General parallel sparse-blocked matrix multiply for linear scaling SCF theory

Computer Physics Communications

Volumn 128, Issue 1, 2000, Pages 93-107

  Challacombe, Matt ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVE FITTING; DATA COMMUNICATION SYSTEMS; DATA HANDLING; HEURISTIC METHODS; MATRIX ALGEBRA; PROBLEM SOLVING;

SELF CONSISTENT FIELD THEORY; SIMPLIFIED DENSITY MATRIX MINIMIZATION; SPARSE BLOCKED MATRIX MULTIPLY;

PARALLEL PROCESSING SYSTEMS;

EID: 0034625292     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4655(00)00074-6     Document Type: Article

References (107)

1. C.A. White, B.G. Johnson, P.M.W. Gill, M. Head-Gordon, Chem. Phys. Lett. 253 (1996) 268.
2. M. Challacombe, E. Schwegler, J. Chem. Phys. 106 (1997) 5526.
3. J.M. Perezjorda, W.T. Yang, J. Chem. Phys. 107 (1997) 1218.
4. K.N. Kudin, G.E. Scuseria, Chem. Phys. Lett. 289 (1998) 611.
5. J.C. Burant, R.E. Stratmann, M.J. Frisch, J. Chem. Phys. 105 (1996) 8969.
6. E. Schwelger, M. Challacombe, M. Head-Gordon, J. Chem. Phys. 106 (1997) 9708.
7. C. Ochsenfeld, C.A. White, M. Head-Gordon, J. Chem. Phys. 109 (1998) 1663.
8. E. Schwegler, Ph.D. thesis, University of Minnessota (1998). http://www.t12.lanl.gov/home/mchalla/.
9. E. Schwelger, M. Challacombe, J. Chem. Phys. 111 (1999) 6223.
10. R.E. Stratmann, G.E. Scuseria, M.J. Frisch, Chem. Phys. Lett. 257 (1996) 213.
11. G. Scuseria, J. Phys. Chem. 103 (1999) 4782.
12. M. Challacombe, J. Chem. Phys. 110 (1999) 2332.
13. S. Huzinaga, Comput. Phys. Rep. 2 (1985) 281.
14. E.R. Davidson, D. Feller, Chem. Rev. 86 (1986) 681.
15. I. Shavitt, Israel J. Chem. 33 (1993) 357.
16. R.D. Bardo, K. Ruddenberg, J. Chem. Phys. 60 (1974) 918.
17. D.F. Feller, K. Ruedenberg, Theo. Chim. Acta 52 (1979) 231.
18. M.W. Schmidt, K. Ruedenberg, J. Chem. Phys. 71 (1979) 3951.
19. S. Huzinaga, M. Klobukowski, Theochem 28 (1986) 403.
20. S. Huzinaga, B. Miguel, Chem. Phys. Lett. 175 (1990) 289.
21. S. Wilson, Can. J. Chem. Rev. 70 (1992) 290.
22. D. Moncrieff, S. Wilson, J. Phys. B 26 (1993) 1605.
23. M. Klobukowski, Can. J. Chem. Rev. 72 (1994) 1741.
24. S. Obara, A. Saika, J. Chem. Phys. 89 (1988) 1540.
25. M. Honda, K. Sato, S. Obara, J. Chem. Phys. 94 (1991) 3790.
26. P.M.W. Gill, Adv. Q. Chem. 25 (1994) 141.
27. E. Schwegler, M. Challacombe, M. Head-Gordon, J. Chem. Phys. 109 (1998) 8764.
28. K.N. Kudin, G.E. Scuseria, J. Chem. Phys. 111 (1999) 2351.
29. X.P. Li, R.W. Nunes, D. Vanderbilt, Phys. Rev. B 47 (1993) 10 891.
30. M.S. Daw, Phys. Rev. B 47 (1993) 10 895.
31. S.Y. Qiu, C.Z. Wang, K.M. Ho, C.T. Chan, J. Phys. Cond. Matt. 6 (1994) 9153.
32. R.W. Nunes, D. Vanderbilt, Phys. Rev. B 50 (1994) 17 611.
33. E. Hernández, M.J. Gillan, Phys. Rev. B 51 (1995) 10 157.
34. J.M. Millam, G.E. Scuseria, J. Chem. Phys. 106 (1997) 5569.
35. A.D. Daniels, J.M. Millam, G.E. Scuseria, J. Chem. Phys. 107 (1997) 425.
36. C.M. Coringe, E. Hernández, M.J. Gillan, I.J. Bush, Comput. Phys. Commun. 94 (1996) 89.
37. D.R. Bowler, I.J. Bush, M.J. Gillan (1999), submitted.
38. D.R. Bowler, M.J. Gillan, Comput. Phys. Commun. 120 (1999) 95.
39. A.H.R. Palser, D.E. Manolopoulos, Phys. Rev. B 58 (1999) 12 704.
40. P. Ordejón, D.A. Drabold, M.P. Grumbach, R.M. Martin, Phys. Rev. B 48 (1993) 14 646.
41. F. Mauri, G. Galli, R. Car, Phys. Rev. B 47 (1993) 9973.
42. F. Mauri, G. Galli, Phys. Rev. B 50 (1994) 4316.
43. S. Itoh, P. Ordejón, R.M. Martin, Comput. Phys. Commun. 88 (1995) 173.
44. J. Kim, F. Mauri, G. Galli, Phys. Rev. B 51 (1995) 1456.
45. P. Ordejón, E. Artacho, J.M. Soler, Phys. Rev. B 53 (1996) 10 441.
46. A. Canning et al., Comput. Phys. Commun. 94 (1996) 89.
47. D. Sánchez-Portal, P. Ordejón, E. Artacho, J.M. Soler, Int. J. Quant. Chem. 65 (1997) 453.
48. E. Artacho et al., Phys. Stat. Sol. B 215 (1999) 809.
49. G. Galli, Cur. Op. Sol. State Mat. Sci. 1 (1996) 864.
50. D.R. Bowler et al., Mod. Sim. Mat. Sci. Eng. 5 (1997) 199.
51. S. Goedecker, Rev. Mod. Phys. 71 (1999) 1085.
52. C.P. Kruskal, L. Rudolph, M. Snir, Theo. Comput. Sci. 64 (1989) 135.
53. G. Manzini, J. Parallel Dist. Comput. 21 (1994) 169.
54. M. Middendorf, H. Schmeck, G. Turner, Austral. Comput. J. 27 (1995) 37.
55. M. Schütz, G. Hetzer, H. Werner, J. Chem. Phys. 111 (1999) 5691.
56. M.R. Field, SIAM J. Sci. Comput. 19 (1998) 27.
57. J. Shadid et al., Parallel Comput. 23 (1997) 1307.
58. M. Ast, R. Fischer, J. Labarta, H. Manz, Adv. Eng. Soft. 29 (1998) 241.
59. B.K. Kendrick, E.F. Hayes, J. Chem. Phys. (1999), to be submitted.
60. S. Goedecker et al., Technical Report No. La-ur-97-1504, Los Alamos National Laboratory, Los Alamos, NM (unpublished).
61. S. Balay, W.D. Gropp, L.C. McInnes, B.f. Smith, in: ManageMent of Parallelism in Object-oriented Numerical Software Libraries. Modern Software Tools in Scientific Computing, E. Arge, A.M. Bruaset, H.P. Langtangen (Eds.) (Birkhauser Press, New York, 1997).
62. J. Dongarra, J. Du Croz, I. Duff, S. Hammarling, ACM Trans. Math. Soft. 16 (1990) 1.
63. J. Bilmes et al., LAPACK Working Note 111, University of Tennessee (unpublished).
64. J. Bilmes, K. Asanović, C. Chin, J. Demmel, in: Proceedings of International Conference on Supercomputing (ACM SIGARC, Vienna, Austria, 1997).
65. J. Bilmes et al., The Phipac WWW Home Page, http://www. icsi.berkeley.edu/̃bilmes/phipac.
66. L.F. Romero, E.L. Zapata, Parallel Comput. 21 (1995) 583.
67. Y. Saad, Iterative Methods for Sparse Linear Systems (PWS Publishing, Boston, 1996).
68. R.S. Tuminaro, J.S. Shadid, S.A. Hutchinson, Conc. Pract. Exp. 10 (1998) 229.
69. L. Colombo, W. Sawyer, Mat. Sci. Eng. B 37 (1996) 228.
70. J.H. Wilkinson, The Algebraic Eigenvalue Problem (Clarendon Press, Oxford, 1965).
71. G.W. Stewart, Introduction to Matrix Computations (Academic Press, London, 1973).
72. M. Benzi, G.H. Golub, BIT 39 (1999) 417.
73. T. Huckle, Appl. Num. Math. 30 (1999) 291.
74. M. Benzi, C.D. Meyer, SIAM J. Sci. Comput. 16 (1995) 1159.
75. M. Benzi, C.D. Meyer, M. Tůma, SIAM J. Sci. Comput. 17 (1996) 1135.
76. M. Benzi, J. Marin, M. Tůma, in: Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific ComPuting, B. Hendrickson et al. (Eds.) (SIAM, Philadelphia, 1999); CD-ROM.
77. M. Benzi, J. Marin, M. Tůma, in: Proc. 4th IMACS International Symposium on Iterative Methods in Scientific Computation II, D.R. Kincaid et al. (Eds.) (IMACS, Austin, TX, 1999).
78. M. Benzi, Personal communication.
79. R. McWeeny, Rev. Mod. Phys. 126 (1962) 1028.
80. S. Pissanetzky, Sparse Matrix Technology (Academic Press, London, 1984).
81. F.G. Gustavson, ACM Trans. Math. Soft. 4 (1978) 250.
82. P. Maslen et al., J. Phys. Chem. A 102 (1998) 2215.
83. Message Passing Interface Forum. MPI: A Message-passing Interface Standard (Version 1.1), 1995, http://www.mpiforum.org.
84. T. Bially, IEEE Trans. Inf. Th. 15 (1969) 658.
85. C. Faloutsos, S. Roseman, in: Proc. 8th ACM Symposium on Principles of Database Systems (ACM Press, Philadelphia, PA, 1989) pp. 247-253.
86. J.R. Pilkington, S.B. Baden, IEEE Trans. Parallel Dist. Systems 7 (1996) 288.
87. C. Ou, S. Ranka, J. Parallel Dist. Comput. 42 (1997) 109.
88. M. Griebel, G. Zumbusch, Parallel Comput. 25 (1999) 827.
89. L.K. Platzman, J.J. Bartholdi, J. ACM 36 (1969) 719.
90. M.G. Norman, P. Moscato, Chaos, Solitons and Fractals 6 (1995) 389.
91. S.G. Nastea, O. Frieder, T. El-Ghazawi, J. Parallel Dist. Comput. 46 (1997) 180.
92. R.L. Rao, S.S. Lyengar, Comput. Math. Appl. 27 (1994) 71.
93. D.W. Walker, S.W. Otto, Concur. Pract. Exp. 8 (1996) 707.
94. M. Challacombe, E. Schwegler, MONDOSCF V0.1, A Suite of Programs for Linear Scaling SCF Theory, unpublished.
95. R. Vuduc, PHIPAC DGEMM tuned for 5 x 5 matrices and Intel LINUX.
96. The ASCI Blue Mountain WWW Page, http://ext.lanl.gov/ projects/asci/bluemtn/.
97. The Portland Group Compilers WWW Page, http://www. pgroup.com/.
98. The Alliance Road Runner WWW Page, http://www.alliance. unm.edu/.
99. Standard Coordinates for Benchmarking Linear Scaling SCF Theory. Water cluster and estane globule series available from http://www.t12.lanl.gov./home/mchalla/.
100. T.R. Gibbs, A. Popolato, LASL Explosive Property Data (University of California Press, Berkeley, 1980) p. 109.
101. P. Pulay, Chem. Phys. Lett. 73 (1980) 393.
102. P. Pulay, J. Comput. Chem. 3 (1982) 556.
103. M.S. Warren, J.K. Salmon, in: Supercomputing '92 (IEEE Comp. Soc., Los Alamitos, 1992) pp. 570-576 (1992 Gordon Bell Prize winner).
104. M.S. Warren, J.K. Salmon, in: Supercomputing '93 (IEEE Comp. Soc., Los Alamitos, 1993) pp. 12-21.
105. J.K. Salmon, M.S. Warren, J. Comput. Phys. 111 (1994) 136.
106. M.S. Warren, J.K. Salmon, Comput. Phys. Commun. 87 (1995).
107. M.S. Warren, J.K. Salmon, in: Seventh SIAM Conference on Parallel Processing for Scientific Computing (SIAM, Philadelphia, 1995).