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Focus CoE - Newsletter 05/2020

Content

1. Welcome

2. How CoEs contribute to COVID-19 research

3. Focus On: POP CoE

4. CoE News

5. Codes

6. Trainings, Workshops & Events

1. Welcome

Dear reader,

European society faces a number of pressing challenges in various areas. The most recent and largest of them is certainly the current Corona crisis. Researchers and institutions all over the world are working on different sub-topics associated with the virus and the disease it causes.

Various European Centres of Excellence (CoEs) and their partners are involved in studies of virus spread, vaccine development, and drug improvement. In particular, an HiDALGO group led by Derek Groen has been working on the simulation of COVID-19 spread in the dense urban areas, as well as on testing effectiveness of different restrictive policies in response to a request from the British National Health Service. This Focus CoE newsletter features contributions of CoEs to COVID-19 research.

Meanwhile, various other urgent topics are arising in research fields such as sociology, economics, ecology and technology. Due to globalisation processes such as the rapid advances in communication technologies or the development of the global labour market, many of these challenges affect a large number of people and are therefore global in nature.
Nowadays, policy makers cannot successfully solve any of those global challenges based alone on their intuition. The HiDALGO project aims to equip stakeholders with advanced solutions for computer-aided evidence-based policy making in the domain of Global Challenges.

The vivid examples of global challenges – explored by HiDALGO use cases – include modelling human migration from conflict zones, designing and developing smart cities, as well as reducing the impact of malicious information in social media. We build numerical models of global challenges and estimate consequences of different policies based on simulations of those models. In order to improve the accuracy of simulations, we have developed detailed social models coupled with such physical models of relevant phenomena, as well as different data sources including streaming data from sensors, mobile networks, social networks, etc. Find here a general overview over the tasks of our project’s work package 6 that deals with the development of Artificial Intelligence and Machine Learning components for our pilot applications.

Besides that, this newsletter presents a comprehensive overview over the recent activities of the CoE POP. Finally, you will find the event section for upcoming trainings, webinars, and summer schools.

Enjoy reading!

Sergiy Gogolenko
Technical Coordinator HiDALGO CoE
HLRS – High Performance Computing Center Stuttgart

2. How CoEs contribute to COVID-19 research

Various HPC CoEs are actively contributing to the research on COVID-19 in very different research areas:
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CompBioMed is active in a vast international consortium across Europe and USA working on urgent coronavirus research. Heading CompBioMed’s efforts in this collaboration is Prof Peter Coveney and the Centre for Computational Science (CCS) at University College London (UCL), together with Leibniz Rechenzentrum (LRZ) and the Gauss Centre for Supercomputing (GCS).

>> Find out more about CompBioMed and Coronavirus
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Unquestionably, a discovery of a vaccine and cure will be of paramount importance for long-term control of the spread of the disease. In support of the efforts, BioExcel experts are partnering with numerous international initiatives by bringing all of their advanced software applications and expertise.

>> Find out more about BioExcel and Coronavirus
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HiDALGO CoE has established a local flu and Coronavirus simulator. It is an agent-based model that approximates the viral spread of COVID-19 at the subnational level.

>> Find out more about the HiDALGO simulator
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Various partners of the EXCELLERAT CoE are supporting measures in COVID-19 research. An overview was published in the project's latest newsletter.

>> Overview: how EXCELLERAT partners support the fight against COVID-19 [PDF]

3. Focus On: POP CoE

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An Introduction to POP CoE

The Performance Optimisation and Productivity (POP) EU Centre of Excellence provides a free parallel application performance profiling and optimisation service to all customers based in Europe. This is to help parallel applications increase their performance to tackle more challenging problems and at greater scale. We are nearly half-way through the three-year project, which is providing performance insights into applications across all scales and many scientific domains.
This CoE is comprised of eight partners with expertise in parallel code development and profiling, spanning all disciplines but mainly in computational science. Three of the partners develop their own application profiling tools: BSC develops Extrae/Paraver, Université de Versailles develops MAQAO and Juelich are one of the developers of Scalasca.

>> More information on POP CoE
Using the POP Application Profiling Service

If you have a parallel application and would like to know its performance characteristics or it is not scaling to your expectation, the POP service can help you. We offer two services:

1. Performance assessment: this service gives a high-level overview of the application performance, as well as providing insight into what is limiting the scaling. Recommendations are made on how best to address the performance issues;
2. Proof of concept: this implements a code to test the effectiveness of the improvements recommended in the Performance Assessment. In some cases, the optimisations are implemented if they are simple to achieve.

Learn more about using the above services: pop-helpdesk@bsc.es or pop-coe.eu/services
Latest Case Studies
Case Study 1: 190x strong-scaling speed-up of HemeLB simulation on SuperMUC-NG

HemeLB is an open-source lattice-Boltzmann code for simulation of large-scale three-dimensional fluid flow in complex sparse geometries such as those found in vascular networks. It is written in C++ using MPI by UCL and developed within the EU H2020 HPC CompBioMed CoE for computational biomedicine as their flagship code. Click here to read more about this case study.
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Case Study 2: 25% Faster time-to-solution for Urban Microclimate Simulations for Rheologic GmbH

Rheologic is an Austrian company providing CFD (Computational Fluid Dynamics) services and solutions for complex flows. Rheologic develop new solvers for the OpenFOAM-framework, in this case uhiSolver (Urban Heat Island Solver). This is a program to forecast local conditions (e.g. thermal comfort) during the hottest days of summer in densely built urban areas including the cooling effects of plants and water surfaces due to evaporation.

POP CoE found that the performance was very good already with super-linear speedup. However, using the POP methodology we identified room for improving the load balance of the application to further boost the performance.

Click here to read more about this case study.
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>> Read more successful POP CoE Case Studies.
POP CoE on the web
website twitter email youtube 

4. CoE News

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Publication: Computational approaches to therapeutic antibody design: established methods and emerging trends
>> Read More
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ChEESE awarded almost 110M core hours for earthquake, volcano and tsunami research
>> Read More
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AI-driven integrative biology for accelerating therapeutic drug discoveries to treat SARS-CoV-2
>> Read More
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An interview with Massimo Noro, Director of Business Development at STFC
>> Read More

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EoCoE is hiring: Engineer for High Performance Computing & Data Analysis
>> Read More
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New podcast episode: Why do aeronautics benefit from HPC simulations? An interview with Pipistrel Aircraft
>> Listen on Soundcloud
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How HiDALGO uses the power of AI and Machine Learning to
approach solutions for major global challenges
>> Read More [PDF]
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Recap: MaX Webinar on “How to use Quantum ESPRESSO on new GPU-based HPC systems”
>> Read More
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New episode of video series POPCast featuring an interview with Ania Brown, Research Software Engineer at Oxford e-Research Centre.
>> Watch on Youtube

5. Codes

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SIESTA is a first-principles materials simulation program based on density-functional theory (DFT). It was one of the first codes to enable the treatment of large systems with first-principles electronic-structure methods, which opened up new research avenues in many disciplines. Apart from its natural habitats of materials physics and chemistry, SIESTA has also become popular among scientists in geosciences, biology and engineering.

SIESTA's efficiency stems from the use of strictly localised basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave methods.

>> Read more about the SIESTA code here
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The official release of GROMACS 2020.2 is available. This release fixes several issues found since the last patch release of GROMACS 2020. BioExcel encourages all users of the 2020 series to update to 2020.2.

>> More on the new GROMACS release

6. Trainings, Workshops & Events

Check out the upcoming trainings, workshops & events for May & June 2020 below - or visit the Focus CoE Event Calendar and the HPC Training Registry for all future events.
May & June 2020:
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09 June 2020:
Preparing to run biomolecular QM/MM simulations with CP2K using AmberTools Online

11 June 2020:
Webinar: The HADDOCK2.4 server – new features and a guided demo

22 June - 26 June 2020:
Remote BioExcel Summer School on Biomolecular Simulations
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10 June 2020
Webinar: Accelerated hydrologic modeling: ParFlow GPU implementation
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30 June 2020
Virtual Workshop on Emerging Technologies for Weather and Climate Modelling
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27 May 2020
Managing, simplifying and disseminating High-Throughput computational materials science with AiiDA, AiiDA lab, and the Materials Cloud Archive
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70569 Stuttgart | Germany
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