{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/293d2fe0f013f2dde7a588a9d3341cbc0/petraenderle", "tags" : [ "2017","computing","parallel","sfb716","sfb716-d9","simulation","vis(us)","visus:pfluegdk" ], "intraHash" : "93d2fe0f013f2dde7a588a9d3341cbc0", "interHash" : "fae1172c4b41349915db2961bcba50af", "label" : "Load balancing with p4est for Short-Range Molecular Dynamics with ESPResSo", "user" : "petraenderle", "description" : "", "date" : "2018-06-19 13:58:28", "changeDate" : "2018-06-19 12:07:14", "count" : 2, "pub-type": "inbook", "journal": "Advances in Parallel Computing","publisher":"IOS Press", "year": "2017", "url": "http://ebooks.iospress.nl/volumearticle/48637", "author": [ "Malte Brunn","Colin W. Glass","Michael Lahnert","Miriam Mehl","Dirk Pflüger" ], "authors": [ {"first" : "Malte", "last" : "Brunn"}, {"first" : "Colin W.", "last" : "Glass"}, {"first" : "Michael", "last" : "Lahnert"}, {"first" : "Miriam", "last" : "Mehl"}, {"first" : "Dirk", "last" : "Pflüger"} ], "editor": [ "Sanzio Bassini","Marco Danelutto","Patrizio Dazzi","Gerhard R. Joubert","Frans Peters" ], "editors": [ {"first" : "Sanzio", "last" : "Bassini"}, {"first" : "Marco", "last" : "Danelutto"}, {"first" : "Patrizio", "last" : "Dazzi"}, {"first" : "Gerhard R.", "last" : "Joubert"}, {"first" : "Frans", "last" : "Peters"} ], "volume": "Volume 32: Parallel Computing is Everywhere","pages": "455-464", "language" : "English", "eventtitle" : "International Parallel Computing Conference (ParCo) 2017; Bologna, Italy", "eventdate" : "12-15 September 2017", "doi" : "10.3233/978-1-61499-843-3-455", "bibtexKey": "brunn2017balancing" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2126f35b3dc5e36c0d63a461eb07e23c3/clausbraun", "tags" : [ "GPGPU","GPU","Markov-Chain","Monte-Carlo","SimTech","architectures","computer","heterogeneous","hybrid","molecular","myown","parallel","simulation","thermodynamics" ], "intraHash" : "126f35b3dc5e36c0d63a461eb07e23c3", "interHash" : "8b3986f798c6d3bc3d644b3a4e79b147", "label" : "Acceleration of Monte-Carlo Molecular Simulations on Hybrid Computing Architectures", "user" : "clausbraun", "description" : "", "date" : "2018-03-19 16:15:07", "changeDate" : "2018-03-19 15:32:04", "count" : 7, "pub-type": "inproceedings", "booktitle": "Proceedings of the 30th IEEE International Conference on Computer Design (ICCD'12)","publisher":"IEEE Computer Society", "year": "2012", "url": "", "author": [ "Claus Braun","Stefan Holst","Hans-Joachim Wunderlich","Juan Manuel Castillo","Joachim Gross" ], "authors": [ {"first" : "Claus", "last" : "Braun"}, {"first" : "Stefan", "last" : "Holst"}, {"first" : "Hans-Joachim", "last" : "Wunderlich"}, {"first" : "Juan Manuel", "last" : "Castillo"}, {"first" : "Joachim", "last" : "Gross"} ], "pages": "207--212","abstract": "Markov-Chain Monte-Carlo (MCMC) methods are an important class of simulation techniques, which execute a sequence of simulation steps, where each new step depends on the previous ones. Due to this fundamental dependency, MCMC methods are inherently hard to parallelize on any architecture. The upcoming generations of hybrid CPU/GPGPU architectures with their multi-core CPUs and tightly coupled many-core GPGPUs provide new acceleration opportunities especially for MCMC methods, if the new degrees of freedom are exploited correctly. \r\nIn this paper, the outcomes of an interdisciplinary collaboration are presented, which focused on the parallel mapping of a MCMC molecular simulation from thermodynamics to hybrid CPU/GPGPU computing systems. While the mapping is designed for upcoming hybrid architectures, the implementation of this approach on an NVIDIA Tesla system already leads to a substantial speedup of more than 87x despite the additional communication overheads.", "file" : "http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2012/ICCD_BraunHWCG2012.pdf", "doi" : "http://dx.doi.org/10.1109/ICCD.2012.6378642", "bibtexKey": "BraunHWCG2012" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2a102ad88594647037e1fc695a9f77c90/clausbraun", "tags" : [ "GPGPU","SimTech","apoptosis","modeling","myown","numerical","parallel","particle","receptor-clustering","simulation" ], "intraHash" : "a102ad88594647037e1fc695a9f77c90", "interHash" : "da3df25277c913d9e4301ee4eebe7f58", "label" : "Parallel Simulation of Apoptotic Receptor-Clustering on GPGPU Many-Core Architectures", "user" : "clausbraun", "description" : "", "date" : "2018-03-19 16:15:07", "changeDate" : "2018-03-19 15:22:27", "count" : 2, "pub-type": "inproceedings", "booktitle": "Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'12)", "year": "2012", "url": "", "author": [ "Claus Braun","Markus Daub","Alexander Schöll","Guido Schneider","Hans-Joachim Wunderlich" ], "authors": [ {"first" : "Claus", "last" : "Braun"}, {"first" : "Markus", "last" : "Daub"}, {"first" : "Alexander", "last" : "Schöll"}, {"first" : "Guido", "last" : "Schneider"}, {"first" : "Hans-Joachim", "last" : "Wunderlich"} ], "pages": "1--6","abstract": "Apoptosis, the programmed cell death, is a physiological process that handles the removal of unwanted or damaged cells in living organisms. The process itself is initiated by signaling through tumor necrosis factor (TNF) receptors and ligands, which form clusters on the cell membrane. The exact function of this process is not yet fully understood and currently subject of basic research. Different mathematical models have been developed to describe and simulate the apoptotic receptor-clustering.\r\nIn this interdisciplinary work, a previously introduced model of the apoptotic receptor-clustering has been extended by a new receptor type to allow a more precise description and simulation of the signaling process. Due to the high computational requirements of the model, an ef?cient algorithmic mapping to a modern many-core GPGPU architecture has been developed. Such architectures enable high-performance computing (HPC) simulation tasks on the desktop at low costs. The developed mapping reduces average simulation times from months to days (peak speedup of 256x), allowing the productive use of the model in research.", "file" : "http://www.iti.uni-stuttgart.de//fileadmin/rami/files/publications/2012/BIBM_BraunDSSW2012.pdf", "doi" : "http://dx.doi.org/10.1109/BIBM.2012.6392661", "bibtexKey": "BraunDSSW2012" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b9d42307aff55f949dce3efdc063ee86/clausbraun", "tags" : [ "Euler-Maruyama","GPU","SimTech","adaptive","aggregation","approximation","computing","heterogeneous","ligand-receptor-model","multi-timescale","myown","parallel","particle","simulation" ], "intraHash" : "b9d42307aff55f949dce3efdc063ee86", "interHash" : "8b3950b9a31a28b554ce868d67598d14", "label" : "Adaptive Parallel Simulation of a Two-Timescale-Model for Apoptotic Receptor-Clustering on GPUs", "user" : "clausbraun", "description" : "", "date" : "2018-03-19 16:15:07", "changeDate" : "2018-03-19 15:21:25", "count" : 5, "pub-type": "inproceedings", "booktitle": "Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'14)", "year": "2014", "url": "", "author": [ "Alexander Schöll","Claus Braun","Markus Daub","Guido Schneider","Hans-Joachim Wunderlich" ], "authors": [ {"first" : "Alexander", "last" : "Schöll"}, {"first" : "Claus", "last" : "Braun"}, {"first" : "Markus", "last" : "Daub"}, {"first" : "Guido", "last" : "Schneider"}, {"first" : "Hans-Joachim", "last" : "Wunderlich"} ], "pages": "424--431","abstract": "Computational biology contributes important solutions for major biological challenges. Unfortunately, most applications in computational biology are highly computeintensive and associated with extensive computing times. Biological problems of interest are often not treatable with traditional simulation models on conventional multi-core CPU systems. This interdisciplinary work introduces a new multi-timescale simulation model for apoptotic receptor-clustering and a new parallel evaluation algorithm that exploits the computational performance of heterogeneous CPU-GPU computing systems. For this purpose, the different dynamics involved in receptor-clustering are separated and simulated on two timescales. Additionally, the time step sizes are adaptively refined on each timescale independently.\r\n This new approach improves the simulation performance significantly and reduces computing times from months to hours for observation times of several seconds.", "file" : "http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2014/BIBM_SchoeBDSW2014.pdf", "doi" : "http://dx.doi.org/10.1109/BIBM.2014.6999195", "bibtexKey": "SchoeBDSW2014" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2dffb2a37e29a0efe71208a49226516a6/c.niethammer", "tags" : [ "dynamics","highly","molecular","parallel","programming","scalable","simulation","simulations","vectorization" ], "intraHash" : "dffb2a37e29a0efe71208a49226516a6", "interHash" : "a0dbaf1fbdff3c8d5401f74e8d6a7aad", "label" : "591 TFLOPS Multi-trillion Particles Simulation on SuperMUC", "user" : "c.niethammer", "description" : "", "date" : "2017-12-12 09:58:14", "changeDate" : "2017-12-12 08:58:14", "count" : 3, "pub-type": "inbook", "booktitle": "Supercomputing: 28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013. Proceedings","publisher":"Springer Berlin Heidelberg","address":"Berlin, Heidelberg", "year": "2013", "url": "https://doi.org/10.1007/978-3-642-38750-0_1", "author": [ "Wolfgang Eckhardt","Alexander Heinecke","Reinhold Bader","Matthias Brehm","Nicolay Hammer","Herbert Huber","Hans-Georg Kleinhenz","Jadran Vrabec","Hans Hasse","Martin Horsch","Martin Bernreuther","Colin W. Glass","Christoph Niethammer","Arndt Bode","Hans-Joachim Bungartz" ], "authors": [ {"first" : "Wolfgang", "last" : "Eckhardt"}, {"first" : "Alexander", "last" : "Heinecke"}, {"first" : "Reinhold", "last" : "Bader"}, {"first" : "Matthias", "last" : "Brehm"}, {"first" : "Nicolay", "last" : "Hammer"}, {"first" : "Herbert", "last" : "Huber"}, {"first" : "Hans-Georg", "last" : "Kleinhenz"}, {"first" : "Jadran", "last" : "Vrabec"}, {"first" : "Hans", "last" : "Hasse"}, {"first" : "Martin", "last" : "Horsch"}, {"first" : "Martin", "last" : "Bernreuther"}, {"first" : "Colin W.", "last" : "Glass"}, {"first" : "Christoph", "last" : "Niethammer"}, {"first" : "Arndt", "last" : "Bode"}, {"first" : "Hans-Joachim", "last" : "Bungartz"} ], "editor": [ "Julian Martin Kunkel","Thomas Ludwig","Hans Werner Meuer" ], "editors": [ {"first" : "Julian Martin", "last" : "Kunkel"}, {"first" : "Thomas", "last" : "Ludwig"}, {"first" : "Hans Werner", "last" : "Meuer"} ], "pages": "1--12","abstract": "Anticipating large-scale molecular dynamics simulations (MD) in nano-fluidics, we conduct performance and scalability studies of an optimized version of the code ls1 mardyn. We present our implementation requiring only 32 Bytes per molecule, which allows us to run the, to our knowledge, largest MD simulation to date. Our optimizations tailored to the Intel Sandy Bridge processor are explained, including vectorization as well as shared-memory parallelization to make use of Hyperthreading. Finally we present results for weak and strong scaling experiments on up to 146016 Cores of SuperMUC at the Leibniz Supercomputing Centre, achieving a speed-up of 133k times which corresponds to an absolute performance of 591.2 TFLOPS.", "isbn" : "978-3-642-38750-0", "doi" : "10.1007/978-3-642-38750-0_1", "bibtexKey": "Eckhardt2013" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cdcc9c23758fe8aad2fd902ccc79b611/c.niethammer", "tags" : [ "MD","hlrs","myown","parallel","program","programming","simulation","spmt" ], "intraHash" : "cdcc9c23758fe8aad2fd902ccc79b611", "interHash" : "e55164114995631b666027f82d58105e", "label" : "ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems", "user" : "c.niethammer", "description" : "", "date" : "2015-11-20 15:34:49", "changeDate" : "2015-11-20 14:34:49", "count" : 3, "pub-type": "article", "journal": "Journal of Chemical Theory and Computation", "year": "2014", "url": "/brokenurl# http://dx.doi.org/10.1021/ct500169q ", "author": [ "Christoph Niethammer","Stefan Becker","Martin Bernreuther","Martin Buchholz","Wolfgang Eckhardt","Alexander Heinecke","Stephan Werth","Hans-Joachim Bungartz","Colin W. Glass","Hans Hasse","Jadran Vrabec","Martin Horsch" ], "authors": [ {"first" : "Christoph", "last" : "Niethammer"}, {"first" : "Stefan", "last" : "Becker"}, {"first" : "Martin", "last" : "Bernreuther"}, {"first" : "Martin", "last" : "Buchholz"}, {"first" : "Wolfgang", "last" : "Eckhardt"}, {"first" : "Alexander", "last" : "Heinecke"}, {"first" : "Stephan", "last" : "Werth"}, {"first" : "Hans-Joachim", "last" : "Bungartz"}, {"first" : "Colin W.", "last" : "Glass"}, {"first" : "Hans", "last" : "Hasse"}, {"first" : "Jadran", "last" : "Vrabec"}, {"first" : "Martin", "last" : "Horsch"} ], "volume": "10","number": "10","pages": "4455-4464", "doi" : "10.1021/ct500169q", "eprint" : "http://dx.doi.org/10.1021/ct500169q", "bibtexKey": "niethammer2014mardyn" } ] }