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@inproceedings{1839944, author = {Višňovský, Vladimír and Spišaková, Viktória and Hozzová, Jana and Oľha, Jaroslav and Trapl, Dalibor and Spiwok, Vojtěch and Hejtmánek, Lukáš and Křenek, Aleš}, address = {Brusel}, booktitle = {Proc. ESM 2021}, editor = {Armenia S., Geril P.}, keywords = {Docker; Jupyter notebook; Kubernetes; Molecular force field; Protein folding; Reproducibility; Workflow}, howpublished = {paměťový nosič}, language = {eng}, location = {Brusel}, isbn = {978-94-92859-18-1}, pages = {42-45}, publisher = {EUROSIS}, title = {Complex simulation workflows in containerized high-performance environment}, year = {2021} }
TY - JOUR ID - 1839944 AU - Višňovský, Vladimír - Spišaková, Viktória - Hozzová, Jana - Oľha, Jaroslav - Trapl, Dalibor - Spiwok, Vojtěch - Hejtmánek, Lukáš - Křenek, Aleš PY - 2021 TI - Complex simulation workflows in containerized high-performance environment PB - EUROSIS CY - Brusel SN - 9789492859181 KW - Docker KW - Jupyter notebook KW - Kubernetes KW - Molecular force field KW - Protein folding KW - Reproducibility KW - Workflow N2 - utting-edge research involving in-silico simulations often requires to use many heterogeneous software tools made by different developers, resulting in complex, custom-made pipelines of various scripts and programs. Such pipelines are nearly impossible to be reproduced by other research groups, jeopardizing both quality and acceptance of such research results. Starting with two in-house use cases in computational chemistry, we identified a common pattern applicable for other applications as well, and we designed and implemented a solution based on Jupyter notebooks to drive the simulation, Docker containers to package all software dependencies, and Kubernetes execution environment to run several cooperating containers which build up the whole application. ER -
VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL, Vojtěch SPIWOK, Lukáš HEJTMÁNEK a Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. \textit{Proc. ESM 2021}. Brusel: EUROSIS, 2021, s.~42-45. ISBN~978-94-92859-18-1.
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