1
|
Luk OO, Lakhlili J, Hoenen O, von Toussaint U, Scott BD, Coster DP. Towards validated multiscale simulations for fusion. Philos Trans A Math Phys Eng Sci 2021; 379:20200074. [PMID: 33775143 DOI: 10.1098/rsta.2020.0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Harnessing energy produced by thermonuclear fusion reactions has the potential to provide a clean and inexpensive source of energy to Earth. However, throughout the past seven decades, physicists learned that creating our very own fusion energy source is very difficult to achieve. We constructed a component-based, multiscale fusion workflow to model fusion plasma inside the core of a tokamak device. To ensure the simulation results agree with experimental values, the model needs to undergo the process of verification, validation and uncertainty quantification (VVUQ). This paper will go over the VVUQ work carried out in the multiscale fusion workflow (MFW), with the help of the EasyVVUQ software library developed by the VECMA project. In particular, similarity of distributions from simulation and experiment is explored as a validation metric. Such initial validation measures provide insights into the accuracy of the simulation results. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.
Collapse
Affiliation(s)
- O O Luk
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - J Lakhlili
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - O Hoenen
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | | | - B D Scott
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - D P Coster
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| |
Collapse
|
2
|
Groen D, Arabnejad H, Jancauskas V, Edeling WN, Jansson F, Richardson RA, Lakhlili J, Veen L, Bosak B, Kopta P, Wright DW, Monnier N, Karlshoefer P, Suleimenova D, Sinclair R, Vassaux M, Nikishova A, Bieniek M, Luk OO, Kulczewski M, Raffin E, Crommelin D, Hoenen O, Coster DP, Piontek T, Coveney PV. VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations. Philos Trans A Math Phys Eng Sci 2021; 379:20200221. [PMID: 33775151 PMCID: PMC8059654 DOI: 10.1098/rsta.2020.0221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 05/04/2023]
Abstract
We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and uncertainty quantication (UQ). It enables users to verify key aspects of their applications, systematically compare and validate the simulation outputs against observational or benchmark data, and run simulations conveniently on any platform from the desktop to current multi-petascale computers. In this sequel to our paper on VECMAtk which we presented last year [1] we focus on a range of functional and performance improvements that we have introduced, cover newly introduced components, and applications examples from seven different domains such as conflict modelling and environmental sciences. We also present several implemented patterns for UQ/SA and V&V, and guide the reader through one example concerning COVID-19 modelling in detail. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.
Collapse
Affiliation(s)
- D. Groen
- Department of Computer Science, Brunel University London, London, UK
- Centre for Computational Science, University College London, London, UK
| | - H. Arabnejad
- Department of Computer Science, Brunel University London, London, UK
| | | | - W. N. Edeling
- Centrum Wiskunde and Informatica, Amsterdam, The Netherlands
| | - F. Jansson
- Centrum Wiskunde and Informatica, Amsterdam, The Netherlands
- Department of Geoscience and Remote Sensing, Delft University of Technology, Delft, The Netherlands
| | - R. A. Richardson
- Centre for Computational Science, University College London, London, UK
- Netherlands eScience Center, Amsterdam, The Netherlands
| | - J. Lakhlili
- Max Planck Institute for Plasma Physics - Garching, Munich, Germany
| | - L. Veen
- Netherlands eScience Center, Amsterdam, The Netherlands
| | - B. Bosak
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - P. Kopta
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - D. W. Wright
- Centre for Computational Science, University College London, London, UK
| | - N. Monnier
- CEPP - Center for Excellence in Performance Programming, Atos Bull, Rennes, France
| | - P. Karlshoefer
- CEPP - Center for Excellence in Performance Programming, Atos Bull, Rennes, France
| | - D. Suleimenova
- Department of Computer Science, Brunel University London, London, UK
| | - R. Sinclair
- Centre for Computational Science, University College London, London, UK
| | - M. Vassaux
- Centre for Computational Science, University College London, London, UK
| | - A. Nikishova
- Computational Science Lab, Institute for Informatics, University of Amsterdam, Amsterdam, The Netherlands
| | - M. Bieniek
- Centre for Computational Science, University College London, London, UK
| | - Onnie O. Luk
- Max Planck Institute for Plasma Physics - Garching, Munich, Germany
| | - M. Kulczewski
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - E. Raffin
- CEPP - Center for Excellence in Performance Programming, Atos Bull, Rennes, France
| | - D. Crommelin
- Centrum Wiskunde and Informatica, Amsterdam, The Netherlands
- Korteweg-de Vries Institute for Mathematics, Amsterdam, The Netherlands
| | - O. Hoenen
- Max Planck Institute for Plasma Physics - Garching, Munich, Germany
| | - D. P. Coster
- Max Planck Institute for Plasma Physics - Garching, Munich, Germany
| | - T. Piontek
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - P. V. Coveney
- Centre for Computational Science, University College London, London, UK
- Computational Science Lab, Institute for Informatics, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
3
|
Luk OO, Hoenen O, Perks O, Brabazon K, Piontek T, Kopta P, Bosak B, Bottino A, Scott BD, Coster DP. Application of the extreme scaling computing pattern on multiscale fusion plasma modelling. Philos Trans A Math Phys Eng Sci 2019; 377:20180152. [PMID: 30967036 PMCID: PMC6388005 DOI: 10.1098/rsta.2018.0152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 05/18/2023]
Abstract
The extreme scaling pattern of the ComPat project is applied to a multi-scale workflow relevant to the magnetically confined fusion problem. This workflow combines transport, turbulence and equilibrium codes (together with additional auxiliaries such as initial conditions and numerical module), which aims at calculating the behaviour of a fusion plasma on long (transport) time scales based on information from much faster (turbulence) time scales. Initial findings of profile measurements are reported in this paper and indicate that, depending on the chosen performance metric for defining 'cost', such as time to completion, efficiency and total energy consumption of the mutliscale workflow, different choices on the number of cores would be made when determining the optimal execution configuration. A variant of the workflow which increases the inherent parallelism is presented, and shown to produce equivalent results at (typically) lower cost compared with the original workflow. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.
Collapse
Affiliation(s)
- O. O. Luk
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - O. Hoenen
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | | | | | - T. Piontek
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - P. Kopta
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - B. Bosak
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - A. Bottino
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - B. D. Scott
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - D. P. Coster
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| |
Collapse
|
4
|
Voitsekhovitch I, Hatzky R, Coster D, Imbeaux F, McDonald DC, Fehér TB, Kang KS, Leggate H, Martone M, Mochalskyy S, Sáez X, Ribeiro T, Tran TM, Gutierrez-Milla A, Aniel T, Figat D, Fleury L, Hoenen O, Hollocombe J, Kaljun D, Manduchi G, Owsiak M, Pais V, Palak B, Plociennik M, Signoret J, Vouland C, Yadykin D, Robin F, Iannone F, Bracco G, David J, Maslennikov A, Noé J, Rossi E, Kamendje R, Heuraux S, Hölzl M, Pinches SD, Da Silva F, Tskhakaya D. Recent EUROfusion Achievements in Support of Computationally Demanding Multiscale Fusion Physics Simulations and Integrated Modeling. Fusion Science and Technology 2018. [DOI: 10.1080/15361055.2018.1424483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- I. Voitsekhovitch
- United Kingdom Atomic Energy Authority, CCFE, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - R. Hatzky
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - D. Coster
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - F. Imbeaux
- CEA, Institute for Magnetic Fusion Research, F-13108 Saint-Paul-lez-Durance, France
| | - D. C. McDonald
- United Kingdom Atomic Energy Authority, CCFE, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
- EUROfusion Programme Management Unit, Garching, Germany
| | - T. B. Fehér
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - K. S. Kang
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | | | - M. Martone
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - S. Mochalskyy
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - X. Sáez
- Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - T. Ribeiro
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - T.-M. Tran
- Swiss Plasma Centre (SPC), 1015 Lausanne, Switzerland
| | | | - T. Aniel
- CEA, Institute for Magnetic Fusion Research, F-13108 Saint-Paul-lez-Durance, France
| | - D. Figat
- Poznan Supercomputing and Networking Center, Poznan, Poland
| | - L. Fleury
- CEA, Institute for Magnetic Fusion Research, F-13108 Saint-Paul-lez-Durance, France
| | - O. Hoenen
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - J. Hollocombe
- United Kingdom Atomic Energy Authority, CCFE, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - D. Kaljun
- University of Ljubljana, Kongresni trg 12-1000, Ljubljana, Slovenia
| | - G. Manduchi
- Consorzio RFX, Corso Stati Uniti 4, 35127 Padova, Italy
| | - M. Owsiak
- Poznan Supercomputing and Networking Center, Poznan, Poland
| | - V. Pais
- National Institute for Laser, Plasma and Radiation Physics, P.O. Box MG-36, 077125 Magurele, Bucharest, Romania
| | - B. Palak
- Poznan Supercomputing and Networking Center, Poznan, Poland
| | - M. Plociennik
- Poznan Supercomputing and Networking Center, Poznan, Poland
| | - J. Signoret
- CEA, Institute for Magnetic Fusion Research, F-13108 Saint-Paul-lez-Durance, France
| | - C. Vouland
- CEA, Institute for Magnetic Fusion Research, F-13108 Saint-Paul-lez-Durance, France
| | - D. Yadykin
- Chalmers University of Technology, S-41296 Göteborg, Sweden
| | - F. Robin
- CEA-DRF, Centre de Saclay, 91191 Gif-sur-Yvette, France
| | | | | | - J. David
- CEA-DRF, Centre de Saclay, 91191 Gif-sur-Yvette, France
| | - A. Maslennikov
- CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno, Bologna, Italy
| | - J. Noé
- CEA-DRF, Centre de Saclay, 91191 Gif-sur-Yvette, France
| | - E. Rossi
- CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno, Bologna, Italy
| | - R. Kamendje
- EUROfusion Programme Management Unit, Garching, Germany
- Graz University of Technology, Institut fuer Theoretische Physik—Computational Physics, A-8010 Graz, Austria
| | - S. Heuraux
- CNRS-Université de Lorraine, Institute Jean Lamour UMR 7198, BP 70239 F-54506, Vandoeuvre, France
| | - M. Hölzl
- Max-Planck-Institut für Plasmaphysik, Garching D-85748, Germany
| | - S. D. Pinches
- ITER Organization, Route de Vinon-sur-Verdon, CS 90 046, 13067 St Paul Lez Durance Cedex, France
| | - F. Da Silva
- Instituto de Plasmas e Fusão Nuclear—Laboratório Associado, 1046-001 Lisboa, Portugal
| | - D. Tskhakaya
- Vienna University of Technology, Institute of Applied Physics, Fusion@ÖAW, A-1040 Vienna, Austria
| |
Collapse
|
5
|
Borgdorff J, Ben Belgacem M, Bona-Casas C, Fazendeiro L, Groen D, Hoenen O, Mizeranschi A, Suter JL, Coster D, Coveney PV, Dubitzky W, Hoekstra AG, Strand P, Chopard B. Performance of distributed multiscale simulations. Philos Trans A Math Phys Eng Sci 2014; 372:rsta.2013.0407. [PMID: 24982258 PMCID: PMC4084531 DOI: 10.1098/rsta.2013.0407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.
Collapse
Affiliation(s)
- J Borgdorff
- Computational Science, Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M Ben Belgacem
- Computer Science Department, University of Geneva, 1227 Carouge, Switzerland
| | - C Bona-Casas
- Department of Applied Mathematics, University of A Coruña, 15001 A Coruña, Spain
| | - L Fazendeiro
- Department of Earth and Space Sciences, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - D Groen
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - O Hoenen
- Max-Planck-Institut für Plasmaphysik, 85748 Garching, Germany
| | - A Mizeranschi
- Nano Systems Biology, School of Biomedicine, University of Ulster, Coleraine BTS2 1SA, UK
| | - J L Suter
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - D Coster
- Max-Planck-Institut für Plasmaphysik, 85748 Garching, Germany
| | - P V Coveney
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - W Dubitzky
- Nano Systems Biology, School of Biomedicine, University of Ulster, Coleraine BTS2 1SA, UK
| | - A G Hoekstra
- Computational Science, Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands National Research University ITMO, Kronverkskiy prospekt 49, 197101 St Petersburg, Russia
| | - P Strand
- Department of Earth and Space Sciences, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - B Chopard
- Computer Science Department, University of Geneva, 1227 Carouge, Switzerland
| |
Collapse
|