Verified Exascale Computing for Multiscale Applications

Livrables

A detailed and comprehensive report on the dissemination actions that will be carried out by the project.

Report on the implementation of non-intrusive VVUQ techniques

Report the progress in employing non-intrusive VVUQ techniques in the multi-scale scientific applications (Task 4.2).

Review Dissemination activity from the first half of the project and propose actions for the second half, including an update of dissemination action plan and innovation plan.

Final Report on VECMA Infrastructure

A document describing the final status of the VECMA computing infrastructure

Final report on multiscale UQP and V&V

A final and consolidated description of UQPs for multiscale UQ and a report on their scaling to the exascale A final formal set of procedures for multiscale VV and their implementation as VVPs

Documentation and tutorials accompanying the deep-track release of the VECMA toolkit

This is a living deliverable providing documentation and tutorials on the deeptrack release of the VECMA toolkit It will first be produced in M24 and updated in M30 and M36 Community feedback on previous versions will be used to guide the direction of subsequent versions

Final Dissemination and Innovation Report

A review of the Dissemination and Innovation activity of the second half of the project

Full release of the entire VECMA toolkit

The software release of the VECMA toolkit containing deeptrack functionalities including unit and functional tests Community feedback on the M24 release will be used to shape this main release and this process will be documented as part of this deliverable

First Report on VECMA Infrastructure

A document summarising the status of the project infrastructure. It will include information about unified operational procedures, a list of available resources and deployed services with a description of modifications and extensions introduced to these services to facilitate access to resources and to support specific VECMA needs and requirements.

Report on the fast-track implementation of the VECMA toolkit

A short written report presenting the architecture of the VECMA toolkit, reporting on the current status of the technical development, a list of anticipated features for the fast-track release and a provisional list of envisioned features for the deep-track release.

Quality Assurance Plan

To manage and support the quality control with the project, a documented Quality Assurance Plan will be set up and maintained to monitor all deliverables before finalising them. The deliverable also contains a detailed risk analysis and contingency planning, including a log of risks and associated issues.

Report on advanced multiscale UQ algorithms, including intrusive approaches, and mapping thereof in UQPs and first results on V&V

Description of algorithms developed in Task 23 and resulting UQPs developed in Task 24 as well as scalable UQPs for the exascale In addition an account of formal procedures for multiscale VV will be provided

Interim Report Innovation Management Activities

A report on our initial setting up of framework and results of exploitation activities undertaken in the first half of the project together with engagements and involvement with the wider cPPP community.

Project Handbook

To ensure a consistent implementation of the management of the project, UCL will produce a project procedure handbook that will be readily accessible to all Partners.

Innovation Plan

A detailed innovation plan, to be adhered to by all members of the consortium, to promote the innovation and commercialisation aspects of this project.

Architecture of the VECMA system

A document presenting the overall technical architecture of the VECMA system with description of distinct functional layers as well as relationships between external components and software developed in the project.

Business Plan

A Business Plan for the project will be produced in month 30

Report on Application Software Readiness

Report the specific requirements of the applications as identified during Task 4.1.

Report on the implementation of non-intrusive and intrusive VVUQ techniques

Report on the experiences of implementing VVUQ techniques in the multiscale scientific applications Tasks 42 and 43 as well as using the VVUQ primitives to decrease application uncertainty Task 44

Data Management Plan

A Data Management Plan for the project will be produced in the first 6 months.

Fast-track release of the VECMA toolkit

The software release of the VECMA toolkit containing the fast-track functionalities, including unit and functional tests, as well as documentation and tutorials.

Preliminary deep-track release of the VECMA toolkit

A preliminary software release of the VECMA toolkit now also containing deeptrack functionalities including unit and functional tests

Publications

“Accelerating heterogeneous multiscale simulations of advanced materials properties with graph-based clustering”,

Auteurs: M. Vassaux, K. Gopalakrishnan, R. C. Sinclair, R. A. Richardson and P. Coveney,
Publié dans: Advanced Theory and Simulations,, Numéro 4, 2, 2000234, 2020, ISSN 2513-0390
Éditeur: Wiley Online Library
DOI: 10.1002/adts.202000234

“Reproducible validation and replication studies in nanoscale physics”, . 379, 20200068 (2021), DOI:10.1098/rsta.2020.0068

Auteurs: N. C. Clementi and L. A. Barba,
Publié dans: Phil. Trans. R. Soc. A, 2020, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0068

“TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing”

Auteurs: M. Bieniek, A. Bhati, S. Wan and P. V. Coveney,
Publié dans: J. Chem. Theory Comput, Numéro 17, 2, 1250–1265, 2021, ISSN 1549-9626
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

“The fundamental principles of reproducibility”,

Auteurs: Odd Erik Gundersen,
Publié dans: Phil. Trans. R. Soc. A, Numéro 379, 20200210, 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0210

“How policy decisions affect refugee journeys in South Sudan: A study using automated ensemble simulations”, (2020), DOI:

Auteurs: D. Suleimenova and D. Groen,
Publié dans: Journal of Artificial Societies and Social Simulation, Numéro 23 (1) 2, 2020, ISSN 1460-7425
Éditeur: University of Surrey
DOI: 10.18564/jasss.4193

“Sensitivity-driven simulation development: a case study in forced migrationo”, Phil. Trans. R. Soc. A. 379, 20200409 (2021),

Auteurs: D. Suleimenova, H. Arabnejad, W. N. Edeling and D. Groen,
Publié dans: Phil. Trans. R. Soc. A., 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0077

“The case for free and open source software in research and scholarship”,

Auteurs: L. Fortunato and M. Galassi,
Publié dans: Phil. Trans. R. Soc. A., Numéro 379, 20200079, 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0079

“Uncertainty Quantification for Multiscale Fusion Plasma Simulations with VECMA Toolkit”,

Auteurs: J. Lakhlili, O.Hoenen, O. Luk, D. Coster,
Publié dans: ICCS 2020, Lecture Notes in Computer Science, Numéro 12143, 2020, ISSN 1611-3349
Éditeur: Springer LINK
DOI: 10.1007/978-3-030-50436-6_53

“The importance of uncertainty quantification in model reproducibility”, Phil. Trans. R. Soc. A. 379, 20200071 (2021), DOI:10.1098/rsta.2020.0071

Auteurs: V. Volodina and P. Challenor,
Publié dans: Phil. Trans. R. Soc. A. 379, 20200071 (2021),, 2020, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0071

“Towards validated multiscale simulations for fusion”

Auteurs: O. O. Luk, J. Lakhlili, O. Hoenen, U. von Toussaint, B. D. Scott and D. P. Coster,
Publié dans: Phil. Trans. R. Soc. A. 3, 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0074

“Building a Turbulence-Transport workflow incorporating uncertainty quantification for predicting core profiles in a tokamak plasma”

Auteurs: D. P. Coster, R. Fischer, O. Hoenen, J. Lakhlili, O. O. Luk, R. Preuss, B. D. Scott, and U. Toussaint,
Publié dans: Nuclear Fusion, Numéro Volume 61, Number 12, 2021, ISSN 0029-5515
Éditeur: Institute of Physics Publishing
DOI: 10.1088/1741-4326/ac359f

“Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit”, (2021),

Auteurs: D. Suleimenova, H. Arabnejad, W. N. Edeling, D. Coster, O. O. Luk, J. Lakhlili, V. Jancaskas, M Kulczewski, L. Veen, D. Ye, P. Zun, V. Krzhizhanovskaya, A. Hoekstra, D. Crommelin, P. V. Coveney, D. Groen,
Publié dans: J. Comput. Sci., Numéro Volume 53, July 2021, 101402, 2021, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2021.101402

“Learning from reproducing computational results: introducing three principles and the Reproduction Package”, DOI:

Auteurs: M. S. Krafczyk, A. Shi, A. Bhaskar, D. Marinov and V. Stodden,
Publié dans: Phil. Trans. R. Soc. A. 379, 20200069 (2021),, 2021, ISSN 1471-2962
Éditeur: Royal Soc.
DOI: 10.1098/rsta.2020.0069

Mastering the scales: a survey on the benefits of multiscale computing software

Auteurs: Derek Groen, Jaroslaw Knap, Philipp Neumann, Diana Suleimenova, Lourens Veen, Kenneth Leiter
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180147, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0147

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

Auteurs: Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 3/1, 2019, Page(s) 1900195, ISSN 2513-0390
Éditeur: Advanced Theory and Simulations
DOI: 10.1002/adts.201900195

Predicting queue wait time probabilities for multi-scale computing

Auteurs: Vytautas Jancauskas, Tomasz Piontek, Piotr Kopta, Bartosz Bosak
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180151, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0151

A New Pathology in the Simulation of Chaotic Dynamical Systems on Digital Computers

Auteurs: Bruce M. Boghosian, Peter V. Coveney, Hongyan Wang
Publié dans: Advanced Theory and Simulations, Numéro 2/12, 2019, Page(s) 1900125, ISSN 2513-0390
Éditeur: Advanced Theory and Simulations
DOI: 10.1002/adts.201900125

Multiscale modelling, simulation and computing: from the desktop to the exascale

Auteurs: Alfons G. Hoekstra, Simon Portegies Zwart, Peter V. Coveney
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180355, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0355

Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis

Auteurs: A. Nikishova, L. Veen, P. Zun, A. G. Hoekstra
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180154, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0154

Semi-intrusive uncertainty propagation for multiscale models

Auteurs: Anna Nikishova, Alfons G. Hoekstra
Publié dans: Journal of Computational Science, Numéro 35, 2019, Page(s) 80-90, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2019.06.007

Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis

Auteurs: Anna Nikishova, Lourens Veen, Pavel Zun, Alfons G. Hoekstra
Publié dans: Cardiovascular Engineering and Technology, Numéro 9/4, 2018, Page(s) 761-774, ISSN 1869-408X
Éditeur: Springer Pub. Co.,
DOI: 10.1007/s13239-018-00372-4

Micromechanical exfoliation of graphene on the atomistic scale

Auteurs: Robert C. Sinclair, James L. Suter, Peter V. Coveney
Publié dans: Physical Chemistry Chemical Physics, Numéro 21/10, 2019, Page(s) 5716-5722, ISSN 1463-9076
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c8cp07796g

Toward High Fidelity Materials Property Prediction from Multiscale Modeling and Simulation

Auteurs: Maxime Vassaux, Robert C. Sinclair, Robin A. Richardson, James L. Suter, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 3/1, 2019, Page(s) 1900122, ISSN 2513-0390
Éditeur: Advanced Theory and Simulations
DOI: 10.1002/adts.201900122

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders

Auteurs: Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Publié dans: Journal of Chemical Theory and Computation, Numéro 15/5, 2019, Page(s) 3316-3330, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

The heterogeneous multiscale method applied to inelastic polymer mechanics

Auteurs: M. Vassaux, R. A. Richardson, P. V. Coveney
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180150, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0150

Multiscale computing for science and engineering in the era of exascale performance

Auteurs: Alfons G. Hoekstra, Bastien Chopard, David Coster, Simon Portegies Zwart, Peter V. Coveney
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180144, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0144

Sensitivity analysis based dimension reduction of multiscale models

Auteurs: Anna Nikishova, Giovanni E. Comi, Alfons G. Hoekstra
Publié dans: Mathematics and Computers in Simulation, Numéro 170, 2020, Page(s) 205-220, ISSN 0378-4754
Éditeur: Elsevier BV
DOI: 10.1016/j.matcom.2019.10.013

Big data: the end of the scientific method?

Auteurs: Sauro Succi, Peter V. Coveney
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 377/2142, 2019, Page(s) 20180145, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2018.0145

The Role of Graphene in Enhancing the Material Properties of Thermosetting Polymers

Auteurs: Maxime Vassaux, Robert C. Sinclair, Robin A. Richardson, James L. Suter, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 2/5, 2019, Page(s) 1800168, ISSN 2513-0390
Éditeur: Wiley online
DOI: 10.1002/adts.201800168

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

Auteurs: David W. Wright, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Publié dans: Scientific Reports, Numéro 9/1, 2019, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-019-41758-1

Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold

Auteurs: Robert C. Sinclair, Peter V. Coveney
Publié dans: Journal of Chemical Information and Modeling, Numéro 59/6, 2019, Page(s) 2741-2745, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.9b00114

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Auteurs: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 3/1, 2019, Page(s) 1900194, ISSN 2513-0390
Éditeur: Wiley Online Library
DOI: 10.1002/adts.201900194

“Reducing data-driven dynamical subgrid scale models by physical constraints”, 201, 104470 (2020),

Auteurs: W. Edeling, D. Crommelin,
Publié dans: Journal of Computers & Fluids,, Numéro 201, 104470, 2021, ISSN 0045-7930
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.compfluid.2020.104470

“Collective knowledge: organizing research projects as a database of reusable components and portable workflows with common interfaces”,

Auteurs: G. Fursin,
Publié dans: Phil. Trans. R. Soc. A., 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0211

Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations

Auteurs: Derek Groen, Robin A. Richardson, David W. Wright, Vytautas Jancauskas, Robert Sinclair, Paul Karlshoefer, Maxime Vassaux, Hamid Arabnejad, Tomasz Piontek, Piotr Kopta, Bartosz Bosak, Jalal Lakhlili, Olivier Hoenen, Diana Suleimenova, Wouter Edeling, Daan Crommelin, Anna Nikishova, Peter V. Coveney
Publié dans: Computational Science – ICCS 2019 - 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part IV, Numéro 11539, 2019, Page(s) 479-492, ISBN 978-3-030-22746-3
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-22747-0_36

A Coupled Food Security and Refugee Movement Model for the South Sudan Conflict

Auteurs: Christian Vanhille Campos, Diana Suleimenova, Derek Groen
Publié dans: Computational Science – ICCS 2019 - 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part V, Numéro 11540, 2019, Page(s) 725-732, ISBN 978-3-030-22749-4
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-22750-0_71

Towards Data-Driven Dynamic Surrogate Models for Ocean Flow

Auteurs: Wouter Edeling, Daan Crommelin
Publié dans: Proceedings of the Platform for Advanced Scientific Computing Conference, 2019, Page(s) 1-10, ISBN 9781-450367707
Éditeur: ACM
DOI: 10.1145/3324989.3325713

Reduced model-error source terms for fluid flow”,

Auteurs: W. N. Edeling, D. Crommelin
Publié dans: UNCECOMP19 Conference, Preprint (2019), 2019
Éditeur: UNCECOMP19 Conference
DOI: 10.13140/rg.2.2.36773.35048

Towards modelling the effect of evolving violence on forced migration

Auteurs: D. Groen, D. Bell, H. Arabnejad, D. Suleimenova, S. E. J. Taylor, and A. Anagnostou
Publié dans: 2019
Éditeur: Proceedings of the 2019 Winter Simulation Conference

B. Bosak, T. Piontek, P. Karlshoefer, E. Raffin, J. Lakhlili, P. Kopta, “Verification, Validation and Uncertainty Quantification of Large-Scale Applications with QCG-PilotJob”

Auteurs: B. Bosak, T. Piontek, P. Karlshoefer, E. Raffin, J. Lakhlili, P. Kopta,
Publié dans: Lecture Notes in Computer Science,, Numéro 12746, 2021
Éditeur: Computer Science, ICCS 2021,

“Performing Validation, Verification, and Sensitivity Analysis on Multiscale Fusion Plasma Simulations with the VECMA Toolkit”,

Auteurs: O. O. Luk, J. Lakhlili, U. Toussaint, L. E. Veen, Y. Yudin, O. Hoenen, B. D. Scott, D. P. Coster,
Publié dans: 2021
Éditeur: 47th EPS Conference on Plasma Physics (2021)

Reducing data-driven dynamical subgrid scale models by physical constraints

Auteurs: W. N. Edeling, D. Crommelin
Publié dans: 2020
Éditeur: Computers & Fluids
DOI: 10.13140/rg.2.2.11045.86245

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