high performance computing on graphics processing units: hgpu.org

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

Nilay Khare, Alind Khare and Farhan Khan

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Tags: Algorithms, Bioinformatics, Biology, BLAST, CUDA, Hadoop, nVidia, nVidia Quadro 2000, nVidia Quadro 600, Tesla C2075

December 3, 2017 by hgpu

A Hybrid-parallel Architecture for Applications in Bioinformatics

Jan Christian Kassens

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, FPGA, nVidia, nVidia GeForce GTX 780 Ti, Thesis

December 3, 2017 by hgpu

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Ernst Joachim Houtgast, Vlad-Mihai Sima, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, FPGA, OpenCL, Smith-Waterman algorithm

November 26, 2017 by hgpu

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

Data-Parallel Flattening by Expansion

IA-SpGEMM: An Input-aware Auto-tuning Framework for Parallel Sparse Matrix-Matrix Multiplication

MGPUSim: Enabling Multi-GPU Performance Modeling and Optimization

TensorNetwork: A library for easy and efficient manipulation of tensor networks

TensorNetwork for Machine Learning

triSYCL: Generic system-wide modern C++ for heterogeneous platforms with SYCL from Khronos Group

SYCL Code Generation for Multigrid Methods

Dynamic Distribution Pruning for Efficient Network Architecture Search

Tinker-HP: High Performance Massively Parallel Evolution of Tinker

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel’s HPC Architectures: a Living Review [Article v1.0]

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high performance computing on graphics processing units: hgpu.org

Parallel scalable simulations of biological neural networks using TensorFlow: A beginner’s guide

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences

Interactive GPU active contours for segmenting inhomogeneous objects

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Molecular dynamics recipes for genome research

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

A Hybrid-parallel Architecture for Applications in Bioinformatics

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Accelerating Genomics Research with OpenCL and FPGAs

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

Recent source codes

Data-Parallel Flattening by Expansion

IA-SpGEMM: An Input-aware Auto-tuning Framework for Parallel Sparse Matrix-Matrix Multiplication

MGPUSim: Enabling Multi-GPU Performance Modeling and Optimization

TensorNetwork: A library for easy and efficient manipulation of tensor networks

triSYCL: Generic system-wide modern C++ for heterogeneous platforms with SYCL from Khronos Group

PSST: A Tutorial for Parallelised Scalable Simulations in TensorFlow

MUSE: Miami University Simulation Environment

Pressure Point Analysis framework

Dynamic Distribution Pruning for Efficient Network Architecture Search

Tinker-HP: High Performance Massively Parallel Evolution of Tinker

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Featured events

7th International Workshop on OpenCL, 2019

Distributed Heterogeneous Programming in C/C++ (DHPCC++), 2019

3rd International Workshop on Theoretical Approaches to Performance Evaluation, Modeling and Simulation (TAPEMS), 2019

International Conference on Frontiers of Neural Networks (ICFNN), 2019

International Conference on Frontiers of Artificial Intelligence and Machine Learning (FAIML), 2019