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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.


PFLOTRAN relative strong scaling efficiency for the IFRC problem scenario where the efficiency for the entire simulation (Total) is divided into the Flow, Geochemical Transport, and Other (i.e., initialization, I/O) components. Ideal efficiency is 1.0. The superlinear efficiency for Flow is likely due to caching effects. Note that beyond 128 processes, the size of the IFRC flow problem on each process is too small to expect good scalability (i.e., well below 10 K flow dofs/process).
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fig11: PFLOTRAN relative strong scaling efficiency for the IFRC problem scenario where the efficiency for the entire simulation (Total) is divided into the Flow, Geochemical Transport, and Other (i.e., initialization, I/O) components. Ideal efficiency is 1.0. The superlinear efficiency for Flow is likely due to caching effects. Note that beyond 128 processes, the size of the IFRC flow problem on each process is too small to expect good scalability (i.e., well below 10 K flow dofs/process).

Mentions: [66]The IFRC scenario domain is discretized with 432 K grids cells measuring . At one and 10 dofs per grid cell, the total number of flow and geochemical transport dofs are 432 K and 4.32 M, respectively. Simulations were run on 32–16,384 Jaguar XK6 processor cores incremented by powers of 2. Figure 10 presents the total wall-clock time required to complete the simulation versus the number of processes employed where the total time is divided between Flow, Geochemical Transport, and time spent in Other portions of the code (the major contributors being initialization and checkpointing). The slope of ideal speedup is plotted for comparison purposes. The corresponding relative strong scaling efficiencies are shown in Figure 11. The overall scalability of the code is near linear (Total efficiency % in Figure 1) out to 512 processes. Beyond 512 processes, the scalability of the flow solution and Other portions of the code begins to degrade dramatically.


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

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

PFLOTRAN relative strong scaling efficiency for the IFRC problem scenario where the efficiency for the entire simulation (Total) is divided into the Flow, Geochemical Transport, and Other (i.e., initialization, I/O) components. Ideal efficiency is 1.0. The superlinear efficiency for Flow is likely due to caching effects. Note that beyond 128 processes, the size of the IFRC flow problem on each process is too small to expect good scalability (i.e., well below 10 K flow dofs/process).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig11: PFLOTRAN relative strong scaling efficiency for the IFRC problem scenario where the efficiency for the entire simulation (Total) is divided into the Flow, Geochemical Transport, and Other (i.e., initialization, I/O) components. Ideal efficiency is 1.0. The superlinear efficiency for Flow is likely due to caching effects. Note that beyond 128 processes, the size of the IFRC flow problem on each process is too small to expect good scalability (i.e., well below 10 K flow dofs/process).
Mentions: [66]The IFRC scenario domain is discretized with 432 K grids cells measuring . At one and 10 dofs per grid cell, the total number of flow and geochemical transport dofs are 432 K and 4.32 M, respectively. Simulations were run on 32–16,384 Jaguar XK6 processor cores incremented by powers of 2. Figure 10 presents the total wall-clock time required to complete the simulation versus the number of processes employed where the total time is divided between Flow, Geochemical Transport, and time spent in Other portions of the code (the major contributors being initialization and checkpointing). The slope of ideal speedup is plotted for comparison purposes. The corresponding relative strong scaling efficiencies are shown in Figure 11. The overall scalability of the code is near linear (Total efficiency % in Figure 1) out to 512 processes. Beyond 512 processes, the scalability of the flow solution and Other portions of the code begins to degrade dramatically.

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.