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

The provision of high performance compute and data resources on a grid has often been the primary concern of grid resource providers, with the network links used to connect them only a secondary matter. Certain large scale distributed scientific simulations, especially ones which involve cross-site runs or interactive visualisation and steering capabilities, often require high quality of service, high bandwidth, low latency network interconnects between resources. In this paper, we describe three applications which require access to such network infrastructure, together with the middleware and policies needed to make them possible.

[1]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[2]  Peter V. Coveney,et al.  The application hosting environment: Lightweight middleware for grid-based computational science , 2007, Comput. Phys. Commun..

[3]  Peter V. Coveney,et al.  Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[4]  Petr Holub,et al.  Distributed and collaborative visualization of large data sets using high-speed networks , 2006, Future Gener. Comput. Syst..

[5]  William Jones,et al.  On the application of computer simulation techniques to anionic and cationic clays: A materials chemistry perspective , 2006 .

[6]  P. V. Coveney,et al.  Emergence of rheological properties in lattice Boltzmann simulations of gyroid mesophases , 2006 .

[7]  Jon MacLaren,et al.  HARC: The Highly-Available Resource Co-allocator , 2007, OTM Conferences.

[8]  Peter V. Coveney,et al.  Intercalation and in situ polymerization of poly(alkylene oxide) derivatives within M+-montmorillonite (M = Li, Na, K) , 2006 .

[9]  Shantenu Jha,et al.  Using Lambda Networks to Enhance Performance of Interactive Large Simulations , 2006, 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06).

[10]  Peter Clarke,et al.  The ESLEA Circuit Reservation Software , 2007 .

[11]  Robert L. Grossman,et al.  Data mining middleware for wide-area high-performance networks , 2006, Future Gener. Comput. Syst..

[12]  Joe Mambretti,et al.  AMROEBA: Computational astrophysics modeling enabled by dynamic lambda switching , 2006, Future Gener. Comput. Syst..

[13]  David Snelling,et al.  Explicit Trust Delegation: Security for dynamic Grids , 2004 .

[14]  Ian T. Foster,et al.  Overview of the I-Way: Wide-Area Visual Supercomputing , 1996, Int. J. High Perform. Comput. Appl..

[15]  Ian T. Foster,et al.  MPICH-G2: A Grid-enabled implementation of the Message Passing Interface , 2002, J. Parallel Distributed Comput..

[16]  Peter V. Coveney,et al.  Simulation of hydrated Li+-, Na+- and K+-montmorillonite/polymer nanocomposites using large-scale molecular dynamics , 2004 .

[17]  Peter V. Coveney,et al.  Facilitating User Access to the Grid: A Lightweight Application Hosting Environment for Grid Enabled Computational Science , 2006, 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06).

[18]  Peter V. Coveney,et al.  Large-scale molecular dynamics study of montmorillonite clay : Emergence of undulatory fluctuations and determination of material properties , 2007 .

[19]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[20]  D. Branton,et al.  Unzipping kinetics of double-stranded DNA in a nanopore. , 2002, Physical review letters.

[21]  Masahiko Jinno,et al.  The first functional demonstration of optical virtual concatenation as a technique for achieving Terabit networking , 2006, Future generations computer systems.

[22]  Thomas Soddemann.  Job Management Enterprise Application , 2006, Euro-Par Workshops.

[23]  Shantenu Jha,et al.  NEKTAR, SPICE and Vortonics: using federated grids for large scale scientific applications , 2006, 2006 IEEE Challenges of Large Applications in Distributed Environments.

[24]  S M Pickles,et al.  A practical toolkit for computational steering , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[25]  Christos Bouras,et al.  Performance issues of bandwidth management in ATM networks , 2003, Int. J. Commun. Syst..

[26]  Ian T. Foster,et al.  The Anatomy of the Grid: Enabling Scalable Virtual Organizations , 2001, Int. J. High Perform. Comput. Appl..

[27]  Shantenu Jha,et al.  SPICE: Simulated Pore Interactive Computing Environmen , 2005, ACM/IEEE SC 2005 Conference (SC'05).

[28]  Michael M. Resch,et al.  Metacomputing across intercontinental networks , 2001, Future Gener. Comput. Syst..

[29]  Peter V Coveney,et al.  Scientific Grid computing , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[30]  Gregory A Voth,et al.  Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations. , 2005, The Journal of chemical physics.

[31]  Thomas Soddemann.  Science gateways to DEISA: user requirements, technologies, and the material sciences and plasma physics gateway , 2007, Concurr. Comput. Pract. Exp..

[32]  Carlos R. Mechoso,et al.  Running a climate model in a heterogeneous, distributed computer environment , 1994, Proceedings of 3rd IEEE International Symposium on High Performance Distributed Computing.

[33]  Jon MacLaren.  Co-allocation of compute and network resources using HARC , 2007 .

[34]  S. Joseph,et al.  Simulating movement of tRNA into the ribosome during decoding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Mark Carson,et al.  NIST Net: a Linux-based network emulation tool , 2003, CCRV.

[36]  P. Coveney,et al.  Chirality and domain growth in the gyroid mesophase , 2006, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[37]  Ian T. Foster.  Globus Toolkit Version 4: Software for Service-Oriented Systems , 2005, NPC.

[38]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[39]  Thomas Soddemann.  Science gateways to DEISA: user requirements, technologies, and the material sciences and plasma physics gateway: Research Articles , 2007 .

[40]  E. Lindahl,et al.  Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. , 2000, Biophysical journal.

[41]  Leslie Lamport,et al.  Consensus on transaction commit , 2004, TODS.