Detailed Information on Publication Record
2021
Complex simulation workflows in containerized high-performance environment
VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL et. al.Basic information
Original name
Complex simulation workflows in containerized high-performance environment
Authors
VIŠŇOVSKÝ, Vladimír (703 Slovakia, belonging to the institution), Viktória SPIŠAKOVÁ (703 Slovakia, belonging to the institution), Jana HOZZOVÁ (703 Slovakia, belonging to the institution), Jaroslav OĽHA (703 Slovakia, belonging to the institution), Dalibor TRAPL (203 Czech Republic), Vojtěch SPIWOK (203 Czech Republic), Lukáš HEJTMÁNEK (203 Czech Republic, belonging to the institution) and Aleš KŘENEK (203 Czech Republic, guarantor, belonging to the institution)
Edition
Brusel, Proc. ESM 2021, p. 42-45, 4 pp. 2021
Publisher
EUROSIS
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
Belgium
Confidentiality degree
není předmětem státního či obchodního tajemství
Publication form
storage medium (CD, DVD, flash disk)
RIV identification code
RIV/00216224:14610/21:00119698
Organization unit
Institute of Computer Science
ISBN
978-94-92859-18-1
UT WoS
000848790600007
Keywords in English
Docker; Jupyter notebook; Kubernetes; Molecular force field; Protein folding; Reproducibility; Workflow
Tags
Tags
International impact, Reviewed
Změněno: 30/3/2023 14:31, Mgr. Alena Mokrá
V originále
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.
In Czech
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.
Links
| GA19-16857S, research and development project |
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