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add starting point for ISC'25 tutorial submission on CernVM-FS + EESSI
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2 changes: 2 additions & 0 deletions isc25/EESSI/Makefile
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all:
pdflatex main.tex
19 changes: 19 additions & 0 deletions isc25/EESSI/abstract.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?

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.

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.

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.
18 changes: 18 additions & 0 deletions isc25/EESSI/attendance.tex
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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.

%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)

% 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

% 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
12 changes: 12 additions & 0 deletions isc25/EESSI/audience.tex
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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}
92 changes: 92 additions & 0 deletions isc25/EESSI/cv-alan.tex
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%===============================================================================
% Alan
%===============================================================================

\subsection{CV for Alan \'O Cais}

\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}

\subsection*{Education}

\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}

\subsection*{Professional Experience}

\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}

\subsection*{Tools and Projects}

\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}

\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}

\subsection*{Selected Publications}

\paragraph{Conference Papers}

\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}

\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}

\paragraph{Journal Papers}

\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}

\newpage
99 changes: 99 additions & 0 deletions isc25/EESSI/cv-bob.tex
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%===============================================================================
% Bob
%===============================================================================

\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}

\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}

\subsection*{Professional Experience}
\begin{description}
\item[] 2011--present: HPC Expert, University of Groningen (The Netherlands)
\end{description}

\subsection*{Tools and Projects}

\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}

\subsection*{Conferences, Workshops and Tutorials}

\begin{itemize}

\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}}}

\end{itemize}

\subsection*{Selected Publications}

\paragraph{Conference Papers}

\begin{itemize}

\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).

\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).

\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.

\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.

\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).

\end{itemize}

\paragraph{Journal Articles}

\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. 2023,
\url{https://doi.org/10.1002/spe.3075}

\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}

\end{itemize}
81 changes: 81 additions & 0 deletions isc25/EESSI/cv-eli.tex
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%===============================================================================
% Eli
%===============================================================================

\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}

\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}

\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}

\subsection*{Tools and Projects}

\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}}}

\end{itemize}

\subsection*{Conferences, Workshops and Tutorials}

\begin{itemize}

\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.


\end{itemize}

\subsection*{Selected Publications}

\begin{itemize}

\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

\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}

\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



\end{itemize}
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