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Understanding the Power of Evolutionary Computation for GPU Code Optimization

Jhe-Yu Liou, Muaaz Awan, Steven Hofmeyr, Stephanie Forrest, Carole-Jean Wu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Evolutionary Computations, Neural and Evolutionary Computing, nVidia, nVidia GeForce GTX 1080 Ti, Package, performance portability, Sequence alignment, Tesla P100, Tesla V100

September 4, 2022 by hgpu

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack

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Tags: AMD Radeon Instinct MI100, ATI, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce RTX 3090, OpenCL, Package, Sequence alignment, Tesla A100

May 22, 2022 by hgpu

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

Manuel Costanzo, Enzo Rucci, Carlos Garcia Sanchez, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX Titan X, nVidia GeForce RTX 2070, Sequence alignment, Smith-Waterman algorithm, SYCL

March 27, 2022 by hgpu

FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours

Shenggan Cheng, Ruidong Wu, Zhongming Yu, Binrui Li, Xiwen Zhang, Jian Peng, Yang You

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Tags: Biology, Computer science, CUDA, Machine learning, nVidia, nVidia A100, Package

March 6, 2022 by hgpu

NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics

Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis

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Tags: Biology, Chemistry, CUDA, GeForce RTX 2080 Ti, Machine learning, Molecular dynamics, Molecular simulation, Neural networks, nVidia, Package

January 23, 2022 by hgpu

linus: Conveniently explore, share, and present large-scale biological trajectory data from a web browser

Johannes Waschke, Mario Hlawitschka, Kerim Anlas, Vikas Trivedi, Ingo Roeder, Jan Huisken, Nico Scherf

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Tags: Biology, OpenCL, Package, PyOpenCL, Python

January 10, 2021 by hgpu

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar Hernandez, Jeremy C. Smith, Ada Sedova

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Tags: Biology, Biomolecules, Computational biology, CUDA, molecular docking, nVidia, nVidia DGX-2, nVidia GeForce RTX 2080 Ti, OpenCL, supercomputer, Tesla V100

July 12, 2020 by hgpu

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli

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Tags: AMD Radeon RX Vega 56, ATI, Biology, Chemistry, Energy-efficient computing, Heterogeneous systems, molecular docking, nVidia, OpenCL, Tesla V100

March 1, 2020 by hgpu

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Tesla V100

February 16, 2020 by hgpu

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

Saptarshi Soham Mohanta, Collins Assisi

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Tags: Biology, Computer science, CUDA, Deep learning, Differential equations, Machine learning, Neural networks, nVidia, ODEs, Ordinary differential equations, Package, Partial differential equations, PDEs, Python, TensorFlow, Tutorial

June 12, 2019 by hgpu

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

Huihui Zou, Shanjiang Tang, Ce Yu, Hao Fu, Yusen Li, Wenjie Tang

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Tags: Algorithms, APU, Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 750, OpenCL, Sequence alignment, Smith-Waterman algorithm

December 9, 2018 by hgpu

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

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

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

November 25, 2018 by hgpu

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PipeCNN: An OpenCL-based FPGA Accelerator for Convolutional Neural Networks

An OpenCL-Based FPGA Accelerator for Faster R-CNN

MFC: High-fidelity multiphase flow simulation

Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform

Magicube

Efficient Quantized Sparse Matrix Operations on Tensor Cores

Morpheus: Dynamic matrix type and algorithms for sparse matrices

Exploiting dynamic sparse matrices for performance portable linear algebra operations

Energon-AI: Large-scale model inference

EnergonAI: An Inference System for 10-100 Billion Parameter Transformer Models

segTACO

Sgap: Towards Efficient Sparse Tensor Algebra Compilation for GPU

ScalSALE: Scalable SALE Benchmark Framework for Supercomputers

SCALSALE: Scalable SALE Benchmark Framework for Supercomputers

Lina: High Level Analysis Tool for FPGA Accelerators

Lina: a fast design optimisation tool for software-based FPGA programming

GEVO: GPU code optimization using EVOlutionary computation

Understanding the Power of Evolutionary Computation for GPU Code Optimization

GPU Multiversion B-Tree

Fully Concurrent GPU Data Structures

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