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Final MICROCARD workshop and Cardiac Physiome meeting September 2024
The last MICROCARD workshop was organized together with the annual meeting of the Cardiac Physiome Society, on 12 to 14 September 2024 in Freiburg im Breisgau, Germany. It was part of a cluster of events around MICROCARD hotspot Karlsruhe:
- 4-6 September: the Virtual Physiological Human (VPH) meeting in Stuttgart
- 8-11 September: the Computing in Cardiology (CinC) meeting in Karlsruhe
- 12-14 September: Cardiac Physiome and MICROCARD Meeting in Freiburg.
Thursday 12 September
Cardiac Physiome sessions
Friday 13 September
Cardiac Physiome sessions
Saturday 14 September
Morning: Cardiac Physiome sessions
| 13:00 | Welcome. Mark Potse |
| 13:15 | A word from the EuroHPC JU. Matteo Mascagni |
| 13:30 | Parallel-in-time methods for cardiac electrophysiology. Giacomo Rosilho de Souza |
| 13:45 | BDDC and GDSW scalable preconditioners for the cardiac EMI model. Ngoc Mai Monica Huynh |
| 14:00 | Algebraic Multigrid solvers for the cardiac EMI model on hybrid CPU–GPU architectures. Edoardo Centofanti |
| 14:15 | Efficient Simulation of Cardiac Electrophysiology at cellular level. Fatemeh Chegini |
| 14:30 | Load Balancing and automatic resource dimensioning for generated ionic model kernels. Vincent Alba |
| 15:15 | Automatic failure detection and restart in openCARP. Nicolas Ducarton |
| 15:30 | Finite Volume Methods and Numerical Simulations for the Cell-by-Cell Bidomain Model in Cardiac Electrophysiology. Zeina Chehade |
| 15:45 | The Challenge of the Low Precision Processor Trend - Computational Linear Algebra on Modern Architectures. Hartwig Anzt |
| 16:00 | Distributed Preconditioning Efforts in Ginkgo. Fritz Göbel |
| 16:15 | Distributed memory parallel simulator of the EMI model. James Trotter |
| 16:30 | Closing words |
| 16:45 | General Assembly meeting (private) |
MICROCARD Summer School
A summer school was organized on June 24-26 2024, in conjuction with the Simula Summer school in Computational Physiology.
Program:
| Mark Potse Introduction to the MICROCARD project | |
| Olivier Bernus: The role of cardiac microstructure in arrhythmias: Insights from experimental and clinical studies | |
| Eva Rog-Zielinska: 3D time-resolved electron microscopy: a contradiction in terms? | |
| Corentin Prigent: Meshing & MMG tutorial | |
| Edward Vigmond & Hermenegild Arevalo: openCARP tutorial | |
| Pietro Benedusi & Alessandro Gatti: Cell-by-cell modeling tutorial |
For further information see the dedicated website.
3rd MICROCARD Workshop on 4 and 5 July 2023
On the 4th and 5th of July 2023 our third workshop will take place on the main campus of Strasbourg University.
Meeting link: https://u-bordeaux-fr.zoom.us/j/89450683300
Tuesday 4 July
| 08:30 | welcome coffee |
| 09:00 | welcome and introduction |
| Vincent Loechner (Université de Strasbourg) [slides] and Mark Potse (Université de Bordeaux) [slides] | |
| 09:30 | invited presentation |
| Loop Optimization: A Matter of Art and Science | |
| Cédric Bastoul (Qualcomm) | |
| 11:00 | session 1: Geometry |
| Deep learning techniques for the instance segmentation of cardiomyocytes [slides] | |
| Fabio Frangiamore (Orobix) | |
| Cardiac Microstructure: Insights from 3D Confocal Microscopy | |
| Joachim Greiner (University of Freiburg and KIT) | |
| Meshing with Mmg [slides] | |
| Algiane Froehly (Inria) | |
| 12:30 | lunch |
| 14:00 | session 2: openCARP |
| Web interface for cardiac simulations [slides] | |
| Tomas Stary (KIT) | |
| Simulated Excitation Patterns in the Atria and Their Corresponding Electrograms [slides] | |
| Joshua Steyer (KIT) | |
| Adaptive higher-order time integration and BDDC preconditioning; EMI in openCARP [slides] | |
| Fatemeh Chegini (ZIB) | |
| 16:00 | session 3: open discussion |
| chair: Martin Weiser (ZIB) | |
| topics include test cases for microCARP, end-user interaction | |
| 17:00 | General Assembly meeting (GA members only) |
| 18:30 | social event |
Wednesday 5 July
| 08:30 | welcome coffee |
| 09:00 | special invited session on the EMI model |
| Operator preconditioning for the EMI equations [slides] | |
| Miroslav Kuchta (Simula) | |
| Cell-based modeling and simulation of electrical and chemical interplay in excitable tissue [slides] | |
| Ada Ellingsrud (Simula) | |
| From EMI to KNP-EMI: spectral properties and scalable solvers [slides] | |
| Pietro Benedusi (Simula) | |
| 10:30 | break |
| 11:00 | session 4: modeling |
| The Need for Microscale Modelling of Atrial Fibrillation | |
| Edward Vigmond (Université de Bordeaux) | |
| Investigating implicit and explicit methods for serial and parallel integration of stiff ionic models [slides] | |
| Giacomo Rosilho de Souza (U. Pavia) | |
| Finite Volume Methods for the EMI Model of Electrocardiology : From Admissible to General Meshes [slides] | |
| Zeina Chehade (Université de Bordeaux) | |
| 12:30 | lunch |
| 14:00 | session 5: code optimization |
| CUDA and ROCm GPU Ionic Models: Raw Performance and Energy Performance [slides] | |
| Arun Thangamani (Université de Strasbourg) | |
| Ionic models implementation update: multi-target (CPU+GPU), StarPU interface, and code improvements [slides] | |
| Raphaël Colin (Université de Strasbourg) and Vincent Alba (Université de Bordeaux) | |
| Fault tolerance for distributed application | |
| Amina Guermouche (Bordeaux INP) | |
| 15:30 | break |
| 16:00 | session 6: solvers |
| Recent Ginkgo development and the 1.6.0 release [slides] | |
| Terry Cojean and Pratik Nayak (KIT) | |
| BDDC preconditioning in Ginkgo - a status update [slides] | |
| Fritz Göbel | |
| Scalable multilevel preconditioners for cell-by-cell and Bidomain cardiac models [slides] | |
| Luca Pavarino and Ngoc Mai Monica Huynh (U. Pavia) | |
| 17:30 | closing |
| 17:30 | Executive Board meeting (EB members only) |
WP3+5 meeting in Berlin, March 16 and 17, 2023
For 16 and 17 March 2023 the members of WP3 and WP5 are planning a live meeting at ZIB in Berlin. For practical information see the hints for visitors.
Thursday 16 March
| 09:00 | opening session |
| 09:30 | spatial discretization status |
| 11:30 | time discretization status |
| 14:00 | preconditioner status |
| 16:00 | modularization concept discussion |
| 17:00 | µCARP software structure and concepts |
Thursday 17 March
| 09:00 | joint paper planning / scheduling |
| 10:30 | hands-on implementation and design |
| 13:30 | recap of insights gained and consequences for algorithmic development |
| 15:30 | report and project review planning pair programming and paper writing |
2nd MICROCARD Workshop on 6 and 7 July 2022
On the 6th and 7th of July 2022 our second workshop took place in the amphitheatre of the Liryc institute in Pessac, near Bordeaux. Below the final program of the meeting is shown.
Wednesday 6 July
| 09:30 | opening session |
| Welcome, introduction, and state of the project | |
| Mark Potse, coordinator | |
| 10:15 | keynote lecture: The Long and Winding Road Toward Efficient High-Performance Computing |
| William Jalby (LI PARAD laboratory, U. Versailles Saint-Quentin/U. Paris Saclay) | |
| 11:00 | coffee break |
| 11:15 | numerical schemes |
| Boundary element and explicit stabilized methods for the cell-by-cell model in electrophysiology | |
| Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause | |
| Higher-order time integration with algebraic adaptivity in the cell-by-cell model | |
| Fatemeh Chegini and Martin Weiser | |
| 12:15 | lunch break |
| 13:30 | HPC code development |
| Porting the openCARP framework to modern accelerators leveraging Ginkgo's GPU capabilities | |
| Fritz Göbel | |
| Expansion of the openCARP DevOps toolchain for easier development, maintenance and usage | |
| Marie Houillon | |
| 14:30 | automated code generation (private session) |
| Data layout transformation and vectorization of ionic models | |
| Arun Thangamani | |
| 15:00 | Towards a GPU code generation of ionic models |
| Tiago Trevisan Jost | |
| 15:30 | coffee break |
| 16:00 | General Assembly (private) |
| This meeting takes place in the Salle du conseil and is only accessible to GA members. |
Thursday 7 July
| 09:30 | invited presentations |
| Visualising cardiomyocyte nanostructure during health and disease | |
| Eva Rog-Zielinska (Uni. Freiburg, MICROCARD EAB member) | |
| MicroCT in translational cardiology | |
| Richard Walton (Liryc) | |
| 10:20 | optimization of ionic models |
| Handling load, architecture and precision heterogeneity for ionic models | |
| Denis Barthou, Marie-Christine Counilh, and Vincent Alba | |
| 11:00 | coffee break |
| 11:20 | mesh adaptation - chair: Axel Loewe |
| Introduction to remeshing | |
| Algiane Froehly | |
| Development of a massively parallel remeshing code for exascale geometries | |
| Francesco Brarda and Algiane Froehly | |
| A practical algorithm to build geometric models of cardiac muscle structure | |
| Mark Potse, Luca Cirrottola, and Algiane Froehly | |
| 12:20 | clinical view |
| The fibrillating heart | |
| Mélèze Hocini (Liryc, MICROCARD EAB member) | |
| 12:40 | lunch break |
| 13:30 | solvers and preconditioners - chair: Simone Pezzuto |
| 13:30 | A scalable BDDC preconditioner for the cardiac cell-by-cell model with a hybrid discontinuous Galerkin discretization |
| Luca Pavarino, Simone Scacchi, Ngoc Mai Monica Huynh, Fatemeh Chegini, and Martin Weiser | |
| 14:00 | Parallel nonlinear solvers for implicit time discretizations in cardiac electrophysiology |
| Ngoc Mai Monica Huynh, Nicolás A. Barnafi, Luca Pavarino, and Simone Scacchi | |
| 14:30 | visit of the experimental platforms at Liryc |
| 15:15 | coffee break |
| 15:30 | Inter-WP discussion on the implementation of the cell-by-cell model |
| This meeting takes place in the Salle du conseil and is limited to 30 participants. |
PersonalizeAF workshop on 4 and 5 July 2022
The ITN PersonalizeAF will organize a workshop in July 2022, just before ours, at the same location.
Liryc summer school on cardiac electrophysiology, 27 June - 1 July 2022
The next Liryc summer school on cardiac electrophysiology will be held in the last week of June 2022 at the Liryc institute in Pessac, near Bordeaux. It is expected to be an on-site event.
1st MICROCARD Workshop on 4 February 2022
| 13:00 | Welcome and introduction to MICROCARD [Mark Potse, coordinator] |
| 13:15 | keynote: 3D imaging of myocardial architecture using immunolabeling and confocal microscopy [Frank Sachse] |
| 14:05 | Deep learning approach for the segmentation of cardiomyocytes [Andrea Dorizza] |
| 14:25 | break |
| 14:40 | First results on the impact of dynamic power capping on performance and power consumption [Amina Guermouche] |
| 15:00 | Choice of a linear solver and preconditioner for µCARP [Hartwig Anzt] |
| 15:20 | FEM Discretization and Implementation of the Cell-by-Cell Model [Fatemeh Chegini] |
| 15:40 | break |
| 16:00 | Lifting the code generation of ionic models to novel compiler technology [Tiago Trevisan Jost] |
| 16:20 | Overview of the numerical scheme for µCARP [Yves Coudière] |
| 16:40 | discussion |
MICROCARD Kick-off meeting on 19 April 2021
| 13:00 | Welcome and presentation of the project [Mark Potse, coordinator] |
| 13:30 | Welcome by the director of Liryc [Pierre Jaïs] |
| 13:45 | Presentation of the EuroHPC Joint Undertaking [Daniel Opalka, project officer] |
| 14:00 | break |
| 14:30 | presentation of the teams |
| Modeling team at Liryc [Mark Potse] | |
| STORM team at Inria [Denis Barthou] | |
| MMG consortium [Algiane Froehly] | |
| CAMUS team at Université de Strasbourg/Inria [Vincent Loechner] | |
| SIMULA [Xing Cai] | |
| Università degli studi di Pavia [Luca Pavarino] | |
| Università della Svizzera italiana [Rolf Krause] | |
| Biomedical Engineering at KIT [Axel Loewe] | |
| Steinbuch Centre for Computing at KIT [Hartwig Anzt] | |
| Zuse Institute Berlin [Martin Weiser] | |
| MEGWARE [Axel Auweter] | |
| Numericor [Aurel Neic] | |
| Orobix [Luca Antiga] | |
| 15:30 | keynote: Cardiac electrophysiology and arrhythmia [Olivier Bernus, scientific director of Liryc] |
| 16:15 | conclusion [Mark Potse] |