Workflow issues in atomistic simulations

Molecular Simulation

Volumn 31, Issue 5, 2005, Pages 323-328

  Chapman, C ^a   Wakelin, J ^b   Artacho, E ^b   Dove, M T ^b   Calleja, M ^b   Bruin, R ^b   Emmerich, W ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b Department of Earth Sciences ^*

Author keywords

CML; Combinatorial problems; Grid; Workflow

Indexed keywords

COMBINATORIAL MATHEMATICS; COMPUTATION THEORY; COMPUTER SIMULATION; MINERALS; PROBLEM SOLVING; RELAXATION PROCESSES; SOIL POLLUTION;

CHEMICAL MARKUP LANGUAGE (CML); COMBINATORIAL PROBLEMS; GRID; WORKFLOW;

ATOMIC PHYSICS;

EID: 20544439359     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/08927020500065223     Document Type: Article

References (21)

1. M.T. Dove, M. Calleja, J. Wakelin, K. Trachenko, G. Ferlat, P. Murray-Rust, N.H. de Leeuw, Z. Du, G.D. Price, P.B. Wilson, J.P. Brodholt, M. Alfredsson, A. Marmier, R.P. Tyer, L.J. Blanshard, R.J. Allan, K. Kleese van Dam, I.T. Todorov, W. Smith, V.N. Alexandrov, G.J. Lewis, A. Thandavan, S.M. Hasan. Environment from the molecular level: an escience testbed project. Proceedings of UK e-Science All Hands Meeting 2003, pp. 302-305, (EPSRC, ISBN 1-904425-11-9).
2. S. Wells, M. Alfredsson, J. Bowe, J. Brodholt, R. Bruin, M. Calleja, R. Catlow, D. Cooke, M. Dove, Z. Du, S. Kerisit, N. de Leeuw, A. Marmier, S. Parker, D. Price, B. Smith, H. Spohr, I. Todorov, K. Trachenko, J. Wakelin, K. Wright. Science outcomes from the use of grid tools in the eminerals project. Proc. Of the All Hands Meeting 2004, Nottingham (2004).
3. HPCxm capability computing, documentation, http://www.hpcx.ac. uk/support/documentation/index.html
4. A. Garcia, P. Murray-Rust, J. Wakelin. The use of XML and CML in computational chemistry and physics programs. Proceedings of the UK e-Science All Hands Meeting 2004, pp. 1111-1114 (2004), (ISBN 1-904425-21-6).
5. R.P. Tyer, L.J. Blanshard, K. Kleese van Dam, R.J. Allan, A.J. Richards, M.T. Dove. Building the eMinerals minigrid. Proceedings of UK e-Science All Hands Meeting 2003, pp. 483-487, (EPSRC, ISBN 1-904425-11-9).
6. M. Calleja, L. Blanshard, R. Bruin, C. Chapman, A. Thandavan, R. Tyer, P. Wilson, V. Alexandrov, R.J. Allen, J. Brodholt, M.T. Dove, W. Emmerich, K. Kleese van Dam. Grid tool integration within the eMinerals project. Proceedings of the UK e-Science All Hands Meeting 2004, pp. 812-817 (2004), (ISBN 1-904425-21-6).
7. M. Calleja, R. Bruin, M.G. Tucker, M.T. Dove, R.P. Tyer, L.J. Blanshard, K. Kleese van Dam, R.J. Allan, C. Chapman, W. Emmerich, P.B. Wilson, J.P. Brodholt, N. Thandavan, V.N. Alexandrov. Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid. Mol. Simul., (in press).
8. The globus project. (2003), http://www.globus.org/toolkit
9. I. Foster, C. Kesselman. Globus: a meta-computing infrastructure toolkit. Int. J. Supercomput. Appl., (1997).
10. R.W. Moore, C. Baru. Virtualization services for data grids, Chapter 11. In Grid Computing: Making The Global Infrastructure a Reality, F. Berman, A.J.G. Hey, G. Fox (Eds), John Wiley (2003).
11. M. Doherty, K. Kleese, M. Williams, B. Strong, L. Blanshard, R. Tyer, T. Folkes, D. Corney, A. Sansum, M. Bly, N. White. SRB in action. Proceedings of UK e-Science All Hands Meeting 2003, pp. 51-58, (EPSRC, ISBN 1-904425-11-9).
12. M. Livny, K. Miller, T. Tannenbaum, D. Wright. Condor-a distributed job scheduler. In Beowulf Cluster Computing with Linux, Thomas Sterling (Ed.), The MIT Press, (2002).
13. Condor Team, Condor version 6.7.0 manual. University of Wisconsin-Madison. (2003), http://www.cs.wisc.edu/condor/manual/v6.7/
14. P. Wilson, W. Emmerich, J. Brodholt. Leveraging HTC for UK eScience with very large condor pools: demand for transforming untapped power into results. Proceedings of the UK e-Science All Hands Meeting 2004, pp. 308-315 (2004), (ISBN 1-904425-21-6).
15. P. Murray-Rust, H. Rzepa. Chemical markup, XML and the worldwide web. 2. Information objects and the CMLDOM. J. Chem. Inf. Comput. Sci., (2001).
16. Y. Zhang, P. Murray-Rust, M.T. Dove, R.C. Glen, H.S. Rzepa, J.A. Townsend, S. Tyrrell, J. Wakelin, E.G. Willighagen. JUMBO-an XML infrastructure for eScience. Proceedings of the UK e-Science All Hands Meeting 2004, pp. 930-934 (2004), (ISBN 1-904425-21-6).
17. J. Wakelin, P. Murray-Rust, S. Tyrrell, Y. Zhang, H.S. Rzepa, A. Garcia. CML tools and information flow in atomic scale simulations. Mol. Simul., (in press).
18. I. Foster, C. Kesselman, J. Nick, S. Tuecke. The physiology of the grid: an open grid services architecture for distributed systems integration. Globus Project (2002)
19. I. Foster, J. Frey, S. Graham, S. Tuecke, K. Czajkowski, D. Ferguson, F. Leymann, M. Nally, I. Sedukhin, D. Snelling, T. Storey, W. Vambenepe, S. Weerawarana, Modelling stateful resources with web services. Version 1.1, IBM (2004)
20. T. Andrews, F. Curbera, H. Dholakia, Y. Goland, J. Klein, F. Leymann, K. Liu, D. Roller, D. Smith, S. Thatte, I. Trickovic, S. Weerawarana. Business process execution language for web services. (2003), Specification v1.1, ftp://www6.software.ibm. com/software/developer/library/ws-bpel.pdf
21. C. Chapman, P. Wilson, T. Tannenbaum, M. Farrellee, M. Livny, J. Brodholt, W. Emmerich. Condor services for the global grid: interoperability between OGSA and condor. Proc. Of the All Hands Meeting 2004, Nottingham (2004).