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Verified Exascale Computing for Multiscale Applications

Deliverables

Detailed Dissemination Action plan

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).

Interim Dissemination Report

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.

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.

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.

Report on Application Software Readiness

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

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.

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Publications

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

Author(s): M. Vassaux, K. Gopalakrishnan, R. C. Sinclair, R. A. Richardson and P. Coveney,
Published in: Advanced Theory and Simulations,, 4, 2, 2000234, 2020, ISSN 2513-0390
Publisher: 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

Author(s): N. C. Clementi and L. A. Barba,
Published in: Phil. Trans. R. Soc. A, 2020, ISSN 1364-503X
Publisher: 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”

Author(s): M. Bieniek, A. Bhati, S. Wan and P. V. Coveney,
Published in: J. Chem. Theory Comput, 17, 2, 1250–1265, 2021, ISSN 1549-9626
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

“The fundamental principles of reproducibility”,

Author(s): Odd Erik Gundersen,
Published in: Phil. Trans. R. Soc. A, 379, 20200210, 2021, ISSN 1364-503X
Publisher: 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:

Author(s): D. Suleimenova and D. Groen,
Published in: Journal of Artificial Societies and Social Simulation, 23 (1) 2, 2020, ISSN 1460-7425
Publisher: 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),

Author(s): D. Suleimenova, H. Arabnejad, W. N. Edeling and D. Groen,
Published in: Phil. Trans. R. Soc. A., 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0077

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

Author(s): L. Fortunato and M. Galassi,
Published in: Phil. Trans. R. Soc. A., 379, 20200079, 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0079

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

Author(s): J. Lakhlili, O.Hoenen, O. Luk, D. Coster,
Published in: ICCS 2020, Lecture Notes in Computer Science, 12143, 2020, ISSN 1611-3349
Publisher: 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

Author(s): V. Volodina and P. Challenor,
Published in: Phil. Trans. R. Soc. A. 379, 20200071 (2021),, 2020, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0071

“Towards validated multiscale simulations for fusion”

Author(s): O. O. Luk, J. Lakhlili, O. Hoenen, U. von Toussaint, B. D. Scott and D. P. Coster,
Published in: Phil. Trans. R. Soc. A. 3, 2021, ISSN 1364-503X
Publisher: 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”

Author(s): D. P. Coster, R. Fischer, O. Hoenen, J. Lakhlili, O. O. Luk, R. Preuss, B. D. Scott, and U. Toussaint,
Published in: Nuclear Fusion, Volume 61, Number 12, 2021, ISSN 0029-5515
Publisher: Institute of Physics Publishing
DOI: 10.1088/1741-4326/ac359f

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

Author(s): 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,
Published in: J. Comput. Sci., Volume 53, July 2021, 101402, 2021, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2021.101402

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

Author(s): M. S. Krafczyk, A. Shi, A. Bhaskar, D. Marinov and V. Stodden,
Published in: Phil. Trans. R. Soc. A. 379, 20200069 (2021),, 2021, ISSN 1471-2962
Publisher: Royal Soc.
DOI: 10.1098/rsta.2020.0069

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

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

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

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

Predicting queue wait time probabilities for multi-scale computing

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

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

Author(s): Bruce M. Boghosian, Peter V. Coveney, Hongyan Wang
Published in: Advanced Theory and Simulations, 2/12, 2019, Page(s) 1900125, ISSN 2513-0390
Publisher: Advanced Theory and Simulations
DOI: 10.1002/adts.201900125

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

Author(s): Alfons G. Hoekstra, Simon Portegies Zwart, Peter V. Coveney
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 377/2142, 2019, Page(s) 20180355, ISSN 1364-503X
Publisher: 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

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

Semi-intrusive uncertainty propagation for multiscale models

Author(s): Anna Nikishova, Alfons G. Hoekstra
Published in: Journal of Computational Science, 35, 2019, Page(s) 80-90, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2019.06.007

Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis

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

Micromechanical exfoliation of graphene on the atomistic scale

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

Toward High Fidelity Materials Property Prediction from Multiscale Modeling and Simulation

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

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

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

The heterogeneous multiscale method applied to inelastic polymer mechanics

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

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

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

Sensitivity analysis based dimension reduction of multiscale models

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

Big data: the end of the scientific method?

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

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

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

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

Author(s): David W. Wright, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-41758-1

Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold

Author(s): Robert C. Sinclair, Peter V. Coveney
Published in: Journal of Chemical Information and Modeling, 59/6, 2019, Page(s) 2741-2745, ISSN 1549-9596
Publisher: 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

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

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

Author(s): W. Edeling, D. Crommelin,
Published in: Journal of Computers & Fluids,, 201, 104470, 2021, ISSN 0045-7930
Publisher: 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”,

Author(s): G. Fursin,
Published in: Phil. Trans. R. Soc. A., 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0211

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

Author(s): 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
Published in: Computational Science – ICCS 2019 - 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part IV, 11539, 2019, Page(s) 479-492, ISBN 978-3-030-22746-3
Publisher: 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

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

Towards Data-Driven Dynamic Surrogate Models for Ocean Flow

Author(s): Wouter Edeling, Daan Crommelin
Published in: Proceedings of the Platform for Advanced Scientific Computing Conference, 2019, Page(s) 1-10, ISBN 9781-450367707
Publisher: ACM
DOI: 10.1145/3324989.3325713

Reduced model-error source terms for fluid flow”,

Author(s): W. N. Edeling, D. Crommelin
Published in: UNCECOMP19 Conference, Preprint (2019), 2019
Publisher: UNCECOMP19 Conference
DOI: 10.13140/rg.2.2.36773.35048

Towards modelling the effect of evolving violence on forced migration

Author(s): D. Groen, D. Bell, H. Arabnejad, D. Suleimenova, S. E. J. Taylor, and A. Anagnostou
Published in: 2019
Publisher: 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”

Author(s): B. Bosak, T. Piontek, P. Karlshoefer, E. Raffin, J. Lakhlili, P. Kopta,
Published in: Lecture Notes in Computer Science,, 12746, 2021
Publisher: Computer Science, ICCS 2021,

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

Author(s): O. O. Luk, J. Lakhlili, U. Toussaint, L. E. Veen, Y. Yudin, O. Hoenen, B. D. Scott, D. P. Coster,
Published in: 2021
Publisher: 47th EPS Conference on Plasma Physics (2021)

Reducing data-driven dynamical subgrid scale models by physical constraints

Author(s): W. N. Edeling, D. Crommelin
Published in: 2020
Publisher: Computers & Fluids
DOI: 10.13140/rg.2.2.11045.86245