Fully parallel mesh I/O using PETSc DMPlex with an application to waveform modeling

DOI10.1137/20M1332748zbMATH Open1462.65005arXiv2004.08729OpenAlexW3134579658MaRDI QIDQ5857724FDOQ5857724

Authors: Vaclav Hapla, Matthew G. Knepley, Michael Afanasiev, Christian Böhm, Martin van Driel, Lion Krischer, Andreas Fichtner 

Publication date: 7 April 2021

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Abstract: Large-scale PDE simulations using high-order finite-element methods on unstructured meshes are an indispensable tool in science and engineering. The widely used open-source PETSc library offers an efficient representation of generic unstructured meshes within its DMPlex module. This paper details our recent implementation of parallel mesh reading and topological interpolation (computation of edges and faces from a cell-vertex mesh) into DMPlex. We apply these developments to seismic wave propagation scenarios on Mars as an example application. The principal motivation is to overcome single-node memory limits and reach mesh sizes which were impossible before. Moreover, we demonstrate that scalability of I/O and topological interpolation goes beyond 12'000 cores, and memory-imposed limits on mesh size vanish.

Full work available at URL: https://arxiv.org/abs/2004.08729

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zbMATH Keywords

directed acyclic graphunstructured meshpartitioningspectral-element methodparallel I/OPETScDMPlexseismic waveform modelingtopological interpolation

Mathematics Subject Classification ID

Applications of graph theory (05C90) Parallel numerical computation (65Y05) Wave equation (35L05) Mesh generation, refinement, and adaptive methods for the numerical solution of initial value and initial-boundary value problems involving PDEs (65M50) Software, source code, etc. for problems pertaining to numerical analysis (65-04)

Cites Work

• DOLFIN: automated finite element computing
• p4est: scalable algorithms for parallel adaptive mesh refinement on forests of octrees
• Title not available (Why is that?)
• MFEM: a modular finite element methods library
• PetIGA: a framework for high-performance isogeometric analysis
• Firedrake, automating the finite element method by composing abstractions
• A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs
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• A spectral element method for fluid dynamics: Laminar flow in a channel expansion
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• The Finite Element Method: Theory, Implementation, and Applications
• A compact adjacency-based topological data structure for finite element mesh representation
• OCTREE-BASED HEXAHEDRAL MESH GENERATION
• Efficient implementation of high-order finite elements for Helmholtz problems
• Recursive algorithms for distributed forests of octrees
• Efficient mesh management in firedrake using PETSc DMPlex
• Mesh data structure selection for mesh generation and FEA applications
• Unstructured geometric multigrid in two and three dimensions on complex and graded meshes
• An Augmented Lagrangian Preconditioner for the 3D Stationary Incompressible Navier--Stokes Equations at High Reynolds Number

Cited In (7)

• PETSc DMNetwork: a library for scalable network PDE-based multiphysics simulations
• Scalable FEA on non-conforming assembly mesh
• Efficient mesh management in firedrake using PETSc DMPlex
• A Numerical study of Landau damping with PETSc-PIC
• Efficient N-to-M checkpointing algorithm for finite element simulations
• Ray decomposition radiation transport for high performance computing
• Developing a geodynamics simulator with PETSc

Uses Software

• DistDLB
• SIERRA
• PETSc
• METIS
• DOLFIN
• FEniCS
• ParMETIS
• p4est
• PT-Scotch
• MFEM
• FEAPpv
• PetIGA
• Firedrake
• Oracle
• DMPlex
• GitHub
• AxiSEM
• EXODUS II

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