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Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN.

Hammond GE, Lichtner PC, Mills RT - Water Resour Res (2014)

Bottom Line: [1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer.PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field.Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

View Article: PubMed Central - PubMed

Affiliation: Applied Systems Analysis and Research, Sandia National Laboratories Albuquerque, New Mexico, USA.

ABSTRACT

[1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's parallel layout and code design, PFLOTRAN's parallel performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

No MeSH data available.


Wall-clock time for geochemical transport versus process count for 3.1 M copper leaching scenario.
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fig05: Wall-clock time for geochemical transport versus process count for 3.1 M copper leaching scenario.

Mentions: [52]The 3.1 M scenario, with 64 times as many grid cells as the 49 K scenario in the z-dimension of identical length, was run on 32–16384 XK6 processor cores, again incremented by powers of 2. Figure 5 illustrates the wall-clock simulation time for the 3.1 M copper leaching scenario. With the minimum number of processes at 32, the nodes are fully packed leaving no room for the improved memory/cache efficiency that was exhibited below 16 processes in the 49 K scenario.


Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN.

Hammond GE, Lichtner PC, Mills RT - Water Resour Res (2014)

Wall-clock time for geochemical transport versus process count for 3.1 M copper leaching scenario.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257577&req=5

fig05: Wall-clock time for geochemical transport versus process count for 3.1 M copper leaching scenario.
Mentions: [52]The 3.1 M scenario, with 64 times as many grid cells as the 49 K scenario in the z-dimension of identical length, was run on 32–16384 XK6 processor cores, again incremented by powers of 2. Figure 5 illustrates the wall-clock simulation time for the 3.1 M copper leaching scenario. With the minimum number of processes at 32, the nodes are fully packed leaving no room for the improved memory/cache efficiency that was exhibited below 16 processes in the 49 K scenario.

Bottom Line: [1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer.PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field.Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

View Article: PubMed Central - PubMed

Affiliation: Applied Systems Analysis and Research, Sandia National Laboratories Albuquerque, New Mexico, USA.

ABSTRACT

[1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's parallel layout and code design, PFLOTRAN's parallel performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

No MeSH data available.