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Applications of Massively Parallel Systems
Volume 52, Number 1/2, 2008
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Blue Matter: Scaling of N-body simulations to one atom per node - References
by B. G.
Fitch
,
A.
Rayshubskiy
,
M.
Eleftheriou
,
T. J. C.
Ward
,
M. E.
Giampapa
,
M. C.
Pitman
,
J. W.
Pitera
,
W. C.
Swope
,
and R. S.
Germain
References
M. Karplus and J. A. McCammon, “Molecular Dynamics Simulations of Biomolecules,”
Nat. Struct. Biol.
9
, No. 9, 646–652 (2002).
D. Frenkel and B. Smit,
Understanding Molecular Simulation: From Algorithms to Applications
, Academic Press, San Diego, CA, 1996.
Y. Sugita and Y. Okamoto, “Replica-Exchange Molecular Dynamics Method for Protein Folding,”
Chem. Phys. Lett.
314
, 141–151 (1999).
M. Eleftheriou, A. Rayshubskiy, J. W. Pitera, B. G. Fitch, R. Zhou, and R. S. Germain, “Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L,”
Proceedings of the 5th IEEE International Workshop on High Performance Computational Biology
, Rhodes Island, Greece, 2006; see
http://www.hicomb.org/HiCOMB2006/papers/HICOMB2006-08.pdf
.
J. S. Bader and D. Chandler, “Computer Simulation Study of the Mean Forces Between Ferrous and Ferric Ions in Water,”
J. Phys. Chem.
96
, No. 15, 6423–6427 (1992).
R. W. Hockney and J. W. Eastwood,
Computer Simulation Using Particles
, Taylor & Francis Group, New York, 1988.
T. Darden, D. York, and L. Pedersen, “Particle Mesh Ewald: An
N
-log(
N
) Method for Ewald Sums in Large Systems,”
J. Chem. Phys.
98
, No. 12, 10089–10092 (1993).
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “A Smooth Particle Mesh Ewald Method,”
J. Chem. Phys.
103
, No. 19, 8577–8593 (1995).
M. Deserno and C. Holm, “How to Mesh Up Ewald Sums. I. A Theoretical and Numerical Comparison of Various Particle Mesh Routines,”
J. Chem. Phys.
109
, No. 18, 7678–7693 (1998).
A. F. Voter, “Parallel Replica Method for Dynamics of Infrequent Events,”
Phys. Rev. B
57
, No. 22, R13985–R13988 (1998).
M. R. Shirts and V. S. Pande, “Mathematical Analysis of Coupled Parallel Simulations,”
Phys. Rev. Lett.
86
, No. 22, 4983–4987 (2001).
M. Tuckerman, B. J. Berne, and G. J. Martyna, “Reversible Multiple Time Scale Molecular Dynamics,”
J. Chem. Phys.
97
, No. 3, 1990–2001 (1992).
R. Zhou, E. Harder, H. Xu, and B. J. Berne, “Efficient Multiple Time Step Method for Use with Ewald and Particle Mesh Ewald for Large Biomolecular Systems,”
J. Chem. Phys.
115
, No. 5, 2348–2358 (2001).
W. C Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, “A Computer Simulation Method for the Calculation of Equilibrium Constants for the Formation of Physical Clusters of Molecules: Application to Small Water Clusters,”
J. Chem. Phys.
76
, No. 1, 637–649 (1982).
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, M. C. Pitman, and R. S. Germain, “Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics,”
Proceeding of the ACM/IEEE Conference on Supercomputing
, Tampa, FL, 2006; see
http://sc06.supercomputing.org/schedule/pdf/pap246.pdf
.
A. Gara, M. A. Blumrich, D. Chen, G. L.-T. Chiu, P. Coteus, M. E. Giampapa, R. A. Haring, et al.,
“Overview of the Blue Gene/L System Architecture,”
IBM J. Res. & Dev.
49
, No. 2/3, 195–212 (2005).
L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, “NAMD2: Greater Scalability for Parallel Molecular Dynamics,”
J. Comp. Phys.
151
, No. 1, 283–312 (1999).
J. C. Phillips, G. Zheng, S. Kumar, and L. V. Kale, “NAMD: Biomolecular Simulation on Thousands of Processors,”
Proceedings of the ACM/IEEE Conference on Supercomputing
, New York, NY, 2002, p. 36.
S. Plimpton, “Fast Parallel Algorithms for Short-Range Molecular Dynamics,”
J. Comp. Phys.
117
, No. 1, 1–19 (1995).
S. Plimpton and B. Hendrickson, “A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems,”
J. Comp. Chem.
17
, No. 3, 326–337 (1996).
B. Hendrickson and S. Plimpton, “Parallel Many-Body Simulations Without All-to-All Communication,”
J. Parallel Distrib. Comp.
27
, No. l, 15–25 (1995).
M. Snir, “A Note on N-Body Computations with Cutoffs,”
Theory of Computing Systems
37
, No. 2, 295–318 (2004).
D. E. Shaw, “A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions,”
J. Comp. Chem.
26
, No. 13, 1318–1328 (2005).
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, et al., “Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L,”
Research Report RC-23688
, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, August 2005.
R. S. Germain, B. Fitch, A. Rayshubskiy, M. Eleftheriou, M. C. Pitman, F. Suits, M. Giampapa, and T. J. C. Ward, “Blue Matter on Blue Gene/L: Massively Parallel Computation for Biomolecular Simulation,”
Proceedings of the 3rd IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis
, Jersey City, NJ, 2005, pp. 207–212.
K. J. Bowers, R. O. Dror, and D. E. Shaw, “The Midpoint Method for Parallelization of Particle Simulations,”
J. Chem. Phys.
124
, No. 18, 184109–184109-11 (2006).
K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, et al., “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference, on Supercomputing
, Tampa, FL, 2006; see
http://sc06.supercomputing.org/schedule/pdf/pap259.pdf
.
F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, et al.,
“Blue Gene: A Vision for Protein Science Using a Petaflop Supercomputer,”
IBM Syst. J.
40
, No. 2, 310–327 (2001).
W. C. Swope, J. W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, et al., “Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a
β
‐Hairpin Peptide,”
J. Phys. Chem. B
108
, No. 21, 6582–6594 (2004).
M. C. Pitman, F. Suits, A. D. MacKerell, Jr., and S. E. Feller, “Molecular-Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol,”
Biochemistry
43
, No. 49, 15318–15328 (2004).
M. C. Pitman, A. Grossfield, F. Suits, and S.E. Feller, “Role of Cholesterol and Polyunsaturated Chains in Lipid-Protein Interactions: Molecular Dynamics Simulation of Rhodopsin in a Realistic Membrane Environment,”
J. Am. Chem. Soc.
127
, No. 13, 4576–4577 (2005).
M. C. Pitman, F. Suits, K. Gawrisch, and S. E. Feller, “Molecular Dynamics Investigation of Dynamical Properties of Phosphatidylethanolamine Lipid Bilayers,”
J. Chem. Phys.
122
, No. 24, 244715–244715-10 (2005).
F. Suits, M. C. Pitman, and S. E. Feller, “Molecular Dynamics Investigation of the Structural Properties of Phosphatidylethanolamine Lipid Bilayers,”
J. Chem. Phys.
122
, No. 24, 244714–244714-9 (2005).
A. Grossfield, S. E. Feller, and M. C. Pitman, “A Role for Direct Interactions in the Modulation of Rhodopsin by ω-3 Polyunsaturated Lipids,”
Proc. Nad. Acad. Sci.
103
, No. 13, 4888–4893 (2006).
M. Eleftheriou, R. S. Germain, A. K. Royyuru, and R. Zhou, “Thermal Denaturing of Mutant Lysozyme with both the OPLSAA and the CHARMM Force Fields,”
J. Am. Chem. Soc.
128
, No. 41, 13388–13395 (2006).
K. Martinez-Mayorga, M. C. Pitman, A. Grossfield, S. E. Feller, and M. F. Brown, “Retinal Counterion Switch Mechanism in Vision Evaluated by Molecular Simulations,”
J. Am. Chem. Soc.
128
, No. 51, 16502–16503 (2006).
M. Eleftheriou, B. Fitch, A. Rayshubskiy, T. J. C. Ward, and R. Germain, “Performance Measurements of the 3D FFT on the Blue Gene/L Supercomputer,”
Proceedings of Euro-Par 2005
, Lisbon, Portugal, 2005, pp. 795–803.
D. Greer, “Industry Trends: Chip Makers Turn to Multicore Processors,”
IEEE Computer
38
, No. 5, 11–13 (2005).
V. E. Taylor, R. L. Stevens, and K. E. Arnold, “Parallel Molecular Dynamics: Implications for Massively Parallel Machines,”
J. Parallel Distrib. Comput.
45
, No. 2, 166–175 (1997).
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, et al., “Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L,”
Proceedings of the International Conference on Computational Science
, Reading, England, 2006, pp. 846–854.
G. M. Amdahl, “Validity of the Single Processor Approach to Achieving Large Scale Computing Capabilities,”
Proceedings of the AFIPS Conference
, Anaheim, CA, 1967, pp. 483–485.
B. G. Fitch, R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, et al., “Blue Matter, an Application Framework for Molecular Simulation on Blue Gene,”
J. Parallel Distrib. Comput.
63
, No. 7/8, 759–773 (2003).
R. S. Germain, Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, T. J. C. Ward, and B. G. Fitch,
“Early Performance Data on the Blue Matter Molecular Simulation Framework,”
IBM J. Res. & Dev.
49
, No. 2/3, 447–456 (2005).
H. C. Andersen, “Rattle: A ‘Velocity' Version of the SHAKE Algorithm for Molecular Dynamics Calculations,”
J. Comp. Phys.
52
, No. 1, 24–34 (1983).
M. E. Giampapa, R. Bellofatto, M. A. Blumrich, D. Chen, M. B. Dombrowa, A. Gara, R. A. Haring, et al.,
“Blue Gene/L Advanced Diagnostics Environment,”
IBM J. Res. & Dev.
49
, No. 2/3, 319–332 (2005).
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, M. C. Pitman, and R. S. Germain, “Progress in Scaling Biomolecular Simulations to Petaflop Scale Platforms,”
Proceedings of the International Euro-Par Workshops
, Dresden, Germany, 2006, pp. 279–288.
M. Deserno and C. Holm, “How to Mesh Up Ewald Sums. II. An Accurate Error Estimate for the Particle-Particle-Particle-Mesh Algorithm,”
J. Chem. Phys.
109
, No. 18, 7694–7701 (1998).
J. C. Sexton and D. H. Weingarten, “Hamiltonian Evolution for the Hybrid Monte Carlo Algorithm,”
Nuclear Phys. B
380
, No. 3, 665–677 (1992).
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