PetFMM-A dynamically load-balancing parallel fast multipole library

International Journal for Numerical Methods in Engineering

Volumn 85, Issue 4, 2011, Pages 403-428

  Cruz, Felipe A ^a   Knepley, Matthew G ^b   Barba, L A ^c  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF CHICAGO   (United States)

^c Boston University   (United States)

Author keywords

Dynamic load balancing; Fast multipole method; Hierarchical algorithms; Order N algorithms; Parallel computing; Particle methods; Vortex method

Indexed keywords

DYNAMIC LOAD BALANCING; FAST MULTIPOLE METHOD; HIERARCHICAL ALGORITHM; ORDER-N ALGORITHMS; PARALLEL COMPUTING; PARTICLE METHODS; VORTEX METHODS;

DYNAMIC LOADS; NETWORK MANAGEMENT; OPEN SYSTEMS; PARALLEL ARCHITECTURES; SOFTWARE ARCHITECTURE; VORTEX FLOW;

ALGORITHMS;

EID: 78650545454     PISSN: 00295981     EISSN: 10970207     Source Type: Journal    
DOI: 10.1002/nme.2972     Document Type: Article

References (32)

1. Hockney RW, Eastwood JW. Computer Simulation Using Particles. McGraw-Hill: New York, 1981.
2. Barnes J, Hut P. A hierarchical O(N log N) force-calculation algorithm. Nature 1986; 324:446-449. DOI: 10.1038/324446a0.
3. Appel AW. An efficient program for many-body simulation. SIAM Journal on Scientific and Statistical Computing 1985; 6(1):85-103. DOI: 10.1137/0906008.
4. Greengard L, Rokhlin V. A fast algorithm for particle simulations. Journal of Computational Physics 1987; 73(2):325-348. DOI: 10.1016/0021-9991.
5. Carrier J, Greengard L, Rokhlin V. A fast adaptive multipole algorithm for particle simulations. SIAM Journal on Scientific and Statistical Computing 1988; 9(4):669-686. DOI: 10.1137/0909044.
6. Anderson CR. An implementation of the fast multipole method without multipoles. SIAM Journal on Scientific and Statistical Computing 1992; 13(4):923-947. DOI: 10.1137/0913055.
7. Ying L, Biros G, Zorin D. A kernel-independent adaptive fast multipole algorithm in two and three dimensions. Journal of Computational Physics 2004; 196(2):591-626. DOI: 10.1016/j.jcp.2003.11.021.
8. Gimbutas Z, Rokhlin V. A generalized fast multipole method for nonoscillatory kernels. SIAM Journal on Scientific Computing 2002; 24(3):796-817. DOI: 10.1137/S1064827500381148.
9. Fong W, Darve E. The black-box fast multipole method. Journal of Computational Physics 2009; 228(23):8712-8725. DOI: 10.1016/j.jcp.2009.08.031. URL:.
10. Skeel RD, Tezcan I, Hardy DJ. Multiple grid methods for classical molecular dynamics. Journal of Computational Chemistry 2002; 23(6):673-684. DOI: 10.1002/jcc.10072.
11. Balay S, Buschelman K, Eijkhout V, Gropp WD, Kaushik D, Knepley M, Curfman-McInnes L, Smith BF, Zhang H. PETSc user's manual. Technical Report ANL-95/11-Revision 3.0.0, Argonne National Laboratory, 2008.
12. Brooks B, Bruccoleri R, Olafson D, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry 1983; 4:187-217. DOI: 10.1002/jcc.540040211.
13. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 2005; 26:1781-1802. DOI: 10.1002/jcc.20289.
14. Greengard L, Gropp WD. A parallel version of the fast multipole method. Computers and Mathematics with Applications 1990; 20(7):63-71.
15. Ying L, Biros G, Zorin D, Langston H. A new parallel kernel-independent fast multipole method. Supercomputing, 2003 ACM/IEEE Conference. IEEE Computer Society: Silver Spring, MD, 2003; 14. DOI: 10.1109/SC.2003.10013.
16. Havé P. A parallel implementation of the fast multipole method for Maxwell's equations. International Journal for Numerical Methods in Fluids 2003; 43(8):839-864. DOI: 10.1002/fld.534.
17. Ogata S, Campbell TJ, Kalia RK, Nakano A, Vashishta P, Vemparala S. Scalable portable implementation of the fast multipole method on parallel computers. Computer Physics Communications 2003 153(3):445-461. DOI: 10.1016/S0010-4655(03)00246-7.
18. Kurzak J, Pettitt BM. Massively parallel implementation of a fast multipole method for distributed memory machines. Journal of Parellel and Distributed Computing 2005; 65(7):870-881. DOI: 10.1016/j.jpdc.2005.02.001.
19. Warren MS, Salmon JK. A parallel hashed oct-tree N-body algorithm. Proceedings of the 1993 ACM/IEEE Conference on Supercomputing. ACM: New York, 1993; 12-21.
20. Beatson R, Greengard L. A short course on fast multipole methods. Wavelets, Multilevel Methods and Elliptic PDEs. Oxford University Press: Oxford, 1997; 1-37. Available from: [August 2009].
21. Cruz FA, Barba LA. Characterization of the accuracy of the fast multipole method in particle simulations. International Journal for Numerical Methods in Engineering 2009; 79(13):1577-1604. DOI: 10.1002/nme.2611.
22. Sohn A, Biswas R. Special issue on dynamic load balancing: guest editors' introduction. Journal of Parallel and Distributed Computing 1997; 47:99-101.
23. Rankin WT. DPMTA-Distributed parallel multipole tree algorithm, 2002. Available from: [May 2009].
24. Rankin WT. Efficient parallel implementations of multipole-based N-body algorithms. Ph.D. Thesis, Department of Electrical and Computer Engineering, Duke University, 1999.
25. Karypis G, Kumar V. ParMETIS: Parallel graph partitioning and sparse matrix ordering library. Technical Report 97-060, Department of Computer Science, University of Minnesota, 1997. Available from:.
26. Karypis G, Kumar V. A parallel algorithm for multilevel graph partitioning and sparse matrix ordering. Journal of Parallel and Distributed Computing 1998; 48:71-85.
27. Chan E, Heimlich M, Purkayastha A, van de Geijn R. Collective communication: theory, practice, and experience. Concurrent Computing: Practice and Experience 2007; 19(13):1749-1783. DOI: 10.1002/cpe.v19:13.
28. Knepley MG, Karpeev DA. Mesh algorithms for PDE with Sieve I: mesh distribution. Scientific Programming 2009; 17(3):215-230. DOI: 10.3233/SPR-2009-0249.
29. Barba LA, Leonard A, Allen CB. Advances in viscous vortex methods-meshless spatial adaption based on radial basis function interpolation. International Journal for Numerical Methods in Fluids 2005; 47(5):387-421. DOI: 10.1002/fld.811.
30. Barba LA, Leonard A. Emergence evolution of tripole vortices from net-circulation initial conditions. Physics of Fluids 2007; 19(1):017 101. DOI: 10.1063/1.2409734.
31. Cipra BA. The best of the 20th century: editors name top 10 algorithms. SIAM News 2000; 33(4):1-3.
32. Teng SH. Provably good partitioning and load balancing algorithms for parallel adaptive N-body simulation. SIAM Journal on Scientific Computing 1998; 19(2):635-656. DOI: 10.1137/S1064827595288942.