A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics
Abstract
Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.
- Authors:
-
- University of Southern California, Los Angeles, CA (United States)
- Publication Date:
- Research Org.:
- Univ. of Southern California, Los Angeles, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); Defense Threat Reduction Agency (DTRA); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1538203
- Alternate Identifier(s):
- OSTI ID: 1550232
- Grant/Contract Number:
- SC0010609; SC0014607; HDTRA1-14-1-0074; FG02-13ER16415
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Computer Physics Communications
- Additional Journal Information:
- Journal Volume: 219; Journal Issue: C; Journal ID: ISSN 0010-4655
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; kinetic Monte Carlo simulation; divide-and-conquer algorithm; parallel computing
Citation Formats
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, and Vashishta, Priya. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics. United States: N. p., 2017.
Web. doi:10.1016/j.cpc.2017.05.028.
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, & Vashishta, Priya. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics. United States. https://doi.org/10.1016/j.cpc.2017.05.028
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, and Vashishta, Priya. Tue .
"A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics". United States. https://doi.org/10.1016/j.cpc.2017.05.028. https://www.osti.gov/servlets/purl/1538203.
@article{osti_1538203,
title = {A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics},
author = {Byun, Hye Suk and El-Naggar, Mohamed Y. and Kalia, Rajiv K. and Nakano, Aiichiro and Vashishta, Priya},
abstractNote = {Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.},
doi = {10.1016/j.cpc.2017.05.028},
journal = {Computer Physics Communications},
number = C,
volume = 219,
place = {United States},
year = {Tue Jun 27 00:00:00 EDT 2017},
month = {Tue Jun 27 00:00:00 EDT 2017}
}
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