Pegasus Workflow Management System Research Articles

The Pegasus workflow management system: Translational computer science in practice

Translational research (TR) has been extensively used in the health science domain, where results from laboratory research are translated to human studies and where evidence-based practices are adopted in real-world settings to reach broad communities. In computer science, much research stops at the result publication and dissemination stage without moving to the evaluation in real settings at scale and feeding the gained knowledge back to research. Additionally, there is a lack of steady funding and incentives to broadly promote translational computer science (TCS) in practice. In this paper, we present how, throughout its lifespan, the Pegasus workflow management system project has incorporated the principles of translational computer science. We report on our experience on building a strong, long-term engagement with a broad range of science communities to establish mutually beneficial relationships between the core R&D team and these communities.

Neural network based multi-objective evolutionary algorithm for dynamic workflow scheduling in cloud computing

Workflow scheduling is a largely studied research topic in cloud computing, which targets to utilize cloud resources for workflow tasks by considering the objectives specified in QoS. In this paper, we model dynamic workflow scheduling problem as a dynamic multi-objective optimization problem (DMOP) where the source of dynamism is based on both resource failures and the number of objectives which may change over time. Software faults and/or hardware faults may cause the first type of dynamism. On the other hand, confronting real-life scenarios in cloud computing may change number of objectives at runtime during the execution of a workflow. In this study, we propose a prediction-based dynamic multi-objective evolutionary algorithm, called NN-DNSGA-II algorithm, by incorporating artificial neural network with the NSGA-II algorithm. Additionally, five leading non-prediction based dynamic algorithms from the literature are adapted for the dynamic workflow scheduling problem. Scheduling solutions are found by the consideration of six objectives: minimization of makespan, cost, energy and degree of imbalance; and maximization of reliability and utilization. The empirical study based on real-world applications from Pegasus workflow management system reveals that our NN-DNSGA-II algorithm significantly outperforms the other alternatives in most cases with respect to metrics used for DMOPs with unknown true Pareto-optimal front, including the number of non-dominated solutions, Schott’s spacing and Hypervolume indicator.

The Evolution of the Pegasus Workflow Management Software

Since 2001, the Pegasus Workflow Management System has evolved into a robust and scalable system that automates the execution of a number of complex applications running on a variety of heterogeneous, distributed high-throughput, and high-performance computing environments. Pegasus was built on the principle of separation between the workflow description and workflow execution, providing the ability to port and adapt the workflow based on the target execution environment. Through its user-driven research and development, it has adapted to the needs of a number of scientific communities, utilizing and developing novel algorithms and software engineering solutions. This paper describes the evolution of Pegasus over time and provides motivations behind the design decisions. It concludes with selected lessons learned.

A New Hybrid Fault Tolerance Approach for Internet of Things

In the Distributed Management Task Force, DMTF, the management software in the Internet of things (IoT) should have five abilities including Fault Tolerance, Configuration, Accounting, Performance, and Security. Given the importance of IoT management and Fault Tolerance Capacity, this paper has introduced a new architecture of Fault Tolerance. The proposed hybrid architecture has used all of the reactive and proactive policies simultaneously in its structure. Another objective of the current paper was to develop a measurement indicator to measure the fault tolerance capacity in different architectures. The CloudSim simulator has been used to evaluate and compare the proposed architecture. In addition to CloudSim, another simulator was implemented that was based on the Pegasus-Workflow Management System (WMS) in order to validate the architecture that is proposed in this article. Finally, fuzzy inference systems were designed in a third step to model and evaluate the fault tolerance in various architectures. Based on the results, the positive effect of using various combined Reactive and Proactive policies in increasing the fault tolerance in the proposed architecture has been prominently evident and confirmed.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

BackgroundWith the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed “PGen”, an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way.ResultsWe have developed both a Linux version in GitHub (https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), (http://soykb.org/Pegasus/index.php). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser (http://soykb.org/NGS_Resequence/NGS_index.php) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers.ConclusionPGen workflow has been optimized for the most efficient analysis of soybean data using thorough testing and validation. This research serves as an example of best practices for development of genomics data analysis workflows by integrating remote HPC resources and efficient data management with ease of use for biological users. PGen workflow can also be easily customized for analysis of data in other species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1227-y) contains supplementary material, which is available to authorized users.

Pegasus in the Cloud: Science Automation through Workflow Technologies

The Pegasus Workflow Management System maps abstract, resource-independent workflow descriptions onto distributed computing resources. As a result of this planning process, Pegasus workflows are portable across different infrastructures, optimizable for performance and efficiency, and automatically map to many different storage systems and data flows. This approach makes Pegasus a powerful solution for executing scientific workflows in the cloud.

Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization

This paper presents a cost optimization model for scheduling scientific workflows on IaaS clouds such as Amazon EC2 or RackSpace. We assume multiple IaaS clouds with heterogeneous virtual machine instances, with limited number of instances per cloud and hourly billing. Input and output data are stored on a cloud object store such as Amazon S3. Applications are scientific workflows modeled as DAGs as in the Pegasus Workflow Management System. We assume that tasks in the workflows are grouped into levels of identical tasks. Our model is specified using mathematical programming languages (AMPL and CMPL) and allows us to minimize the cost of workflow execution under deadline constraints. We present results obtained using our model and the benchmark workflows representing real scientific applications in a variety of domains. The data used for evaluation come from the synthetic workflows and from general purpose cloud benchmarks, as well as from the data measured in our own experiments with Montage, an astronomical application, executed on Amazon EC2 cloud. We indicate how this model can be used for scenarios that require resource planning for scientific workflows and their ensembles.

Pegasus, a workflow management system for science automation

Modern science often requires the execution of large-scale, multi-stage simulation and data analysis pipelines to enable the study of complex systems. The amount of computation and data involved in these pipelines requires scalable workflow management systems that are able to reliably and efficiently coordinate and automate data movement and task execution on distributed computational resources: campus clusters, national cyberinfrastructures, and commercial and academic clouds. This paper describes the design, development and evolution of the Pegasus Workflow Management System, which maps abstract workflow descriptions onto distributed computing infrastructures. Pegasus has been used for more than twelve years by scientists in a wide variety of domains, including astronomy, seismology, bioinformatics, physics and others. This paper provides an integrated view of the Pegasus system, showing its capabilities that have been developed over time in response to application needs and to the evolution of the scientific computing platforms. The paper describes how Pegasus achieves reliable, scalable workflow execution across a wide variety of computing infrastructures.

HUBzero and Pegasus: integrating scientific workflows into science gateways

SummaryIn this paper, we described the benefits and the challenges of integrating existing scientific workflow technologies into science gateways. Scientific workflow managers are powerful tools for handling large computational tasks. Domain scientists find it difficult to create new workflows, so many tasks that could benefit from workflow automation are often avoided or performed by hand. Two technologies have come together to bring the benefits of workflow to the masses. The Pegasus Workflow Management System can manage workflows comprised of millions of tasks, all the while recording data about the execution and intermediate results so that the provenance of the final result is clear. The HUBzero platform for scientific collaboration provides a venue for building and delivering tools to researchers and educators. With the press of a button, these tools can launch Pegasus workflows on national computing infrastructures and bring results back for plotting and visualization. As a result, the combination of Pegasus and HUBzero is bringing high‐throughput computing to a much wider audience. Copyright © 2014 John Wiley & Sons, Ltd.

A Case Study into Using Common Real-Time Workflow Monitoring Infrastructure for Scientific Workflows

Scientific workflow systems support various workflow representations, operational modes, and configurations. Regardless of the system used, end users have common needs: to track the status of their workflows in real time, be notified of execution anomalies and failures automatically, perform troubleshooting, and automate the analysis of the workflow results. In this paper, we describe how the Stampede monitoring infrastructure was integrated with the Pegasus Workflow Management System and the Triana Workflow Systems, in order to add generic real time monitoring and troubleshooting capabilities across both systems. Stampede is an infrastructure that provides interoperable monitoring using a three-layer model: (1) a common data model to describe workflow and job executions; (2) high-performance tools to load workflow logs conforming to the data model into a data store; and (3) a common query interface. This paper describes the integration of Stampede monitoring architecture with Pegasus and Triana and shows the new analysis capabilities that Stampede provides to these workflow systems. The successful integration of Stampede with these workflow engines demonstrates the generic nature of the Stampede monitoring infrastructure and its potential to provide a common platform for monitoring across scientific workflow engines.

RseqFlow: workflows for RNA-Seq data analysis

We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps. http://genomics.isi.edu/rnaseq wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu Supplementary data are available at Bioinformatics online.

Adaptive workflow processing and execution in Pegasus

AbstractWorkflows are widely used in applications that require coordinated use of computational resources. Workflow definition languages typically abstract over some aspects of the way in which a workflow is to be executed, such as the level of parallelism to be used or the physical resources to be deployed. As a result, a workflow management system has the responsibility of establishing how best to execute a workflow given the available resources. The Pegasus workflow management system compiles abstract workflows into concrete execution plans, and has been widely used in large‐scale e‐Science applications. This paper describes an extension to Pegasus whereby resource allocation decisions are revised during workflow evaluation, in the light of feedback on the performance of jobs at runtime. The contributions of this paper include: (i) a description of how adaptive processing has been retrofitted to an existing workflow management system; (ii) a scheduling algorithm that allocates resources based on runtime performance; and (iii) an experimental evaluation of the resulting infrastructure using grid middleware over clusters. Copyright © 2009 John Wiley & Sons, Ltd.