Large scale computational science on federated international grids: The role of switched optical networks

Future Generation Computer Systems

Volumn 26, Issue 1, 2010, Pages 99-110

  Coveney, P V ^a   Giupponi, G ^a   Jha, S ^b   Manos, S ^a   MacLaren, J ^b   Pickles, S M ^c   Saksena, R S ^a   Soddemann, T ^d   Suter, J L ^a   Thyveetil, M ^a   Zasada, S J ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d MAX PLANCK INSTITUT FÜR PLASMAPHYSIK   (Germany)

Author keywords

Computational chemistry; Distributed applications; Grid computing; Network communications; Switched optical networks

Indexed keywords

COMPUTATIONAL CHEMISTRY; COMPUTATIONAL SCIENCE; DATA RESOURCES; DISTRIBUTED APPLICATIONS; GRID RESOURCE PROVIDER; HIGH BANDWIDTH; HIGH QUALITY; INTERNATIONAL GRIDS; LOW-LATENCY NETWORKS; NETWORK COMMUNICATIONS; NETWORK INFRASTRUCTURE; NETWORK LINKS; OPTICAL NETWORKS; SCIENTIFIC SIMULATIONS; SWITCHED OPTICAL NETWORKS; VISUALISATION;

COMPUTER SCIENCE; GRID COMPUTING; LIGHT TRANSMISSION; MIDDLEWARE; OPTICAL MATERIALS; QUALITY OF SERVICE;

SWITCHING CIRCUITS;

EID: 69749117302     PISSN: 0167739X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.future.2008.09.013     Document Type: Article

References (77)

1. In: Coveney P.V. (Ed). Scientific grid computing. Philosophical Transactions of the Royal Society A 363 (2005)
2. Foster I., Kesselman C., and Tuecke S. The anatomy of the grid: Enabling scalable virtual organizations. International Journal of Supercomputer Applications 15 (2001) 3-23
3. Uklight network. http://www.uklight.ac.uk
4. Hirano A., Renambot L., Jeong B., Leigh J., Verlo A., Vishwanath V., Singh R., Aguilera J., Johnson A., and DeFanti T.A. The first functional demonstration of optical virtual concatenation as a technique for achieving terabit networking. Future Generation Computer Systems 22 (2006) 876-883
5. Mambretti J., Gold R., Yeh F., and Chen J. AMROEBA: Computational astrophysics modeling enabled by dynamic lambda switching. Future Generation Computer Systems 22 (2006) 949-954
6. Grossman R.L., Gu Y., Hanley D., Sabala M., Mambretti J., Szalay A., Thakar A., Kumazoe K., Yuji O., and Lee M. Data mining middleware for wide-area high-performance networks. Future Generation Computer Systems 22 (2006) 940-948
7. Pickles S.M., Brooke J.M., Costen F.C., Gabriel E., Müller M., Resch M., and Ord S.M. Metacomputing across intercontinental networks. Future Generation Computer Systems 17 8 (2001) 911-918
8. Pickles S., Haines R., Pinning R., and Porter A. A practical toolkit for computational steering. Philosophical Transactions of the Royal Society A 363 1833 (2005) 1843-1853
9. Karonis N., Toonen B., and Foster I. MPICH-G2: A grid-enabled implementation of the message passing interface. Journal of Parallel and Distributed Computing 63 5 (2003) 551-563
10. Coveney P.V., Saksena R.S., Zasada S.J., McKeown M., and Pickles S. The application hosting environment: Lightweight middleware for grid-based computational science. Computer Physics Communications 176 6 (2007) 406-418
11. S. Graham, A. Karmarkar, J. Mischkinsky, I. Robinson, I. Sedukin, Web Services Resource Framework, Tech. Rep., OASIS Technical Report. 2006. http://docs.oasis-open.org/wsrf/wsrf-ws_resource-1.2-spec-os.pdf
12. Job Submission Description Language Specification, OGF. http://forge.gridforum.org/projects/jsdl-wg/document/draft-ggf-jsdl-spec /en/21
13. http://gridsam.sourceforge.net
14. WSRF Lite. http://www.sve.man.ac.uk/research/AtoZ/ILCT
15. S.J. Zasada, R. Saksena, P.V. Coveney, M. Mc Keown, S. Pickles, Facilitating user access to the grid: A lightweight application hosting environment for grid enabled computational science, in: Second IEEE International Conference on e-Science and Grid Computing, 2006, pp. 50-58
16. UK National Grid Service. http://www.ngs.ac.uk/
17. DEISA Grid. http://www.deisa.org/
18. S.J. Zasada, B.G. Cheney, R.S. Saksena, J.L. Suter, P.V. Coveney, J.W. Essex, Production level scientific simulation management on international federated grids, in: Proceedings of the TeraGrid 07 Conference, 2007
19. Foster I. Globus toolkit version 4: Software for service-oriented systems. Network and Parallel Computing (2005) 2-13
20. The UNICORE Project. http://www.unicore.org
21. The Open Grid Forum. http://www.ogf.org
22. I. Foster, H. Kishimoto, A. Savva, D. Berry, A. Djaoui, A. Grimshaw, B. Horn, F. Maciel, F. Siebenlist, R. Subramaniam, et al. The open grid services architecture, Global Grid Forum Draft, draft-ggf-ogsa-ogsa-011, September 23
23. Teragrid Science Gateways Program. http://www.teragrid.org/programs/sci_gateways/
24. Java Specification Request 168, JSR-168 (Portlet Specification). http://jcp.org/en/jsr/detail?id=168
25. Job Management Enterprise Application, JMEA. http://sourceforge.net/projects/jmea
26. T. Soddemann, Job management enterprise application, JMEA, in: Proceedings of the Euro-Par 2006 Workshop, 2007, pp. 253-262
27. C.R. Mechoso, J.D. Farrara, J.A. Spahr, Running a climate model in a heterogeneous, distributed computer environment, in: Proceedings of the Third IEEE International Symposium on High Performance Distributed Computing, 1994, pp. 79-84
28. DeFanti T., Foster I., Papka M., Stevens R., and Kuhfuss T. Overview of the I-WAY: Wide area visual supercomputing. International Journal of Supercomputer Applications 10 (1996) 123-130
29. Soddemann T. Science gateways to DEISA: User requirements, technologies, and the material sciences and plasma physics gateway: Research articles. Concurrency and Computation: Practice & Experience 19 6 (2007) 839-850
30. Apache Axis. http://ws.apache.org/axis
31. Apache Hivemind. http://hivemind.apache.org/
32. CondorG. http://www.cs.wisc.edu/condor/condorg/
33. GridFTP. http://www.globus.org/toolkit/docs/4.0/data/gridftp/
34. Snelling D., Van Den Berghe S., and Qian Li V. Explicit Trust Delegation: Security for dynamic Grids. Fujitsu Scientific and Technical Journal 40 2 (2004) 282-294
35. Bouras C., Chantzi C., Kapoulas V., Panagopoulos A., Sampraku I., and Sevasti A. Performance issues of bandwidth management in ATM networks. International Journal of Communication Systems 16 (2003) 151-169
36. HARC The Highly-Available Resource Co-allocator. http://www.cct.lsu.edu/~maclaren/HARC
37. J. MacLaren, M.M. Keown, S. Pickles, Co-allocation, fault tolerance and grid computing, in: Proceedings of the UK e-Science All Hands Meeting 2006, pp. 155-162
38. J. MacLaren, Co-allocation of compute and network resources using HARC, in: Proceedings of Lighting the Blue Touchpaper for UK e-Science: Closing Conference of the ESLEA Project, PoS(ESLEA)016, 2007. http://pos.sissa.it/archive/conferences/041/016/ESLEA_016.pdf
39. Gray J., and Lamport L. Consensus on transaction commit. ACM TODS 31 1 (2006) 130-160
40. Hutanu A., Allen G., Beck S.D., Holub P., Kaiser H., Kulshrestha A., Liška M., MacLaren J., Matyska L., Paruchuri R., Prohaska S., Seidel E., Ullmer B., and Venkataraman S. Distributed and collaborative visualization of large data sets using high-speed networks. Future Generation Computer Systems, The International Journal of Grid Computing: Theory, Methods and Applications 22 8 (2006) 1004-1010
41. EnLIGHTened Computing Highly-dynamic Applications Driving Adaptive Grid Resources. http://www.enlightenedcomputing.org
42. NW-Grid: the NorthWest Grid. http://www.nw-grid.ac.uk/
43. TeraGrid. http://www.teragrid.org/
44. A.C. Davenhall, P.E.L. Clarke, N. Pezzi, L. Liang, The ESLEA circuit reservation software, in: Proceedings of Lighting the Blue Touchpaper for UK e-Science: closing conference of ESLEA Project', PoS(ESLEA)015, 2007. http://pos.sissa.it/archive/conferences/041/015/ESLEA_015.pdf
45. http://www.hpcx.ac.uk
46. Iperf. http://dast.nlanr.net/Projects/Iperf
47. High performance enabled SSH/SCP. http://www.psc.edu/networking/projects/hpn-ssh
48. Lubensky D.K., and Nelson D.R. Physical Review E 31917 65 (1999)
49. Metzler R., and Klafter J. Biophysical Journal 2776 85 (2003)
50. Howorka S., and Bayley H. Biophysical Journal 3202 83 (2002)
51. Meller A., et al. Physics Review Letters 3435 86 (2003)
52. Sauer-Budge A.F., et al. Physics Review Letters 90 23 (2003) 238101
53. Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nature Structural Biology 9 9 (2002) 646-652
54. S. Jha, P.V. Coveney, M.J. Harvey, R. Pinning, SPICE: Simulated Pore Interactive Computing Environment, in: Proceedings of the 2005 ACM/IEEE conference on Supercomputing
55. B. Boghosian, P.V. Coveney, S. Dong, L. Finn, S. Jha, G. Karniadakis, N. Karonis, Nektar, SPICE and Vortonics - Using federated grids for large scale scientific applications, in: Proceedings of Challenges of Large Applications in Distributed Environments (CLADE) 2006, Paris, vol. IEEE Catalog Number: 06EX13197, 2006, pp. 32-42, ISBN 1-4244-0420-7
56. M.J. Harvey, S. Jha, M.A. Thyveetil, P.V. Coveney, Using lambda networks to enhance performance of interactive large simulations, in: 2nd IEEE International Conference on e-Science and Grid Computing, Amsterdam, 4-6 December 2006
57. Philips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., and Schilten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 26 (2005) 1781-1802
58. Humphrey W., Dalke A., and Schulten K. VMD-Visual Molecular Dynamics. Journal of Molecular Graphics 14 (1996) 33-38
59. Carson M., and Santay D. NISTNet-A linux-based network emulation tool. Computer Communication Review 6 (2003) 111-126
60. Chin J., and Coveney P.V. Chirality and domain growth in the gyroid mesophase. Proceedings of the Royal Society of London Series A 462 (2006) 3575-3600
61. Giupponi G., Harting J., and Coveney P.V. Emergence of rheological properties in lattice Boltzmann simulations of gyroid mesophases. Europhysics Letters 73 (2006) 533-539
62. Harting J., Chin J., Venturoli M., and Coveney P.V. Large-scale lattice Boltzmann simulations of complex fluids: Advances through the advent of computational grids. Philosophical Transactions of the Royal Society A. 1833 (2005) 1895-1915
63. Gropp W., Lusk E., and Skjellum A. Using MPI (1994), MIT Press pp. 59-97
64. M. Venturoli, M.J. Harvey, G. Giupponi, P.V. Coveney, R.L. Pinning, A.R. Porter, S.M. Pickles, Robust grid-based environment for large scale lattice-Boltzmann simulations, in: Proceedings of the UK e-Science All Hands Meeting, 2005. http://www.allhands.org.uk/2005/proceedings/papers/465.pdf
65. Boghosian B., Finn L.I., and Coveney P.V. Moving the data to the computation: Multi-site distributed parallel computation. http://www.realitygrid.org/publications/GD3.pdf
66. Starlight network. http://www.startap.net/starlight/
67. HECToR. http://www.hector.ac.uk
68. Vortonics. http://hilbert.math.tufts.edu/~bruceb/VORTONICS/index.html
69. + montmorillonite/polymer nanocomposites using large-scale molecular dynamics. Chemical Physics Letters 389 4-6 (2004) 261-267
70. Greenwell H.C., Jones W., Coveney P.V., and Stackhouse S. On the application of computer simulation techniques to anionic and cationic clays: A materials chemistry perspective. Journal of Materials Chemistry 16 8 (2006) 706-723
71. Suter J., Coveney P., Greenwell H., and Thyveetil M.-A. Large-scale molecular dynamics study of montmorillonite clay: Emergence of undulatory fluctuations and determination of material properties. Journal of Physical Chemistry C 111 23 (2007) 8248-8259
72. Greenwell H., Bowden A., Chen B., Boulet P., Evans J., Coveney P., and Whiting A. Intercalation and in situ polymerization of poly (alkylene oxide) derivatives within M-montmorillonite (M=Li,Na,K). Journal of Materials Chemistry 16 (2006) 1082-1094
73. Lindahl E., and Edholm O. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophysical Journal 79 1 (2000) 426-433
74. Chang R., Ayton G., and Voth G. Multiscale coupling of mesoscopic-and atomistic-level lipid bilayer simulations. The Journal of Chemical Physics 122 (2005) 244716
75. Farrel A., and Bryskin I. GMPLS: Architecture and Applications (2006), Morgan Kaufmann, Amsterdam
76. Sanbonmatsu K.Y., Joseph S., and Tung C.-S. Simulating movement of tRNA into the ribosome during decoding. PNAS 102 44 (2005) 15854-15859
77. A.C. Davenhall, P.E.L. Clarke, N. Pezzi, L. Liang, The ESLEA circuit reservation software, in: Proceedings of Lighting the Blue Touchpaper for UK e-Science: Closing Conference of ESLEA Project, PoS(ESLEA)015, 2007