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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 49 K copper leaching scenario. The Ideal Slope lines represent the slope of ideal speedup, which is essentially linear between 8–128 processes.
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fig03: Wall-clock time for geochemical transport versus process count for 49 K copper leaching scenario. The Ideal Slope lines represent the slope of ideal speedup, which is essentially linear between 8–128 processes.

Mentions: [48]The 49 K scenario was run on 1–1024 Jaguar XK6 processor cores incremented by powers of 2. Figure 3 illustrates the wall-clock time versus the number of processes employed for fully implicit geochemical transport. The dashed lines in the figure illustrate the slope of ideal or linear speedup, but not ideal performance itself. It is clear from the figures that scalability (or speedup) is less than ideal between 1–8 and 128–1024 processes.


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 49 K copper leaching scenario. The Ideal Slope lines represent the slope of ideal speedup, which is essentially linear between 8–128 processes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig03: Wall-clock time for geochemical transport versus process count for 49 K copper leaching scenario. The Ideal Slope lines represent the slope of ideal speedup, which is essentially linear between 8–128 processes.
Mentions: [48]The 49 K scenario was run on 1–1024 Jaguar XK6 processor cores incremented by powers of 2. Figure 3 illustrates the wall-clock time versus the number of processes employed for fully implicit geochemical transport. The dashed lines in the figure illustrate the slope of ideal or linear speedup, but not ideal performance itself. It is clear from the figures that scalability (or speedup) is less than ideal between 1–8 and 128–1024 processes.

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.