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:

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)
11:00coffee 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

25 November 2024: new open positions

As our new Centre of Excellence is taking off, two positions are open on our jobs page. There are more to come next month or next year!

MICROCARD restarts in November 2024

The MICROCARD project ended on 30 September but MICROCARD will be reborn as a Centre of Excellence on 1 November 2024. It will be funded by EuroHPC call HORIZON-EUROHPC-JU-2023-COE-03.

25 September 2024: Thesis defense Arun Thangamani

Arun Thangamani successfully defended his thesis "Optimized Code Generation of Parallel and Polyhedral Loop Nests using MLIR" at the University of Strasbourg. This is the first thesis supported completely by the MICROCARD project.


more news

Agenda

Thursday 5 December

16:00 MICROCARD-2 Executive Board meeting

Friday 13 December

10:00 (!) monthly WP1 technical meeting

Tuesday 17 December

15:00 Monthly WP2+3 meeting

Wednesday 18 December

Castiel-2 and HPC3 meetings


full agenda

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