Abstract
We address the problem of generating a many-nucleon basis for ab initio nuclear structure modeling, which quickly becomes a significant runtime bottleneck for large model spaces. We first analyze the original basis generation algorithm, which does not employ multi-threading parallel paradigm. Based on the analysis, we propose and empirically evaluate a new efficient scalable basis generation algorithm. We report a reduction of basis generation runtime by a factor of 42 on the Blue Waters supercomputer and by two orders of magnitude on our test-bed computer system with Broadwell CPUs.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
https://sourceforge.net/projects/lsu3shell/ (In the time of writing this paper, latest updates were included in the LSU3develop repository branch).
- 2.
Note that the simulation mode does not reflect the runtime of the MPI_Allreduce communication operation. However, such a reduction of a small array is generally very fast. For instance, on Blue Waters it takes up to few seconds even if majority of the nodes are involved [9].
References
Dytrych, T., Launey, K., Draayer, J., Maris, P., Vary, J., Saule, E., Catalyurek, U., Sosonkina, M., Langr, D., Caprio, M.: Collective modes in light nuclei from first principles. Phys. Rev. Lett. 111(25), 252501 (2013). https://doi.org/10.1103/PhysRevLett.111.252501
Dytrych, T., Maris, P., Launey, K., Draayer, J., Vary, J., Langr, D., Saule, E., Caprio, M., Catalyurek, U., Sosonkina, M.: Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei. Comput. Phys. Commun. 207, 202–210 (2016). https://doi.org/10.1016/j.cpc.2016.06.006
Elliott, J.P.: Collective motion in the nuclear shell model. I. Classification schemes for states of mixed configurations. Proc. Roy. Soc. Lond. A: Math. Physi Eng. Sci. 245(1240), 128–145 (1958). https://doi.org/10.1098/rspa.1958.0072
Elliott, J.P.: Collective motion in the nuclear shell model. II. The introduction of intrinsic wave-functions. Proc. Roy. Soc. Lond. A: Math. Phys. Eng. Sci. 245(1243), 562–581 (1958). https://doi.org/10.1098/rspa.1958.0101
Elliott, J.P., Harvey, M.: Collective motion in the nuclear shell model. III. The calculation of spectra. Proc. Roy. Soc. Lond. A: Math. Phys. Eng. Sci. 272(1351), 557–577 (1963). https://doi.org/10.1098/rspa.1963.0071
Epelbaum, E., Krebs, H., Lee, D., Meißner, U.G.: Ab initio calculation of the Hoyle state. Phys. Rev. Lett. 106, 192501 (2011). https://doi.org/10.1103/PhysRevLett.106.192501
Hagen, G., Papenbrock, T., Hjorth-Jensen, M.: Ab initio computation of the 17F proton halo state and resonances in A = 17 nuclei. Phys. Rev. Lett. 104, 182501 (2010). https://doi.org/10.1103/PhysRevLett.104.182501
Kleinrock, L.: Computer Applications. Queueing Systems, vol. 2, 1st edn. Wiley-Interscience, Hoboken (1976)
Langr, D., Tvrdík, P., Šimeček, I., Dytrych, T.: Downsampling algorithms for large sparse matrices. Int. J. Parallel Prog. 43(5), 679–702 (2014). https://doi.org/10.1007/s10766-014-0315-8
Maris, P., Sosonkina, M., Vary, J.P., Ng, E., Yang, C.: Scaling of ab-initio nuclear physics calculations on multicore computer architectures. Procedia Comput. Sci. 1(1), 97–106 (2010). https://doi.org/10.1016/j.procs.2010.04.012
Navrátil, P., Vary, J.P., Barrett, B.R.: Properties of 12C in the ab initio nuclear shell model. Phys. Rev. Lett. 84, 5728–5731 (2000). https://doi.org/10.1103/PhysRevLett.84.5728
Quaglioni, S., Navrátil, P.: Ab initio many-body calculations of n-3H, n-4He, p-3,4He, and n-10Be scattering. Phys. Rev. Lett. 101, 092501 (2008). https://doi.org/10.1103/PhysRevLett.101.092501
Rosensteel, G., Rowe, D.J.: Nuclear Sp(3, R) model. Phys. Rev. Lett. 38, 10–14 (1977). https://doi.org/10.1103/PhysRevLett.38.10
Acknowledgements
This work was supported by the Czech Science Foundation under Grant No. 16-16772S. This work is also part of the “Collaborative Research: Innovative ab initio symmetry-adapted no-core shell model for advancing fundamental physics and astrophysics” PRAC allocation support by NSF (award number ACI-1516338), and is part of the Blue Waters sustained-petascale computing project, which is supported by NSF (awards OCI-0725070 and ACI-1238993) and the state of Illinois (Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications). The authors acknowledge support from J.P. Draayer from the Louisiana State University, P. Tvrdík from the Czech Technical University in Prague, P. Vrchota from Výzkumný a zkušební letecký ústav, a.s., and M. Pajr from IHPCI.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this paper
Cite this paper
Langr, D., Dytrych, T., Oberhuber, T., Knapp, F. (2018). Efficient Parallel Generation of Many-Nucleon Basis for Large-Scale Ab Initio Nuclear Structure Calculations. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds) Parallel Processing and Applied Mathematics. PPAM 2017. Lecture Notes in Computer Science(), vol 10778. Springer, Cham. https://doi.org/10.1007/978-3-319-78054-2_32
Download citation
DOI: https://doi.org/10.1007/978-3-319-78054-2_32
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-78053-5
Online ISBN: 978-3-319-78054-2
eBook Packages: Computer ScienceComputer Science (R0)