IDCHP et Biologie. Demi-journée de la FIL

IDCHP et Biologie. Demi-journée de la FIL

Matinée du 31 mars. Demi journée du thème Informatique distribuée et calcul haute performance (IDCHP) de la Fédération Informatique de Lyon

Le 31 mars à 10h00 en virtuel. Informations de connexion vous serons communiqué à partir de votre mail d’inscription. 
Informations disponibles également ici:

Séminaire IDCHP et…

Les demi-journées « IDCHP et… » mêlent exposés au cœur du thème et ouvertures à d’autres communautés.

Les exposés visent en général un public large et, si possible, jeune : la présentation des problématiques d’IDCHP va en effet de pair avec l’effort de formation et la motivation des vocations : la transmission d’une culture qui situe les compétences et offre les opportunités de collaboration. C’est l’ambition du thème.

Séminaire IDCHP et biologie

Matinée du mercredi 31 mars 2021

L’inscription est gratuite mais obligatoire sur le formulaire accessible [ici]

Les informations de connexion pour les exposés et discussions seront transmises aux inscrits.

Emmanuel Godard

Panorama des Modèles de Calcul Distribué : Des réseaux sans-fil aux systèmes biologiques. (A Distributed Computing Models Panorama : From wireless networks to biological systems)
We present a panorama of modern distributed computing models. These models are highly diverse being introduced for many different application contexts : internet communication networks, HPC, manycores machines, vehicular networks, etc. We show that there exists common notions to organize this variety and that most models are fortunately computationnaly equivalent to (variant of) others. We will in particular focus on an elegant model that has been defined and redefined in many contexts, from highly dynamic networks to shared registers. We also expose how distributed models can escape the digital world, going eg from wireless networks to biological systems.  

Loïc Paulevé

Formal methods for capturing dynamics of biological networks
The prediction of behaviors of biological systems is a tremendous challenge at the intersection of multiple disciplines, including mathematics and computer science. Processes such as cellular differentiation involve many actors at the molecular and genetic level, and whereas global knowledge exists on their pairwise interactions, their observation provides limited information for devising a precise model. In this talk, I’ll give an overview of formal methods around the /qualitative/ modelling of dynamics of biological networks which offers coarse-grained but robust predictions. Motivated by applications in cellular reprogramming, I’ll focus on Boolean networks with questions related to the update schedule of nodes and its influence on reachability and stability properties.  


Pour toutes questions merci de contacter Xavier Urbain et/ou Eddy Caron.

Posted in FIL

Entretiens Jacques Cartier – Colloque : “Effets rebonds dans le numérique. Comment les détecter ? Comment les mesurer ? Comment les éviter ?”

2 Novembre 2020 – 9h00-12h00 (Heure Québec / Canada) // 15h00-18h00 (Heure Française)

Organisé par le Centre Jacques Cartier, l’Ecole Normale Supérieure de Lyon, Inria, le laboratoire LIP, l’Université de Sherbrooke, le CIRAIG et le GDS EcoInfo avec des intervenants franco-québécois en sciences du numérique et en sciences humaines et sociales.

Plus d’informations :

Avalon is contributing to LLVM OpenMP/runtime

Philippe Virouleau, funding thanks to EoCoE-II project, has proposed patches to LLVM OpenMP/runtime in order to provide better control and performances of OpenMP task execution. First accepted patch was pushed in LLVM master branch ( It solves an side effect due to the task throttling heuristic that serializes task execution. It may  cripple the application performance in some specific task graph scenarios, like the ones detailed in section 4.2 from this paper published at IWOMP 2018 (the full text can be found here). In such cases not having the full task graph prevent some opportunities for cache reuse between successive tasks.

Mid term goals are to transfer some important and innovative features mostly already available in libKOMP



Avalon at the TILECS Workshop

Avalon at the TILECS Workshop

Towards an Infrastructure for Large-Scale Experimental Computer Science

3 et 4 juillet, Campus Grenoble, France

More information about SILECS and the TILECS Workshop:

Laurent Lefevre (Avalon / Speaker) and Georges Da Costa with Christian Perez (Avalon / Chairman)

SILECS is a research infrastructure being built to gather the efforts of several testbeds.


The Avalon team are involved in this impressive project.

Farah Ait Salaht, Eddy Caron, Marcos Dias de assuncao, Laurent Lefevre (speaker), Matthieu Imbert, Christian Perez  (Session Chairman) was at this workshop.

Journée STIP Inria – Rencontre Avalon

The STIP Inria day started

Journée Ateliers Valorisation organisé par le STIP (Service Transfert Innovation et Partenariat ) Inria le 18 juin au LIP.

Organisation: STIP Inria (Helena Jerôme, Philippe Broun)

Intervenants: Pascale Vicat Blanc, Olivier Arsene, Xavier Blot

Lieu: Salle de réunion du M7


9h-12h : ateliers d’introduction à l’entrepreneuriat, présentations des dispositifs Inria (accompagnement, financement…), témoignage et retour d’expérience et échanges avec Pascale Vicat Blanc, scientifique-entrepreneure Inria (spécialisée dans le Cloud Computing)
13h15-16h15 : Ateliers en groupe basés entre autre sur une méthode de créativité : choix d’une techno/sujet dans les sujets scientifiques de l’équipe Avalon et sur les domaines d’applications des résultats de recherches, pour illustrer l’atelier, construction d’un livrable utile aux participants (encore à définir)

Participants: Marouane Azzouz, Dorra Boughzala, Eddy Caron, Alexandre Da Silva Veith, Felipe De Souza, Zakaria Fraoui, Mohamed Hamnache, Zeina Houmani, Cyril Séguin.

The day in live

10h15 : The Marshmallow Challenge

Organized by Beyond Lab (Xavier Blot and Olivier Arsene)

18 minutes to build the Marshmallow Tower …

Alexandre, Zeina and Felipe Team



Cyril, Dorra and Zakaria Team








And the winner is …

Cyril, Dorra and Zakaria Team

10h35: What’s STIP Inria can do for you [Philippe Broun]

Philippe Broun’s Talk – What’s the STIP can do for you

If you are lost in Innovation world… Who ya gonna call?










10h57: Start’up experience: an amazing human adventure [Pascale Vicat-Blanc]

The Pascale Vicat-Blanc’s start-up experience









12h15: Beyond Lab introduction [Xavier Blot and Olivier Arsene]

The website:

Beyond lab introduction


Lunch … discussions continue with the help of a good Pizza …








14h05-16h45 Workshop to introduce three Avalon’s projects

A game with three teams.

Stage 1: Elevator pitch

SeeDep, SkyData and FogMonitoring

Stage 2: Team, appropriate, go beyond… Find the value

Each team try to find the value of an other project.

Stage 3: Final Pitch and Strategy


Thesis Defense – Hadrien Croubois

Hadrien Croubois: Toward an autonomic engine for scientific workflows and elastic Cloud infrastructure

Everyone is welcome to attend Hadrien Croubois’s thesis defense, which will take place Tuesday 16th October at 14h at Salle des thèse (ENS de Lyon).

You are also invited to the cocktail that follows the defense.


Eddy Caron, ENS de Lyon

Committee members:

Noël De Palma, Université Jospeh Fourier, reviewer
Johan Montagnat, CNRS, Laboratoire I3S UMR 7271, reviewer
Luciana Arantes, Université Sorbonne, examiner
Frédéric Desprez, Inria, examiner
Pushpinder Kaur Chouhan,Ulster University, examiner


The constant development of scientific and industrial computation infrastructures requires the concurrent development of scheduling and deployment mechanisms to manage such infrastructures. Throughout the last decade, the emergence of the Cloud paradigm raised many hopes, but achieving full platform autonomicity is still an ongoing challenge.

Work undertaken during this Ph.D. aimed at building a workflow engine that integrated the logic needed to manage workflow execution and Cloud deployment on its own. More precisely, we focus on Cloud solutions with a dedicated Data as a Service (DaaS) data management component. Our objective was to automate the execution of workflows submitted by many users on elastic Cloud resources.

This contribution proposes a modular middleware infrastructure and details the implementation of the underlying modules:

  • A workflow clustering algorithm that optimises data locality in the context of DaaS-centered communications;
  • A dynamic scheduler that executes clustered workflows on Cloud resources;
  • A deployment manager that handles the allocation and deallocation of Cloud resources according to the workload characteristics and users’ requirements.

All these modules have been implemented in a simulator to analyse their behaviour and measure their effectiveness when running both synthetic and real scientific workflows. We also implemented these modules in the DIET middleware to give it new features and prove the versatility of this approach. Simulation running the WASABI workflow (waves analysis based inference, a framework for the reconstruction of gene regulatory networks) showed that our approach can decrease the deployment cost by up to 44% while meeting the required deadlines.

Phd Crossover

Phd Crossover

LIP & LBMC – Avalon & Gandrillon – Hadrien & Arnaud –

En octobre vous pouvez découvrir le crossover entre la thèse d’Hadrien Croubois (Avalon) du laboratoire de l’Informatique du Parallélisme (LIP) de l’ENS  et d’Arnaud Bonnafoux (Gandrillon) du Laboratoire de Biologie Moléculaire de la Cellule (LBMC) de l’ENS.


Commencez par découvrir le vendredi 12 octobre 2018, à 14h à l’ENS de Lyon site Monod (salle de réunion M6) comment Arnaud Bonnafoux a conçu WASABI. (Plus d’information ici)

au LIP

Puis venez découvrir le mardi 16 octobre 2018, à 14h à l’ENS de Lyon site Monod (salle des thèses) comment le moteur de workflow d’Hadrien Croubois est profitable aux besoins en calcul de WASABI. (Plus d’information ici)

Thesis Defense — Pedro Silva

Everyone is welcome to attend Pedro Silva’s thesis defense, which will take place next Monday 11th December at 14h at Salle Place de l’Ecole (1, Place de l’École, 69003).

On the mapping of distributed applications onto multiple Clouds.

Christian Perez, Inria
Frédéric Desprez, Inria

Committee members:
Patricia PASCAL-STOLF, IUT de Blagnac, reviewer
Emmanuel Jeannot, Inria, reviewer
Christine Morin, Inria, examiner
Erik Elmroth, University of Umea – Sweden, examiner

You are also invited to the cocktail that follows the defense at the
LIP’s coffee area (coin café) (46 Allée d’Italie, 3rd floor).


The Cloud has become a very popular platform for deploying distributed applications. Today, virtually any credit card holder can have access to Cloud services. There are many different ways of offering Cloud services to customers. In this thesis we specially focus on the Infrastructure as a Service (IaaS), a model that, usually, proposes virtualized computing resources to costumers in the form of virtual machines (VMs).
Thanks to its attractive pay-as-you-use cost model, it is easier for customers to outsource hosting infrastructures and benefit of
savings related to upfront investments and maintenance costs. Also, customers can have access to features such as scalability, availability, and reliability, which previously were almost exclusive for large companies.

To place a distributed application on the Cloud, a customer must first consider the mapping between her application (or its parts) to the target infrastructure. She needs to take into consideration cost, resource, and communication constraints to select the most suitable set of VMs, from private and public Cloud providers. However, defining a mapping manually may be a challenge in large-scale or time constrained scenarios since the number of possible configuration explodes. The large offer of Cloud providers in the market and eventual advantages of having an application deployed over different Cloud sites, like redundancy and reachability, for example, make this challenge even more complex. Furthermore, when automating the mapping definition, scalability issues must be taken into account since this problem is a generalization of the graph homomorphism problem, which is NP-complete.

In this thesis we address the problem of calculating initial and reconfiguration placements for distributed applications over possibly multiple Clouds. Our objective is to minimize renting and migration costs while satisfying applications’ resource and communication constraints. We concentrate on the mapping between applications and Cloud infrastructures. Using an incremental approach, we split the problem into three different parts and propose efficient heuristics that can compute good quality placements very quickly for small and large scenarios. First we model the problem as a communication oblivious problem and propose vector packing based heuristics able to calculate initial placement solutions. Then, we extend our application and infrastructure models by introducing communication constraints, and propose a graph homomorphism based heuristic to calculate initial placement solutions. In the last part, we introduce application reconfiguration to our models and propose a heuristic able to calculate communication and reconfiguration aware placement solutions.

These heuristics have been extensively evaluated against state of the art approaches such as MIP solvers and meta-heuristics. We show through simulations that the proposed heuristics manage to compute solutions in a few seconds that would take many hours or days for other approaches to compute.