High Performance Computing in Life Sciences, Engineering And Physics

Deliverables

ETHICS

Clearence of Ethics issues according to the Ethics requirements

Scientific publications report

Report on scientific publications from WP1 – WP5

Final project report

Report on project activities and results

Dissemination and outreach plan

Targeted plan for dissemination and outreach activity As suggested in the proposal UC will lead the deliverable

draft period report

draft first Periodic report to be delivered before the MTR

Final Dissemination report

Annual report of dissemination activities As suggested in the proposal UC will lead the deliverable

Progress report

First progress report

Report on workshops

Training description and evaluation As suggested in the proposal TCD will lead the deliverable

ATLANTIS project HiPOP website

Report on content of the EU-USA ATLANTIS project portal

Report on conference

Report on scientific results with emphasis on the project outcomes As suggested in the proposal UC will lead the deliverable

Report on potential exascale architectures

Evaluation of HPC architectures for exascale using lattice QCD kernels As suggested in the proposal JUELICH will lead the deliverable

Year-3 Dissemination report

Annual report of dissemination activities As suggested in the proposal UC will lead the deliverable

Protein/DNA interactions explored by molecular simulation

Investigation of the effect of in vivo post-translational modifications (PTMs) on the interaction between platinated DNA- formed in cells undergoing anticancer treatment of cisplatin – and its target protein HMGB1.

Algorithms for suspension hydrodynamics

Report on pseudo-spectral and Lattice Boltzmann algorithms for suspension hydrodynamics

Year-1 Dissemination report

Annual report of dissemination activities As suggested in the proposal UC will lead the deliverable

Lattice Boltzmann Algorithms

Report on the effect of thermal fluctuations in multiphase fluids

Turbulence models in LBM

Report on the adaptation of LBM codes to model turbulence using LE/testing on accelerators

Report on HPC architecture and technology trends

Market analysis of trends for HPC architectures and technologies As suggested in the proposal JUELICH will lead the deliverable

Continuum model for population genetics

Description of the process of development a hybrid approach that, while retaining the features of the continuum Fisher approach, it can allow to quantitatively study genetics evolution.

Report on shared courses

Assessment of educational effectiveness node-shared courses As suggested in the proposal TCD will lead the deliverable

Hadron spectrum and resonances

Publications on Hadron spectrum and resonance parameters As suggested in the proposal TCD will lead the deliverable

Year-2 Dissemination report

Annual report of dissemination activities As suggested in the proposal UC will lead the deliverable

String Breaking from Lattice QCD with up, down and strange sea quarks

Description of testing of the code, application for computer time at ICHEC in Ireland, and analysis of string breaking.

Hybrid Monte-Carlo algorithms

Report on the parallelized and optimized algorithms to explore rare events in hydrodynamics

Report on Ph.D. awards

List of Ph.D. awarded thesis

Career Development Plan (CDP)

CDP on the career path of each ESR

Coarse Grain /All Atoms code

Implementation of adaptive resolution schemes and AMBER-based force

Supervisory board

Supervisory board for the Network

Domain decomposition (DD) algorithm

Prototype asynchronous algebraic DD for preconditioning communication-avoiding Krylov-subspace methods

Deflation algorithm

Prototype deflation-based method incorporating multilevel representation of the deflation subspace

Nucleon structure and BSM physics

Results and publication on nucleon and BSM observables

Quantum Mechanics (QM)/Molecular mechanics (MM) codes

Optimization of selected QM/MM codes for scaling on BlueGene/Q

Time-like form factors

Preliminary results on time-like form factors As suggested in the proposal DESY will lead the deliverable

New approaches for disconnected diagrams

Publication of results of disconnected graphs for nucleon structure As suggested in the proposal DESY will lead the deliverable

QCD algorithms

Scalability of deflation-based methods in large-scale QCD computations

Kick-off meeting and SB meeting at CyI

Report on the event. Stakeholder meeting for project kick-off

Multigrid algorithms

Prototype asynchronous algebraic multigrid for preconditioning communication-avoiding Krylov-subspace methods

Report on LBM codes

Publication on improvement of LBM

Multilevel methods

Publication on convergence behaviour of asynchronous multilevel methods

Project training portal

Assembly of training material for the portal maintained at CyI

GPCRs and SMIs

Publication of mosquito GPCRs and SMIs As suggested in the proposal ICL will lead the deliverable

Project dissemination material

Showcase for students and the general public As suggested in the proposal UC will lead the deliverable

MTR

Midterm review meeting

Further development of QM/MM codes for exascale

Development of new parallel strategies for multiscale QM/MM molecular dynamics algorithms suitable for exascale machines. As suggested in the proposal IBM will lead the deliverable

Project website

EJD project website

Publications

Performance and portability of accelerated lattice Boltzmann applications with OpenACC

Author(s): Calore, E., Gabbana, A., Kraus, J., Schifano, S. F. and Tripiccione, R.
Published in: Concurrency and Computation: Practice and Experience, Issue 28, 2016, Page(s) 3485–3502, ISSN 1532-0626
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpe.3862

Adaptive aggregation-based domain decomposition multigrid for twisted mass fermions

Author(s): Alexandrou, C., Bacchio, S., Finkenrath, J., Frommer, A., Kahl, K., and Rottmann, M.
Published in: Physical Review D, Issue 94, 2016, Page(s) 114509, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/physrevd.94.114509

Massively parallel lattice–Boltzmann codes on large GPU clusters

Author(s): Calore, E., Gabbana, A., Kraus, J., Pellegrini, E., Schifano, S. and Tripiccione, R.
Published in: Parallel Computing, Issue 58, 2016, Page(s) 1 - 24, ISSN 0167-8191
Publisher: Elsevier BV
DOI: 10.1016/j.parco.2016.08.005

Isospin-0 ππ s-wave scattering length from twisted mass lattice QCD

Author(s): Liu, L., Bacchio, S., Dimopoulos, P., Finkenrath, J., Frezzotti, R., Helmes, C., Jost, C., Knippschild, B., Kostrzewa, B., Liu, H., Ottnad, K., Petschlies, M., Urbach, C. & Werner, M.
Published in: Physical Review D, Issue 10.1103/PhysRevD.96.054516, 2017, ISSN 1824-8039
Publisher: American Physical Society

Systematic uncertainties in parton distribution functions from lattice QCD simulations at the physical point

Author(s): Constantia Alexandrou, Krzysztof Cichy, Martha Constantinou, Kyriakos Hadjiyiannakou, Karl Jansen, Aurora Scapellato, Fernanda Steffens
Published in: Physical Review D, Issue 99/11, 2019, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/PhysRevD.99.114504

Pion vector form factor from lattice QCD at the physical point

Author(s): C. Alexandrou, S. Bacchio, P. Dimopoulos, J. Finkenrath, R. Frezzotti, K. Jansen, B. Kostrzewa, M. Mangin-Brinet, F. Sanfilippo, S. Simula, C. Urbach, U. Wenger
Published in: Physical Review D, Issue 97/1, 2018, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/PhysRevD.97.014508

Charm quark effects on the strong coupling extracted from the static force

Author(s): Salvatore Calì, Francesco Knechtli, Tomasz Korzec, Haralambos Panagopoulos
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 10002, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817510002

Software and DVFS Tuning for Performance and Energy-Efficiency on Intel KNL Processors

Author(s): Enrico Calore, Alessandro Gabbana, Sebastiano Schifano, Raffaele Tripiccione
Published in: Journal of Low Power Electronics and Applications, Issue 8/2, 2018, Page(s) 18, ISSN 2079-9268
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/jlpea8020018

Computation of parton distributions from the quasi-PDF approach at the physical point

Author(s): Constantia Alexandrou, Simone Bacchio, Krzysztof Cichy, Martha Constantinou, Kyriakos Hadjiyiannakou, Karl Jansen, Giannis Koutsou, Aurora Scapellato, Fernanda Steffens
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 14008, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817514008

Effects of a strong magnetic field on the QCD flux tube

Author(s): Claudio Bonati, Salvatore Calì, Massimo D’Elia, Michele Mesiti, Francesco Negro, Andrea Rucci, Francesco Sanfilippo
Published in: Physical Review D, Issue 98/5, 2018, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/PhysRevD.98.054501

Progress in computing parton distribution functions from the quasi-PDF approach

Author(s): Constantia Alexandrou, Krzysztof Cichy, Martha Constantinou, Kyriakos Hadjiyiannakou, Karl Jansen, Haralambos Panagopoulos, Aurora Scapellato, Fernanda Steffens
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 06021, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817506021

Simulating twisted mass fermions at physical light, strange, and charm quark masses

Author(s): Constantia Alexandrou, Simone Bacchio, Panagiotis Charalambous, Petros Dimopoulos, Jacob Finkenrath, Roberto Frezzotti, Kyriakos Hadjiyiannakou, Karl Jansen, Giannis Koutsou, Bartosz Kostrzewa, Mariane Mangin-Brinet, Giancarlo Rossi, Silvano Simula, Carsten Urbach
Published in: Physical Review D, Issue 98/5, 2018, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/PhysRevD.98.054518

Transversity parton distribution functions from lattice QCD

Author(s): Constantia Alexandrou, Krzysztof Cichy, Martha Constantinou, Karl Jansen, Aurora Scapellato, Fernanda Steffens
Published in: Physical Review D, Issue 98/9, 2018, ISSN 2470-0010
Publisher: American Physical Sciences
DOI: 10.1103/PhysRevD.98.091503

Hybrid Monte Carlo algorithm for sampling rare events in space-time histories of stochastic fields

Author(s): G. Margazoglou, L. Biferale, R. Grauer, K. Jansen, D. Mesterházy, T. Rosenow, R. Tripiccione
Published in: Physical Review E, Issue 99/5, 2019, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/physreve.99.053303

Multigrid accelerated simulations for Twisted Mass fermions

Author(s): Simone Bacchio, Constantia Alexandrou, Jacob Finkerath
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 02002, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817502002

Optimization of lattice Boltzmann simulations on heterogeneous computers

Author(s): E Calore, A Gabbana, SF Schifano, R Tripiccione
Published in: The International Journal of High Performance Computing Applications, Issue 33/1, 2017, Page(s) 124-139, ISSN 1094-3420
Publisher: SAGE Publications
DOI: 10.1177/1094342017703771

Effects of thermal fluctuations in the fragmentation of a nanoligament

Author(s): X. Xue, M. Sbragaglia, L. Biferale, F. Toschi
Published in: Physical Review E, Issue 98/1, 2018, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/PhysRevE.98.012802

π γ → π π transition and the ρ radiative decay width from lattice QCD

Author(s): Constantia Alexandrou, Luka Leskovec, Stefan Meinel, John Negele, Srijit Paul, Marcus Petschlies, Andrew Pochinsky, Gumaro Rendon, Sergey Syritsyn
Published in: Physical Review D, Issue 98/7, 2018, ISSN 2470-0010
Publisher: American Physical Society
DOI: 10.1103/PhysRevD.98.074502

Energy-efficiency evaluation of Intel KNL for HPC workloads

Author(s): Calore, E.; Gabbana, A.; Schifano, S. F.; Tripiccione, R.
Published in: Journal of Low Power Electronics and Applications, Issue 7, 2018, ISSN 2079-9268
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3233/978-1-61499-843-3-733

Simulation of an ensemble of N f = 2 + 1 + 1 twisted mass cloverimproved fermions at physical quark masses

Author(s): Jacob Finkenrath, Constantia Alexandrou, Simone Bacchio, Panagiotis Charalambous, Petros Dimopoulos, Roberto Frezzotti, Karl Jansen, Bartosz Kostrzewa, Giancarlo Rossi, Carsten Urbach
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 02003, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817502003

String breaking by light and strange quarks in QCD

Author(s): John Bulava, Ben Hörz, Francesco Knechtli, Vanessa Koch, Graham Moir, Colin Morningstar, Mike Peardon
Published in: Physics Letters B, Issue 793, 2019, Page(s) 493-498, ISSN 0370-2693
Publisher: Elsevier BV
DOI: 10.1016/j.physletb.2019.05.018

Kinetic approach to relativistic dissipation

Author(s): A. Gabbana, M. Mendoza, S. Succi, R. Tripiccione
Published in: Physical Review E, Issue 96/2, 2017, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/PhysRevE.96.023305

Instanton based importance sampling for rare events in stochastic PDEs

Author(s): Lasse Ebener, Georgios Margazoglou, Jan Friedrich, Luca Biferale, Rainer Grauer
Published in: Chaos: An Interdisciplinary Journal of Nonlinear Science, Issue 29/6, 2019, Page(s) 063102, ISSN 1054-1500
Publisher: American Institute of Physics
DOI: 10.1063/1.5085119

Numerical evidence of electron hydrodynamic whirlpools in graphene samples

Author(s): A. Gabbana, M. Mendoza, S. Succi, R. Tripiccione
Published in: Computers & Fluids, Issue 172, 2018, Page(s) 644-650, ISSN 0045-7930
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compfluid.2018.02.020

Relativistic dissipation obeys Chapman-Enskog asymptotics: Analytical and numerical evidence as a basis for accurate kinetic simulations

Author(s): A. Gabbana, D. Simeoni, S. Succi, R. Tripiccione
Published in: Physical Review E, Issue 99/5, 2019, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/PhysRevE.99.052126

Lattice Boltzmann simulations of droplet dynamics in time-dependent flows

Author(s): F. Milan, M. Sbragaglia, L. Biferale, F. Toschi
Published in: The European Physical Journal E, Issue 41/1, 2018, ISSN 1292-8941
Publisher: Springer Verlag
DOI: 10.1140/epje/i2018-11613-0

Prospects for the Detection of Electronic Preturbulence in Graphene

Author(s): A. Gabbana, M. Polini, S. Succi, R. Tripiccione, F. M. D. Pellegrino
Published in: Physical Review Letters, Issue 121/23, 2018, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.121.236602

Flux tubes in N f = 2 + 1 QCD with external magnetic fields

Author(s): Claudio Bonati, Salvatore Calì, Massimo D’Elia, Michele Mesiti, Francesco Negro, Andrea Rucci, Francesco Sanfilippo
Published in: EPJ Web of Conferences, Issue 175, 2018, Page(s) 12008, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/201817512008

Multigrid approach in shifted linear systems for the non-degenerated twisted mass operator

Author(s): Constantia Alexandrou, Simone Bacchio, Jacob Finkenrath
Published in: Computer Physics Communications, Issue 236, 2019, Page(s) 51-64, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2018.10.013

Light-Cone Parton Distribution Functions from Lattice QCD

Author(s): Constantia Alexandrou, Krzysztof Cichy, Martha Constantinou, Karl Jansen, Aurora Scapellato, Fernanda Steffens
Published in: Physical Review Letters, Issue 121/11, 2018, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.121.112001

Multiscale velocity correlations in turbulence and Burgers turbulence: Fusion rules, Markov processes in scale, and multifractal predictions

Author(s): Jan Friedrich, Georgios Margazoglou, Luca Biferale, Rainer Grauer
Published in: Physical Review E, Issue 98/2, 2018, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/PhysRevE.98.023104

Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes

Author(s): Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Paolo Carloni
Published in: Journal of Chemical Theory and Computation, Issue 15/3, 2019, Page(s) 2101-2109, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00040

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

Author(s): Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Alejandro Giorgetti, Paolo Carloni
Published in: Journal of Chemical Theory and Computation, Issue 13/11, 2017, Page(s) 5647-5657, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.7b00508

Evaluation of DVFS techniques on modern HPC processors and accelerators for energy-aware applications

Author(s): Enrico Calore, Alessandro Gabbana, Sebastiano Fabio Schifano, Raffaele Tripiccione
Published in: Concurrency and Computation: Practice and Experience, 2017, Page(s) e4143, ISSN 1532-0626
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpe.4143

Towards a unified lattice kinetic scheme for relativistic hydrodynamics

Author(s): A. Gabbana, M. Mendoza, S. Succi, R. Tripiccione
Published in: Physical Review E, Issue 95/5, 2017, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/PhysRevE.95.053304

A study of the radiative transition ππ → πγ∗ with lattice QCD.

Author(s): Leskovec, L., Alexandrou, C., Koutsou, G., Meinel, S., Negele, J. W., Paul, S., Petschlies, M., Pochinsky, A., Rendon, G. and Syritsyn, S.
Published in: Proceedings of Science (LATTICE2016), 2016, Page(s) 159, ISSN 1824-8039
Publisher: SISA (Scuola Internazionale Superiore di Studi Avanzati)

DDalphaAMG for twisted mass fermions

Author(s): Bacchio, S., Alexandrou, C., Finkenrath, J., Frommer, A., Kahl, K. and Rottmann, M.
Published in: Proceedings of Science (LATTICE2016), 2016, Page(s) 259, ISSN 1824-8039
Publisher: SISA (Scuola Internazionale Superiore di Studi Avanzati)

Impact of dynamical charm quarks

Author(s): Tomasz Korzec, Francesco Knechtli, Salvatore Cali, Björn Leder, Graham Moir
Published in: Proceedings of 34th annual International Symposium on Lattice Field Theory — PoS(LATTICE2016), 2017, Page(s) 126
Publisher: Sissa Medialab
DOI: 10.22323/1.256.0126

Early Experience on Using Knights Landing Processors for Lattice Boltzmann Applications

Author(s): Enrico Calore, Alessandro Gabbana, Sebastiano Fabio Schifano, Raffaele Tripiccione
Published in: Parallel Processing and Applied Mathematics - 12th International Conference, PPAM 2017, Lublin, Poland, September 10-13, 2017, Revised Selected Papers, Part I, Issue 10777, 2018, Page(s) 519-530, ISBN 978-3-319-78023-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-78024-5_45

String breaking with 2+1 dynamical fermions using the stochastic LapH method

Author(s): V. Koch, J. Bulava, B. Hörz, F. Knechtli, G. Moir, C. Morningstar and M. Peardon
Published in: 2018
Publisher: Cornell University

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