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Multi-Level Parallelization of the Fragment Molecular Orbital Method in GAMESS

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Recent Advances of the Fragment Molecular Orbital Method

Abstract

The parallelization of the fragment molecular orbital (FMO) method implemented in GAMESS is reviewed for Cray/Intel, IBM Blue Gene, and Fujitsu supercomputers. Various strategies for load balancing are compared. A basic OpenMP implementation of FMO is described and its parallel efficiency is reported. The two-level generalized distributed data interface is extended to an arbitrary number of levels and applied using three levels to an FMO Hessian calculation at the level of second-order Møller–Plesset (MP2) theory.

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Acknowledgements

We thank Dr. Ryan Olson for contributing code to the multilevel GDDI. VM thanks Intel Parallel Computing Centers program for funding. DGF and HU thank the Next-Generation Supercomputer (NGS) project funded by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan. This work was supported by the Office of Science, U.S. Department of Energy, under Contract DE-AC02-06CH11357. MSG acknowledges support from the US Department of Energy Exascale Computing Project. This research was in part supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.

Author information

Authors and Affiliations

  1. Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1/3, Moscow, 119991, Russia

    Vladimir A. Mironov

  2. Argonne National Laboratory, Computational Science Division, Argonne, IL, 60439, USA

    Yuri Alexeev

  3. CD-FMat, National Institute of Advanced Industrial Science and Technology, Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan

    Dmitri G. Fedorov

  4. Institute for Molecular Science, National Institute of Natural Sciences, 2F Hulic Kamiyacho Building, 4-3-13 Toranomon, Minato-ku, Tokyo, 105-0001, Japan

    Hiroaki Umeda

  5. Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan

    Hiroaki Umeda

  6. Cray Japan Inc., 15F Hibiya Daibiru, 1-2-2, Uchisaiwai-Cho, Chiyoda-ku, Tokyo, 100-0011, Japan

    Hiroaki Umeda

  7. Academic & Research Computing, Worcester Polytechnic Institute, Worcester, MA, 01609, USA

    Spencer Pruitt

  8. Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA, 50011, USA

    Alexander Gaenko & Mark S. Gordon

  9. Advanced Research Computing, University of Michigan, 3550 Rackham, 915 E. Washington St., Ann Arbor, MI, 48109-1070, USA

    Alexander Gaenko

Authors
  1. Vladimir A. Mironov
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  2. Yuri Alexeev
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  3. Dmitri G. Fedorov
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  4. Hiroaki Umeda
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  5. Spencer Pruitt
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  6. Alexander Gaenko
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  7. Mark S. Gordon
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Corresponding author

Correspondence to Yuri Alexeev .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo, Japan

    Yuji Mochizuki

  2. Graduate School of System Informatics, Kobe University, Kobe, Japan

    Shigenori Tanaka

  3. School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan

    Kaori Fukuzawa

Glossary

GAMESS

general atomic and molecular electronic structure system

QM

quantum-mechanical

FMO

fragment molecular orbital

HPC

high-performance computing

MPI

message passing interface

OpenMP

open multi-processing

HF

Hartree–Fock

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Mironov, V.A. et al. (2021). Multi-Level Parallelization of the Fragment Molecular Orbital Method in GAMESS. In: Mochizuki, Y., Tanaka, S., Fukuzawa, K. (eds) Recent Advances of the Fragment Molecular Orbital Method. Springer, Singapore. https://doi.org/10.1007/978-981-15-9235-5_30

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