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seminaire passé seminar

[SEMINAR] May 30 2023 – DENERGIUM 🧑‍🏫 Hervé MATHIEU

🧑‍🏫 Hervé MATHIEU – cofunder of DENERGIUM
🌎 May 30 2023
☕️ 4:00 PM
🏢 Maison de la Simulation, Batiment Digiteo Saclay, Salle Mandelbrot
🔗 https://www.linkedin.com/company/denergium/ 
🔗 https://www.denergium.com

Abstract

DENERGIUM est une startup créée début 2023. DENERGIUM est une entreprise technologique, un éditeur de logiciels et un acteur environnemental positif. DENERGIUM a pour mission de rendre plus efficace l’utilisation des infrastructures informatiques. Pour cela DENERGIUM s’appuie sur une technologie issue d’Inria, qui à partir de données énergétiques acquises dans un datacenter et d’algorithmes avancés (modèles mathématiques, IA) permet d’apporter des optimisations aux gestionnaires de datacenter mais aussi aux utilisateurs des datacenters. Notre marché est l’ensemble des infrastructures informatiques opérant du calcul massif (HPC, IA, BigData). DENERGIUM est accompagnée par Inria Startup Studio, Unitec et Ovhcloud startup program.

A partir d’une démonstration d’EnergyScopium optimize, nous pourrons échanger sur la problématique de l’optimisation énergétique dans l’usage des clusters de calcul : configuration matérielle et logicielle des serveurs, lancement des calculs, choix des bibliothèques logicielles, développement logiciel.

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seminaire passé seminar

[SEMINAR] May 16 2023 – Development and GPU porting efforts for a high-performance low-Mach CFD solver based on unstructured adaptive grids 🧑‍🏫 Patrick BEGOU and Vincent MOUREAU

🧑‍🏫 Patrick BEGOU – Research Engineer at LEGI, UMR 5519
🧑‍🏫 Vincent MOUREAU, CNRS research fellow at CORIA, UMR6614
🌎 May 16 2023
☕️ 9:30 AM
🏢 Maison de la Simulation, Batiment Digiteo Saclay, Salle Mandelbrot

Abstract

With the steady increase of the power of parallel super-computers, 3D unsteady simulations offer a great potential to study turbulent flows. However, the simulation of highly non-linear phenomena such as turbulence, primary atomization or premixed flames requires very accurate numerical methods and high resolution to capture vortex and interface dynamics. While most direct numerical simulations of turbulent flows are carried out with structured grids or Cartesian-based Adaptive Mesh Refinement, recent advances in numerical methods for tetrahedron-based meshes and parallel mesh adaptation strategies raise the attractiveness of unstructured grids. The use of tetrahedra has two advantages for practical configurations: complex geometries are easily meshed and the mesh is locally more isotropic than Cartesian grids. The first part of the presentation will be focused on the development of highly-efficient dynamic adaptation of tetrahedron-based unstructured grids and on projection methods for low-Mach number flows which can cope with adaptive grids. The proposed methodology, which heavily relies on the remeshing library MMG (www.mmgtools.org) has been thoroughly optimized to reach good performances with grids of several billion cells on more than 10 000 cores. This dynamic mesh adaptation strategy has been implemented in the YALES2 code (www.coria-cfd.fr) and applied to the modeling of turbulent flows in many configurations. In these academic and industrial applications, the local mesh adaptation enabled a drastic reduction of the CPU cost compared to the fixed-grid approach and enabled to reach unprecedented mesh resolutions. The second part of the presentation will be dedicated to the efforts to port these methodologies to GPUs while continuing promoting fast development and innovation from a community of non-GPU experts.

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Non classé seminaire passé seminar

[SEMINAR] January 2023 – Simulations numériques ab initio de l’irradiation ionisante de la matière 🧑‍🏫 Auréllien de la Lande

🧑‍🏫 Aurélien de la Lande, CNRS
🌎 January 25 2023

Nous avons développé à l’Institut de Chimie Physique d’Orsay des approches de simulation ab initio originales pour simuler le dépôt d’énergie par des ions rapides ou des photons XUV dans des systèmes moléculaires de grandes tailles, tels que ceux rencontrés en biologie1. Durant ce séminaire, nous intro- duirons les équations du mouvement des électrons dans le cadre de la théorie de la fonctionnelle de la densité2. 

Nos codes de simulation reposent sur de nouveaux algorithmes de la théorie de la fonctionnelle de la densité dépendant du temps permettant de simuler des systèmes de taille nanométrique et inhomo- gènes3,4. L’une des astuces principales est de recourir à des densités électroniques auxiliaires permettant de calculer la répulsion coulombienne et les effets liés à la nature quantique des électrons (échange et corrélation). Le couplage avec la librairie ScaLapack permet une réduction importante du cout de calcul du propagateur3. Pour aller plus loin une interface avec la libraire Magma a récemment été réalisée. La réduction du coût de calcul est remarquable et permet d’entrevoir des applications sans précédent en terme de taille de systèmes simulés. 

J’illustrerai l’apport de ces approches par diverses études récentes du groupe. Un premier exemple a trait à l’irradiation comparée d’oligomères d’ADN solvatés par des protons, de noyaux d’hélium ou de carbone (Fig. 1)5. L’étude a permis de mettre en évidence des processus clés de l’étape physique de l’irradiation ; par exemple le mécanisme d’ionisation par flux-et-reflux du nuage électronique, la localisation des électrons secondaires ou encore les probabilités d’ionisation des bases d’ADN ou du solvant5. Dans un second exemple je mettrai en évidence un effet de taille remarquable lors le processus d’ionisation d’acide aminés, de peptides et de protéines par des photons ionisant XUV. Cette découverte permet de faire des hypothèses sur les sites d’ionisation primaires possibles du milieu cellulaire par ce type de rayonnement. 

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seminaire passé

[SEMINAR] March 2020 – Two-level Coarse Corrected Optimized Schwarz Methods using PETSc 🧑‍🏫 Serge Van Criekingen

🧑‍🏫 Serge Van Criekingen, IDRIS, France
🌎 March 2020

Abstract

Parallel Schwarz-type domain decomposition methods are based on an iterative process where, at each iteration, a local solve is simultaneously performed on each of the (possibly overlapping) subdomains, using interface values previously computed on neighboring subdomains. The reference method in this framework is the Restricted Additive Schwarz (RAS) method, implemented as a preconditioner in the PETSc library. Using existing PETSc tools, we here implement two improvements to this method: a new coarse correction to obtain a two-level scalable method, as well as optimized transmission conditions, resulting in an Optimized 2-level Restricted Additive Schwarz method.

The first improvement, namely the introduction of a coarse correction to insure scalability, is wellknown and due to that fact that, in the case of elliptic problems, information is only transferred from each subdomain to its direct neighbors at each iteration of a 1-level method such as RAS. This makes the number of iterations grow with the number of subdomains. Scalability is achieved by introducing a coarse grid on which a reduced-size calculation is performed, yielding a coarse correction at each iteration of the solution process. Such a 2-level method permits global propagation of the iterative corrections throughout the entire domain, leading to the scalability of the method. Many choices for the coarse grid point locations are possible, and we here follow a method introduced by M.J. Gander et al. yielding a reduced number of iterations.

The second improvement, namely optimized transmission conditions, stems from the idea that the transmission conditions used in the iterative process at subdomain interfaces can also be chosen such as to reduce the number of iterations. In our case, we consider Robin transmission conditions instead of the classical Dirichlet ones, i.e. a well-chosen combination of Dirichlet and Neumann values at subdomain interfaces. A good choice of the Robin coefficient representing the relative weight of Dirichlet and Neumann values permits minimizing the number of iterations, which led to the name Optimized Schwarz Methods.

We combine these two improvements and apply them to a 2D Laplace test case up to 16,384 CPU cores. We obtain substantially improved computation times, comparable to the ones obtained with the multigrid library HYPRE interfaced by PETSc. This is significant in that Schwarz-type domain decomposition methods were up to now not considered competitive with multigrid methods on this type of problem. Furthermore, we extend the method to non-symmetric problems, adding an advection term to the Laplacian, and investigate various ways of adapting the coarse space.

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seminaire passé

[SEMINAR] March 2019 – Emulating quantum computers 🧑‍🏫 Victor Alessandrini

🧑‍🏫 Victor Alessandrini, Maison de la Simulation, France
🌎 March 2019

Abstract:

There is today increasing consensus on the fact that quantum computing – an emerging data processing technology – may in the future play a significant role (with not yet fully understood boundaries) in high performance scientific computing. The simulation of quantum computers on standard computing platforms is today a necessary step to understand, assess, and develop quantum algorithms for computation, paving the way for the eventual future adoption of this disruptive technology. Emulation software will remain useful for some time to validate results of the earlier quantum computing platforms, and to help tuning application quantum codes. We will present a fully portable C++ emulation library under development for more than one year. The library disposes of three interfaces: a shared memory version running on SMP nodes, a MPI extension enabling access to a larger number of qubits, and a Python wrapper of the C++ library. A significant pedagogical effort is implemented in the documentation. Besides the traditional C++ class documentation, we are producing strategic higher level documentation and pedagogical papers on applications, including Jupyter notebooks. This seminar will propose first an introduction to quantum computing, explaining the fundamental differences with classical computing, underlining the strong features as well as the limiting bottlenecks of the technology. We will present next a short and very high level overview of the emulation library, focusing on a few major strategic choices. Then, the issues involved in quantum algorithms will be illustrated with a quantum chemistry example used in the validation tests of the software. Finally, we will conclude with a rapid overview of different areas in which quantum algorithm research is evolving (quantum chemistry, condensed matter physics, combinatorial optimization, fault tolerant quantum computing,…).

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Non classé seminaire passé

[SEMINAR] February 2019 – Hercules 🧑‍🏫 Olivier Bressand

🧑‍🏫 Olivier Bressand, CEA-DAM, France
🌎 February 2019

Abstract

Hercules is a CEA-DAM platform for managing data produced by simulation codes. It integrates different I/O services to read, write in parallel database in the framework of protection / recovery, intercode (coupling or code sequence) and post-processing (visualization and analysis). It is based on a data model that covers many domains of simulation (structured, unstructured, AMR-block, AMR-tree based, multi-fluid, laser, atom, Euler, Lagrange, ale, 1D, 2D, 3D) and provides services to produce, filter, and disaggregate data in the sequential or parallel HPC application.

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Non classé seminaire passé

[SEMINAR] February 2019 – MPC, The Multi-Processor Computing Framework 🧑‍🏫 Julien Jaeger

🧑‍🏫 Julien Jaeger, CEA-DAM, France
🌎 February 2019

Abstract

The MPC (Multi-Processor Computing) framework provides a unified parallel runtime designed to improve the scalability and performances of applications running on clusters of (very) large multiprocessor/multicore NUMA nodes. Thanks to its design, MPC allows mixed-mode programming models and efficient interaction with the HPC software stack. MPC provides implementations for the MPI, OpenMP and POSIX Threads standards. All these standards can be mixed together in an efficient way, thanks to process virtualization, and the sharing of information and resources

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seminaire passé

[SEMINAR] February 2019 – PaDaWan 🧑‍🏫 Julien CAPUL

🧑‍🏫 Julien CAPUL, CEA-DAM, France
🌎 February 2019

PaDaWAn is an infrastructure providing in-memory data exchange between applications and a simple configuration model to switch from a file-based workflow to an in-transit workflow. The infrastructure is currently based on CEA-DAM Hercule parallel I/O libray by providing an ABI-compatible library to intercept simulation data in a transparent way and to facilitate integration into existing simulation codes and tools.

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seminaire passé

[SEMINAR] January 2013 – Gestion des IO parallèle en modélisation du climat – la bibliothèque XIOS 🧑‍🏫 Yann MEURDESOIF

🧑‍🏫 Yann Meurdesoif, Researcher at the Laboratoire des Sciences du Climat et l’Environnement (LSCE)
🌎 January 2013

Abstract:

XIOS est un nouvel outil développé à l’IPSL (Institut Pierre Simon Laplace) destiné à gérer efficacement les sorties fichiers des modèles de simulations climatiques. Il vise deux principaux objectifs :

  • Souplesse d’utilisation, grâce à une description externe des I/O sous forme d’un fichier XML hiérarchisé et d’une API fortran permettant de compléter ces informations à partir des codes.
  • Performance : des cœurs de calculs sont exclusivement dédiés à la gestion des écritures via une technologie client/serveur, les données étant transmises des clients (code de calcul) vers les serveurs (cœurs I/O) par des communications MPI asynchrones non bloquantes. L’écriture des fichiers se fait alors en tâche de fond, en même temps que les calculs. Lors des phases d’écriture, XIOS exploite également le parallélisme du système de fichier via l’utilisation des bibliothèques netcdf4/hdf5 parallèle, permettant à plusieurs processus d’écrire simultanément dans un même fichier, et agrégeant ainsi la bande passante I/O vers les supports matériels.

Slides:

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Non classé seminaire passé

[SEMINAR] December 2012 – Software optimization for petaflops/s scale Quantum Monte Carlo simulations 🧑‍🏫 by Anthony SCEMAMA

🧑‍🏫 Anthony Scemama, Research Engineer at the Laboratoire de Chimie et de Physique Quantiques of IRSAMC
🌎 December 2012

Quantum chemistry is known to be one of the grand challenges of modern science since many fundamental and applied fields are concerned (drug design, micro-electronics, nanosciences,…). To investigate all these fascinating problems is a tremendous task since highly accurate solutions of the fundamental underlying Schrödinger equation for a (very) large number of electrons need to be determined. The use of Quantum Monte Carlo methods is an emerging alternative approach to usual methods since they can take advantage of massively parallel architectures. In this talk the QMC=Chem program we develop in Toulouse will be presented, as well as the different strategies we used to reach the petaflops/s scale.

Slides :