@inproceedings{2107, author = {{Grunzke, Richard and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, André and Gesing, Sandra and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Krüger, Jens and Kruse, Martin and Müller-Pfefferkorn, Ralph and Schäfer, Patrick and Schuller, Bernd and Steinke, Thomas and Zink, Andreas}}, booktitle = {{Proc. UNICORE Summit}}, title = {{{A Data Driven Science Gateway for Computational Workflows}}}, year = {{2012}}, } @inproceedings{1789, author = {{Kaiser, Jürgen and Meister, Dirk and Brinkmann, André and Effert, Sascha}}, booktitle = {{Proc. Symp. on Mass Storage Systems and Technologies (MSST)}}, pages = {{1--12}}, publisher = {{IEEE}}, title = {{{Design of an exact data deduplication cluster}}}, doi = {{10.1109/MSST.2012.6232380}}, year = {{2012}}, } @inproceedings{2171, author = {{Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, André and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Krüger, Jens and Müller-Pfefferkorn, Ralph and Schäfer, Patrick and Steinke, Thomas}}, booktitle = {{Proc. EGI Community Forum}}, title = {{{The MoSGrid Community From National to International Scale}}}, year = {{2012}}, } @article{2172, author = {{Thielemans, Kris and Tsoumpas, Charalampos and Mustafovic, Sanida and Beisel, Tobias and Aguiar, Pablo and Dikaios, Nikolaos and W Jacobson, Matthew}}, journal = {{Physics in Medicine and Biology}}, number = {{4}}, pages = {{867--883}}, publisher = {{IOP Publishing}}, title = {{{STIR: Software for Tomographic Image Reconstruction Release 2}}}, doi = {{10.1088/0031-9155/57/4/867}}, volume = {{57}}, year = {{2012}}, } @article{2173, author = {{Redif, Soydan and Kasap, Server}}, journal = {{Int. Journal of Electronics}}, number = {{12}}, pages = {{1646--1651}}, publisher = {{Taylor & Francis}}, title = {{{Parallel algorithm for computation of second-order sequential best rotations}}}, doi = {{10.1080/00207217.2012.751343}}, volume = {{100}}, year = {{2012}}, } @article{2174, author = {{Kasap, Server and Benkrid, Khaled}}, journal = {{Journal of Computers}}, number = {{6}}, pages = {{1312--1328}}, publisher = {{Academy Publishers}}, title = {{{Parallel Processor Design and Implementation for Molecular Dynamics Simulations on a FPGA Parallel Computer}}}, volume = {{7}}, year = {{2012}}, } @article{2176, author = {{Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, André and Gesing, Sandra and Grunzke, Richard and Jäkel, René and Kohlbacher, Oliver and Krüger, Jens and Dos Santos Vieira, Ines}}, journal = {{Studies in Health Technology and Informatics}}, pages = {{142--151}}, publisher = {{IOP Publishing}}, title = {{{Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway}}}, doi = {{10.3233/978-1-61499-054-3-142}}, volume = {{175}}, year = {{2012}}, } @inproceedings{2178, author = {{Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, André and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Krüger, Jens and Müller-Pfefferkorn, Ralph and Schäfer, Patrick and Steinke, Thomas}}, booktitle = {{Proceedings of Science}}, title = {{{A Science Gateway Getting Ready for Serving the International Molecular Simulation Community}}}, volume = {{PoS(EGICF12-EMITC2)050}}, year = {{2012}}, } @misc{587, author = {{Plessl, Christian and Platzner, Marco and Agne, Andreas and Happe, Markus and Lübbers, Enno}}, publisher = {{Awareness Magazine}}, title = {{{Programming models for reconfigurable heterogeneous multi-cores}}}, year = {{2012}}, } @inproceedings{2106, abstract = {{Although the benefits of FPGAs for accelerating scientific codes are widely acknowledged, the use of FPGA accelerators in scientific computing is not widespread because reaping these benefits requires knowledge of hardware design methods and tools that is typically not available with domain scientists. A promising but hardly investigated approach is to develop tool flows that keep the common languages for scientific code (C,C++, and Fortran) and allow the developer to augment the source code with OpenMPlike directives for instructing the compiler which parts of the application shall be offloaded the FPGA accelerator. In this work we study whether the promise of effective FPGA acceleration with an OpenMP-like programming effort can actually be held. Our target system is the Convey HC-1 reconfigurable computer for which an OpenMP-like programming environment exists. As case study we use an application from computational nanophotonics. Our results show that a developer without previous FPGA experience could create an FPGA-accelerated application that is competitive to an optimized OpenMP-parallelized CPU version running on a two socket quad-core server. Finally, we discuss our experiences with this tool flow and the Convey HC-1 from a productivity and economic point of view.}}, author = {{Meyer, Björn and Schumacher, Jörn and Plessl, Christian and Förstner, Jens}}, booktitle = {{Proc. Int. Conf. on Field Programmable Logic and Applications (FPL)}}, keywords = {{funding-upb-forschungspreis, funding-maxup, tet_topic_hpc}}, pages = {{189--196}}, publisher = {{IEEE}}, title = {{{Convey Vector Personalities – FPGA Acceleration with an OpenMP-like Effort?}}}, doi = {{10.1109/FPL.2012.6339370}}, year = {{2012}}, } @article{2108, author = {{Schumacher, Tobias and Plessl, Christian and Platzner, Marco}}, issn = {{0141-9331}}, journal = {{Microprocessors and Microsystems}}, keywords = {{funding-altera}}, number = {{2}}, pages = {{110--126}}, title = {{{IMORC: An Infrastructure and Architecture Template for Implementing High-Performance Reconfigurable FPGA Accelerators}}}, doi = {{10.1016/j.micpro.2011.04.002}}, volume = {{36}}, year = {{2012}}, } @inproceedings{615, abstract = {{Due to the continuously shrinking device structures and increasing densities of FPGAs, thermal aspects have become the new focus for many research projects over the last years. Most researchers rely on temperature simulations to evaluate their novel thermal management techniques. However, the accuracy of the simulations is to some extent questionable and they require a high computational effort if a detailed thermal model is used.For experimental evaluation of real-world temperature management methods, often synthetic heat sources are employed. Therefore, in this paper we investigated the question if we can create significant rises in temperature on modern FPGAs to enable future evaluation of thermal management techniques based on experiments in contrast to simulations. Therefore, we have developed eight different heat-generating cores that use different subsets of the FPGA resources. Our experimental results show that, according to the built-in thermal diode of our Xilinx Virtex-5 FPGA, we can increase the chip temperature by 134 degree C in less than 12 minutes by only utilizing about 21% of the slices.}}, author = {{Happe, Markus and Hangmann, Hendrik and Agne, Andreas and Plessl, Christian}}, booktitle = {{Proceedings of the International Conference on Reconfigurable Computing and FPGAs (ReConFig)}}, pages = {{1--8}}, publisher = {{IEEE}}, title = {{{Eight Ways to put your FPGA on Fire – A Systematic Study of Heat Generators}}}, doi = {{10.1109/ReConFig.2012.6416745}}, year = {{2012}}, } @inproceedings{591, abstract = {{One major obstacle for a wide spread FPGA usage in general-purpose computing is the development tool flow that requires much higher effort than for pure software solutions. Convey Computer promises a solution to this problem for their HC-1 platform, where the FPGAs are configured to run as a vector processor and the software source code can be annotated with pragmas that guide an automated vectorization process. We investigate this approach for a stereo matching algorithm that has abundant parallelism and a number of different computational patterns. We note that for this case study the automated vectorization in its current state doesn’t hold its productivity promise. However, we also show that using the Vector Personality can yield a significant speedups compared to CPU implementations in two of three investigated phases of the algorithm. Those speedups don’t match custom FPGA implementations, but can come with much reduced development effort.}}, author = {{Kenter, Tobias and Plessl, Christian and Schmitz, Henning}}, booktitle = {{Proceedings of the International Conference on ReConFigurable Computing and FPGAs (ReConFig)}}, pages = {{1--8}}, publisher = {{IEEE}}, title = {{{Pragma based parallelization - Trading hardware efficiency for ease of use?}}}, doi = {{10.1109/ReConFig.2012.6416773}}, year = {{2012}}, } @inproceedings{609, abstract = {{Today's design and operation principles and methods do not scale well with future reconfigurable computing systems due to an increased complexity in system architectures and applications, run-time dynamics and corresponding requirements. Hence, novel design and operation principles and methods are needed that possibly break drastically with the static ones we have built into our systems and the fixed abstraction layers we have cherished over the last decades. Thus, we propose a HW/SW platform that collects and maintains information about its state and progress which enables the system to reason about its behavior (self-awareness) and utilizes its knowledge to effectively and autonomously adapt its behavior to changing requirements (self-expression).To enable self-awareness, our compute nodes collect information using a variety of sensors, i.e. performance counters and thermal diodes, and use internal self-awareness models that process these information. For self-awareness, on-line learning is crucial such that the node learns and continuously updates its models at run-time to react to changing conditions. To enable self-expression, we break with the classic design-time abstraction layers of hardware, operating system and software. In contrast, our system is able to vertically migrate functionalities between the layers at run-time to exploit trade-offs between abstraction and optimization.This paper presents a heterogeneous multi-core architecture, that enables self-awareness and self-expression, an operating system for our proposed hardware/software platform and a novel self-expression method.}}, author = {{Happe, Markus and Agne, Andreas and Plessl, Christian and Platzner, Marco}}, booktitle = {{Proceedings of the Workshop on Self-Awareness in Reconfigurable Computing Systems (SRCS)}}, pages = {{8--9}}, title = {{{Hardware/Software Platform for Self-aware Compute Nodes}}}, year = {{2012}}, } @inproceedings{567, abstract = {{Heterogeneous machines are gaining momentum in the High Performance Computing field, due to the theoretical speedups and power consumption. In practice, while some applications meet the performance expectations, heterogeneous architectures still require a tremendous effort from the application developers. This work presents a code generation method to port codes into heterogeneous platforms, based on transformations of the control flow into function calls. The results show that the cost of the function-call mechanism is affordable for the tested HPC kernels. The complete toolchain, based on the LLVM compiler infrastructure, is fully automated once the sequential specification is provided.}}, author = {{Barrio, Pablo and Carreras, Carlos and Sierra, Roberto and Kenter, Tobias and Plessl, Christian}}, booktitle = {{Proceedings of the International Conference on High Performance Computing and Simulation (HPCS)}}, pages = {{559--565}}, publisher = {{IEEE}}, title = {{{Turning control flow graphs into function calls: Code generation for heterogeneous architectures}}}, doi = {{10.1109/HPCSim.2012.6266973}}, year = {{2012}}, } @inproceedings{612, abstract = {{While numerous publications have presented ring oscillator designs for temperature measurements a detailed study of the ring oscillator's design space is still missing. In this work, we introduce metrics for comparing the performance and area efficiency of ring oscillators and a methodology for determining these metrics. As a result, we present a systematic study of the design space for ring oscillators for a Xilinx Virtex-5 platform FPGA.}}, author = {{Rüthing, Christoph and Happe, Markus and Agne, Andreas and Plessl, Christian}}, booktitle = {{Proceedings of the International Conference on Field Programmable Logic and Applications (FPL)}}, pages = {{559--562}}, publisher = {{IEEE}}, title = {{{Exploration of Ring Oscillator Design Space for Temperature Measurements on FPGAs}}}, doi = {{10.1109/FPL.2012.6339370}}, year = {{2012}}, } @inproceedings{2180, author = {{Beisel, Tobias and Wiersema, Tobias and Plessl, Christian and Brinkmann, André}}, booktitle = {{Proc. Workshop on Computer Architecture and Operating System Co-design (CAOS)}}, keywords = {{funding-enhance}}, title = {{{Programming and Scheduling Model for Supporting Heterogeneous Accelerators in Linux}}}, year = {{2012}}, } @article{2177, author = {{Grad, Mariusz and Plessl, Christian}}, journal = {{Int. Journal of Reconfigurable Computing (IJRC)}}, publisher = {{Hindawi Publishing Corp.}}, title = {{{On the Feasibility and Limitations of Just-In-Time Instruction Set Extension for FPGA-based Reconfigurable Processors}}}, doi = {{10.1155/2012/418315}}, year = {{2012}}, } @article{13546, author = {{Riefer, A. and Rauls, E. and Schmidt, Wolf Gero and Eberhard, J. and Stoll, I. and Mattay, J.}}, issn = {{1098-0121}}, journal = {{Physical Review B}}, number = {{16}}, title = {{{2-Aminopyrimidine-silver(I) based organic semiconductors: Electronic structure and optical response}}}, doi = {{10.1103/physrevb.85.165202}}, volume = {{85}}, year = {{2012}}, } @article{13545, author = {{Landmann, M and Rauls, E and Schmidt, Wolf Gero}}, issn = {{0953-8984}}, journal = {{Journal of Physics: Condensed Matter}}, title = {{{The electronic structure and optical response of rutile, anatase and brookite TiO2}}}, doi = {{10.1088/0953-8984/24/19/195503}}, volume = {{24}}, year = {{2012}}, }