PRACE Scientific Conference 2012

The 2012 PRACE Scientific Conference will be held on Sunday, June 17, in Hamburg, Germany.

Top European scientists will highlight advances in large scale simulation and key results obtained with support by PRACE, the Partnership for Advanced Computing in Europe. The European Commission and the PRACE director will present Europe’s vision for HPC.

Scientist and researchers from academia and industry are cordially invited to participate, learn from colleagues what can be achieved using PRACE services and indentify opportunities for future PRACE supported projects. The programme will include a short meeting of the User Forum which will provide an opportunity for users and those considering applying for PRACE resources to discuss issues with the PRACE management and members of the Scientific Steering Committee.

This year PRACE partners with ISC, the International Supercomputing Conference, maximizing the value for PRACE and ISC’12 attendees. Participation in the PRACE programme on Sunday is free of charge. However, all participants should register via the ISC registration. After the end of the sessions PRACE and ISC invite you to an informal get-together with colleagues from Asia-Pacific participating in the Asia-Pacific day organised in parallel by ISC.

The conference takes place at the Radisson Blu Hotel close to the Congress Center Hamburg. For more information please contact praceday2012-oc(at)

- Registration: Closed.


08:30 – 09:00 Registration

09:00 – 09:15 Welcome

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Richard Kenway

Richard Kenway, Chair of PRACE Scientific Steering Committee & Conference Chairman

Professor Richard Kenway chairs the PRACE Scientific Steering Committee, which advises PRACE on all scientific and technical matters, particularly the peer review process for allocating PRACE resources.

Professor Kenway is Tait Professor of Mathematical Physics at the University of Edinburgh and Chairman of EPCC. His research explores non-perturbative aspects of theories of elementary particles using computer simulation, particularly the strong interactions of quarks and gluons. As a University Vice-Principal, he is responsible for promoting advanced computing to benefit academia and industry, including provision of the UK’s HECToR and DiRAC HPC services. He is a founding member of the UK e-Infrastructure Leadership Council.

09:15 – 09:45 PRACE: computing for scientific breakthroughs

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Maria Ramalho

Maria Ramalho, Chairman of the Board of Directors, PRACE AISBL

Maria F. Ramalho is Managing Director of PRACE: Partnership for Advanced Computing in Europe. PRACE, the European Research Infrastructure provides access to world class high-performance computing (HPC) resources to researchers from around the world through a peer review process. Maria holds a Ph.D. in electronic engineering from the University of London, U.K. and a B.Sc. in Mathematics/Computer Science from the University of Coimbra, Portugal. In the past she has worked for Alcatel Research Labs and for a private research Lab in Brussels, Belgium. In 2004 she was hired by the European Commission Directorate General Information Society as Project Officer. Maria Ramalho joined PRACE in 2011 after having worked with an interest group to create the European Technology Platform on High-Performance Computing. She strongly supports and promotes research breakthroughs using HPC, the adoption of HPC by European industry, the added-value of Information and Communication Technologies in public utility sectors (e.g. education, health, civil protection) and the integration of computational sciences in academic curricula at graduate and postgraduate level.

09:45 – 10:15 The European HPC Strategy
Kostas Glinos, Head of Unit “GÉANT & e-Infrastructure”, European Commission

10:15 – 10:45 Coffee Break

10:45 – 11:30 A Fast and Scalable Low Dimensional Solver for Charged Particle Dynamics in Large Particle Accelerators

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Ineichen Yves

Yves Ineichen, Paul Scherrer Institut , PRACE Award Winner

Yves Ineichen is a PhD student at the ETH Zurich. He received is Msc from the Computer Science Department, ETH Zurich, Switzerland in 2008. Between 2008 — 2010, he worked as research assistant at ETH Zurich and visiting student at the Los Alamos National Lab. He started his PhD in January 2010.Read abstract …

Authors: Yves Ineichen, Andreas Adelmann, Costas Bekas, Alessandro Curioni & Peter Arbenz

AbstractThis paper demonstrates how HPC can be used in real time to tune the operation of particle accelerators, which are invaluable tools for research in the basic and applied sciences, in fields such as materials science, chemistry, the biosciences, particle physics, nuclear physics and medicine. The design, commissioning, and operation of accelerator facilities is a non-trivial task, due to the large number of control parameters and the complex interplay of several conflicting design goals. The team from IBM Research, Paul Scherrer Institute and ETH Zürich achieved strong and weak scalability improvement on BlueGene/P of two orders of magnitude for the most heavily used component of the optimisation framework, which computes the evolving shape of the bunches of particles in the beam. This enables thousands of such calculations to be performed in a matter of minutes, creating close to on-line optimisation capability.

11:30 – 12:00 Excess proton at water/hydrophobic interfaces: A Car-Parrinello MD study

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Paolo Carloni

Paolo Carloni, German Research School for Simulation Sciences GmbH

Paolo Carloni obtained his PhD in Chemistry at the University of Florence in 1993. He was head of the Statistical and Biological Physics sector in SISSA (Italy) till 2009 when he moved to the University of Aachen (Germany) to lead the Computational Biophysics sector of the GRS at the FZ-Juelich. Since 2012 he is also Director of the Computational Biomedicine lab (IAS-5) at FZ-Jülich. His research focuses on molecular simulations and bioinformatics approaches to molecular biophysics, molecular medicine and structural genomics. He has published more than 175 papers and one edited book.Read abstract …

Project leader: Paolo Carloni, German Research School for Simulation Sciences GmbH, Jülich, Germany
Collaborators: Emiliano Ippoliti, German Research School for _ Simulation Sciences GmbH, Jülich, Germany / Yana Vereshchaga, German Research School for Simulation Sciences GmbH, Jülich, Germany

Recent experimental evidence shows unambiguously that, at room conditions, excess protons are located close to hydrophobic surfaces in liquid mixtures, in contrast to intuitive considerations. Shedding light on structural and energetic facets of this issue is crucial to describe correctly key biochemical processes such as protein folding and ligand/target interactions. So far, approaches have been mostly used classical modeling or empirical quantum-mechanical methods. The latter have suggested that the process is driven by enthalpy, which overcompensates the entropy penalty. First principle study reported so far did not address the energetics of the processes. Here we plan to perform ab initio molecular dynamics of an excess proton in the presence of a water/decane mixture as used experimentally. We plan to calculate the free energy of the process using thermodynamic integration and determine at which distance from the surface it is most probable that the proton localizes.

PRACE Resource awarded: 40 468 480 core-hours

12:00 – 12:30 A dislocation dynamics study of dislocation cell formation and interaction between a low angle grain boundary and an in-coming dislocation

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Bing Liu

Bing Liu, Max-Planck-Institut für Eisenforschung

Bing Liu received his B.S. in Metallurgical Engineering from University of Science and Technology Beijing in 2004 and his M.S. in Physical Metallurgy from RWTH Aachen University in 2009. He is currently a Ph.D. candidate at Max-Planck-Institut für Eisenforschung. His research interests include dislocation dynamics simulations of dislocation—interface interactions and crystal plasticity modeling of metal forming.Read abstract …

Project leader: Dierk Raabe, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
Collaborators: Franz Roters, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany / Bing Liu, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany

Discrete Dislocation Dynamics (DDD) models simulate explicitly the motion, multiplication and interaction of dislocation lines, the carrier of plasticity in crystalline materials, in response to an applied load. This project aims to study the dislocation physics during plastic deformation of metals, focusing on the microstructure evolution (cell structure formation) and the interaction between a low angle grain boundary (LAGB) and an in-coming dislocation.
To simulate the dislocation cell structure formation, both the sample volume and the amount of plastic deformation have to exceed the most computationally expensive simulations (volume: 5 µm on a side; plastic deformation 1.7%) run on Thunder and Blue Gene/L computers at the Lawrence Livermore National Laboratory.
When the wall dislocations and the dislocation loop have the same Burgers vector but on different glide planes (collinear relation), they form a junction with zero Burgers vector (partial annihilation). The collinear dislocation interaction has been reported to be stronger than all other types of dislocation interactions (self interaction, coplanar interaction, interaction leading to non-zero junctions). The finding from our simulations of the interaction between a low angle grain boundary (dislocation wall) and dislocation loops is that: the partial annihilation of wall dislocation and in-coming dislocation loop makes dislocation loop transmission easy and leads to strong interactions at the dislocation wall, and junction formation pins the dislocation loop at the dislocation wall, and strong multiplication events happen outside the dislocation wall region. Both dislocation density and plastic strain increase faster in the junction case than in the collinear case. It is important to further study how the interaction depends on the dislocation spacing of wall dislocations, or in other words the angle of the LAGB. Currently the dislocation spacing is 1000b (b is the magnitude of the Burgers vector), and the use of smaller dislocation spacing (100b) would request the number of DOF to increase 100 times (the number of dislocations x10, and the number of segments per dislocation x10).
Additionally, we would like to study the (average) migration velocity of a clean and solitary LAGB in contrast to the (messy) case when concurrent activity of numerous dislocation loops destroys the neat boundary structure. Both cases are investigated under the same applied stress. Experimental observations suggest a massive reduction in the migration rate in the latter case. Likely, the generation of low-mobility junctions slows down a disrupted boundary. The messy case (dislocation wall with massively-tangled dense dislocation network) needs the computational capability of the Blue Gene/P.

PRACE Resource awarded: 15 600 000 core-hours

12:30 – 13:30 Lunch Break

13:30 – 14:15 PRACE User Forum with Q&A

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Turlough Downes

Chairman: Turlough Downes, Dublin City University & Dublin Institute for Advanced Studies, Ireland

Turlough Downes received his PhD in computational astrophysics in 1997 from Trinity College, Dublin. After pursuing post-doctoral research in the University of Utrecht he became Hitachi Lecturer for High Performance Computing at Trinity College, Dublin where he lectured until 2000. He then moved to Dublin City University (DCU) where he is now a Senior Lecturer. Since 2008 he has spent roughly half of his time with the Dublin Institute for Advanced Studies (DIAS) under a cost-sharing agreement between DCU and DIAS.Read more…

This short session is intended to give PRACE users an opportunity todiscuss their experiences of applying for, and using, PRACE resources.The emphasis will be on identifying issues of concern which are commonto a number of users. One example of such an issue is the opening ofPRACE resources to teams from outside the EU and associated states. TheProgramme Committee of the User Forum will then feed these concernsdirectly to the relevant PRACE committees with a view to having themaddressed.

14:15 – 14:45 Droplet growth by coalescence in turbulent clouds: kinetics, fluctuations, and universality

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Jeremie Bec

Jeremie Bec, Observatoire de la Côte d’Azur

After defending a PhD in 2002 on basic aspects of physics and hydrodynamics at the Observatoire de la Côte d’Azur, I was a postdoctoral fellow at the Institute for Advanced Study in Princeton and at the University La Sapienza in Rome where I acquired an expertise on dissipative dynamical systems and critical phenomena. Since I was hired by CNRS in 2005 in Nice, I have mainly worked on turbulent transport and mixing. In 2009 the European Research Council awarded me a starting independent researcher grant to study the effect of fluctuations and extreme events in atmospheric transport.Read abstract …

Project leader: Jeremie Bec, Observatoire de la Côte d’Azur, Nice, France
Collaborators: Holger Homann, Observatoire de la Côte d’Azur, Nice, France / Samriddhi Sankar Ray, Observatoire de la Côte d’Azur, Nice, France / Rainer Grauer, Ruhr-University Bochum, Bochum, Germany

Warm clouds are constituted of small water droplets that do not follow exactly the turbulent airflow but have inertia. They thus react with some delay to the fluid motion and feel gravity, so that they distribute non-uniformly in space and can have very large velocity differences. Consequently the rate of collision and growth by coalescence of such droplets cannot be predicted by simple arguments and the timescales of precipitation are often under-estimated. Our objective is to investigate this issue by a direct numerical simulation of coalescing particles that are passively transported by a homogeneous isotropic turbulent flow.While atmospheric scientists attach importance to account simultaneously for all processes to be as much realistic as possible, the proposed approach simplifies the main mechanisms to obtain a better handling of fundamental questions. The novelty of the intended work originates in extending and adapting to the problem of rain formation the statistical physics tools developed for Lagrangian turbulence. The main ingredient of such approaches is the statistical Lagrangian formalism developed during the last decade, which consists in reformulating transport and mixing problems in terms of averages along particle paths. The key task is then to estimate the cumulative weights of fluctuations along trajectories or to determine the probability of the events giving a dominating contribution to the statistics. This method has two advantages: first, it is well adapted for dealing with systems that are far from equilibrium, and second, it allows controlling the history of individual particle paths. The problem of estimating time scale of rain formation in warm clouds requires tools that cope with these two difficulties.
In order to accompany and validate such analytical modelings, we will perform state-of-the-art numerical simulations of a cloud portion. For being ensured that the airflow turbulence is sufficiently developed, we plan to integrate the fluid phase on a $2048^3$ periodic grid with a high-accuracy pseudo-spectral solver. To match particle loading encountered in strato-cumulus, one billion particles will be seeded in the flow with an initial size distribution that mimics observations and which will be centered around a typical radius equal to one twentieth of the dissipative Kolmogorov scale. The system will then be evolved using an efficient collision detection algorithm and performing particle mergers that conserve mass and momentum. The simulation will be evolved for at least fifty large-scale turnover time to obtain a typical size of particle that has increased by at least one order of magnitude. The objective is to measure timescales for the growth of droplets and to highlight universal properties of the size distribution in the large-time asymptotics. Such measurements will confirm or refute the validity of predictions from standard mean-field kinetic models.

PRACE Resource awarded: 50 000 000 core-hours

14:45 – 15:15 Predictive full-scale fast ignition with PW plasma amplified laser pulses

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Ricardo Fonseca

Ricardo Fonseca, Instituto Superior Técnico, Lisbon

Ricardo A. Fonseca was born in Lisbon, Portugal on September 11th, 1973. He received his degree in Physics Engineering from the Instituto Superior T’ecnico in 1996 and joined the Laser and Plasma Group at this institute. In 2000 he spent one year at the University of California Los Angeles working on the numerical modelling of high intensity laser plasma interactions. He obtained his PhD in Physics from the Technical University of Lisbon in 2002, on the subject of Laser-Plasma Electron Accelerators. He is a researcher for the Instituto de Plasmas e Fus ao Nuclear and in 2003 he took up a permanent position at the Instituto Superior de Ci^encias do Trabalho e da Empresa in Lisbon, where he is currently an Associate Professor. He has published over 100 papers in leading scientific journals. He was awarded the Oscar Buneman award in 2000. He was the chairman of the 21st International Conference on Numerical Simulation of Plasmas, ICNSP’09.

Read abstract …

Project leader: Luis O. Silva, Instituto Superior Técnico, Lisbon, Portugal
Collaborators: Warren Mori, University of California Los Angeles, Los Angeles, United States / Raoul Trines, Rutherford Appleton Laboratory, Didcot, UK / Frederico Fiuza, Instituto Superior Técnico, Lisbon, Portugal / Ricardo Fonseca, Instituto Superior Técnico, Lisbon, Portugal

Fusion energy is regarded as a possible long-term energy solution for humanity, capable of providing the energy resources to drive economic growth and social development. Fast ignition is one of the most promising and exciting inertial confinement fusion schemes to improve the viability of inertial fusion energy as a practical energy source. Even if up to now experiments have been limited to laser energies still far from ideal conditions for ignition and simulations, which are extremely complex due to the different temporal and spatial scales involved, have been limited to reduced scales/simplified models, in the very near future we expect transformative results as novel laser systems are now coming online, with the National Ignition Facility and, in the near future, the ESFRI roadmap project HiPER (High Power laser Energy Research), reaching the conditions required for ignition. In this proposal, and using massively parallel simulations, we aim to perform, for the first time with realistic target properties (e.g. density, temperature, dimensions) and the correct simulation dimensionality, and with realistic ultra-intense laser pulses obtained from Raman amplification, self-consistent fast ignition simulations including all the relevant microphysics/particle dynamics, taking advantage of the novel hybrid model incorporated into the state-of-the-art relativistic particle-in-cell massively parallel code OSIRIS, with the goal of identifying possible paths to demonstrate fast ignition as an efficient scheme for inertial fusion energy.

PRACE Resource awarded: 31 000 000 core-hours

15:15 – 15:45 Coffee Break

15:45 – 16:15 Turbulent entrainment due to a plume impinging on a density interface
Maarten van Reeuwijk, Imperial College London

Read abstract …

Project leader: Maarten van Reeuwijk, Imperial College London, London, UK
Collaborators: Harm Jonker, Delft University of Technology, Delft, The Netherlands / Gary Hunt, Imperial College London, London, UK

The entrainment of fluid across density interfaces is a fundamental physical process with applications throughout the natural sciences and engineering. This process is of importance in density stratified environments which are subject to regions of localized turbulence. For example, in oceanic and atmospheric contexts, turbulent entrainment has a bearing on the rate of deepening of oceanic and atmospheric mixed layers, respectively. This then has a direct impact on the concentration of pollutants released in the atmosphere or trapped in a mixed layer in the ocean. As entrainment involves a transport of fluid between layers, it has widespread applications in water-air quality problems. However, despite its significance, existing entrainment laws, which couple an entrainment velocity to a turbulence intensity and density contrast between the layers, are subject to very significant uncertainties and currently there is no consensus in the literature regarding which is correct or the most appropriate. With laboratory measurements of entrainment rates in identical apparatus varying by orders of magnitude, this then presents the scientific community with real concerns and throws into question many models and modeling approaches which rely on a specification of such entrainment rates. This proposal aims to pin down the entrainment law for localized turbulent patches using direct numerical simulation (DNS).
An improved entrainment law for localized turbulent patches will enable enhanced predictive capability. One pertinent example is the low-energy design of ventilation in buildings. Here, the turbulent entrainment across a thermal interface – an interface separating a cool lower region in a room from the warmer upper region – as is typically induced by a thermal plume rising from localized heat sources, is an extremely important mechanism as it plays a significant role in determining the temperature distribution in the room and thus, the comfort of occupants. Optimization of the energy-efficiency in a ventilated building is only possible if the simplified models typically used to provide design guidance are accurate.

PRACE Resource awarded: 30 000 000 core-hours

16:15 – 16:45 Ab initio Simulations of Turbulence in Fusion Plasmas

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Frank Jenko

Frank Jenko, Max Planck Institute for Plasma Physics

The work of Prof. Jenko (Max Planck Institute for Plasma Physics at Garching near Munich, Germany) centers around the topics of plasma turbulence, computational physics, and high performance computing – with applications to both fusion energy research and astrophysics. In his group, one of the leading “gyrokinetic” plasma turbulence codes has been developed (see This GENE code is used by a large number of researchers world-wide on a variety of different platforms on up to about 300,000 cores. He is the author of more than 150 publications and has won several awards including an Excellence Grant by the European Research Council.Read abstract …

Project leader: Frank Jenko, Max Planck Institute for Plasma Physics (IPP), Garching, Germany
Collaborators: Tobias Görler, Max Planck Institute for Plasma Physics (IPP), Garching, Germany / Florian Merz, Max Planck Institute for Plasma Physics (IPP), Garching, Germany / Daniel Told, Max Planck Institute for Plasma Physics (IPP), Garching, Germany / Moritz Johannes Pueschel, Max Planck Institute for Plasma Physics (IPP), Garching, Germany / Stephan Brunner, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland / Michael Barnes, Trinity College, University of Oxford, Oxford, UK

The world-wide demand of electricity is projected to increase by about a factor of six throughout the 21st century. At the same time, the use of fossile fuels will have to be reduced. At present, we still have no silver bullet which can be used to close this gap. Fusion energy is an attractive option in this context, and high-performance simulations play a key role for its further development. The present project represents an important contribution to the European effort to employ Petascale (and later Exascale) computing for fusion energy applications. Its main goal is to use the latest version of the plasma turbulence code GENE to perform a number of millenium-type simulations which are closely linked to the international flagship fusion experiment ITER – one of the most challenging scientific projects to date and currently under construction in Southern France. The first target is to perform the first physically comprehensive simulations of the ASDEX Upgrade tokamak at Garching, presently one of the world’s leading fusion devices and conceptually very similar to ITER, although about four time smaller in the linear dimensions. The second question to be addressed is the dependence of the turbulent transport on the system size. Given that ITER is expected to benefit from the fact that it will be significantly larger than all existing fusion devices, this is a key issue to ensure the project’s success. Since the theoretical understanding of it is still far from complete, these simulations will provide very valuable insights.

PRACE Resource awarded: 50 000 000 core-hours

16:45 – 17:00 Closing Remarks
Richard Kenway, Chair of PRACE Scientific Steering Committee & Conference Chairman

17:30 – 18:30 Networking Event together with ISC’12 Asia Day

- Program: Download here (pdf)

PRACE Award 2012

The PRACE Award will be presented at the ISC’12 Opening Session on Monday, June 18, 2012:…

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