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Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl

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Tags: Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti

July 5, 2016 by hgpu

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie

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Tags: Algorithms, Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C1060, Tesla C2075

October 24, 2013 by hgpu

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Thai V. Hoang, Xavier Cavin, David W. Ritchie

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Tags: Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C2075

September 28, 2013 by hgpu

Experience of parallelizing cryo-EM 3D reconstruction on a CPU-GPU heterogeneous system

Linchuan Li, Xingjian Li, Guangming Tan, Mingyu Chen, Peiheng Zhang

Tags: Algorithms, Computer science, Cryo-EM, CUDA, Data parallelism, GPU cluster, Heterogeneous systems, MPI, nVidia, Performance, Tesla C2050

August 24, 2011 by hgpu

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Source codes

Tags: ATI, ATI Radeon HD 5970, Biology, Cryo-EM, Molecular modeling, nVidia, nVidia GeForce GTX 470, OpenCL, Package, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

Xiaokang Zhang, Xing Zhang, Z. Hong Zhou

Tags: Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Hemant D. Tagare, Andrew Barthel, Fred J. Sigworth

Tags: Algorithms, Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Experience of parallelizing cryo-EM 3D reconstruction on a CPU-GPU heterogeneous system

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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