Complex simulation workflows in containerized high-performance environment

VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL, Vojtěch SPIWOK, Lukáš HEJTMÁNEK and Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. Proc. ESM 2021. Brusel: EUROSIS, 2021, p. 42-45. ISBN 978-94-92859-18-1.

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

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Belgium
• Confidentiality degree: is not subject to a state or trade secret
• 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: rivok
• Tags: International impact, Reviewed

Abstract

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.

Abstract (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: Name: Zpřesnění molekulárně mechanických potenciálů léčivům podobných molekul metodou property map

Investor: Czech Science Foundation, Correction of molecular mechanics potentials of drug-like molecules by property map