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Newsletter #09 - March 2021
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Content
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2. News from the Centres of Excellence
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3. Introducing the CoE Flagship Codes
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4. Trainings, Webinars, Workshops & Events
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1. Introduction
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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.
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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.
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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.
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Alfonso Valencia, ICREA Prof.
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Barcelona Supercomputing Center (BSC)
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2. News from the Centres of Excellence
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Promoting Women’s Research in Computational Biology: A Conversation with Eva Alloza
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Video: ChEESE celebrates the International Day of Women and Girls in Science 2021 >> Watch here
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CoEC project website is online >> Check out here
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Blog post: Designing tools for Exascale simulation >> Read More
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Uncertainty in CovidSim epidemic simulation >> Read More
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CompBioMed joins the LEXIS project Open Call >> Read More
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Implementation of High-Dimensional Neural Network Potentials >> Read More
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February Module of the Month: ALL library implementation in HemeLB, a CoE collaboration >> Read More
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New publication about the results of the DYAMOND initiative >> Read More
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The use of in-situ analysis tools by EXCELLERAT >> Read More
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New content arrived: FocusCoE prepared this overview of the Use Cases provided by the CoEs >> Read More
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New CoE RAISE: Research on AI- and Simulation-Based Engineering at Exascale >> Read More
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New website section "Science & MaX": collection of the scientific papers produced by the materials science community using the MaX flagship codes >> Discover here
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AiiDAlab, an intuitive infrastructure for computational workflows >> Read More
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Identifying best ways to scale up personalised medicine data analysis tools for use on modern HPC platforms >> Read More
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POP’s OpenMP Metrics: a Case Study >> Read More
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POP for Astronomy - 40% Reduction in Execution Time for the PIERNIK Code >> Read More
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Performance Improvements by More Than 30% and a Data Race Fixed for CalculiX Code >> Read More
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3. Introducing the CoE Flagship Codes
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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.
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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.
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Want to know more about the CoEs flagship codes, tools and software packages?
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4. Trainings, Webinars, Workshops & Events
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Check out the trainings, webinars, workshops & events below, and visit the CoE Event Calendar for all future events.
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8-9 April & 15-16 April, 2021
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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.
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Höchstleistungsrechenzentrum Stuttgart (HLRS) | Nobelstraße 19
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70569 Stuttgart | Germany
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