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1st SimLab Porting Workshop 2010

Jülich Supercomputing Centre
9 - 11 June 2010

Topics | Agenda

SimLab Porting Workshop 2010

The Simulation Laboratories (SimLab) at JSC are research and support groups with expertise in advanced simulation techniques needed for tackling computational intensive scientific challenges. Currently the following scientific areas are represented at JSC: Biology, Molecular Systems, Climate, and Plasma Physics. One of their main tasks is to actively engage with national and European scientific groups, helping them to harness the world-class supercomputer facilities available at JSC.

The aim of this introductory workshop is to support users in the usage of JSC's high performance computing (HPC) facilities. Advanced porting techniques for both supercomputers JUROPA (Intel Nehalem cluster) and JUGENE (IBM Blue Gene/P) at JSC will be presented. Further focus will be on the special needs related to HPC techniques of the SimLabs: Biology, Climate, Molecular Systems, and Plasma Physics. Computational methods as well as programming techniques are covered by the selected talks and intensive hands-on tutorials during the first two days. Access to both machines will be provided during the workshop. The last third day, each SimLab will arrange discussion groups to consider future SimLab activities, like support actions and proposals, community oriented development and workshops.


The agenda covers the following topics

  • introduction to SimLabs and HPC systems at JSC
  • hands-on tutorials for optimal porting on JUROPA and JUGENE, including

    • torus network
    • simdization
    • parallel IO
    • HPC tools (scalasca, vtunes, ihpct, totalview, unicore)
  • lectures on computational methods from the SimLab fields, including

    • Parallel Computational Chemistry: ab-initio Methods
    • Parallel Particle Methods in Plasma Physics
    • Fast Coulomb Solver
    • Inverse Methods in Atmospheric Sounding
    • Simulating Protein Structure Formation using Monte Carlo
  • talks on current state-of-the-art HPC methods
  • discussion sessions on future SimLab activities


Please apply for participation by sending an email to covering

  • your institute and current position
  • your scientific fields of interest
  • your HPC experience

Registrations are only considered before 20 May 2010, and due to available space, the maximal number of participants is limited.


For any questions concerning the workshop please send an e-mail to or contact us directly

Priv.-Doz. Dr. Paul Gibbon
Institute for Advanced Simulation
Jülich Supercomputing Centre
Forschungszentrum Jülich GmbH
52425 Jülich
+49 (0) 2461 61 1499
+49 (0) 2461 61 6656


Wednesday, 9 June 2010

09:00 - 09:15Welcome and Registration
Paul Gibbon
09:15 - 10:00Introduction to Simulation Laboratories
Paul Gibbon
10:00 - 10:45Introduction to JSC's HPC Facilities
Lukas Arnold
10:45 - 11:00Coffee Break
11:00 - 11:30Simulating Protein Structure Formation using Monte Carlo
Olav Zimmermann
11:30 - 12:30Porting juropa I
Jan Meinke, Sandipan Mohanty, Wolfgang Frings
12:30 - 13:30Lunch Break
13:30 - 17:30Porting juropa II
Jan Meinke, Sandipan Mohanty, Wolfgang Frings

Thursday, 10 June 2010

09:00 - 09:35Parallel Computational Chemistry: ab-initio Methods
Thomas Müller
09:35 - 10:10Inverse Methods in Atmospheric Sounding
Lars Hoffmann
10:10 - 10:45Fast Coulomb Solver
Godehard Sutmann
10:45 - 11:00Coffee Break
11:00 - 11:35Parallel Particle Methods in Plasma Physics
Paul Gibbon
11:35 - 12:10SimLabs at KIT, meeting a Challenge
Frank Schmitz
12:10 - 13:15Lunch Break
13:15 - 17:30Porting jugene
Lukas Arnold

Friday, 11 June 2010

09:00 - 10:00High Performance Supercomputing in Molecular Medicine
Paolo Carloni
10:00 - 10:45Electrostatic Effects in Ionic Liquids and Biomolecular Systems
Maxim Fedorov
10:45 - 11:00Coffee Break
11:00 - 12:00SimLab Meetings
12:00 - 12:30Goodby
12:30 - 13:30Lunch