TY - CHAP A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Balasko, Akos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Herres-Pawlis, Sonja A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver T1 - Granular Security for a Science Gateway in Structural Bioinformatics T2 - Proc. IWSG-Life 2011 Y1 - 2011 ER - TY - CHAP A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Proc. of Grid Workflow Workshop 2011, Cologne, Germany Y1 - 2011 UR - http://CEUR-WS.org/Vol-826/paper02.pdf VL - 826 PB - CEUR Workshop Proceedings ER - TY - CHAP A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, Andre A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - The MoSGrid Community – From National to International Scale T2 - EGI Community Forum 2012 Y1 - 2012 ER - TY - CHAP A1 - Gesing, Sandra A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Krüger, Jens A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin A1 - Kohlbacher, Oliver T1 - A Science Gateway for Molecular Simulations T2 - EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts Y1 - 2011 SP - 94 EP - 95 ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering T2 - Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/SAAHPC.2012.12 SP - 74 EP - 83 ER - TY - CHAP A1 - Grunzke, Richard A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Kruse, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Steinke, Thomas A1 - Zink, Andreas T1 - A Data Driven Science Gateway for Computational Workflows T2 - Proceedings of the UNICORE Summit Y1 - 2012 CY - Dresden, Germany ER - TY - CHAP A1 - Wende, Florian A1 - Noack, Matthias A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Zitzlsberger, Georg A1 - Newburn, Chris J. ED - Dutot, Pierre-Francois ED - Trystram, Denis T1 - Portable SIMD Performance with OpenMP* 4.x Compiler Directives N2 - Effective vectorization is becoming increasingly important for high performance and energy efficiency on processors with wide SIMD units. Compilers often require programmers to identify opportunities for vectorization, using directives to disprove data dependences. The OpenMP 4.x SIMD directives strive to provide portability. We investigate the ability of current compilers (GNU, Clang, and Intel) to generate SIMD code for microbenchmarks that cover common patterns in scientific codes and for two kernels from the VASP and the MOM5/ERGOM application. We explore coding strategies for improving SIMD performance across different compilers and platforms (Intel® Xeon® processor and Intel® Xeon Phi™ (co)processor). We compare OpenMP* 4.x SIMD vectorization with and without vector data types against SIMD intrinsics and C++ SIMD types. Our experiments show that in many cases portable performance can be achieved. All microbenchmarks are available as open source as a reference for programmers and compiler experts to enhance SIMD code generation. Y1 - 2016 SN - 978-3-319-43659-3 U6 - https://doi.org/10.1007/978-3-319-43659-3_20 VL - Euro-Par 2016: Parallel Processing: 22nd International Conference on Parallel and Distributed Computing PB - Springer International Publishing ER - TY - CHAP A1 - Schmidtke, Robert A1 - Laubender, Guido A1 - Steinke, Thomas T1 - Big Data Analytics on Cray XC Series DataWarp using Hadoop, Spark and Flink T2 - CUG Proceedings Y1 - 2016 ER - TY - CHAP A1 - Wende, Florian A1 - Marsman, Martijn A1 - Steinke, Thomas T1 - On Enhancing 3D-FFT Performance in VASP T2 - CUG Proceedings Y1 - 2016 ER - TY - CHAP A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Kramer, Tobias A1 - Steinke, Thomas T1 - DM-HEOM: A Portable and Scalable Solver-Framework for the Hierarchical Equations of Motion T2 - 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018) N2 - Computing the Hierarchical Equations of Motion (HEOM) is by itself a challenging problem, and so is writing portable production code that runs efficiently on a variety of architectures while scaling from PCs to supercomputers. We combined both challenges to push the boundaries of simulating quantum systems, and to evaluate and improve methodologies for scientific software engineering. Our contributions are threefold: We present the first distributed memory implementation of the HEOM method (DM-HEOM), we describe an interdisciplinary development workflow, and we provide guidelines and experiences for designing distributed, performance-portable HPC applications with MPI-3, OpenCL and other state-of-the-art programming models. We evaluated the resulting code on multi- and many-core CPUs as well as GPUs, and demonstrate scalability on a Cray XC40 supercomputer for the PS I molecular light harvesting complex. Y1 - 2018 SN - 978-1-5386-5555-9 U6 - https://doi.org/10.1109/IPDPSW.2018.00149 N1 - Best Paper Award SP - 947 EP - 956 ER -