Computing Patterns for High Performance Multiscale Computing

Livrables

Interim Report on Instantiating Computing Patterns for HPMC Applications

Interim report about our progress in employing multiscale computing patterns in actual scientific applications. It will contain an assessment of the efficacy of the patterns as well as recommendations and best practices for their instantiation.

Report on Application Software Readiness

Report the specific requirements of the applications as identified during Task 3.1.

Quality Assurance Plan

To manage and support the project Quality Control, 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.

First Dissemination Report

Review events and dissemination results of past year and proposes actions for the coming one, including update of dissemination action plan.

First progress report on the Experimental Execution Environment

This deliverable will present the progress in the installation, configuration, and usage of the Experimental Execution Environment. This deliverable will also include the first version of the ComPat Experimental Execution Environment user guide.

Report on integration of ComPat services with multiscale coupling libraries and patterns

A document describing the final integration of ComPat services with multiscale coupling libraries and patterns including references to ComPat applications executed on the ComPat Pan-European Experimental Execution Environment.

Report and software on design of tools and required actions to support performance tools for multiscale

Report on an analyses of the requirements for the tools (debug, profile and analyse performance) and design and architecture of a solution appropriate to support the multiscale patterns.

Architecture of the ComPat system

A document describing the overall architecture of the ComPat system including relationships between developed in the project toolkits and services.

Report on Existing Software Suitability and Adaptation

Report on what software will be used in the project, how it compares to other software packages, and outline a detailed plan for their adaptation and integration, as well as report on MML implementation and status report on implementation of the multiscale computing patterns.

Final report on the Experimental Execution Environment

An update of deliverable D6.3.

Final report on high level tools, including performance profiling and modelling

Report on the status of the tools, and on the validation of the impact of measurement and analysis on the applications – and on the accuracy of the modelling tools as applied to simulations at the scales of machines available during the latter months of the project.

Report on the assessment of operational procedures and definition of the ComPat operational model
Report on Instantiating Computing Patterns and performance measurements and prediction of HPMC Application

Report on the performance of all selected multiscale applications as measured on the Experimental Execution Environment and other available resources. It will give a detailed account of various metrics of resource usage, including wall clock time, data throughput, scalability and energy consumption. It will furnish detailed performance predictions for all selected multiscale applications on future exascale systems. This report will, as a major outcome of this project, present a forecast of the actual impact that exascale resources may have on future science applications by leveraging extreme parallelism.

Final Report on Multiscale Computing Patterns, including their Performance

Final report on the performance of all selected multiscale applications as measured on the Experimental Execution Environment and selected production environments. It will give a detailed account of various metrics of resource usage, including wall clock time, data throughput, scalability and energy consumption. It will also provide a detailed account on the performance prediction models.

First Report on Multiscale Computing Patterns and Algorithms

First report on the algorithms and components used to construct the Multiscale Computing Patterns, details of the actual implementation, and preliminary results on performance measurements.

First Report on status of performance profiling of multiscale simulations

First report on an analysis of the changes and impact on the initial simulations using the initial tools, including any architectural changes required since D4.1.

First Report on ComPat middleware services

A document summarizing the status of development of services offering a set of key capabilities for toolkits and patterns from WP2, including QoS on computational Tier-0/1 resources, dynamic multi-cluster co-allocation of resources, energy optimization and multi-cluster deployment and execution of ComPat multiscale simulations consisting of cooperating sub-models.

Third Dissemination Report

Review events and dissemination results of second project period.

Second Dissemination Report

Review events and dissemination results and propose actions for the coming one, including update of dissemination action plan.

Detailed Dissemination Action plan
Project Handbook

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

Publications

High-throughput Binding Affinity Calculations at Extreme Scales

Auteurs: Dakka, Jumana; Turilli, Matteo; Wright, David W; Zasada, Stefan J; Balasubramanian, Vivek; Wan, Shunzhou; Coveney, Peter V; Jha, Shantenu
Publié dans: BioMed Central, Numéro 1, 2018
Éditeur: Springer Nature

Multiscale Computing for Science and Engineering in the Era of Exascale Performance

Auteurs: A. G. Hoekstra, B. Chopard, D. Coster, S. Portegies Zwar, P. V. Coveney
Publié dans: 2018
Éditeur: The Royal Society Publishing
DOI: 10.1098/rsta.2018.0144

The heterogeneous multiscale method applied to inelastic polymer mechanics

Auteurs: M. Vassaux, R. Richardson, P. V. Coveney
Publié dans: 2018
Éditeur: The Royal Society Publishing
DOI: 10.1098/rsta.2018.0150

Application of the Extreme Scaling Computing Pattern on Multiscale Fusion Plasma Modelling

Auteurs: O. O. Luk, O. Hoenen, O. Perks, K. Brabazon, T. Piontek, P. Kopta, B. Bosak, A. Bottino, B. D. Scott, D. P. Coster
Publié dans: 2018
Éditeur: The Royal Society
DOI: 10.1098/rsta.2018.0152

ComPat Framework for Multiscale Simulations Applied to Fusion Plasmas

Auteurs: O. Luk, O. Hoenen, A. Bottino, B. Scott, D. Coster
Publié dans: Computer Physics Communications, 2018
Éditeur: Elsevier

Load Balancing Massively Parallel Cell-based Blood Flow Simulations

Auteurs: S. Alowayyed, V. Azizi, G. Zavodszky and A. G. Hoekstra
Publié dans: Computer Physics Communications, 2018
Éditeur: Elsevier

Predicting Queue Wait Time Probabilities for Multi-Scale Computing

Auteurs: V. Jancauskas, T. Piontek, P. Kopta, B. Bosak
Publié dans: Philosophical Transactions of the Royal Society, 2018
Éditeur: The Royal Society

Development of a multiscale simulation approach for forced migration

Auteurs: D. Groen
Publié dans: ICCS 2018, Springer Lecture Notes in Computer Science (LNCS), 2018
Éditeur: Springer

Modelling Refugees Escaping Violent Events: A Feasibility Study From An Input Data Perspective

Auteurs: N. T. Chan, D. Suleimenova, D. Bell, D. Groen
Publié dans: Proceedings of the Operational Research Society Simulation Workshop 2018, 2018
Éditeur: The Operational Research Society

Big Data: the End of the Scientific Method?

Auteurs: Sauro Succi, Peter V. Coveney
Publié dans: Phil Trans R Soc (Series A), 2018
Éditeur: The Royal Society
DOI: 10.1098/rsta.2018.0145

A Distributed Multi-agent Market Place for HPC Compute Cycle Resource Trading”

Auteurs: S. J. Zasada and P. V. Coveney
Publié dans: CoRR, 2015
Éditeur: Cornell University Library

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

Auteurs: D. Groen, J. Knap, P. Neumann, D. Suleimenova, L. Veen, K. Leiter
Publié dans: Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 2018
Éditeur: The Royal Society
DOI: 10.1098/rsta.2018.0147

SiMon: Simulation Monitor for Computational Astrophysics

Auteurs: Penny Xuran Qian, Maxwell Xu Cai, Simon Portegies Zwart, Ming Zhu
Publié dans: Publications of the Astronomical Society of the Pacific, Numéro 129/979, 2017, Page(s) 094503, ISSN 0004-6280
Éditeur: University of Chicago Press
DOI: 10.1088/1538-3873/aa7c49

Uncertainty Quantification in Alchemical Free Energy Methods

Auteurs: Agastya P. Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter V. Coveney
Publié dans: Journal of Chemical Theory and Computation, Numéro 14/6, 2018, Page(s) 2867-2880, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.7b01143

The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition

Auteurs: R. Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V. Coveney
Publié dans: Frontiers in Immunology, Numéro 8, 2017, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2017.00797

Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells

Auteurs: Gábor Závodszky, Britt van Rooij, Victor Azizi, Alfons Hoekstra
Publié dans: Frontiers in Physiology, Numéro 8, 2017, Page(s) 563, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2017.00563

Validation of Patient-Specific Cerebral Blood Flow Simulation Using Transcranial Doppler Measurements

Auteurs: Derek Groen, Robin A. Richardson, Rachel Coy, Ulf D. Schiller, Hoskote Chandrashekar, Fergus Robertson, Peter V. Coveney
Publié dans: Frontiers in Physiology, Numéro 9, 2018, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00721

Load balancing of parallel cell-based blood flow simulations

Auteurs: S. Alowayyed, G. Závodszky, V. Azizi, A.G. Hoekstra
Publié dans: Journal of Computational Science, Numéro 24, 2018, Page(s) 1-7, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2017.11.008

Stability of exomoons around the Kepler transiting circumbinary planets

Auteurs: Adrian S Hamers, Maxwell X Cai, Javier Roa, Nathan Leigh
Publié dans: Monthly Notices of the Royal Astronomical Society, Numéro 480/3, 2018, Page(s) 3800-3811, ISSN 0035-8711
Éditeur: Blackwell Publishing Inc.
DOI: 10.1093/mnras/sty2117

Multiscale computing in the exascale era

Auteurs: Saad Alowayyed, Derek Groen, Peter V. Coveney, Alfons G. Hoekstra
Publié dans: Journal of Computational Science, Numéro 22, 2017, Page(s) 15-25, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2017.07.004

Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation

Auteurs: Robert C. Sinclair, James L. Suter, Peter V. Coveney
Publié dans: Advanced Materials, Numéro 30/13, 2018, Page(s) 1705791, ISSN 0935-9648
Éditeur: United Nations Industrial Developement Organization
DOI: 10.1002/adma.201705791

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

Auteurs: Inti Pelupessy, Ben van Werkhoven, Arjen van Elteren, Jan Viebahn, Adam Candy, Simon Portegies Zwart, Henk Dijkstra
Publié dans: Geoscientific Model Development, Numéro 10/8, 2017, Page(s) 3167-3187, ISSN 1991-9603
Éditeur: Copernicus Publications
DOI: 10.5194/gmd-10-3167-2017

Numerical verification of the microscopic time reversibility of Newton’s equations of motion: Fighting exponential divergence

Auteurs: Simon F. Portegies Zwart, Tjarda C.N. Boekholt
Publié dans: Communications in Nonlinear Science and Numerical Simulation, Numéro 61, 2018, Page(s) 160-166, ISSN 1007-5704
Éditeur: Elsevier BV
DOI: 10.1016/j.cnsns.2018.02.002

Chemically Specific Multiscale Modeling of the Shear-Induced Exfoliation of Clay–Polymer Nanocomposites

Auteurs: James L. Suter, Peter V. Coveney
Publié dans: ACS Omega, Numéro 3/6, 2018, Page(s) 6439-6445, ISSN 2470-1343
Éditeur: ACS
DOI: 10.1021/acsomega.8b00542

A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data

Auteurs: Pavel S. Zun, Tatiana Anikina, Andrew Svitenkov, Alfons G. Hoekstra
Publié dans: Frontiers in Physiology, Numéro 8, 2017, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2017.00284

The signatures of the parental cluster on field planetary systems

Auteurs: Maxwell Xu Cai, Simon Portegies Zwart, Arjen van Elteren
Publié dans: Monthly Notices of the Royal Astronomical Society, Numéro 474/4, 2017, Page(s) 5114-5121, ISSN 0035-8711
Éditeur: Blackwell Publishing Inc.
DOI: 10.1093/mnras/stx3064

The dynamics of stellar discs in live dark-matter haloes

Auteurs: M S Fujii, J Bédorf, J Baba, S Portegies Zwart
Publié dans: Monthly Notices of the Royal Astronomical Society, Numéro 477/2, 2018, Page(s) 1451-1471, ISSN 0035-8711
Éditeur: Blackwell Publishing Inc.
DOI: 10.1093/mnras/sty711

PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling

Auteurs: Miguel O. Bernabeu, Martin L. Jones, Rupert W. Nash, Anna Pezzarossa, Peter V. Coveney, Holger Gerhardt, Claudio A. Franco
Publié dans: Biophysical Journal, Numéro 114/9, 2018, Page(s) 2052-2058, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2018.03.032

The Oceanographic Multipurpose Software Environment

Auteurs: Inti Pelupessy, Ben van Werkhoven, Arjen van Elteren, Jan Viebahn, Adam Candy, Simon Portegies Zwart, Henk Dijkstra
Publié dans: Geoscientific Model Development Discussions, 2016, Page(s) 1-36, ISSN 1991-962X
Éditeur: EGU
DOI: 10.5194/gmd-2016-178

Stability of multiplanetary systems in star clusters

Auteurs: Maxwell Xu Cai (蔡栩), M. B. N. Kouwenhoven, Simon F. Portegies Zwart, Rainer Spurzem
Publié dans: Monthly Notices of the Royal Astronomical Society, Numéro 470/4, 2017, Page(s) 4337-4353, ISSN 0035-8711
Éditeur: Blackwell Publishing Inc.
DOI: 10.1093/mnras/stx1464

Simulations of stripped core-collapse supernovae in close binaries

Auteurs: Alex Rimoldi, Simon Portegies Zwart, Elena Maria Rossi
Publié dans: Computational Astrophysics and Cosmology, Numéro 3/1, 2016, ISSN 2197-7909
Éditeur: Springer
DOI: 10.1186/s40668-016-0015-4

Hemocell: a high-performance microscopic cellular library

Auteurs: Gábor Zavodszky, Britt van Rooij, Victor Azizi, Saad Alowayyed, Alfons Hoekstra
Publié dans: Procedia Computer Science, Numéro 108, 2017, Page(s) 159-165, ISSN 1877-0509
Éditeur: Elsevier
DOI: 10.1016/j.procs.2017.05.084

The evolution of hierarchical triple star-systems

Auteurs: Silvia Toonen, Adrian Hamers, Simon Portegies Zwart
Publié dans: Computational Astrophysics and Cosmology, Numéro 3/1, 2016, ISSN 2197-7909
Éditeur: Springer
DOI: 10.1186/s40668-016-0019-0

On the calculation of equilibrium thermodynamic properties from molecular dynamics

Auteurs: Peter V. Coveney, Shunzhou Wan
Publié dans: Physical Chemistry Chemical Physics, Numéro 18/44, 2016, Page(s) 30236-30240, ISSN 1463-9076
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c6cp02349e

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, 2018, ISSN 1869-408X
Éditeur: Springer Pub. Co.,
DOI: 10.1007/s13239-018-00372-4

The origin of interstellar asteroidal objects like 1I/2017 U1 ‘Oumuamua

Auteurs: Simon Portegies Zwart, Santiago Torres, Inti Pelupessy, Jeroen Bédorf, Maxwell X Cai
Publié dans: Monthly Notices of the Royal Astronomical Society: Letters, Numéro 479/1, 2018, Page(s) L17-L22, ISSN 1745-3933
Éditeur: Blackwell Publishing
DOI: 10.1093/mnrasl/sly088

Multiscale modeling: recent progress and open questions

Auteurs: Bastien Chopard, Jean-Luc Falcone, Pierre Kunzli, Lourens Veen, Alfons Hoekstra
Publié dans: Multiscale and Multidisciplinary Modeling, Experiments and Design, Numéro 1/1, 2018, Page(s) 57-68, ISSN 2520-8160
Éditeur: Springer
DOI: 10.1007/s41939-017-0006-4

Patterns for High Performance Multiscale Computing

Auteurs: S. Alowayyed, T. Piontek, J.L. Suter, O. Hoenen, D. Groen, O. Luk, B. Bosak, P. Kopta, K. Kurowski, O. Perks, K. Brabazon, V. Jancauskas, D. Coster, P.V. Coveney, A.G. Hoekstra
Publié dans: Future Generation Computer Systems, Numéro 91, 2019, Page(s) 335-346, ISSN 0167-739X
Éditeur: Elsevier BV
DOI: 10.1016/j.future.2018.08.045

Towards the virtual artery: a multiscale model for vascular physiology at the physics–chemistry–biology interface

Auteurs: Alfons G. Hoekstra, Saad Alowayyed, Eric Lorenz, Natalia Melnikova, Lampros Mountrakis, Britt van Rooij, Andrew Svitenkov, Gábor Závodszky, Pavel Zun
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 374/2080, 2016, Page(s) 20160146, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2016.0146

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

Auteurs: Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Ian Wall, Darren Green, Paul Bamborough, Peter V. Coveney
Publié dans: Journal of Chemical Theory and Computation, Numéro 13/2, 2017, Page(s) 784-795, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.6b00794

FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures

Auteurs: Derek Groen, Agastya P. Bhati, James Suter, James Hetherington, Stefan J. Zasada, Peter V. Coveney
Publié dans: Computer Physics Communications, Numéro 207, 2016, Page(s) 375-385, ISSN 0010-4655
Éditeur: Elsevier BV
DOI: 10.1016/j.cpc.2016.05.020

Mechanism of Exfoliation and Prediction of Materials Properties of Clay–Polymer Nanocomposites from Multiscale Modeling

Auteurs: James L. Suter, Derek Groen, Peter V. Coveney
Publié dans: Nano Letters, Numéro 15/12, 2015, Page(s) 8108-8113, ISSN 1530-6984
Éditeur: American Chemical Society
DOI: 10.1021/acs.nanolett.5b03547

LB3D: A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids

Auteurs: S. Schmieschek, L. Shamardin, S. Frijters, T. Krüger, U.D. Schiller, J. Harting, P.V. Coveney
Publié dans: Computer Physics Communications, 2017, ISSN 0010-4655
Éditeur: Elsevier BV
DOI: 10.1016/j.cpc.2017.03.013

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

Auteurs: Shunzhou Wan, Agastya P. Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram, Sharan K. Bagal, Peter V. Coveney
Publié dans: Journal of Chemical Information and Modeling, Numéro 57/4, 2017, Page(s) 897-909, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.6b00780

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

Auteurs: Agastya P. Bhati, Shunzhou Wan, David W. Wright, Peter V. Coveney
Publié dans: Journal of Chemical Theory and Computation, Numéro 13/1, 2016, Page(s) 210-222, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.6b00979

Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations

Auteurs: Dakka, Jumana; Farkas-Pall, Kristof; Turilli, Matteo; Wright, David W; Coveney, Peter V; Jha, Shantenu
Publié dans: arXiv, Numéro 1, 2018
Éditeur: arXiv

From Thread to Transcontinental Computer: Disturbing Lessons in Distributed Supercomputing

Auteurs: Derek Groen, Simon Portegies Zwart
Publié dans: 2015 IEEE 11th International Conference on e-Science, 2015, Page(s) 565-571, ISBN 978-1-4673-9325-6
Éditeur: IEEE
DOI: 10.1109/eScience.2015.81

Optimization of Multiscale fusion Plasma Simulations within the ComPat Framework

Auteurs: O. Luk, O. Hoenen, A. Bottino, B. Scott, D. Coster
Publié dans: EPS Proceedings, Numéro P1, 2018, Page(s) 1102, ISBN 979-10-96389-08-7
Éditeur: European Physical Society

Astrophysical Recipes: the Art of AMUSE

Auteurs: S. Portegies Zwart and S. McMillan
Publié dans: AAS IOP Astronomy, 2018
Éditeur: IOP

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