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Jobs

We expect to open about 20 positions for PhD students, postdocs, and engineers. Most of these positions will be opened in 2021, a few more in 2022.

All open positions will be published on EURAXESS and on national and local platforms. In addition we will give an overview here.

Currently open positions

Engineer - Task parallelization of a cardiac simulation code

WP2. Location: Bordeaux.

The detailed meshes of cardiac tissue that this project requires will have unprecedented size and an unprecedented level of parallelism. To run simulations efficiently, massive parallellism is required and due to the large scale of the simulation, the execution has to be resilient to possible faults and requires a checkpoint/restart strategy.

The engineer will be in charge of the parallelization of the code. This parallelization will rely on MPI and StarPU [1]. More particularly, the engineer will have to write the parallelism as a parallel task graph, optimize it and evaluate its performance. Lastly, an evaluation of the method for partial checkpointing based on such task graph will be conducted. The different steps during this mission are:

1. Parallelization in StarPU+MPI of the OpenCarp simulation code;
2. Adaptation to a newly developed fault-resilient version of StarPU; and
3. Maintenance of the parallelization scheme as the code is modified by others to handle heart models with sub-cellular resolution.

Expired offers

Engineer - Mesh generation of cardiac meshes at cellular scale

WP7. Location: Bordeaux.

The MICROCARD project will require large and detailed meshes of cardiac tissue structure to perform simulations on. The engineer will be in charge of the development of the open source toolchain for the generation of 3D tetrahedral meshes for the project test cases. Starting from segmented data (voxels labeled as vessels, myocyte, fibroblast…) provided by project partners, this person will develop robust tools for:

1. Building tetrahedral meshes from 3D image voxels;
2. Data filtering and cleaning;
3. Explicit discretization of cellular domains by isovalue discretization and mesh improvement and adaptation (implementation within the parallel open source remesher ParMmg and the sequential remesher Mmg).

Postdoc - Parallel isovalue discretization and mesh adaptation on hybrid architectures

WP7. Location: Bordeaux.

The detailed meshes of cardiac tissue that the MICROCARD project requires will have unprecedented size, ultimately in the order of 10¹² elements. To create such meshes, powerful parallel mesh generation software must be developed.

The open source software ParMmg, based on iterative calls of the serial remesher Mmg over sub-meshes, allows to adapt a mesh using a distributed algorithm based on the MPI standard. The post-doctoral researcher will be in charge of writing a new task-based algorithm, and then implementing it using the StarPU task scheduler. This will allow the software to make efficient use of both hybrid parallelization paradigms and new heterogeneous architectures.

Future positions

The following positions are expected to be opened if all goes well.

Postdoc - Modelling of Atrial Fibrillation at a very Fine Scale

WP8. Location: Bordeaux, Starting: 1/1/2022

Atrial fibrillation (AF) remains difficult to treat as the recurrence rate after ablation remains high. This project will look at the influence of structural and electrical heterogeneity on AF at an unprecedented scale, both the triggering and maintenance.

The postdoc will create very high resolution atrial models incorporating shape, fibre architecture, fibrosis and electrical remodelling data. A major challenge will be working with the large datasets produced, including their analysis and visualization. The person for this position is expected to have a strong knowledge of both computer modelling/numerical methods and electrophysiology, with a proficiency in analyzing data.

For information please contact Dr Edward Vigmond at IHU Liryc.