We demonstrate that the Qbox code supports unprecedented large-scale First-Principles Molecular Dynamics (FPMD) applications on the BlueGene/L supercomputer. Qbox is an FPMD implementation specifically designed for large-scale parallel platforms such as BlueGene/L. Strong scaling tests for a Materials Science application show an 86% scaling efficiency between 1024 and 32,768 CPUs. Measurements of performance by means of hardware counters show that 36% of the peak FPU performance can be attained.

References

[1]

{1} R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985). For a review, see e.g. M. Parrinello, "From Silicon to RNA: the Coming of Age of First-Principles Molecular Dynamics" Sol. St. Comm. 103, 107 (1997).

Crossref

Google Scholar

[2]

{2} W. Kohn and L. J. Sham, Phys. Rev. A140, 1133 (1965).

Crossref

Google Scholar

[3]

{3} T. Ogitsu, E. Schwegler, F. Gygi, and G. Galli, Phys. Rev. Lett. 91, 175502 (2003).

Crossref

Google Scholar

[4]

{4} F. Gygi, "Qbox: a large-scale parallel implementation of First-Principles Molecular Dynamics" (LLNL preprint, 2005).

Google Scholar

[5]

{5} N. R. Adiga et al., "An overview of the BlueGene/L supercomputer" SC2002 - High Performance Networking and Computing, 2002.

Digital Library

Google Scholar

[6]

{6} L. Bachega, S. Chatterjee, K. Dockser, J. Gunnels, M. Gupta, F. Gustavson, C. Lapkowski, G. Liu, M. Mendell, C. Wait, T. J. C. Ward, "A High-Performance SIMD Floating Point Unit Design for BlueGene/L: Architecture, Compilation, and Algorithm Design" PACT, 2004.

Digital Library

Google Scholar

[7]

{7} L. S. Blackford, J. Choi, A. Cleary, E. D'Azevedo, J. Demmel, I. Dhillon, J. Dongarra, S. Hammarling, G. Henry, A. Petitet, K. Stanley, D. Walker, R. C. Whaley, "ScaLAPACK Users' Guide" SIAM, Philadelphia, (1997).

Digital Library

Google Scholar

[8]

{8} These caches are not coherent in "co-processor mode" operation, but the advantages and disadvantages of this property are beyond the scope of this paper.

Google Scholar

[9]

{9} M. Frigo and S. G. Johnson, "FFTW: an adaptive software architecture for the FFT", Proceedings of ICASSP 1998, Vol.3, pages 1381-1384.

Crossref

Google Scholar

[10]

{10} J. Lorenz, S. Kral, F. Franchetti, C. W. Ueberhuber, "Vectorization techniques for the BlueGene/L double FPU", IBM Journal of Research and Development, Vol. 49, No. 2/3, 2005, pages 437-446.

Digital Library

Google Scholar

[11]

{11} S. Kral: FFTW-GEL Homepage: http://www.complang.tuwien.ac.at/skral/fftwgel.html

Google Scholar

[12]

{12} Franchetti, S. Kral, J. Lorenz, C. W. Ueberhuber: Efficient Utilization of SIMD Extensions, Proceedings of the IEEE Special Issue on "Program Generation, Optimization, and Adaptation," Vol. 93, No. 2, 2005, pages 409-425.

Google Scholar

Cited By

View all

Bhatele AJain NMubarak MGamblin TJin DLiu JKale L(2019)Analyzing Cost-Performance Tradeoffs of HPC Network Designs under Different Constraints using SimulationsProceedings of the 2019 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/3316480.3325516(1-12)Online publication date: 29-May-2019
https://dl.acm.org/doi/10.1145/3316480.3325516
Jain NBhatele AHowell LBöhme DKarlin ILeón EMubarak MWolfe NGamblin TLeininger MMohr BRaghavan P(2017)Predicting the performance impact of different fat-tree configurationsProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3126908.3126967(1-13)Online publication date: 12-Nov-2017
https://dl.acm.org/doi/10.1145/3126908.3126967
Holmes DMohror KGrant RSkjellum ASchulz MBland WSquyres JDongarra JHolmes DCollis ALarsson Träff JSmith L(2016)MPI SessionsProceedings of the 23rd European MPI Users' Group Meeting10.1145/2966884.2966915(121-129)Online publication date: 25-Sep-2016
https://dl.acm.org/doi/10.1145/2966884.2966915
Show More Cited By

Index Terms

Recommendations

Large-scale electronic structure calculations of high-Z metals on the BlueGene/L platform
SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing

First-principles simulations of high-Z metallic systems using the Qbox code on the BlueGene/L supercomputer demonstrate unprecedented performance and scaling for a quantum simulation code. Specifically designed to take advantage of massively-parallel ...
Parallel molecular dynamics: communication requirements for massively parallel machines
FRONTIERS '95: Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation (Frontiers'95)

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems, from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good ...
Dual-level parallelism for ab initio molecular dynamics: Reaching teraflop performance with the CPMD code

We show teraflop performance of the fully featured ab initio molecular dynamics code CPMD on an IBM pSeries 690 cluster. A mixed distributed-memory, coarse-grained parallel approach using the MPI library and shared-memory, fine-grained parallelism using ...

Comments

Information & Contributors

Information

Published In

SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing

November 2005

829 pages

ISBN:1595930612

General Chair:
William Kramer

Publisher

IEEE Computer Society

United States

Publication History

Published: 12 November 2005

Check for updates

Author Tag

Electronic structure. Molecular Dynamics. Ab initio simulations. First-principles simulations. Parallel computing. BlueGene/L.

Qualifiers

Article

Conference

SC '05

Sponsor:

SIGARCH
IEEE-CS

SC '05: International Conference for High Performance Computing, Networking, Storage and Analysis

November 12 - 18, 2005

Acceptance Rates

SC '05 Paper Acceptance Rate 62 of 260 submissions, 24%;

Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

18
Total Citations
View Citations
319
Total Downloads

Downloads (Last 12 months)2
Downloads (Last 6 weeks)0

Reflects downloads up to 01 Sep 2024

Other Metrics

View Author Metrics

Citations

Cited By

View all

Bhatele AJain NMubarak MGamblin TJin DLiu JKale L(2019)Analyzing Cost-Performance Tradeoffs of HPC Network Designs under Different Constraints using SimulationsProceedings of the 2019 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/3316480.3325516(1-12)Online publication date: 29-May-2019
https://dl.acm.org/doi/10.1145/3316480.3325516
Jain NBhatele AHowell LBöhme DKarlin ILeón EMubarak MWolfe NGamblin TLeininger MMohr BRaghavan P(2017)Predicting the performance impact of different fat-tree configurationsProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3126908.3126967(1-13)Online publication date: 12-Nov-2017
https://dl.acm.org/doi/10.1145/3126908.3126967
Holmes DMohror KGrant RSkjellum ASchulz MBland WSquyres JDongarra JHolmes DCollis ALarsson Träff JSmith L(2016)MPI SessionsProceedings of the 23rd European MPI Users' Group Meeting10.1145/2966884.2966915(121-129)Online publication date: 25-Sep-2016
https://dl.acm.org/doi/10.1145/2966884.2966915
Nomura KKalia RNakano AVashishta PShimamura KShimojo FKunaseth MMessina PRomero NDamkroger TDongarra J(2014)Metascalable quantum molecular dynamics simulations of hydrogen-on-demandProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.59(661-673)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/SC.2014.59
Jia WFu JCao ZWang LChi XGao WWang L(2013)Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machinesJournal of Computational Physics10.1016/j.jcp.2013.05.005251(102-115)Online publication date: 1-Oct-2013
https://dl.acm.org/doi/10.1016/j.jcp.2013.05.005
Wang LWu YJia WGao WChi XWang LLathrop SCosta JKramer W(2011)Large scale plane wave pseudopotential density functional theory calculations on GPU clustersProceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/2063384.2063479(1-10)Online publication date: 12-Nov-2011
https://dl.acm.org/doi/10.1145/2063384.2063479
Bronevetsky GGyllenbaal JDe Supinski B(2009)CLOMPInternational Journal of Parallel Programming10.1007/s10766-009-0096-737:3(250-265)Online publication date: 1-Jun-2009
https://dl.acm.org/doi/10.1007/s10766-009-0096-7
Bronevetsky GGyllenhaal JDe Supinski B(2008)CLOMPProceedings of the 4th international conference on OpenMP in a new era of parallelism10.5555/1789826.1789829(13-25)Online publication date: 12-May-2008
https://dl.acm.org/doi/10.5555/1789826.1789829
Wang LLee BShan HZhao ZMeza JStrohmaier EBailey DTeller P(2008)Linearly scaling 3D fragment method for large-scale electronic structure calculationsProceedings of the 2008 ACM/IEEE conference on Supercomputing10.5555/1413370.1413437(1-10)Online publication date: 15-Nov-2008
https://dl.acm.org/doi/10.5555/1413370.1413437
De Supinski BSchulz MBulatov VCabot WChan BCook ADraeger EGlosli JGreenough JHenderson KKubota ALouis SMiller BPatel MSpelce TStreitz FWilliams PYates RYoo AAlmasi GBhanot GGara AGunnels JGupta MMoreira JSexton JWalkup BArcher CGygi FGermann TKadau KLomdahl PRendleman CWelcome MMclendon WHendrickson BFranchetti FKral SLorenz JÜberhuber CChow EÇatalyürek Ü(2008)BlueGene/L applicationsInternational Journal of High Performance Computing Applications10.1177/109434200708502522:1(33-51)Online publication date: 1-Feb-2008
https://dl.acm.org/doi/10.1177/1094342007085025
Show More Cited By

View Options

Get Access

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Cited By

Index Terms

Recommendations

Large-scale electronic structure calculations of high-Z metals on the BlueGene/L platform

Parallel molecular dynamics: communication requirements for massively parallel machines

Dual-level parallelism for ab initio molecular dynamics: Reaching teraflop performance with the CPMD code

Comments

Published In

Sponsors

Publisher

Publication History

Check for updates

Author Tag

Qualifiers

Conference

Acceptance Rates

Other Metrics

Article Metrics

Other Metrics

Cited By

Login options

Full Access

PDF

eReader

Abstract

References

Cited By

Index Terms

Recommendations

Large-scale electronic structure calculations of high-Z metals on the BlueGene/L platform

Parallel molecular dynamics: communication requirements for massively parallel machines

Dual-level parallelism for ab initio molecular dynamics: Reaching teraflop performance with the CPMD code

Comments

Information

Published In

Sponsors

Publisher

Publication History

Check for updates

Author Tag

Qualifiers

Conference

Acceptance Rates

Contributors

Other Metrics

Bibliometrics

Article Metrics

Other Metrics

Citations

Cited By

Get Access

Login options

Full Access

View options

PDF

eReader

Figures

Other

Share

Share this Publication link

Share on social media

Affiliations