Autumn 2012 inSiDE • Vol. 10 No. 2 Innovatives Supercomputing in Deutschland ContentsEditorial is published two times a year by The GAUSS Editorial Centre for Supercomputing (HLRS, JSC, LRZ) Welcome to this new issue of InSiDE, touch with a wider community is part Publishers the journal on innovative Supercomputing of two further contributions: A report on Prof. Dr. A. Bode | Prof. Dr. Dr. Th. Lippert | Prof. Dr.-Ing. Dr. h.c. Dr. h.c. M. M. Resch in Germany published by the Gauss ISC'12 shows the strong interaction Centre for Supercomputing (GCS). We of GCS with the international supercom- Editor are well into our 10th year and continue puting community. Introducing the newly F. Rainer Klank, HLRS [email protected] to look back a little bit. This time we created SICOS GmbH we show how small have invited the Chairman of the Board and medium sized enterprises can be Design of GCS Prof. Dr. Heinz-Gerd Hegering supported in their usage of HPC systems. Antje A. Häusser, HLRS [email protected] for an interview on High Performance Stefan Steinbach, HLRS [email protected] Computing in Germany and Europe. Again we present a rich section on Linda Weinmann, HLRS [email protected] applications running on the GCS systems. Prof. Hegering not only looks back on the Ranging from Computational Fluid history of High Performance Computing. Dynamics to astrophysical simulations He and the Leibniz Computing Centre the eight contributions clearly show the (LRZ) also have good reason to celebrate need for compute power and the poten- and look positively towards the future. tial of HPC simulation for both basic LRZ inaugurated its new system called and applied science. The growing "SuperMUC" in July. Following the GCS strength of GCS in HPC research is high- strategy SuperMUC introduces a new lighted by the seven project descriptions architecture to users in Europe and that show how various groups at Garching, Germany. Emphasizing Germany’s role Jülich and Stuttgart contribute to the as a leader in European High Performance progress in HPC research. Computing LRZ and GCS were also proud to present the SuperMUC to be GCS has made big steps over the last Europe’s number one system in the TOP years. The co-operation with PRACE has • Prof. Dr. 500 list. So the spiral of performance in extended its reach into Europe and has A. Bode (LRZ) Germany is working as designed and allowed us to contribute to European the Jülich Supercomputing Centre (JSC) research and development substantially. • Prof. Dr. Dr. Th. Lippert (JSC) and the High Performance Computing GCS is committed to continuing these Center Stuttgart (HLRS) are both preparing efforts. In the field of HPC research GCS • Prof. Dr.-Ing. Dr. h.c. Dr. h.c. for their next step. is moving forward both in European and M. M. Resch (HLRS) national large scale research programs. The work of GCS is a major part of the European PRACE initiative. Results of With this, we look forward to a bright the 4th Pan-European call for user pro- future for supercomputing in Germany posals are presented in this issue. and hope you enjoy reading. Showing off these results and getting in 2 Autumn 2012 • Vol. 10 No. 2 • inSiDE Autumn 2012 • Vol. 10 No. 2 • inSiDE 3 Contents ContentsEditorial Contents News » "SuperMUC", Europe's fastest Supercomputer, 6 inaugurated at the 50th Anniversary of LRZ » Optimizing the Energy-to-Solution on 62 SandyBridge Systems » Interview with Prof. Hegering 8 » ParaPhrase − Parallel Patterns for Adaptive 66 » PRACE: Results of the 4th Regular Call 11 Heterogeneous Multicore Systems » GCS @ ISC'12 12 » H4H – Hybrid for HPC 68 » SICOS: HPC and more for Industry 14 » The SIOX Project 70 Applications » Performance Dynamics of Massively Parallel 72 Codes » Simulation of Nasal Cavity Flows for Virtual Surgery 16 Environments » PRACE – Third Implementation Phase Project 74 started » Numerical Investigation of the Flow Field about 24 the VFE-2 Delta-Wing Systems » Simulating Blood Cells and Blood Flow 28 » JUQUEEN: The most recent Blue Gene 76 Architecture at Jülich » Direct Numerical Simulations of turbulent 34 Rayleigh-Bénard Convection » Virtual Reality and Visualization at the Leibniz 80 Supercomputing Centre » Development and Validation of Thermal Simulation 38 Models for Li-Ion Batteries in Hybrid and Pure Centres 82 Electric Vehicles Activities 88 » Matter-Antimatter Asymmetry and the Search 42 for fundamental Laws of Physics with JUGENE Courses 106 » Theoretical Mechanochemistry: Stressing 48 Authors 112 Molecules in the "Virtual Lab" » Global MHD Simulations of protostellar Jets with 54 radiative Effects Projects » LRZ Validation-Suite for Life Science 58 4 Autumn 2012 • Vol. 10 No. 2 • inSiDE Autumn 2012 • Vol. 10 No. 2 • inSiDE 5 News News While High Performance Computing was "SuperMUC", Europe's fastest in the beginning and is at the heart of Supercomputer, inaugurated at LRZ, LRZ also is the general IT service provider for Munich’s universities and th the 50 Anniversary of LRZ serves more than 100,000 customers in the Munich area. Prof. Dr. Heinz-Gerd Hegering, past Chairman of LRZ for sciencists. On July 20, 2012, LRZ more than twenty years, at the celebra- celebrated the inauguration of SuperMUC tion of the 50th anniversary gave an and its 50th anniversary. Several overview on the evolution of the many hundred guests attended the event to- different services offered by LRZ. Figure 4: The first LRZ building. Figure 5: The LRZ building in gether with Prof. Dr. Annette Schavan, the centre of Munich. Germany’s Federal Minister for Science LRZ always has been a pioneer in infor- and Education, and Dr. Wolfgang mation technology e.g., communication Heubisch, Bavaria’s Minister of State networks, long term archiving, High for Research, Science and the Arts. Performance Computing in general and today with a special focus on energy In 1962, the Bavarian Academy of Sci- efficiency. Thus, SuperMUC, manufac- ences founded a "Commission for tured by IBM, is the first computer of Figure 6: The LRZ building after the extension 2009-2011 in Garching near Munich. Electronic Computing”, which was later its class that is completely cooled with renamed to “Commission for Informatics”. hot water. LRZ is a leading expert in which is stressed by the fact that the This Commission for Informatics the field of warm water cooling of com- Federal Government of Germany and Figure 1: Prof. Dr. Arndt “SuperMUC”, LRZ’s new supercomputer established and runs the Leibniz-Rechen- puters. The extension of the computer the Free State of Bavaria jointly spent Bode, Chairman of LRZ, is ranked no. 1 in Europe and no. 4 in zentrum LRZ (Leibniz Supercomputing building has been equipped with the more than 80 Million Euro for the present Martina Koederitz, the world as announced on the Interna- Centre). Starting in a residential necessary infrastructure for this innova- configuration of SuperMUC and about General Manager IBM Germany, Federal Minister tional Suprecomputing Conference at building in Munich, it moved to a new tive and highly energy-efficient way to 50 Million Euro for the extensions of the for Science and Education Hamburg on June, 18th, 2012, by and larger building near the famous run computers from SuperMUC to buildings of LRZ. SuperMUC is now Prof. Dr. Annette Schavan Prof. Dr. Hans Meurer, co-founder of Karlsplatz “Stachus” in the centre of Linux clusters. available for academia in Germany as part • L u d g e r P a l m and Bavaria’s Minister the Top500 list of supercomputers Munich a few years later. In 2006, of the Gauss Centre for Supercomputing of State for Research, Science and the Arts (www.top500.org). LRZ had to move again, now to a much Federal Minister Prof. Dr. Annette GCS and for many researchers in 24 Leibniz Dr. Wolfgang Heubisch. larger facility on the campus in Garching, Schavan as well as Minister of State member states via the Partnership for Supercomputing SuperMUC, as described in detail in our north of Munich, which had to be ex- Dr. Wolfgang Heubisch pointed out Advanced Computing in Europe, PRACE. Centre (LRZ) last issue, delivers 3 PetaFlop/s peak tended further already in 2009 to 2011 the importance of High Performance performance to Germany’s and Europe’s to its current impressive size. Computing for Germany and Bavaria Figure 2: Prof. Dr. Hans Meuer, co-founder of the Top500 list, Figure 3: Celebrating the 50th anniversary of LRZ and the Figure 7: Prof. Dr. Heinz-Gerd Hegering, LRZ’s Chairman for Figure 8: Ministers Schavan and Heubisch putting their hands on the handing the certificates to Martina Koederitz, General Manager inauguration of “SuperMUC” with Ministers Prof. Dr. Annette more than 30 years, at the ceremony. warm-water cooling of SuperMUC. IBM Germany, and to Prof. Dr. Arndt Bode, Chairman of LRZ. Schavan and Dr. Wolfgang Heubisch. 6 Autumn 2012 • Vol. 10 No. 2 • inSiDE Autumn 2012 • Vol. 10 No. 2 • inSiDE 7 News News Interview with Prof. Hegering Prof. Hegering, you have been the chair- nario: it provides the most extensive HPC systems are never stand-alone cate that significant amount of funding man of the board of the Gauss Centre system base in the Petaflop-range, has installations but are enmeshed in an for the project PetaGCS. for Supercomputing (GCS) for the the role of PMO in the PRACE projects, infrastructure of networks and data last 4 years. What have been the major and held until just recently also the handling systems. How do you see the When we look at the national level we changes over that time? role of the council chairman in PRACE development of this overall infrastruc- find that Germany has a well-estab- AISBL.