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WP 1 Software integration and provision

This work package will develop and deploy a complete DevOps toolchain as the basis for the overall aim of the MICROCARD project: a production-ready simulation platform for cardiac electrophysiology at the cellular scale on future exascale computers. Moreover, it will integrate the advances regarding parallelization, discretization, resilience, energy consumption, and tailored numerical schemes in the openCARP software stack.

People

leaders: Axel Loewe, Aurel Neic

faculty: Nico Mittenzwey, Xing Cai, Mark Potse, Simone Pezzuto, Martin Weiser, Vincent Loechner, Luca Antiga, Luca Pavarino

staff: Jorge P. Sánchez Arciniegas, Fatemeh Chegini

Tasks

Task 1.1 Software interoperability, bundling and maintenance

Task 1.2 Continuous Integration and Deployment

Task 1.3 High-Performance Data Output

Task 1.4 Simple and Secure Access & Collaboration

WP 2 Task-based parallelization

Task-based parallelization is needed to obtain the flexibility required for our code to scale to thousands of compute nodes that may be equipped with thousands of processors each, with different architectures such as CPUs, GPUs, and other accelerators. The objective of this work package is therefore to provide a parallel and task-based formulation of the application. In addition, this formulation will be able to deal with hardware failures of some nodes during the execution.

People

leaders: Denis Barthou, Vincent Loechner

faculty: Emmanuelle Saillard, Mark Potse, Bérenger Bramas, Luca Antiga, Martin Weiser, Yves Coudière

staff: Fatemeh Chegini

Tasks

Task 2.1 Parallel task-graph expression

Task 2.2 Hiding MPI communication latency

Task 2.3 Adaptation of automatic checkpoint placement strategy

Task 2.4 Evaluation of the resilience

WP 3 Numerical discretization and implementation of the cell-by-cell model

This work package will develop suitable discretization schemes to turn the system of partial differential equations that describes the current flow in the tissue into a system of algebraic equations. These schemes need to be numerically efficient in terms of convergence order, sparsity, and condition numbers, but also well suited for current and future HPC architectures in terms of parallelization and vectorization opportunities as well as energy demand and incurred communication.

People

leaders: Martin Weiser, Simone Pezzuto

faculty: Yves Coudière

staff: Fatemeh Chegini

Tasks

Task 3.1 Space discretization

Task 3.2 Time discretization

Task 3.3 Adaptivity

Task 3.4 Coupling to bidomain

Task 3.5 Implementation of μCARP

WP 4 Production-ready high performance linear solver technology

This work package will develop custom linear solvers, adapted to the needs of the numerical scheme and working in collaboration with the preconditioners developed in WP5. The solvers will be deployed in the Ginkgo open-source sparse linear algebra library, to make them available to all computational science research.

People

leaders: Hartwig Anzt, Simone Scacchi

faculty: Xing Cai, Vincent Loechner

staff: Terry Cojean

Description

In this work package, we will develop and implement iterative linear solvers meeting the requirements of the MICROCARD simulation ecosystem. This entails efficiently exploiting the compute power available in next-generation manycore processors, scaling to large processor counts, reduced communication and synchronization overheads, and flexibility in accepting different preconditioner types (WP5) and integrating into the MICROCARD software stack (WP1). Production-ready implementations of the iterative linear solvers will be deployed in the Ginkgo open-source sparse linear algebra library, therewith making the solver technology available to all computational science research. A special focus will be put on portability and platform-specific energy considerations. The Continuous Integration (CI) service provided by MEGWARE will form the basis for the solver development for non-standard and prototype hardware, with an emphasis on the technology developed in the European Processor Initiative (EPI). Thanks to a unique technology with high-resolution power measurement this server will notably help us to move to a multi-objective optimization accounting not only for runtime but also for energy balance.

Tasks

Task 4.1 Assessment of linear solver requirements

Task 4.2 Hardware-aware high performance linear solver development

Task 4.3 Linear solver preconditioner integration

Task 4.4 Linear solver application integration

WP 5 Tailored preconditioners

The effective solution of the PDE systems employed in MICROCARD on HPC architectures requires highly scalable iterative solvers and preconditioners that are tailored to the problem and to each other. In this work package we will develop the preconditioners, which will work with the linear solvers developed in WP4.

People

leaders: Luca Pavarino, Rolf Krause

faculty: Simone Scacchi, Stefano Gualandi, Raffaella Guglielmann, Piero Colli-Franzone, Hartwig Anzt

staff: Fatemeh Chegini

Description

In order to fully exploit the pre-exascale and exascale parallel machines targeted by this project, our primary concern will be to obtain weak scalability, i.e. maintaining per-element performance with a large number of model elements. We will also target strong scaling, i.e. the best speedup for a fixed problem size with respect to the number of processors.

Weak scalability for reaction-diffusion problems is typically achieved by using multilevel preconditioners, such as multigrid (MG) and domain decomposition (DD) preconditioners. We will design, implement, and validate novel preconditioners based on recent advances in one-level and multilevel methods. Our strategy will be to explore both several multiplicative levels (such as in MG methods) and a few additive levels (such as in DD methods). Our preconditioners will be tailored to the specific choice of both space-time discretization (WP 3) and iterative solvers (WP4).

Tasks

Task 5.1 One-level preconditioners

Task 5.2 DD preconditioners

Task 5.3 MG preconditioners

Task 5.4 Compressed communication

WP 6 Code generation for heterogeneous architectures

High-performance computers rely more and more on innovative techniques such as vector units and massive but functionally limited parallelism. To obtain optimal performance from these systems it is necessary to write specially adapted code. In this work package we will develop tools that can write such code automatically, based on higher-level descriptions of the functionality.

People

leaders: Vincent Loechner, Denis Barthou

faculty: Xing Cai, Bérenger Bramas

staff:

Description

This work package will build a bridge from a high-level model representation convenient for ionic model experts to an optimized implementation that exploits both target architecture resources and properties of the scientific problem (computation patterns, resilience to approximation). We will design a compiler infrastructure to translate an equational formulation extended with domain-specific information to a code that aims to be efficient in both execution time and energy dissipation. Our objective is (1) to maximize productivity by allowing users to express the scientific problem rather than the implementation details and (2) to maximize flexibility. Our strategy is to rely on a dedicated compiler front end, and on new research extending state-of-the-art code generation and runtime techniques to statically and dynamically optimize the application.

Tasks

Task 6.1 Compilation scheme for equational formulation

Task 6.2 Parallel source code generation

Task 6.3 Adaptive code optimization

Task 6.4 Runtime resources and heterogeneity management

WP 7 Mesh generation

The simulations that our software is to perform will require exceptionally large meshes. In this work package we will develop adapted segmentation tools and a high-performance version of the parMMG meshing software, using the same task-based parallelization methods as for the simulation code itself.

People

leaders: Algiane Froehly, Luca Antiga

faculty: Raffaella Guglielmann, Nicolas Barral, Luca Cirrottola

staff:

Description

This work package will provide the tools to create the extremely large meshes needed for the macroscopic cell-by-cell models in the MICROCARD project. We will develop a new version of the parMMG meshing software using a task-based parallellization paradigm, based on the same tools and expertise as the simulation software in the project, and able to run on large heterogeneous supercomputers. We will further develop the automated image segmentation and mesh construction toolchain that will be needed for the use cases.

Tasks

Task 7.1 segmentation and mesh preparation

Task 7.2 parallelization of meshing software

WP 8 Use cases

In this work package the tools that are developed in the project will be road-tested on four different use cases, involving pathologies such as atrial fibrillation and mycardial infarction.

People

leaders: Hermenegild Arevalo, Edward Vigmond

faculty: Axel Loewe, Mark Potse

staff:

Description

The purpose of this work package is to test the developed modeling technologies in the most realistic and demanding way, by using them for cardiological research projects in the hands of researchers who are experienced in applied modeling studies, in collaboration with cardiologists or physiologists.

Tasks

Task 8.1 Role of heterogeneous re-modeling during ischemia in promoting arrhythmias

Task 8.2 The effect of microscopic tissue structure on clinical electrograms

Task 8.3 Relation between macroscopic conduction properties and microstructural defects

Task 8.4 The effects of micro- and macro-structure on atrial fibrillation

Task 8.5 Arrhythmia in idiopathic cardiomyopathies

WP 9 Project outreach: dissemination and exploitation

This work package concentrate our efforts to share what we learn and develop during the project, to different audiences ranging from specialists in different domains to students at different levels, and interested citizens.

People

leaders: Mark Potse, Axel Loewe

project manager: Anne-Cécile Huby

faculty: Raffaella Guglielmann

staff:

Description

This work package aims at ensuring

  • engagement with and uptake of the MICROCARD software by the users,
  • project dissemination towards the different stakeholders,
  • sustainability of the developed software after the project ends, and
  • management of IP and data to support the exploitation strategy.
  • Tasks

    Task 9.1 Engagement with the direct user community

    Task 9.2 Engagement with the end user community

    Task 9.3 Dissemination activities

    Task 9.4 Exploitation & sustainability

    Task 9.5 Knowledge management (IP and data)

    WP 10 Project management

    This last work package serves the scientific and financial coordination, risk management, quality assurance, and reporting of the project.

    People

    scientific coordinator: Mark Potse

    scientific and technical manager: Yves Coudière

    project manager: Anne-Cécile Huby

    faculty: Vincent Loechner, Luca Pavarino, Axel Loewe, Hartwig Anzt, Rolf Krause, Xing Cai, Martin Weiser, Luca Antiga

    staff:

    Description

    This work package will ensure that MICROCARD achieves its stated objectives within the given resources and time schedule. The goals are to

  • provide a strategic vision for the project, manage the risks, and ensure the highest level of quality for the scientific deliverables;
  • coordinate and monitor the project implementation, in accordance with the signed grant agreement;
  • enhance the visibility of the project via a clear visual identity and online presence.
  • Tasks

    Task 10.1 Scientific coordination, quality assurance and risk monitoring

    Task 10.2 Project management and EC reporting

    Task 10.3 Overall project communication and branding

    Latest news

    Friday 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.


    more news

    Agenda

    1 April 2021

    Project start

    12 to 16 April 2021

    2021 Exascale Computing Project Annual Meeting

    19 and 20 April 2021 13:00 to 17:00 CET

    MICROCARD kick-off meeting (online)


    full agenda

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