PUMA publications for /user/diglezakis/hpc-computinghttps://puma.ub.uni-stuttgart.de/user/diglezakis/hpc-computingPUMA RSS feed for /user/diglezakis/hpc-computing2024-03-29T01:13:45+01:00DATENPOLITIK, OPEN SCIENCE
UND DATENINFRASTRUKTUREN: AKTUELLE
ENTWICKLUNGEN IM EUROPÄISCHEN RAUMhttps://puma.ub.uni-stuttgart.de/bibtex/2f449f1d02cc32a1ad8bcffb347297c7d/diglezakisdiglezakis2022-10-17T17:47:43+02:00dataSpaces eosc europa forschungsdaten gaiaX hpc-computing 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> (Eds.) </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 RAUM2022dataSpaces eosc europa forschungsdaten gaiaX hpc-computing politik Like a rainbow in the dark: metadata annotation for HPC applications in the age of dark datahttps://puma.ub.uni-stuttgart.de/bibtex/2a01fba3c690fedfaaa51e2be254cafb6/diglezakisdiglezakis2021-02-09T17:31:47+01:00automated forschungsdaten hpc-computing metadata tools <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 data2021automated forschungsdaten hpc-computing metadata tools 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.Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineeringhttps://puma.ub.uni-stuttgart.de/bibtex/2ab2ddb1039b00ff1b73c9ab682a82aae/diglezakisdiglezakis2020-12-07T15:02:15+01:00forschungsdaten hpc-computing metadata molecularSimulation ontologie <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> and 4 other author(s). </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Journal of Chemical & 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>December 2019<meta content="December 2019" itemprop="datePublished"/></span></em>)</span>Mon Dec 07 15:02:15 CET 2020Journal of Chemical {\&} Engineering Datadec31313--1329Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering652019forschungsdaten hpc-computing metadata molecularSimulation ontologie Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering | Journal of Chemical & Engineering DataAiiDA: automated interactive infrastructure and database for computational sciencehttps://puma.ub.uni-stuttgart.de/bibtex/2c7971d8d6a474e4c5bf8a30d62d04ede/diglezakisdiglezakis2017-09-12T15:52:49+02:00forschungsdaten framework hpc-computing metadata repository software softwareLizenzMotivation reproducibility <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> and <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 1112016forschungsdaten framework hpc-computing metadata repository software softwareLizenzMotivation reproducibility 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.