A GPU acceleration of 3-D Fourier reconstruction in cryo-EM
Identifikátory výsledku
Kód výsledku v IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F19%3A00109272" target="_blank" >RIV/00216224:14610/19:00109272 - isvavai.cz</a>
Výsledek na webu
<a href="https://journals.sagepub.com/doi/10.1177/1094342019832958" target="_blank" >https://journals.sagepub.com/doi/10.1177/1094342019832958</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1177/1094342019832958" target="_blank" >10.1177/1094342019832958</a>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
A GPU acceleration of 3-D Fourier reconstruction in cryo-EM
Popis výsledku v původním jazyce
Cryo-electron microscopy is a popular method for macromolecules structure determination. Reconstruction of a 3-D volume from raw data obtained from a microscope is highly computationally demanding. Thus, acceleration of the reconstruction has a great practical value. In this article, we introduce a novel graphics processing unit (GPU)-friendly algorithm for direct Fourier reconstruction, one of the main computational bottlenecks in the 3-D volume reconstruction pipeline for some experimental cases (particularly those with a large number of images and a high internal symmetry). Contrary to the state of the art, our algorithm uses a gather memory pattern, improving cache locality and removing race conditions in parallel writing into the 3-D volume. We also introduce a finely tuned CUDA implementation of our algorithm, using auto-tuning to search for a combination of optimization parameters maximizing performance on a given GPU architecture. Our CUDA implementation is integrated in widely used software Xmipp, version 3.19, reaching 11.4× speedup compared to the original parallel CPU implementation using GPU with comparable power consumption. Moreover, we have reached 31.7× speedup using four GPUs and 2.14×–5.96× speedup compared to optimized GPU implementation based on a scatter memory pattern.
Název v anglickém jazyce
A GPU acceleration of 3-D Fourier reconstruction in cryo-EM
Popis výsledku anglicky
Cryo-electron microscopy is a popular method for macromolecules structure determination. Reconstruction of a 3-D volume from raw data obtained from a microscope is highly computationally demanding. Thus, acceleration of the reconstruction has a great practical value. In this article, we introduce a novel graphics processing unit (GPU)-friendly algorithm for direct Fourier reconstruction, one of the main computational bottlenecks in the 3-D volume reconstruction pipeline for some experimental cases (particularly those with a large number of images and a high internal symmetry). Contrary to the state of the art, our algorithm uses a gather memory pattern, improving cache locality and removing race conditions in parallel writing into the 3-D volume. We also introduce a finely tuned CUDA implementation of our algorithm, using auto-tuning to search for a combination of optimization parameters maximizing performance on a given GPU architecture. Our CUDA implementation is integrated in widely used software Xmipp, version 3.19, reaching 11.4× speedup compared to the original parallel CPU implementation using GPU with comparable power consumption. Moreover, we have reached 31.7× speedup using four GPUs and 2.14×–5.96× speedup compared to optimized GPU implementation based on a scatter memory pattern.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Návaznosti výsledku
Projekt
<a href="/cs/project/EF16_013%2F0001802" target="_blank" >EF16_013/0001802: CERIT Scientific Cloud</a><br>
Návaznosti
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Ostatní
Rok uplatnění
2019
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
The International Journal of High Performance Computing Applications
ISSN
1094-3420
e-ISSN
1741-2846
Svazek periodika
33
Číslo periodika v rámci svazku
5
Stát vydavatele periodika
US - Spojené státy americké
Počet stran výsledku
12
Strana od-do
948-959
Kód UT WoS článku
000484527300014
EID výsledku v databázi Scopus
2-s2.0-85062825004