The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States
Molecular dynamics calculations composed of many independent simulations are frequently encountered in free energy simulations, as well as many other simulation approaches. In principal, the availability of a large number of independent tasks should make possible the development of highly scalable parallel code that executes these tasks concurrently. This paper discusses the use of processor groups to write simulation codes of this type and describes results a code that evaluates the volume dependence of the Helmholtz free energy for clusters of an immiscible fluid in a solvent. The results show that very high levels of scalability can be achieved using processor groups with corresponding reductions in the time to completion. The main limitation to scaling appears to be load imbalance due to variations in the execution times of the individual tasks.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 908948
- Report Number(s):
- PNNL-SA-51253; KP1303000; TRN: US200722%%828
- Journal Information:
- Journal of Chemical Theory and Computation, 3(2):583-592, Vol. 3, Issue 2
- Country of Publication:
- United States
- Language:
- English
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