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MICROCARD News

8 November 2023: paper on a boundary integral formulation for the cell-by-cell model

The article Boundary integral formulation of the cell-by-cell model of cardiac electrophysiology was published in Engineering Analysis with Boundary Elements. See a one-minute introduction here on LinkedIn!

The three-dimensional cell-by-cell models that we want to simulate in the MICROCARD project require huge resources, so it is interesting to also investigate alternatives. In this paper, Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause reformulated the problem on the cellular membrane alone, thanks to a boundary integral formulation. This formulation allows to drastically reduce the problem size, as Giacomo explains in this one-minute clip.

Admittedly these are two-dimensional tests, the method is not easy to implement, and it would be hard to extend it to millions of cells in three dimensions. But if we find solutions for these problems, it will greatly facilitate simulations of whole-heart electrophysiology, which are now too big even for the largest supercomputers on the planet.

1 September 2023: Euro-par conference 2023 in Limassol, Cyprus

Terry Cojean, Fritz Göbel and Hartwig Anzt won a best poster award at the 29th International European Conference on Parallel and Distributed Computing (Euro-Par) which took place from 28 August to 1 September 2023 in Limassol, Cyprus.

The prize-winning poster was entitled BDDC Preconditioning in the Project MICROCARD and reported on the implementation of BDDC preconditioners in the Ginkgo linear algebra library. BDDC preconditioners are numerical methods that are crucial for simulating cardiac electrophysiology at the super-high resolution and scale that our project needs. The prize shows that the actual implementation of these methods (translating math to efficient code) is not only enjoyed by the users, but also by fellow computer scientists.

25 August 2023: ICIAM 2023 meeting in Tokyo

Ten presentations are given by MICROCARD members at the 10th International Congress on Industrial and Applied Mathematics (ICIAM 2023), which takes place in Tokyo from 20 to 25 August.

In his talk Implementing Platform Portable Solvers and Preconditioners for Cardiac Simulations in the MICROCARD Project, Fritz Göbel showed how the Ginkgo library is accelerating the openCARP software, in particular for the new BDDC preconditioners that we use for cell-by-cell models.

Ngoc Mai Monica Huynh discussed the mathematics behind these preconditioners in her presentation Scalable multilevel preconditioners for hybrid-DG discretizations of nonlinear cell-by-cell cardiac models while Luca Pavarino discussed this class of preconditioners in general, in Scalable domain decomposition solvers for cardiac reaction-diffusion cell-by-cell models.

Fatemeh Chegini showed how these methods are actually used to run cell-by-cell models comprising several hundreds of cells in her talk entitled Higher Order Time Integration for EMI Cardiac Electrophysiology Simulations with Nested Subset Selection and BDDC Preconditioning.

(more to come)

5 July 2023: sad news

We recently learned that Professor Piero Colli Franzone passed away in June 2023 at the age of 76. Piero Colli Franzone was an Emeritus professor of Numerical Analysis at the Department of Mathematics of the University of Pavia. He received a degree in Mathematics from the University of Pavia in 1969. He is well known for his numerous contributions to the field of computational electrocardiology, in particular for his work on the bidomain model, the complex shape of local unipolar electrograms (in collaboration with Bruno Taccardi), eikonal equations, inverse problems and anisotropic front propagation. He contributed to MICROCARD as an adviser in the Pavia group.

4 and 5 July 2023: the 3rd MICROCARD workshop in Strasbourg!

19 to 22 June 2023: FIMH meeting in Lyon

Seven of us attended the 12th Functional Imaging and Modeling of the Heart (FIMH) meeting in Lyon, where Simone Pezzuto and Lia Gander (USI) presented MICROCARD work. The biannual FIMH meetings combine mathematics with medical imaging and cardiac modeling or simulation. All of these fields play a role in our project, next to HPC of course.

Thanks to rapid rail connections, none of us had to fly to get there, from Karlsruhe, Bordeaux, Lugano or Pavia. Mark Potse came by bicycle from Bordeaux as, he says, "it's on my way to Strasbourg anyway".

19-21 June 2023: the 7th ECCOMAS Young Investigators Conference in Porto

The ECCOMAS Young Investigators Conference provides young researchers working in computational science and engineering fields an opportunity to present their research and to network in a young and dynamic environment. Two of our post-docs presented their ongoing works within the MICROCARD project.

Giacomo Rosilho de Souza presented a Boundary Element discretization for the cell-by-cell model, jointly proposed with Simone Pezzuto and Rolf Krause.

Ngoc Mai Monica Huynh presented results related to BDDC preconditioners for composite discontinuous Galerkin discretizations of the same model, a joint work with Luca Pavarino, Simone Scacchi, Fatemeh Chegini and Martin Weiser.

6 June 2023: COUPLED PROBLEMS meeting in Chania

Martin Weiser presented our latest developments in numerical methods for cell-by-cell heart models at the International Conference on Computational Methods for Coupled Problems in Science and Engineering (COUPLED PROBLEMS 2023) meeting in Chania, Greece. The conclusions, briefly:

• multirate integration and spectral deferred correction (SDC) methods play exceedingly well together
• multirate SDC is a cheap and simple method for cardiac simulation
• tailored BDDC preconditioners are highly effective for cell-by-cell models

The multirate and SDC methods were developed by Fatemeh Chegini and Martin Weiser at the Zuse Institute Berlin, while the BDCC methods are the work of Ngoc Mai Monica Huynh, Simone Scacchi and Luca Pavarino at Università di Pavia.

In the accompanying conference proceedings paper we will also show that we improved our methods (developed by Mark Potse, Algiane Froehly and Luca Cirrottola) to create synthetic models of cardiac tissue, so that we can now generate models comprising thousands of cells.

24 to 26 May 2023: openCARP workshop in Karlsruhe

A large delegation of MICROCARD members attended the openCARP workshop in Karlsruhe from 24 to 26 May, 2023. MICROCARD builds on openCARP and some of its developments also benefit the original software. Vincent Loechner presented the Limpet-MLIR framework which makes ionic model computations in openCARP several times faster and energy-efficient, and is making the use of more precise and compute-intensive models feasible. Martin Weiser presented the numerical approach that MICROCARD is taking and Fatemeh Chegini discussed how this is implemented in the openCARP code. Finally, Laetitia Mottet and Corentin Prigent gave a short course on the Mmg meshing software, a crucial element of the MICROCARD project and of possible use to many openCARP users as well.

16 and 17 March 2023: live meeting on numerics in Berlin

Participants in work packages 3 and 5 met at the Zuse Institute in Berlin to discuss the state of research and software development in space and time discretizations as well as preconditioners. Also on the agenda were concrete implementation aspects such as the modularization concept, software structure, and code, planned joint papers and reports. Overall it was an intense and very productive meeting, that the participants enjoyed very much. (more photos on LinkedIn)

26 February to 3 March 2023: SIAM CSE meeting in Amsterdam

Martin Weiser, Simone Pezzuto and Ngoc Mai Monica Huynh presented MICROCARD results at the SIAM Conference on Computational Science and Engineering (CSE23) in Amsterdam, The Netherlands. Several other members attended the meeting.

More about Simone's work can be read in the manuscript "Boundary Integral Formulation of the Cell-by-Cell Model of Cardiac Electrophysiology" which is curently under review.

13 December 2022: Mmg release 5.7.0

Mmg version 5.7.0 was released. Mmg is a set of tools and software libraries that we use to construct and improve meshes of cardiac tissue on which we can run our simulations. The release features developments that are crucial for the MICROCARD project, such as 64-bit integers, necessary for meshes with more than a few billion elements. In addition there are several improvements and new features for the isosurfacing functionality.

30 November 2022: Our first Periodic Report submitted

Today we submitted the first of our two Periodic Reports to EuroHPC. This report covers the first 18 months of the project.

MICROCARD's goal is to develop software that can simulate the heart cell by cell, that is at micrometer resolution, on exascale supercomputers. The first 18 months of the project were characterized by the construction of building blocks, a prototype implementation of the cell-by-cell model, and the design of the exascale-ready code that will integrate these building blocks. Functionality that we need has been added to the existing software libraries on which the project builds, and is already available for others to use. Examples are recent releases of the ParMmg code, the Ginkgo linear algebra library, and the openCARP cardiac simulation software.

In addition we worked on the interpretation of imaging data to construct tissue geometries, and we developed a code that can produce artificial geometries that are much larger than would be possible with microscope images. We also developed alternative numerical approaches to the mathematical problem, methods to distribute computational work on millions of processors, and strategies to reduce the energy consumption of our code.

The project has supported the publication of 8 journal papers so far, and as many presentations at scientific conferences. We have also participated in events aimed at a larger audience. We regularly post news about our project here on our website and on LinkedIn.

The image does not show our Periodic Report, nor one of us. It is a 1969 photo of software engineering pioneer Margaret Hamilton standing beside a listing of the software, developed by her and the team she led, for the Apollo space program.

15 November 2022: #RESET webinar

The lack of gender equality in academia is a serious problem both from moral and from practical points of view. This is especially the case in computer science. Even though the first computer programmer ever was a woman, the first programming language was invented by a woman, the first compiler was invented by a woman, and the software that sent the first men to the moon was developed by women, the western world has since the 1980s become convinced that computer science is unsuitable, inhospitable, or unattractive for women. This leads to many missed vocations and unused talent, hurting projects like ours.

Therefore MICROCARD participated as a case study in the 3rd webinar on Gender Equality in Research organized by the project #RESET I Redesigning Equality and Scientific Excellence Together. These webinars aim to provide guidance and tools to integrate gender and diversity concepts into research projects.

Presentations were given by researchers from a variety of disciplines, as well as experts on gender inclusivity, and EC Policy Officer Athanasia Moungou. Our project coordinator Mark Potse presented the MICROCARD project and its efforts to strive for gender equality in our fields of research. Other projects that were highlighted included Critical ChangeLab, presented by Eva Durall and feast2030, presented by Aleksandra Rozalska, while Dalila Chenaf-Nicet talked about Gender and unintentional discrimination.

The recording of this webinar is now available on Youtube.

13 November 2022: Ginkgo release 1.5.0

Version 1.5.0 of the Ginkgo library for sparse linear algebra on CPUs and GPUs was released. It includes several improvements relevant to the MICROCARD project, such as multi-node support for all matrix formats and most solvers; full DPC++/SYCL support, and GPU-resident sparse direct solvers.

17 October 2022: Anatomic lesson by Dr José A. Cabrera

Several MICROCARD members attended an online interactive cardiac anatomy lesson given by Dr José Cabrera, a world-renowned expert in the percutaneous treatment of heart rhythm problems, for students in the MSc program Electromechanical Heart Diseases given at the Liryc institute in Bordeaux.

In these sessions, which Dr Cabrera performs for Liryc about yearly, he demonstrates human or animal heart samples to highlight the structures that are most interesting for cardiac electrophysiologists. Professional cameras and lighting techniques are used to allow the audience to look over the teacher's shoulder and to zoom in when needed.

For many of us, this was an unusual experience. Emmanuelle Saillard (computer scientist): "He mentioned a lot more names than I can remember, but it was impressive to see a heart this way. Frankly, I didn't expect this."

14 October 2022: Aslak Tveito will step down as director of Simula

Simula Research Laboratories announced that its CEO Aslak Tveito will step down in January 2023, after having led Simula for more than 20 years. Dr Tveito plans to spend more time on his research, which includes the "EMI Framework", the concept of modeling electrically active tissue on a cellular scale with separate intracellular and extracellular spaces, which also underlies the MICROCARD project. We think that this could be very good news for cardiology and neurology research.

October 2022: Simone Pezzuto becomes an assistant professor in Trento

The next MICROCARD member to move is Simone Pezzuto, who left USI to become an assistant professor at Università di Trento. Fortunately for us, he too will maintain a relationship with USI that allows him to participate fully in the project.

In Trento, Simone will in the Department of Mathematics. Next to his research work he will teach a 9-ECTS course in Mathematical Biology, for MSc students in Mathematics.

September 2022: Amina Guermouche is now an associate professor at Bordeaux INP

Many good things are happening to MICROCARD members this year. Amina Guermouche, until recently a research engineer at Inria, won a position as maître de conférences (associate professor) at the engineering school Bordeaux INP. Next to her new teaching duties she will continue working on the MICROCARD project, but most of her tasks will be taken over by Mariem Makni who moved from WP7 to WP2.

Francesco Brarda, who worked as an engineer on WP7, left for a PhD student position at Emory University. To replace him and Mariem, Laetitia Mottet and Corentin Prigent will join us in October.

July 2022: Hartwig Anzt nominated director of the Innovative Computing Laboratory

It is now official: Hartwig Anzt, one of our Work Package leaders, is the new director of the Innovative Computing Laboratory at the University of Tennessee. In this position he is succeeding Jack Dongarra, laureate of the 2021 Turing Award. We are very proud of this prestigious nomination and relieved to know that Hartwig has retained a part-time professorship at the Karlsruhe Institute of Technology, which allows him and his team members to continue participating in the MICROCARD project.

6 and 7 July 2022: the first in-person MICROCARD workshop

On the 6th and 7th of July 2022 our second workshop took place, this time face-to-face in the amphitheatre of the Liryc institute in Pessac, near Bordeaux. The meeting opened with an introduction by project coordinator Mark Potse followed by a keynote lecture by the computer scientist Professor William Jalby. Twelve presentations were given by project members, about their work in the project. Two presentations were planned to be given by members of our end-user advisory board, Eva Rog-Zielinska and Carol Ann Remme, but as Dr Remme had to cancel at the last minute, Dr Richard Walton from Liryc stood in with a presentation about micro-CT imaging. The meeting was completed with a guided tour of the experimental platforms of the Liryc institute. The complete program of the workshop is available on the events page.

We received 37 participants on-site and a dozen more online. Four of us had to return home due to a canceled train in Germany, one was forced to spend an unforeseen night at an airport hotel in Spain, and one made it barely ahead of a railway strike in France. In the end, only one presentation had to be given online.

June 2022: MICROCARD in Hamburg, Oslo, Paris, Milan, Budapest, and online

This month, the MICROCARD project was presented at the Teratec Forum 2022 on 14 and 15 June in Paris, and at the 5th Workshop on Heterogeneous and Low-Power Data Center technologies in the EuroHPC Projects Context (HeLP–DC) which is part of the HiPEAC meeting in Budapest on June 20–22.

Amina Guermouche presented MICROCARD results at the 4th Workshop on Resource Arbitration for Dynamic Runtimes (RADR), part of the IEEE IPDPS meeting. In her talk "Combining Uncore Frequency and Dynamic Power Capping to Improve Power Savings" she discussed new methods to reduce power consumption of large-scale computations by automatically adapting the speed of different computer parts to the needs of the program. The IPDPS meeting was 100% online this year.

Marie Houillon talked about the integration of the Ginkgo library in the openCARP software at the ISC High Performance meeting on May 29 to June 2 in Hamburg.

Giacomo Rosilho de Souza and Mark Potse presented MICROCARD work at the ECCOMAS meeting on 5-9 June in Oslo.

Giacomo will also present work on parallel-in-time methods at the CMBE meeting on 27-29 June in Milan.

1 June 2022: News from the ISC22 meeting

The ISC High Performance meeting took place from May 29 to June 2 in Hamburg. MICROCARD was present in several ways: Partner and supercomputer manufacturer MEGWARE took part in the exposition. Marie Houillon presented the integration of the Ginkgo library in the openCARP software, which is an important step in our work. And we were happy to see that EuroHPC executive director Anders Dam Jensen mentioned us specifically in his presentation.

Also at ISC22, Jack Dongarra unveiled the new top-500 of the world's fastest supercomputers. It included the first acknowledged exascale supercomputer, and had the recently installed French supercomputer Adastra in the top-10 with 46 Pflop/s. We will need exascale machines for our work and although we'll probably not get our hands on them soon, this first instance is good news for us.

Prior to the ISC meeting Dr Dongarra, whom we also know as creator of famous linear algebra software packages such as LINPACK and winner of the 2021 Turing Award, had made a visit to our partner KIT where he gave a lecture at the Steinbuch Computing Center, introduced by his former pupil Hartwig Anzt. The photo shows Hartwig Anzt, Steinbuch director Martin Frank, and Jack Dongarra between the racks of the HoreKa supercomputer at KIT. In the background, from left to right, Stefano Maurogiovanni, Vasilis Georgiou, Rached Chaaben, and Mike Tsai.

19 May 2022: Local meeting in Bordeaux

Today the project members in Bordeaux had a bilingual, interdisciplinary, interinstitutional and inter-work package meeting. Presentations by Emmanuelle Saillard (WP2), Zeina Chehade (WP3), Vincent Alba (WP2), Algiane Froehly (WP7), Francesco Brarda (WP7), and Mark Potse (WP7) represented the multidisciplinary character of the project, covering mathematical proofs, code optimization, large-scale parallel remeshing, and construction of tissue models. It was great to benefit from the wide range of expertise present.

9 May 2022: Interview with Stefano Maurogiovanni, ERASMUS+ intern at KIT

Stefano Maurogiovanni is an MSc student at the University of Pavia who is currently doing an internship in the group of Hartwig Anzt at KIT, where he is implementing a distributed solver based on algebraic multigrid (AMG) methods in the Ginkgo library, to support the MICROCARD project. In this article published by KIT Stefano and his colleague Rached Chaaben talk about their experience at KIT's Steinbuch Centre for Computing.

In Pavia Stefano is directed by Stefano Gualandi and Luca Pavarino. His stay at KIT was made possible by the ERASMUS+ program of the European Union and strengthens the collaboration within the MICROCARD project.

29 April 2022: MICROCARD leading the way in European supercomputing

MICROCARD is one of nine European supercomputing projects showcased in the brochure Leading the way in European supercomputing issued by CORDIS on behalf of the European Commission. These short stories give an easy to understand overview of what problems supercomputers are solving today.

9 April 2022: follow us on LinkedIn

We're now on LinkedIn as Project MICROCARD

Upcoming: summer school on cardiac electrophysiology

The Liryc summer school on cardiac electrophysiology is now open for registation. It will take place shortly before our project workshop in July 2022, at the same location. It is combined with a 2-day meeting of the PersonalizeAF project.

4 February 2022: first MICROCARD workshop

Our first project workshop took place on 4 February 2021. This edition was fully online; we hope for an in-person meeting in the summer.

22 December 2021

The European Processor Initiative writes: "The main result of general-purpose processor activities in EPI phase one, the Rhea processor, will be instrumental for the launch of European exascale supercomputers in 2023."

Friday 10 December 2021: our first conference abstracts

Our first conference abstracts have been submitted to the ECCOMAS meeting taking place in Oslo, Norway, June 2022, and to the WCCM-APCOM meeting in Yokohama, Japan, August 2022.

Tuesday 31 August 2021

The 2021 edition of the ETP4HPC handbook of European High-Performance Computing Projects is published, covering MICROCARD among 68 European HPC projects. If you don't like ads and cookies you can also download it in PDF format here.

Friday 27 August 2021

One new job opening in Lugano and two other positions still open on our jobs page.

Friday 2 July 2021

One new job opening and three other positions still open on our jobs page.

Wednesday 14 April 2021: funding complete

Today the German BMBF confirmed that the project will be co-funded from their side, so now we are sure that the project is completely funded.

12 February 2021

Today the Austrian FFG signed the funding contract for our Austrian partner, Numericor. Thus, five of the six national funding agencies that are involved have confirmed their co-funding for the project. Only the German BMBF is still working on it.

18 December 2020: Grant Agreement signed, ready for take-off!

This week the Grant Agreement for the MICROCARD project was signed by EuroHPC and by the partner institutes. We are now sure that the project will start on 1 April 2021.

24 September 2020

The project made its first public appearance today at the TERATEC Forum.

14 July 2020

The EU confirms that the MICROCARD project passed the evaluation stage. This means that it will be funded, if all of the parties agree with the Grant Agreement that is now to be prepared.

14 January 2020

After 3 months of very intensive work the MICROCARD proposal was submitted to EuroHPC.