https://puma.ub.uni-stuttgart.de/group/researchcode/hpc-computingPUMA RSS feed for /group/researchcode/hpc-computing2026-04-16T17:29:43+02:00https://puma.ub.uni-stuttgart.de/bibtex/24297669772239848ef5163a19989129e/diglezakisdiglezakis2024-12-05T14:42:20+01:00tool hpc-computing neuromuscular simulation <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Benjamin Maier" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/0"><span itemprop="name">B. Maier</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Dominik Göddeke" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/1"><span itemprop="name">D. Göddeke</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Felix Huber" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/2"><span itemprop="name">F. Huber</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Thomas Klotz" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/3"><span itemprop="name">T. Klotz</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Oliver Röhrle" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/4"><span itemprop="name">O. Röhrle</span></a></span>, </span> und <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Miriam Schulte" itemprop="url" href="/person/159bf2fc78694127b4507b54213450ee5/author/5"><span itemprop="name">M. Schulte</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Journal of Computational Science</span>, </em> </span>(<em><span>2024<meta content="2024" itemprop="datePublished"/></span></em>)</span>Thu Dec 05 14:42:20 CET 2024Journal of Computational Science102291OpenDiHu: An efficient and scalable framework for biophysical simulations of the neuromuscular system792024tool hpc-computing neuromuscular simulation The versatile neuromuscular system, consisting of skeletal muscles and the nervous system, enables human to perform crucial everyday tasks. To investigate its functioning and dysfunctioning with computer simulations, highly resolved, multi-scale models are favorable, whose numerical solutions demand for high performance computing. We present OpenDiHu, a versatile, high-performance computing, open source software framework for detailed, systemic simulations of skeletal muscles and their recruitment mechanisms. OpenDiHu allows to solve a variety of multi-scale models, including 3D muscle mechanics, measurable electromyographic signals, action potential propagation in the muscle tissue, subcellular bio-chemo-electrical processes, and the neural drive to the muscle. All these components can be combined with a wide range of numerical solution schemes into comprehensive simulation setups for the entire system. Experiments on up to almost 27000 cores demonstrate the efficiency and parallel scalability of OpenDiHu. This enables in silico experiments at very high spatial and temporal resolutions.https://puma.ub.uni-stuttgart.de/bibtex/2fe5c27bfa323a45b3c97de8f81f88da2/diglezakisdiglezakis2024-11-06T08:56:02+01:00hpc-computing metadata crawler NFDI4ING extraction <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Christian Stemmer" itemprop="url" href="/person/1960db829af8e246ca25a1582ec3583a7/author/0"><span itemprop="name">C. Stemmer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Nils Hoppe" itemprop="url" href="/person/1960db829af8e246ca25a1582ec3583a7/author/1"><span itemprop="name">N. Hoppe</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Benjamin Farnbacher" itemprop="url" href="/person/1960db829af8e246ca25a1582ec3583a7/author/2"><span itemprop="name">B. Farnbacher</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ralev Radoslav" itemprop="url" href="/person/1960db829af8e246ca25a1582ec3583a7/author/3"><span itemprop="name">R. Radoslav</span></a></span>, </span> und <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Giuseppe Chiapparino" itemprop="url" href="/person/1960db829af8e246ca25a1582ec3583a7/author/4"><span itemprop="name">G. Chiapparino</span></a></span></span>. </span><span class="additional-entrytype-information">(<em><span>2021<meta content="2021" itemprop="datePublished"/></span></em>)<em>[000][29*][000].</em></span>Wed Nov 06 08:56:02 CET 2024[000][29*][000]A metadata crawler for simulation data management2021hpc-computing metadata crawler NFDI4ING extraction HOMER (HPMC tool for Ontology-based Metadata Extraction and Re-use).https://puma.ub.uni-stuttgart.de/bibtex/2f449f1d02cc32a1ad8bcffb347297c7d/diglezakisdiglezakis2022-10-17T17:47:43+02:00forschungsdaten europa hpc-computing eosc dataSpaces gaiaX politik <span data-person-type="editor" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="editor"><a title="Rat für Informationsinfrastrukturen (RfII)" itemprop="url" href="/person/15cc4f24a957c5ea9516dc1bb3efc4c9c/editor/0"><span itemprop="name">R. für Informationsinfrastrukturen (RfII)</span></a></span></span> (Hrsg.) </span><span class="additional-entrytype-information">(<em><span>2022<meta content="2022" itemprop="datePublished"/></span></em>)</span>Mon Oct 17 17:47:43 CEST 2022DATENPOLITIK, OPEN SCIENCE UND DATENINFRASTRUKTUREN: AKTUELLE ENTWICKLUNGEN IM EUROPÄISCHEN RAUM2022forschungsdaten europa hpc-computing eosc dataSpaces gaiaX politik https://puma.ub.uni-stuttgart.de/bibtex/2a01fba3c690fedfaaa51e2be254cafb6/diglezakisdiglezakis2021-02-09T17:31:47+01:00forschungsdaten hpc-computing metadata tools automated <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Schembera" itemprop="url" href="/person/1b6eac40c2b6d9e29e99c8eece7d9e01b/author/0"><span itemprop="name">B. Schembera</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">The Journal of Supercomputing</span>, </em> </span>(<em><span>2021<meta content="2021" itemprop="datePublished"/></span></em>)</span>Tue Feb 09 17:31:47 CET 2021The Journal of SupercomputingLike a rainbow in the dark: metadata annotation for HPC applications in the age of dark data2021forschungsdaten hpc-computing metadata tools automated The deluge of dark data is about to happen. Lacking data management capabilities, especially in the field of supercomputing, and missing data documentation (i.e., missing metadata annotation) constitute a major source of dark data. The present work contributes to addressing this challenge by presenting ExtractIng, a generic automated metadata extraction toolkit. Existing metadata information of simulation output files scattered through the file system, can be aggregated, parsed and converted to the EngMeta metadata model. Use cases from computational engineering are considered to demonstrate the viability of ExtractIng. The evaluation results show that the metadata extraction is simulation-code independent in the sense that it can handle data outputs from various fields of science, is easy to integrate into simulation workflows and compatible with a multitude of computational environments.https://puma.ub.uni-stuttgart.de/bibtex/2ab2ddb1039b00ff1b73c9ab682a82aae/diglezakisdiglezakis2020-12-07T15:02:15+01:00forschungsdaten hpc-computing metadata ontologie molecularSimulation <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Martin Thomas Horsch" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/0"><span itemprop="name">M. Horsch</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Christoph Niethammer" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/1"><span itemprop="name">C. Niethammer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Gianluca Boccardo" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/2"><span itemprop="name">G. Boccardo</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Paola Carbone" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/3"><span itemprop="name">P. Carbone</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Silvia Chiacchiera" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/4"><span itemprop="name">S. Chiacchiera</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Mara Chiricotto" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/5"><span itemprop="name">M. Chiricotto</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Joshua D. Elliott" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/6"><span itemprop="name">J. Elliott</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Vladimir Lobaskin" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/7"><span itemprop="name">V. Lobaskin</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Philipp Neumann" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/8"><span itemprop="name">P. Neumann</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Peter Schiffels" itemprop="url" href="/person/1bcb2f3681bb3cff5c214b58d19429556/author/9"><span itemprop="name">P. Schiffels</span></a></span></span> und 4 andere Autor(en). </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Journal of Chemical &amp; Engineering Data</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">65 </span></span>(<span itemprop="issueNumber">3</span>): <span itemprop="pagination">1313--1329</span></em> </span>(<em><span>Dezember 2019<meta content="Dezember 2019" itemprop="datePublished"/></span></em>)</span>Mon Dec 07 15:02:15 CET 2020Journal of Chemical {\&} Engineering Data1231313--1329Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering652019forschungsdaten hpc-computing metadata ontologie molecularSimulation Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering | Journal of Chemical & Engineering Datahttps://puma.ub.uni-stuttgart.de/bibtex/2c7971d8d6a474e4c5bf8a30d62d04ede/diglezakisdiglezakis2017-09-12T15:52:49+02:00framework forschungsdaten hpc-computing metadata software reproducibility softwareLizenzMotivation repository <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Giovanni Pizzi" itemprop="url" href="/person/18aa55fa398b71ec36da3eb98d8fff42e/author/0"><span itemprop="name">G. Pizzi</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Andrea Cepellotti" itemprop="url" href="/person/18aa55fa398b71ec36da3eb98d8fff42e/author/1"><span itemprop="name">A. Cepellotti</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Riccardo Sabatini" itemprop="url" href="/person/18aa55fa398b71ec36da3eb98d8fff42e/author/2"><span itemprop="name">R. Sabatini</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Nicola Marzari" itemprop="url" href="/person/18aa55fa398b71ec36da3eb98d8fff42e/author/3"><span itemprop="name">N. Marzari</span></a></span>, </span> und <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Boris Kozinsky" itemprop="url" href="/person/18aa55fa398b71ec36da3eb98d8fff42e/author/4"><span itemprop="name">B. Kozinsky</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Computational Materials Science</span>, </em> </span>(<em><span>2016<meta content="2016" itemprop="datePublished"/></span></em>)</span>Tue Sep 12 15:52:49 CEST 2017Computational Materials Science 218 - 230AiiDA: automated interactive infrastructure and database for computational science 1112016framework forschungsdaten hpc-computing metadata software reproducibility softwareLizenzMotivation repository Abstract Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from computer science to manage, preserve, and share these computational efforts. We illustrate here our paradigm sustaining such vision, based around the four pillars of Automation, Data, Environment, and Sharing. We then discuss its implementation in the open-source AiiDA platform (http://www.aiida.net), that has been tuned first to the demands of computational materials science. AiiDA’s design is based on directed acyclic graphs to track the provenance of data and calculations, and ensure preservation and searchability. Remote computational resources are managed transparently, and automation is coupled with data storage to ensure reproducibility. Last, complex sequences of calculations can be encoded into scientific workflows. We believe that AiiDA’s design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows.