Conference Programme and Abstracts...Tuesday 20 May - 09:00 to 13:00 - Aula Master Alternative cooling technologies and heat re-use session 09:00 – 09:20 C1: Immersion cooling (PSNC)

1Barcelona, 20 - 22 May 2014

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PRACE Composite - 210x210 .indd 1 02/05/2014 10:27Conference Programme and Abstracts

Barcelona, 20 - 22 May 2014

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Table of Contents

Welcome ....................................................................................................................... 3

Committees ....................................................................................................................... 4

General Information ............................................................................................................... 5

Useful Information ................................................................................................................. 7

Location Map ....................................................................................................................... 8

Workshop on exascale and PRACE prototypes ................................................................. 12

Meeting Programme ............................................................................................................ 13

Abstracts ..................................................................................................................... 14

Plenary Session ........................................................................................... 15

Opening & Welcome .................................................................................... 18

Computer Science ....................................................................................... 20

Life Science ................................................................................................. 23

Chemistry / Materials Science ..................................................................... 25

Environmental Science ................................................................................ 28

Automotive / Engineering ............................................................................ 29

Astrophysics / Mathematics ......................................................................... 32

SHAPE ........................................................................................................ 34

Plenary Session ........................................................................................... 40

Poster Session .................................................................................................................... 43

List of authors ..................................................................................................................... 55

Media Sponsors................................................................................................................... 60


www.prace-ri.eu HPC for Innovation

WHEN SCIENCE MEETS INDUSTRY

Welcome Dear Participant,

It is a great pleasure for us to welcome you to the PRACE Scientific and Industrial Conference 2014 - the first edition of the PRACE days – which is hosted by PRACE and the Barcelona Supercomputing Center (BSC) under the motto:

HPC for Innovation – when Science meets Industry

What better city than Barcelona, which was recently awarded the European capital of innovation prize 2014, to host this conference combining the well-known, but previously separate, PRACE Scientific Conferences and PRACE Industrial Seminars!

The Barcelona Supercomputing Centre is also proud to welcome this high-level scientific and industrial con-ference to the North Campus of the Universitat Politècnica de Catalunya (UPC). With MareNostrum, Spain’s first Tier-0 system, close by, participants to PRACEdays14 will enjoy the unique combination of Barcelona’s excellent hospitality as well as excellent science and research.

With one satellite event – a Workshop on Exascale and PRACE Prototypes – and two joint meetings – an open session of the PRACE User Forum and the bi-annual meeting of the PRACE Industrial Advisory Commi-ttee – PRACEdays14 have already shown their importance to the wider scientific and industrial communities.

For the main conference, we have lined-up an impressive group of speakers from Europe and beyond, who will present their advancements in HPC-supported science and engineering. Included in our programme are also two keynotes from distinguished American researchers, as well as a plenary address from the European Commission who have been supporting PRACE since its inception. The topic “Centres of Excellence” will be jointly presented by representatives of PRACE, ETP4HPC and the European Commission on Tuesday 20 May.

On Wednesday 21 May, we are very honoured that Maria Luisa Poncela, Secretary General for Science, Technology and Innovation, and President of the Barcelona Supercomputing Center since 2012, will formally open the conference. In the afternoon, you will have a choice of 8 parallel streams dedicated to various indus-trial and scientific topics. We recommend you try to join at least one presentation from the SHAPE stream, as this innovative HPC access programme for SMEs has already yielded ground-breaking results!

Last, but not least, on Thursday 22 May, a moderated panel will discuss the economic and scientific impact of collaboration between science and industry, coming full circle and closing the conference by referring to the motto of this edition.

A social programme including a sight-seeing tour through Barcelona will offer some entertainment and oppor-tunities to convene and connect in a more informal setting.

We would like to take this opportunity to thank all those who have made this event possible: the Organisation and Programme Committee, the PRACE Board of Directors, the PRACE Scientific Steering Committee, the PRACE Industrial advisory Committee, the User Forum, the team at Barcelona Supercomputing Center, and many others. I also want to thank the speakers and contributors without whom we would not have been able to offer you this complete and in-depth programme.

Wishing you a fruitful and inspiring conference!

Yours sincerely,

Catherine Rivière Sergi Girona Chair of the PRACE Council Chair of the PRACE Board of Directors

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Committees

Organisation & Programme Committee (OPC)

Dietmar Erwin Chair of the Organisation & Programme Committee

Sergi Girona Chair of the PRACE Board of Directors

Marjolein Oorsprong PRACE Communications Officer Renata Giménez BSC

Sara Ibáñez BSC

Kenneth Ruud Chair of the PRACE SSC

Jürgen Kohler Chair of the PRACE IAC

Andres Rhod Gregersen Vice-Chair of the PRACE IAC

Gustavo Yepes Chair of the PRACE User Forum

Turlough Downes Outgoing Chair of the PRACE User Forum

Scientific Steering Committee (SSC)

Paolo Carloni

Giovanni Ciccotti

Christoph Dellago

Sylvie Joussaume

Richard Kenway

Dimitri Komatitsch

Petros Koumoutsakos

Christian Lang

Ben Moore

Antonio Navarra

Maurizio Otraviani

Ignacio Pagonabarraga Mora

Olivier Pironneau

Simon Portegies Zwart

Kenneth Ruud (Chair)

Wolfgang Schröder

Christof Schütte

Erik Landahl

Luís Silva

Joost VandeVondele

Claudio Zannoni




General Information

PRACEdays14 From Tuesday 20 May to Thursday 22 May 2014 Venue

Vertex Building of the North Campus of the Universitat Politècnica de Catalunya (UPC)

Pl. Eusebi Güell 6

08034 Barcelona

Spain

Workshop on exascale and PRACE prototypes

From Monday 19 May to Tuesday 20 May 2014

Venue

Aula Master - A3 Building of the North Campus of the Universitat Politècnica de Catalunya (UPC)

Jordi Girona, 1-3

08034 Barcelona

Spain

Technical Secretariat Location

In the Auditori Hall – Vertex Building: Tuesday 20 May to Thursday 22 May

Technical Secretariat Desk Schedule

Tuesday 20 May 09:00 to 19:00

Wednesday 21 May 08:30 to 18:30

Thursday 22 May 08:30 to 15:30

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Meeting Rooms

Workshop on Exascale and PRACE prototypes PRACEdays14

Monday 19 May

Tuesday 20 May

Tuesday 20 May

Wednesday 21 May

Thursday 22 May

AM Aula Master Auditori Auditori

Auditori PM Aula Master Auditori Sala d’actes VS213

VS208 VS214 VS217

Coffee breaks and lunches

PRACEdays14 coffee breaks and lunches will be served in the Hall of the Auditori. Workshop coffee breaks will be served in the room close to the Aula Master.

Sightseeing bus Tour and Dinner

Date: Wednesday 21 May 2014 Departure time: 18:00 from Vertex Building

You will enjoy seeing some of the most beatiful places of Barcelona like Casa Milà, Casa Batlló, Cristobal Colon’s square, Barcelona’s skyline from Montjuic and many others.

Dinner at Restaurant La Barceloneta

The secret of Restaurante Barceloneta’s cuisine on a menu, elaborated on the basic recipes of traditional seafood cooking.

Simple recipes, meticulously prepared by experienced professionals using the best ingredients, with fish and shellfish, always freshly caught, along with selected raw vegetables brought in directly from the markets. Internet access

There will be free wi-fi Internet Access at the meeting venue. Access keys will be available at the Technical Secretariat Desk.

Insurance

The registration fee does not include the insurance of participants against accidents, illness, cancellation, theft, property loss or damage.

Participants are advised to take out adequate personal travel insurance.




Useful Information About Barcelona

Barcelona is a dynamic, welcoming city and one of the major economic and business centres of Spain and the Mediterranean Europe. The Catalan capital has a modern hotel infrastructure and boasts first rate shops and leisure, cultural and tourist attractions; all these traits have made Barcelona a first-class tourist destination, and the ideal place for meetings and congresses.

Barcelona enjoys a Mediterranean climate with mild, sunny winters, warm summers and relatively low rainfall. Temperatures during May are usually mild (18-22 degrees Celsius).

Getting around

Barcelona has a complete public transport network including metro, tramway, buses and local trains. Sants Station is a multi-modal station (train, bus and metro). From Sants Station you can go by high-speed train to Madrid or Seville.

With an Hola BCN! travel card for 2, 3, 4 or 5 days you can make unlimited journeys in Barcelona and the metropolitan area with public transport. This includes metro and bus (TMB), local train (FGC), tram (TRAM) and regional train (Rodalies de Catalunya).

Use it on the Rodalies train to and from the airport too!

Unfortunately, pickpocketing is a fact of traveling life, also in Barcelona. Be aware of your surroundings and keep your valuables safe at all times.

From the airport

An aerobus departs every 5 minutes from Barcelona airport and stops at Plaza España and Plaça Catalunya (city centre)

Taxis

Taxis in Barcelona may be ordered by phone, picked up at authorized taxi stands or flagged down on the street. Taxis must usually be paid in cash though some accept credit cards.

Radio taxi: +34 933 033 033

Taxi for disabled people: +34 935 519 368

Commercial Opening Times

In general, banks and savings banks open from 08:30 to 14:00 from Monday to Friday. There are many ATMs all over the city.

Shopping centres are open Monday-Saturday from 10:00 to 22:00

Useful Telephone Numbers

For emergencies: 112 Municipal Police: 092

Renfe (Spanish Railway) Customer Service +34 902 320 320

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Location Map

Vertex BuildingPRACEdays14 Venue

A3 BuildingWorkshop Venue

L3 - Bus H6 - Tram (T1-T2-T3)

MareNostrum




CO

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A3 Building

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Vertex Building - Main Floor

SALA D’ACTES - VS ROOMSENTRANCEAUDITORI ENTRANCE

VERTEX BUILDING ENTRANCE

Vertex Building - Floor -1

AUDITORI

SALA D’ACTES

AUDITORI




Vertex Building - Floor -2

VS208

VS217

VS213

VS214

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Workshop on exascale and PRACE prototypes

Monday 19 May - 14:00 to 18:00 - Aula Master14:00 – 14:20 Welcome and opening

Prototypes (session 1)

14:20 – 14:40 P1: On-die integrated CPU and GPU (PSNC) – Radek Januszewski

14:40 – 15:00 P2: Eurora (Cineca) – Carlo Cavazzoni

15:00 – 15:20 P3: Scalable Hybrid (CSC) - Sami Saarinen 15:20 – 16:00 Discussion panel prototypes P1, P2 and P3

16:00 – 16:40 Coffee break

Prototypes (session 2)

16:40 – 17:00 P4: Mont-Blanc (BSC) – Alex Ramírez

17:00 – 17:20 P5: DEEP and DEEP-ER (JSC) – Estela Suárez

17:20 – 18:00 Discussion panel prototypes P4 and P5

Tuesday 20 May - 09:00 to 13:00 - Aula Master Alternative cooling technologies and heat re-use session

09:00 – 09:20 C1: Immersion cooling (PSNC) – Radek Januszewski

09:20 – 09:40 C2: Cold plate technology (CINECA) – Carlo Cavazzoni 09:40 – 10:00 C3: Direct hot-water cooling and heat re-use (LRZ) – Torsten Wilde

10:00 – 10:30 Discussion panel prototypes C1, C2 and C3

10:30 – 11:00 Coffee break

11:00 – 11:20 X1: Exascale integrated I/O subsystem (JSC) – Michael Stephan

11:20 – 11:40 X2: The case of ARM+GPU (BSC) – Filippo Mantovani

11:40 – 12:00 Discussion panel about X1 and X2

12:00 – 13:00 Discussion, wrap-up and workshop outcomes




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User Forum General Meeting

Tuesday 20 May - 13:30 to 15:30 - Auditori User Forum General Meeting

The PRACE User Forum is an independent entity where PRACE users can discuss their experiences and express their future needs from the PRACE HPC services and resources. The User Forum takes the outcomes of these discussions to PRACE on behalf of the User Community. The Forum has visibility in different social networks, such as LinkedIn and Twitter (@PRACEuserforum) on which all PRACE users are very welcome to start discussions and express their concerns. Besides this online activity, the User Forum also organizes an open session within the PRACEdays conference in which users can raise their opinions, suggestions and criticisms in front of the PRACE representatives.

Gustavo Yepes is an University Professor at the Department of Theoretical Physics of the Universidad Autonoma de Madrid. He is an expert in numerical Cosmology and Astrophysics. He has been working in this field since the late 80’s and has been an active user of most of the HPC systems that have been available for scientific research both in Europe and the US, including the present PRACE infrastructures. He is currently the Chair of the PRACE User Forum Programme Committee.




Abstracts

Plenary Session

Tuesday 20 May - 16:00 to 18:15 - Auditori In silico exploration of the most extreme scenarios in astrophysics and in the laboratory: from gamma ray bursters to ultra intense lasers Luís O. Silva, Instituto Superior Técnico, Lisbon, Portugal

I will describe how massively parallel simulations are advancing our understanding of extreme scenarios where ultra intense flows of particles and light, in the laboratory and in astrophysics, combined with nonlinear relativistic effects define the complex evolution of the system. After presenting the algorithms describing the collective dynamics of charged particles in intense fields that allows for the use of the largest supercomputers in the World, I will cover recent progresses in relativistic shocks and cosmic ray acceleration in extreme astrophysical events, advanced plasma based accelerators for intense x-ray sources, and novel ion acceleration mechanisms for cancer therapy and fusion energy. I will show how petaflop scale simulations, combined with unique astronomical observatories and the emergence of multi PetaWatt laser systems, are triggering and opening novel exciting opportunities for innovation and new avenues for scientific discovery.

Luís O. Silva is Professor of Physics at Instituto Superior Técnico, Lisbon, Portugal, where he leads the Group for Lasers and Plasmas. He obtained his degrees (MSc 1992, PhD 1997 and Habilitation 2005) from IST. He was a post-doctoral researcher at the University of California Los Angeles from 1997 to 2001. His scientific contributions are focused in the interaction of intense beams of particles and lasers with plasmas, from a fundamental point of view and towards their applications for secondary sources for biology and medicine.

Luís O. Silva has authored more than 150 papers in refereed journals and three patents, and has given in-vited talks at the major plasma physics conferences and served on the program and selection committees of conferences and prizes in Europe, US and Japan. He is a member of the International Scientific Advisory Board of ELI – Beamlines, of the Scientific Steering Committee of PRACE, and of the National Council for Science and Technology (reporting to the Prime Minister of Portugal). He has supervised 6 PhD students and 7 post-doctoral fellows whose work has led to several national and international prizes. He was PI in more than 20 projects funded by the Portuguese Science Foundation, ESA and EU, in EU supercomputing projects, by NVIDIA, and the Rutherford Appleton Laboratory. He was awarded an Advanced Grant from the European Research Council in 2010, being the youngest in “Fundamental Constituents of Matter” and one of the youngest scientists overall to be awarded an Advanced Grant.

He was awarded the 2011 Scientific Prize of the Technical University of Lisbon, the IBM Scientific Prize 2003, the 2001 Abdus Salam ICTP Medal for Excellence in Nonlinear Plasma Physics by a Young Researcher, and the Gulbenkian Prize for Young Researchers in 1994. He was elected Fellow of the American Physical Soci-ety and to the Global Young Academy in 2009.

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ETP4HPC – European Technology Platform for HPC Jean-François Lavignon, ETP4HPC

ETP4HPC, the European Technology Platform (ETP) for High-Performance Computing (HPC) (www.etp4h-pc.eu) is an organisation led by European HPC Technology providers with an objective to build a competitive HPC value chain in Europe. ETP4HPC also included HPC research centres and end-users. It has issues a Strategic Research Agenda (SRA) which outlines the research priorities of European HPC on its way to achieve Exascale capabilities within the Horizon 2020 Programme. ETP4HPC is also one of the partners of the Contractual Public-Partnership (cPPP) for HPC (together with the European Commission) the aim of which is building a competitive HPC Eco-system in Europe based on the provision of Technologies, Infra-structure and Applications.

ETP4HPC intends to play a key role in the coordination of the European HPC Eco-system. Our intention is to form a project team that will respond to the Commission’s FETHPC-2 -2014(Part A) Call on that topic.

The objective of this parallel session it to:

- Outline the assumptions and suggestions of the SRA - Explain the concept of the cPPP and how it will affect the European HPC arena - Discuss the preparations for the Coordination of the HPC strategy call as above.

Jean-François Lavignon joined Bull in 1998, where he is in charge of collaborative R&D. At Bull, he has been involved in research strategy and developing emerging businesses. Be-fore joining Bull he served in several positions related to IT research. He has experience in parallel computing, computer architecture and signal and image processing. Jean-François Lavignon graduated from Ecole Polytechnique in 1984 and ENSTA (Ecole Nationale des Techniques Avancées) in 1986. He then spent one year at Stanford University as invited re-searcher. He is now the Chairman of ETP4HPC, the European Technology Platform for HPC.

PRACE and HPC Centers of Excellence working in synergy Sergi Girona, PRACE Leonardo Flores Añover, European Commission Jean-François Lavignon, ETP4HPC

Under the Work Programme 2014 – 2015 of the new Horizon 2020 EU Research and Innovation programme, the European Commission launched Call EINFRA 5-2015, entitled “Centers of Excellence for Computing Applications”.

This Call invites the establishment of a limited number of Centers of Excellence (CoE) to ensure EU compet-itiveness in the application of HPC for addressing scientific, industrial or societal challenges.

PRACE will co-operate with the HPC CoE, finding synergies in the efforts of both parties, including the iden-tification of suitable applications for co-design initiatives relevant to the development of HPC technologies.

This session will present and explain Call EINFRA-5-2015 and open the floor to participants to identify and bring forward the services and possible synergies required.




Sergi Girona is Chair of the Board of Directors of PRACE, as well as Director of the Oper-ations Department of the Barcelona Supercomputing Center (BSC). He belongs to the BoD of PRACE since its creation in 2010, and currently is both its Chair and Managing Director.

He holds a PhD in Computer Science from the Technical University of Catalunya. In 2001, EASi Engineering was founded and Sergi became the Director of the company for Spain, and the R&D Director for the German headquarters.

In 2004, he joined BSC for the installation of MareNostrum in Barcelona. MareNostrum was the largest supercomputer in Europe at that time, and it maintained this position for 3 years. Sergi was responsible for the site preparation and the coordination with IBM for the system installation. Currently, he is managing the Operations group with the responsibilities for User Support and System Administration of the different HPC systems at BSC.

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Plenary Session

Wednesday 21 May - 09:00 to 12:30 - AuditoriOpening and Welcome

Maria Luisa Poncela, Secretary General for Science, Technology and Innovation. President of the Barcelona Supercomputing Center since 2012.

She studied Economics with a major in Business Administration at the University of Zaragoza, graduating in 1982. She is a member of the Senior State Corps of Sales Engineers and Economists since 1989 and of the State Corps of Business Graduates since 1984.

She has been for years a Member of the Board of Directors of several business companies such as the Cen-tre for Development of the Industrial Technology (CDTI), the Institute for Diversification and Energy Savings (IDEA), the Spanish Company of Reinforcement (CERSA) and the Large Telescope of the Canary Island (GRANTECAN). At the same time, she has served as Chair of the Ministry of Science and Technology in the Board of Directors of the Spanish Agency for Consumer Affairs, Food Safety and Nutrition, and as member of the Advisory Board of the Spanish Medicine Agency.

Moreover, she has been speaker of different conferences, courses and seminars and she is the author of various articles.

Catherine Rivière, CEO of GENCI, France. Chair of the PRACE Council. She graduated from ENSIMAG, Ecole Nationale Supérieure d’Informatique et de Mathéma-tiques Appliquées of Grenoble in 1983.

In 1983, she joined the French Institute of Petroleum (IFP) located at Rueil Malmaison.

In 1996, she was appointed as Deputy Manager of the Exploration Production Business Unit.

In 2001, she joined as CEO Tech’Advantage, a service company and a subsidiary of IFP.

Currently and since 2007, she holds a position of CEO of GENCI (Grand Equipement National de Calcul In-tensif) in charge of the coordination of the national academic high performance computing facilities.

In June 2012, Catherine Riviere was appointed as Council Chair of PRACE Aisbl (Partnership for Advanced Computing in Europe) which links 25 countries, and in which France is represented by GENCI.

Building an Ecosystem to Accelerate Data-Driven Innovation Francine Berman, Rensselaer Polytechnic Institute, United States

Digital data has transformed the world as we know it, creating a paradigm shift from information-poor to infor-mation-rich that impacts nearly every area of modern life. Nowhere is this more apparent than in the research community. Today, digital data from high performance computers, scientific instruments, sensors, audio and video, social network communications and many other sources are driving our ability to discover, innovate, and understand the world around us.

In order to best utilize this data, an ecosystem of technical, social and human infrastructure is needed to support digital research data now and in the future. In this talk, we discuss the opportunities and challenges for the stewardship and support of the digital data needed to drive research and innovation in today’s world.




Dr. Francine Berman is the Edward P. Hamilton Distinguished Professor in Computer Science at Rensselaer Polytechnic Institute. She is a Fellow of the Association of Computing Machinery (ACM) and a Fellow of the IEEE. In 2009, Dr. Berman was the inaugural recipient of the ACM/IEEE-CS Ken Kennedy Award for “influential leadership in the design, development, and deployment of national-scale cyberinfrastructure.”

Prior to joining Rensselaer, Dr. Berman was the High Performance Computing Endowed Chair in the Jacobs School of Engineering at UC San Diego. From 2001 to 2009, Dr. Berman served

as Director of the San Diego Supercomputer Center (SDSC) where she led a staff of 250+ interdisciplinary scientists, engineers, and technologists. From 2009 to 2012, she served as Vice President for Research at Rensselaer Polytechnic Institute, stepping down in 2012 to lead U.S. participation in the Research Data Alli-ance (RDA), an emerging international organization created to accelerate global data sharing and exchange. Dr. Berman is co-Chair of the inaugural leadership Council of the RDA and Chair of RDA/United States.

Dr. Berman currently serves as co-Chair of the National Academies Board on Research Data and Informa-tion, as Vice-Chair of the Anita Borg Institute Board of Trustees, and is a member of the National Science Foundation CISE Advisory Board. From 2007-2010, she served as co-Chair of the US-UK Blue Ribbon Task Force for Sustainable Digital Preservation and Access. For her accomplishments, leadership, and vision, Dr. Berman was recognized by the Library of Congress as a “Digital Preservation Pioneer”, as one of the top women in technology by BusinessWeek and Newsweek, and as one of the top technologists by IEEE Spectrum.

Drive safe, green and smart: HPC-Applications for sustainable mobility. Alexander F. Walser, Automotive Simulation Centre Stuttgart, Germany

The automotive industry is facing the challenge of sustainable mobility. This is a demanding task character-ized by fulfilling legal safety requirements globally increasing, improving fuel economy, reducing CO2, noise emissions and pollutants just as increasing consumer demands. In recent years numerical simulation made its way in the design phase of automotive development and production as a useful tool for faster problem analysis and reduction of cost and product development time. High Performance Computing (HPC) is signifi-cant in the automotive industry for competitiveness and innovation. HPC is used in areas where high-perfor-mance computing power is needed to solve computationally intensive problems e.g. computational fluid dy-namics (external aerodynamics, coolant flow or in-cylinder combustion) and dynamic finite element analysis (crashworthiness and occupant safety simulation). New aspects such as cloud computing or big and smart data will increase the research and innovation challenges of HPC for the automotive industry. Optimizing pro-cess chains, closing methodical gaps and increasing forecast quality, the cooperation between science and industry through sustainable partnerships in the industrial pre-competitive collaborative research is needed. Pioneering cooperation between science and industry, the Automotive Simulation Center Stuttgart - asc(s - was founded in 2008. The asc(s business model is based on the Competence Network principle. With its 23 members (OEMs, ISVs, IHVs, research facilities and natural members) the asc(s is a transfer platform set-ting trends for the interaction of science and industry in Europe. The asc(s offers an environment to develop new software applications, scalable algorithms and tools to make HPC systems easy-to-use and to make researchers highly innovative and productive. Linking specific practical projects with the numerical basic re-search ensures a rapid economic availability of research results with high quality and provides new impulses for product development.

Alexander F. Walser is managing director at the Automotive Simulation Center Stuttgart e.V. – asc(s. He received a diploma in Civil Engineering in the subject area modelling and simula-tion methods from University of Stuttgart in 2011. After completing his studies he worked on research projects in the field of structural mechanics, crashworthiness, shape and topology optimization. Since 2013 he is responsible for acquiring and managing HPC-projects and new research fields at the asc(s.

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European HPC strategy Augusto Burgueño Arjona, European Commission, Belgium

With its communication on HPC of February 2012, the Commission committed to an ambitious action plan for European leadership in HPC. In May 2013, the Council invited the Commission to develop and elaborate its plans for HPC and to explore all possible support for academic and industrial research and innovation under Horizon 2020. Since then, the first calls of Horizon 2020 have been launched and the HPC Public-Private Partnership with ETP4HPC has been formally launched. There is however much more work ahead of us. In my presentation I will delineate the expected contributions of all HPC stakeholders to make Europe Union’s vision on HPC a reality.

Dr. Augusto Burgueño Arjona is currently Head of Unit “eInfrastructure” at European Commission Directorate General for Communications Networks, Content and Technology and General manager and coach at Coach Mundi ASBL.

Previously he served as Head of Unit “Finance” Directorate General for Communications Networks, Content and Technology at European Commission and Head of inter-Directorate General Task Force IT Planning Office at European Commission.

Computer Science

Wednesday 21 May – 13:30 to 15:30 - Auditori

Large Scale Graph Analytics Pipeline Cristiano Malossi, IBM Research - Zurich, Rüschlikon, SwitzerlandYves Ineichen, IBM Research - Zurich, Rüschlikon, SwitzerlandCostas Bekas, IBM Research - Zurich, Rüschlikon, SwitzerlandAlessandro Curioni, IBM Research - Zurich, Rüschlikon, Switzerland In recent years, graph analytics has become one of the most important and ubiquitous tools for a wide variety of research areas and applications. Indeed, modern applications such as ad hoc wireless telecommunication networks, or social networks, have dramatically increased the number of nodes of the involved graphs, which now routinely range in the tens of millions and out-reaching to the billions in notable cases. We developed novel near linear (O(N)) methods for sparse graphs with N nodes estimating: - the most important nodes in a graph, the subgraph centralities, and - spectrograms, that is the density of eigenvalues of the adjacency matrix of the graph in a certain unit of space. The method to compute subgraph centralities employs stochastic estimation and Krylov subspace tech-niques to drastically reduce the complexity which, using standard methods, is typically O(N3). This technique allows to approximate centralities fast, highly scalable and accurately, and thereby opens the way for cen-trality based big data graph analytics that would have been nearly impossible with standard techniques. This can be employed to identify possible bottlenecks, for example in the European street network with 51 million nodes in only a couple of minutes on only 16 threads.

Spectrograms are powerful in capturing the essential structure of graphs and provide a natural and human readable (low dimensional) representation for comparison. How about comparing graphs that are almost similar? Of course, this is a massive dimensionality reduction, however at the same time the shape of the spectrogram yields a tremendous wealth of information. In order to tackle arising big data challenges an efficient utilization of available HPC resources is key. Both developed methods exhibit an efficient parallelization on multiple hierarchical levels. For example, computing




Cristiano Malossi received his B.Sc. in Aerospace Engineering and his M.Sc. in Aeronautical Engineering from the Politecnico di Milano (Italy) in 2004 and 2007, respectively.After working one year on computational geology problems in collaboration with ENI (the main Italian oil and energy company), he moved to Switzerland where in 2012 he got his Ph.D. in Applied Mathematics from the Swiss Federal Institute of Technology in Lausanne (EPFL), with a thesis focused on the development of algorithms and mathematical methods for the numerical simulation of cardiovascular problems.In July 2013 Cristiano joined IBM Research - Zurich as Postdoctoral Researcher of the Computational Sciences group in the Mathematical and Computational Science department. His main research interests include: High Performance Computing, Energy-Aware Algorithms and Architectures, Numerical Analysis, Computational Fluid Dynamics, Aircraft Design, Computational Geology, and Cardiovascular Simulations.

Big models simulations and optimization through HPC. An effective way of improving performances for cloud targeted services. Gino Perna, Enginsoft, Italy Alberto Bassanese, Enginsoft, Italy Stefano Odorizzi, Enginsoft, Italy Carlo Janna, M3E, Italy

Woven fabric composites have been object of several researches investigating their mechanical properties since their introduction in the aeronautic and industrial applications more than twenty years ago: their good conformability makes them the material of choice for complex geometries. Fatigue problems are very complicated because fibers are bundled in yarns that are interlaced to form a specific pattern so the complex geometry of the fabric architecture strongly affects which one of the constituents fails first and the way a local failure propagates up to cause the final failure of the entire lamina. By dealing with the problem just in terms of mean (macro) stresses at laminate level as if the material was homogeneous anisotropic, it is not possible to embrace the stress concentrations and the intra-laminar shear stresses within each component. Multi-Scale analysis approaches are therefore the obvious way to link macroscopic and microscopic structural behaviours of composite materials. However, numerous are the parameters controlling the final composite mechanical properties. These parameters are typically the fiber architecture and the volume fraction, the mechanical properties of the fiber, the matrix and the fiber-matrix interface. FEA and continuously enhanced hardware performances, nowadays hardware’s multi-core architectures have been offering a convenient solution to the problem of modelling by accounting for their inherently multi-scale structural nature to the point that Virtual Prototyping can nowadays almost replace some of the physical tests required for the mechanical characterization of different material systems.

To solve the problem and perform optimization of the whole structure a great number of computational cores are required but one of the main obstacles are performances in mechanical analysis, that should be removed to try to perform at the same level as CFD codes. New conjugate gradient techniques are very promising in those scenarios to cut down considerably computational time thus leaving space for more analyses and optimization studies to maximize performances and design better and safe products.

the spectrogram can be parallelized on three levels: bins and matrix-vector products can be computed independently, and the each matrix-vector product can be computed in parallel. The combination of a highly scalable implementation and algorithmic improvements enable us to tackle big data analytics problems that are nearly impossible to solve with standard techniques.A broad spectrum of applications in industrial and societal challenges can profit from fast graph analytics, for example routing and explorative visualization. We continuously focus our efforts to extend the coverage of our massively parallel graph analytics software stack to a variety of application domains in science and industry.

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Gino Perna is HPC and It Manager at Enginsoft. He obtained his MSc degree in Civil Engineering at Padua University in 1986. In addition to his duties at Enginsoft he has teaching duties at the University of Trento, mostly focused on Computer Programming. His knowledge goes through Mechanical & CFD simulations with last few years spent in the field of HPC and CAE.

Mont-Blanc – Engaging Industry in low-energy HPC technology design process Alex Ramirez, Barcelona Supercomputing Center, Spain Marcin Ostasz, Barcelona Supercomputing Center, Spain

The aim of the Mont-Blanc project has been to design a new type of computer architecture capable of setting future global High-Performance Computing (HPC) standards, built from energy efficient solutions used in embedded and mobile devices. This will help address the Grand Challenge of energy consumption and en-vironment protection, as well as potentially help Europe achieve leadership in world-class HPC technologies and satisfy the European industry’s need for low-power HPC.

The project has been in operation since Oct 2011. The European Commission has recently granted an ad-ditional 8 million Euro to extend the project activities until 2016. This will enable further development of the OmpSs parallel programming model to automatically exploit multiple cluster nodes, transparent application check pointing for fault tolerance, support for ARMv8 64-bit processors, and the initial design of the Mont-Blanc Exascale architecture. Several new partners have joined this second phase of Mont-Blanc, including Allinea, STMicroelectronics, INRIA, University of Bristol, and University of Stuttgart.

Mont-Blanc are looking for members of the European HPC industrial user eco-system to join our Industrial End-User Group (IUG). As the project produces novel HPC technologies and solutions (i.e. low-energy HPC), it will request the members of the IUG to validate these products and provide feedback to the projects in order to align its objectives, deliverables and address issues such as end-user compatibility. An Industrial End-User Group coordinator has been appointed to coordinate this process. The IUG will consist of representatives of various industries, including, but not limited to Automotive, Energy, Oil/Gas, Aerospace, Pharma, and Finan-cial.

The objective of this session is to: - Familiarise the audience with the IUG: membership rules and obligations,

- Explain the processes of testing the Mont-Blanc technology, - Share the latest project results, - Instigate other industrial organisations to join or work closely with the IUG, and Collect feedback and suggestions in relation to the IUG.

The session will have two parts: - Technical – explaining the project, its achievements and the latest results available as above, - Moderated discussion on the current and future work of the IUG.




Alex Ramirez is a Tenured Associated Professor at Universitat Politecnica de Catalunya, and Computer Architecture Research Manager at Barcelona Supercomputing Center where he leads the the Mont-Blanc EU project, targeting Exascale HPC systems, and developing the first HPC cluster prototypes built on low-power ARM processors.

He has graduated 10 PhD students, and published over 150 papers in international confer-ences and journals (H index 24) in compiler optimizations, processor microarchitecture, multicore architecture, multithreading processors, parallelizations strategies, and energy-ef-ficient cluster computing.

He has participated as Principal Investigator in 11 European projects, and 7 industrially funded projects. His research has been featured in The Wall Street Journal, Wired, Financial Times, Scientific Computing, Scien-tific Computing World, HPC Wire, Slashdot, ComputerWorld, and others. In 2010 he received the first Award to a Young Researcher by the Spanish Academy of Engineering.

Marcin Ostasz graduated from the Technical University of Budapest at the Faculty of Elec-tronics with an MSc degree and he also holds a Master of Business Administration (MBA) degree awarded by Oxford Brookes University in the UK. Marcin has over 13 years of com-bined experience gained at various technical, project management, operations manage-ment, business analysis and process improvement positions with organisations such as Nokia, American Power Conversion, Dell, GE and Barclays Bank. Marcin is currently work-ing at Barcelona Supercomputing Centre as a business analyst. His tasks include supporting projects and organisations such as PRACE, the European Technology Platform, EUDAT and Mont-Blanc. He specialises in managing industrial relations, road-mapping, workshop man-agement and business analysis.

Life Sciences

Wednesday 21 May - 16:00 to 17:20 - Auditori

Numerical Simulation of sniff in the respiratory system Hadrien Calmet, Barcelona Supercomuting Center, Spain

Direct numerical simulation (DNS) in the human nose-throat is a great challenge. As far as the author knows, this is the first time that DNS is carry out in all the respiratory system. This massive simulation is very useful to obtain a high level of detail in all the human nose-throat. The flow structure, the turbulence or the power spectrum could be post-processed anywhere along the human conduct. Is the guarantee also, that the inflow along the airway will be realistic. Simplified boundary conditions are not necessary.

Here a subject-specific model of the domain that extends from the face to the third branch generation in the lung is used to carry out the simulation. This model is coming from an extraction of Computed Tomography (CT). The inlet boundary condition is a profile on time of the flow rate during sniff (peak at 30l/min), it is mod-eled with statistic analysis of a few patients.

When two unstructured meshes with finely resolved boundary layers are used, there are 44 millions and 350 millions of elements. The second is the result of a first using an parallel algorithm to produce an uniform mesh multiplication, resulting finer mesh. The second mesh is used to detail the turbulence analysis and ensure sufficient resolution of the first. Due to a lighter data analysis, the first mesh is generally used for the description of the flow.

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The complex flow forces to analyse each part of the large airways separately and is tending to explain the main characteristics and main features of each region. The time scale is different in the nose and in the throat, the physic also is different. In addition a large number of turbulence statistics are computed and the main feature of the flow for each region is performed with the power spectra in few set points of each region and compared with the two different meshes.

Hadrien Calmet is a researcher at the Barcelona Supercomputing Center (CASE depart-ment), Barcelona, Spain since October 2006. He works on:

-Pre-processing (mesh with Ansys ICEM), structured, unstructured, hybrid. Aerodynamic, hydrodynamic, hemodynamic and engineering problems -Post-processing (visualization) with Paraview, In-visu -Film editor with Final Cut Pro for animations and documentary about Science.

His research topics are: Bio-mechanics, Extraction of Vortex. Implementation of In-house CFD code with MPI, HDF5 libraries.

Large scale DFT simulation of a mesoporous silica based drug delivery system Massimo Delle Piane, University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Centre, Torino, Italy Marta Corno, University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Sur-faces) Centre, Torino, Italy Alfonso Pedone, University of Modena and Reggio Emilia, Department of Chemistry, Modena, Italy Piero Ugliengo, University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Sur-faces) Centre, Torino, Italy

Mesoporous materials are characterized by an ordered pore network with high homogeneity in size and very high pore volume and surface area. Among silica-based mesoporous materials, MCM-41 is one of the most studied since it was proposed as a drug delivery system. Notwithstanding the relevance of this topic, the at-omistic details about the specific interactions between the surfaces of the above materials and drugs and the energetic of adsorption are almost unknown.

We resort to a computational ab-initio approach, based on periodic Density Functional Theory (DFT), to sim-ulate the features of the MCM-41 mesoporous silica material with respect to adsorption of ibuprofen, starting from our previous models of a silica-drug system. We sampled the potential energy surface of the drug-silica system by docking the drug on different spots on the pore walls of a realistic MCM model. The drug loading was then gradually increased resulting in an almost complete surface coverage. Furthermore, we performed ab-initio molecular dynamics simulations to check the stability of the interaction and to investigate the drug mobility.

Through our simulations we demonstrated that ibuprofen adsorption seems to follow a quasi-Langmuirian model. Particularly, we revealed that dispersion (vdW) interactions play a crucial role in dictating the features of this drug/silica system. Finally, simulations of IR and NMR spectra provided useful information to interpret ambiguous experimental data.

Simulations of this size (up to almost 900-1000 atoms), at this accurate (and onerous) level of theory, were possible only thanks to the computational resources made available by the PRACE initiative. We have demon-strated that the evolution of HPC architectures and the continuous advancement in the development of more efficient computational chemistry codes have been able to take the Density Functional Theory approach out of the realm of “small” chemical systems, directly into a field that just a few years ago was an exclusive of the




much less computationally demanding Molecular Mechanics methods. This opens the path to the accurate ab-initio simulation of complex chemical problems (in material science and beyond) without many of the sim-plifications that were necessary in the recent past.

Massimo Delle Piane has a Master Degree in Industrial Biotechnology and is now a PhD student at the Department of Chemistry, University of Torino, Italy, under the supervision of Prof. Piero Ugliengo. His thesis is devoted to quantum mechanical modeling of the interac-tion between biomolecules and oxide surfaces, with particular interest in the study of silica based materials for drug delivery purposes. He has been directly involved in two PRACE project, for a total of 60 million core hours. He also collaborates with the developers of the CRYSTAL simulation code, developed in the same department by the group headed by Prof. Roberto Dovesi.

Chemistry / Materials Science

Wednesday 21 May – 13:30 to 15:30 - Sala d’Actes

Ab initio modelling of the adsorption in giant Metal-Organic Frameworks: from small mole-cules to drugs Bartolomeo Civalleri, Department of Chemistry, University of Torino, Torino, Italy M. Ferrabone, Department of Chemistry, University of Torino, Torino, Italy R. Orlando, Department of Chemistry, University of Torino, Torino, Italy Metal-Organic Frameworks (MOFs) are a new class of materials that are expected to play a huge impact in the development of next-generation technologies. They consist of inorganic nodes connected through or-ganic linkers to form a porous three-dimensional framework. The combination of different nodes and linkers makes MOFs very versatile materials with promising applications in many fields, including: gas adsorption, catalysis, photo-catalysis, drug delivery, sensing and nonlinear optics.

We will show results on the ab-initio modeling of the adsorptive capacity of the so-called giant MOFs. They possess pores with a very large size and, in turn, a huge surface area. Among giant MOFs, the most repre-sentative one is probably MIL-100. It ideally crystallizes in a non-primitive cubic lattice with 2788 atoms in the primitive cell. MIL-100 is characterized by the presence of a large number of coordinatively unsaturated metal atoms exposed at the inner surface of the pores that are crucial in determining its adsorption capacity. In particular, we are investigating MIL-100 for its ability of capture carbon dioxide, which is one of the hottest topic in MOFs research, and the adsorption of large molecules such as drugs, for drug delivery purposes. The project is ongoing and available results will be shown.

Giant MOFs, with thousands of atoms in the unit cell, represent a tremendous challenge for current ab-initio calculations. The use of Tier-0 computer resources provided by PRACE is essential to tack-le this challenging problem. All calculations have been carried out with the B3LYP-D method by us-ing the massive parallel (MPP) version of the ab-initio code CRYSTAL (http://www.crystal.unito.it/).

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Bartolomeo Civalleri graduated in chemistry (1995) and received his Ph.D. in chemistry (1999) from the University of Torino. Since 2002, he joined the Theoretical Chemistry group at the University of Torino as a faculty researcher. His current research is focused on ab-in-itio modelling in solid state chemistry with particular interest in metal-organic frameworks, hydrogen storage materials and molecular crystals. He is also involved in the development of the CRYSTAL code.

Ab Initio Quantum Chemistry on Graphics Processing Units: Rethinking Algorithms for Massively Parallel Architectures Jörg Kussmann, University of Munich (LMU), Germany Simon Maurer, University of Munich (LMU), Germany Christian Ochsenfeld, University of Munich (LMU), Germany Conventional ab initio calculations are limited in their application to molecular systems containing only a few hundred atoms due to their unfavorable scaling behavior, which is at least cubical [O(N3)] for the most simple mean-field approximations (Hartree-Fock, Kohn-Sham density functional theory). In the last two de-cades, a multitude of methods has been developed that reduce the scaling behavior to linear for systems with a significant HOMO-LUMO gap, allowing for the computation of molecular properties of systems with more than 1000 atoms on single-processor machines.

The advent of general-purpose GPUs (GPGPU) in recent years promised significant speed-ups for scientific high-performance computing. However, quantum chemical methods seem to pose a particularly difficult case due to the heavy demand of computational resources. Thus, first implementations of the rate-determining integral routines on GPUs were strongly limited to very small basis sets and employed intermediate sin-gle-precision quantities. Furthermore, a straightforward and efficient adaptation of O(N) integral algorithms for GPUs is not possible due to their inherent book-keeping, branching, random memory access, and process interdependency.

We present general strategies and specific algorithms to efficiently utilize GPUs for electronic structure calcu-lations with the focus on a fine-grained data organization for efficient workload distribution, reducing inter-pro-cess communication to a minimum, and minimizing the use of local memory.

Thus, we are able to use large basis sets and double-precision-only GPU-kernels in contrast to previously suggested algorithms. The benefits of our approach will be discussed for the example of the calculation of the exchange matrix, which is the by far most time-consuming step in SCF calculations.

Here, we recently proposed a linear-scaling scheme based on pre-selection (PreLinK) which has been prov-en to be highly suitable for massively parallel architectures.

Thus, we are able to perform SCF calculations on GPUs using larger basissets to determine not only en-ergies and gradients, but also static and dynamic higher order properties like NMR shieldings or excitation energies. Apart from discussing the performance gain as compared to conventional ab initio calculations on a single server, we also compare different architectures based on CUDA, OpenCL, MPI/OpenMP, and MPI/CUDA.

Furthermore, we present the – to our knowledge – first efficient use of GPUs for post-HF methods beyond the mere use of GPUs for linear algebra operations at the example of second-order Møller-Plesset perturbation theory (MP2).




Jörg Kussmann received a PhD in Theoretical Chemistry from the University of Tübingen. After pursuing post-doctoral research at the Pennsylvania State University, he became a research scientist in the Theoretical Chemistry Group at the University of Munich (LMU).

His main focus is the extension of the applicability of quantum chemical methods to larger systems or longer time-scales by developing low- or ideally linear-scaling ab initio methods and the utilization of modern computing architectures, especially graphics processing units (GPU).

Shedding Light On Lithium/Air Batteries Using Millions of Threads On the BG/Q Supercomputer Teodoro Laino, IBM Research – Zurich, Rüschlikon, Switzerland V. Weber, IBM Research – Zurich, Rüschlikon, Switzerland A. Curioni, IBM Research – Zurich, Rüschlikon, Switzerland

In 2009, IBM Research embarked into an extremely challenging project, the ultimate goal of which is to deliver a new type of battery that will allow to drive an electric vehicle for 500 miles without intermediate recharging. The battery considered the most promising candidate to achieve this goal is based on lithium and oxygen, commonly known as Lithium/Air battery, potentially delivering energy densities one order of magnitude larger than state-of-the-art electrochemical cells.

With few exceptions carbonate-based electrolytes, for instance propylene carbonate (PC) or ethylene car-bonate (EC), have been the preferred choice for most experimental setups related to Lithium/Air batteries to date. By using massively parallel molecular dynamics simulations, we modeled the reactivity of a surface of Li2O2 in contact with liquid PC, revealing the high susceptibility of PC to chemical degradation by the peroxide anion.

Moreover, by using increasingly detailed and realistic simulations we were able to provide an understanding of the molecular processes undergoing at the cathode of the Li/Air cell, showing that the electrolyte holds the key role in non-aqueous Lithium/Air batteries in producing the appropriate reversible electrochemical reduction.

A crucial point when modeling such complex systems is the level of accuracy of DFT calculations, which is key for improving the predictive capabilities of molecular modeling studies and for addressing material dis-covery challenges.

In order to achieve a reliable level of accuracy we implemented a novel parallelization scheme for a highly efficient evaluation of the Hartree–Fock exact exchange (HFX) in ab initio molecular dynamics simulations, specifically tailored for condensed phase simulations. We show that our solutions can take great advantage of the latest trends in HPC platforms, such as extreme threading, short vector instructions and highly dimen-sional interconnection networks. Indeed, all these trends are evident in the IBM Blue Gene/Q supercomputer. We demonstrate an unprecedented scalability up to 6,291,456 threads (96 BG/Q racks) with a near perfect parallel efficiency, which represents a more than 20-fold improvement as compared to the current state of the art. In terms of reduction of time to solution we achieved an improvement that can surpass a 10-fold decrease of runtime with respect to directly comparable approaches.

By using the PBE0 hybrid functional (HFX), so to enhance the accuracy of DFT based molecular dynamics, we characterized the reactivity of different classes of electrolytes with solid Li2O2. In this talk, we present an effective way to screen different solvents with respect to their intrinsic chemical stability versus Li2O2 solid particles [3]. Based on these results, we proposed alternative solvents with enhanced stability to ensure an appropriate reversible electro-chemical reaction and finally contribute to the optimization of a key technology for electric vehicles.

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Dr. Teodoro Laino, Research Staff Member - Mathematical and Computational Sciences, IBM Research – Zurich.

Teodoro Laino received his degree in theoretical chemistry in 2001 (University of Pisa and Scuola Normale Superiore di Pisa) and a doctorate in 2006 in computational chemistry at the Scuola Normale Superiore di Pisa, Italy. His doctoral thesis, entitled “Multi-Grid QM/MM Approaches in ab initio Molecular Dynamics” was supervised by Prof. Dr. Michele Parrinello - one of the pioneers in this field.

From 2006 to 2008 he worked as a post-doctoral researcher in the research group of Prof. Dr. Jürg Hutter at the University of Zurich, where he developed algorithms for ab initio and classical molecular dynamics simulations. Since 2008 he has been working in the department of Mathematical and Computational Scienc-es at the IBM Research Laboratory in Zurich. The focus of his research is on complex molecular dynamics simulations for industrial-related problems in the field of energy storage, life sciences and nano-electronics.

Environmental Science

Wednesday 21 May – 16:00 to 17:20 - Sala d’Actes

Next generation pan-European climate models for multi- and many-core architecture Jun She, Danish Meteorological Institute Jacob Weismann Poulsen, Danish Meteorological Institute Per Berg, Danish Meteorological Institute Lars Jonasson, Danish Meteorological Institute

To generate more consistent and accurate climate information for climate adaptation and mitigation, high res-olution coupled atmosphere-ocean-ice models are needed in large regional scale, e.g., pan-European and Arctic-N. Atlantic scales. The computational load of these models can be hundreds times heavier than current global coupled models (e.g. those used in IPCC AR5). The vision is to make the regional coupled models ef-ficient on multi-and many-core architecture. To reach this goal, the most challenging part is the ocean model optimization as the model domain is highly irregular with straits of a few hundred meter width to open ocean in a scale of a few thousand kilometres. Based on achievements made in PRACE project ECOM-I (Next generation pan-European coupled climate-ocean model – phase 1), this presentation will show methods and results in optimizing a pan-European two-way nested ocean-ice model, with focusing on coding standard, I/O, halo communication, load balance and multi-grid nesting. The optimization was tested on different archi-tectures e.g. Curie Thin, CRAY XT5/XT6 and Xeon Phi etc. The results also show that different model setups lead to very different computational complexity. A single real domain setup for Baffin Bay shows scalability to 16000 cores and Amdahl ratio of >99.5%. However, a pan-European setup with 10 interconnected nesting domains only reaches scalability of less than two thousand and Amdahl ratio 92%. Key issues on evaluating computational performance of models, such as run2run reproducibility, scalability, Amdahl ration and their relation with job size, ratio of computational points (wet points) and multi-grids will be addressed. Finally a roadmap for next generation pan-European coupled climate models for many-core architecture is discussed.

Jun She received a PhD Lanzhou University in 1991 in Climate Dynamics. He has worked on oceanography and climate modeling in China, Japan, USA on and Denmark in part 20 years. Since 2007 he has been a science manager at DMI’s Centre for Ocean and Ice. He has (co-) authored 50 publications on modeling weather, ocean, wave, climate, marine eco-systems, and optimal design of observational networks.




Optimizing an Earth Science Atmospheric Application with the OmpSs Programming Model George S. Markomanolis, Barcelona Supercomputing Center, Spain

The Earth Sciences Department of the Barcelona Supercomputing Center (BSC) is working on the devel-opment of a new chemical weather forecasting system based on the NCEP/NMMB multiscale meteorologi-cal model. In collaboration with the National Centers for Environmental Prediction (NOAA/NCEP/EMC), the NASA Goddard Institute for Space Studies (NASA/GISS), and the University of California Irvine (UCI), the group is implementing aerosol and gas chemistry inlined within the NMMB model. The new modeling sys-tem, namely NMMB/BSC Chemical Transport Model (NMMB/BSC-CTM), is a powerful tool for research in physico-chemical processes occurring in the atmosphere and their interactions. We present our efforts on porting and optimizing the NMMB/BSC-CTM model. This work is done under Severo Ochoa program and the purpose is to prepare the model for large scale experiments and increase the resolution of the executed do-main. However, in order to achieve high scalability of our application is needed to optimize the various parts of the code. It is well known through the discussion about the exascale era that the coprocessors will play an important role. Currently there are two main types of coprocessors, GPUs and Intel Xeon Phi. In order to use both approaches without the need to rewrite most of the code, the programming model OmpSs, which is developed at BSC-CNS, is used. Through this procedure we extend the usage of our model by porting part of our code to be executed on GPUs and Xeon Phi coprocessors. The performance analysis tool Paraver is used to identify the bottleneck functions. Afterwards, the corresponding code is ported in OpenCL either optimized for being executed on GPUs and Xeon Phi respectively. We execute our model with various con-figurations in order to test it under extreme load by enabling the chemistry modules which take under consid-eration much more species (water, aerosols, gas) and we observe that the bottleneck functions depend on each case. We solve load balancing issues and whenever possible we take advantage of the available cores from NVIDIA GPU and Intel Xeon Phi. To the best of our knowledge, the use of the programming model Om-pSs on an earth science application with future purpose to be used operationally is without any precedence.

George S. Markomanolis received his PhD in Computer Science from INRIA/ENS de Lyon in 2014 on Performance Evaluation and Prediction of Parallel Applications. He holds a MSc. in Computational Science from University of Athens, Greece and a BSc. in Mathematics from University of Ioannina, Greece. He has been external collaborator to Wolfgang Pauli institute in Vienna Austria where he parallelized some serial applications from the physics field. After-wards, he worked at CNRS’ computing center of the national institute of nuclear and particle physics at France as engineer. Currently, he is senior engineer at Barcelona Supercomput-ing Center at Earth Sciences department and his work is to optimize an Atmospheric model and prepare it for the exascale machines. This work is done under Severo Ochoa program.

Automotive / Engineering

Wednesday 21 May – 13:30 to 15:30 - Room VS208

INCITE in the International Research Community Julia C. White, INCITE, United States

The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program promotes unprecedented scientific and engineering simulations through extremely large awards of computer time on high-performance computers that are among the most powerful in the world. Successful INCITE projects de-liver high-impact science that could not otherwise be achieved without access to leadership-class systems at the US Department of Energy’s Argonne and Oak Ridge Leadership Computing Facilities. INCITE does not distinguish between funding sources or country of affiliation, instead selecting the research of highest impact from the worldwide community of researchers.

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Julia C. White, INCITE program manager, will highlight the history of the INCITE program and the role of international researchers over the program’s ten-year history. White will describe the importance of a broad geographical diversity of not just proposal applicants, but of peer-review panels that assess applications and even the INCITE program itself.

Paul Messina of Argonne National Laboratory will speak about industry use of leadership-class resources; White will focus on international access to these resources through the INCITE program.

Julia C. White is the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program manager. INCITE is a peer-review allocation program to award time on the US Department of Energy’s leadership-class supercomputers at Oak Ridge and Argonne National Laboratories. INCITE enables researchers around the world to carry out unprec-edented scientific and engineering simulations. White provides leadership and oversight of INCITE from the call for proposals through peer-review and final awards. She previously held management roles at Oak Ridge and Pacific Northwest National Laboratories and at Physi-cal Review B, an international journal specializing in condensed-matter phenomena and-materials physics. White holds a Ph.D. in chemistry from Indiana University-Bloomington and an MBA from the University of Tennessee-Knoxville.

High fidelity multiphase simulations studying primary breakup Mathis Bode, RWTH Aachen University, Germany

A variety of flows encountered in industrial configurations involve both liquid and gas. Systems to atomize liq-uid fuels, such as diesel injection systems, are one example. The performance of a particular technical design depends on a cascade of physical processes, originating from the nozzle internal flow, potential cavitation, turbulence, and the mixing of a coherent liquid stream with a gaseous ambient environment. This mixing stage is critical, and the transfer occurring between liquid and gas is governed by an interface topology.

The most serious gap in understanding of spray formation is primary breakup, but it is also the first physical process to be modeled. This means that uncertainties in the modeling of primary breakup will influence, for example, the design and performance of atomizers in diesel combustion systems all the way down to emis-sion and pollutant formation.

Typical diesel injection systems have outlet diameters of the order of 100 micrometers and the resulting smallest droplets and turbulent structures are even much smaller. This illustrates two of the major problems for studying primary breakup: First, experiments characterizing the atomization process are very difficult due to the small length scales. Second, huge meshes are required for simulating primary breakup because of the necessity to resolve the broad spectrum of length scales in play within a single simulation. Thus, studying primary breakup is not possible without using massively parallel code frameworks.

We use the CIAO code which was already run on up to 65000 parallel cores on SuperMuc in connection with recently developed highly accurate interface tracking methods. This so-called 3D unsplit forward/backward Volume-of-Fluid method that is coupled to a level set approach overcomes the traditional issues of mass con-servation and interface curvature computation in the context of multiphase simulations. Due to its robustness, it also enables the simulation of arbitrarily high density ratios.

In this project, a novel approach combining spatial and temporal jet simulations of multiphase flows is used to study primary breakup from first principles. The results of these high fidelity multiphase simulations are used to further the understanding and accurate modeling of primary breakup in turbulent spray formation of industrial relevance.




Mathis Bode is a research assistant and Ph.D. student in Prof. Pitsch’s group at the Institute for Combustion Technology at RWTH Aachen University. He received his Master of Science in Mechanical Engineering from RWTH Aachen University in 2012. His research interests include high fidelity simulations of multiphase flows on massively parallel computers.

Fluid saturation of hydrocarbon reservoirs and scattered waves: Numerical experiments and field study Vladimir A. Tcheverda, Novosibirsk State University, Russia V. Lisitsa, Novosibirsk State University, Russia A. Merzlikina, Novosibirsk State University, Russia G. Reshetova, Novosibirsk State University, Russia

Over the last decade the use of scattered waves took a significant place among the wide range of modern seismic techniques. But so far their main area of application is spatial localization of clusters of subseis-mic-scale heterogeneities, like cracks, fractures and caverns, in other words these waves are using just in order to say “yes” or “no” to the presence of this microstructure. Therefore the main goal of our efforts within the framework of the PRACE Project Grant 2012071274 (supercomputer HERMIT at Stutgart University) is to understand which kind of knowledge about the fine structure of the target object like a cavernous fractured reservoir can be achieved from this constituent of the full seismic wave field. The key instrument for the study-ing the scattering and diffraction of seismic waves in realistic models is a full scale numerical simulation. In order to describe correctly waves’ propagation in media with heterogeneities of both large scale (3D hetero-geneous background) and fine scaIe (distribution of caverns and fracture corridors) we apply finite-difference schemes with local refinement in time and space. On this base we are able to simulate wave propagation in very complicated realistic models of 3D heterogeneous media with subseismic heterogeneities.

This simulation was done for realistic digital model derived from all available data about some specific depos-its. It happens that fluid saturation has very specific impact in synthetic seismic image which can be used as predictive criterion in real life data processing and interpretation. This criterion is confirmed by real life deep well.

Professor Dr. Vladimir A. Tcheverda is Head of the Department of Computational Methods in Geophysics, at the Trofimuk Institute of Petroleum Geology and Geophysics of the Sibe-rian Branch of the Russian Academy of Sciences in Novosibirsk. He is Full Professor at the Mathematical Department of the Novosibirsk State University (NSU) and chair of “Mathemat-ical Methods in Geophysics”.

His current research interests are: True amplitude prestack migration and full waveform inversion; Newton - like approaches to resolve non-linear ill-posed problems and their application for reliable numerical reso-lution of inverse problems of wave propagation for heterogeneous elastic media (multicomponent seismic data inversion and imaging); finite-difference/finite element simulation of seismic wave propagation through multiscale media (cavernous fractured reservoirs).

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Astrophysics and mathematics


EAGLE: Simulating the formation of the Universe Richard Bower, Durham University, United Kingdom

The EAGLE (Evolution and Assembly of Galaxies and their Environments) project aims to create a realistic virtual universe on the PRACE computers. Through a suite of state of the art hydrodynamic simulations, the calculations allow us to understand how the stars and galaxies we see today have grown out of small quantum fluctuations that are seeded in the big bang. The simulations track and evolve dark matter and dark energy using physical processes such as metal dependant gas cooling, the formation of stars, the explosion of supernovae and the evolution of giant black holes. The resolution of the simulations is sufficient to resolve the onset of the Jeans instability in galactic disks, allowing us to study the formation of individual galaxies in detail. At the same time the largest calculation simulates a volume that is 100 Mpc on each side, recreating the full range of galaxy environments from the isolated dwarves to dense rich galaxy clusters.

During my talk I will explain why this is a formidable challenge. The physics of galaxy formation couples the large scale force of gravity to the physics of star formation and black hole accretion. In principle, the simulation needs to cover a dynamic range of at least 108 in length scale (from 100 Mpc to 1 pc). To make matters worse, these scales are strongly coupled. While the small-scale phenomena are driven by large scale collapse, the small scale also generate feedback by generating gas flows on large scales. Even with large computer time allocations on the fastest computers available today, this is impossible and we must adopt a multi-scale approach.

A key philosophy of the EAGLE simulations has been to use the simplest possible sub-grid models for star formation and black hole accretion, and for feedback from supernovae and AGN. Using a stochastic approach, efficient feedback is achieved without hydrodynamic decoupling of resolution elements. The small number of parameters in these models are calibrated by requiring that the simulations match key observed properties of local galaxies. Having set the parameters using the local Universe, I will show that the simulations reproduce the observed evolution of galaxy properties extremely well.

The resulting universe provides us with deep insight into the formation of galaxies and black holes. In particular, we can use the simulations to understand the relationship between local galaxies and their progenitors at higher redshift and to understand the role of interactions between galaxies and the AGN that they host. I will present an overview of some of the most important results from the project, and discuss the computational challenges that we have met during the project. In particular, we found it necessary to develop a new flavour of the Smooth Particle Hydrodynamics (SPH) framework in order to avoid artificial surface tension terms.

The improved formulation has the potential to influence other areas of numerical astronomy and could also be used in more industrial applications such as turbine design or tsunami prevention where the SPH tech-nique is commonly used.

The EAGLE project has shown that it is possible to simulate the Universe in unprecedented realism using an extremely simple approach to the multi-scale problem. It has allowed us to meet the grand challenge of understanding the origin of galaxies like our own Milky Way. I will briefly describe what can be learned from the novel approach to sub-grid physics and potentially applied to other areas.




Prof. Richard Bower studies the Universe, aiming to understand the formation and evolu-tion of galaxies. His work covers both theoretical and observational aspects, ranging from the development of new observing techniques to the creation of new theoretical models for the interaction of galaxies and the black holes that they host. Most recently,

he has been developing multi-scale techniques that allow direct hydrodynamic simulation of galaxies within a representative volume of the Universe. This program, the EAGLE project, has created a fascinating virtual universe which captures the properties of the observed universe well.

Prof. Bower holds a Professorship at the Institute of Computational Cosmology at Durham University. He lectures courses in Cosmology and Astronomical Statistics as well as developing new course material in computational physics. He is also a part of the Ordered Universe project, a collaboration between physicists and historians investigating the 13th century scientific works of Robert Grosseteste.

A massively parallel solver for discrete Poisson-like problems Yvan Notay, University of Brussels, Belgium

AGMG (AGgregation-based algebraic MultiGrid solver) is a software package that solves large sparse sys-tems of linear equations; it is especially well suited for discretized partial differential equations. AGMG is an algebraic solver that can be used black box and thus substitute for direct solvers based on Gaussian elimi-nation. It uses a method of the multigrid type with coarse grids obtained automatically by aggregation of the unknowns. Sequential AGMG is scalable in the sense that the time needed to solve a system is (under known conditions) proportional to the number of unknowns.

AGMG is also a parallel solver since the beginning of the project in 2008. Within the framework of a PRACE project, we faced the challenge to port it on massively parallel systems, with up to several hundred thou-sands of cores. Some relatively simple yet not straightforward adaptations were needed. Thanks to them, we obtained excellent weak scalability results: when the size of the linear system to solve is increased pro-portionally to the number of cores, the time is first essentially constant, and then increases but moderately, the penalty never exceeding a factor of 2 (this maximal factor is seen on JUQUEEN when using more than 370,000 cores, that is, more than 80% of the machine ranked eighth in the top 500 supercomputer list). More importantly, when considering scalability results, one should never forget that their relevance depends on the quality of the sequential code one starts from. And comparative tests show that, on a single node, our solver is more than 3 times faster than HYPRE, which is often considered as the reference parallel solver for the considered type of linear systems.

Yvan Notay holds a PhD in Applied Science from the University of Brussels (ULB). He spent most of his career at the F.R.S.-FNRS, with ULB as main place of work. He is Research Di-rector since 2007. He is an expert in numerical linear algebra, especially in iterative methods for the solution of (very) large sparse linear systems. Outside his research community, he is mainly known as the author of the AGMG software package. This latter offers to non-experts a fairly easy to use implementation of an algebraic multigrid method, which solves linear systems from scalar elliptic PDEs in linear time.

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SHAPE


SHAPE: SME HPC Adoption Programme in Europe The adoption of HPC technologies in order to perform wide numerical simulation activities, investigate com-plex phenomena and study new prototypes is crucial to help SMEs to innovate products, processes and services and thus to be more competitive.

SHAPE, the SME HPC Adoption Programme in Europe is a new pan-European programme supported by PRACE. The Programme aims to raise awareness about HPC among European SMEs and provide them with the expertise necessary to take advantage of the innovation possibilities created by HPC, thus increasing their competitiveness. The programme allows SMEs to benefit from the expertise and knowledge developed within the top-class PRACE research infrastructure.

The programme aims to deploy progressively a set of complementary services towards SMEs such as in-formation, training, access to computational expertises for co developing a concrete industrial project to be demonstrated using PRACE HPC resources.

The SHAPE Pilot is a trial programme issued to prove the viability and the value of the SHAPE Programme, with the objective to refine the details of the initiative and prepare its launch in a fully operational way. The Pilot works with ten selected SMEs to introduce HPC-based tools and techniques into their business, opera-tional, or production environment.

This session presents some preliminary results of the Pilot, showing the work carried out together with the selected SMEs to adopt HPC solutions.

Agenda

The SHAPE Programme for Competitive SMEs in Europe Giovanni Erbacci, PRACE 3IP WP5 leader, CINECA, (Italy) Design improvement of a rotary turbine supply chamber through CFD analysis Roberto Vadori, Thesan, (Italy), Claudio Arlandini, CINECA, (Italy) Electromagnetic simulation for large model using HPC José-Maria Tamayo-Palau, Nexio Simulation, (France) Novel HPC technologies for rapid analysis in bioinformatics Paul Walsh, Nsilico, (Ireland) HPC application to improve the comprehension of ballistic impacts behaviour on composite materials Paolo Cavallo, AMET srl, (Italy), Claudio Arlandini, CINECA, (Italy) Airflow Simulations in Clean Rooms with OpenFOAM Ralph Eisenschmid, OPTIMA pharma, (Germany) LES turbulence models in race boat sail Gonzalo Kouyoumdjian, Juan Yacht Design SL, (Spain), Herbert Owen, BSC, (Spain)




Giovanni Erbacci graduated in Computer Science at the University of Pisa in Italy. Since 1999 to 2011 he coordinated the HPC Group, responsible for HPC support and consultancy in CINECA, promoting HPC activities and methodologies, co-operating both with academic institutions and European initiatives.

Currently he leads the HPC Projects Division in the Supercomputing Applications and Inno-vation Department at CINECA, supporting research and infrastructure HPC projects, both at European and national level. G.E. participated in different EC projects since the IV FP; and he is active in PRACE since the beginning.

He is a member of the PRACE Technical Board and in PRACE 3IP leads the Services for Industrial Users & SMEs activity.

Giovanni Erbacci has a wide experience in the field of computational sciences, parallel architectures, parallel programming models, scaling applications, performance evaluation. Since 1992, he organises and directs the CINECA’s Summer School on Parallel Computing.

Giovanni Erbacci is the author or the co-author of several papers published in journals and conference pro-ceedings and he is a member of the ACM.

Design improvement of a rotary turbine supply chamber through CFD analysis Roberto Vadori, Thesan Claudio Arlandini, CINECA

This work deals with the optimization of a volumetric machine. The machine is under active development, and a prototype is already working and fully monitored in an experimental mock-loop setup. This prototype oper-ates under controlled conditions on a workbench, giving as an output the efficiency of the machine itself. Main goal is to obtain an increased efficiency through the design and realization of the moving chambers in which fluid flows. In order to obtain such a task, an extensive CFD modeling and simulation is required to perform virtual tests on different design solutions to measure the physical quantities assessing the performance of a given geometry. The final goal is to design a better geometry of the different components, mainly the supply and exhaust chambers, cutting down time and resources needed to realize a physical prototype and to limit the physical realization only on a single geometry of choice. The modeling should allow then, through an op-timization strategy, to perform parametric studies of key parameters of the design of the moving chambers in which fluid flows, in order to identify the main geometrical parameters able to drive the optimal configuration. High Performance Computing facilities and Open-Source tools, such as OpenFOAM, are therefore of capi-tol interest to handle the complex physical model under consideration and to perform a sufficient amount of design configuration analysis.

Roberto Vadori graduated in 1989 with a degree in Mechanical Engineering from Politecni-co di Torino. where he got a PhD on Machine Design in 1995. In the same year he became Assistant Professor in Engineering Faculty, group of Machine Design. Starting from 2000 he gave lectures on Computational Mechanics at University of Rome „La Sapienza“, Fraunhofer Institut Bremen, and Kaiserslauten University. During the year 2001 he moved to Modena University, as Associate Professor. In 2003 he started to work in Industry, namely in Altair Engineering as a Researcher in the Methodology and Training Group.

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He kept the tenure of Finite Element Method classes from 2004 till 2007 in Politecnico di Torino, site of Alessandria and he was invited lecturer during all the academic years in the Course of Chassis Design of Engineering Faculty, Politecnico di Torino and the PhD Summer School in Machine Design. He his author of more than 80 papers published in referred national and international journals. Currently he holds the position of director of numerical and mathematical modelling and design activities in Thesan and Savio.

Claudio Arlandini got a PhD in Nuclear Astrophysics at the University of Heidelberg. He worked as business manager in the area of IT infrastructure management and data center operations at CILEA Interuniversity Consortium, and since the merging of CILEA in CINECA he is involved in simulation and technology transfer services for industries. He was WP9 “Industrial Applications Support” Leader In PRACE2IP and he is coordinator of CINECA ac-tivities in the I4MS Project Fortissimo.

Electromagnetic simulation for large model using HPC José-Maria Tamayo-Palau, NEXIO Simulation Pascal de-Reseguir, NEXIO Simulation

Nexio Simulation has recently started migrating from an electromagnetic simulation software (CAPITOLE-EM) developed for regular Personal Computers to High Performance Computing systems (CAPITOLE-HPC). This has been possible thanks first to the French HPC-PME initiative and then to the European Shape project. HPC-PME initiative is a project targeted to help and encourage Small and Medium size Enterprises (SME) towards HPC. Under the Shape project we expect to scale-up this initial step in the sense of computational time, resource usage and optimization.

The industry has become more and more exigent asking for simulation of very large problems. In particular, in the electromagnetic environment, we can fall very rapidly into full linear systems with several millions of un-knowns. The solution of these systems requires some matrix compression techniques based on the physics of the problem and mathematical algorithms. When these techniques are not enough it claims for the use of HPC with a good number of CPUs and a large amount of memory. The main workload in the migration to HPC systems is the parallelization of the code, trying to optimize the machine usage as well as a good memory treatment depending on the architecture of the particular machine.

José M. Tamayo was born in Barcelona, Spain, on October 23, 1982. He received the de-gree in mathematics and the degree in telecommunications engineering from the Universitat Politècnica de Catalunya (UPC), Barcelona, both in 2006. He received the Ph.D. degree in telecommunications engineering from the Universitat Politècnica de Catalunya (UPC), Bar-celona, in 2011.From 2004 to 2011, he stayed at the Telecommunications Department, Universitat Politècni-ca de Catalunya (UPC), Barcelona.

From April 2011 to April 2012 he worked as a postdoc at DEOS department, ISAE, Toulouse, France. In May 2012, he joint Entares Engineering, now Nexio Simulation, Toulouse, France. His current research interests include accelerated numerical methods for solving electromagnetic problems.




Novel HPC technologies for rapid analysis in bioinformatics Paul Walsh, Nsilico, Ireland

NSilico is an Irish based SME that develops software to the life sciences sector, providing bioinformatics and medical informatics systems to a range of clients. One of the major challenges that their users face is the exponential growth of high-throughput genomic sequence data and the associated computational demands to process such data in a fast and efficient manner. Genomic sequences contain gigabytes of nucleotide data that require detailed comparison with similar sequences in order to determine the nature of functional, structural and evolutionary relationships. In this regard Nsilico has been working with computational experts from CINES (France) and ICHEC (Ireland) under the PRACE SHAPE programme to address a key problem that is the rapid alignment of short DNA sequences to reference genomes by deploying the Smith-Waterman algorithm on an emerging many-core technology, the Intel Xeon Phi co-processor. This presentation will give an overview of the technical challenges that have been overcome during this project, performance achieve-ments and implications, as well as our immensely positive experience in working with PRACE within this successful collaboration.

Dr Paul Walsh is the Chief Technology Officer of NSilico (www.nsilico.com), provider of the world’s most easy-to-use data management and analytics software for the life sciences and health care industries. He is also a Research Fellow in the Cork Institute of Technology (CIT) and a Senior Visiting Research Fellow at the University of Edinburgh where he manages research in medical informatics and bioinformatics.

He holds a Ph.D., M.Sc. and B.Sc. Hons in Computer Science from the National University of Ireland and has a long list of publications including outstanding paper awards. He was recently awarded a distinction in Project Management and has consulted on a wide range of projects ranging from start-up technology com-panies to managing projects for global corporations. He is funded under national and international research schemes such as the EU FP7 program where he oversees research in data analytics, machine learning and high performance computing. He sits on numerous committees and editorial boards including Landes Sciences Journal Bioengineered (https://www.landesbioscience.com/journals/bioe/). His latest research is focussed on bringing innovative high performance computation techniques to bear on big data problem in bioinformatics.

HPC application to improve the comprehension of ballistic impacts behaviour on composite materials Paolo Cavallo, AMET Claudio Arlandini, CINECA

The damage phenomenon occurring on composite materials when subjected to a ballistic impact is a com-plex problem.

Therefore, the understanding of the influence of the parameters describing the material behavior is not a straightforward task; moreover, due to the fact that these influences are mutually connected, the task of de-signing a new structure with improved characteristics in terms of resistance to ballistic impacts is a very hard one. Only resorting to a massive use of DOE analyses, supported by suitable computing resources, may lead to a better understanding of the problem and to a definition of the parameters mostly influencing the physical phenomenon.

We present an overview of the methodology used in this research together with the first results obtained, and their relevance in the context of composite materials industrial manufacturing.

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Paolo Cavallo got a MSc in Nuclear Engineering at Politecnico di Torino. He has more than 20 years of experience in CAE and methodologies development. He was Project Manager at FIAT Research Center, Technical Director at Altair Engineering Italy, and General Manager at ISDG Research Center. He is now Technical Director of AMET Srl. AMET’s mission is to provide its customers with best-in-class solutions – i.e. methodologies, technologies and engineering services – for the design and development of industrial products, exploiting an integrated multi-domain model-based approach, to assure optimum system performance.

Claudio Arlandini got a PhD in Nuclear Astrophysics at the University of Heidelberg. He worked as business manager in the area of IT infrastructure management and data center operations at CILEA Interuniversity Consortium, and since the merging of CILEA in CINECA he is involved in simulation and technology transfer services for industries. He was WP9 “Industrial Applications Support” Leader In PRACE2IP and he is coordinator of CINECA ac-tivities in the I4MS Project Fortissimo.

PRACE SHAPE Project: OPTIMA pharma GmbH Ralph Eisenschmid, OPTIMA pharma GmbH B. Große-Wöhrmann, Bärbel, HLRS OPTIMA pharma produces and develops filling and packaging machines for pharmaceutical products. Ster-ile filling lines are enclosed in clean rooms, and a detailed and reliable knowledge of the airflow inside the clean rooms would enhance the design of the filling machines and support the CAE job. The goal of this project is to simulate the airflow with OpenFOAM meeting the requirements of industrial production.

We looked for the best strategy for the generation of very large meshes including domain decomposition and reconstruction using the standard tools provided by OpenFOAM. Then, we tested and compared different turbulence models on large meshes and studied the scalability of the relevant OpenFOAM solvers. Overall, we found a compromise between the required mesh resolution and the feasible mesh size which allows reli-able simulations of the airflow in the entire clean room. We found serial tools like decomposePar as walltime- and memory-critical bottlenecks in performing CFD with OpenFOAM on large grids with mesh sizes larger than 50 M cells. Results will be presented at the talk.

Ralph Eisenschmid, born in Germany, studied and graduated in Process Engineering at the University of Stuttgart. With long term experience in R&D and plant engineering, he entered Optima pharma in 2011 as R&D engineer for process development. In 2012 he successful-ly introduced numerical methods and simulations at Optima pharma by using commercial multiphysics toolboxes. With friendly help and consulting of HLRS members (HPC center of the University of Stuttgart) he discovered the advantages and performance of opensource toolboxes like OpenFOAM in CFD issues. Since 2013 he is running CFD simulations on large HPC systems at the HLRS. His first experiences in HPC started in running air flow simulations in clean rooms with OpenFOAM.




Testing LES turbulence models in race boat sail SHAPE Pilot Project – with the involvement of Juan Yacht Design Herbert Owen, Barcelona Supercomputing Centre, Spain

Currently, race boat design depends more heavily on the CFD modeling of turbulent free surface flows than on tank and wind tunnel testing. Simulations are cheaper, faster and more reliable than traditional tests for boat design. Enhanced flow visualization and force decomposition, provides much richer information than the one measurable in tank tests leading to a much better understanding of the flow phenomena. The early adoption of RANS CFD has been a key competitive advantage in the design of America’s Cup and Volvo Ocean Race wining boats. Nowadays commercial RANS CFD codes have become standard practice and more innovative simulation tools would provide a technological advantage. RANS models work well for most problems but their accuracy is reduced when there are important regions of separated flow. This happens at the boat sails for certain wind directions. Large eddy simulation (LES) turbulence models are needed for such flows.

In this work, we test LES models implemented in the finite element CFD code Alya for the flow around boat sails in conditions where RANS models fail. Alya uses a Variational Multiscale formulation that can take into account the LES modeling relying only on the numerical model. Alternatively eddy viscosity models such as the WALE model can be used. The results obtained with these models will be compared to results obtained with RANS on the same mesh to allow the company JYD to have a better idea of the advantages this new technology could contribute to their work and the feasibility of incorporating it to their available tools.

Herbert Owen, graduated in Mechanical Engineer at the Universidad de Buenos Aires, Ar-gentina. He received his in PhD in Civil Engineering from the Technical University of Catalo-nia (UPC), Barcelona, Spain. 2009.He started his research activity in Computational Fluid Dynamics as a Junior Researcher at the Center for Industrial Research of the Techint Organization, a company involved in steel-making in Argentina in 1999.

In 2003 he moved to Barcelona to start his PhD on “A Finite Element Model for Free Surface and Two Fluid Flows on Fixed Meshes” at the UPC Technical University of Catalo- nia which he finished in 2009. Then he moved to the Barcelona Supercomputing Center where he continues to work mainly in Computational Fluid Dynamics using the Finite Element Method and participates in the development of the parallel code Alya.He is author of more than ten articles in reviewed journals and a similar number of conference publications. His main research areas are: free surface and two fluid flows, mould filling problems, ship hydrodynamics, turbu-lence modeling, pressure segregation schemes and finite element stabilization techniques.

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Plenary Session

Thursday 22 May - 09:00 to 12:30 - Auditori

Observing the bacterial membrane through molecular modeling and simulation Matteo Dal Peraro, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)

The physical and chemical characterization of biological membranes is of fundamental importance for under-standing the functional role of lipid bilayers in shaping cells and organelles, steering vesicle trafficking and promoting cellular signaling. In bacteria this cellular envelop is highly complex, providing a robust barrier to permeation and mechanical stress and an active defense to external attack. With the constant emergence of drug resistant strains that poses a serious threat to global health, understanding the fine molecular details of the bacterial cellular wall is of crucial importance to aid the development of innovative and more efficient antimicrobial drugs. In this context, molecular modeling and simulation stand as powerful resources to probe the properties of membranes at atomistic level. In this talk I will present the efforts of my laboratory (i) to cre-ate better models of bacterial membrane constituents, (ii) to develop efficient tools for assembling realistic bacterial membrane systems, and (iii) to investigate their interactions with signaling protein complexes and antimicrobial peptides, exploiting the computational power of current HPC resources.

Matteo Dal Peraro, Ph.D. is Tenure Track Assistant Professor at the School of Life Scienc-es, Ecole Polytechnique Fédérale de Lausanne (EPFL). He is Head of the Laboratory for Biomolecular Modeling (LBM). His research at the LBM, within the Interfaculty Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.

Observations on the evolution of HPC for Science and Industry Paul Messina, Argonne Leadership Computing Facility (ALCF) of Argonne National Laboratory

Scientific computing has advanced dramatically during the last four decades, despite several upheavals in computer architectures. The evolution of high-end computers in the next decade will again pose challenges as well as opportunities. The good news is that many applications are able to utilize today’s massive levels of parallelism, as will be shown by presenting a sampling of varied scientific, engineering, and industrial ap-plications that are using high-end systems at the Argonne Leadership Computing Facility and other centers.

As we look towards the use of exascale computers, availability of application software and building blocks is as always a key factor. This is especially the case for industrial users but is also true for many academic and research laboratory users. Support is needed to enable the transition of widely used codes, programming frameworks, and libraries to new platforms and evolution of capabilities to support the increased complexity of the applications that are enabled by the more powerful systems.

Providing access to state-of-the-art systems -- and training on their use -- to interested industrial and aca-demic researchers in an effect approach and should be used more widely. Training is also an important factor in enabling the productive use of HPC. Few university courses teach scientists and engineers how to use ef-fectively leading-edge HPC platforms, software engineering practices, how to build and maintain community codes, what high-quality software tools and building blocks are available, and how to work in teams -- yet all those skills are necessary in the use of HPC.




Finally, close involvement of applications experts in guiding the design of future hardware and software, supplemented by funding to address development of key technologies and features, has proven to be effective and will be needed more than ever in the exascale era and beyond.

Dr. Paul Messina is Director of Science at the Argonne Leadership Computing Facility (ALCF) of Argonne National Laboratory. Previously, Dr. Messina served as founding Director of California Institute of Technology’s (Caltech) Center for Advanced Computing Research, as Assistant Vice President for Scientific Computing, and as Faculty Associate for Scientific Computing, Caltech.

While at Caltech he conceived, formed, and led the Consortium for Concurrent Supercomputing, which created and operated the Intel Touchstone Delta System, at that time the world’s most powerful scientific computer, and held a joint appointment at the Jet Propulsion Laboratory as Manager of High-Performance Computing and Communications. During his Caltech years he also served as Principal Investigator for the CASA gigabit network testbed, as Chief Architect for the National Partnership for Advanced Computational Infrastructure (NPACI), as principal investigator for the Scalable I/O Initiative, and as co-principal investigator for the National Virtual Observatory and TeraGrid.

During a leave from Caltech in 1999-2000, he led the DOE-NNSA Accelerated Strategic Computing Initiative.

In his first association with Argonne from 1973-1987, he held a number of positions in the Applied Mathemat-ics Division and was the founding Director of the Mathematics and Computer Science Division.

Economic and scientific impact of collaboration between science and industry Moderator: Tom Wilkie, Europa Science Ltd., United Kingdom

Panel: Luis O. Silva, Argonne Leadership Computing Facility, United States Jean-François Lavignon, Argonne Leadership Computing Facility, United States Michael Papka, Argonne Leadership Computing Facility, United States Francine Berman, Rensselaer Polytechnic Institute, United States Alexander Frederic Walser, Automotive Simulation Centre Stuttgart, Germany Augusto Burgueño Arjona, European Commission, Belgium Matteo Dal Peraro, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) Kenneth Ruud, Chair of the PRACE SSC Jürgen Kohler, Chair of the PRACE IAC

Panel Discussion:One of the overarching goals of Horizon 2020 is to foster economic growth and create jobs in Europe. By con-necting science and innovation, Horizon 2020 is helping to achieve this while putting emphasis on excellent science, industrial leadership, and tackling societal challenges.

The panelists will discuss opportunities and challenges for improving the collaboration between science and industry to achieve this goal. Successful examples, best practices and lessons lear-ned will be presented from different perspectives and the role of funding agencies will be explained.

Tom Wilkie. An award-winning senior science writer and national newspaper journalist, Dr Tom Wilkie co-founded Europa Science in 2002. With a background in mathematics and the owner of a PhD in the theory of elementary particle physics, he is a former Features Editor of New Scientist, former Science Editor for The Independent, and former Head of Bio-Medical Ethics at the Welcome Trust. He now serves as Editor-In-Chief across all Europa Science publications.

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Michael E. Papka, PhD is a computer scientist whose research is focused on the visu-alization and analysis of large data from simulation and experimental sources. His in-terests include the use of advanced technology to enhance this research and to enable scientific collaboration. He is the director of the Argonne Leadership Computing Facility (ALCF), home to one of the world’s fastest supercomputers dedicated to open science, and the deputy associate laboratory director of the Computing, Environment and Life Sciences (CELS) directorate at Argonne, where he supports programmatic efforts that contribute to or benefit from high performance computing. In addition to his duties and research efforts at Argonne, Mike is a member of the computer science faculty at North-ern Illinois University, where he teaches courses on data visualization, data structures, and algorithm analysis. He is also a senior fellow of the University of Chicago/Argonne

Computation Institute. Mike earned a master’s degree and doctorate in computer science from the University of Chicago, a master’s degree in computer science and electrical engineering from the University of Illinois at Chicago, and a bachelor’s degree in physics from Northern Illinois University.




PRACEdays14 Poster Session (Tuesday 20 May 2014, 18:30 – 19:30) The posters will be on display throughout the conference

Perturbation-Response Scanning method reveals hot residues responsible for conformational transitions of human serum transferrin protein (Material Science)

Haleh AbdizadehSabanci University

(Turkey)

Old-fashioned CPU optimisation of a fluid simulation for investigating turbophoresis (Mechanical engineering [CFD])John Donners

SURFsara(Netherlands)

Toward next stage of design method of polymer nano-composites using x-ray scattering analysis and large-scale simulations by supercomputing (Material Science)

Katsumi HagitaNational Defense Academy

(Japan)

The development of scalable unstructured high-accuracy and adaptive discretisations for Large Eddy Simulation of turbomachinery flows (Aeronautics / Aerospace)

Koen HillewaertCenaero(Belgium)

Accelerating Simulations of Hydrogen Rich Systems by a Factor of 2.5 (Life Sciences)Himanshu Khandelia

University of Southern Denmark(Denmark)

Self-consistent charge carrier mobility calculation in organic semiconductors with explicit polaron treatment (Material Science)

Ivan KondovKarlsruhe Institute of Technology

(Germany)

CFD Simulations by Open Source Software (Engineering)Tomas KozubekIT4Innovations

(Czech Republic)

Simulating an Electrodialysis Desalination Process with HPC (Engineering)Kannan MasilamaniUniversity Siegen

(Germany)

GPGPU based Lanczos algorithm for large symmetric eigenvalue problems (Computer Science)Vishal Mehta

Trinity College Dublin(Ireland)

Car body design in crash: a new optimization challenge (Engineering)Marc ParienteRenault SA

(France)

Harnessing Performance Variability for HPC Applications (Computer Architecture / Earth Sciences)Antoni Portero

IT4Innovations(Czech Republic)

Engineering simulations at CSUC (Engineering)Pere Puigdomènech

CSUC(Spain)

Solving Large non-Symmetric Eigenvalue problems using GPUs (Computer Science)Teemu Rantalaiho

University of Helsinki(Finland)

High Performance Computing aspects of acoustic simulations of an air-intake system in OpenFOAM (Engineering)Jan Schmalz

University of Duisburg-Essen(Germany)

Linear Algebra Library for heterogeneous computing in scientific discovery (Mathematics / Engineering)Thomas Soddemann

Fraunhofer Institute for Algorithms and Scientific Computing SCAI(Germany)

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Poster Session

Wednesday 21 May - 18:30 to 20:00 - Auditori Hall Perturbation-Response Scanning method reveals hot residues responsible for conforma-tional transitions of human serum transferrin protein Haleh Abdizadeh, Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul Ali Rana Atilgan, Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul Canan Atilgan, Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul

Proteins usually undergo conformational changes between structurally different forms to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that medi-ate the conformational movements between different regions of the protein. In the present work, we have employed Perturbation- Response Scanning (PRS) method based on the linear response theory in order to predict the key residues involved in protein conformational transitions. The key functional sites are identified as the residues whose perturbations largely influence the conformational transition between the initial and target conformations. Ten different states of the human serum transferrin (hTF) protein in apo, holo and par-tially open forms under different initial conditions have been used as case studies to identify critical residues responsible for closed- partially open- open transitions. The results show that the functionally important res-idues mainly are confined to highly specific regions. Interestingly, we observe a rich mixture of both conser-vation and variability within the identified sites. In addition, perturbation directionality is an important factor in recovering the conformational change, implying that highly selective binding must occur near these sites to invoke the necessary conformational change.

Moreover, our extensive Molecular Dynamics (MD) simulations of holo hTF in physiological and en-dosomal pH are in remarkable agreement with experimental observations. Our results indicate do-main motions in the N-lobe as well as domain rigidity in the C-lobe at physiological pH. However, the C lobe goes through more flexible dynamics at low pH, achieved as a result of protonation of pKa upshift-ed residues. This flexibility in turn leads to the selective release of iron within this cellular compartment.

Haleh Abdizadeh is a research assistant at the Computational Materials Science Labora-tory, Sabanci University, Turkey working on her PhD. She received her M.Sc. in Polymers Engineering from Amirkabir University of Technology, Iran. Currently, her research focuses on structural dynamics of proteins to detect conformational changes and allosteric modula-tion of function in ferric binding proteins.




Old-fashioned CPU optimisation of a fluid simulation for investigating turbophoresis John Donners, SURFsara Hans Kuerten, TU/e

Turbulent flows with embedded particles occur frequently in the environment and in industry. These flows have richer physics than flow of a single-phase fluid and new numerical simulation techniques have been de-veloped in recent years. One of the main interests of this research is turbophoresis, the tendency of particles to migrate in the direction of decreasing turbulence. This principle tends to segregate particles in a turbulent flow toward the wall region and is expected to increase the deposition rate onto a surface. High-resolution simulations with a spectral model are used to correctly predict the particle equation of motion in models that do not resolve all turbulent scales.

Long integrations are required to reach statistical equilibrium of the higher-order moments of the particle velocities. Most of the runtime of the spectral model is taken up by Fourier transforms and collective com-munications. To reach the required performance, the MPI-only parallellization scheme was extended with the use of MPI datatypes, multi-threaded FFTW calls and OpenMP parallellization. To maximize efficiency, MPI communication and multi-threaded FFTW calls are overlapped: the master thread is used to complete the blocking collective communication, while computations are split across the other threads. To accomplish this overlap, communication and computation of multiple variables is interleaved. When no communication is required, computations are split across all threads. The core count was increased by a factor of 5.2, while the total runtime could be reduced by a factor of 6.7.

Faster simulations allow for a tighter loop of hypothesis building and testing, which result in faster scientific discovery. The parallellization techniques presented here only require relatively small modifications to the code, without introducing revolutionary new paradigms for accelerators. This can keep the focus of the scien-tist on the generation of knowledge.

John Donners received his PhD in oceanography at Utrecht University in 2005. He was a research scientist doing climate modelling on the Earth Simulator in Yokohama for the UK-Japan climate collaboration from 2004 to 2008. He then joined SURFsara as a consul-tant for supercomputing. His tasks include the parallellization, optimization and scaling of HPC applications on national and European HPC systems.

Toward next stage of design method of polymer nano-composites by X-ray scattering analysis and large-scale simulations on supercomputers Katsumi Hagita, National Defense Academy of Japan

Polymer Nano-Composites (PNC), ex. polymer films and tire rubber, is widely used in our usual life. Geom-etry of nano-fillers has much important role to tune its function. Recently, nano-science and technology can perform molecular level control of synthesis to make various branching of polymer, modification of end of polymer and grafting to a substrate or a nano-particle, and observation of nano space from nano-meter to submicron meter. With benefits of recent progress of massively parallel supercomputing, virtual experiments to study effect by polymer architecture, morphology of nano particles can be performed for basic science by current top supercomputers and will be for R&D of industrial products by future top supercomputers. We proposed an approach combined X-ray scattering analysis and large scale simulations of bead spring model of PNC. Overview of our simulation model and approach, and results are shown in my Poster Presentation. This work is partially supported by JHPCN (Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures) in JAPAN for efficient and advanced use of networked supercomputers.

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Dr. Katsumi Hagita is lecturer in Department of Applied Physics, National Defense Academy of JAPAN. I received Ph. D degree in Physics from Keio University, Japan on March, 2001. My research interests are polymer physics and polymer material science as well as data analysis based on statistical physics and large scale simulations as computational physics.

The development of scalable unstructured high-resolution discretisations for Large Eddy Simulation of turbomachinery flows Koen Hillewaert, Cenaero Corentin Carton de Wiart, Cenaero.

To allow the design for more reliable off-design operation, higher overall efficiency and lower environmental nuisance of jet engines, more precise CFD tools will be required in complement to the currently available tools.

The industry state of the art in CFD is largely based on statistical turbulence modeling. Scale-resolving ap-proaches on the other hand compute (large) turbulent flow structures directly, thereby removing turbulence modeling altogether (Direct Numerical Simulation/DNS) or reducing its scope to the smaller turbulent struc-tures, which are more universal in nature (Large Eddy Simulation/LES). Given the limitation of statistical mod-els to the prediction of near-design aerodynamic performance, there is a need for scale-resolving approaches for the prediction of off-design aerodynamic performance, noise generation, combustion, transitional flows ...

The stumbling block towards an industrial use of DNS and LES is the huge computational cost. The detailed representation of turbulent flow structures impose huge resolution and accuracy requirements, unobtainable by the low order discretisation methods currently used in industry. High resolution codes used for the funda-mental study of turbulence are on the other hand not sufficiently flexible to tackle real industrial geometries, and often do not provide possibilities for adaptive resolution, which could drastically enhance solution reliabil-ity. The combination of high performance computing to adaptive unstructured high-resolution codes promises a breakthrough in modeling capabilities.

This talk discusses the recent developments in the development of the discontinuous Galerkin Method for the large-scale DNS and LES of turbomachinery flows. Due to its elementwise defined discontinuous inter-polation, this method features high accuracy on unstructured meshes, excellent serial and (strong) parallel performance and high flexibility for adaptive resolution. The main focus of the talk will be the further assess-ment of the LES models on benchmark test cases as well as the assessment of the benefits of local or-der-adaptation currently persued in the PRACE project ‘PadDLES’. Furthermore, serial and parallel efficiency optimisation will be discussed.

Koen Hillewaert is the team leader of the Argo group at Cenaero. His group has been active for several years in the industrialisation and large scale deployment of implicit high-order discontinuous Galerkin methods for the DNS and LES of industrial flows. The group has benefited from PRACE resources in the industrial pilot project noFUDGE (transitional flow in a LP turbine) and the currently running two year project PadDLES (demonstration of p-vari-able discretisations for LES). The group was furthermore involved in the European research projects Adigma and IDIHOM on the industrialisation of high-order methods.

Koen is the head developer of the Argo code, responsible for discretisation and computational efficiency as-pects. He is one of the organisers of the workshop on higher-order methods for CFD. Koen is currently also vice-chair of the PRACE user forum.




Accelerating Simulations of Hydrogen Rich Systems by a Factor of 2.5 Himanshu Khandelia, University of Southern Denmark, Denmark

Biological molecules are hydrogen-rich. Fast vibrations of H-bonded atoms and angles limit the time-step in molecular dynamics simulations to 2 fs. We implement a method to improve performance of all-atom lipid simulations by a factor of 2.5. We extend the virtual sites procedure to POPC lipids, thus permitting a time-step of 5 fs. We test our algorithm on a simple bilayer, on a small peptide in a membrane, and on a large transmembrane protein in a lipid bilayer, the latter requiring the use of HPC at Hector. Membrane properties are mostly unaffected, and the reorientation of a small peptide in the membrane and the lipid binding and ion binding of a large membrane protein are unaffected by the new VS procedure.

The procedure is compatible with the previously implemented virtual sites method for proteins, thus allowing for VS simulations of protein-lipid complexes.

Currently, the method has been implemented for the CHARMM36 force field, and is applicable to other lipids, proteins and force fields, thus potentially accelerating molecular simulations of all lipid-containing biological complexes.

Himanshu Khandelia has a Masters in Biochemical Engineering and Biotechnology from the Indian Institute of Technology, Delhi, after which he pursued a PhD in Chemical Engi-neering from the University of Minnesota. HK moved to Denmark in 2006 for a postdoc, and is currently Associate Professor at MEMPHYS, Center for Biomembrane Physics at the University of Southern Denmark, Odense, Denmark. HK is supported by a Lundbeckfonden Young Investigator award which is awarded to 6-8 outstanding young scientists each year. We are interested in the biophysics of membranes, and of membrane associated phenom-ena, such as the mechanism of ion pumping across the membrane, the biogenesis of lipid droplets in the lipid bilayer and drug-membrane interactions. PRACE resources have been instrumental in furthering our research.

Self-consistent charge carrier mobility calculation in organic semiconductors with explicit polaron treatmentPascal Friederich, Karlsruhe Institute of Technology (KIT), Germany Ivan Kondov, Karlsruhe Institute of Technology (KIT), Germany Velimir Meded, Karlsruhe Institute of Technology (KIT), Germany Tobias Neumann, Karlsruhe Institute of Technology (KIT), Germany Franz Symalla, Karlsruhe Institute of Technology (KIT), Germany Angela Poschlad, Karlsruhe Institute of Technology (KIT), Germany Andrew Emerson, SuperComputing Applications and Innovation Dept, Cineca, Italy Vadim Rodin, Sony Deutschland GmbH, Stuttgart Technology Center, Germany Florian von Wrochem, Sony Deutschland GmbH, Stuttgart Technology Center, Germany

Wolfgang Wenzel, Karlsruhe Institute of Technology (KIT), Germany

Whole-device simulation of organic electronics is important for improving device performance. We present a multi-step simulation of electronic processes in organic light-emitting diodes (OLEDs) achieved by multi-scale modelling, i.e. by integrating different simulation techniques covering multiple length scales. A typical model with 3000 molecules consists of about 1000 pairs of charge hopping sites in the core region, which contains about 100 electrostatically interacting molecules. The energy levels of each site depend on the local electrostatic environment yielding a significant contribution to the energy disorder. This effect is explic-itly taken into account in the quantum mechanics sub-model in a self-consistent manner, which represents

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however, a considerable computational challenge. Thus we find that the total number of computationally expensive density functional theory (DFT) calculations needed is very high (about 105). Each of these cal-culations is parallelized using the MPI library and scales up to 1024 Blue Gene/Q cores for small organic molecules of about 50-100 atoms. Next data are exchanged between all contained molecules at each itera-tion of the self-consistence loop to update the electrostatic environment of each site. This requires that the quantum mechanics sub-model is executed on a high-performance computing system employing a special scheduling strategy for a second-level parallelisation of the model. In this study we use this procedure to investigate charge transport in thin films based on the experimentally known electron-conducting small mol-ecule Alq3, but the same model can be applied to, for example, two-component organic guest/host systems.

Ivan Kondov has acquired a master’s degree in theoretical chemistry and chemical physics at the Sofia University and PhD in theoretical physics at the Technical University Chemnitz with thesis on computational studies of electron transfer processes. He has over twelve years experience with scientific computing and simulations. Since 2009 he is heading the Simulation Laboratory NanoMicro at Steinbuch Centre for Computing, Karlsruhe Institute of Technology. His scientific interests range in the broad fields of computational chemistry, computational nanoscience and high performance computing.

CFD Simulations by Open Source Software Tomas Kozubek, National supercomputing center IT4Innovations, VSB – TU Ostrava, Czech Republic Tomas Brzobohaty, National supercomputing center IT4Innovations, VSB – TU Ostrava, Czech Republic Tomas Karasek, National supercomputing center IT4Innovations, VSB – TU Ostrava, Czech Republic

Demand from end users who need to solve their problems which are in many cases very complex is and always has been driving force for developing of new efficient algorithms. This is even more apparent in era of supercomputers. Nowadays high performance computers give their users computational power unimag-inable few years ago. Demand for algorithms able to tame and utilize this power has been lately driving force for parallelization of existing and development of new parallel algorithms.

At this poster examples of engineering problems such as external aerodynamics, urban flow and thermody-namics solved on High Performance Computing (HPC) platform are presented. To obtain high fidelity results numerical models consisting of meshes with huge number of cells has to be created. As a consequence large number of equations has to be solved to obtain final solution. To do so in acceptable time supercomputer Anselm at National supercomputing center IT4Innovations, Czech Republic, was employed. To emphasize advantage of supercomputers when it comes to computational time results of scalability for all cases are presented at this poster as well.

Deployment of open source codes on HPC systems together with development of new algorithms for solving large number of equations will enable researchers and engineers to solve even more challenging problems in many areas and industries such as aerospace, automotive, biomechanics or urban flow.

Tomas Kozubek is a professor of applied mathematics at the VSB Technical University of Ostrava and head of department Libraries for Parallel Computing at IT4Innovations Nation-al supercomputing center. He obtained his PhD in Computer Sciences and Applied Mathe-matics from VSB Technical University of Ostrava. His research interest is in scalable algo-rithms for solving large problems of mechanics, FETI type domain decomposition methods, quadratic programming algorithms and reliable solution of the nonlinear problems.

Tomas is also a local coordinator of the work packages within Partnership for Advanced Computing in Eu-rope (PRACE) project and principal investigator for Czech Republic of EXascale Algorithms and Advanced Computational Techniques (EXA2CT).




Simulating an Electrodialysis Desalination Process with HPC Kannan Masilamani, Siemens AG, Corporate Technology, Erlangen, Germany; Simulation Techniques and Scientific Computing, University of Siegen, Germany J. Zudrop, Simulation Techniques and Scientific Computing, University of Siegen, Germany M. Johannink, Aachener Verfahrenstechnik - Process Systems Engineering, RWTH Aachen University Germany H. Klimach, Simulation Techniques and Scientific Computing, University of Siegen, Germany S. Roller, Simulation Techniques and Scientific Computing, University of Siegen, Germany

Electrodialysis can be use for efficient seawater desalination. For this, an electric field is used in combination with selective membranes to separate salt ions from the seawater. Those membranes are kept apart by a complex spacer structure. Within the spacer filled flow channel, the process involves the transport of ions and the bulk mixture. A multi-species Lattice Boltzmann Method (LBM) for liquid mixture is implemented in our highly scalable simulation framework Adaptable Poly-Engineering Simulator (APES) and deployed on High Performance Computing (HPC) systems to gain some insights to this complex process.

For relevant results, it is necessary to simulate the full device used in the laboratory and industrial scale, which results in simulations with half a billion elements. A performance analysis is done for the method on the Cray XE6 system Hermit, HLRS, Stuttgart.

Kannan Masilamani is a PhD Student under the supervision of Prof. Sabine Roller, University of Siegen

He is working on the BMBF funded project “HISEEM: Highly Efficient Integrated Simulation of Electro-Membrane Processes for Desalination of Sea Water.” And his research focus is the Multi-Species LBM method and it’s coupling with Electrodynamics

GPGPU based Lanczos algorithm for large symmetric eigenvalue problems Vishal Mehta, Trinity College Dublin, Ireland

Eigen value problems are heart of many science and engineering applications. However, they are computa-tionally expensive, especially when the eigenvalue systems are very large. There are techniques like power iteration, Arnoldi’s algorithm, and Lanczos procedure when only few of large or small Eigen values are required.

The use of GPGPU for these computations is challenging. The CUDA computing model and PTX assembly from Nvidia does provide flexible environment for a programmer to use the hardware to its threshold.

The Implicit restarted Lanczos has been developed for an NVIDIA GPU, providing notable speed up over standard shared memory OpenMP model. The salient features include householder transformations for QR decomposition and strum sequencing techniques for eigen values of symmetric tridiagonal matrix. The mem-ory levels like shared memory, caches, and registers have been efficiently used along with highly efficient PTX assemblies. PTX assembly optimization includes reducing registers in use; by managing assembly in-structions pertaining to false shared memory initializations and false movements of values around registers.

Mr. Vishal Mehta has his bachelor’s in Electronics and Communication from Nirma Univer-sity, India and M.Sc. in High Performance Computing from Trinity College Dublin. His active field of research includes heterogeneous computing models and algorithms, High Perfor-mance architectures and Hadoop Distributed File system. He is currently pursuing his M.Sc. degree from Trinity College Dublin. He has previously worked at Space Application Centre, Indian Space Research Organization; porting Synthetic Aperture Radar Algorithms on CUDA platform. He is also a recipient of Government of Ireland award for international scholars (2012) and Nvidia academic research grant (2011).

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Car body design in crash: a new optimization challenge Marc Pariente, Renault SAS Thuy Vuong, Yves Tourbier, Jean Christophe Allain,

IRT System X; ESI-Group

The presentation will focus on the results of a PRACE HPC project initiated in March 2013 and completed in March 2014. The purpose of the project is the optimal design of a vehicle body to reach the safety objective, with representative means and targets that the automakers will use in the next 3-5 years. The project consists of two complementary phases:

- The development of a crash numerical model integrating a more precise representation of the physics than the current models (about 20 MFE, calculated with 1024 cores within 24hrs);

- The use of this model in a design study by optimization techniques in large dimension (about 100 parameters) , and representative of the combinatorial aspects of the industrial issues, such as the re-use of existing parts up to design a new vehicle.

An application of the model reduction techniques in crash will help to conclude on the prospects for large-scale optimization problems with heavy numerical simulations.

Marc Pariente. I am a Mechanical Engineer, I received my degree in 2003 at IFMA (Institut Français de mécanique avancée) located in Clermont-Ferrand (FRANCE). My knowledge is based on mechanics, material, optimization, Finite Element Method… Working at the Re-nault Research department since 2004 first on topics linked with engine ignition and spark plug. Since 2012, I join the research optimization team to work on improvement on car crash model and optimization tools.

Harnessing Performance Variability for HPC Applications Antonio Portero, IT4Innovations National Supercomputer Center, Czech Republic

The overall goal of the HARPA project is to provide architectures for High Performance Computing (HPC)-ori-ented with efficient mechanisms to offer performance dependability guarantees in the presence of unreliable time-dependent variations and aging throughout the lifetime of the system. This will be done by utilizing both proactive (in the absence of hard failures) and reactive (in the presence of hard failures) techniques.

The term “performance dependability guarantee” refers to time-criticality (i.e., meeting deadlines), and a predefined bound on the performance deviation from the nominal specifications in the case of HPC. The promise is to achieve this reliability guarantee with a reasonable energy overhead (e.g. less than 10% average). A significant improvement is hence achieved compared to the SotA, which now provides guarantees at the payoff of at least 50% overhead. In addition, we will provide a better flexibility in the platform design while still achieving power savings of at least 20%. To the best of our knowledge, this is the first project to attempt a holistic approach of providing dependable performance guarantees in HPC systems. This is done while taking into account various non-functional factors, such as timing, reliability, power, and aging effects. The HARPA project aims to address several scientific challenges in this direction:




(i) Shaving margins. Similar to the circuit technique Razor, but with different techniques at the microarchitecture and middleware, our aim is to introduce margin shaving concepts into aspects of a system that are typically over-provisioned for the worst case.

(ii) A more predictable system with real-time guarantees, where needed. The different monitors, knobs, and the HARPA engine will make the target system more predictable and pro-actively act on performance variability prior to hard failures. (iii) Implementation of effective platform monitors and knobs. HARPA will select the appropriate monitors and knobs and their correct implementation to reduce efficiency and performance overheads.

Technical Approach: HARPA Engine Overview Figure shows the main concepts of the HARPA architecture and the main components of an architecture that can provide performance-dependability guarantees. The main elements that distinguish a HARPA-en-abled system are: (i) Monitors and knobs, (ii) User requirements and (iii) HARPA Engine. The HARPA en-gine actuates the knobs to bias the execution flow as desired, based on the state of the system and the performance (timing/throughput) requirements of the application.

The concepts that are to be developed within the HARPA context address the HPC. More specifically, from HPC domain we will use Disaster and Flood Management Simulation.

Web page: www.harpa-project.eu Antonio Portero. He received the Electronic Engineering degree, master in Microelectronics and PhD (Suma Cum Laude) in Computer Science from the Universitat Autònoma de Barcelona (Spain) in 1997, 2000 and 2008 respectively.

Currently, he is Senior Researcher at IT4Innovations National Supercomputer Center, Czech Republic. Before, he was Research Associate at the University of Siena (Italy). He has been involved in several European Projects: HARPA (Harnessing Performance Variability), TERA-FLUX in the area of Future and Emerging Technologies for Tera-device Computing, HiPEAC (High Performance Embedded-system Architecture and Compiler) and ERA (Embedded Re-configurable Architectures).

His current interest includes Computer Architecture themes such as Embedded Systems, Multiprocessors, Memory System Performance, Workload Characterization and Network on Chip. He is HiPEAC member (European Network of Excellence on High Performance and Embedded Architecture and Compilation), IEEE (Institute of Electrical and Electronics Engineers) and ACM (Association for Computing Machinery).

Engineering simulations at CSUC Pere Puigdomènech, Consorci de Serveis Universitaris de Catalunya (CSUC) David Tur, Consorci de Serveis Universitaris de Catalunya (CSUC) Alfred Gil, Consorci de Serveis Universitaris de Catalunya (CSUC) Cristian Gomollon, Consorci de Serveis Universitaris de Catalunya (CSUC)

The Consorci de Serveis Universitaris de Catalunya (CSUC) shares academic, scientific, library, transfer of knowledge and management services to associated entities to improve effectiveness and efficiency by enhancing synergies and economies of scale. The center provide services to public and private universities, research centers and institutes, offering a wide range of services such as supercomputing, communications,

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advanced communications library resources, digital repositories, e-administration and shared services

The HPC&applications area of CSUC offers its knowledge to accademic and industrial users providing technical and scientific support hence they can obtain the maximum benefit of the use of the HPC systems.

The poster will present Benchmark results of most used industrial codes showing performance behaviour in real cases from:

- Ansys FLUENT 14: Truck_111m: Flow around a truck body (DES 111e6 elements) and Donaldson LES (LES 20 e6 elements).

- Pamcrash 2012: Barrier: Entire car crash model (3e6 elements).- ABAQUS 6.12 Explicit and Implicit: Cylinder head-block linear elastic analysis (5e6 elements) and

Wave propagation (10e6 elements). - STAR-CCM + 7.02: Aeroacustic model (60e6 elements).- OpenFOAM 2.0.0: Motorbike fluid dynamics (RANS 70e6 elements).

Pere Puigdomènech Thibaut studied in the Lycée Français de Barcelone and received a degree in Mechanical Engineering from the Escola Tècnica Superior d’Enginyeria Industrial de Barcelona (ETSEIB) at the Universitat Politècnica de Catalunya (UPC).

He is currently working as HPC Engineering Support at the Consorci de Serveis Universitaris de Catalunya (CSUC) in the HPC and Applications Department.

Solving Large non-Symmetric Eigenvalue problems using GPUs Teemu Rantalaiho, Department of Physics and Helsinki Institute of Physics, University of Helsinki, Finland David J. Weir, Department of Physics and Helsinki Institute of Physics, University of Helsinki, Finland Joni M. Suorsa, Department of Physics and Helsinki Institute of Physics, University of Helsinki, Finland

We present an implementation of the Implicitly restarted Arnoldi method (IRAM) with deflation optimized for CUDA capable graphics processing units. The resulting code has been published online and is free to use with two levels of APIs that can be tailored to meet many needs. The IRAM method is a Krylov subspace method that can be used to extract a part of the eigenvalue/vector spectrum of a large nonsymmetric (non hermitean) matrix. Our use case was the extraction of the low-lying eigenvalue distribution of the Wilson-Dirac operator in the context of Lattice QCD and the large amount of computations needed for a single calculation combined with our already CUDA capable QCD code warranted the use of a custom solution for IRAM. Our approach followed the strategy of our QCD code where abstraction of parallel algorithms allows us to decouple the actual scientific code from the underlying hardware; This way one can run the same code on both CPUs and GPUs, greatly reducing development time, which is one of the key performance metrics in production codes.

Benchmarks on a single Tesla k20m (ECC on – 175GB/s mem bw) GPU show that our algorithm runs about 18.5 times faster than ARPACK++ on a single core of a Xeon X5650 @ 2.67GHz (32GB/s) with a 786432 sized system of a sparse (QCD) matrix with about 6 percent of the time spent in matrix-vector multiplies (on the GPU). On this use-case the GPU code achieved 146 Gbytes/s, which is 83 percent of theoretical peak memory bandwidth. Our code supports multiple GPUs through MPI and the code scales well as long as there is enough work to fill the GPUs.




Teemu Rantalaiho received a Master of Science in theoretical physics from University of Helsinki in 2010 and started doctoral studies under Kari Rummukainen later the same year concentrating on computational methods in quantum field theory. Has previously worked nearly a decade in industry doing multiphysics research, applied mathematics and software engineering and software architecture for mobile graphics processors and applications.

Currently investigating technicolor theories using GPU-clusters and developing code as well as investigating inversion methods to study transport coefficients in finite temperature Quantum Field theories.

Recent work also includes contribution to a project to study eigenvalue distributions of the Wilson operator in QCD-like theories. Further interests include parallelization techniques and their application in high performance computing.

High Performance Computing aspects of acoustic simulations of an air-intake system in OpenFOAM® Jan Schmalz, University of Duisburg-Essen, Chair of Mechanics and Robotics, Duisburg, Germany Wojciech Kowalczyk, University of Duisburg-Essen, Chair of Mechanics and Robotics, Duisburg, Germany

Air-intake systems of combustion engines emit sound mainly based on turbulences. But often the acoustic parameters and the sound emission are considered not before an existing prototype. Unfortunately changes of concepts are hardly feasible in that stage of development process. Numerical methods, like finite volume methods for computational fluid dynamics, applied on virtual prototypes are helpful tools during the early stages of product development processes. Concerning the acoustical behavior commonly used methods of computational fluid dynamics are extended to compute e.g. the sound pressure level in the far field at a spe-cific observer point. The contributed data is comparable to the results of common acoustic measurements.

In this paper the open source computational fluid dynamics framework OpenFOAM® is used to solve the com-plex fluid dynamic task of an air-intake system of a combustion engine. Due to the used numerical approach it also has the principle functionality to solve aero acoustic problems. A computational aero acoustic approach based on acoustic analogies is implemented in OpenFOAM® 2.1.1. This novel approach is mainly based on Curle’s acoustic analogy where existing surfaces within the computation domain are rigid and stationary. The CAA approach is added to originally distributed transient incompressible and compressible application solvers, pisoFoam and rhoPimpleFoam respectively, which are both parallelized already and are able to run on several compute cores.

The presented method takes into account the possibility and availability of high performance computing re-sources. It provides the advantage to compute the flow fields, acoustic sources and the corresponding sound propagation in an extended near field on one mesh only which might be done during the first phases in prod-uct development. The specific behavior of parallel computation of acoustical fields in a HPC environment will be discussed by means of the mentioned computing case of an air intake system.

Jan Schmalz is a research assistant and Ph.D. student at the chair of Mechanics and Robot-ics at the University of Duisburg-Essen. He received a diploma in Mechanical Engineering from the University of Applied Sciences Ravensburg-Weingarten in 2006 and after a few years of work experience in the automotive industries and further studies of Mechanical Engineering he received a Master of Science in Mechanical Engineering from the University of Duisburg-Es-sen in 2010. His research interests include computational fluid dynamics applications in high performance computing frameworks and in particular the implementation of computational aero acoustics approaches for parallel computational fluid dynamic simulations.

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Linear Algebra Library for Heterogeneous Computing in Scientific Discovery Thomas Soddemann, Fraunhofer SCAI, Germany

Current hardware configurations evolve more and more to highly heterogeneous environments combining traditional CPU based systems with accelerator boards. Obtaining good performance on such systems is challenging and implies code adaption, integration of new components and using different libraries.

Application domains from various industrial fields including aerospace, automotive, engineering and oil & gas exploration often can be subsumed to simulations solving big sparse linear systems of equations, which can be challenging e.g. due to numerical stability and scalability.

The Library for Accelerated Math Applications (LAMA) accomplishes both: new and altering hardware sys-tems with efficient backends for various architectures and accelerated calculation through a wide set of linear solvers. LAMA affords full sparse BLAS functionality with a maximum of flexibility in hardware and software decisions at the same time. The configuration of the whole LAMA environment can be set up by a Domain Specific Language and can therefore be reconfigured on run time. Concepts of solvers, distributions, matrix formats are exchangeable and users can switch between compute locations e.g. GPU or Intel® MIC. As new hardware architectures and features are hitting the market in much shorter time intervals than ever before it will be necessary to rely on flexible software technologies to adapt these changes and to be able to maintain existing methods in time to benefit from them and stay competitive.

Thomas Soddemann studied physics and mathematics in Paderborn and Freiburg. He re-ceived his Ph.D. in statistical physics from the Johannes-Gutenberg-University Mainz. Later he worked at Johns Hopkins University, Sandia National Labs, and for the Max-Planck-So-ciety’s Supercomputing Centre RZG before he joined Fraunhofer SCAI as group lead HPC. His work focuses on numerical mathematical methods and automated code optimization.




List of Authors

Last Name Affiliation Pages

Abdizahed, Haleh Sabanci University, Turkey 44

Arlandini, Claudio CINECA, Italy 35

Berman, Francine Rensselaer Polytechnic Institute, United States 18

Bode, Mathis RWTH, Aachen University, Germany 30

Bower, Richard Durham University, United Kingdom 32

Burgueño Arjona, Augusto European Commission, Belgium 41

Calmet, Hadrien Barcelona Supercomputing Center, Spain 23

Cavallo, Paolo AMET srl, Italy 37

Civalleri, Bartolomeo University of Torino, Italy 25

Dal Peraro, Matteo School of Life Sciences, EPFL, Switzerland 40

Delle Piane, Massimo University of Torino, Italy 24

Donners, John SURFsara, The Netherlands 45

Eisenschmid, Ralph OPTIMA pharma, Germany 38

Erbacci, Giovanni CINECA, Italy 35

Girona, Sergi PRACE 16

Hagita, Katsumi National Defense Academy, Japan 45

Hillewaert, Koen Cenaero, Belgium 46

Khandelia, Himanshu University of Southern Denmark, Denmark 47

Kondov, Ivan Karlsruhe Institute of Technology (KIT), Germany 48

Kouyoumdjian, Gonzalo Juan Yacht Design SL, Spain 34

Kozubek, Tomas IT4Innovations, Czech Republic 48

Kussmann, Jörg University of Munich (LMU), Germany 26

Laino, Teodoro IBM Research Zurich, Rüschlikon, Switzerland 27

Lavignon, Jean-François ETP4HPC 41

Malossi, Cristiano IBM Research Zurich, Rüschlikon, Switzerland 20

Markomanolis, George Barcelona Supercomputing Center, Spain 29

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Last Name Affiliation Pages

Masilamani, Kannan University Siegen, Germany 49

Mehta, Vishal Trinity College Dublin, Ireland 49

Messina, Paul C. Argonne Leadership Computing Facility, United States 40

Notay, Yvan University of Brussels, Belgium 33

Ostasz, Marcin Barcelona Supercomputing Center, Spain 22

Owen, Herbert Barcelona Supercomputing Center, Spain 39

Papka, Michael Argonne Leadership Computing Facility, United States 41

Pariente, Marc Renault SA, France 50

Perna, Gino Enginsoft SpA, Italy 21

Poncela, María Luisa Ministry of Economy and Competitiveness, Spain 18

Portero, Antoni IT4Innovations, Czech Republic 50

Puigdomènech, Pere Consorci de Serveis Universitaris de Catalunya, Spain 51

Ramírez, Alex Barcelona Supercomputing Center, Spain 22

Rantalaiho, Teemu University of Helsinki, Finland 52

Rivière, Catherine PRACE 18

Schmalz, Jan University of Duisburg-Essen, Germany 53

She, Jun Danish Meteorological Institute, Denmark 28

Silva, Luís O. Instituto Superior Técnico Lisbon, Portugal 15

Soddemann, Thomas Fraunhofer SCAI, Germany 54

Tamayo-Palau, José-Maria Nexio Simulation, France 36

Tchverda, Vladimir Novosibirsk State University, Russia 31

Vadori, Roberto Thesan, Italy 35

Walser, Alexander Frederic Automotive Simulation Centre Stuttgart, Germany 19

Walsh, Paul Nsilico, Ireland 37

White, Julia INCITE, United States 29

Wilkie, Tom Europa Science Ltd., United Kingdom 41




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Conference Programme and Abstracts...Tuesday 20 May - 09:00 to 13:00 - Aula Master Alternative cooling technologies and heat re-use session 09:00 – 09:20 C1: Immersion cooling (PSNC)