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Thursday, February 07

Eliminating Explicit Synchronization from
Molecular Simulations to Improve Scalability

T. P. Straatsma, Pacific Northwest National Laboratory, Richland, Wash.
National Center for Computational Sciences Seminar
10:00 AM — 11:00 AM, Building 4500-N, Weinberg Auditorium
Contact: Linda Gregg (, 865.241.7202


Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern, massively-concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive.

This presentation illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put-notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

About the speaker
Dr. T. P. Straatsma is currently the Chief Scientist and Director of the Extreme Scale Computing Initiative for the Computational Sciences and Mathematics Division of the Pacific Northwest National Laboratory. He holds a Ph.D. in Mathematics and Natural Sciences from the University of Groningen, the Netherlands.