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High Performance Computing on CRESCO infrastructure: research activities and results 2018

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High Performance Computing on

CRESCO infrastructure:

research activities and results 2018

Italian National Agency for New Technologies, Energy and Sustainable Economic Development

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H

IGH

P

ERFORMANCE

C

OMPUTING

ON

CRESCO

INFRASTRUCTURE

:

RESEARCH

ACTIVITY

AND

RESULTS

2018

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Contributions provided by a selection of users of the CRESCO infrastructure

Scientific Editor: Giuseppe Santomauro, ENEA, DTE-ICT-HPC, CR Portici

Acknowledgements: We wish to thank Gianclaudio Ferro for providing the Reporter

system (http://hdl.handle.net/10840/5791) to collect contributions and to build the

Volume

Cover: Amedeo Trolese, ENEA, DTE-ICT, CR Frascati

ISBN: 978-88-8286-390-6

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Contents

1. Foreword 5

2. CRESCO HPC clusters evolution, users and workloads 2008-2018

G.Bracco, S.Migliori, A.Quintiliani, F.Iannone, F.Ambrosino, G.Aprea, A.Colavincenzo, P.D’Angelo, A.Funel, G.Guarnieri, A.Mariano, F.Palombi, S.Pierattini, G.Ponti,

G.Santomauro et al. 6

3. Critical Infrastructure Protection: CRESCO6 Tsunami simulations in Southern Italy

F.Iannone, S.Migliori and DTE-ICT-HPC Team 13

4. Report on the performance on the CRESCO6 cluster of the hybrid OpenMP/MPI orac6.1 molecular dynamics code

P.Procacci and G.Guarnieri 18

5. Effect of bidispersity in polymer chain length on the potential of mean force between nanoparticles in a holopolymer matrix

G.Munaò, A.De Nicola, S.Caputo, G.Donati, A.Pizzirusso, Y.Zhao and G.Milano 23 6. Functionalization of Phosphorene 2D material: a computational investigation

A.Ienco, G.Manca and M.Peruzzini 28

7. Peptide bonds detection via graphene nanogaps: a proof of principle study

G.Zollo, T.Civitarese and A.E.Rossini 32

8. Code parallelization of the optimisation for the local transport’s electrification using job array

G.Chiapparo and M.Celino 45

9. Alpha Spectrometry with inexpensive prototyping board: simulation, design and experimental tests

L.Lepore, G.A.Marzo and L.Gugliermetti 51

10. Run-length performance estimation of the functional regression control chart

F.Centofanti, A.Lepore, A.Menafoglio, B.Palumbo and S.Vantini 55 11. Multiscale modeling of carbon black nanoparticles in polyethylene melts

S.Caputo, A.De Nicola, G.Donati and G.Munaò 59

12. Swap dynamics in kinetically constrained models of the glass transition and in blockaded systems of cold atoms

R.Gutiérrez 62

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12. Swap dynamics in kinetically constrained models of the glass transition and in blockaded systems of cold atoms

R.Gutiérrez 62

13. Mesoporous organosilica, gas sorption investigation by atomistic simulations

A.De Nicola, G.Munaò, A.Pizzirusso, G,Donati, S.Caputo and J.M.Vicent Luna 66 14. Modeling electrical and thermal properties of carbon nanotubes enforced composite

materials

Y.Zhao, G.Donati, A.De Nicola, A.Pizzirusso, G.Munao, S.Caputo and G.Milano 70 15. DNS of a CH4/CO2/O2 Non-Premixed Flame at 300 bar

D.Cecere, E.Giacomazzi, N.Arcidiacono and F.R.Picchia 75 16. Ozone risk assessment to forest in Asia: comparison between different approaches

A.Anav, A.De Marco 88

17. Ab initio simulations of amorphous GeO2 under pressure: a first search for phase transitions

G.Mancini, M.Celino, A.Di Cicco and E.Covino 91

18. Percolation paths through simulated granular superconductors

G.Mancini 97

19. Dynamical complexity as a proxy for the network degree distribution

A.Tlaie, I.Leyva and I.Sendiña-Nadal 103

20. Diffraction line profiles of spherical hollow nanocrystals

E.Burresi and L.Tapfer 108

21. Validation and analysis of the MITO circulation forecast model for the Mediterranean Sea-Black Sea system

G.Sannino, A.Bargagli, A.Carillo, R.Iacono, E.Lombardi, E.Napolitano, M.Palma,

G.Pisacane and M.V.Struglia 112

22. Air quality forecast system over Italy: FORAIR-IT

M.Adani, G.Guarnieri, L.Vitali, M.Mircea, M.D’Isidoro, A.Cappelletti and L.Ciancarella 116 23. Wave diffraction and transmission by submerged breakwater

P.Filianoti and L.Gurnari 120

24. ENEA-INMRI Monte Carlo calculations for the update of the IAEA TRS 398 dosimetry protocol

M.Pimpinella and M.Pinto 125

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24. ENEA-INMRI Monte Carlo calculations for the update of the IAEA TRS 398 dosimetry protocol

M.Pimpinella and M.Pinto 125

25. Recent developments and applications of hybrid MHD-gyrokinetic codes to realistic plasma scenarios

S.Briguglio, G.Fogaccia, G.Vlad and T.Wang 129

26. Silicene on an Insulating Substrate

O.Pulci and P.Gori 134

27. Advanced D1S dynamic code validation through a Shutdown dose rate benchmark experiment at jet

R.Villari, D.Flammini, N.Fonnesu, S.Loreti and G.Mariano 138 28. Comparison between deterministic and stochastic codes on depletion calculations for

an Er-SHB PWR FA

R.Pergreffi, F.Rocchi, A.Guglielmelli and P.Console Camprini 142 29. Improvement of the ENEA Neutron Active Interrogation system performances

G.Gandolfo 147

30. Mapping renewable energy potential map over Lesotho

M.D’Isidoro, G.Briganti, L.Vitali, G.Righini and M.Adani 151 31. Molecular Dynamics Simulation of Peptides for Brain Theranostic Nanosystems

C.Arcangeli, C.Lico, S.Baschieri and M.Mancuso 155

32. Nuclear analysis of the Water Cooled Lithium Lead DEMO reactor

F.Moro, A.Colangeli, A.Del Nevo, D.Flammini, G.Mariano, E.Martelli, R.Mozzillo,

S.Noce and R.Villari 162

33. Ab initio simulation of advanced magnetic materials

F.Totti, A.Albino and F.Buonocore 166

34. Neutronics analyses of DEMO divertor

D.Flammini, R.Villari, F.Moro, N.Fonnesu, G.Mariano and A.Colangeli 170 35. Neutronics analysis for the design and integration of the pellet guiding tube in DEMO

A.Colangeli, R.Villari, F.Moro, D.Flammini, G.Mariano and N.Fonnesu 174 36. Comparative study of the neutronic performances of EU-WCLL and China-WCCB

breeding blanket concepts

P.Chiovaro, A.Del Nevo and P.A.Di Maio 178

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36. Comparative study of the neutronic performances of EU-WCLL and China-WCCB breeding blanket concepts

P.Chiovaro, A.Del Nevo and P.A.Di Maio 178

37. Ab Initio study of Na-Ion Insertion in a High Energy Cathode for Sodium Batteries

M.Pavone, A.Massaro, M.Tuccillo and A.B.Muñoz-García 182 38. Polymer physics and computational approaches to investigate genome spatial

organization

M.Conte, A.Esposito, L.Fiorillo, C.Annunziatella, A.M.Chiariello and S.Bianco 187 39. Monte Carlo Simulations Supporting Studies of PWR’s, Nuclear Criticality Safety and

TAPIRO Research Reactor Simulations

P.Console Camprini and K.W.Burn 194

40. The impact of boron doping on hydrogen storage properties of MgH2

S.Kurko, B.P.Mamula, J.Rmus, J.G.Novakovic and N.Novakovic 198 41. Study of solid molecular deuterium D2 growth for high speed pipegun pellet injector

S.Giusepponi, F.Buonocore, M.Celino, A.Frattolillo and S.Migliori 202 42. Exact Calculation of Extinction Probabilities in Games of Cyclic Dominance

F.Palombi 206

43. Evolution of the Internet at the Autonomous Systems Level During a Decade

A.Funel 213

44. CRESCO ENEA HPC clusters: a working example of a multifabric GPFS Spectrum Scale layout

F.Iannone, F.Ambrosino, G.Bracco, M.De Rosa, A.Funel, G.Guarnieri, S.Migliori,

F.Palombi, G.Ponti and G.Santomauro 222

45. Parallel Text Mining of Large Corpora in GRID Environment - TaLTaC in ENEAGRID infrastructure

S.Migliori, D.Alderuccio, F.Ambrosino, A.Colavincenzo, M.Mongelli, S.Pierattini,

G.Ponti, A.Quintiliani, S.Bolasco, F.Baiocchi and G.De Gasperis 227

46. Author Index 233

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