The ZIH colloquia take place regularly at each 4th Thursday of the month at 15:00 o'clock in the room Willers-Bau A 317.
For additional or extraordinary events time and room are explicitly mentioned.

Next Colloquium:

24. May 2012: Marc Casas Guix (LLNL) "Automatic Phase Detection and Structure Extraction of Parallel Applications"
Tracing is an accepted and well-known approach to understand and improve the performance of high performance computing applications. However, generating and analyzing trace-files obtained from large scale executions can be really problematic due to the large amount of data generated by such massively parallel executions. Thus, automatic methodologies should be applied to reduce the size of the data, ruling out its non-significant or redundant parts and keeping the fundamental ones. In this talk, a solution based on signal processing techniques, Wavelet and Fourier transforms, will be presented. By analyzing the specter of frequencies that appear in applications’ executions, the approach is able to detect the internal structure of parallel executions and to rule out redundant information, reducing by one or two orders of magnitude the data that should be analyzed. Finally, more general considerations regarding high performance computing and the challenges that exascale computing brings will also we made.

Further Colloquia 2012

• 28. June 2012: Bertil Schmidt (Uni Mainz) "Parallel Algorithms and Tools for Bioinformatics on GPUs"
  High-throughput techniques for DNA sequencing have led to a rapid growth in the amount of digital biological data. The current state-of-the-art technology produces 600 billion nucleotides per machine run. Furthermore, the speed and yield of NGS (Next-generation sequencing) instruments continue to increase at a rate beyond Moore's Law, with updates in 2012 enabling 1 trillion nucleotides per run. Correspondingly, sequencing costs (per sequenced nucleotide) continue to fall rapidly, from several billion dollars for the first human genome in 2000 to a forecast US$1000 per genome by the end of 2012. However, to be effective, the usage of NGS for medical treatment will require algorithms and tools for sequence analysis that can scale to billions of short reads. In this talk I will demonstrate how parallel computing platforms based on CUDA-enabled GPUs, multi-core CPUs, and heterogeneous CPU/GPU clusters can be used as efficient computational platforms to design and implement scalable tools for sequence analysis. I will present solutions for classical sequence alignment problems (such as pairwise sequence alignment, BLAST, multiple sequence analysis, motif finding) as well as for NGS algorithms (such as short-read error correction, short-read mapping, short-read clustering).

• 26.July 2012: Lucas Schnorr (CNRS Grenoble/Frankreich)

Past Colloquia 2012

• 26. April 2012 16:00: Thomas Cowan (Direktor des Instituts für Strahlenphysik am Helmholtz-Zentrum Dresden-Rossendorf (HZDR))  "Beschleunigung der Beschleunigung - Lasergetriebene Strahlungsquellen und ihre Anwendungen"
  Neuartige Strahlungsquellen ermöglichen nicht nur neue Einblicke in ultraschnelle Vorgänge in Materie sondern auch deren Kontrolle. Eine derartige Kontrolle erfordert genaues Wissen über die Erzeugung von elektromagnetischer wie Teilchen-Strahlung sowie deren Wechselwirkung mit Materie auf atomarer Ebene. Um dieses Wissen zu vergrößern braucht es eine enge Verbindung von experimentellen Messungen, Datenanalyse und Simulation.
  Der Vortrag stellt neuartige Strahlungsquellen vor und diskutiert ihre Bedeutung in der fundamentalen Forschung ebenso wie ihre zukünftige Anwendung, zum Beispiel in der Krebstherapie. Als Beispiele aktueller Forschung dienen die Beschleunigung von Teilchenstrahlen mit Hilfe von Lasern und die in-vivo Dosimetrie bei der Krebsbehandlung mit Ionenstrahlen. Beide Forschungsgebiete profitieren von der Beschleunigung komplexer Rechenoperationen durch GPUs, sowohl im Bereich der Simulation als auch in der Datenauswertung.
• 22. März 2012: Josef Weidendorfer (TU München): "Architecture Simulation for Programmers"
  To study performance bottlenecks of (parallel) programs, analysis tools usually take advantage of a mix of hardware performance counters and application instrumentation as event source. Real hardware properties are measured, showing details about the symptoms of any performance problem. However, this real view to hardware can be tricky: for the tool, as instrumentation overhead can invalidate the measurement; and for the user, as event types can be difficult to interpret. Architecture simulation can overcome these obstacles and provide more abstract metrics not measurable in legacy processor hardware.
  This talk will focus on using cache simulation for detailed analysis of memory access behavior of programs, and show the benefits of this approach, such as better abstract metrics than just hit/miss ratios for cache exploitation. In this regard, upcoming extensions to the tool suite Callgrind/KCachegrind are shown, as well as research on keeping the simulation slowdown small.
• 23. February 2012: Martin Hofmann-Apitius (Fraunhofer SCAI) "Large-Scale Information Extraction for Biomedical Modelling and Simulation"
  Unstructured information is a huge resource for scientific information. This is in particular true for sciences with a strong empirical background, such as biology, pharmaceutical chemistry or medicine. In my talk, I will give an overview on our work that aims at making scientific information available that is "hidden" in scientific publications (including patents) and medical narratives (electronic patient records). The presentation will cover essentials of information extraction technologies developed in our lab, their implementation in workflows for large-scale production of relevant information and the application of our information extraction technologies in the area of modelling neurodegenerative diseases.

• 
  26. January 2012: Michael Hohmuth (AMD, OSRC): "OS and Architecture Research at the AMD Operating System Research Center: ASF, the Advanced Synchronization Facility" In this talk, I will present the Advanced Synchronization Facility (ASF), an experimental AMD64 architecture extension aimed at one of these trends, parallel computing. ASF is designed to make parallel programming easier by supporting two styles of writing parallel programs: lock-free programming and transactional programming.

Past years:

History 2011
History 2010
History 2009
History 2008
History 1998 - 2007