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add starting point for ISC'25 tutorial submission on CernVM-FS + EESSI
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all: | ||
pdflatex main.tex |
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What if there was a way to avoid having to install a broad range of scientific software from scratch on every HPC | ||
cluster or cloud instance you use or maintain, without compromising on performance? | ||
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Installing scientific software for supercomputers is known to be a tedious and time-consuming task. Especially as the | ||
HPC user community becomes more diverse, computational science expands rapidly, the diversity of system architectures | ||
increases the application software stack continues to deepen. Simultaneously, we see a surge in interest in cloud | ||
computing for scientific computing. Delivering optimised software installations and providing access to these | ||
installations in a reliable, user-friendly, and reproducible way is a highly non-trivial task that affects application | ||
developers, HPC user support teams, and the users themselves. | ||
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This tutorial aims to address these challenges by providing the attendees with the knowledge to stream optimised | ||
scientific software. For this, the tutorial introduces European Environment for Scientific Software Installations | ||
(\emph{EESSI}), a collaboration between various European HPC sites \& industry partners, with the common goal of | ||
creating a shared repository of scientific software installations that can be used on a variety of systems, regardless | ||
of which flavor/version of Linux distribution or processor architecture is used, or whether it’s a full size HPC | ||
cluster, a cloud environment or a personal workstation. | ||
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We cover the usage of EESSI, different ways to accessing EESSI, how to add software to EESSI, and highlight some more | ||
advanced features. We will also show how to engage with the community and contribute to the project. |
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Based on attendance at previous EESSI and EasyBuild events, including the yearly EasyBuild User Meetings (over 30 | ||
attendees in the last physical edition in 2023, close to 100 in 2021 and 2022 in an online setting) and previous | ||
related tutorials (PRACE-VI-SEEM 2017 Spring School with 25-30 attendees, a free online EasyBuild tutorial in June'20 | ||
with about 100 attendees, the half-day ISC'21 tutorial with over 25 attendees, and the in-person (half-day) ISC'22 | ||
EasyBuild tutorial with about 20 attendees, and an online EESSI tutorial in Dec'23 had over 130 registrations), we | ||
anticipate this EESSI tutorial to be well attended with 20-50 attendees. | ||
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%KH I would've gone with 50/25/25, but this works too (maybe better even) | ||
% MG: This was just a blind guess ;) | ||
%KH seems about right I think, we want to keep it beginner-oriented, 25% advanced may be too much... maybe 50/30/20 is less awkward? | ||
% I love how 'awkward' is such an awkward word to type... :D (no, haven't had beer yet) | ||
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% KH: Markus, I'm signing off for tonight... I'll be around tomorrow, definitely in the morning (have a student intern to keep busy in the afternoon, but I'll be around on Slack) | ||
%MG: Yea, I will also stop working soon | ||
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% KH: do we need anything from Maxime? It's probably good to tell him that now, since he'll only be around after 1-2pm tomorrow. | ||
%MG: For the submission, we'll need a short bio (some text) For Alan and the two of us, I will copy from last year unless I receive an update. | ||
% KH I already asked him for a bio. And a picture. I'll mail that too. => DONE |
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This tutorial is intended for | ||
\begin{itemize} | ||
\item End users who want to empower themselves to use a uniform software stack without compromising on | ||
performance, on top of what is provided centrally by the HPC support team; | ||
\item System managers, administrators and user support teams, responsible for the operational aspects of HPC systems and concerned about | ||
hardware optimised scientific software installations; | ||
% \item user support teams who need to provide a consistent central software stack for end users, and want to do so in | ||
% a reproducible way; | ||
\item Cloud and CI users, who want to use a common stack of optimised scientific software installations; | ||
\item System manufacturers and integrators interested in state-of-the-art software installation tools, who want to | ||
leverage the collective expertise incorporated in EasyBuild and EESSI. | ||
\end{itemize} |
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%=============================================================================== | ||
% Alan | ||
%=============================================================================== | ||
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\subsection{CV for Alan \'O Cais} | ||
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\begin{description} | ||
\item[] Centre Européen de Calcul Atomique et Moléculaire (CECAM) | ||
\item[] Avenue de Forel 2, BCH 3103 | ||
\item[] 1015 Lausanne, Switzerland | ||
\item[] [email protected] | ||
\end{description} | ||
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\subsection*{Education} | ||
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\begin{description} | ||
\item[] Ph.D Theoretical Physics, 2005, Trinity College Dublin (Ireland) | ||
\item[] M.Sc. High Performance Computing, 2002, Trinity College Dublin (Ireland) | ||
\item[] B.Sc. Theoretical Physics, 2001, Trinity College Dublin (Ireland) | ||
\end{description} | ||
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\subsection*{Professional Experience} | ||
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\begin{description} | ||
\item[] 2022 - present: Scientific Software Engineer with CECAM | ||
\item[] 2016 - 2021: E-CAM Centre of Excellence Software Manager at J\"ulich Supercomputing Centre (Germany) | ||
\item[] 2010 - 2016: Research Fellow at J\"ulich Supercomputing Centre (Germany) | ||
\item[] 2008 - 2010: Scientific Coordinator at The Cyprus Institute (Cyprus) | ||
\item[] 2006 - 2008: Research Fellow at University of Adelaide (Australia) | ||
\item[] 2005 - 2006: Research Fellow at Trinity College Dublin (Ireland) | ||
\end{description} | ||
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\subsection*{Tools and Projects} | ||
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\begin{itemize} | ||
\item[] \emph{MultiXscale EuroHPC Centre-of-Excellence} | ||
\\steering committee member, technical manager, and work package leader (2023--present) | ||
\\{\small{\url{https://www.multixscale.eu}}} | ||
\item[] \emph{European Environment for Scientific Software Installations (EESSI)} | ||
\\active contributor (2020--present) | ||
\\{\small{\url{https://eessi.io} - \url{https://eessi.io/docs}}} | ||
\item[] \emph{EasyBuild: (scientific) software build and installation framework} | ||
\\developer \& co-maintainer (2013--present) | ||
\\{\small{\url{https://easybuild.io} - \url{https://docs.easybuild.io}}} | ||
\end{itemize} | ||
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\subsection*{Conferences, Workshops and Tutorials} | ||
\begin{itemize} | ||
\item[] \emph{Streaming Optimised Scientific Software: an Introduction to EESSI}, online tutorial in context of | ||
MultiXscale EuroHPC CoE, co-organisor, December 2023 | ||
\\{\small{\url{https://github.com/EESSI/docs/tree/main/talks/20231205-Introduction-to-EESSI-CASTIEL2}}} | ||
\item[] \emph{Best Practices for CernVM-FS in HPC}, online tutorial in context of MultiXscale EuroHPC CoE, co-organisor, December 2023 | ||
\\{\small{\url{https://multixscale.github.io/cvmfs-tutorial-hpc-best-practices}}} | ||
\item[] \emph{Maintaining a Modern Scientific Software Stack Made Easy with EasyBuild} tutorial at ISC'21, June 2021 (\url{https://easybuild.io/tutorial}) | ||
\item[] Organiser of the first \emph{European HPC Training Stakeholder Workshop} (in coordination with the European Commission) | ||
\item[] Instructor at all E-CAM Centre of Excellence \emph{\href{https://www.e-cam2020.eu/events?tribe_paged=1&tribe_event_display=list&tribe-bar-date=2015-10-01&tribe-bar-search=Extended}{Extended Software Development Workshops}} | ||
\item[] Local organizer of the \emph{\href{https://github.com/easybuilders/easybuild/wiki/2nd-EasyBuild-User-Meeting}{2nd EasyBuild User Meeting (EUM'17)}}. J\"ulich. Germany. | ||
\item[]Invited instructor at PRACE seasonal training workshops: | ||
\begin{itemize} | ||
\item[] PRACE Autumn School in HPC Programming Techniques, Athens 25-28 November 2014: Lectures on Profiling and Optimization and Benchmarking | ||
\item[] PRACE Winter School, Tel Aviv 10-13 February 2014: Lectures on Profiling and Optimization and Benchmarking | ||
\item[] Joint HP-SEE, LinkSCEEM-2 and PRACE HPC Summer Training, Athens 13-15 July 2011: Lectures on Profiling and Optimization and Benchmarking | ||
\end{itemize} | ||
\end{itemize} | ||
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\subsection*{Selected Publications} | ||
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\paragraph{Conference Papers} | ||
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\begin{itemize} | ||
\item[] A. \'O Cais, P. Steinbach, \emph{Expanding user communities with HPC Carpentry}. Proceedings of the Workshop on HPC Education and Training for Emerging Technologies at ISC2019, Journal of Computational Science Education. 11. 21-25. | ||
\end{itemize} | ||
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\begin{itemize} | ||
\item[] D. Alvarez, A. O'Cais, M. Geimer, K. Hoste, \emph{Scientific Software Management in Real Life: Deployment of EasyBuild on a Large Scale System}. Proceedings of the 3rd International Workshop on HPC User Support Tools, Salt Lake City, USA, 2016. | ||
\end{itemize} | ||
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\paragraph{Journal Papers} | ||
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\begin{itemize} | ||
\item[] B. Dröge, V. Holanda Rusu, K. Hoste, C. van Leeuwen, A. O'Cais, T. Röblitz, \emph{{EESSI}: {A cross‐platform | ||
ready‐to‐use optimised scientific software stack}}. Software: Practice and Experience, 53(1):176-210, Jan. 2022, | ||
\url{https://doi.org/10.1002/spe.3075} | ||
\item[] MJT Oliveira, N Papior, Y Pouillon, V Blum, E Artacho,\dots, \emph{The {CECAM} electronic structure library and the modular software development paradigm}. | ||
J Chem Phys. 2020;153:024117 | ||
\item[] M.S. Mahbub, (Adelaide U. \& Rajshahi U.), Alan O'Cais, Waseem Kamleh, B.G. Lasscock, Derek B. Leinweber, Anthony G. Williams, \emph{Isolating Excited States of the Nucleon in Lattice QCD}, Phys.Rev.D80:054507,2009. | ||
\item[] M.S. Mahbub, (Adelaide U. \& Rajshahi U.) , Alan O'Cais, Waseem Kamleh, Ben G. Lasscock, Derek B. Leinweber, Anthony G. Williams, (Adelaide U.), \emph{Isolating the Roper Resonance in Lattice QCD}, Phys.Lett.B679:418-422,2009. | ||
\item[] Alexandrou, C., et al., \emph{Evaluation of fermion loops applied to the calculation of the n' mass and the nucleon scalar and electromagnetic form factors}, Computer Physics Communications 183.6 (2012): 1215-1224. | ||
\item[] J. Foley, K. Jimmy Juge, A. O'Cais, M. Peardon, S.M. Ryan and J. I. Skullerud, \emph{Practical all-to-all propagators for lattice QCD}, Comput. Phys. Commun. 172 (2005) 145. | ||
\end{itemize} | ||
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\newpage |
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%=============================================================================== | ||
% Bob | ||
%=============================================================================== | ||
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\subsection{CV for Bob Dr\"oge} | ||
\begin{description} | ||
\item[] Team HPC - Center for Information Technology - University of Groningen | ||
\item[] Nettelbosje 1, 9747 AJ Groningen | ||
\item[] The Netherlands | ||
\item[] [email protected] | ||
\end{description} | ||
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\subsection*{Education} | ||
\begin{description} | ||
\item[] M.Sc. Computing Science (Computational Science and Visualization), 2011, University of Groningen (The Netherlands) | ||
\item[] B.Sc. Applied Mathematics, 2009, University of Groningen (The Netherlands) | ||
\item[] B.Sc. Computing Science, 2008, University of Groningen (The Netherlands) | ||
\end{description} | ||
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\subsection*{Professional Experience} | ||
\begin{description} | ||
\item[] 2011--present: HPC Expert, University of Groningen (The Netherlands) | ||
\end{description} | ||
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\subsection*{Tools and Projects} | ||
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\begin{itemize} | ||
\item[] \emph{MultiXscale EuroHPC Centre-of-Excellence} | ||
\\project partner and task leader (2023--present) | ||
\\{\small{\url{https://www.multixscale.eu}}} | ||
\item[] \emph{European Environment for Scientific Software Installations (EESSI)} | ||
\\active contributor (2020--present) | ||
\\{\small{\url{https://eessi.io} - \url{https://eessi.io/docs}}} | ||
\item[] \emph{EasyBuild: (scientific) software build and installation framework} | ||
\\maintainer and active contributor (2016--present) | ||
\\{\small{\url{https://easybuild.io} - \url{https://docs.easybuild.io}}} | ||
\item[] \emph{Euclid: ESA mission to explore the dark Universe} | ||
\\developer, system administrator, work package lead for SDC-NL infrastructure (2012--present) | ||
\\{\small{\url{https://www.esa.int/Science_Exploration/Space_Science/Euclid}}} | ||
\end{itemize} | ||
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\subsection*{Conferences, Workshops and Tutorials} | ||
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\begin{itemize} | ||
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\item[] \emph{One scientific software stack for all systems, that's EESSI}, talk at SURF Advanced Computing User Day, December 2023, | ||
\\{\small{\url{https://www.surf.nl/en/agenda/advanced-computing-user-day}}} | ||
\item[] \emph{Best Practices for CernVM-FS in HPC}, online tutorial in context of MultiXscale EuroHPC CoE, co-organisor, December 2023 | ||
\\{\small{\url{https://multixscale.github.io/cvmfs-tutorial-hpc-best-practices}}} | ||
\item[] \emph{EESSI: One Scientific Software Stack to Rule Them All}, Talk at FOSDEM'21, February 2021 | ||
\\{\small{\url{https://archive.fosdem.org/2021/schedule/event/eessi/}}} | ||
\item[] co-organisaton of FOSDEM devroom on \emph{HPC, Big Data \& Data Science} (2021), | ||
\url{https://archive.fosdem.org/2021/schedule/track/hpc_big_data_and_data_science} | ||
\item[] \emph{Introduction to CernVM-FS}, online tutorial, co-presenter, January 2021 | ||
\\{\small{\url{https://cvmfs-contrib.github.io/cvmfs-tutorial-2021}}} | ||
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\end{itemize} | ||
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\subsection*{Selected Publications} | ||
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\paragraph{Conference Papers} | ||
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\begin{itemize} | ||
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\item[] O.R. Williams, K. Begeman, D. Boxhoorn, B. Dröge, T.A. Nutma, A. Tsyganov, E.A. Valentijn, W.-J. Vriend, C. Dabin, | ||
\emph{The Euclid Archive Processing and Data Distribution Systems: A Distributed Infrastructure for Euclid and Associated Data}. | ||
Proceedings of the 29th annual conference on Astronomical Data Analysis Software and Systems (ADASS XXIX, Oct 2019). | ||
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\item[] A. Belikov, O. Williams, B. Altieri, D. Boxhoorn, G. Buenadicha, B. Dröge, J. McFarland, S. Nieto, J. Salgado, P. de Teodoro, A. Tsyganov, E. Valentijn, | ||
\emph{The Euclid Archive System: A Datacentric Approach to Big Data}. | ||
Proceedings of 2016 conference on Big Data from Space (BiDS'16). | ||
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\item[] O.R. Williams, K. Begeman, D. Boxhoorn, B. Dröge, A. Tsyganov, J.P. McFarland, E.A. Valentijn, W.J. Vriend, C. Dabin, | ||
\emph{The Role of the Euclid Archive System in the Processing of Euclid and External Data}. | ||
Astronomical Data Analysis Software and Systems XXVI ASP Conference Series, Vol. 521, proceedings of a conference held (16-20 October 2016) at Stazione Marittima Conference Centre, Trieste, Italy. | ||
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\item[] B. Dröge, L. van der Meulen, G. Schoof, | ||
\emph{How far do Dutch people live from attractive nature? An assessment using parallel computing with Python and FOSS4G libraries}. | ||
Geomatics Workbooks : FOSS4G Europe Como 2015. | ||
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\item[] A. Belikov, O. Williams, B. Dröge, A. Tsyganov, D. Boxhoorn, J. McFarland, G. Verdoes Kleijn, E. Valentijn, B. Altieri, C. Dabin, F. Pasian, P. Osuna, | ||
\emph{Euclid Archive System Prototype}. | ||
Proceedings of the 2014 conference on Big Data from Space (BiDS’14). | ||
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\end{itemize} | ||
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\paragraph{Journal Articles} | ||
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\begin{itemize} | ||
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\item[] B. Dröge, V. Holanda Rusu, K. Hoste, C. van Leeuwen, A. O'Cais, T. Röblitz, \emph{{EESSI}: {A cross‐platform | ||
ready‐to‐use optimised scientific software stack}}. Software: Practice and Experience, 53(1):176-210, Jan. 2023, | ||
\url{https://doi.org/10.1002/spe.3075} | ||
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\item[] V. Codreanu, B. Dröge, D. Williams, B. Yasar, F. Yang, B. Liu, F. Dong, O. Surinta, L. Schomaker, J. Roerdink, M. Wiering, \emph{Evaluating automatically parallelized versions of the support vector machine}. | ||
Concurrency Computat.: Pract. Exper., 28: 2274-2294, 2016, | ||
\url{https://doi.org/10.1002/cpe.3413} | ||
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\end{itemize} |
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%=============================================================================== | ||
% Eli | ||
%=============================================================================== | ||
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\subsection{CV for Elisabeth Ortega} | ||
\begin{description} | ||
\item[] HPCNow! | ||
\item[] Carrer de Marie Curie, 8, 14, Nou Barris, 08042 Barcelona | ||
\item[] [email protected] | ||
\end{description} | ||
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\subsection*{Education} | ||
\begin{description} | ||
\item[] Master in Quantum Computing, 2024, Universidad Internacional de la Rioja (Spain) | ||
\item[] PhD in Theoretical and Computational Chemistry, 2015, Universitat Autònoma de Barcelona (Spain) | ||
\item[] BsC in Computer Science, 2015, Universitat Oberta de Catalunya (Spain) | ||
\item[] Masters in Theoretical and Computational Chemistry, 2011, Universitat Rovira i Virgili (Spain) | ||
\item[] BsC in Chemistry, 2009, Universitat Autònoma de Barcelona (Spain) | ||
\end{description} | ||
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\subsection*{Professional Experience} | ||
\begin{description} | ||
\item[] 2022--present: R\&D\&i Manager, HPCNow! (Spain) | ||
\item[] 2018--2024: Assistant Professor in Master of Bioinformatics, Universitat Oberta de Catalunya (Spain) | ||
\item[] 2017--2022: Field Applications Scientist \& Product Owner, Lead Molecular Design (Spain) | ||
\item[] 2015--2017: Software Developer, Lead Molecular Design (Spain) | ||
\item[] 2014--2015: HPC System Administrator, Universitat Autònoma de Barcelona (Spain) | ||
\item[] 2009--2014: PhD Student, Universitat Autònoma de Barcelona (Spain) | ||
\end{description} | ||
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\subsection*{Tools and Projects} | ||
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\begin{itemize} | ||
\item[] \emph{Women in HPC MAR Chapter} | ||
\\Co-founder (2023--present) | ||
\\{\small{\url{https://www.multixscale.eu}}} | ||
\item[] \emph{MultiXscale EuroHPC Centre-of-Excellence} | ||
\\steering comitee member and work package leader (2023--present) | ||
\\{\small{\url{https://www.multixscale.eu}}} | ||
\item[] \emph{Bio Network for training} | ||
\\steering comitee member and work package leader (2023--present) | ||
\\{\small{\url{https://www.biont-training.eu}}} | ||
\item[] \emph{HEROES} | ||
\\project member and work package leader {2022--2023} | ||
\\{\small{\url{https://www.heroes-project.eu}}} | ||
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\end{itemize} | ||
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\subsection*{Conferences, Workshops and Tutorials} | ||
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\begin{itemize} | ||
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\item[] \emph{Bridging the gap between desktop computers and HPC with Open OnDemand}, talk and demo at the 17th Red Española de | ||
Supercomputación Users conference, September 2023. | ||
\item[] \emph{Getting your scientific software everywhere without compromising on performance was never that EESSI}, talk and demo in | ||
Azure booth at ISC-HPC 23, May 2023. | ||
\item[] \emph{HPC in quantum era}, talk in HPCKP Meeting, May 2023. | ||
\item[] \emph{Playing with quantum computers without quantum computers}, talk at the 16th Red Española de Supercomputación | ||
Users conference, September 2022. | ||
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\end{itemize} | ||
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\subsection*{Selected Publications} | ||
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\begin{itemize} | ||
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\item[] Stefano Bonciarelli, Jenny Desantis, Laura Goracci, Lydia Siragusa, Ismael Zamora, Elisabeth Ortega-Carrasco, | ||
\emph{Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase}. | ||
Journal of Chemical Information and Modeling, 61(6):1706-2719, 2021 | ||
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\item[] Victor Munoz Robles, Elisabeth Ortega-Carrasco, Lur Alonso-Cotchico, Jaime Rodriguez-Guerra, Agusti Lledos, Jean-Didier Marechal, \emph{Toward the computational design of artificial metalloenzymes: | ||
From protein–ligand docking to multiscale approaches}. ACS Catalysis, 5(4):2469-2480, 2015, | ||
\url{https://doi.org/10.1021/acscatal.5b00010} | ||
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\item[] Elisabeth Ortega‐Carrasco, Agusti Lledós, Jean‐Didier Maréchal, \emph{Assessing protein–ligand docking for the binding of organometallic compounds to proteins}. | ||
Journal of Computational Chemistry, 35(3):192.198, 2014 | ||
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\end{itemize} |
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