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Performance Analysis of Python-based Finite Volume Solver ANUGA on Modern Architectures

Published: 04 November 2021 Publication History

Abstract

The performance analysis of ANUGA, a Python-based finite volume solver on the unstructured grid for shallow water model in two dimensions, on recent Intel and AMD processor-based HPC clusters, form the focus of the present study. The analysis uses three datasets with different resolutions of the underlying triangular mesh for discretizing the region of interest. The computational workload depends on the resolution of the grid, which impacts the computation time required for the simulation of the flow. The factors influencing the parallel performance: workload distribution across different processes, and the bulk of the data exchange (the communication overhead), are studied systematically. This paper is an account of the preliminary study to understand the impact of the memory hierarchy (due to the relative sizes of cache) available on different architecture on the performance of this application.

References

[1]
M. Arafa, B. Fahim, S. Kottapalli, A. Kumar, L. P. Looi, S. Mandava, A. Rudoff, I. M. Steiner, B. Valentine, G. Vedaraman, and S. Vora. 2019. Cascade Lake: Next generation Intel Xeon scalable processor. IEEE Micro 39, 2 (2019), 29–36. https://doi.org/10.1109/MM.2019.2899330
[2]
Lorenzo Begnudelli and Brett F. Sanders. 2006. Unstructured grid finite-volume algorithm for shallow-water flow and scalar transport with wetting and drying. Journal of Hydraulic Engineering 132 (2006), 371–384. https://doi.org/10.1061/ASCE0733-94292006132:4371
[3]
M. J. Castro, J. A. García-Rodríguez, J. M. González-Vida, and C. Parés. 2006. A parallel 2D finite volume scheme for solving systems of balance laws with nonconservative products: Application to shallow flows. Computer Methods in Applied Mechanics and Engineering 195 (2006), 2788–2815. https://doi.org/10.1016/j.cma.2005.07.007
[4]
Phillip Colella. 2004. Defining software requirements for scientific computing. DARPA HPCS Presentation.
[5]
Intel Corporation. 2021. Intel Trace Analyzer and Collector: MPI Profiling for Cluster Applications. https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/trace-analyzer.html
[6]
G. Davies and S. Roberts. 2015. Open source flood simulation with a 2D discontinuous-elevation hydrodynamic model. In Proceedings of International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, MODSIM 2015, T. Weber, M. J. McPhee, and R. S. Anderssen(Eds.). 2130–2136. https://www.mssanz.org.au/modsim2015/
[7]
J. Doweck, W. Kao, A. K. Lu, J. Mandelblat, A. Rahatekar, L. Rappoport, E. Rotem, A. Yasin, and A. Yoaz. 2017. Inside 6th-Generation Intel Core: New microarchitecture code-named Skylake. IEEE Micro 37, 2 (2017), 52–62. https://doi.org/10.1109/MM.2017.38
[8]
Domenico Ferraro, Pierfranco Costabile, Carmelina Costanzo, Gabriella Petaccia, and Francesco Macchione. 2020. A spectral analysis approach for the a priori generation of computational grids in the 2-D hydrodynamic-based runoff simulations at a basin scale. Journal of Hydrology 582(2020), 124508. https://doi.org/10.1016/j.jhydrol.2019.124508
[9]
Bobby Minola Ginting, Punit Kumar Bhola, Christoph Ertl, Ralf-Peter Mundani, Markus Disse, and Ernst Rank. 2020. Hybrid-parallel simulations and visualisations of real flood and tsunami events using unstructured meshes on high-performance cluster systems. In Advances in Hydroinformatics, Models for Extreme Situations and Crisis Management, SimHydro 2019(Springer Water book series), P. Gourbesville and G. Caignaert (Eds.). 867–888. https://10.1007/978-981-15-5436-0_67
[10]
Bobby Minola Ginting and Ralf-Peter Mundani. 2019. Comparison of shallow water solvers: Applications for dam-break and tsunami cases with reordering strategy for efficient vectorization on modern hardware. Water 11(2019), 639 (1–32). https://doi.org/10.3390/w11040639
[11]
Carlos H. González, Basilio B. Fraguela, Diego Andrade, José A. García, and Manuel J. Castro. 2013. Numerical simulation of pollutant transport in a shallow-water system on the Cell heterogeneous processor. Journal of Supercomputing 65 (2013), 1089–1103. https://doi.org/10.1007/s11227-012-0862-y
[12]
Ioan Hadade, Feng Wang, Mauro Carnevale, and Luca di Mare. 2019. Some useful optimisations for unstructured computational fluid dynamics codes on multicore and manycore architectures. Computer Physics Communications 235 (2019), 305–323. https://doi.org/10.1016/j.cpc.2018.07.001
[13]
George Karypis and Vipin Kumar. 2013. METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering. http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
[14]
D. K. Kaushik and D. E. Keyes. 1999. Efficient parallelization of an unstructured grid solver: A memory-centric approach. Technical Report. Istambul Technical University.
[15]
M. K. Kumashikar, S. G. Bendi, S. Nimmagadda, A. J. Deka, and A. Agarwal. 2017. 14nm Broadwell Xeon® processor family: Design methodologies and optimizations. In 2017 IEEE Asian Solid-State Circuits Conference (A-SSCC). 17–20. https://doi.org/10.1109/ASSCC.2017.8240205
[16]
Asier Lacasta, Mario Morales-Hernández, Javier Murillo, and Pilar García-Navarro. 2015. GPU implementation of the 2D shallow water equations for the simulation of rainfall/runoff events. Environmental Earth Sciences 74 (2015), 7295–7305. https://doi.org/10.1007/s12665-015-4215-z
[17]
Qiuhua Liang. 2010. Flood simulation using a well-balanced shallow flow model. Journal of Hydraulic Engineering 136 (2010), 669–675. https://doi.org/(ASCE)HY.1943-7900.0000219
[18]
Zhanyan Liu, Hongbin Zhang, and Qiuhua Liang. 2019. A coupled hydrological and hydrodynamic model for flood simulation. Hydrology Research 50(2019), 589–606. https://doi.org/10.2166/nh.2018.090
[19]
Jacobo Lobeiras, Moisés Vinās, Margarita Amor, Basilio B. Fraguela, Manuel Arenaz, J. A. García-Rodríguez, and Manuel J. Castro. 2012. Parallelization of shallow water simulations on current multi-threaded systems. International Journal of High Performance Computing Applications 27 (2012), 493–512. https://doi.org/10.1177/1094342012464800
[20]
Sudi Mungkasi and J. B. Budi Darmawan. 2015. Fast and efficient parallel computations using a cluster of workstations to simulate flood flows. In Intelligence in the Era of Big Data: Proceedings of International Conference on Soft Computing, Intelligence Systems, and Information Technology, ICSIIT 2015(Communications in Computer and Information Science, Vol. 516), R. Intan, Chi-Hung Chi, H. N. Palit, and L. W. Santoso (Eds.). 469–477. https://link.springer.com/book/10.1007/978-3-662-46742-8
[21]
Sudi Mungkasi and Stephen Gwyn Roberts. 2011. A finite volume method for shallow water flows on triangular computational grids. In Proceedings of IEEE International Conference on Advanced Computer Science and Information Systems, ICACSIS 2011. 79–84. https://ieeexplore.ieee.org/xpl/conhome/6132213/proceeding
[22]
Ole Møller Nielsen, Stephen G. Roberts, D. Gray, Andrew McPherson, and A. Hitchman. 2005. Hydrodynamic modelling of coastal inundation. In Proceedings of International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, MODSIM 2005, A. Zerger and R. M. Argent (Eds.). 518–523. https://www.mssanz.org.au/modsim05/index.htm
[23]
G. Petaccia, F. Leporati, and E. Torti. 2016. OpenMP and CUDA simulations of Sella Zerbino Dam break on unstructured grids. Computational Geosciences 20 (2016), 1123–1132. https://doi.org/10.1007/s10596-016-9580-5
[24]
Stephen Gwyn Roberts and Ole Møller Nielsen. 2007. Parallelisation of a finite volume method for hydrodynamic inundation modelling. In Proceedings of the 13th Biennial Computational Techniques and Applications Conference, CTAC-2006(ANZIAM Journal, Vol. 48), Wayne Readand A. J. Roberts (Eds.). C558–C572. https://journal.austms.org.au/ojs/index.php/ANZIAMJ/article/view/153
[25]
Stephen G Roberts, Yusuke Oishi, and Michael Li. 2013. High resolution tsunami inundation simulations. In Proceedings of International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, MODSIM 2013, J. Piantadosi, R. S. Anderssen, and J. Boland (Eds.). 310–316. https://www.mssanz.org.au/modsim2013/
[26]
Jonathan Richard Shewchuk. 2005. A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator. https://www.cs.cmu.edu/~quake/triangle.html
[27]
Francisco J. M. Simões. 2011. Finite volume model for two-dimensional shallow environmental flow. Journal of Hydraulic Engineering 137 (2011), 173–182. https://doi.org/10.1061/(ASCE)HY.1943-7900.0000292
[28]
D. Suggs, M. Subramony, and D. Bouvier. 2020. The AMD “Zen 2” processor. IEEE Micro 40, 2 (2020), 45–52. https://doi.org/10.1109/MM.2020.2974217
[29]
András Attila Sulyok, Gábor Dániel Balogh, István Zoltan Reguly, and Gihan R. Mudalige. 2018. Improving locality of unstructured mesh algorithms on GPUs. arXiv:1802.03749 [cs.MS].
[30]
Zhe Weng and Peter E. Strazdins. 2014. Acceleration of a Python-based tsunami modelling application via CUDA and OpenHMPP. In Proceedings of International Symposium on Parallel and Distributed Processing Symposium Workshops, IPDPSW 2014. 1275 –1284. https://ieeexplore.ieee.org/xpl/conhome/6967893/proceeding
[31]
Xinya Ying, Jeff Jorgeson, and Sam S. Y. Wang. 2009. Modeling dam-break flows using finite volume method on unstructured grid. Engineering Applications of Computational Fluid Mechanics 3 (2009), 184–194. https://doi.org/10.1080/19942060.2009.11015264

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IC3-2021: Proceedings of the 2021 Thirteenth International Conference on Contemporary Computing
August 2021
483 pages
ISBN:9781450389204
DOI:10.1145/3474124
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 04 November 2021

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  1. MPI
  2. finite volume method
  3. performance
  4. shallow water model
  5. unstructured grid

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