high performance computing on graphics processing units: hgpu.org

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Accelerating Genomics Research with OpenCL and FPGAs

Chris Rauer, George S. Powley, Mir Ahsan, Nicholas Finamore

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Tags: Algorithms, Biology, Computer science, FPGA, Genomics, OpenCL

October 15, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider

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Tags: Biology, Computer science, Java, Next-Generation sequencing, nVidia, OpenCL, Package, R, Tesla K20

August 26, 2017 by hgpu

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Zelimkhan Gerikhanov

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Tags: AMD Radeon HD 8970 M, ATI, Biology, Biomechanics, FEM, Finite element method, Medicine, MRI, OpenCL, Thesis

August 17, 2017 by hgpu

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Adrian Przybylski, Bjorn Thiel, Jan Keller-Findeisen, Bernd Stock, Mark Bates

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Tags: Biology, Computer science, CUDA, Microscopy, nVidia, nVidia GeForce GTX 1080, Package, Python

August 17, 2017 by hgpu

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

Jesus Perez Serrano, Edans Flavius De Oliveira Sandes, Alba Cristina Magalhaes Alves de Melo, Manuel Ujaldon

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Tags: Bioinformatics, Biology, CUDA, Energy-efficient computing, nVidia, nVidia GeForce GTX 980, Performance, Smith-Waterman algorithm

June 10, 2017 by hgpu

DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing

Weihua Guo, You Xu, Xueyang Feng

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Tags: Biology, Computer science, Deep learning, Medicine, nVidia, nVidia GeForce GTX 1080, Package, Python, TensorFlow

May 11, 2017 by hgpu

Exploration of cyber-physical systems for GPGPU computer vision-based detection of biological viruses

Pascal Libuschewski

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Tags: Biology, Computer vision, Design space exploration, Microscopy, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 560 Ti, nVidia Quadro NVS 3100 M, OpenCL, Thesis, Visualization

April 20, 2017 by hgpu

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

William R. Saunders, James Grant, Eike H. Muller

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Tags: Algorithms, Biology, Chemistry, Code generation, Computer science, CUDA, Differential equations, DSL, Molecular dynamics, nVidia, Package, Partial differential equations, PDEs, Physics, Python, Tesla K20

April 15, 2017 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, Computer science, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm

February 26, 2017 by hgpu

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Felipe Sulser Larraz

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, Databases, Filtering, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm, Thesis

February 2, 2017 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

Accelerating Genomics Research with OpenCL and FPGAs

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing

Exploration of cyber-physical systems for GPGPU computer vision-based detection of biological viruses

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

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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