Focus CoE - Newsletter #05
July 2020


1. Introduction

2. CoE News

3. New EXCELLERAT Service Portal

4. CoE Flagship Codes

5. Trainings, Workshops & Events

1. Introduction

Dear reader,

It is a matter of fact that more and more EU companies use HPC simulation and modelling as drivers for their businesses. Their motivations are manifold and depend on the industry branch. A common driver is the increasing complexity of components and products. To deal with more complex components, higher fidelity simulations are needed. Those simulations require finer geometries, that require better meshes (meshing is still an extremely difficult task impossible to fully automatize), that require better linear algebra and matrix calculus.

Faster computers, like the pre-exascale systems we are eagerly waiting for, are a necessary component, but not the only one. EU industries also need trusted partners in this innovation process. That's why we developed a comprehensive online service portal for EXCELLERAT CoE. It allows us to present our portfolio of services to all relevant stakeholders in a very effective way. Find out more about the new portal in this newsletter.

Furthermore, this issue of the newsletter gives an overview over the latest activities of the ten European CoEs in HPC.

Enjoy reading!

Claudio Arlandini
Coordinator WP5 "Centre Implementation" for EXCELLERAT CoE

2. CoE News

Speed up your biomolecular simulations with workflows using the BioExcel Building Blocks (bioBB) >> Read More

Success Story: SeRC announced as Intel’s first oneAPI academic Center of Excellence >> Read More

BioExcel: A leader in open-source free energy calculation software >> Read More

Available online: BioExcel Webinar #47 - COVID-19 Molecular Structure and Therapeutics Hub >> Read More
First simulations with SeisSol on Marconi100 and Piz Daint >> Read More

ChEESE contributes to Spain´s unique insurance scheme against natural catastrophes >> Read More

ChEESE flagship code XSHELLS simulates geomagnetic reversals with unprecedented realism
>> Read More
Blog post: The World’s Fastest Computer to Join Fight Against COVID-19 >> Read More

Listing: Coronavirus Research Resources >> Read More
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Success Story: Accelerating the design and discovery of materials with tailored properties using first principles high-throughput calculations and automated generation of Wannier functions >> Read More

Webinar series "The importance of being H.P.C. Earnest" is now available on the CECAM Youtube Channel >> Watch here

The CoE PoP and how it can support E-CAM users >> Read More

E-CAM High Throughput Computing Library >> Read More

The CECAM Electronic Structure Library and the modular software development paradigm >> Read More
EoCoE project partner CIEMAT offers positions for 19 predoctoral researchers >> Read More
Slides available: 6th ENES Workshop on High Performance Computing for Climate and Weather (25-26 and 28-29 May, 2020) >> Read More
Check out HiDALGO's talks on multiscale modelling, uncertainty quantification and the reliability of computer simulations >> Read More

HiDALGO poster presented at the ISC20 >> Read More [PDF]
New video "MaX in a nutshell" >> Watch on YouTube

Webinar series on MaX flagship Codes CP2K, Aiida, Yambo and Quantum Espresso is available online >> Watch here

Newly-engineered Materials Cloud Archive unveiled >> Read More
16th POP Guest Webinar: Inclusive Leadership and Inspiring Action and Innovation with Dr Toni Collis (CEO Collis-Holmes Innovations, Chair of Women in High Performance Computing) >> Read More

Blog article: POP and its Role for Materials Modelling >> Read More

New episode of video series POPCast featuring an interview with Phil Tooley, HPC Application Analyst >> Watch on Youtube

Blog article: Tool Time: Using the Python Extrae API to Profile a Region of a Code >> Read More

Blog article: Tool Time: Instantaneous Parallelism in Paraver >> Read More

Blog article: Tool Time: Profiling Parallel HDF5 using Darshan >> Read More

3. New EXCELLERAT Service Portal

We are pleased to announce the launch of EXCELLERAT’s redesigned Service Portal. By presenting a wide variety of resources in an easily-accessible format, the Portal will play an essential role in EXCELLERAT’s mission to create a Centre of Excellence in Engineering.

We have adopted a user-centric approach, and the portal therefore offers separate dashboards tailored towards engineers, software developers, and the general engineering community. Each dashboard quickly directs users to relevant content, and delivers tailored information accordingly. Each page provides a quick route to any related content and offers an easy way to request services from EXCELLERAT.
The Engineers' dashboard is designed for EXCELLERAT’s end-users. It contains technical content and presents the codes, tools, and use cases under development by project partners. There is also a repository of the datasets that have been produced and publicly released by EXCELLERAT.

The Developers' dashboard presents codes and use cases, with accompanying content tailored to the developers of software codes. And importantly, it presents a detailed list of the consulting topics for which EXCELLERAT can provide support.

The Community dashboard brings together content of interest to the entire engineering community. It includes the EXCELLERAT training portfolio, a repository of all material published by EXCELLERAT, advice on accessing events organised by project partners, a Career portal, and funding opportunities for the Engineering community.

Questions or feedback?
Your opinion is important. EXCELLERAT invites you to send your comments about the portal to support@excellerat.eu.

4. CoE Flagship Codes

HemeLB, developed by the team of Prof Peter Coveney at University College London (UK), is a software pipeline that simulates the blood flow through a stent (or other flow diverting device) inserted in a patient’s brain. The aim is to discover how different stent designs (surface patterns) affect the stress the blood applies to the blood vessel, in particular in the region of the aneurysm being treated. The pipeline also allows the motion of magnetically steered particles, for example coated with drugs, to be simulated and estimates made as to where they might statistically end up.

The HemeLB setup tool voxelises the geometry at the given resolution, and HemeLB (lattice-Boltzmann CFD solver) then simulates the fluid flow within that geometry, using the given velocity-time profiles for each inlet. Once complete, the simulation output is analysed using the hemeXtract utility, which can produce images of cross-sectional flow, or 3D shots of wall shear stress distribution in the geometry using ParaView visualisation software.

>> Read more about the HemeLB code
ParFlow is a physics-based 3D parallel hydrologic model, which simulates surface and 3D subsurface flow, based on Richard’s and kinematic wave equations on a finite difference, finite volume grid with a preconditioned, implicit Newton-Krylov solver for the nonlinear PDEs.

ParFlow is not completely rewritten in EoCoE-II, but some code upscaling is planned as well as the activation of the Adaptive Mesh Refinement of the computing grids with the ad hoc numerical scheme and corresponding solver. It is also planned to have a strong effort on IO that will be coordinated with the effort on ensemble runs.

>> Read more about the ParFlow code
>> Latest release v3.7.0 on GitHub

5. Trainings, Workshops & Events

Check out the upcoming trainings, workshops & events below, and visit the Focus CoE Event Calendar for all future events.
03 - 04 September, 2020:
Introduction to GROMACS
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
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15 - 26 February 2021:
Extended Software Development Workshop: Improving bundle libraries
24-28 August 2020
Virtual Summer School on Effective HPC for Climate and Weather
19 - 20 October 2020
Scientific Visualization with COVISE and VISTLE

19 October 2020
Data analytics using machine learning and modal decomposition
01 October 2020
Hackathon: Exploring brand-new technology

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