TY - GEN A1 - Moser, Monika A1 - Haridi, Seif A1 - Shafaat, Tallat A1 - Schütt, Thorsten A1 - Högqvist, Mikael A1 - Reinefeld, Alexander T1 - Transactional DHT Algorithms N2 - We present a framework for transactional data access on data stored in a DHT. It allows to atomically read and write items and to run distributed transactions consisting of a sequence of read and write operations on the items. Items are symmetrically replicated in order to achieve durability of data stored in the SON. To provide availability of items despite the unavailability of some replicas, operations on items are quorum-based. They make progress as long as a majority of replicas can be accessed. Our framework processes transactions optimistically with an atomic commit protocol that is based on Paxos atomic commit. We present algorithms for the whole framework with an event based notation. Additionally we discuss the problem of lookup inconsistencies and its implications on the one-copy serializability property of the transaction processing in our framework. T3 - ZIB-Report - 09-34 KW - Distributed System KW - DHT KW - Paxos KW - Algorithms KW - Storage Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11532 SN - 1438-0064 ER - TY - GEN A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Haridi, Seif A1 - Schütt, Thorsten T1 - Enhanced Paxos Commit for Transactions on DHTs N2 - Key/value stores which are built on structured overlay networks often lack support for atomic transactions and strong data consistency among replicas. This is unfortunate, because consistency guarantees and transactions would allow a wide range of additional application domains to benefit from the inherent scalability and fault-tolerance of DHTs. The Scalaris key/value store supports strong data consistency and atomic transactions. It uses an enhanced Paxos Commit protocol with only four communication steps rather than six. This improvement was possible by exploiting information from the replica distribution in the DHT. Scalaris enables implementation of more reliable and scalable infrastructure for collaborative Web services that require strong consistency and atomic changes across multiple items. T3 - ZIB-Report - 09-28 KW - Paxos KW - Transaktionen KW - DHT KW - strenge Konsistenz KW - Paxos KW - transactions KW - DHT KW - strong consistency Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11448 SN - 1438-0064 ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle T2 - Workshop on Computer Games Y1 - 2013 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Data-flow scheduling for a scalable FLESnet JF - CBM Progress Report 2017 Y1 - 2018 SN - 978-3-9815227-5-4 U6 - https://doi.org/10.15120/GSI-2018-00485 SP - 130 EP - 131 ER - TY - GEN A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Modeling Checkpoint Schedules for Concurrent HPC Applications T2 - CoSaS 2018 International Symposium on Computational Science at Scale Y1 - 2018 ER - TY - CHAP A1 - Weinhold, Carsten A1 - Lackorzynski, Adam A1 - Bierbaum, Jan A1 - Küttler, Martin A1 - Planeta, Maksym A1 - Weisbach, Hannes A1 - Hille, Matthias A1 - Härtig, Hermann A1 - Margolin, Alexander A1 - Sharf, Dror A1 - Levy, Ely A1 - Gak, Pavel A1 - Barak, Amnon A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Lieber, Matthias A1 - Nagel, Wolfgang T1 - FFMK: A Fast and Fault-Tolerant Microkernel-Based System for Exascale Computing T2 - Software for Exascale Computing - SPPEXA 2016-2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-47956-5_16 SP - 483 EP - 516 PB - Springer ER - TY - GEN A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle N2 - The performance of heuristic search algorithms depends crucially on the effectiveness of the heuristic. A pattern database (PDB) is a powerful heuristic in the form of a pre-computed lookup table. Larger PDBs provide better bounds and thus allow more cut-offs in the search process. Today, the largest PDB for the 24-puzzle is a 6-6-6-6 PDB with a size of 486 MB. We created 8-8-8, 9-8-7 and 9-9-6 PDBs that are three orders of magnitude larger (up to 1.4 TB) than the 6-6-6-6 PDB. We show how to compute such large PDBs and we present statistical and empirical data on their efficiency. The largest single PDB gives on average an 8-fold improvement over the 6-6-6-6 PDB. Combining several large PDBs gives on average an 12-fold improvement. T3 - ZIB-Report - 13-21 KW - heuristic search KW - pattern databases Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18095 SN - 1438-0064 ER - TY - JOUR A1 - Enke, Harry A1 - Steinmetz, Matthias A1 - Adorf, Hans-Martin A1 - Beck-Ratzka, Alexander A1 - Breitling, Frank A1 - Brüsemeister, Thomas A1 - Carlson, Arthur A1 - Ensslin, Torsten A1 - Högqvist, Mikael A1 - Nickelt, Iliya A1 - Radke, Thomas A1 - Reinefeld, Alexander A1 - Reiser, Angelika A1 - Scholl, Tobias A1 - Spurzem, Rainer A1 - Steinacker, Jürgen A1 - Voges, Wolfgang A1 - Wambsganß, Joachim A1 - White, Steve T1 - AstroGrid-D: Grid technology for astronomical science JF - New Astronomy Y1 - 2011 UR - http://www.sciencedirect.com/science/article/pii/S1384107610000837 U6 - https://doi.org/10.1016/j.newast.2010.07.005 VL - 16 IS - 2 SP - 79 EP - 93 ER - TY - CHAP A1 - Flik, T. A1 - Reinefeld, Alexander ED - Czichos, Horst ED - Hennecke, Manfred T1 - Rechnerorganisation T2 - Hütte – Das Ingenieurwissen Y1 - 2012 SP - J6 EP - J124 PB - Springer-Verlag Berlin ET - 34 ER - TY - CHAP A1 - Peter, Kathrin A1 - Reinefeld, Alexander T1 - Consistency and fault tolerance for erasure-coded distributed storage systems T2 - Proceedings of the fifth international workshop on Data-Intensive Distributed Computing Date Y1 - 2012 UR - http://doi.acm.org/10.1145/2286996.2287002 U6 - https://doi.org/10.1145/2286996.2287002 SP - 23 EP - 32 PB - ACM CY - New York, NY, USA ER - TY - JOUR A1 - Enke, Harry A1 - Partl, Adrian A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Handling Big Data in Astronomy and Astrophysics JF - Datenbank-Spektrum Y1 - 2012 UR - http://dx.doi.org/10.1007/s13222-012-0099-1 U6 - https://doi.org/10.1007/s13222-012-0099-1 VL - 12 IS - 3 SP - 173 EP - 181 PB - Springer-Verlag ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - An Analysis of SMP Memory Allocators T2 - Proceedings of the 41st International Conference on Parallel Processing Workshops (Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2)) Y1 - 2012 U6 - https://doi.org/10.1109/ICPPW.2012.10 SP - 48 EP - 54 PB - IEEE Computer Society ER - TY - CHAP A1 - Schütt, Thorsten A1 - Döbbelin, Robert A1 - Reinefeld, Alexander T1 - Forward Perimeter Search with Controlled Use of Memory T2 - International Joint Conference on Artificial Intelligence, IJCAI-13, Beijing Y1 - 2013 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Döbbelin, Robert T1 - MR-search: massively parallel heuristic search JF - Concurrency and Computation: Practice and Experience Y1 - 2011 U6 - https://doi.org/10.1002/cpe.1833 VL - 25 IS - 1 SP - 40 EP - 54 ER - TY - CHAP A1 - Stender, Jan A1 - Berlin, Michael A1 - Reinefeld, Alexander ED - Kyriazis, D. ED - Voulodimos, A. ED - Gogouvitis, S. ED - Varvarigou, Theodora A. T1 - XtreemFS – a File System for the Cloud T2 - Data Intensive Storage Services for Cloud Environments Y1 - 2013 UR - http://dx.doi.org/10.4018/978-1-4666-3934-8 U6 - https://doi.org/10.4018/978-1-4666-3934-8 PB - IGI Global ER - TY - GEN A1 - Scheffler, Daniel A1 - Sips, Mike A1 - Behling, Robert A1 - Dransch, Doris A1 - Eggert, Daniel A1 - Fajerski, Jan A1 - Freytag, Johann-Christoph A1 - Griffiths, Patrick A1 - Hollstein, André A1 - Hostert, Patrick A1 - Köthur, Patrick A1 - Peters, Mathias A1 - Pflugmacher, Dirk A1 - Rabe, Andreas A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Segel, Karl T1 - GeoMultiSens – Scalable Multisensoral Analysis of Satellite Remote Sensing Data T2 - ESA Living Planet Symposium, EO Open Science Posters 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 - TY - CHAP A1 - Scheffler, Daniel A1 - Sips, Mike A1 - Behling, Robert A1 - Dransch, Doris A1 - Eggert, Daniel A1 - Fajerski, Jan A1 - Freytag, Johann-Christoph A1 - Griffiths, Patrick A1 - Hollstein, André A1 - Hostert, Patrick A1 - Köthur, Patrick A1 - Peters, Mathias A1 - Pflugmacher, Dirk A1 - Rabe, Andreas A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Segel, Karl T1 - Geomultisens – a common automatic processing and analysis system for multi-sensor satellite data T2 - Advancing Horizons for Land Cover Services Entering the Big Data Era, Second joint Workshop of the EARSeL Special Interest Group on Land Use & Land Cover and the NASA LCLUC Program Y1 - 2016 SP - 18 EP - 19 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM) JF - Journal of Computational Chemistry N2 - Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes. Y1 - 2018 U6 - https://doi.org/doi:10.1002/jcc.25354 VL - 39 IS - 22 SP - 1779 EP - 1794 PB - Wiley Periodicals, Inc. ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reimers, Jeffrey R. A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Yin, Shiwei T1 - Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM JF - Chemical Physics N2 - We analyze the exciton dynamics in PhotosystemI from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Foerster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results. Y1 - 2018 U6 - https://doi.org/10.1016/j.chemphys.2018.05.028 VL - 515 SP - 262 EP - 271 PB - Elsevier B.V. ER -