Abstract
This work details the opportunities and challenges of porting a Petascale, MPI-based application —LAMMPS— to OpenSHMEM. We investigate the major programming challenges stemming from the differences in communication semantics, address space organization, and synchronization operations between the two programming models. This work provides several approaches to solve those challenges for representative communication patterns in LAMMPS, e.g., by considering group synchronization, peer’s buffer status tracking, and unpacked direct transfer of scattered data. The performance of LAMMPS is evaluated on the Titan HPC system at ORNL. The OpenSHMEM implementations are compared with MPI versions in terms of both strong and weak scaling. The results outline that OpenSHMEM provides a rich semantic to implement scalable scientific applications. In addition, the experiments demonstrate that OpenSHMEM can compete with, and often improve on, the optimized MPI implementation.
This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).
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Notes
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For brevity, in this paper we use the simplified nomenclature shmem_put, shmem_get, which are not actual OpenSHMEM functions, but refer to the actual typed operations (like shmem_double_put, shmem_long_get, etc.).
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Acknowledgements
This material is based upon work supported by the U.S. Department of Energy, under contract #DE-AC05-00OR22725, through UT Battelle subcontract #4000123323. The work at Oak Ridge National Laboratory (ORNL) is supported by the United States Department of Defense and used the resources of the Extreme Scale Systems Center located at the ORNL.
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Tang, C., Bouteiller, A., Herault, T., Gorentla Venkata, M., Bosilca, G. (2015). From MPI to OpenSHMEM: Porting LAMMPS. In: Gorentla Venkata, M., Shamis, P., Imam, N., Lopez, M. (eds) OpenSHMEM and Related Technologies. Experiences, Implementations, and Technologies. OpenSHMEM 2014. Lecture Notes in Computer Science(), vol 9397. Springer, Cham. https://doi.org/10.1007/978-3-319-26428-8_8
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