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A general-purpose hierarchical mesh partitioning method with node balancing strategies for large-scale numerical simulations [article]

Fande Kong, Roy H. Stogner, Derek R. Gaston, John W. Peterson, Cody J. Permann, Andrew E. Slaughter, Richard C. Martineau
2018 arXiv   pre-print
In this work, we consider a general-purpose hierarchical partitioner which takes into account the existence of multiple processor cores and shared memory in a compute node while partitioning a graph into  ...  Large-scale parallel numerical simulations are essential for a wide range of engineering problems that involve complex, coupled physical processes interacting across a broad range of spatial and temporal  ...  CONCLUSIONS AND FUTURE WORK A general-purpose hierarchical mesh partitioning method was introduced and discussed for large-scale scientific computing.  ... 
arXiv:1809.02666v2 fatcat:yxfhslx3izbonlh7gyfidyikhi

A numerical method for multiphysics simulations based on hierarchical Cartesian grids

2015 Journal of Fluid Science and Technology  
We present a numerical method based on hierarchical Cartesian grids for the simulation of multiphysics problems, here in particular for the conjugate heat transfer between a fluid and a solid.  ...  The data structures developed for this simulation method allow to account for moving objects and are especially well suited for massive parallelization.  ...  Acknowledgments This work has been financed by the research cluster Fuel production with renewable raw materials (BrenaRo) at RWTH Aachen University as well as by the German Research Foundation (DFG) within  ... 
doi:10.1299/jfst.2015jfst0002 fatcat:nwt33xykpjfbldqnfkyozj3q3q

Dynamic Load Balancing for PIC code using Eulerian/Lagrangian partitioning [article]

Marc Sauget, Guillaume Latu
2017 arXiv   pre-print
This document presents an analysis of different load balance strategies for a Plasma physics code that models high energy particle beams with PIC method.  ...  A comparison of different load balancing algorithms is given: static or dynamic ones. Lagrangian and Eulerian partitioning techniques have been investigated.  ...  Different strategies for load balancing Parallelisation of a PIC code relies to a large extent on the load balancing chosen and the partitioning scheme used.  ... 
arXiv:1706.08362v1 fatcat:cud476qoincjdebv4glq4fwnki

Hardware Locality-Aware Partitioning and Dynamic Load-Balancing of Unstructured Meshes for Large-Scale Scientific Applications

Pavanakumar Mohanamuraly, Gabriel Staffelbach
2020 Proceedings of the Platform for Advanced Scientific Computing Conference  
We present an open-source topology-aware hierarchical unstructured mesh partitioning and load-balancing tool TreePart.  ...  It provides a range of partitioning methods by interfacing with existing shared and distributed memory parallel partitioning libraries.  ...  This work was granted access to the HPC resources of IDRIS under an allocation by GENCI for the Grand Challenges Jean Zay (2019).  ... 
doi:10.1145/3394277.3401851 dblp:conf/pasc/MohanamuralyS20 fatcat:thhnjsb7ufbgbmvmf6abiyzlri

New challenges in dynamic load balancing

Karen D. Devine, Erik G. Boman, Robert T. Heaphy, Bruce A. Hendrickson, James D. Teresco, Jamal Faik, Joseph E. Flaherty, Luis G. Gervasio
2005 Applied Numerical Mathematics  
Data partitioning and load balancing are important components of parallel computations. Many different partitioning strategies have been developed, with great effectiveness in parallel applications.  ...  New models are needed for non-square, non-symmetric, and highly connected systems arising from applications in biology, circuits, and materials simulations.  ...  Numerous strategies for static and dynamic load balancing have been developed, including recursive bisection (RB) methods [1] [2] [3] , space-filling curve (SFC) partitioning [4] [5] [6] [7] [8] and  ... 
doi:10.1016/j.apnum.2004.08.028 fatcat:papkwaxblzcqdi6ove7lwe46ve

Scalability and some optimization of the Finite-volumE Sea ice-Ocean Model, Version 2.0 (FESOM2)

Nikolay V. Koldunov, Vadym Aizinger, Natalja Rakowsky, Patrick Scholz, Dmitry Sidorenko, Sergey Danilov, Thomas Jung
2019 Geoscientific Model Development Discussions  
Furthermore, strategies for improvements in parallel performance are presented and assessed.  ...  Several model enhancements, improving this scalability for large numbers of processes, are described and tested.  ...  Schematics of an HPC cluster for purposes of hierarchic mesh partitioning (left) and a comparison of the total, SSH, and sea-ice scaling for hierarchic (continuous lines) and non-hierarchic (dashed lines  ... 
doi:10.5194/gmd-2018-334 fatcat:vq27gmw63fartpyovb5gb4vno4

Advanced general-purpose computational mechanics system for large-scale analysis and design

Shinobu Yoshimura, Ryuji Shioya, Hirohisa Noguchi, Tomoshi Miyamura
2002 Journal of Computational and Applied Mathematics  
with a 60 million DOF mesh on Hitachi SR2201 (1024 PEs), and nonparametric shape optimization of a support structure for an express way with a one million DOF mesh on a PC cluster (10 PEs).  ...  We have been developing an advanced general-purpose computational mechanics system, named ADVEN-TURE, which is designed to be able to analyze a model of arbitrary shape with a 10 -100 million degrees of  ...  Acknowledgements This work was performed as a part of Research for the Future Program sponsored by the Japan Society for the Promotion of Science.  ... 
doi:10.1016/s0377-0427(02)00536-8 fatcat:dbe7itm7svbuxencxg54alkvuq

Addressing spatiotemporal and computational heterogeneity in structured adaptive mesh refinement

Sumir Chandra, Manish Parashar
2006 Computing and Visualization in Science  
This paper presents hierarchical partitioning, bin-packing based load balancing, and Dispatch structured partitioning strategies to manage the spatiotemporal and computational heterogeneity in SAMR applications  ...  Structured adaptive mesh refinement (SAMR) techniques can provide accurate and costeffective solutions to realistic scientific and engineering simulations modeling complex physical phenomena.  ...  John Hewson, Sandia National Laboratories, Albuquerque, NM, for his help with the methane-air chemical mechanism and generating a self-supporting chemistry module for us.  ... 
doi:10.1007/s00791-006-0028-7 fatcat:4cgjjql7uze5rdehxlhga3f6l4

Scalable adaptive mantle convection simulation on petascale supercomputers

Carsten Burstedde, Omar Ghattas, Michael Gurnis, Georg Stadler, Eh Tan, Tiankai Tu, Lucas C. Wilcox, Shijie Zhong
2008 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis  
With RHEA's adaptive capabilities, we have been able to reduce the number of elements by over three orders of magnitude, thus enabling us to simulate large-scale mantle convection with a finest local resolution  ...  Thus parallel adaptive mesh refinement and coarsening (AMR) is essential. We present RHEA, a new generation mantle convection code designed to scale to hundreds of thousands of cores.  ...  We acknowledge many helpful discussions with hypre developers Rob Falgout and Ulrike Yang, and with George Biros.  ... 
doi:10.1109/sc.2008.5214248 dblp:conf/sc/BursteddeGGSTTWZ08 fatcat:6lxfuvf6znhltfvhkg55yeiqie

Data structures and load balancing for parallel adaptive hp finite-element methods

A.K. Patra, A. Laszloffy, J. Long
2003 Computers and Mathematics with Applications  
Adaptive hp finite-element methods (FEM)  ...  Parallel versions of these methods offer the potential for very accurate solution of large scale physically realistic models of important physical systems.  ...  A final difficulty that is encountered in the design of a solver for use across a large class of parallel architectures is the choice of solution method for best efficiency.  ... 
doi:10.1016/s0898-1221(03)90084-8 fatcat:kfbmcn4sk5eptguihyc5jhmqbm

A scalable parallel finite element framework for growing geometries. Application to metal additive manufacturing

Eric Neiva, Santiago Badia, Alberto F. Martín, Michele Chiumenti
2019 International Journal for Numerical Methods in Engineering  
It is grounded on three building blocks: (1) Hierarchical adaptive mesh refinement with octree-based meshes; (2) a parallel strategy to model the growth of the geometry; (3) state-of-the-art parallel iterative  ...  After verification against a 3D benchmark, a strong-scaling analysis assesses performance and identifies major sources of parallel overhead.  ...  Mesh generation by hierarchical AMR Physical phenomena are often characterized by multiple scales in both space and time.  ... 
doi:10.1002/nme.6085 fatcat:qrctvxbjlja7zl6nq5l3buwqui

FEMS: An Adaptive Finite Element Solver

Alberto Bertoldo
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
FEMS relies on a simple model-driven mesh partitioning strategy, which makes it possible to perform efficient static load balancing on both homogeneous and heterogeneous machines.  ...  We present the software architecture of FEMS, a parallel multifrontal solver for FE applications whose main feature is an install-time training phase where adaptation to the computing platform takes place  ...  partitioning for load balancing purposes, and to optimize communication patterns.  ... 
doi:10.1109/ipdps.2007.370569 dblp:conf/ipps/Bertoldo07 fatcat:gn3biypjwndg3hb7elkecelwwm

Scalability and some optimization of the Finite-volumE Sea ice–Ocean Model, Version 2.0 (FESOM2)

Nikolay V. Koldunov, Vadym Aizinger, Natalja Rakowsky, Patrick Scholz, Dmitry Sidorenko, Sergey Danilov, Thomas Jung
2019 Geoscientific Model Development  
Furthermore, strategies for improvements in parallel performance are presented and assessed.  ...  Several model enhancements improving this scalability for large numbers of processes are described and tested.  ...  We would also like to extend special thanks to Hendryk Bockelmann (DKRZ) for his active support with scaling experiments on large numbers of nodes. Financial support.  ... 
doi:10.5194/gmd-12-3991-2019 fatcat:w6tzezu7dnd3zont55u2aohcne

Productive Parallel Linear Algebra Programming with Unstructured Topology Adaption

Peter Gottschling, Torsten Hoefler
2012 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012)  
For this purpose, we developed a linear algebra library -Parallel Matrix Template Library 4 -based on generic and meta-programming introducing a new paradigm: meta-tuning.  ...  The discretization of complex geometries in unstructured meshes leads to sparse matrices with irregular patterns.  ...  Acknowledgments We thank Sebastian Aland for the CFD example and Thomas Witkowski and Andreas Naumann for the benchmarks with PMTL4 and PETSc.  ... 
doi:10.1109/ccgrid.2012.51 dblp:conf/ccgrid/GottschlingH12 fatcat:q7xojjtnd5elhkhh37f2rghpge

Comparison of Message-Passing and Shared Memory Implementations of the GMRES Method on MIMD Computers

Joanna Płażek, Krzysztof Banaś, Jacek Kitowski
2001 Scientific Programming  
A combined approach, the hybrid programming model suitable for multicomputers with SMP nodes, is introduced.  ...  In this paper we compare different parallel implementations of the same algorithm for solving nonlinear simulation problems on unstructured meshes.  ...  Monika Dekster (AGH Cracow) for her assistance in preparation of the manuscript.  ... 
doi:10.1155/2001/681621 fatcat:odxbcq52w5gytkzb2ywewg5szq
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