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/ |
FocusCoE organizes two workshops at EHPCSW21
With the support of the FocusCoE project, a number of the HPC CoE participated in the first online edition of the EuroHPC Summit Week 2021 (EHPCSW21) in the context of two half-day workshops: the first one was titled “CoEs on the road to Exascale” held on 23 March 2021 and the second one was a training session titled “HPC Education & Training – Perspectives from EU13 Member States” held on Friday 26 March 2021. The high interest in the workshops was reflected by the number of participants from both academia and HPC-related industry, with over 100 participants in total for each workshop.
The session on Tuesday was structured in two parts: the first one started with an overview of FocusCoE project given by Guy Lonsdale, FocusCoE coordinator, followed by a presentation from Edouard Audit (CEA) about the European HPC Centres of Excellence (CoEs) with a focus on their Applications. The second part was organised as a live panel discussion moderated by Erwin Laure (MPCDF) and addressed the status and future of Applications Support in EuroHPC.
“We are glad that various CoEs participated actively in the EuroHPC Summit Week giving them an opportunity to disseminate their latest results as well as to interact with the EHPCSW21 attendees. While we all miss the opportunity for physical events, one of the positive side-effects of the online environment is that it allows many others to view the recordings of our workshops after the event and thus increase the potential impact”, says Guy Lonsdale.
The session on Friday, chaired by Simon Wong (ICHEC), focused on the HPC education and training landscape among the EU13 Member States with individual talks on existing programmes, target communities and industries, and future perspectives. The audience was provided with a range of insights relevant for the development of the European HPC education and training ecosystem.
About the EHPCSW21
The EuroHPC Summit Week (EHPCSW) 2021 gathers the main European HPC stakeholders from technology suppliers and HPC infrastructures to scientific and industrial HPC users in Europe. As in previous years, PRACE, the Partnership for Advanced Computing in Europe, organised the eighth edition of its Scientific and Industrial Conference (PRACEdays21) within the EHPCSW 2021. PRACEdays21 will bring together experts from academia and industry who will present their advancements in HPC-supported science and engineering.
FocusCoE Webinar: Opportunities and Challenges for Industrial Applications
This webinar covers some of the most critical research areas of the European Centres of Excellence (CoE) in high-performance computing, highlighting topics such as physical-mathematical modelling, numerical algorithms and scientific libraries.
It includes several examples of how the CoE’s activities and applications result in tangible benefits to address scientific and industrial challenges.
Speakers & Topics:
- Massimo Celino (ENEA): EoCoE: the European Energy oriented Centre of Excellence in HPC
- Alfredo Buttari (CNRS, France): Parallel block low-rank sparse direct solvers with applications
- Jose Gracia (HLRS, Germany): POP – Performance Analysis as a Service
- Alison Walker (Univ. of Bath, UK): Working with SME on the design of new energy materials
New CoE RAISE: Research on AI- and Simulation-Based Engineering at Exascale
Artificial intelligence (AI) methods are developing at a rapid rate and being progressively applied to numerous workflow stages to solve complex problems. Analysing and processing big data requires high computational power and scalable AI solutions. Therefore, entirely new workflows must be developed from current applications that can be run efficiently on future high-performance computing (HPC) architectures at exascale. To tackle these topics, a new European Centre of Excellence “Research on AI- and Simulation-Based Engineering at Exascale” (CoE RAISE) was founded and is being funded by the EU.
Forschungszentrum Jülich coordinates the CoE RAISE, which was launched on 1 January 2021 with a total budget of around € 5 million. The CoE brings together eleven full partners and two third parties with expertise in AI and HPC.
FocusCoE Workshop at the virtual HiPEAC ’21 conference – the Twitter report
On January 20, FocusCoE organized a workshop at the virtual HiPEAC 2021 event under the topic “The HPC CoE services and applications”. We covered the workshop on Twitter – find our timeline below.
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.
Nature: Simulating the pandemic: What COVID forecasters can learn from climate models
CompBioMed: Coronavirus - Computational Drug Discovery
Cardiotoxicity: supercomputer-basedin silico studies with Alya Red
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.
ETP4HPC handbook 2020 released
The 2020 edition of the ETP4HPC Handbook of HPC projects is available. It offers a comprehensive overview over the European HPC landscape that currently consists of around 50 active projects and initiatives. Amongst these are the 14 Centres of Excellence and FocusCoE, that are also represented in this edition of the handbook.
Meeting the challenges of tomorrow – at scale
With the help of a multi-million funding programme for applications in High Performance Computing, the European Commission aims to address European societal, economic and scientific challenges.
From computing the reduction of noise and fuel for passenger airplanes to assessing the effects of climate change – Applications in High Performance Computing (HPC) help tackle some of the world’s biggest societal, scientific, and economic challenges. The development of the next generation of supercomputing systems – exascale systems, with computing speeds a billion times higher than current desktop computers – targets the future needs of such applications. However, enabling these applications to effectively use ever larger (and increasingly complex) computing systems is a major milestone which has yet to be achieved, keeping in mind that the first pre-Exascale machines will be available in Europe in 2020 according to the announced EuroHPC strategy.
After an investment of 42 M€ in 2015, the European Commission confirmed its support with an additional budget of 74 M€ in December 2018 resulting in 10 operational European HPC Centres of Excellence (CoEs) for computing applications. Achieving excellence in HPC Applications takes a pivotal place – it is the applications that deliver solutions to the aforementioned challenges – in the European HPC Ecosystem alongside the development of Exascale technologies and provision of access to extreme-scale infrastructure. Simultaneously, FocusCoE has been selected as a Coordination and Support Action (CSA) in order to support these CoEs in their mission to contribute to a globally competitive HPC ecosystem. The launch of the new HPC Centres of Excellence continues to support the key role of applications and this is expected to be a crucial element within the EuroHPC Programme.
General Assembly to shape strategic collaboration
In a Workshop organized by FocusCoE on 21st February in Frankfurt, all European HPC CoEs came together to discuss cross-community collaboration, common training activities and concerted outreach to support industry. As one of the main outcomes of the workshop, the establishment of the EU HPC CoE General Assembly was initiated, a body comprising CoE members and other strategic partners. The General Assembly will allow EU HPC CoEs to collaboratively define a strategy for contributions to the EU HPC Ecosystem and plan its implementation.
FocusCoE aims to channel information on CoE contributions to important societal, scientific, and economic challenges across Europe and thus give EU HPC CoEs a unified voice, creating a common understanding of the importance of HPC applications across public, academic, and industrial stakeholders. Additional support services of FocusCoE therefore comprise promotion, support for industrial outreach and business development, and providing cross-area training to the CoEs.
Identifying these cross-area intersections was one of the main objectives of the first EU HPC CoE workshop in Frankfurt. Many CoEs address specific HPC application areas such as Life Sciences, Earth Sciences, Material Sciences, and Engineering. However, other CoEs focus on computational approaches as tools to address challenges across multiple application areas, such as Machine Learning, Code Performance Optimization, and Data Analytics. “With the help of the GA and other support activities”, project coordinator Guy Lonsdale states, “we aim to bring these competences together and support the CoEs to find synergies that help them more effectively fulfill their pivotal role within a globally competitive EU HPC ecosystem”. In the coming months, the CoEs will work together towards their common goal to make today’s largest-scale applications fit for tomorrow’s challenges.