Journal Article10.1524/ZKSU.2009.0033
Large-scale distributed computing for accelerated structure solution
Kenneth Shankland,Thomas A. N. Griffin,J. van de Streek,Jared H. Cole,Norman Shankland,Alastair J. Florence,William I. F. David +6 more
- 01 Sep 2009
- Vol. 30, Iss: 30, pp 227-232
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TL;DR: The DASH structure solution code has been adapted to run on a Univa UD GridMP system in order to distribute simulated annealing runs across hundreds of computers simultaneously with excellent scaling.
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Abstract: Improvements in SDPD methodology have meant that ever more complex structures are being tackled using global optimisation methods. As a very general rule of thumb, the more complex the structure, the more difficult it is to locate the global minimum in the real-space search. This difficulty can, to some extent, be circumvented by running many instances of the search; for stochastic search methods such as simulated annealing, each instance can be run independently of any other. Such search methods are therefore ideally suited to disposition on a distributed grid-type system that makes use of existing networked compute resources. At the Rutherford Appleton Laboratory, the DASH structure solution code has been adapted to run on a Univa UD GridMP system in order to distribute simulated annealing runs across hundreds of computers simultaneously with excellent scaling. The principles outlined are applicable to other structure solution codes and to other grid-type systems, such as the widely used and freely available CONDOR system.
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Citations
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References
DASH: a program for crystal structure determination from powder diffraction data
William I. F. David,Kenneth Shankland,Jacco van de Streek,Elna Pidcock,W. D. Samuel Motherwell,Jason C. Cole +5 more
TL;DR: DASH as discussed by the authors is a user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures and includes algorithms for multiple peak fitting, unit-cell indexing and space-group determination.
597
Molecular, crystallographic and algorithmic factors in structure determination from powder diffraction data by simulated annealing
TL;DR: In this article, a systematic investigation of the influence of algorithmic, crystallographic and molecular factors on the structure solution process was carried out and the results showed that the overall number of successes in solving the crystal structure is close to 100%.
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Characterization of a hybrid Monte Carlo search algorithm for structure determination
TL;DR: The performance of the HMC algorithm on a number of different crystal structures is investigated as a function of its control parameters and a method is suggested for setting these parameters automatically if HMC is to find routine use in the determination of crystal structures.
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Shake-and-Bake on the grid
TL;DR: SnB and BnP programs, which implement the Shake-and-Bake method of molecular structure (SnB) and substructure (BnP) determination, are implemented and run simultaneously on all computational resources on the New York State Grid.
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