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Focus CoE - Newsletter #06
September 2020

Content

1. Introduction

2. CoE News

3. ESiWACE Success Story: Improving weather and climate forecasting with a new NEMO configuration

4. Introducing the CoE Flagship Codes

5. Trainings, Workshops & Events

1. Introduction

Dear reader,

The ongoing Covid-19 pandemic has turned a lot of the public attention back to science and what scientists can do to help society in a time of crisis. Current supercomputers are aiding research by solving complex problems quickly and efficiently, and the upcoming generation of pre-Exascale and Exascale machines will provide us with the computational capability to simulate with unprecedented time-to-solution.

The ChEESE Center of Excellence is focused on testing and deploying time-sensitive services to aid decision makers of the general public during or shortly after a geohazardous event occurs. This includes HPC-based urgent computing for earthquakes, tsunamis and volcanoes, building upon European flagship codes and related workflows.

Related to this, ChEESE is offering two PATC training courses this October on HPC for computational seismology (including tutorials on 4 flagship codes) and on tools and techniques to improve performances of applications in Solid Earth. You can find more information in this newsletter, which also contains the latest news, updates, stories and events of our fellow CoEs.

Enjoy reading!

Dr. Arnau Folch
Coordinator of ChEESE CoE
Barcelona Supercomputing Center (BSC)

2. CoE News

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BioExcel is supporting the development of COVID-19 treatments >> Read More

At the forefront of antibody-antigen complex prediction using information-driven docking in HADDOCK. >> Read More

Webinar recording available - Computational biomolecular simulation workflows with BioExcel building blocks >> Read More
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ChEESE infrastructures and datasets set to be integrated into EUDAT CDI >> Read More

ChEESE presented at the 106th Congresso Nazionale >> Read More
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CompBioMed Associate Partners predicting the impact of closing your local shop on the spread of Covid-19 >> Read More

The nUCLeus Hub: Scalable training in computational biomedicine >> Read More

Cardiotoxicity: supercomputer-based in silico studies with Alya Red >> Read More [PDF]

Video of Webinar #13: “Are we there yet?” — Addressing emerging drug discovery challenges for SARS-CoV-2 with artificial intelligence driven molecular dynamics >> Read More
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Addressing interactive HTC workloads with HPC characteristics: introduction to E-CAM’s HTC library >> Read More

CLstunfti: An extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids >> Read More

E-CAM Industrial Case Study: Calculations for Applications in Photovoltaic Devices >> Read More

Publication: A possible roadmap for the coarse graining and multiscale simulation community >> Read More
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Guest talk at workshop organized by EU H2020 project HPCWE: HPC developments in Alya for Wind Energy Applications >> Watch on YouTube
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Slides available: ESiWACE Virtual Workshop on Emerging Technologies for Weather and Climate Modelling) >> Read More
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Success Story: Full Airplane Simulations on Heterogeneous Architectures >> Read More

Success Story: Enabling parallel mesh adaptation with Treeadapt >> Read More

EXCELLERAT HPC Podcast E03 - How to Improve Autonomous Vehicles with Supercomputer Simulations >> Listen on Soundcloud
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HiDALGO Simulation Tool predicts second wave of COVID-19 >> Read More

HiDALGO offers the possibility of associate partnership to foster collaboration between HiDALGO and other CoEs, projects, companies, or research institutes >> Read More

Check out the new HiDALGO YouTube channel >> Visit Youtube
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Materials Cloud & AiiDA: cornerstones of MARVEL open science strategy, feature in Scientific Data >> Read More

Webinar series on MaX flagship Codes: New developments in SIESTA for high-performance materials simulations >> Recording available here

Newly-engineered Materials Cloud Archive unveiled >> Read More
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Jobs at NOMAD: Several Open Positions for master and PhD students as well as Postdocs at several high-level institutions in Europe >> Read More

Video: NOMAD in a nutshell >> Watch on Youtube

Follow the NOMAD CoE on >> Twitter
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Blog article: Tool Time: Caliper - A Performance Analysis Toolbox in a Library >> Read More

Blog article: Tool Time: Performance Analysis Study with Vampir >> Read More

Blog article: Tool Time: Analyzing Performance Profiles using Hatchet >> Read More

Recap: POP Goes Virtual for 35th VI-HPS Tuning Workshop >> Read More
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Jobs: Postdoc/software engineer positions within TREX Center of Excellence in Exascale Computing >> Read More

Follow TREX on >> Twitter

3. CoEs' success stories - Focus on ESiWACE: Improving weather and climate forecasting with a new NEMO configuration

Quick Summary

  • Industry sector involved: Weather & Climate modelling community in Europe
  • Software and hardware used: NEMO (Nucleus for European Modelling of the Ocean) on Atos Bull Supercomputers at Météo France and at CEA’s Very Large Computing Centre (TGCC)
  • Challenge: NEMO performance and scalability optimisation
  • Solution: Close collaboration between researchers from the community and HPC experts to set up a NEMO configuration to ease and perform profiling, benchmarking and performance optimisation.

Highlighted Centre of Excellence

ESiWACE, the “Centre of Excellence in Simulation of Weather and Climate in Europe” has been funded by the European Commission to substantially improve efficiency and productivity of numerical weather and climate simulation. Overall, the Centre of Excellence prepares the European weather and climate community to make use of future exascale systems in a co-design effort involving modelling groups, computer scientists and HPC industry. For more details on ESiWACE, check out this Youtube video.

Organizations involved

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Atos Center for Excellence in Performance Programming (CEPP) provides expertise and services in High Performance Computing, Artificial Intelligence and Quantum Computing.
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LOCEAN laboratory, part of the CNRS-IPSL, conducts studies on the physical and biogeochemical processes of the ocean and their role in climate in interaction with marine ecosystems.
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CERFACS research center is specialized in modelling and numerical simulation, through its facilities and expertise in high-performance computing.

Challenge

A key model for weather and climate comprehension is NEMO (Nucleus for European Modelling of the Ocean), a modelling framework for research activities and forecasting services in ocean and climate sciences. NEMO is used by a wide variety of applications at global or regional focus, with different resolutions, different numerical schemes, parameterizations and therefore with different performance constraints. The technical challenge here was to find a way to ease the profiling and benchmarking of NEMO for its versatile uses in order to increase the performance of this framework.

Solution

In response to this challenge, ESiWACE has developed a new configuration, adapted to HPC benchmarking, that is polymorphic and can very simply reproduce any use of NEMO.
Thanks to a close collaboration between the Atos CEPP, LOCEAN and CERFACS, a dedicated configuration of NEMO to ease its profiling and benchmarking has been set up.
Many tests of this configuration, including large-scale experiments on the Atos Bull supercomputers at Météo France and CEA’s Very Large Computing Centre (TGCC) have been performed. This resulted in several optimisations improving the performance of the NEMO code in this configuration by up to 38%.

The open source NEMO 4.0, which was released in 2019, benefited from this work and included the following improvements: an automatic MPI sub-domain decomposition, and a rewriting of the communication routines with an optimisation of treatment of the North pole singularity.

Business Impact

Some of the NEMO uses such as weather or climate forecasts are among the key challenges our society must address. Improvements of NEMO numerical performance allow to refine model results, to reduce forecast uncertainties and to better predict high-impact extreme events, thus saving lives. On Earth the Ocean has a huge impact on the atmosphere. Thus, NEMO is widely used coupled with atmospheric models. For example, it is used to simulate ocean eddies, temperature and salinity that play a key role in cyclone intensity and trajectory forecast. Therefore, business impacts of improving NEMO may be indirect but there are significant as they concern everyone and all kinds of companies and entities.

This work benefits society by improving the efficiency and productivity of numerical weather and climate simulation and by preparing them for future exascale systems. It fosters expertise exchanges which enable researchers and industry to be more productive, leading to scientific excellence in Europe, through direct and tight collaborations.

Benefits resulting from this work

  • Simplified profiling and benchmarking of NEMO at different scales to find the most relevant optimisation paths.
  • Up to 38% efficiency and scalability increase of NEMO with the optimized configuration on HPC systems.
  • Reduction in time/cost of ocean simulations for both research and production purpose improving weather and climate predictions, allowing to protect property, interests and saving lives.
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Image: Example of NEMO High Resolution Simulation (ORCA 1/12°) showing here the Sea Surface Salinity in both Atlantic and Pacific Ocean on the equator. Source: https://www.nemo-ocean.eu/

4. Introducing the CoE Flagship Codes

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CODA is a Computational Fluid Dynamics (CFD) software for the solution of the RANS equations on unstructured grids based on second-order finite-volume and higher-order Discontinuous-Galerkin (DG) discretizations. The implementation addresses the efficient utilization of current and upcoming high performance computing clusters. CODA is being co-developed by Airbus, ONERA (the French Aerospace Lab), and the German Aerospace Center (DLR), offering the possibility of contributions from further partners on the basis of individual agreements.

>> Read more about the CODA code
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HADDOCK is a versatile information-driven flexible docking approach for the modelling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it can integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both. The information that can be integrated is quite diverse: interface restraints from NMR or MS, mutagenesis experiments, or bioinformatics predictions; various orientational restraints from NMR and, recently, cryo-electron maps. Currently, HADDOCK allows the modelling of large assemblies consisting of up to 6 different molecules, which together with its rich data support, provides a truly integrative modelling platform.

>> Read more about the HADDOCK code

5. Trainings, Workshops & Events

Check out the upcoming trainings, workshops & events below, and visit the Focus CoE Event Calendar for all future events.
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30 November - 04 December, 2020:
Remote BioExcel Winter School on Biomolecular Simulations
17 – 20 October 2021:
EMBO Workshop: Advances and Challenges in Biomolecular Simulations
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21 October 2020:
Training: PATC: CHEESE Advanced Training on HPC for Computational Seismology

26 - 27 October 2020:
Training: PATC: Tools and techniques to quickly improve performances of HPC applications in Solid Earth

21 November 2020:
Event: Paper presentation & tutorial at the GEOProcessing 2020 conference
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**POSTPONED - NEW DATES NOT YET AVAILABLE**:
HPC for mesoscale simulation

15 - 26 February 2021:
Extended Software Development Workshop: Improving bundle libraries
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06 October, 2020:
Training on High Performance Data Analytics and Visualisation

23 November, 2020:
ESiWACE2 Domain Specific Language (DSL) training
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19 - 20 October 2020
Scientific Visualization with COVISE and VISTLE

** POSTPONED, NEW DATE NOT AVAILABLE YET **
Data analytics using machine learning and modal decomposition
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14 October 2020
Webinar: All-electron DFT using the FLEUR code (more information will be available on the MaX event page soon)

04 January 2021
Advanced School on Materials and molecular Modelling with Quantum ESPRESSO

06 - 09 July 2021
AiiDA School on High-throughput computing
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Winter Term 2020 / 2021 (1st session on 05 November, 2020)
Course on Big Data and Artificial Intelligence in Materials Sciences

06 - 07 October, 2020
NOMAD Repository and Archive – Sharing, Publishing, and Managing Computational Materials Science Data with NOMAD

01 - 02 December, 2020
NOMAD Materials Encyclopedia
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30 September - 02 October, 2020
POP experts will give an overview of the VI-HPS programming tools suite at the 36th VI-HPS Tuning Workshop
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