Executing Long-running Multi-component Applications on Batch Grids

Computational grids are increasingly being used for executing large multi-component scientific applications. The most widely reported advantages of application execution on grids are the performance benefits, in terms of speeds, problem sizes or quality of solutions, due to increased number of processors. We explore the possibility of improved performance on grids without increasing the application’s processor space. For this, we consider grids with multiple batch systems. We explore the challenges involved in and the advantages of executing long-running multi-component applications on multiple batch sites with a popular multi-component climate simulation application, CCSM, as the motivation.We have performed extensive simulation studies to estimate the single and multi-site execution rates of the applications for different system characteristics.Our experiments show that in many cases, multiple batch executions can have better execution rates than a single site execution.

A Multi-layer Perceptron based Non-linear Mixture Model to estimate class abundance from mixed pixels

Sub-pixel classification is essential for the successful description of many land cover (LC) features with spatial resolution less than the size of the image pixels. A commonly used approach for sub-pixel classification is linear mixture models (LMM). Even though, LMM have shown acceptable results, pragmatically, linear mixtures do not exist. A non-linear mixture model, therefore, may better describe the resultant mixture spectra for endmember (pure pixel) distribution. In this paper, we propose a new methodology for inferring LC fractions by a process called automatic linear-nonlinear mixture model (AL-NLMM). AL-NLMM is a three step process where the endmembers are first derived from an automated algorithm. These endmembers are used by the LMM in the second step that provides abundance estimation in a linear fashion. Finally, the abundance values along with the training samples representing the actual proportions are fed to multi-layer perceptron (MLP) architecture as input to train the neurons which further refines the abundance estimates to account for the non-linear nature of the mixing classes of interest. AL-NLMM is validated on computer simulated hyperspectral data of 200 bands. Validation of the output showed overall RMSE of 0.0089±0.0022 with LMM and 0.0030±0.0001 with the MLP based AL-NLMM, when compared to actual class proportions indicating that individual class abundances obtained from AL-NLMM are very close to the real observations.

Phylogenetic Predictions on Grids

A phylogenetic or evolutionary tree is constructed from a set of species or DNA sequences and depicts the relatedness between the sequences. Predictions of future sequences in a phylogenetic tree are important for a variety of applications including drug discovery, pharmaceutical research and disease control. In this work, we predict future DNA sequences in a phylogenetic tree using cellular automata. Cellular automata are used for modeling neighbor-dependent mutations from an ancestor to a progeny in a branch of the phylogenetic tree. Since the number of possible ways of transformations from an ancestor to a progeny is huge, we use computational grids and middleware techniques to explore the large number of cellular automata rules used for the mutations. We use the popular and recurring neighbor-based transitions or mutations to predict the progeny sequences in the phylogenetic tree. We performed predictions for three types of sequences, namely, triose phosphate isomerase, pyruvate kinase, and polyketide synthase sequences, by obtaining cellular automata rules on a grid consisting of 29 machines in 4 clusters located in 4 countries, and compared the predictions of the sequences using our method with predictions by random methods. We found that in all cases, our method gave about 40% better predictions than the random methods.

Middleware for Long-running Applications on Batch Grids. Student Research Symposium poster

Computational grids with multiple batch systems (batch grids) can be powerful infrastructures for executing long-running multicomponent parallel applications. In this paper, we have constructed a middleware framework for executing such long-running applications spanning multiple submissions to the queues on multiple batch systems. We have used our framework for execution of a foremost long-running multi-component application for climate modeling, the Community Climate System Model (CCSM). Our framework coordinates the distribution, execution, migration and restart of the components of CCSM on the multiple queues where the component jobs of the different queues can have different queue waiting and startup times.

Incentive Compatible Mechanisms for Resource Procurement in Computational Grids with Rational resource Providers

In a computational grid, the presence of grid resource providers who are rational and intelligent could lead to an overall degradation in the efficiency of the grid. In this paper, we design incentive compatible grid resource procurement mechanisms which ensure that the efficiency of the grid is not affected by the rational behavior of resource providers.In particular, we offer three elegant incentive compatible mechanisms for this purpose: (1) G-DSIC (Grid-Dominant Strategy Incentive Compatible) mechanism (2) G-BIC (Grid-Bayesian Nash Incentive Compatible) mechanism (3) G-OPT(Grid-Optimal) mechanism which minimizes the cost to the grid user, satisfying at the same time, (a) Bayesian incentive compatibility and (b) individual rationality. We evaluate the relative merits and demerits of the above three mechanisms using game theoretical analysis and numerical experiments.

An Efficient MPI_Allgather for Grids

Allgather is an important MPI collective communication. Most of the algorithms for allgather have been designed for homogeneous and tightly coupled systems. The existing algorithms for allgather on Gridsystems do not efficiently utilize the bandwidths available on slow wide-area links of the grid. In this paper, we present an algorithm for allgather on grids that efficiently utilizes wide-area bandwidths and is also wide-area optimal. Our algorithm is also adaptive to gridload dynamics since it considers transient network characteristics for dividing the nodes into clusters. Our experiments on a real-grid setup consisting of 3 sites show that our algorithm gives an average performance improvement of 52% over existing strategies.

Coupled Climate Model on Grids

Community Climate System Model (CCSM) is a Multiple Program Multiple Data (MPMD) parallel global climate model comprising atmosphere, ocean, land, ice and coupler components. The simulations have a time-step of the order of tens of minutes and are typically performed for periods of the order of centuries. These climate simulations are highly computationally intensive and can take several days to weeks to complete on most of today’s multi-processor systems. ExecutingCCSM on grids could potentially lead to a significant reduction in simulation times due to the increase in number of processors. However, in order to obtain performance gains on grids, several challenges have to be met. In this work,we describe our load balancing efforts in CCSM to make it suitable for grid enabling.We also identify the various challenges in executing CCSM on grids. Since CCSM is an MPI application, we also describe our current work on building a MPI implementation for grids to grid-enable CCSM.

Electrochemical performance of mixed crystallographic phase nanotubes and nanosheets of titania and titania-carbon/silver composites for lithium-ion batteries

The role of homogeneity in ex situ grown conductive coatings and dimensionality in the lithium storage properties of TiO(2) is discussed here. TiO(2) nanotube and nanosheet comprising of mixed crystallographic phases of anatase and TiO(2) (B) have been synthesized by an optimized hydrothermal method. Surface modifications of TiO(2) nanotube are realized via coating the nanotube with Ag nanoparticles and amorphous carbon. The first discharge cycle capacity (at current rate = 10 mA g(-1)) for TiO(2) nanotube and nanosheet were 355 mAh g(-1) and 225 mAhg(-1), respectively. The conductive surface coating stabilized the titania crystallographic structure during lithium insertion-deinsertion processes via reduction in the accessibility of lithium ions to the trapping sites. The irreversible capacity is beneficially minimized from 110 mAh g(-1) for TiO(2) nanotubes to 96 mAh g(-1) and 57 mAhg(-1) respectively for Ag and carbon modified TiO(2) nanotubes. The homogeneously coated amorphous carbon over TiO(2) renders better lithium battery performance than randomly distributed Ag nanoparticles coated TiO(2) due to efficient hopping of electrons. (C) 2011 Elsevier B.V. All rights reserved.

Application-oriented adaptive MPI_Bcast for grids

Due to the importance of collective communications in scientific parallel applications, many strategies have been devised for optimizing collective communications for different kinds of parallel environments. There has been an increasing interest to evolve efficient broadcast algorithms for computational grids. In this paper, we present application-oriented adaptive techniques that take into account resource characteristics as well as the application's usage of broadcasts for deriving efficient broadcast trees. In particular, we consider two broadcast parameters used in the application, namely, the broadcast message sizes and the time interval between the broadcasts. The results indicate that our adaptive strategies can provide 20% average improvement in performance over the popular MPICH-G2's MPI_Bcast implementation for loaded network conditions.

Functionalized and Postfunctionalizable Porous Polymeric Films through Evaporation-Induced Phase Separation Using Mixed Solvents

Condensation of water droplets during rapid evaporation of a polymer solution, under humid conditions, has been known to generate uniformly porous polymer films. Similar porous films are also formed when a solution of the polymer in THF containing small amounts of water, is allowed to evaporate rapidly under air flow; this suggests that water droplets may be formed during the final stages of film formation. In the presence of added surfactants, the interface of water droplets could become lined with the surfactants and consequently the internal walls of the pores generated, upon removal of the water, could become decorated with the hydrophilic head groups of the surfactant molecules. In a series of carefully designed experiments, we have examined the effect of added surfactants, both anionic and cationic, on the formation of porous PMMA films; the films were prepared by evaporating a solution of the polymer in THF containing controlled amounts of aqueous surfactant solutions. We observed that the average size of the pores decreases with increasing surfactant concentration, while it increases with increasing amounts of added water. The size of the pores and their distribution were examined using AFM and IR imaging methods. Although IR imaging possessed inadequate resolution to confirm the presence of surfactants at the pore surface, exchange of the inorganic counterion, such as the sodium-ion of SDS, with suitable ionic organic dyes permitted the unequivocal demonstration of the presence of the surfactants at the interface by the use of confocal fluorescence microscopy.

Mixed ionic and electronic conduction in zirconia and its applications in metallurgy

Mixed ionic and electronic conduction in Zr02-based solid electrolytes was studied.The effect of impurities and second-phase particles on the mixed conduction parameter, P,, was measured for different types of ZrOZ electrolytes. The performance of solid-state sensors incorporating ZrOZ electrolytes is sometimes limited by electronic conduction in ZrOZ, especially at temperatures >I800 K. Methods for eliminating or minimizing errors in measured emf due to electronically driven transport of oxygen anions are discussed. Examples include probes for monitoring oxygen content in liquid steel as well as the newly developed sulfur sensor based on a ZrOz(Ca0) + CaS electrolyte. The use of mixed conducting ZrOZ as a semipermeable membrane or chemically selective sieve for oxygen at high temperatures is discussed. Oxygen transport from liquid iron to CO + C& gas mixtures through a ZrOZ membrane driven by a chemical potential gradient, in the absence of electrical leads or imposed potentials, was experimentally observed.