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Final MICROCARD workshop and Cardiac Physiome meeting September 2024

The last MICROCARD workshop will be organized together with the annual meeting of the Cardiac Physiome Society, on 12 to 14 September 2024 in Freiburg im Breisgau, Germany. It will be part of a supercluster of events around MICROCARD hotspot Karlsruhe:

Stuttgart and Freiburg are a 45 minutes and 1 hour train raide away from Karlsruhe, respectively, so it's easy to attend all three meetings.

Thursday 12 September

Cardiac Physiome sessions

Friday 13 September

Cardiac Physiome sessions

Saturday 14 September

MICROCARD sessions with presentations by Joshua Steyer, Tomáš Starý, Andréa Alexander, Mark Potse, Fatemeh Chegini (tbc), Zeina Chehade, ... (more to come)

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)
11:00coffee break
11:15numerical 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
12:15lunch 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
14:30automated 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
15:30coffee 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)
10:20optimization of ionic models
Handling load, architecture and precision heterogeneity for ionic models
Denis Barthou, Marie-Christine Counilh, and Vincent Alba
11:00coffee break
11:20mesh 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
12:20clinical view
The fibrillating heart
Mélèze Hocini (Liryc, MICROCARD EAB member)
12:40lunch break
13:30solvers 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
14:30visit of the experimental platforms at Liryc
15:15coffee 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]

LinkedIn: @project MICROCARD

Twitter: @P_Microcard

Latest news

13 September: Interview with Fatemeh Chegini

Latest in a series of interviews with young MICROCARD members, our interview with Fatemeh Chegini was posted on LinkedIn today.


more news

Agenda

15 to 19 July

46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society in Orlando, Florida, USA

Friday 19 July

10:00 WP2+6 meeting

Friday 26 July

14:00 WP7 meeting


full agenda

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