorithm

July 25, 2011 by hgpu

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Shucai Xiao, A.M. Aji, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, Cell processor, CUDA, Data parallelism, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

July 23, 2011 by hgpu

Parallelizing the Cellular Potts Model on graphics processing units

Jose J. Tapia, Roshan M. D'Souza

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Tags: Biology, Computational biology, CUDA, nVidia, Tesla C1060

July 22, 2011 by hgpu

Accelerating Partitional Algorithms for Flow Cytometry on GPUs

Jeremy Espenshade, Andrew Pangborn, Gregor von Laszewski, Douglas Roberts, James S. Cavenaugh

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Tags: Algorithms, Biology, Clustering, CUDA, nVidia, Tesla C870

July 18, 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

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high performance computing on graphics processing units: hgpu.org

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

High-performance biocomputing for simulating the spread of contagion over large contact networks

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Hardware accelerators for biocomputing: A survey

Accelerated simulation of spiking neural networks using GPUs

Unifying stream based and reconfigurable computing to design application accelerators

Near-real-time simulations of biolelectric activity in small mammalian hearts using graphical processing units

High-Throughput Sequence Translation Using CUDA

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Parallelizing the Cellular Potts Model on graphics processing units

Accelerating Partitional Algorithms for Flow Cytometry on GPUs

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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