Bastien Chopard

University of Geneva, Genève, Geneva, Switzerland

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Publications (181)128.72 Total impact

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    ABSTRACT: We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale component-based execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading codes. We demonstrate its local and distributed computing capabilities and compare its performance to MUSCLE 1, file copy, MPI, MPWide, and GridFTP. The local throughput of MPI is about two times higher, so very tightly coupled code should use MPI as a single submodel of MUSCLE 2; the distributed performance of GridFTP is lower, especially for small messages. We test the performance of a canal system model with MUSCLE 2, where it introduces an overhead as small as 5% compared to MPI.
    Journal of Computational Science. 09/2014; 5(5):719–731.
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    Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 08/2014; 372(2021).
  • Alfons Hoekstra, Bastien Chopard, Peter Coveney
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    ABSTRACT: We argue that, despite the fact that the field of multiscale modelling and simulation has enjoyed significant success within the past decade, it still holds many open questions that are deemed important but so far have barely been explored. We believe that this is at least in part due to the fact that the field has been mainly developed within disciplinary silos. The principal topics that in our view would benefit from a targeted multidisciplinary research effort are related to reaching consensus as to what exactly one means by 'multiscale modelling', formulating a generic theory or calculus of multiscale modelling, applying such concepts to the urgent question of validation and verification of multiscale models, and the issue of numerical error propagation in multiscale models. Moreover, we believe that this would, in principle, also lay the foundation for more efficient, well-defined and usable multiscale computing environments. We believe that multidisciplinary research to fill in the gaps is timely, highly relevant, and with substantial potential impact on many scientific disciplines.
    Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 08/2014; 372(2021).
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    ABSTRACT: Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.
    Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 08/2014; 372(2021).
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    ABSTRACT: We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology.
    Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 08/2014; 372(2021).
  • Hitomi Anzai, Bastien Chopard, Makoto Ohta
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    ABSTRACT: Stent insertion for cerebral aneurysm has been studied using ideal and realistic aneurysms in recent years. Stent insertion aims at reducing the flow in an aneurysm. To minimize the average velocity in an aneurysm, we applied optimization to the strut position in a realistic aneurysm based on computational fluid dynamics. The result shows the effect on velocity reduction of strut placement in the inflow area.
    Journal of Flow Control, Measurement & Visualization 04/2014; 2(2):67-77.
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    ABSTRACT: Background: A modern technique for the treatment of cerebral aneurysms involves insertion of a flow diverter stent. Flow stagnation, produced by the fine mesh structure of the diverter, is thought to promote blood clotting in an aneurysm. However, apart from its effect on flow reduction, the insertion of the metal device poses the risk of occlusion of a parent artery. One strategy for avoiding the risk of arterial occlusion is the use of a device with a higher porosity. To aid the development of optimal stents in the view point of flow reduction maintaining a high porosity, we used lattice Boltzmann flow simulations and simulated annealing optimization to investigate the optimal placement of stent struts. Method: We constructed four idealized aneurysm geometries that resulted in four different inflow characteristics and employed a stent model with 36 unconnected struts corresponding to the porosity of 80%. Assuming intracranial flow, steady flow simulation with Reynolds number of 200 was applied for each aneurysm. Optimization of strut position was performed to minimize the average velocity in an aneurysm while maintaining the porosity. Results: As the results of optimization, we obtained non-uniformed structure as optimized stent for each aneurysm geometry. And all optimized stents were characterized by denser struts in the inflow area. Conclusion: The variety of inflow patterns that resulted from differing aneurysm geometries led to unique strut placements for each aneurysm type. Keywords: Cerebral aneurysm, Flow diverter, Design optimization, Computational fluid dynamics.
    Journal of Biomechanical Engineering 04/2014; · 1.52 Impact Factor
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    ABSTRACT: Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning (ML) methods. On one hand the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, on the other hand models built by ML are hard to interpret and do not increase biological knowledge. Therefore we developed a novel method based on patterns discovery and decision trees to predict PTMs. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and N(α)-terminal acetylation (N-Ac), two of the most common PTMs. The resulting classifiers perform well when compared to existing models. On a set of eukaryotic proteins they display a cross-validated MCC of 0.83 (IMC) and 0.65 (N-Ac). When used to predict potential substrates of NatB and NatC our classifiers display better performance than the state of the art. Moreover we present an analysis of the model predicting IMC for H. sapiens proteins and demonstrate that we are able to extract experimentally known facts without prior knowledge. Those results validate the fact that our method produces white box models. Predictors for IMC and N-Ac and all datasets are freely available at: http://terminus.unige.ch/. jean-luc.falcone@unige.ch.
    Bioinformatics 03/2014; · 5.47 Impact Factor
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    ABSTRACT: Fragments associated with explosive volcanic eruptions range from microns to meters in diameter, with the largest ones following ballistic trajectories from the eruptive vent. Recent field observations suggest that bombs ejected during Strombolian eruptions may collide while airborne. We developed a Discrete Event Simulator to study numerically the impact of such collisions on hazard assessment. We show that the area where bombs can land might be significantly increased when collisions occur. As a consequence, if collisions are dominant, the deposition distance cannot be used to estimate important eruption parameters, such as exit speed.
    Computers & Geosciences 01/2014; 63:62–69. · 1.83 Impact Factor
  • Mohamed Ben Belgacem, Bastien Chopard
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    ABSTRACT: In this paper, we report on the experimental results of running a large, tightly coupled, distributed multiscale computation over a hybrid High Performance Computing (HPC) infrastructures. We connected EC2 based cloud clusters located in USA to university clusters located in Switzerland. We ran a concurrent multiscale MPI based application on this infrastructure and measured the overhead induced by extending our HPC clusters with EC2 resources. Our results indicate that accommodating some parts of the multiscale computation on cloud resources can lead to low performance without a proper adjustment of CPUs power and workload. However, by enforcing a load-balancing strategy one can benefit from the extra Cloud resources.
    Future Generation Computer Systems 01/2014; · 2.64 Impact Factor
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    ABSTRACT: We present a very detailed numerical simulation of the Rhone river in the Geneva area, using a Lattice Boltzmann (LB) modeling approach. The simulations of water ways are important to better predict and control their behavior when subject to exceptional event or new management strategies. Here, we investigate the current computing limits of using a three-dimensional (3D), free surface model to simulate a high resolution flow over a long section of the river, on a massively parallel computer. We argue that in a near future, computers will be powerful enough to tackle such a simulation. We also compare our results with a two-dimensional (2D) shallow water model to determine in which range a 3D free surface approach provides better insights. Finally, we discuss the advantage of a multi-scale approach for this type of problems.
    International Journal of Modern Physics C 12/2013; 24(12):40008-. · 0.62 Impact Factor
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    ABSTRACT: A lattice Boltzmann method is proposed to simulate the blending of two fluids in static, laminar mixers. The method uses a mesh-based algorithm to solve for the fluid flow, and a meshless technique to trace the interface between the blended fluids. This hybrid approach is highly accurate, because the position of the interface can be traced beyond the resolution of the grid. The numerical diffusion is negligible in this model, and it is possible to reproduce mixing patterns that contain more than one hundred striations with high fidelity. The implementation of this method in the massively parallel library Palabos is presented, and simulation results are compared with experimental data to emphasize the accuracy of the results.
    International Journal of Modern Physics C 12/2013; 24(12):40009-. · 0.62 Impact Factor
  • Georgia Ionescu, Bastien Chopard
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    ABSTRACT: We model a virtual scientific community in which authors publish and cite articles. Citations are attributed according to a preferential attachment mechanism. From the numerical simulations, the h-index can be computed. This bottom-up approach reproduces well real bibliometric data. We consider two versions of our model. (1) The single-scientist is controlled by two parameters which can be tuned to reproduce the value of the h-index of many real scientists. Moreover, this model shows how the h-index grows with the number of citations, for a fixed number of articles. We also define an average h-index that can be used to compare the scientific productivity of institutions of different sizes. (2) The multi-scientist model considers a population of scientists and allows us to study the impact of removing citations from the low h-index researchers on the community. Simulations on real bibilometric data, as well as the predictions of the model, show that the h-index eco-system can be strongly affected by such a filtering.
    Physics of Condensed Matter 10/2013; 86(10). · 1.28 Impact Factor
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    ABSTRACT: Inherently complex problems from many scientific disciplines require a multiscale modeling approach. Yet its practical contents remain unclear and inconsistent. Moreover, multiscale models can be very computationally expensive, and may have potential to be executed on distributed infrastructure. In this paper we propose firm foundations for multiscale modeling and distributed multiscale computing. Useful interaction patterns of multiscale models are made predictable with a submodel execution loop (SEL), four coupling templates, and coupling topology properties. We enhance a high-level and well-defined Multiscale Modeling Language (MML) that describes and specifies multiscale models and their computational architecture in a modular way. The architecture is analyzed using directed acyclic task graphs, facilitating validity checking, scheduling distributed computing resources, estimating computational costs, and predicting deadlocks. Distributed execution using the multiscale coupling library and environment (MUSCLE) is outlined. The methodology is applied to two selected applications in nanotechnology and biophysics, showing its capabilities.
    Journal of Parallel and Distributed Computing 04/2013; 73(4):465–483. · 1.12 Impact Factor
  • Procedia Computer Science. 01/2013; 18:1106 - 1115.
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    ABSTRACT: This paper considers a multiscale description of thrombus formation and its simplified numerical implementation in the case of cerebral aneurysms. In particular, we extend previously introduced generic 2D models towards 3D patient specific aneurysm geometries. The multiscale amplification method contributes to considerably reducing simulation time. This allows us to achieve a mesh resolution high enough to resolve details of the stent geometry which is triggering flow conditions to induce clotting. Simulation results presented in this paper are qualitatively in a good agreement with clinical observations.
    Procedia Computer Science. 01/2013; 18:1006.
  • B. Chopard, V.T. Pham, L. Lefèvre
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    ABSTRACT: We consider a Galilean transformation of the lattice Boltzmann model for shallow water flows. In this new reference frame, the velocity lattice is asymmetrical but it is possible to simulate flows with Froude number larger than 1 and to model the transition from a torrential to a fluvial regime.
    Computers & Fluids 01/2013; 88:225–231. · 1.47 Impact Factor
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    ABSTRACT: We present a prototype software to virtually deploy pipeline flow diverting stents in intracranial vessels with aneurysms. The final objective is to understand the biological and biomechanical mechanisms underlying the stent-induced clot formation within the aneurysm. The weaving pattern of the selected pipeline stent is described w.r.t. cylindrical coordinates. Patient-specific 3D vascular geometry is extracted by a level-set image segmentation algorithm. A deformable cylindrical simplex mesh model is used to simulate the virtual stent positioning. A continuous Right Generalized Cylinder model is then used to obtain the mapping of the stent geometry onto the deformed cylindrical surface. Meshes representing the vessel/aneurysm surface and the filaments of the stent are used as input to simulate the fluid dynamics without and with the virtual stent. Lattice Boltzmann method is used to solve the equations. We show preliminary visual results on a first patient.
    MICCAI-Workshop on Computer Assisted Stenting; 10/2012
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    ABSTRACT: Grid refinement has been addressed by different authors in the lattice Boltzmann method community. The information communication and reconstruction on grid transitions is of crucial importance from the accuracy and numerical stability point of view. While a decimation is performed when going from the fine to the coarse grid, a reconstruction must performed to pass form the coarse to the fine grid. In this context, we introduce a decimation technique for the copy from the fine to the coarse grid based on a filtering operation. We show this operation to be extremely important, because a simple copy of the information is not sufficient to guarantee the stability of the numerical scheme at high Reynolds numbers. Then we demonstrate that to reconstruct the information, a local cubic interpolation scheme is mandatory in order to get a precision compatible with the order of accuracy of the lattice Boltzmann method.These two fundamental extra-steps are validated on two classical 2D benchmarks, the 2D circular cylinder and the 2D dipole–wall collision. The latter is especially challenging from the numerical point of view since we allow strong gradients to cross the refinement interfaces at a relatively high Reynolds number of 5000. A very good agreement is found between the single grid and the refined grid cases.The proposed grid refinement strategy has been implemented in the parallel open-source library Palabos.
    Journal of Computational Physics 05/2012; 231(14):4808–4822. · 2.14 Impact Factor
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    ABSTRACT: A modern technique to treat cerebral aneurysms is to insert a flow diverter in the parent artery. In order to produce an optimal design of such devices, we consider a methodology combining simulated annealing optimization and lattice Boltzmann simulations. Our results surpass, in terms of stent efficiency, those obtained in the recent literature with an other optimization method. Although our approach is still in 2D, it demonstrates the potential of the method. We give some hint on how the 3D cases can be investigated.
    Journal of Computational Science. 01/2012; 3(s 1–2):1–7.

Publication Stats

2k Citations
128.72 Total Impact Points

Institutions

  • 1970–2014
    • University of Geneva
      • • Department of Computer Science
      • • Department of Inorganic, Analytical, and Applied Chemistry
      • • Department of Theoretical Physics
      Genève, Geneva, Switzerland
  • 2009
    • University of Amsterdam
      • Department of Computational Science
      Amsterdam, North Holland, Netherlands
    • École Polytechnique Fédérale de Lausanne
      Lausanne, Vaud, Switzerland
  • 1998
    • Massachusetts Institute of Technology
      • Laboratory for Computer Science
      Cambridge, MA, United States