High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Large Scale Distributed Testing for Fault Classification and Isolation

Developing confidence in the quality of software is an increasingly difficult problem. As the complexity and integration of software systems increases, the tools and techniques used to perform quality assurance (QA) tasks must evolve with them. To date, several quality assurance tools have been developed to help ensure of quality in modern software, but there are still several limitations to be overcome. Among the challenges faced by current QA tools are (1) increased use of distributed software solutions, (2) limited test resources and constrained time schedules and (3) difficult to replicate and possibly rarely occurring failures. While existing distributed continuous quality assurance (DCQA) tools and techniques, including our own Skoll project, begin to address these issues, new and novel approaches are needed to address these challenges. This dissertation explores three strategies to do this. First, I present an improved version of our Skoll distributed quality assurance system. Skoll provides a platform for executing sophisticated, long-running QA processes across a large number of distributed, heterogeneous computing nodes. This dissertation details changes to Skoll resulting in a more robust, configurable, and user-friendly implementation for both the client and server components. Additionally, this dissertation details infrastructure development done to support the evaluation of DCQA processes using Skoll -- specifically the design and deployment of a dedicated 120-node computing cluster for evaluating DCQA practices. The techniques and case studies presented in the latter parts of this work leveraged the improvements to Skoll as their testbed. Second, I present techniques for automatically classifying test execution outcomes based on an adaptive-sampling classification technique along with a case study on the Java Architecture for Bytecode Analysis (JABA) system. One common need for these techniques is the ability to distinguish test execution outcomes (e.g., to collect only data corresponding to some behavior or to determine how often and under which conditions a specific behavior occurs). Most current approaches, however, do not perform any kind of classification of remote executions and either focus on easily observable behaviors (e.g., crashes) or assume that outcomes' classifications are externally provided (e.g., by the users). In this work, I present an empirical study on JABA where we automatically classified execution data into passing and failing behaviors using adaptive association trees. Finally, I present a long-term case study of the highly-configurable MySQL open-source project. Exhaustive testing of real-world software systems can involve configuration spaces that are too large to test exhaustively, but that nonetheless contain subtle interactions that lead to failure-inducing system faults. In the literature covering arrays, in combination with classification techniques, have been used to effectively sample these large configuration spaces and to detect problematic configuration dependencies. Applying this approach in practice, however, is tricky because testing time and resource availability are unpredictable. Therefore we developed and evaluated an alternative approach that incrementally builds covering array schedules. This approach begins at a low strength, and then iteratively increases strength as resources allow reusing previous test results to avoid duplicated effort. The results are test schedules that allow for successful classification with fewer test executions and that require less test-subject specific information to develop

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Real-time and fault tolerance in distributed control software

Closed loop control systems typically contain multitude of spatially distributed sensors and actuators operated simultaneously. So those systems are parallel and distributed in their essence. But mapping this parallelism onto the given distributed hardware architecture, brings in some additional requirements: safe multithreading, optimal process allocation, real-time scheduling of bus and network resources. Nowadays, fault tolerance methods and fast even online reconfiguration are becoming increasingly important. All those often conflicting requirements, make design and implementation of real-time distributed control systems an extremely difficult task, that requires substantial knowledge in several areas of control and computer science. Although many design methods have been proposed so far, none of them had succeeded to cover all important aspects of the problem at hand. [1] Continuous increase of production in embedded market, makes a simple and natural design methodology for real-time systems needed more then ever

Online Fault Classification in HPC Systems through Machine Learning

As High-Performance Computing (HPC) systems strive towards the exascale goal, studies suggest that they will experience excessive failure rates. For this reason, detecting and classifying faults in HPC systems as they occur and initiating corrective actions before they can transform into failures will be essential for continued operation. In this paper, we propose a fault classification method for HPC systems based on machine learning that has been designed specifically to operate with live streamed data. We cast the problem and its solution within realistic operating constraints of online use. Our results show that almost perfect classification accuracy can be reached for different fault types with low computational overhead and minimal delay. We have based our study on a local dataset, which we make publicly available, that was acquired by injecting faults to an in-house experimental HPC system.Comment: Accepted for publication at the Euro-Par 2019 conferenc

Finding Faulty Functions From the Traces of Field Failures

Corrective maintenance, which rectifies field faults, consumes 30-60% time of software maintenance. Literature indicates that 50% to 90% of the field failures are rediscoveries of previous faults, and that 20% of the code is responsible for 80% of the faults. Despite this, identification of the location of the field failures in system code remains challenging and consumes substantial (30-40%) time of corrective maintenance. Prior fault discovery techniques for field traces require many pass-fail traces, discover only crashing failures, or identify faulty coarse grain code such as files as the source of faults. This thesis (which is in the integrated article format) first describes a novel technique (F007) that focuses on identifying finer grain faulty code (faulty functions) from only the failing traces of deployed software. F007 works by training the decision trees on the function-call level failed traces of previous faults of a program. When a new failed trace arrives, F007 then predicts a ranked list of faulty functions based on the probability of fault proneness obtained via the decision trees. Second, this thesis describes a novel strategy, F007-plus, that trains F007 on the failed traces of mutants (artificial faults) and previous faults. F007-plus facilitates F007 in discovering new faulty functions that could not be discovered because they were not faulty in the traces of previously known actual faults. F007 (including F007-plus) was evaluated on the Siemens suite, Space program, four UNIX utilities, and a large commercial application of size approximately 20 millions LOC. F007 (including the use of F007-plus) was able to identify faulty functions in approximately 90% of the failed traces by reviewing approximately less than 10% of the code (i.e., by reviewing only the first few functions in the ranked list). These results, in fact, lead to an emerging theory that a faulty function can be identified by using prior traces of at least one fault in that function. Thus, F007 and F007-plus can correctly identify faulty functions in the failed traces of the majority (80%-90%) of the field failures by using the knowledge of faults in a small percentage (20%) of functions