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ASAGI: A Parallel Server for Adaptive Geoinformation

Authors:

Sebastian Rettenberger,

Oliver Meister,

Alice-Agnes GabrielAuthors Info & Claims

EASC '16: Proceedings of the Exascale Applications and Software Conference 2016

Article No.: 2, Pages 1 - 9

https://doi.org/10.1145/2938615.2938618

Published: 26 April 2016 Publication History

Abstract

We present ASAGI, an open-source library with a simple interface to access Cartesian material and geographic datasets in massively parallel simulations with dynamically adaptive mesh refinement (AMR). ASAGI distributes geographic datasets over all compute nodes storing only a portion of the dataset on each node. An automatic replication mechanism copies the data between nodes to assure fast local access even after load migration in the application. We demonstrate ASAGI's preparedness for up-to-petascale simulations in three use cases. We simulate a Tsunami on 512 cores and a porous media flow on up to 8,192 cores of SuperMUC with the AMR framework sam(oa)2. We also run an earthquake simulation with SeiSol on 65,536 cores. For all applications, ASAGI provides large complex 3D material datasets required for the realistic scenarios. The NUMA-awareness of ASAGI turned out to be especially useful for the hybrid MPI+OpenMP parallelization of both codes.

References

[1]

Conventions for the standardization of NetCDF files, 1995. http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html, Accessed: 2016-02-11.

[2]

The GEBCO_08 Grid, version 20100927, 2010. http://www.gebco.net.

[3]

J. Dinan, P. Balaji, D. Buntinas, D. Goodell, W. Gropp, and R. Thakur. An implementation and evaluation of the MPI 3.0 one-sided communication interface. Concurrency and Computation: Practice and Experience, 2016.

Digital Library

[4]

A. Gabriel and C. Pelties. Simulating large-scale earthquake dynamic rupture scenarios on natural fault zones using the ADER-DG method. In EGU General Assembly Conference Abstracts, volume 16 of EGU General Assembly Conference Abstracts, page 10572, May 2014. poster abstract.

[5]

P. Galvez, J.-P. Ampuero, L. A. Dalguer, S. N. Somala, and T. Nissen-Meyer. Dynamic earthquake rupture modelled with an unstructured 3-D spectral element method applied to the 2011 M9 Tohoku earthquake. Geophysical Journal International, 198(2):1222--1240, 2014.

[6]

D. L. George and R. J. LeVeque. Finite volume methods and adaptive refinement for global tsunami propagation and local inundation. Science of Tsunami Hazards, 24:319--328, 2006.

[7]

A. Heinecke, A. Breuer, S. Rettenberger, M. Bader, A.-A. Gabriel, C. Pelties, A. Bode,W. Barth, X.-K. Liao, K. Vaidyanathan, M. Smelyanskiy, and P. Dubey. Petascale high order dynamic rupture earthquake simulations on heterogeneous supercomputers. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis SC14, pages 3--14, New Orleans, LA, USA, Nov. 2014. IEEE.

Digital Library

[8]

A. Humphrey, D. Sunderland, T. Harman, and M. Berzins. Radiative heat transfer calculation on 16384 GPUs using a reverse Monte Carlo ray tracing approach with adaptive mesh refinement. In The 17th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2016), 2016. accepted.

[9]

M. D. Kohler, H. Magistrale, and R. W. Clayton. Mantle heterogeneities and the SCEC reference three-dimensional seismic velocity model version 3. Bulletin of the Seismological Society of America, 93(2):757--774, 2003.

[10]

O. Meister and M. Bader. 2D adaptivity for 3D problems: Parallel SPE10 reservoir simulation on dynamically adaptive prism grids. Journal of Computational Science, 9:101--106, 2015.

[11]

MPI Forum. MPI: A message passing interface standard. Version 2.0, May 1998.

[12]

A. K. Patra, A. Bauer, C. Nichita, E. B. Pitman, M. Sheridan, M. Bursik, B. Rupp, A. Webber, A. Stinton, L. Namikawa, et al. Parallel adaptive numerical simulation of dry avalanches over natural terrain. Journal of Volcanology and Geothermal Research, 139(1):1--21, 2005.

[13]

A. Plesch, C. Tape, R. Graves, P. Small, G. Ely, and J. Shaw. Updates for the CVM-H including new representations of the offshore Santa Maria and San Bernardino basin and a new Moho surface. In 2011 Southern California Earthquake Center Annual Meeting, Proceedings and Abstracts, volume 21, page 214, 2011.

[14]

S. Popinet. Quadtree-adaptive tsunami modelling. Ocean Dynamics, 61(9):1261--1285, 2011.

[15]

S. Popinet. Adaptive modelling of long-distance wave propagation and fine-scale flooding during the Tohoku tsunami. Natural Hazards and Earth System Sciences, 12(4):1213--1227, 2012.

[16]

J. Rudi, A. C. I. Malossi, T. Isaac, G. Stadler, M. Gurnis, P. W. J. Staar, Y. Ineichen, C. Bekas, A. Curioni, and O. Ghattas. An extreme-scale implicit solver for complex PDEs: Highly heterogeneous flow in earth's mantle. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC '15, pages 5:1--5:12, New York, NY, USA, 2015. ACM.

Digital Library

[17]

O. Sahni, K. E. Jansen, C. A. Taylor, and M. S. Shephard. Automated adaptive cardiovascular flow simulations. Engineering with Computers, 25(1):25--36, 2008.

[18]

SeisSol, 2016. http://www.seissol.org/.

[19]

E. Strohmaier, J. Dongarra, H. Simon, and M. Meuer. Top500 list, November 2015. http://www.top500.org.

[20]

M. P. Süss and J. H. Shaw. P wave seismic velocity structure derived from sonic logs and industry reflection data in the Los Angeles basin, California. Journal of Geophysical Research: Solid Earth, 108(B3), 2003. 2170.

[21]

A. S. Tanenbaum. Modern operating systems (2. ed.). Prentice Hall, 2001.

Digital Library

[22]

K. Unterweger, R. Wittmann, P. Neumann, T. Weinzierl, and H.-J. Bungartz. Integration of FULLSWOF2D and PeanoClaw: adaptivity and local time-stepping for complex overland flows. In Recent trends in computational engineering - CE2014: optimization, uncertainty, parallel algorithms, coupled and complex problems., pages 181--195. Springer, 2015.

Cited By

Palgunadi KGabriel AGaragash DUlrich TMai P(2024)Rupture Dynamics of Cascading Earthquakes in a Multiscale Fracture NetworkJournal of Geophysical Research: Solid Earth10.1029/2023JB027578129:3Online publication date: 19-Mar-2024
https://doi.org/10.1029/2023JB027578
Li DGabriel A(2024) Linking 3D Long‐Term Slow‐Slip Cycle Models With Rupture Dynamics: The Nucleation of the 2014 M w 7.3 Guerrero, Mexico Earthquake AGU Advances10.1029/2023AV0009795:2Online publication date: 30-Mar-2024
https://doi.org/10.1029/2023AV000979
Taufiqurrahman TGabriel ALi DUlrich TLi BCarena SVerdecchia AGallovič F(2023)Dynamics, interactions and delays of the 2019 Ridgecrest rupture sequenceNature10.1038/s41586-023-05985-x618:7964(308-315)Online publication date: 24-May-2023
https://doi.org/10.1038/s41586-023-05985-x
Show More Cited By

ASAGI: A Parallel Server for Adaptive Geoinformation
1. Applied computing
  1. Physical sciences and engineering

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cover image ACM Other conferences

EASC '16: Proceedings of the Exascale Applications and Software Conference 2016

April 2016

59 pages

ISBN:9781450341226

DOI:10.1145/2938615

Copyright © 2016 ACM.

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 the author(s) 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: 26 April 2016

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EASC '16: Exascale Applications and Software Conference 2016

April 26 - 29, 2016

Stockholm, Sweden

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Cited By

Palgunadi KGabriel AGaragash DUlrich TMai P(2024)Rupture Dynamics of Cascading Earthquakes in a Multiscale Fracture NetworkJournal of Geophysical Research: Solid Earth10.1029/2023JB027578129:3Online publication date: 19-Mar-2024
https://doi.org/10.1029/2023JB027578
Li DGabriel A(2024) Linking 3D Long‐Term Slow‐Slip Cycle Models With Rupture Dynamics: The Nucleation of the 2014 M w 7.3 Guerrero, Mexico Earthquake AGU Advances10.1029/2023AV0009795:2Online publication date: 30-Mar-2024
https://doi.org/10.1029/2023AV000979
Taufiqurrahman TGabriel ALi DUlrich TLi BCarena SVerdecchia AGallovič F(2023)Dynamics, interactions and delays of the 2019 Ridgecrest rupture sequenceNature10.1038/s41586-023-05985-x618:7964(308-315)Online publication date: 24-May-2023
https://doi.org/10.1038/s41586-023-05985-x
Rekoske JGabriel AMay D(2023)Instantaneous Physics‐Based Ground Motion Maps Using Reduced‐Order ModelingJournal of Geophysical Research: Solid Earth10.1029/2023JB026975128:8Online publication date: 11-Aug-2023
https://doi.org/10.1029/2023JB026975
Ulrich TGabriel AMadden E(2022)Stress, rigidity and sediment strength control megathrust earthquake and tsunami dynamicsNature Geoscience10.1038/s41561-021-00863-515:1(67-73)Online publication date: 17-Jan-2022
https://doi.org/10.1038/s41561-021-00863-5
Madden EUlrich TGabriel A(2022)The State of Pore Fluid Pressure and 3‐D Megathrust Earthquake DynamicsJournal of Geophysical Research: Solid Earth10.1029/2021JB023382127:4Online publication date: 2-Apr-2022
https://doi.org/10.1029/2021JB023382
Biemiller JGabriel AUlrich T(2022)The Dynamics of Unlikely Slip: 3D Modeling of Low‐Angle Normal Fault Rupture at the Mai'iu Fault, Papua New GuineaGeochemistry, Geophysics, Geosystems10.1029/2021GC01029823:5Online publication date: 25-May-2022
https://doi.org/10.1029/2021GC010298
Aniko Wirp SGabriel ASchmeller MH. Madden Evan Zelst IKrenz Lvan Dinther YRannabauer L(2021)3D Linked Subduction, Dynamic Rupture, Tsunami, and Inundation Modeling: Dynamic Effects of Supershear and Tsunami Earthquakes, Hypocenter Location, and Shallow Fault SlipFrontiers in Earth Science10.3389/feart.2021.6268449Online publication date: 24-Jun-2021
https://doi.org/10.3389/feart.2021.626844
Palgunadi KGabriel AUlrich TLópez-Comino JMai P(2020)Dynamic Fault Interaction during a Fluid-Injection-Induced Earthquake: The 2017 Mw 5.5 Pohang EventBulletin of the Seismological Society of America10.1785/0120200106110:5(2328-2349)Online publication date: 4-Aug-2020
https://doi.org/10.1785/0120200106
Madden EBader MBehrens Jvan Dinther YGabriel ARannabauer LUlrich TUphoff CVater Svan Zelst I(2020)Linked 3-D modelling of megathrust earthquake-tsunami events: from subduction to tsunami run upGeophysical Journal International10.1093/gji/ggaa484224:1(487-516)Online publication date: 10-Oct-2020
https://doi.org/10.1093/gji/ggaa484
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