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).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
- 2.
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.).
References
Using the GNI and DMAPP APIs. Technical Report S-2446-3103, Cray Inc. (2011). http://docs.cray.com/books/S-2446-3103/S-2446-3103.pdf
OpenSHMEM application programming interface (version 1.2). Technical report, Open Source Software Solutions, Inc. (OSSS) (2015). http://www.openshmem.org
Barriuso, R., Knies, A.: SHMEM’s user’s guide for C. Technical report, Cray Research Inc. (1994)
Gerstenberger, R., Besta, M., Hoefler, T.: Enabling highly-scalable remote memory access programming with MPI-3 one sided. Sci. Program. 22(2), 75–91 (2014). doi:10.3233/SPR-140383
Jose, J., Potluri, S., Subramoni, H., Lu, X., Hamidouche, K., Schulz, K., Sundar, H., Panda, D.K.: Designing scalable out-of-core sorting with hybrid MPI+PGAS programming models. In: Proceedings of the 8th International Conference on Partitioned Global Address Space Programming Models, PGAS 2014, pp. 7:1–7:9. ACM, New York (2014). doi:10.1145/2676870.2676880
Jose, J., Potluri, S., Tomko, K., Panda, D.K.: Designing scalable graph500 benchmark with hybrid MPI+OpenSHMEM programming models. In: Kunkel, J.M., Ludwig, T., Meuer, H.W. (eds.) ISC 2013. LNCS, vol. 7905, pp. 109–124. Springer, Heidelberg (2013)
Li, M., Lin, J., Lu, X., Hamidouche, K., Tomko, K., Panda, D.K.: Scalable MiniMD design with hybrid MPI and OpenSHMEM. In: Proceedings of the 8th International Conference on Partitioned Global Address Space Programming Models, PGAS 2014, pp. 24:1–24:4. ACM, New York (2014). doi:10.1145/2676870.2676893
Li, M., Lu, X., Potluri, S., Hamidouche, K., Jose, J., Tomko, K., Panda, D.: Scalable graph500 design with MPI-3 RMA. In: 2014 IEEE International Conference on Cluster Computing (CLUSTER), pp. 230–238, September 2014. doi:10.1109/CLUSTER.2014.6968755
MPI Forum. MPI: A Message-Passing Interface Standard (Version 2.2). High Performance Computing Center Stuttgart (HLRS), September 2009
Plimpton, S.: Parallel FFT package. Technical report, Sandia National Labs. http://www.sandia.gov/~sjplimp/docs/fft/README.html
Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117(1), 1–19 (1995). doi:10.1006/jcph.1995.1039
Poole, S.W., Hernandez, O.R., Kuehn, J.A., Shipman, G.M., Curtis, A., Feind, K.: OpenSHMEM - toward a unified RMA model. In: Padua, D.A. (ed.) Encyclopedia of Parallel Computing, pp. 1379–1391. Springer, Heidelberg (2011). doi:10.1007/978-0-387-09766-4_490
Pophale, S., Nanjegowda, R., Curtis, T., Chapman, B., Jin, H., Poole, S., Kuehn, J.: OpenSHMEM Performance and Potential: An NPB Experimental Study. In: Proceedings of the 6th Conference on Partitioned Global Address Space Programming Model, PGAS 2012. ACM, New York (2012)
Vetter, J.S., McCracken, M.O.: Statistical scalability analysis of communication operations in distributed applications. SIGPLAN Not. 36(7), 123–132 (2001). doi:10.1145/568014.379590
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
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
Download citation
DOI: https://doi.org/10.1007/978-3-319-26428-8_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-26427-1
Online ISBN: 978-3-319-26428-8
eBook Packages: Computer ScienceComputer Science (R0)