Meshing

Authors: R. Borrella, J.C. Cajasa , G. Houzeauxa  and M.Vazqueza
aBarcelona Supercomputing Center – Centro Nacional de Supercomputación, Spain

 

Abstract: Larger supercomputers allow the resolution of more complex problems that require denser and thus also larger meshes. In this context, and extrapolating to the Exascale paradigm, meshing operations such as generation, deformation, adaptation/regeneration or partition/load balance, become a critical issue within the simulation workflow. In this paper we focus on the mesh partitioning, presenting the work carried out in the context of a PRACE Preparatory Access Project to enable a Space Filling Curve (SFC) based partitioner in the computational mechanics code Alya. In particular, we have run our tests on the MareNostrum III supercomputer of the Barcelona Supercomputing Center. SFC partitioning is a fast and scalable alternative to the standard graph based partitioning and in some cases provides better solutions. We show our approach at implementing a parallel SFC based partitioner. We have avoided any computing or memory bottleneck in the algorithm, while we have imposed that the solution achieved is independent (discounting rounding off errors) of the number of parallel processes used to compute it.

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Authors: B. Eguzkitzaa*, M. Garcíaa , G J.C.Cajasa , S. Marrasb, G. Houzeauxa, B. Sainte-Rosec
aBarcelona Supercomputing Center – Centro Nacional de Supercomputación, Spain

bStanford University, Department of Geophysics, Stanford, CA, U.S.A

cThe Ocean Cleanup, Operations Maritime Research, Delft, Netherland

Abstract: The Ocean Cleanup (www.theoceancleanup.com) is a foundation that develops technologies to extract plastic pollution from the oceans and prevent more plastic debris from entering ocean waters. The main technology is the Ocean Cleanup Array which utilizes long floating barriers to capture and concentrate the plastic such that the system is a passive barrier. Computational Fluid Dynamics (CFD) is being used to study the catch efficiency debris of different sizes and densities, the transport of plastic along the containment boom, and the forces acting on it in order to determine the appropriate shape for their passive barrier concept. A study for the wave and boom influence on particle trajectories has to be done with CFD to investigate the effects of wind-and- wave- induced turbulence on the boom capture efficiently as well as to include the interaction between particles and the dynamic structure in the CFD analyses. The objective of this PRACE project is to simulate the flow dynamic around the buoyancy body and the flexible skirt as well as the interaction of the plastic debris with the skirt. This simulation is a very strong multi-physics coupled problem carried out by Alya code: Navier-stokes equations in a turbulence regime, free surface, solid mechanics and particle Lagrangian transport have to be solved. On one hand, we have analysed the performance of the code solving this kind of complex problems in terms of computational efficiency. On the other hand, we have overcome the physical and numerical difficulties presented in the simulation.

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Authors: A. Gargallo-Peiróa*, H. Owena , G. Houzeauxa , X. Rocaa
aBarcelona Supercomputing Center – Centro Nacional de Supercomputación

Carrer de Jordi Girona, 29-31, 08034 Barcelona, Spain (Spain)

Abstract: We present the implementation in the Alya code of a method to refine a mesh in parallel while preserving the curvature of a target topography. Our approach starts by generating a coarse linear mesh of the computational domain. Then, the former coarse mesh is curved to match the curvature of the target geometry. Finally, the curved mesh is given to the improved Alya code that now reads the curved mesh, partitions it, and sends the subdomain meshes to the slaves. The result is a finer linear mesh obtained in parallel with improved geometric accuracy. The main application of the obtained finer linear mesh is to compute a steady state flow solution on complex topographies.

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Authors: J.C. Cajasaa, G. Houzeauxa and B. Eguzkitzaa
aBarcelona Supercomputing Center – Centro Nacional de Supercomputación

aaNEXUS II Building, c/ Jordi Girona 29, 08034 Barcelona (Spain)

Abstract: Domain Composition Methods are techniques to couple local solutions of physical problems, solved on local meshes, to obtain a global solution on the union of these meshes. This work consisted in implementing such techniques at the algebraic level, making the coupling independent of the physics to be considered. This approach enables us to solve multi-domain and multi-physics problems, using both single and multi-code approaches. Both explicit and implicit coupling were implemented, for surface and volume couplings. The implementation was carried out for distributed memory supercomputers, using MPI. Several physical examples demonstrate the reliability of the proposed implementation.

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Authors: Yusuf Yılmaz,Can Özturan, Oğuz Tosun, Ali Haydar Özer, Seren Soner
Dept. of Computer Engineering, BogaziciUniversity, Istanbul, Turkey

Abstract: The main goal of this project is to develop a parallel tetrahedral mesh generator based on existing sequential mesh generation software. As sequential mesh generation software, the Netgen mesh generator was used due to its availability as LGPL open source software and its wide user base. Parallel mesh generation routines were developed using the MPI libraries and the C++ language. The parallel mesh generation algorithms developed proceed by decomposing the whole geometry into a number of sub-geometries sequentially on a master node at the beginning and then mesh each sub-geometry in parallel on multiple processors. Three methods were implemented. The first decomposes the CAD geometry and produces conforming surface sub-meshes that are sent to other processors for volume mesh generation. The second and third methods are refinement based methods that also make use of the CAD geometry information. Advantages and disadvantages of each method are discussed. Parallel repartitioning also need to be done in the first method. To facilitate distributed element movements in parallel, a migration algorithm that utilizes “owner updates” rule is developed. Timing results obtained on the Curie supercomputer are presented. In particular, results show that by using a refinement based method, one can generate over a billion element meshes in under a minute.

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Authors: PavlaKabelikova, Ales Ronovsky, Vit Vondraka
Dept. of Applied Mathematics,VSB-Technical University of Ostrava, Tr. 17. listopadu 15, 708 00Ostrava, Czech Republic

Abstract: In this whitepaper, a new mesh multiplication package developed for Code_Saturne is described. The package implements parallel global refinement of hexahedral meshes for Code_Saturne to allow creating meshes with more than 1 billion cells. This enables running Code_Saturne’s extremely large CFD simulations on PRACE Tier-0 systems. The effectiveness of the implemented multiplication algorithm is demonstrated on practical examples, which were carried out on CURIE system at CEA.

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Authors: G.Houzeaux,R.delaCruz, M.V ́azquez

Barcelona Supercomputing Center,Edificio NEXUS I, Gran Capit ́an 2-4, 08034 Barcelona, Spain

Abstract: The objective of the present project is to implement a parallel uniform mesh multiplication in a HPC code developed atBarcelona Supercomputing Center named Alya. The mesh multiplication consists in subdividing recursively the mesh inparallel in order to obtain a refined mesh from an initial ”coarse” mesh. This mesh multiplication should be implementedefficiently to be used the fly, thus avoiding treating huge geometry files. In addition, the post-process can be carried outin a straightfoward way at any level of the mesh multiplication.

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Author: ValentinPavlov*
Rila Solutions EAD, Acad. G. Bonchevstr., bl. 27, Sofia 1113, Bulgaria

Abstract: The SPECFEM3D package simulates seismic wave propagation using a parallel implementation of a variation of the Galerkin procedure called Spectral Element Method (SEM). The advantage of this method is that it produces a diagonal mass matrix which allows for quick explicit solving of the seismic wave equations. The drawback is that using an explicit method the solver is not stable unless the Courant-Friedrichs-Lewy (CFL) condition for convergence holds, imposing a certain inequality relation between the time step and spatial size of the spectral elements. The internal mesher provided with the package uses a partitioning approach that directly links the number of parallel solver tasks with the spatial size of the elements. For any given mesh, increasing the number of parallel processes leads to decreasing the element size, and via the CFL condition to decreasing the time step. This directly compromises the scalability of the solver by requiring more time steps for the same amount of work with no gain in performance. The goal of this project is to improve the scalability of the package by reconsidering the partitioning approach of the internal mesher. We analyze the existing approach and propose a new one, based on using the SCOTCH partitioning library, already integrated in the workflow for solving the problem on externally generated mesh. Our results indicate that the modified partitioning scheme leads to substantial performance benefits for regional modeling with the internal mesher in petascale environments. We validate the results by running the examples included in the package and observe that the solver produces identical synthetic seismograms when run with meshes generated by the original and modified internal mesher.

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Disclaimer

These whitepapers have been prepared by the PRACE Implementation Phase Projects and in accordance with the Consortium Agreements and Grant Agreements n° RI-261557, n°RI-283493, or n°RI-312763.

They solely reflect the opinion of the parties to such agreements on a collective basis in the context of the PRACE Implementation Phase Projects and to the extent foreseen in such agreements. Please note that even though all participants to the PRACE IP Projects are members of PRACE AISBL, these whitepapers have not been approved by the Council of PRACE AISBL and therefore do not emanate from it nor should be considered to reflect PRACE AISBL’s individual opinion.

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© 2014 PRACE Consortium Partners. All rights reserved. This document is a project document of a PRACE Implementation Phase project. All contents are reserved by default and may not be disclosed to third parties without the written consent of the PRACE partners, except as mandated by the European Commission contracts RI-261557, RI-283493, or RI-312763 for reviewing and dissemination purposes.

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