TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics
Abstract
Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family of molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code showsmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1329851
- Report Number(s):
- LA-UR-13-28342
Journal ID: ISSN 1049-3301
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- ACM Transactions on Modeling and Computer Simulation
- Additional Journal Information:
- Journal Volume: 25; Journal Issue: 3; Journal ID: ISSN 1049-3301
- Publisher:
- Association for Computing Machinery
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; Computer Science; Material Science; temperature-accelerated dynamics (TAD) method
Citation Formats
Mniszewski, Susan M., Junghans, Christoph, Voter, Arthur F., Perez, Danny, and Eidenbenz, Stephan J. TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics. United States: N. p., 2015.
Web. doi:10.1145/2699715.
Mniszewski, Susan M., Junghans, Christoph, Voter, Arthur F., Perez, Danny, & Eidenbenz, Stephan J. TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics. United States. https://doi.org/10.1145/2699715
Mniszewski, Susan M., Junghans, Christoph, Voter, Arthur F., Perez, Danny, and Eidenbenz, Stephan J. Thu .
"TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics". United States. https://doi.org/10.1145/2699715. https://www.osti.gov/servlets/purl/1329851.
@article{osti_1329851,
title = {TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics},
author = {Mniszewski, Susan M. and Junghans, Christoph and Voter, Arthur F. and Perez, Danny and Eidenbenz, Stephan J.},
abstractNote = {Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family of molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.},
doi = {10.1145/2699715},
journal = {ACM Transactions on Modeling and Computer Simulation},
number = 3,
volume = 25,
place = {United States},
year = {Thu Apr 16 00:00:00 EDT 2015},
month = {Thu Apr 16 00:00:00 EDT 2015}
}
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Works referencing / citing this record:
Speculation and replication in temperature accelerated dynamics
journal, February 2018
- Zamora, Richard J.; Perez, Danny; Voter, Arthur F.
- Journal of Materials Research, Vol. 33, Issue 7