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FocusCoE Hosts Intel OneAPI Workshop for the EU HPC CoEs
On March 2, 2022 FocusCoE hosted Intel for a workshop introducing the oneAPI development environment. In all, over 40 researchers representing the EU HPC Centres of Excellence (CoEs)were able to attend the single day workshop to gain an overview of OneAPI. The 8 presenters from Intel gave presentations through the day covering the OneAPI vision, design, toolkits, a use case with GROMACS (which is already used by some of the EU HPC CoEs), and specific tools for migration and debugging.
Launched in 2019, the Intel OneAPI cross-industry, open, standards-based unified programming model is being designed to deliver a common developer experience across accelerator architectures. With the time saved designing for specific accelerators, OneAPI is intended to enable faster application performance, more productivity, and greater innovation. As summarized on Intel’s OneAPI website, “Apply your skills to the next innovation, and not to rewriting software for the next hardware platform.” Given the work that EU HPC CoEs are currently doing to optimise codes for Exascale HPC systems, any tools that make this process faster and more efficient can only boost CoEs capacity for innovation and preparedness for future heterogeneous systems.
The OneAPI industry initiative is also encouraging collaboration on the oneAPI specification and compatible oneAPI implementations. To that end, Intel is investing time and expertise into events like this workshop to give researchers the knowledge they need not only to use but help improve OneAPI. The presenters then also make themselves available after the workshop to answer questions from attendees on an ongoing basis. Throughout our event, participants were continuously able to ask questions and get real-time answers as well as offers for further support from software architects, technical consulting engineers, and the researcher who presented a use case. Lastly, the full video and slides from presentations are available below for any CoEs who were unable to attend or would like a second look at the detailed presentations.

SIMAI 2021
The 2020 edition of the bi-annual congress of the Italian Society of Applied and Industrial Mathematics (SIMAI) has been held in Parma, hosted by the University of Parma, from August 30 to September 3, 2021, in a hybrid format (physical and online). The conference aimed to bring together researchers and professionals from academia and industry that are active in the study of mathematical and numerical models and their application to industry and general real-life problems, stimulate interdisciplinary research in applied mathematics, and foster interactions between the scientific community and industry. Six plenary lectures have been covering a wide range of topics. In this edition, a posters session was also organized to broaden the opportunity to disseminate the results of interesting research. A large part of the conference was dedicated to minisymposia, autonomously organized around specific topics by their respective promoters. Furthermore, an Industrial Session gathering together both academic and industrial researchers was organized, particularly with more than 70 industry representatives focusing on mathematical problems encountered in R&D areas.
Within the SIMAI conference, the minisymposium on HPC, European High-Performance Scientific Computing: Opportunities and Challenges for Applied Mathematics” was organized by ENEA within the framework of project FocusCoE, and a contribution to the aforementioned Industrial Session was given through a talk on results on Hydropower production modelling obtained by project EoCoE. In the minisymposium agenda of 3th of September (9:30-12:00), five presentations (20 min + 5 min Q) have been made from CoEs representatives: Ignatio Pagonabarraga (CoE: E-CAM), Alfredo Buttari (CoE: EoCoE), Francesco Buonocore (CoE: EoCoE), Pasqua D’Ambra (CoEs: EoCoE. EUROHPC project:TEXTAROSSA), Tomaso Esposti Ongaro (CoE: ChEESE). The number of sustained participants has been ca. 25.
The FocusCoE contribution within the industrial session of September 1 (17:50-18:15) has been made through a talk of prof. Bruno Majone (CoEs: EoCoE) presented by Andrea Galletti (CoEs: EoCoE) titled “Detailed hydropower production modelling over large-scale domains: the HYPERstreamHS framework”.
CoEs at Teratec Forum 2021 and ISC21
With the support of FocusCoE, a number of HPC CoEs will give short presentations at the virtual PRACE booth in the following two HPC-related events: Teratec Forum 2021 and ISC2021 that will take place towards the end of this month. See the schedule below for more details. Please reserve the slots in your calendars, registration details will be provided on the PRACE website soon!
“We are happy to see that FocusCoE was able to help the HPC CoEs to have a significant presence at this year’s editions of ISC and Teratec Forum, two major HPC events, enabled through our good synergies with PRACE”, says Guy Lonsdale, FocusCoE coordinator.
Teratec Forum 2021 schedule
Date / Event | Time slot CEST | Title | Speaker | Organisation |
Tue 22 June | 11:00 – 11:15 | EoCoE-II: Towards exascale for Energy | Edouard Audit, EoCoE-II coordinator | CEA (France) |
| 14:30 – 14:45 | POP CoE: Free Performance Assessments for the HPC Community | Bernd Mohr | Jülich Supercomputing Centre |
Thu 24 June | 13:45 – 14:00 | EXCELLERAT – paving the way for the evolution towards Exascale | Amgad Dessoky / Sophia Honisch | HLRS |
ISC 2021 schedule
Date / Event | Time slot CEST | Title | Speaker | Organisation |
Thu 24 June | 13:45 – 14:00 | EXCELLERAT – paving the way for the evolution towards Exascale | Amgad Dessoky / Sophia Honisch | HLRS |
Fri 25 June | 11:00 – 11:15 | The Center of Excellence for Exascale in Solid Earth (ChEESE) | Alice-Agnes Gabriel | Geophysik, University of Munich |
| 15:30 – 15:45 | EoCoE-II: Towards exascale for Energy | Edouard Audit, EoCoE-II coordinator | CEA (France) |
Tue 29 June | 11:00 – 11:15 | Towards a maximum utilization of synergies of HPC Competences in Europe | Bastian Koller, HLRS | HLRS |
Wed 30 June | 10:45 -11:00 | CoE | Dr.-Ing. Andreas Lintermann | Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH |
Thu 1 July | 11:00 -11:15 | POP CoE: Free Performance Assessments for the HPC Community | Bernd Mohr | Jülich Supercomputing Centre |
| 14:30 -14:45 | TREX: an innovative view of HPC usage applied to Quantum Monte Carlo simulations | Anthony Scemama (1), William Jalby (2), Cedric Valensi (2), Pablo de Oliveira Castro (2) | (1) Laboratoire de Chimie et Physique Quantiques, CNRS-Université Paul Sabatier, Toulouse, France (2) Université de Versailles St-Quentin-en-Yvelines, Université Paris Saclay, France |
Please register to the short presentations through the PRACE event pages here:
PRACE Virtual booth at Teratec Forum 2021 | PRACE Virtual booth at ISC2021 |
prace-ri.eu/event/teratec-forum-2021/ | prace-ri.eu/event/praceisc-2021/ |
List of innovations by the CoEs, spotted by the EU innovation radar


Title: Biobb, biomolecular modelling building Blocks |
Market maturity: Exploring |
Project: BioExcel |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF MANCHESTER – UNITED KINGDOM |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA) – SPAIN |
Title: GROMACS, a versatile package to perform molecular dynamics |
Market maturity: Exploring |
Project: BioExcel |
Innovation Topic: Excellent Science |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
Title: HADDOCK, a versatile information-driven flexible docking approach for the modelling of biomolecular complexes |
Market maturity: Exploring |
Project: BioExcel |
Innovation Topic: Excellent Science |
UNIVERSITEIT UTRECHT – NETHERLANDS |
Title: PMX, a versatile (bio-) molecular structure manipulation package |
Market maturity: Exploring |
Project: BioExcel |
Innovation Topic: Excellent Science |
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV – GERMANY |

Title: Faster Than Real Time (FTRT) environment for high-resolution simulations of earthquake generated tsunamis |
Market maturity: Tech ready |
Market creation potential: High |
Project: ChEESE |
Innovation Topic: Excellent Science |
UNIVERSIDAD DE MALAGA – SPAIN |
TECHNISCHE UNIVERSITAET MUENCHEN – GERMANY |
ISTITUTO NAZIONALE DI GEOFISICA E VULCANOLOGIA – ITALY |
Title: Probabilistic Seismic Hazard Assessment (PSHA) |
Market maturity: Exploring |
Project: ChEESE |
Innovation Topic: Excellent Science |
LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN – GERMANY |
TECHNISCHE UNIVERSITAET MUENCHEN – GERMANY |
ISTITUTO NAZIONALE DI GEOFISICA E VULCANOLOGIA – ITALY |
Title: Urgent Computing services for the impact assessment in the immediate aftermath of an earthquake |
Market maturity: Tech Ready |
Market creation potential: High |
Project: ChEESE |
Innovation Topic: Excellent Science |
EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH – SWITZERLAND |
BULL SAS – FRANCE |

Title: Alya, HemeLB, HemoCell, OpenBF, Palabos-Vertebroplasty simulator, Palabos – Flow Diverter Simulator, BAC, HTMD, Playmolecule, Virtual Assay, CT2S, Insigneo Bone Tissue Suit |
Market maturity: Exploring |
Project: CompBioMed |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
UNIVERSITY COLLEGE LONDON – UNITED KINGDOM |
ACELLERA LABS SL – SPAIN |

Title: E-CAM software repository |
Market maturity: Exploring |
Project: E-CAM |
Innovation Topic: Excellent Science |
ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE – SWITZERLAND |
UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN – IRELAND |
UNITED KINGDOM RESEARCH AND INNOVATION – UNITED KINGDOM |
Title: E-CAM Training offer on effective use of HPC simulations in quantum chemistry |
Market maturity: Exploring |
Project: E-CAM |
Innovation Topic: Excellent Science |
ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE – SWITZERLAND |
UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN – IRELAND |
FREIE UNIVERSITAET BERLIN – GERMANY |
Title: Improved Simulation Software Packages for Molecular Dynamics |
Market maturity: Exploring |
Project: E-CAM |
Innovation Topic: Excellent Science |
SCIENCE AND TECHNOLOGY FACILITIES COUNCIL – UNITED KINGDOM |
TECHNISCHE UNIVERSITAET WIEN – AUSTRIA |
UNIVERSITEIT VAN AMSTERDAM – NETHERLANDS |
Title: Improved software modules for Meso– and multi–scale modelling |
Market maturity: Exploring |
Project: E-CAM |
Innovation Topic: Excellent Science |
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV – GERMANY |
FREIE UNIVERSITAET BERLIN – GERMANY |

Title: Code auditing, optimization and performance assessment services for energy-oriented HPC simulations |
Market maturity: Exploring |
Project: EoCoE |
Innovation Topic: Excellent Science |
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV – GERMANY |
FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V. – GERMANY |
Title: Consultancy Services for using HPC Simulations for Energy related applications |
Market maturity: Exploring |
Project: EoCoE |
Innovation Topic: Excellent Science |
COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES – FRANCE |
FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V. – GERMANY |

Table: New coupled earth system model |
Market maturity: Tech Ready |
Project: ESiWACE |
Innovation Topic: Excellent Science |
BULL SAS – FRANCE |
MET OFFICE – UNITED KINGDOM |
EUROPEAN CENTRE FOR MEDIUM-RANGE WEATHER FORECASTS – UNITED KINGDOM |

Title:AMR capability and Accelerated Computing in AVBP code |
Market maturity: Exploring |
Project: EXCELLERAT |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
CERFACS CENTRE EUROPEEN DE RECHERCHE ET DE FORMATION AVANCEE EN CALCUL SCIENTIFIQUE SOCIETE CIVILE – FRANCE |
Title: AMR capability in Alya code to enable advanced simulation services for engineering |
Market maturity: Tech Ready |
Project: Excellerat |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
Title: Data Exchange & Workflow Portal: secure, fast and traceable online data transfer between data generators and HPC centers |
Market maturity: Tech Ready |
Market creation potential: High |
Project: Excellerat |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
Title: FPGA Acceleration for Exascale Applications based on ALYA and AVBP codes |
Market maturity: Tech Ready |
Market creation potential: Noteworthy |
Project: Excellerat |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
Title: Open source mode decomposition toolkit for exascale data analysis |
Market maturity: Tech Ready |
Project: Excellerat |
Innovation Topic: Excellent Science |
RHEINISCH-WESTFAELISCHE TECHNISCHE HOCHSCHULE AACHEN – GERMANY |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
SSC SERVICES GMBH – GERMANY |
Title:Use of GASPI to improve performance of CODA |
Market maturity: Tech Ready |
Project: Excellerat |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
Title: GPU acceleration in TPLS to exploit the GPU-based architectures for Exascale |
Market maturity: Tech Ready |
Project: Excellerat |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
Title: In-Situ Analysis of CFD Simulations |
Market maturity: Tech Ready |
Market creation potential: High |
Project: Excellerat |
Innovation Topic: Excellent Science |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V. – GERMAN |
Title: Interactive in situ visualization in VR |
Market maturity: Tech Ready |
Market creation potential: High |
Project: Excellerat |
Innovation Topic: Excellent Science |
UNIVERSITY OF STUTTGART – GERMANY |
Title: Machine Learning Methods for Computational Fluid Dynamics (CFD) Data |
Market maturity: Tech Ready |
Market creation potential: Noteworthy |
Project: Excellerat |
Innovation Topic: Excellent Science |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |
FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V. – GERMAN |
Title: Parallel I/O in TPLS using PETSc library |
Market maturity: Tech Ready |
Project: Excellerat |
Innovation Topic: Excellent Science |
THE UNIVERSITY OF EDINBURGH – UNITED KINGDOM |
RHEINISCH-WESTFAELISCHE TECHNISCHE HOCHSCHULE AACHEN – GERMANY |
KUNGLIGA TEKNISKA HOEGSKOLAN – SWEDEN |

Title: Highly scalable Material Science Simulation Codes |
Market maturity: Exploring |
Project: MaX |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
E4 COMPUTER ENGINEERING SPA – ITALY |
Title: Quantum Simulation as a Service |
Market maturity: Exploring |
Market creation potential: Noteworthy |
Project: MaX |
Innovation Topic: Excellent Science |
EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH – SWITZERLAND |
CINECA CONSORZIO INTERUNIVERSITARIO – ITALY |
Title: Simulation Code Optimisation and Scaling |
Market maturity: Exploring |
Project: MaX |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH – SWITZERLAND |

Title: Novel Materials Discovery (NOMAD) Repository |
Market maturity: Business Ready |
Project: NoMaD |
Innovation Topic: Excellent Science |
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV – GERMANY |
HUMBOLDT-UNIVERSITAET ZU BERLIN – GERMANY |
BAYERISCHE AKADEMIE DER WISSENSCHAFTEN – GERMANY |
Title: NOMAD Encyclopedia Service: allows users to see, compare, explore, and understand computed materials data |
Market maturity: Tech Ready |
Project: NoMaD |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV – GERMANY |
HUMBOLDT-UNIVERSITAET ZU BERLIN – GERMANY |
Title: An ICT platform prototype for systematically tracing public sentiment, its evolution towards a policy, its components and arguments linked to them. |
Market maturity: Tech Ready |
Project: NOMAD |
Innovation Topic: Smart & Sustainable Society |
ATHENS TECHNOLOGY CENTER ANONYMI BIOMICHANIKI EMPORIKI KAI TECHNIKI ETAIREIA EFARMOGON YPSILIS TECHNOLOGIAS – GREECE |
NATIONAL CENTER FOR SCIENTIFIC RESEARCH “DEMOKRITOS” – GREECE |
CRITICAL PUBLICS LTD – UNITED KINGDOM |

Title: Customer-Specific Performance Analysis for Parallel Codes |
Market maturity: Exploring |
Project: POP |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
UNIVERSITAET STUTTGART – GERMANY |
Title: Repository of powerful tools (codes, pattern/best-practice descriptions, experimental results) for the HPC community |
Market maturity: Exploring |
Project: POP |
Innovation Topic: Excellent Science |
BARCELONA SUPERCOMPUTING CENTER – CENTRO NACIONAL DE SUPERCOMPUTACION – SPAIN |
TERATEC – FRANCE |
E-CAM: Industry training at the MESOSCALE
To further expand the portfolio of activities targeted at industrialists, E-CAM has established a series of new events targeted at training interested industrial researchers on the simulation and modelling techniques implemented in specific codes and in the direct use of this software for their industrial applications.
The first event of this series will focus on the area of meso- and multiscale simulations and on the flagship code DL_MESO:

Industry Training at the MESOSCALE
22nd – 25th March 2021
Online / UKRI STFC Daresbury Laboratory
Website: https://www.cecam.org/workshop-details/1074
In this workshop we will introduce DL_MESO: a software package for mesoscale simulations. Usage of the software will be gradually presented, starting with tutorials based on theoretical background and following up with hands-on sessions. We will focus on the Dissipative Particle Dynamics (DPD) methodology, exploring the different capabilities of DL_MESO_DPD via practical examples that reflect daily industrial challenges.
DL_MESO has been used for a wide range of problems of both scientific and industrial interest. The code is used, for example, in projects with Unilever, Syngenta and Infineum – to develop DPD parameterisation strategies and simulation protocols to predict important properties of newly-devised surfactant-based formulations; with IBM Research Europe – to model nanofluidic multiphase. The code developers themselves will provide the training. The event is co-organized by Formeric, a company that helps industrial users to study their own formulated projects, primarily by developing a software platform to make it easier for them to access DPD simulations and modelling tools.
As part of the event, UKRI STFC offers a 6-month one seat free licence of DL_MESO 2.7 to be used soon after the end of the event, which will help testing the software.
Don’t miss this opportunity to be trained by the experts on the methods and on the codes themselves! Register for event at
www.cecam.org/workshop-details/1074/
[su_button url=”https://www.e-cam2020.eu/wp-content/uploads/2021/02/Flyer_E-CAM_STFC_event.pdf” size=”14″]Download event flyer[/su_button]
January Module of the Month: MaZe, Mass-Zero Constrained Dynamics for Orbital Free Density Functional Theory
Description
The program performs Orbital-Free Density Functional Theory Molecular Dynamics (OF-DFT-MD) using the Mass-Zero (MaZe) constrained molecular dynamics approach described in [1].
This method enforces, at each time step, the Born-Oppenheimer condition that the system relaxes instantaneously to the ground state through the formalism of massless constraints. The adiabatic separation between the degrees of freedom is enforced rigorously, and the algorithm is symplectic and time-reversible in both physical and additional set of degrees of freedom.
The computation of the electronic density is carried out in reciprocal space through a plane-waves expansion so that the mass-zero degrees of freedom are associated to the Fourier coefficients of the electronic density field. The evolution of the ions is performed using Velocity-Verlet algorithm, while the SHAKE algorithm is used for computation of the additional degrees of freedom. The code can sample the NVE and the NVT ensemble, the latter through a Langevin thermostat.
The code was optimised to run on HPC machines, as explained in the software documentation. The proposed optimisations allow a reduction of the execution time by roughly 50% compared to the original version of the code.

Practical application
The code is intended for condensed matter physicists and for material scientists and it can be used for various purposes related to the subject. Even though some analysis tools are included in the package, the main goal of the software is to produce particles trajectories to be analysed in post-production by means of external software.
MaZe implements the orbital-free formulation of density functional theory, in which the optimisation of the energy functional is performed directly in terms of the electronic density without use of Kohn-Sham orbitals. This feature avoids the need for satisfying the orthonormality constraint among orbitals and allows the computational complexity of the code to scale linearly with the dimensionality of the system. The accuracy of the simulation relies on the choice of the kinetic energy functional, which has to be provided in terms of the electronic density alone.
Documentation and source code
The complete documentation is at this location. The source code is available from the E-CAM Gitlab under the MaZe project (software is under embargo until publication leveraging the developments is achieved. Contact code developers or info@e-cam2020.eu for more information.)
References
[1] Sara Bonella, Alessandro Coretti, Rodolphe Vuilleumier, Giovanni Ciccotti, “Adiabatic motion and statistical mechanics via mass-zero constrained dynamics”, Phys. Chem. Chem. Phys. 2020, 22, 10775-10785 DOI: 10.1039/D0CP00163E
Pre-print version (open access): https://arxiv.org/abs/2001.03556
Mesoscale simulation of billion atom complex systems using thousands of GPGPUS's
Short description
Results & Achievements
Objectives


Use Case Owner
Dr. Jony Castagna, computer scientist at UKRI STFC Daresbury Laboratory, E-CAM programmer
E-CAM Newsletter December 2020



How EU projects work on supercomputing applications to help contain the corona virus pandemic
The Centres of Excellence in high-performance computing are working to improve supercomputing applications in many different areas: from life sciences and medicine to materials design, from weather and climate research to global system science. A hot topic that affects many of the above-mentioned areas is, of course, the fight against the corona virus pandemic.
There are rather obvious challenges for those EU projects that are developing HPC applications for simulations in medicine or in the life sciences, like CompBioMed (Biomedicine) BioExcel (Biomolecular Research), and PerMedCoE (Personalized Medicine). But also other projects from scientific areas, that you would, at first sight, not directly relate to research on the pandemic, are developing and using appropriate applications to model the virus and its spread, and support policy makers with computing-heavy simulations. For example, did you know that researchers can simulate the possible spread of the virus on a local level, taking into account measures like closing shops or quarantining residents?
This article gives an overview over the various ways in which EU projects are using supercomputing applications to tackle and support the global challenge of containing the pandemic.
Simulations for better and faster drug development
CompBioMed is an EU-funded project working on applications for computational biomedicine. It is part of a vast international consortium across Europe and USA working on urgent coronavirus research. “Modelling and simulation is being used in all aspects of medical and strategic actions in our fight against coronavirus. In our case, it is being harnessed to narrow down drug targets from billions of candidate molecules to a handful that can be clinically trialled”, says Peter Coveney from University College London (UCL) who is heading CompBioMed’s efforts in this collaboration. The goal is to accelerate the development of antiviral drugs by modelling proteins that play critical roles in the virus life cycle in order to identify promising drug targets.
Secondly, for drug candidates already being used and trialled, the CompBioMed scientists are modelling and analysing the toxic effects that these drugs may have on the heart, using supercomputing resources required to run simulations on such scales. The goal is to assess the drug dosage and potential interactions between drugs to provide guidance for their use in the clinic.
Finally, the project partners analysed a model used to inform the UK Government’s response to the pandemic. It has been found to contain a large degree of uncertainty in its predictions, leading it to seriously underestimate the first wave. “Epidemiological modelling has been and continues to be used for policy-making by governments to determine healthcare interventions”, says Coveney. “We have investigated the reliability of such models using HPC methods required to truly understand the uncertainty and sensitivity of these models.” As a conclusion, a better public understanding of the inherent uncertainty of models predicting COVID-19 mortality rates is necessary, saying they should be regarded as “probabilistic” rather than being relied upon to produce a particular and specific outcome.
Researchsquare: Model uncertainty and decision making: Predicting the Impact of COVID-19 Using the CovidSim Epidemiological Code
Arxiv.org: Scalable HPC and AI Infrastructure for COVID-19 Therapeutics
Arxiv.org: IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads
BioExcel is an EU-funded project developing some of the most popular applications for modelling and simulations of biomolecular systems. Along with code development, the project builds training programmes to address competence gaps in extreme-scale scientific computing for beginners, advanced users and system maintainers.
When COVID-19 struck, BioExcel launched a series of actions to support the community on SARS-CoV-2 research, with an extensive focus on facilitating collaborations, user support, and providing access to HPC resources at partner centers. BioExcel partnered with Molecular Sciences Software Institute to establish the COVID-19 Molecular Structure and Therapeutics Hub to allow researchers to deposit their data and review other group’s submissions as well.
During this period, there was an urgent demand for diagnostics and sharing of data for COVID-19 applications had become vital more than ever. A dedicated BioExcel-CV19 web-server interface was launched to provide access to study molecules involved in the COVID-19 disease. This allowed the project to be a part of open access initiative promoted by the scientific community to make research accessible.
Recently, BioExcel endorsed the EU manifesto for COVID-19 Research launched by European Commission as part of their response to the coronavirus outbreak.
Modelling the electronic structure of the protease
MaX (MAterials design at the eXascale) is a European Centre of Excellence aiming at materials modelling, simulations, discovery and design on the exascale supercomputing architectures.
Though the main interest of the MaX flagship codes is then centered on materials science, the CoE is participating in the fight against SARS-CoV-2. Given the critical pandemic situation that the world is currently facing, an unprecedented effort is being devoted to the study of SARS-CoV-2 by researchers from different scientific communities and groups worldwide. From the biomolecular standpoint, particular focus is being devoted to the main protease, as well as to the spike protein. As such, it is an important potential antiviral drug target: if its function is inhibited, the virus remains immature and non-infectious. Using fragment-based screening, researchers have identified a number of small compounds that bind to the active site of the protease and can be used as a starting point for the development of protease inhibitors.

Among other quantities, MaX researchers now have the possibility to model the electronic structure of the protease in contact with a potential docked inhibitor, and provide new insights on the interactions between them by selecting specific amino-acids that are involved in the interaction and characterizing their polarities. This new approach proposed by the MaX scientists is complementary to the docking methods used up to now and based on in-silico research of the inhibitor. Biological systems are naturally composed of fragments such as amino-acids in proteins or nitrogenous bases in DNA.
With this approach, it is possible to evaluate whether the amino acid-based fragmentation is consistent with the electronic structure resulting from the QM computation. This is an important indicator for the end-user, as it enables to evaluate the quality of the information associated with a given fragment. Then, QM observables on the system’s fragments can be obtained, which are based on a population analysis of electronic density of the system, projected on the amino-acid.
A novelty that this approach enables is the possibility of quantifying the strength of the chemical interaction between the different fragments. It is possible to select a target region and identify which fragments of the systems interact with this region by sharing electrons with it.
“We can reconstruct the fragmentation of the system in such a way as to focus on an active site in a specific portion of the protein”, says Luigi Genovese from CEA (Commissariat à l’énergie atomique et aux énergies alternatives) who is heading Max’s efforts on this topic. “We think this modelling approach could inform efforts in protein design by granting access to variables otherwise impervious to observation.”
Improving drug design and biosensors
The project E-CAM supports HPC simulations in industry and academia through software development, training and discussion in simulation and modeling. Project members are currently following two approaches to add to the research on the corona virus.
Firstly, the SARS-CoV-2 virus that causes COVID-19 uses a main protease to be functional. One of the drug targets currently under investigation is an inhibitor for this protease. While efforts on simulations of binding stability and dynamics are being conducted, not much is known of the dynamical transitions of the binding-unbinding reaction. Yet, this knowledge is crucial for improved drug design. E-CAM aims to shed light on these transitions, using a software package developed by project teams at the University of Amsterdam and the Ecole Normale Superieure in Lyon.
Secondly, E-CAM contributes to the development of the software required to design a protein-based sensor for the quick detection of COVID-19. The sensor, developed at the partner University College Dublin with the initial purpose to target influenza, is now being adapted to SARS-CoV-2. This adaptation needs DNA sequences as an input for suitable antibody-epitope pairs. High-performance computing is required to identify these DNA sequences to design and simulate the sensors prior to their expression in cell lines, purification and validation.
Studying COVID-19 infections on the cell level
The project PerMedCoE aims to optimise codes for cell-level simulations in high-performance computing, and to bridge the gap between organ and molecular simulations. The project started in October 2020.
“Multiscale modelling frameworks prove useful in integrating mechanisms that have very different time and space scales, as in the study of viral infection, human host cell demise and immune cells response. Our goal is to provide such a multiscale modelling framework that includes infection mechanisms, virus propagation and detailed signalling pathways,” says Alfonso Valencia, PerMedCoE project coordinator at the Barcelona Supercomputing Center.
The project team has developed a use case that focusses on studying COVID-19 infections using single-cell data. The work was presented to the research community at a specialized virtual conference in November, the Disease Map Community Meeting. “This use case is a priority in the first months of the project”, says Valencia.
On the technical level, disease maps networks will be converted to models of COVID-19 and human cells from the lung epithelium and the immune system. Then, the team will use omics data to personalise models of different patients’ groups, differentiated for example by age or gender. These data-tailored models will then be incorporated into a COVID-focussed version of the open source cell-level simulator PhysiCell.
Supporting policy makers and governments
The HiDALGO project focusses on modelling and simulating the complex processes which arise in connection with major global challenges. The researchers have developed the Flu and Coronavirus Simulator (FACS) with the objective to support decision makers to provide an appropriate response to the current pandemic situation taking into account health and care capabilities.
FACS is guided by the outcomes of SEIR (Susceptible-Exposed-Infectious-Recovered) models operating at national level. It uses geospatial data sources from Openstreet Map to approximate the viral spread in crowded places, while trading the potential routes to reach them.
In this way, the simulator can model the COVID-19 spread at local level to provide estimations of infections and hospital arrivals, given a range of public health interventions, going from no interventions to lockdowns. Public authorities can use the results of the simulations to identify peaks of contagion, set appropriate measures to reduce spread and provide necessary means to hospitals to prevent collapses. “FACS has enabled us to forecast the spread of COVID-19 in regions such as the London Borough of Brent. These forecasts have helped local National Health Service Trusts to more effectively plan out health and care services in response to the pandemic.” says Derek Groen from the HiDALGO project partner Brunel University London.
Wired: Why London’s Tier 2 lockdown couldn’t be borough by borough
The Guardian: As other cities go into lockdown, why isn’t London having a second wave?
HiPEAC Magazine: Simulating COVID-19 andflu spread using HiDALGO
HiDALGO website: Pandemic Use Case
HiDALGO establishes a local flu and coronavirus detector
Cordis – EU research results: London calling: Simulation tool predicts second wave of COVID-19
EXCELLERAT is a project that is usually focussing on supercomputing applications in the area of engineering. Nevertheless, a group of researchers from EXCELLERAT’s consortium partner SSC-Services GmbH, an IT service provider in Böblingen, Germany and the High-Performance Computing Center Stuttgart (HLRS) are also providing measures to contain the pandemic by supporting the German Federal Institute for Population Research (Bundesinstitut für Bevölkerungsforschung, BiB).
The scientists have developed an intelligent data transfer platform, which enables the BiB to upload data, perform computing-heavy simulations on the HLRS’ supercomputer Hawk, and download the results. The platform supports the work of BiB researchers in predicting the demand for intensive care units during the COVID-19 pandemic. “Nowadays, organisations face various issues while dealing with HPC calculations, HPC in general or even the access to HPC resources,” said Janik Schüssler, project manager at SSC Services. “In many cases, calculations are too complex and users do not have the required know-how with HPC technologies. This is the challenge that we have taken on. The BiB’s researchers had to access HLRS’s Hawk in a very complex way. With the help of our new platform, they can easily access Hawk from anywhere and run their simulations remotely.”
“This platform is part of EXCELLERAT’s overall strategy and tools development, which not only addresses the simulation part of engineering workflows, but provides users the necessary means to optimise their work”, said Bastian Koller, Project Coordinator of EXCELLERAT and HLRS’s Managing Director. “Extending the applicability of this platform to further use cases outside of the engineering domain is a huge benefit and increases the impact of the work performed in EXCELLERAT.”
LearnHPC: dynamic creation of HPC infrastructure for educational purposes
Abstract
In a newly successful PRACE-ICEI proposal, E-CAM, FocusCoE, HPC Carpentry and EESSI join forces to bring HPC resources to the classroom in a simple, secure and scalable way. Our plan is to reproduce the model developed by the Canadian open-source software project Magic Castle. The proposed solution creates virtual HPC infrastructure(s) in a public cloud, in this case on the Fenix Research Infrastructure, and generates temporary event-specific HPC clusters for training purposes, including a complete scientific software stack. The scientific software stack is fully optimised for the available hardware and will be provided by the European Environment for Scientific Software Installations (EESSI).
Description
EU-wide requirements for HPC training are exploding as the adoption of HPC in the wider scientific community gathers pace. However, the number of topics that can be thoroughly addressed without providing access to actual HPC resources is very limited, even at the introductory level. In cases where such access is available, security concerns and the overhead of the process of provisioning accounts make the scalability of this approach questionable.
EU-wide access to HPC resources on the scale required to meet the training needs of all countries is an objective that we attempt to address with this project. The proposed solution essentially provisions virtual HPC system(s) in a public cloud, in this case on the Fenix Research Infrastructure. The infrastructure will dynamically create temporary event-specific HPC clusters for training purposes, including a scientific software stack. The scientific software stack will be provided by the European Environment for Scientific Software Installations (EESSI) which uses a software distribution system developed at CERN, CernVM-FS, and makes a research-grade scalable software stack available for a wide set of HPC systems, as well as servers, desktops and laptops (including MacOS and Windows!).
The concept is built upon the solution of Compute Canada, Magic Castle, which aims to recreate the Compute Canada user experience in public clouds (there is even a presentation where the main developer creates a cluster just by talking to his phone!). Magic Castle uses the open-source software Terraform and HashiCorp Language (HCL) to define the virtual machines, volumes, and networks that are required to replicate a virtual HPC infrastructure.
In addition to providing a dynamically provisioned HPC resource, the project will also offer a scientific software stack provided by EESSI. This model is also based on a Compute Canada approach and enables replication of the EESSI software environment outside of any directly related physical infrastructure.
Our adaption of Magic Castle aims to recreate the EESSI HPC user experience, for training purposes, on the Fenix Research Infrastructure. After deployment, the user is provided with a complete HPC cluster software environment including a Slurm scheduler, a Globus Endpoint, JupyterHub, LDAP, DNS, and a wide selection of research software applications compiled by experts with EasyBuild.
The architecture of the solution is best represented by the graphic below (taken from the Compute Canada documentation at https://github.com/ComputeCanada/magic_castle/tree/master/docs):

With the resources made available to the project, we plan to run 6 HPC training events from January to July 2021. These training events are connected to the Centres of Excellence E-CAM and FocusCoE and with HPC Carpentry.