@inproceedings{NoackFochtSteinke2019, author = {Noack, Matthias and Focht, Erich and Steinke, Thomas}, title = {Heterogeneous Active Messages for Offloading on the NEC SX-Aurora TSUBASA}, booktitle = {2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Heterogeneity in Computing Workshop (HCW 2019)}, year = {2019}, abstract = {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.}, language = {en} } @misc{StallingSteinke1996, author = {Stalling, Detlev and Steinke, Thomas}, title = {Visualization of Vector Fields in Quantum Chemistry}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2124}, number = {SC-96-01}, year = {1996}, abstract = {\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.}, language = {en} } @misc{BaumannBuschGottschewskietal.1997, author = {Baumann, Wolfgang and Busch, Hubert and Gottschewski, J{\"u}rgen and Steinke, Thomas and St{\"u}ben, Hinnerk}, title = {Berliner Landesh{\"o}chstleistungsrechner Parallelrechner Cray T3D/T3E: Betrieb, Nutzung, Projekte, Perspektiven f{\"u}r den Ausbau}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5504}, number = {TR-97-08}, year = {1997}, abstract = {Seit fast drei Jahren betreibt das Konrad-Zuse-Zentrum f{\"u}r Informationstechnik Berlin (ZIB) Parallelrechner der h{\"o}chsten Leistungsklasse im normalen Rechenzentrumsbetrieb. Bereits im Mai 1995 hat das ZIB {\"u}ber seine Erfahrungen mit dem damals leistungsst{\"a}rksten Parallelrechner Deutschlands berichtet. Das Gesamtkonzept des ZIB sieht weiterhin einen H{\"o}chstleistungsrechner 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 f{\"u}r 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.}, language = {de} } @inproceedings{SteinkePeterBorchert2010, author = {Steinke, Thomas and Peter, Kathrin and Borchert, Sebastian}, title = {Efficiency Considerations of Cauchy Reed-Solomon Implementations on Accelerator and Multi-Core Platforms}, booktitle = {Symposium on Application Accelerators in High Performance Computing (SAAHPC)}, address = {Knoxville, USA}, year = {2010}, language = {en} } @misc{BirkenheuerBlunkBreuersetal.2010, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and d. Santos Vieira, I. and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Kr{\"u}ger, Jens and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid - A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science}, journal = {6. German Conference on Chemoinformatics}, year = {2010}, language = {en} } @inproceedings{KruegerBirkenheuerBlunketal.2010, author = {Kr{\"u}ger, Jens and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {Molecular Simulation Grid}, booktitle = {6. German Conference on Chemoinformatics}, publisher = {Gesellschaft Deutscher Chemiker (GDCh)}, year = {2010}, language = {en} } @article{MayKreuchwigSteinkeetal.2010, author = {May, Patrick and Kreuchwig, A. and Steinke, Thomas and Koch, Ina}, title = {PTGL: a database for secondary structure-based protein topologies}, volume = {38}, journal = {Nucleic Acids Res.}, pages = {D326 -- 330}, year = {2010}, language = {en} } @inproceedings{DickmannKasparLoehnhardtetal.2009, author = {Dickmann, Frank and Kaspar, Mathias and L{\"o}hnhardt, Benjamin and Kepper, Nick and Viezens, Fred and Hertel, Frank and Lesnussa, Michael and Mohammed, Yassene and Thiel, Andreas and Steinke, Thomas and Bernarding, Johannes and Krefting, Dagmar and Knoch, Tobias and Sax, Ulrich}, title = {Visualization in Health Grid Environments: A Novel Service and Business Approach}, volume = {5745}, booktitle = {GECON}, publisher = {Springer}, doi = {10.1007/978-3-642-03864-8_12}, pages = {150 -- 159}, year = {2009}, language = {en} } @article{BauerRotherMooretal.2009, author = {Bauer, Raphael and Rother, Kristian and Moor, Peter and Reinert, Knut and Steinke, Thomas and Bujnicki, Janusz and Preissner, Robert}, title = {Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors}, volume = {2}, journal = {Algorithms}, number = {2}, doi = {10.3390/a2020692}, pages = {692 -- 709}, year = {2009}, language = {en} } @inproceedings{MayKlauBaueretal.2007, author = {May, Patrick and Klau, Gunnar and Bauer, Markus and Steinke, Thomas}, title = {Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs}, volume = {4360}, booktitle = {GCCB}, editor = {Dubitzky, W.}, publisher = {Springer}, pages = {19 -- 32}, year = {2007}, language = {en} }