Large-scale first-principles molecular dynamics simulations on the BlueGene/L platform using the Qbox code

Proceedings of the ACM/IEEE 2005 Supercomputing Conference, SC'05

Volumn 2005, Issue , 2005, Pages

  Gygi, François ^a   Yates, Robert K ^a   Lorenz, Juergen ^b   Draeger, Erik W ^a   Franchetti, Franz ^c   Ueberhuber, Christoph W ^b   Sexton, James C ^d   De Supinski, Bronis R ^a   Kral, Stefan ^b   Gunnels, John A ^d  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^c CARNEGIE MELLON UNIVERSITY   (United States)

^d IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

Ab initio simulations; BlueGene L; Electronic structure; First principles simulations; Molecular dynamics; Parallel computing

Indexed keywords

AB INITIO SIMULATIONS; BLUEGENE/L; FIRST PRINCIPLES SIMULATIONS; PARALLEL PLATFORMS;

ELECTRONIC STRUCTURE; MATERIALS SCIENCE; MOLECULAR DYNAMICS; PARALLEL PROCESSING SYSTEMS; SUPERCOMPUTERS;

NATURAL SCIENCES COMPUTING;

EID: 33845422522     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SC.2005.40     Document Type: Conference Paper

References (13)

1. R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985).
2. 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).
3. W. Kohn and L.J.Sham, Phys. Rev. A140, 1133 (1965).
4. T. Ogitsu, E. Schwegler, F. Gygi, and G. Galli, Phys. Rev. Lett. 91, 175502 (2003).
5. F. Gygi, "Qbox: a large-scale parallel implementation of First-Principles Molecular Dynamics" (LLNL preprint, 2005).
6. N. R. Adiga et al., "An overview of the BlueGene/L supercomputer" SC2002 - High Performance Networking and Computing, 2002.
7. 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.
8. 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).
9. 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.
10. M. Frigo and S. G. Johnson, "FFTW: an adaptive software architecture for the FFT", Proceedings of ICASSP 1998, Vol.3, pages 1381-1384
11. 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
12. S. Kral: FFTW-GEL Homepage: http://www.complang.tuwien.ac.at/skral/ fftwgel.html
13. Franchetti, S. Krai, 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.