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  <doc>
    <id>918</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2006-05-18</completedDate>
    <publishedDate>2006-05-18</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">THESEUS - Protein Structure Prediction at ZIB</title>
    <abstract language="eng">THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004.</abstract>
    <identifier type="serial">06-24</identifier>
    <identifier type="opus3-id">918</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-9184</identifier>
    <author>Patrick May</author>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>06-24</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Protein Structure Prediction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Bioinformatics</value>
    </subject>
    <collection role="ddc" number="000">Informatik, Informationswissenschaft, allgemeine Werke</collection>
    <collection role="msc" number="92-08">Computational methods</collection>
    <collection role="msc" number="92E10">Molecular structure (graph-theoretic methods, methods of differential topology, etc.)</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/918/ZR-06-24.pdf</file>
    <file>https://opus4.kobv.de/opus4-zib/files/918/ZR-06-24.ps</file>
  </doc>
  <doc>
    <id>1556</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2012-07-05</completedDate>
    <publishedDate>2012-07-05</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Novel Hybrid Approach to Automatically Determine Kernel Interface Data Volumes</title>
    <abstract language="eng">Scheduling algorithms for heterogeneous platforms make scheduling decisions based on several metrics. One of these metrics is the amount of data to be transferred from and to the accelerator. However, the automated determination of this metric is not a simple task. A few schedulers and runtime systems solve this problem by using regression models, which are imprecise though. Our novel approach for the determination of data volumes removes this limitation and thus provides a solution to obtain exact information.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-15569</identifier>
    <author>Sebastian Dreßler</author>
    <submitter>Sebastian Dreßler</submitter>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>12-23</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>function parameter analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>function parameter sizes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>heterogeneous systems</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>scheduling metrics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>tool flow</value>
    </subject>
    <collection role="ccs" number="D.">Software</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2011-ENHANCE">2011-ENHANCE</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1556/kdv_dressler_steinke_zibreport.pdf</file>
  </doc>
  <doc>
    <id>4218</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-08-26</completedDate>
    <publishedDate>2013-08-26</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU</title>
    <abstract language="eng">Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer&#13;
from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86&#13;
multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we&#13;
describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im&#13;
plementations of the Swendsen-Wang algorithm are demonstrated.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42187</identifier>
    <identifier type="doi">10.1145/2503210.2503254</identifier>
    <enrichment key="SourceTitle">Appeared in: 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</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Florian Wende</author>
    <submitter>Florian Wende</submitter>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-44</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Swendsen-Wang Multi-Cluster Algorithm</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Ising Model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Xeon Phi</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>GPGPU</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Connected Component Labeling</value>
    </subject>
    <collection role="ccs" number="B.">Hardware</collection>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
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    <file>https://opus4.kobv.de/opus4-zib/files/4218/wende_steinke.pdf</file>
  </doc>
  <doc>
    <id>4222</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
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    <completedDate>2013-08-30</completedDate>
    <publishedDate>2013-08-30</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects</title>
    <abstract language="eng">Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually  implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42224</identifier>
    <identifier type="doi">10.1007/978-3-642-54420-0_25</identifier>
    <enrichment key="SourceTitle">Appeared in:  Euro-Par 2013: Parallel Processing Workshops. Lecture Notes in Computer Science 8374. 2014, pp. 249-258</enrichment>
    <author>Sebastian Dreßler</author>
    <submitter>Sebastian Dreßler</submitter>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-46</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>memory footprint</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-linear objects</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>static analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>dynamic analysis</value>
    </subject>
    <collection role="ccs" number="E.">Data</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2013-Many-Core-HPC">2013-Many-Core-HPC</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4222/DresslerSteinke-MemoryFootprint.pdf</file>
  </doc>
  <doc>
    <id>7230</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>e25851</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>Emerging Architectures in Computational Chemistry</issue>
    <volume/>
    <type>article</type>
    <publisherName>Wiley Online Library</publisherName>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-12-19</completedDate>
    <publishedDate>2018-12-19</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">OpenMP in VASP: Threading and SIMD</title>
    <abstract language="eng">The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes.&#13;
Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node.&#13;
We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme.&#13;
We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version, as well as a 2x increased performance of collective operations using the multiple-endpoint MPI feature.&#13;
The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9x performance gain on AVX512 platforms with the Intel compiler.</abstract>
    <parentTitle language="deu">International Journal of Quantum Chemistry</parentTitle>
    <identifier type="doi">10.1002/qua.25851</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SubmissionStatus">in press</enrichment>
    <enrichment key="AcceptedDate">2018-12-19</enrichment>
    <submitter>Florian Wende</submitter>
    <author>Florian Wende</author>
    <author>Martijn Marsman</author>
    <author>Jeongnim Kim</author>
    <author>Fedor Vasilev</author>
    <author>Zhengji Zhao</author>
    <author>Thomas Steinke</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2013-Many-Core-HPC">2013-Many-Core-HPC</collection>
  </doc>
  <doc>
    <id>3415</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Granular Security for a Science Gateway in Structural Bioinformatics</title>
    <parentTitle language="eng">Proc. IWSG-Life 2011</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sandra Gesing</author>
    <author>Richard Grunzke</author>
    <author>Akos Balasko</author>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>André Brinkmann</author>
    <author>Gregor Fels</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Peter Kacsuk</author>
    <author>Miklos Kozlovszky</author>
    <author>Jens Krüger</author>
    <author>Lars Packschies</author>
    <author>Patrick Schäfer</author>
    <author>Bernd Schuller</author>
    <author>Johannes Schuster</author>
    <author>Thomas Steinke</author>
    <author>Anna Szikszay Fabri</author>
    <author>Martin Wewior</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Oliver Kohlbacher</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
  </doc>
  <doc>
    <id>3419</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>826</volume>
    <type>conferenceobject</type>
    <publisherName>CEUR Workshop Proceedings</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">MoSGrid: Progress of Workflow driven Chemical&#13;
Simulations</title>
    <parentTitle language="eng">Proc. of Grid Workflow Workshop 2011, Cologne, Germany</parentTitle>
    <identifier type="url">http://CEUR-WS.org/Vol-826/paper02.pdf</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>Andre Brinkmann</author>
    <author>Gregor Fels</author>
    <author>Sandra Gesing</author>
    <author>Richard Grunzke</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Oliver Kohlbacher</author>
    <author>Jens Krüger</author>
    <author>Ulrich Lang</author>
    <author>Lars Packschies</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Johannes Schuster</author>
    <author>Thomas Steinke</author>
    <author>Klaus Dieter Warzecha</author>
    <author>Martin Wewior</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
  </doc>
  <doc>
    <id>3421</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>0</issue>
    <volume>-</volume>
    <type>article</type>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Solutions for biomedical grid computing – Case studies from the D-Grid project Services@MediGRID</title>
    <parentTitle language="eng">Journal of Computational Science</parentTitle>
    <identifier type="doi">10.1016/j.jocs.2011.06.006</identifier>
    <identifier type="url">http://www.sciencedirect.com/science/article/pii/S1877750311000603</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Frank Dickmann</author>
    <author>Jürgen Falkner</author>
    <author>Wilfried Gunia</author>
    <author>Jochen Hampe</author>
    <author>Michael Hausmann</author>
    <author>Alexander Herrmann</author>
    <author>Nick Kepper</author>
    <author>Tobias Knoch</author>
    <author>Svenja Lauterbach</author>
    <author>Jörg Lippert</author>
    <author>Kathrin Peter</author>
    <author>Eberhard Schmitt</author>
    <author>Ulrich Schwardmann</author>
    <author>Juri Solodenko</author>
    <author>Dietmar Sommerfeld</author>
    <author>Thomas Steinke</author>
    <author>Anette Weisbecker</author>
    <author>Ulrich Sax</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
  </doc>
  <doc>
    <id>3407</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">The MoSGrid Community – From National to International Scale</title>
    <parentTitle language="eng">EGI Community Forum 2012</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sandra Gesing</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Georg Birkenheuer</author>
    <author>Andre Brinkmann</author>
    <author>Richard Grunzke</author>
    <author>Peter Kacsuk</author>
    <author>Oliver Kohlbacher</author>
    <author>Miklos Kozlovszky</author>
    <author>Jens Krüger</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Thomas Steinke</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
  </doc>
  <doc>
    <id>3408</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>Suppl 1</issue>
    <volume>3</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science</title>
    <parentTitle language="eng">Journal of Cheminformatics 2011</parentTitle>
    <identifier type="doi">10.1186/1758-2946-3-S1-P14</identifier>
    <identifier type="url">http://www.jcheminf.com/content/3/S1/P14</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>Andre Brinkmann</author>
    <author>Ines dos Santos Vieira</author>
    <author>Gregor Fels</author>
    <author>Sandra Gesing</author>
    <author>Richard Grunzke</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Oliver Kohlbacher</author>
    <author>Jens Krüger</author>
    <author>Ulrich Lang</author>
    <author>Lars Packschies</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Hans-Günther Schmalz</author>
    <author>Thomas Steinke</author>
    <author>Klaus Dieter Warzecha</author>
    <author>Martin Wewior</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
  </doc>
  <doc>
    <id>3409</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>94</pageFirst>
    <pageLast>95</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Science Gateway for Molecular Simulations</title>
    <parentTitle language="eng">EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sandra Gesing</author>
    <author>Peter Kacsuk</author>
    <author>Miklos Kozlovszky</author>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>Andre Brinkmann</author>
    <author>Gregor Fels</author>
    <author>Richard Grunzke</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Jens Krüger</author>
    <author>Lars Packschies</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Thomas Steinke</author>
    <author>Anna Szikszay Fabri</author>
    <author>Klaus Dieter Warzecha</author>
    <author>Martin Wewior</author>
    <author>Oliver Kohlbacher</author>
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    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
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  <doc>
    <id>3389</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
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    <language>eng</language>
    <pageFirst>74</pageFirst>
    <pageLast>83</pageLast>
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    <completedDate>--</completedDate>
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    <title language="eng">On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering</title>
    <parentTitle language="eng">Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on</parentTitle>
    <identifier type="doi">10.1109/SAAHPC.2012.12</identifier>
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    <author>Florian Wende</author>
    <author>Frank Cordes</author>
    <author>Thomas Steinke</author>
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    <language>eng</language>
    <pageFirst/>
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    <volume>PoS(EGICF12-EMITC2)050</volume>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
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    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Science Gateway Getting Ready for Serving the International Molecular Simulation Community</title>
    <parentTitle language="eng">Proceedings of Science</parentTitle>
    <identifier type="url">http://pos.sissa.it/archive/conferences/162/050/EGICF12-EMITC2_050.pdf</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sandra Gesing</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Georg Birkenheuer</author>
    <author>André Brinkmann</author>
    <author>Richard Grunzke</author>
    <author>Peter Kacsuk</author>
    <author>Oliver Kohlbacher</author>
    <author>Miklos Kozlovszky</author>
    <author>Jens Krüger</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Thomas Steinke</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
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  <doc>
    <id>3392</id>
    <completedYear>2012</completedYear>
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    <language>eng</language>
    <pageFirst>21</pageFirst>
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    <pageNumber/>
    <edition/>
    <issue>Suppl 1</issue>
    <volume>4</volume>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
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    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment</title>
    <parentTitle language="eng">Journal of Cheminformatics</parentTitle>
    <identifier type="doi">10.1186/1758-2946-4-S1-P21</identifier>
    <identifier type="url">http://www.jcheminf.com/content/4/S1/P21</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>André Brinkmann</author>
    <author>Ines dos Santos Vieira</author>
    <author>Gregor Fels</author>
    <author>Sandra Gesing</author>
    <author>Richard Grunzke</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Oliver Kohlbacher</author>
    <author>Jens Krüger</author>
    <author>Ulrich Lang</author>
    <author>Lars Packschies</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Thomas Steinke</author>
    <author>Klaus Dieter Warzecha</author>
    <author>Martin Wewior</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
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  <doc>
    <id>3393</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics</title>
    <parentTitle language="eng">Journal of Grid Computing</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sandra Gesing</author>
    <author>Richard Grunzke</author>
    <author>Jens Krüger</author>
    <author>Georg Birkenheuer</author>
    <author>Martin Wewior</author>
    <author>Patrick Schäfer</author>
    <author>Bernd Schuller</author>
    <author>Johannes Schuster</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Sebastian Breuers</author>
    <author>Akos Balasko</author>
    <author>Miklos Kozlovszky</author>
    <author>Anna Szikszay Fabri</author>
    <author>Lars Packschies</author>
    <author>Peter Kacsuk</author>
    <author>Dirk Blunk</author>
    <author>Thomas Steinke</author>
    <author>André Brinkmann</author>
    <author>Gregor Fels</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>René Jäkel</author>
    <author>Oliver Kohlbacher</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
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    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
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  <doc>
    <id>3394</id>
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    <pageLast/>
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    <publisherName/>
    <publisherPlace>Dresden, Germany</publisherPlace>
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    <completedDate>--</completedDate>
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    <title language="eng">A Data Driven Science Gateway for Computational Workflows</title>
    <parentTitle language="eng">Proceedings of the UNICORE Summit</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Richard Grunzke</author>
    <author>Georg Birkenheuer</author>
    <author>Dirk Blunk</author>
    <author>Sebastian Breuers</author>
    <author>André Brinkmann</author>
    <author>Sandra Gesing</author>
    <author>Sonja Herres-Pawlis</author>
    <author>Oliver Kohlbacher</author>
    <author>Jens Krüger</author>
    <author>Martin Kruse</author>
    <author>Ralph Müller-Pfefferkorn</author>
    <author>Patrick Schäfer</author>
    <author>Bernd Schuller</author>
    <author>Thomas Steinke</author>
    <author>Andreas Zink</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2009-MosGrid">2009-MosGrid</collection>
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  <doc>
    <id>3400</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
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    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>9</pageLast>
    <pageNumber/>
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    <issue/>
    <volume/>
    <type>article</type>
    <publisherName>Springer Berlin / Heidelberg</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Energy consumption of CUDA kernels with varying thread topology</title>
    <parentTitle language="eng">Computer Science - Research and Development</parentTitle>
    <identifier type="url">http://dx.doi.org/10.1007/s00450-012-0230-4</identifier>
    <identifier type="doi">10.1007/s00450-012-0230-4</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sebastian Dreßler</author>
    <author>Thomas Steinke</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2011-ENHANCE">2011-ENHANCE</collection>
  </doc>
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    <id>3375</id>
    <completedYear>2013</completedYear>
    <publishedYear>2013</publishedYear>
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    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>poster</type>
    <publisherName/>
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    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated Analysis of Complex Data Objects</title>
    <parentTitle language="eng">28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013</parentTitle>
    <note>Posterbeitrag</note>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sebastian Dreßler</author>
    <author>Thomas Steinke</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2011-ENHANCE">2011-ENHANCE</collection>
  </doc>
  <doc>
    <id>6073</id>
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    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
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    <type>reportzib</type>
    <publisherName/>
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    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-10-31</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">KART – A Runtime Compilation Library for Improving HPC Application Performance</title>
    <abstract language="eng">The effectiveness of ahead-of-time compiler optimization heavily depends on the amount of available information at compile time. Input-specific information that is only available at runtime cannot be used, although it often determines loop counts, branching predicates and paths, as well as memory-access patterns. It can also be crucial for generating efficient SIMD-vectorized code. This is especially relevant for the many-core architectures paving the way to exascale computing, which are more sensitive to code-optimization. We explore the design-space for using input-specific information at compile-time and present KART, a C++ library solution that allows developers to compile, link, and execute code (e.g., C, C++ , Fortran) at application runtime. Besides mere runtime compilation of performance-critical code, KART can be used to instantiate the same code multiple times using different inputs, compilers, and options. Other techniques like auto-tuning and code-generation can be integrated into a KART-enabled application instead of being scripted around it. We evaluate runtimes and compilation costs for different synthetic kernels, and show the effectiveness for two real-world applications, HEOM and a WSM6 proxy.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-60730</identifier>
    <identifier type="doi">10.1007/978-3-319-67630-2_29</identifier>
    <enrichment key="SourceTitle">Appeared in: ISC High Performance Workshops 2017: IXPUG Workshop "Experiences on Intel Knights Landing at the One Year Mark" LNCS 10524, 2017</enrichment>
    <author>Matthias Noack</author>
    <submitter>Matthias Noack</submitter>
    <author>Florian Wende</author>
    <author>Georg Zitzlsberger</author>
    <author>Michael Klemm</author>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-48</number>
    </series>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2013-Many-Core-HPC">2013-Many-Core-HPC</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6073/kart_zr.pdf</file>
  </doc>
  <doc>
    <id>6054</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>Euro-Par 2016: Parallel Processing: 22nd International Conference on Parallel and Distributed Computing</volume>
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    <publisherName>Springer International Publishing</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Portable SIMD Performance with OpenMP* 4.x Compiler Directives</title>
    <abstract language="eng">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.</abstract>
    <identifier type="isbn">978-3-319-43659-3</identifier>
    <identifier type="doi">10.1007/978-3-319-43659-3_20</identifier>
    <enrichment key="Series">LNCS</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <editor>Pierre-Francois Dutot</editor>
    <submitter>Florian Wende</submitter>
    <author>Florian Wende</author>
    <editor>Denis Trystram</editor>
    <author>Matthias Noack</author>
    <author>Thomas Steinke</author>
    <author>Michael Klemm</author>
    <author>Georg Zitzlsberger</author>
    <author>Chris J. Newburn</author>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="2013-Many-Core-HPC">2013-Many-Core-HPC</collection>
    <collection role="projects" number="2013-SECOS">2013-SECOS</collection>
  </doc>
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