twitter linkedin 

Newsletter #09 - March 2021


1. Introduction

2. News from the Centres of Excellence

3. Introducing the CoE Flagship Codes

4. Trainings, Webinars, Workshops & Events

1. Introduction

Dear Reader,

Only in the recent years the biomedical research community started to exploit HPC to study the biological mechanisms behind diseases, but still only a fraction is aware of what HPC can do for them. The growing complexity of the problems they deal with will make HPC an increasing need for all. This is a huge community still not familiar with HPC, and dealing with use cases that have a potential big impact to make decisions of medical relevance, such as the choice of the right drug to treat a specific tumor, given clinical and omics information from a certain patient.

PerMedCoE (HPC/Exascale Centre of Excellence in Personalised Medicine), which started in October 2020, has the mission to bring together the core of biomedical research towards HPC, and will do so by upgrading current computational biology methods to the HPC/Exascale era. At the same time, it will raise awareness amongst these software tools' potential users on the new possibilities that such methods, scaled-up to exploit HPC capabilities, open to their research in the personalised medicine area.

We are of course not alone in this exciting adventure, as PerMedCoE was born with an ecosystem of HPC Centres of Excellence at its heart, conceived to bridge the molecular- and organ-level simulations from CompBioMed and BioExcel. The project walks hand in hand with these CoEs from the biomedical area, and also with POP and HiDALGO, having some of their key experts working together since day one.

In this newsletter, among other topics, you will find links to an overview of the CoEs' use cases. We contribute with our study to uncover the cross-talk between SARS-CoV-2 and human cells, aiming at a better understanding of COVID-19, a topic which is in all our minds these days.

Stay safe,

Alfonso Valencia, ICREA Prof.
Coordinator of PerMedCoE
Barcelona Supercomputing Center (BSC)

2. News from the Centres of Excellence

Promoting Women’s Research in Computational Biology: A Conversation with Eva Alloza
>> Read More

Official release of GROMACS 2021 code >> Read More
News article: Probing the earth subsurface >> Read More

Video: ChEESE celebrates the International Day of Women and Girls in Science 2021 >> Watch here
CoEC project website is online >> Check out here

Blog post: Designing tools for Exascale simulation >> Read More
Uncertainty in CovidSim epidemic simulation >> Read More

CompBioMed joins the LEXIS project Open Call >> Read More
Implementation of High-Dimensional Neural Network Potentials >> Read More

February Module of the Month: ALL library implementation in HemeLB, a CoE collaboration
>> Read More
New publication about the results of the DYAMOND initiative >> Read More
The use of in-situ analysis tools by EXCELLERAT >> Read More
New content arrived: FocusCoE prepared this overview of the Use Cases provided by the CoEs >> Read More

New CoE RAISE: Research on AI- and Simulation-Based Engineering at Exascale >> Read More
HiDALGO Success Story: Covid-19 Modelling >> Discover here

HiDALGO Success Story: Migration Issues >> Discover here
New website section "Science & MaX": collection of the scientific papers produced by the materials science community using the MaX flagship codes >> Discover here

Overview: News on MaX flagship codes >> Read More

AiiDAlab, an intuitive infrastructure for computational workflows >> Read More
Discover the NOMAD tutorial series playlist >> Watch on Youtube
Identifying best ways to scale up personalised medicine data analysis tools for use on modern HPC platforms >> Read More
POP’s OpenMP Metrics: a Case Study >> Read More

POP for Astronomy - 40% Reduction in Execution Time for the PIERNIK Code >> Read More

Performance Improvements by More Than 30% and a Data Race Fixed for CalculiX Code >> Read More

3. Introducing the CoE Flagship Codes

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method. CP2K is written in Fortran 2008 and can be run efficiently in parallel using a combination of multi-threading, MPI, and CUDA. It is freely available under the GPL license. It is therefore easy to give the code a try, and to make modifications as needed.

>> Read more
SUMO (Simulation of Urban MObility) is an open-source program (licenced under GPL2) for traffic simulation. Its simulation model is microscopic, that is, each vehicle is explicitly modelled, has its own route and moves individually over the network. It is mainly developed by the Institute of Transportation Systems, located at German Aerospace Center. Among other features, it allows the existence of different types of vehicles, roads with several lanes, traffic lights, graphical interface to view the network and the entities that are being simulated, and interoperability with other applications at run-time through an API.

>> Learn More
Want to know more about the CoEs flagship codes, tools and software packages?

>> Discover them all here <<

4. Trainings, Webinars, Workshops & Events

Check out the trainings, webinars, workshops & events below, and visit the CoE Event Calendar for all future events.
30 March, 2021:
Webinar: Applying the Accelerated Weight Histogram method to alchemical transformations

07-11 June, 2021:
BioExcel Summer School on Biomolecular Simulations

17-20 October, 2021:
EMBO Workshop: Advances and Challenges in Biomolecular Simulations
26 April, 2021:
Physics-based earthquake modeling and engineering workshop (EGU21)

29 April, 2021:
Towards Exascale Supercomputing in Solid Earth Geoscience and Geohazards (EGU21)

13 April, 2021:
CompBioMed’s 15th e-seminar will focus on Performance Optimisation and Productivity (POP) services for HPC application developers

15-17 September, 2021:
CompBioMed Conference 2021
11-15 October, 2021:
High performance computing for simulation of complex phenomena

11-22 October, 2021:
Improving bundle libraries
12-16 April, 2021:
Numerical methods for Large Eddy Simulation

04 May, 2021:
Fortran for High Performance Computing

05 - 08 July 2021
Minisymposium at PASC 21 - Extreme CFD for Engineering Applications
26 March, 2021:
EHPCSW21: HPC education and training – perspectives from EU13 Member States

GPU Hackathons in Europe 2021

Spring 2021 (dates tba)
MaX school on Advanced Materials and Molecular Modelling with Quantum ESPRESSO

8-9 April & 15-16 April, 2021
Virtual school on electronic excitations in solids and nanostructures using the Yambo code

17-21 May, 2021
Advanced school on Quantum Transport using SIESTA

Summer 2021 (dates tba):
First-principles simulations of materials with SIESTA

06 - 09 July 2021
Introduction to running reproducible workflows with AiiDA
13 - 14 April, 2021:
NOMAD Online Tutorial Series: Workflow Management - Part 1

01 - 03 November, 2021
Joint NOMAD - E-CAM Workshop: Modeling materials at realistic space and time scales via optimal exploitation of exascale computers and AI

15-19 November, 2021:
High-throughput workflows for materials science with the Atomic Simulation Environment and Fireworks
pop png
19 - 21 April, 2021
Training on POP performance analysis, methodology and tools for women and underrepresented groups in the HPC community
This newsletter is part of the project Focus CoE. Focus CoE has received funding from the European Union’s Horizon 2020 research and innovation programme under the grant agreement Nº 823964.
Unsubscribe | Manage subscription

Höchstleistungsrechenzentrum Stuttgart (HLRS) | Nobelstraße 19
70569 Stuttgart | Germany