TY - CHAP A1 - Stahlberg, Eric A1 - Popig, Daryl A1 - Ryle, Debie A1 - Babst, Michael A1 - Anderson, Mohammed A1 - Steinke, Thomas T1 - Molecular Simulations with Hardware Accelerators T2 - Reconfigurable Systems Summer Institute 2007 (RSSI 2007) Y1 - 2007 CY - National Center for Supercomputing Applications, Urbana/Illinois ER - TY - CHAP A1 - May, Patrick A1 - Krause, F. A1 - Ehrlich, C. A1 - Maaskola, J. A1 - Steinke, Thomas T1 - ZIB threading pipeline - A webservice-based, distributed structure prediction workflow. T2 - Proceedings of the German Conference on Bioinformatics (GCB) Y1 - 2005 SP - 125 EP - 126 ER - TY - CHAP A1 - Michalsky, E. A1 - Goede, A. A1 - Preissner, Robert A1 - May, Patrick A1 - Steinke, Thomas T1 - A distributed pipeline for structure prediction T2 - CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy Y1 - 2004 SP - 112 EP - 114 ER - TY - CHAP A1 - Rother, Kristian A1 - Müller, Heiko A1 - Trißl, Silke A1 - Koch, Ina A1 - Steinke, Thomas A1 - Preissner, Robert A1 - Frömmel, Cornelius A1 - Leser, Ulf ED - Rahm, Erhard T1 - Columba: Multidimensional Data Integration of Protein Annotations T2 - Data Integration in the Life Sciences, First International Workshop, DILS 2004, Leipzig, Germany, March 25-26 Y1 - 2004 U6 - https://doi.org/10.1007/978-3-540-24745-6_11 VL - 2994 SP - 156 EP - 171 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Trißl, Silke A1 - Rother, Kristian A1 - Müller, Heiko A1 - Steinke, Thomas A1 - Koch, Ina A1 - Preissner, Robert A1 - Frömmel, Cornelius A1 - Leser, Ulf T1 - Columba: an integrated database of proteins, structures, and annotations JF - BMC Bioinformatics Y1 - 2005 U6 - https://doi.org/10.1186/1471-2105-6-81 VL - 6 SP - 81 EP - 92 ER - TY - CHAP A1 - May, Patrick A1 - Kallies, B. A1 - Steinke, Thomas T1 - THESEUS – a parallel threading core for highthroughput protein structure prediction T2 - Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC) Y1 - 2005 ER - TY - CHAP A1 - May, Patrick A1 - Steinke, Thomas A1 - Meyer, Michael T1 - THESEUS: A Parallel Threading Core T2 - Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow Y1 - 2004 SP - 199 ER - TY - CHAP A1 - Rother, Kristian A1 - Trissl, S. A1 - Müller, H. A1 - May, Patrick A1 - Heek, R. A1 - Preissner, Robert A1 - Steinke, Thomas A1 - Koch, Ina A1 - Leser, Ulf A1 - Frömmel, Cornelius ED - Christophe, C. ED - Lenhof, H.-P. ED - Sagot, M.-F. T1 - Columba - A Database of Annotations of Protein Structure T2 - ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics Y1 - 2003 SP - 109 EP - 110 ER - TY - CHAP A1 - May, Patrick A1 - Ehrlich, Hans-Christian A1 - Steinke, Thomas ED - Lehner, Wolfgang ED - Meyer, Norbert ED - Streit, Achim ED - Stewart, Craig T1 - ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services T2 - Euro-Par 2006 Workshops Y1 - 2006 UR - http://dx.doi.org/10.1007/11823285_121 VL - 4375 SP - 1148 EP - 1158 PB - Springer ER - TY - JOUR A1 - Kolbeck, Björn A1 - May, Patrick A1 - Schmidt-Goenner, T. A1 - Steinke, Thomas A1 - Knapp, E. T1 - Connectivity independent protein-structure alignment: a hierarchical approach JF - BMC Bioinformatics Y1 - 2006 VL - 7 SP - 510 ER - TY - CHAP A1 - Steinke, Thomas A1 - Reinefeld, Alexander T1 - Experiences with High-Level Programming of FPGAs on Cray XD1 T2 - CUG Proceedings Y1 - 2006 ER - TY - JOUR A1 - Cordes, Frank A1 - Preissner, Robert A1 - Steinke, Thomas T1 - How Does a Protein Work? JF - BioTOPics J. of Biotechnology Berlin-Brandenburg Y1 - 2003 VL - 18 IS - 2 SP - 4 EP - 5 ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - CHAP A1 - Wende, Florian A1 - Noack, Matthias A1 - Schütt, Thorsten A1 - Sachs, Stephen A1 - Steinke, Thomas T1 - Application Performance on a Cray XC30 Evaluation System with Xeon Phi Coprocessors at HLRN-III T2 - Cray User Group Y1 - 2015 ER - TY - CHAP A1 - Baumann, Wolfgang A1 - Laubender, Guido A1 - Läuter, Matthias A1 - Reinefeld, Alexander A1 - Schimmel, Christian A1 - Steinke, Thomas A1 - Tuma, Christian A1 - Wollny, Stefan ED - Vetter, Jeffrey S. T1 - HLRN-III at Zuse Institute Berlin T2 - Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two Y1 - 2015 UR - http://www.crcpress.com/product/isbn/9781498700627 SN - 9781498700627 SP - 81 EP - 114 PB - Chapman and Hall/CRC ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - Concurrent Kernel Execution on Xeon Phi within Parallel Heterogeneous Workloads T2 - Euro-Par 2014: Parallel Processing. 20th International Conference, Porto, Portugal, August 25-29, 2014, Proceedings Y1 - 2014 UR - http://www.springer.com/computer/swe/book/978-3-319-09872-2 U6 - https://doi.org/10.1007/978-3-319-09873-9_66 VL - 8632 SP - 788 EP - 799 ER - TY - CHAP A1 - Wende, Florian A1 - Laubender, Guido A1 - Steinke, Thomas T1 - Integration of Intel Xeon Phi Servers into the HLRN-III Complex: Experiences, Performance and Lessons Learned T2 - CUG2014 Proceedings Y1 - 2014 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU T2 - Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013 Y1 - 2013 U6 - https://doi.org/http://dx.doi.org/10.1145/2503210.2503254 ER - TY - GEN A1 - Benkrid, Khaled A1 - El-Araby, Esam A1 - Huang, Miaoqing A1 - Sano, Kentaro A1 - Steinke, Thomas T1 - High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing T2 - International Journal of Reconfigurable Computing Y1 - 2012 U6 - https://doi.org/10.1155/2012/104963 VL - 2012 SP - 1 EP - 2 ER - TY - CHAP A1 - Noack, Matthias A1 - Wende, Florian A1 - Steinke, Thomas A1 - Cordes, Frank T1 - A Unified Programming Model for Intra- and Inter-Node Offloading on Xeon Phi Clusters T2 - SC '14: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis. SC14, November 16-21, 2014, New Orleans, Louisiana, USA N2 - Standard offload programming models for the Xeon Phi, e.g. Intel LEO and OpenMP 4.0, are restricted to a single compute node and hence a limited number of coprocessors. Scaling applications across a Xeon Phi cluster/supercomputer thus requires hybrid programming approaches, usually MPI+X. In this work, we present a framework based on heterogeneous active messages (HAM-Offload) that provides the means to offload work to local and remote (co)processors using a unified offload API. Since HAM-Offload provides similar primitives as current local offload frameworks, existing applications can be easily ported to overcome the single-node limitation while keeping the convenient offload programming model. We demonstrate the effectiveness of the framework by using it to enable a real-world application from the field of molecular dynamics to use multiple local and remote Xeon Phis. The evaluation shows good scaling behavior. Compared with LEO, performance is equal for large offloads and significantly better for small offloads. Y1 - 2014 UR - http://dl.acm.org/citation.cfm?id=2683616 U6 - https://doi.org/10.1109/SC.2014.22 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Reinefeld, Alexander ED - Reinders, James ED - Jeffers, Jim T1 - Concurrent Kernel Offloading T2 - High Performance Parallelism Pearls Y1 - 2014 UR - http://store.elsevier.com/High-Performance-Parallelism-Pearls/James-Reinders/isbn-9780128021187/ SN - 978-0128021187 N1 - Target publication date: Nov, 2014 PB - Morgan Kaufman, Elsevier ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Reinefeld, Alexander T1 - The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing N2 - With the growing number of hardware components and the increasing software complexity in the upcoming exascale computers, system failures will become the norm rather than an exception for long-running applications. Fault-tolerance can be achieved by the creation of checkpoints during the execution of a parallel program. Checkpoint/Restart (C/R) mechanisms allow for both task migration (even if there were no hardware faults) and restarting of tasks after the occurrence of hardware faults. Affected tasks are then migrated to other nodes which may result in unfortunate process placement and/or oversubscription of compute resources. In this paper we analyze the impact of unfortunate process placement and oversubscription of compute resources on the performance and scalability of two typical HPC application workloads, CP2K and MOM5. Results are given for a Cray XC30/40 with Aries dragonfly topology. Our results indicate that unfortunate process placement has only little negative impact while oversubscription substantially degrades the performance. The latter might be only (partially) beneficial when placing multiple applications with different computational characteristics on the same node. T3 - ZIB-Report - 15-05 KW - Fault-tolerance KW - Process placement KW - Oversubscription Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53560 SN - 1438-0064 ER - TY - JOUR A1 - Heinze, Rieke A1 - Dipankar, Anurag A1 - Henken, Cintia Carbajal A1 - Moseley, Christopher A1 - Sourdeval, Odran A1 - Trömel, Silke A1 - Xie, Xinxin A1 - Adamidis, Panos A1 - Ament, Felix A1 - Baars, Holger A1 - Barthlott, Christian A1 - Behrendt, Andreas A1 - Blahak, Ulrich A1 - Bley, Sebastian A1 - Brdar, Slavko A1 - Brueck, Matthias A1 - Crewell, Susanne A1 - Deneke, Hartwig A1 - Di Girolamo, Paolo A1 - Evaristo, Raquel A1 - Fischer, Jürgen A1 - Frank, Christopher A1 - Friederichs, Petra A1 - Göcke, Tobias A1 - Gorges, Ksenia A1 - Hande, Luke A1 - Hanke, Moritz A1 - Hansen, Akio A1 - Hege, Hans-Christian A1 - Hose, Corinna A1 - Jahns, Thomas A1 - Kalthoff, Norbert A1 - Klocke, Daniel A1 - Kneifel, Stefan A1 - Knippertz, Peter A1 - Kuhn, Alexander A1 - van Laar, Thriza A1 - Macke, Andreas A1 - Maurer, Vera A1 - Mayer, Bernhard A1 - Meyer, Catrin I. A1 - Muppa, Shravan K. A1 - Neggers, Roeland A. J. A1 - Orlandi, Emiliano A1 - Pantillon, Florian A1 - Pospichal, Bernhard A1 - Röber, Niklas A1 - Scheck, Leonhard A1 - Seifert, Axel A1 - Seifert, Patric A1 - Senf, Fabian A1 - Siligam, Pavan A1 - Simmer, Clemens A1 - Steinke, Sandra A1 - Stevens, Bjorn A1 - Wapler, Kathrin A1 - Weniger, Michael A1 - Wulfmeyer, Volker A1 - Zängl, Günther A1 - Zhang, Dan A1 - Quaas, Johannes T1 - Large-eddy simulations over Germany using ICON: a comprehensive evaluation JF - Quarterly Journal of the Royal Meteorological Society N2 - Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model. Y1 - 2017 U6 - https://doi.org/10.1002/qj.2947 VL - 143 IS - 702 SP - 69 EP - 100 ER -