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.

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.

Adaptive Executions of Multi-Physics Coupled Applications on Batch Grids

Long running multi-physics coupled parallel applications have gained prominence in recent years. The high computational requirements and long durations of simulations of these applications necessitate the use of multiple systems of a Grid for execution. In this paper, we have built an adaptive middleware framework for execution of long running multi-physics coupled applications across multiple batch systems of a Grid. Our framework, apart from coordinating the executions of the component jobs of an application on different batch systems, also automatically resubmits the jobs multiple times to the batch queues to continue and sustain long running executions. As the set of active batch systems available for execution changes, our framework performs migration and rescheduling of components using a robust rescheduling decision algorithm. We have used our framework for improving the application throughput of a foremost long running multi-component application for climate modeling, the Community Climate System Model (CCSM). Our real multi-site experiments with CCSM indicate that Grid executions can lead to improved application throughput for climate models.

Large improvements in application throughput of long-running multi-component applications using batch grids

Computational grids with multiple batch systems (batch grids) can be powerful infrastructures for executing long-running multi-component parallel applications. In this paper, we evaluate the potential improvements in throughput of long-running multi-component applications when the different components of the applications are executed on multiple batch systems of batch grids. We compare the multiple batch executions with executions of the components on a single batch system without increasing the number of processors used for executions. We perform our analysis with a foremost long-running multi-component application for climate modeling, the Community Climate System Model (CCSM). We have built a robust simulator that models the characteristics of both the multi-component application and the batch systems. By conducting large number of simulations with different workload characteristics and queuing policies of the systems, processor allocations to components of the application, distributions of the components to the batch systems and inter-cluster bandwidths, we show that multiple batch executions lead to 55% average increase in throughput over single batch executions for long-running CCSM. We also conducted real experiments with a practical middleware infrastructure and showed that multi-site executions lead to effective utilization of batch systems for executions of CCSM and give higher simulation throughput than single-site executions. Copyright (c) 2011 John Wiley & Sons, Ltd.

Modified current space vector based powerline communication method for distributed inverters interfaced smart grids

The following paper presents a Powerline Communication (PLC) Method for grid interfaced inverters, for smart grid application. The PLC method is based on the concept of the composite vector which involves multiple components rotating at different harmonic frequencies. The pulsed information is modulated on the fundamental component of the grid current as a specific repeating sequence of a particular harmonic. The principle of communication is same as that of power flow, thus reducing the complexity. The power flow and information exchange are simultaneously accomplished by the interfacing inverters based on current programmed vector control, thus eliminating the need for dedicated hardware. Simulation results have been shown for inter-inverter communication, both under ideal and distorted conditions, using various harmonic modulating signals.

A Networked Control Systems Perspective for Wide-Area Monitoring Control of Smart Power Grids

This paper presents a networked control systems (NCS) framework for wide area monitoring control of smart power grids. We consider a scenario in which wide area measurements are transmitted to controllers at remote locations. We model the effects of delays and packet dropouts due to limited communication capabilities in the grid. We also design a robust networked controller to damp wide-area oscillations based on information obtained from Wide Area Monitoring Systems (WAMS), and analyze the improvement in system stability due to networked control. With communication integration being an important feature of the smart grid, detailed consideration of the effects of communication is essential in the control design for future power systems. We believe that this work is an essential step in this direction.

Holistic Measures for Evaluating Prediction Models in Smart Grids

The performance of prediction models is often based on ``abstract metrics'' that estimate the model's ability to limit residual errors between the observed and predicted values. However, meaningful evaluation and selection of prediction models for end-user domains requires holistic and application-sensitive performance measures. Inspired by energy consumption prediction models used in the emerging ``big data'' domain of Smart Power Grids, we propose a suite of performance measures to rationally compare models along the dimensions of scale independence, reliability, volatility and cost. We include both application independent and dependent measures, the latter parameterized to allow customization by domain experts to fit their scenario. While our measures are generalizable to other domains, we offer an empirical analysis using real energy use data for three Smart Grid applications: planning, customer education and demand response, which are relevant for energy sustainability. Our results underscore the value of the proposed measures to offer a deeper insight into models' behavior and their impact on real applications, which benefit both data mining researchers and practitioners.