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FocusCoE - Newsletter #07
November 2020


1. Introduction

2. News from the Centres of Excellence

3. HiPEAC conference 2021 workshop: The HPC CoE services and applications

4. Introducing the CoE Flagship Codes

5. Trainings, Webinars, Workshops & Events

1. Introduction

Dear Reader,

With the start of CoEC, PerMedCoE, NOMAD and TREX at the beginning of October, there are now 14 European Centres of Excellence (CoEs) for High Performance Computing applications, promoting the use of upcoming extreme-scale and exascale computing capabilities and scaling up existing parallel codes towards exascale performance. We’re pleased to mention that we expect the start of a fifteenth CoE to be formally announced very soon!

In FocusCoE, we have decided to enhance our communication support for the CoEs by presenting their joint work and results on a single website that was launched a few weeks ago: The objective is to increase the visibility of the whole set of CoEs, document their combined impact and make it easier for interested parties to find their results and services. Information on the FocusCoE project is still there, but it’s in just one of the several areas of the new website.

Furthermore, we were quite active in recent weeks in find ways of supporting the CoEs in joint activities at (virtual) conferences and events. The plans for the near future include the CAE 2020 conference and our joint workshop at the HiPEAC '21 event.

Hope to meet you there, at least on screen - and now, enjoy reading!

Guy Lonsdale
FocusCoE Project Coordinator
scapos AG, Germany

2. News from the Centres of Excellence

BioExcel’s approach to targeting the RNA-dependent polymerase of SARS-CoV-2
>> Read More

BioExcel Facebook page launched >> Follow and like

Celebrating 5 years of BioExcel >> Read More
POP and ChEESE work together to improve Probabilistic Volcanic Hazard Assessment pilot demonstrator >> Read More

From research to societal relevance: How ChEESE and urgent computing may enhance INGV´s hazard forecasting >> Read More
Press release: New Centre of Excellence CoEC targets breakthroughs in combustion through Exascale computing >> Read More

Work with CoEC? Job openings for PhD students >> Read More
VECMA and CompBioMed join forces to predict the impact of COVID >> Read More

Publication: Papers originally submitted to the CompBioMed Conference 2019 have now been published via the Royal Society Interface Focus >> Read More
Comics & Science? The E-CAM issue: an experiment in dissemination >> Read More

E-CAM article on the EU Research Magazine >> Read More
Euronews panel discussion with ESiWACE work package leader Peter Dueben: "How can artificial intelligence help to fight climate change?" >> Watch on Youtube
Success Story: Towards an increased accuracy in the automotive field simulations >> Read More

Blog post: High-performance computing challenge: How can engineers effectively leverage HPC technology? >> Read More
Newsletter article: The Flu and Coronavirus Simulator (FACS) >> Read More [PDF]
Video repository: Learn more about the NOMAD Laboratory and its influence on and significance for materials science >> Read More
EXCELLERAT, MaX and POP at the International CAE Conference 2020 >> Read More
Press release: New CoE for Personalized Medicine launched >> Read More

Follow PerMedCoE on >> Twitter and >> LinkedIn
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588x and 488x Execution Time Speedups of a Volcanic Hazard Assessment Code >> Read More

Tool Time: memP - Parallel Heap Profiling >> Read More
Press Release: New CoE TREX to push research in quantum chemistry simulations a step further >> Read More

Follow TREX on >> LinkedIn

3. HiPEAC conference 2021 workshop: "The HPC CoE services and applications"

The goal of this workshop is to present the latest updates of services provided by several HPC CoEs including EXCELLERAT, EoCoE, ChEESE, HiDALGO, BioExcel and CompBioMed. Organized and supported by FocusCoE, this session will present the latest updates of these HPC CoEs to the HiPEAC community.

10:00 – 10:10 Welcome and FocusCoE introduction, Guy Lonsdale, Scapos
10:10 – 10:25 FPGAs and scientific computing: A match made in heaven?, Nick Brown (EPCC) EXCELLERAT
10:25 – 10:40 Renewable energy in the exascale era, Edouard Audit (CEA), EoCoE
10:40 – 10:55 The HPC synergy for Solid Earth Science, Arnau Folch (BSC) ChEESE
11:00 – 11:30 Coffee break (30min)
11:30 – 11:45 HPC and Big Data Technologies for Global Systems, Javi Nieto (ATOS) HiDALGO
11:45 – 12:00 Meeting User Needs in HPC: Why, What and How in the Life Sciences, Rossen Apostolov (KTH), BioExcel
12:00 – 12:15 Developing HPC services for the biomedical community, Marco Verdicchio, SURFsara – CompBioMed

12:30 – 12:50 Joint Co-Design panel
Chaired by: Guy Lonsdale, Scapos
* CompBioMed: Marco Verdicchio (SURFsara)
* Excellerat: Ivan Spisso (CINECA)
* ChEESE: Soline Laforet (Bull Atos)
* Hidalgo: Javi Nieto (Atos)
* BioExcel: Berk Hess (KTH)

12:50 – 13:00 Wrap-up and conclusions, Guy Lonsdale (Scapos)

Register to this event here:

4. Introducing the CoE Flagship Codes

HemoCell, developed by the team of Prof Alfons Hoekstra at the University of Amsterdam (NL), is a high-performance library to simulate the transport properties of dense cellular suspensions, such as blood. It contains validated material model for red blood cells and additional support for further cell types (white blood cells, platelets). HemoCell is computationally capable of handling a large domain size with a high number of cells (> 10^4-10^6 cells). The code is currently installed and optimised for Cartesius, Lisa, and SuperMUC (Leibniz Supercomputing Centre system), and can be used by anyone with a valid account and CPU allocation on any of these systems.

>> Read more about the HemoCell code
The OpenIFS programme at Centre for Medium-Range Weather Forecasts (ECMWF) provides academic and research institutions with an easy-to-use version of the ECMWF Integrated Forecasting System model (OpenIFS model), the single column model (SCM) and the offline-surface model (OSM). The OpenIFS model provides the full forecast capability of IFS, supporting software and documentation but without the data assimilation system. ESiWACE supports the integration of OpenIFS in the Earth System Model (EC-Earth) and thus allows a more frequent update of the atmospheric model component following the ECMWF model upgrades. Further, compute performance enhancements provided with OpenIFS in ESiWACE can be tested more easily within the EC-Earth framework.

>> Learn more about OpenIFS

5. Trainings, Webinars, Workshops & Events

Check out the trainings, webinars, workshops & events below, and visit the CoE Event Calendar for all future events.
30 November - 04 December, 2020:
Remote BioExcel Winter School on Biomolecular Simulations
Webinar Videos:
BioExcel Webinar #49: Molecular movies made easy with Molywood
BioExcel Webinar #50: Using competencies to guide training and professional development
02 December 2020:
E-seminar on Molecular visualisation using PyMOL
18 - 22 January 2021:
HPC for mesoscale simulation

15 - 19 March 2021
Simulation of open systems in Chemistry, Pharma, Food Science and Immuno-diagnostics: Rare-event methods at constant chemical potentials including constant pH
Webinar Video
EoCoE webinar: A64FX processor - streaming kernels and sparse matrix vector multiplication
05 - 08 July 2021
Minisymposium at PASC 21 - Extreme CFD for Engineering Applications
04 January 2021
Advanced School on Materials and molecular Modelling with Quantum ESPRESSO

06 - 09 July 2021
AiiDA School on High-throughput computing
01 - 02 December, 2020
Tutorial: NOMAD Materials Encyclopedia
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27 November, 2020
POP Webinar: PyPOP - An Interactive Tool for Performance Assessment

07 - 11 December, 2020
POP 37th VI-HPS Tuning Workshop
This newsletter is part of the project Focus CoE. Focus CoE has received funding from the European Union’s Horizon 2020 research and innovation programme under the grant agreement Nº 823964.
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