Certain aspects of the methodology of genetic algorithms for global structural optimization of clusters were studied. Through systematic investigations of Lennard-Jones clusters with up to 100 atoms, several modifications were made to the genetic algorithm introduced by Deaven and Ho [Phys. ReV. Lett. 1995, 75, 288]. These modifications result in improved efficiency of the search procedure and in certain cases lead to determination of globally optimal structures that previous genetic algorithm studies have not found. The modifications include the following: twinning mutations, add-and-etch processes where a cluster of a given number of atoms is grown beyond that size and subsequently etched, and seeding of the initial parental population with selected structural motifs, in conjunction with randomly chosen configurations.
Known challenges for petascale machines are that (1) the costs of I/O for high performance applications can be substantial, especially for output tasks like checkpointing, and (2) noise from I/O actions can inject undesirable delays into the runtimes of such codes on individual compute nodes. This paper introduces the flexible 'DataStager' framework for data staging and alternative services within that jointly address (1) and (2). Data staging services moving output data from compute nodes to staging or I/O nodes prior to storage are used to reduce I/O overheads on applications' total processing times, and explicit management of data staging offers reduced perturbation when extracting output data from a petascale machine's compute partition. Experimental evaluations of DataStager on the Cray XT machine at Oak Ridge National Laboratory establish both the necessity of intelligent data staging and the high performance of our approach, using the GTC fusion modeling code and benchmarks running on 1000+ processors.
SUMMARYApplications running on leadership platforms are more and more bottlenecked by storage input/output (I/O). In an effort to combat the increasing disparity between I/O throughput and compute capability, we created Adaptable IO System (ADIOS) in 2005. Focusing on putting users first with a service oriented architecture, we combined cutting edge research into new I/O techniques with a design effort to create near optimal I/O methods. As a result, ADIOS provides the highest level of synchronous I/O performance for a number of mission critical applications at various Department of Energy Leadership Computing Facilities. Meanwhile ADIOS is leading the push for next generation techniques including staging and data processing pipelines. In this paper, we describe the startling observations we have made in the last half decade of I/O research and development, and elaborate the lessons we have learned along this journey. We also detail some of the challenges that remain as we look toward the coming Exascale era.
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