TY - CHAP A1 - Noack, Matthias A1 - Focht, Erich A1 - Steinke, Thomas T1 - Heterogeneous Active Messages for Offloading on the NEC SX-Aurora TSUBASA T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Heterogeneity in Computing Workshop (HCW 2019) N2 - The NEC SX-Aurora TSUBASA is a new generation of vector processing architectures that combines a standard Intel Xeon host with the newly developed NEC Vector Engine co-processor cards. One way to use these co-processors is offloading suitable parts of the program from the host to the Vector Engines. Currently, the only vendor-provided offloading solutions are the low-level Vector Engine Offloading (VEO) library, and a builtin reverse-offloading mechanism named VHcall. In this work, we extend the portable Heterogeneous Active Messages (HAM) based HAM-Offload framework with support for the NEC SX-Aurora TSUBASA. Therefore, we design, implement, and evaluate two messaging protocols aimed at minimising offloading cost. This sheds some light on how to achieve fast communication between host CPU and the Vector Engines of the NEC SX-Aurora TSUBASA. Compared with VEO, the DMA-based protocol reduces offloading overhead by a factor of 13×. The resulting framework enables users to write portable offload applications with low overhead, that do neither require a language extension like OpenMP, nor a special language like OpenCL. Existing HAM-Offload applications are now ready to run on the NEC SX-Aurora TSUBASA. Y1 - 2019 ER - TY - GEN A1 - Stalling, Detlev A1 - Steinke, Thomas T1 - Visualization of Vector Fields in Quantum Chemistry N2 - \small Many interesting phenomena in molecular systems like interactions between macro-molecules, protein-substrate docking, or channeling processes in membranes are gouverned to a high degree by classical Coulomb or van-der-Waals forces. The visualization of these force fields is important for verifying numerical simulations. Moreover, by inspecting the forces visually we can gain deeper insight into the molecular processes. Up to now the visualization of vector fields is quite unusual in computational chemistry. In fact many commercial software packages do not support this topic at all. The reason is not that vector fields are considered unimportant, but mainly because of the lack of adequate visualization methods. In this paper we survey a number of methods for vector field visualization, ranging from well-known concepts like arrow or streamline plots to more advanced techniques like line integral convolution, and show how these can be applied to computational chemistry. A combination of the most meaningful methods in an interactive 3D visualization environment can provide a powerful tool box for analysing simulations in molecular dynamics. T3 - ZIB-Report - SC-96-01 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2124 ER - TY - GEN A1 - Baumann, Wolfgang A1 - Busch, Hubert A1 - Gottschewski, Jürgen A1 - Steinke, Thomas A1 - Stüben, Hinnerk T1 - Berliner Landeshöchstleistungsrechner Parallelrechner Cray T3D/T3E: Betrieb, Nutzung, Projekte, Perspektiven für den Ausbau N2 - Seit fast drei Jahren betreibt das Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) Parallelrechner der höchsten Leistungsklasse im normalen Rechenzentrumsbetrieb. Bereits im Mai 1995 hat das ZIB über seine Erfahrungen mit dem damals leistungsstärksten Parallelrechner Deutschlands berichtet. Das Gesamtkonzept des ZIB sieht weiterhin einen Höchstleistungsrechner als unabdingbaren Bestandteil des High Performance Scientific Computing (HPSC) im ZIB vor. Der vorliegende Bericht beschreibt die aktuelle Konfiguration, Betriebserfahrungen und die Rechnernutzung sowie typische Rechenleistungen, die für einzelne Anwendungsprogramme erzielt wurden. Beschreibungen der Forschungsgebiete mit den Forschungsgruppen, die den Rechner nutzen und die Anforderungen an den Rechnerausbau, die sich aus deren Arbeiten herleiten, beschließen den Bericht. T3 - ZIB-Report - TR-97-08 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5504 ER - TY - CHAP A1 - Steinke, Thomas A1 - Peter, Kathrin A1 - Borchert, Sebastian T1 - Efficiency Considerations of Cauchy Reed-Solomon Implementations on Accelerator and Multi-Core Platforms T2 - Symposium on Application Accelerators in High Performance Computing (SAAHPC) Y1 - 2010 UR - http://saahpc.ncsa.illinois.edu/10/papers/paper_12.pdf CY - Knoxville, USA ER - TY - GEN A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - d. Santos Vieira, I. A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Kruber, Nico A1 - Krüger, Jens A1 - Lang, U. A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid – A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science T2 - 6. German Conference on Chemoinformatics Y1 - 2010 N1 - Free software session and poster ER - TY - CHAP A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Kruber, Nico A1 - Lang, U. A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - Molecular Simulation Grid T2 - 6. German Conference on Chemoinformatics Y1 - 2010 PB - Gesellschaft Deutscher Chemiker (GDCh) ER - TY - JOUR A1 - May, Patrick A1 - Kreuchwig, A. A1 - Steinke, Thomas A1 - Koch, Ina T1 - PTGL: a database for secondary structure-based protein topologies JF - Nucleic Acids Res. Y1 - 2010 VL - 38 SP - D326 EP - 330 ER - TY - CHAP A1 - Dickmann, Frank A1 - Kaspar, Mathias A1 - Löhnhardt, Benjamin A1 - Kepper, Nick A1 - Viezens, Fred A1 - Hertel, Frank A1 - Lesnussa, Michael A1 - Mohammed, Yassene A1 - Thiel, Andreas A1 - Steinke, Thomas A1 - Bernarding, Johannes A1 - Krefting, Dagmar A1 - Knoch, Tobias A1 - Sax, Ulrich T1 - Visualization in Health Grid Environments: A Novel Service and Business Approach T2 - GECON Y1 - 2009 U6 - https://doi.org/10.1007/978-3-642-03864-8_12 VL - 5745 SP - 150 EP - 159 PB - Springer ER - TY - JOUR A1 - Bauer, Raphael A1 - Rother, Kristian A1 - Moor, Peter A1 - Reinert, Knut A1 - Steinke, Thomas A1 - Bujnicki, Janusz A1 - Preissner, Robert T1 - Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors JF - Algorithms Y1 - 2009 U6 - https://doi.org/10.3390/a2020692 VL - 2 IS - 2 SP - 692 EP - 709 ER - TY - CHAP A1 - May, Patrick A1 - Klau, Gunnar A1 - Bauer, Markus A1 - Steinke, Thomas ED - Dubitzky, W. T1 - Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs T2 - GCCB Y1 - 2007 VL - 4360 SP - 19 EP - 32 PB - Springer ER -