Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches

Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost on the time taken for reinstating the job and the risk of losing data and execution accomplished by the job before it failed. Approaches which can proactively detect computing core failures and take action to relocate the computing core's job onto reliable cores can make a significant step towards automating fault tolerance. Method: This paper describes an experimental investigation into the use of multi-agent approaches for fault tolerance. Two approaches are studied, the first at the job level and the second at the core level. The approaches are investigated for single core failure scenarios that can occur in the execution of parallel reduction algorithms on computer clusters. A third approach is proposed that incorporates multi-agent technology both at the job and core level. Experiments are pursued in the context of genome searching, a popular computational biology application. Result: The key conclusion is that the approaches proposed are feasible for automating fault tolerance in high-performance computing systems with minimal human intervention. In a typical experiment in which the fault tolerance is studied, centralised and decentralised checkpointing approaches on an average add 90% to the actual time for executing the job. On the other hand, in the same experiment the multi-agent approaches add only 10% to the overall execution time.Comment: Computers in Biology and Medicin

On data skewness, stragglers, and MapReduce progress indicators

We tackle the problem of predicting the performance of MapReduce applications, designing accurate progress indicators that keep programmers informed on the percentage of completed computation time during the execution of a job. Through extensive experiments, we show that state-of-the-art progress indicators (including the one provided by Hadoop) can be seriously harmed by data skewness, load unbalancing, and straggling tasks. This is mainly due to their implicit assumption that the running time depends linearly on the input size. We thus design a novel profile-guided progress indicator, called NearestFit, that operates without the linear hypothesis assumption and exploits a careful combination of nearest neighbor regression and statistical curve fitting techniques. Our theoretical progress model requires fine-grained profile data, that can be very difficult to manage in practice. To overcome this issue, we resort to computing accurate approximations for some of the quantities used in our model through space- and time-efficient data streaming algorithms. We implemented NearestFit on top of Hadoop 2.6.0. An extensive empirical assessment over the Amazon EC2 platform on a variety of real-world benchmarks shows that NearestFit is practical w.r.t. space and time overheads and that its accuracy is generally very good, even in scenarios where competitors incur non-negligible errors and wide prediction fluctuations. Overall, NearestFit significantly improves the current state-of-art on progress analysis for MapReduce

Fuzzy C-Mean And Genetic Algorithms Based Scheduling For Independent Jobs In Computational Grid

The concept of Grid computing is becoming the most important research area in the high performance computing. Under this concept, the jobs scheduling in Grid computing has more complicated problems to discover a diversity of available resources, select the appropriate applications and map to suitable resources. However, the major problem is the optimal job scheduling, which Grid nodes need to allocate the appropriate resources for each job. In this paper, we combine Fuzzy C-Mean and Genetic Algorithms which are popular algorithms, the Grid can be used for scheduling. Our model presents the method of the jobs classifications based mainly on Fuzzy C-Mean algorithm and mapping the jobs to the appropriate resources based mainly on Genetic algorithm. In the experiments, we used the workload historical information and put it into our simulator. We get the better result when compared to the traditional algorithms for scheduling policies. Finally, the paper also discusses approach of the jobs classifications and the optimization engine in Grid scheduling

Towards Operator-less Data Centers Through Data-Driven, Predictive, Proactive Autonomics

Continued reliance on human operators for managing data centers is a major impediment for them from ever reaching extreme dimensions. Large computer systems in general, and data centers in particular, will ultimately be managed using predictive computational and executable models obtained through data-science tools, and at that point, the intervention of humans will be limited to setting high-level goals and policies rather than performing low-level operations. Data-driven autonomics, where management and control are based on holistic predictive models that are built and updated using live data, opens one possible path towards limiting the role of operators in data centers. In this paper, we present a data-science study of a public Google dataset collected in a 12K-node cluster with the goal of building and evaluating predictive models for node failures. Our results support the practicality of a data-driven approach by showing the effectiveness of predictive models based on data found in typical data center logs. We use BigQuery, the big data SQL platform from the Google Cloud suite, to process massive amounts of data and generate a rich feature set characterizing node state over time. We describe how an ensemble classifier can be built out of many Random Forest classifiers each trained on these features, to predict if nodes will fail in a future 24-hour window. Our evaluation reveals that if we limit false positive rates to 5%, we can achieve true positive rates between 27% and 88% with precision varying between 50% and 72%.This level of performance allows us to recover large fraction of jobs' executions (by redirecting them to other nodes when a failure of the present node is predicted) that would otherwise have been wasted due to failures. [...

Discovering Job Preemptions in the Open Science Grid

The Open Science Grid(OSG) is a world-wide computing system which facilitates distributed computing for scientific research. It can distribute a computationally intensive job to geo-distributed clusters and process job's tasks in parallel. For compute clusters on the OSG, physical resources may be shared between OSG and cluster's local user-submitted jobs, with local jobs preempting OSG-based ones. As a result, job preemptions occur frequently in OSG, sometimes significantly delaying job completion time. We have collected job data from OSG over a period of more than 80 days. We present an analysis of the data, characterizing the preemption patterns and different types of jobs. Based on observations, we have grouped OSG jobs into 5 categories and analyze the runtime statistics for each category. we further choose different statistical distributions to estimate probability density function of job runtime for different classes.Comment: 8 page