Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

Integration of BPM systems

New technologies have emerged to support the global economy where for instance suppliers, manufactures and retailers are working together in order to minimise the cost and maximise efficiency. One of the technologies that has become a buzz word for many businesses is business process management or BPM. A business process comprises activities and tasks, the resources required to perform each task, and the business rules linking these activities and tasks. The tasks may be performed by human and/or machine actors. Workflow provides a way of describing the order of execution and the dependent relationships between the constituting activities of short or long running processes. Workflow allows businesses to capture not only the information but also the processes that transform the information - the process asset (Koulopoulos, T. M., 1995). Applications which involve automated, human-centric and collaborative processes across organisations are inherently different from one organisation to another. Even within the same organisation but over time, applications are adapted as ongoing change to the business processes is seen as the norm in today’s dynamic business environment. The major difference lies in the specifics of business processes which are changing rapidly in order to match the way in which businesses operate. In this chapter we introduce and discuss Business Process Management (BPM) with a focus on the integration of heterogeneous BPM systems across multiple organisations. We identify the problems and the main challenges not only with regards to technologies but also in the social and cultural context. We also discuss the issues that have arisen in our bid to find the solutions

PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

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

Towards the Integration of Value and Coordination Models - Position Paper -

Cross-organizational collaborations have a high complexity.\ud Modelling these collaborations can be done from di®erent perspectives.\ud For example, the value perspective represents expected value exchanges\ud in a collaboration while the coordination perspective represents the order\ud in which these exchanges occur. How to maintain consistency between\ud di®erent models during design time as well as runtime constitutes a chal-\ud lenging topic. De¯ning criteria and de¯nitions re°ecting the relation be-\ud tween these models during the entire life cycle is not straightforward.\ud Di®erent criteria are used for di®erent models since each model captures\ud a speci¯c aspect of the collaboration. In this paper we investigate the\ud challenges arising when addressing the problem of maintaining adequate\ud and consistent models of a collaboration during the entire life cycle of\ud a collaboration. We propose a framework in which we connect business\ud layer, process layer and implementation layer, presenting the direction\ud for solving this multifaceted problem. We will describe several challenges\ud we anticipate to encounter while implementing our framework

Composition and Self-Adaptation of Service-Based Systems with Feature Models

The adoption of mechanisms for reusing software in pervasive systems has not yet become standard practice. This is because the use of pre-existing software requires the selection, composition and adaptation of prefabricated software parts, as well as the management of some complex problems such as guaranteeing high levels of efficiency and safety in critical domains. In addition to the wide variety of services, pervasive systems are composed of many networked heterogeneous devices with embedded software. In this work, we promote the safe reuse of services in service-based systems using two complementary technologies, Service-Oriented Architecture and Software Product Lines. In order to do this, we extend both the service discovery and composition processes defined in the DAMASCo framework, which currently does not deal with the service variability that constitutes pervasive systems. We use feature models to represent the variability and to self-adapt the services during the composition in a safe way taking context changes into consideration. We illustrate our proposal with a case study related to the driving domain of an Intelligent Transportation System, handling the context information of the environment.Work partially supported by the projects TIN2008-05932, TIN2008-01942, TIN2012-35669, TIN2012-34840 and CSD2007-0004 funded by Spanish Ministry of Economy and Competitiveness and FEDER; P09-TIC-05231 and P11-TIC-7659 funded by Andalusian Government; and FP7-317731 funded by EU. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

McRunjob: A High Energy Physics Workflow Planner for Grid Production Processing

McRunjob is a powerful grid workflow manager used to manage the generation of large numbers of production processing jobs in High Energy Physics. In use at both the DZero and CMS experiments, McRunjob has been used to manage large Monte Carlo production processing since 1999 and is being extended to uses in regular production processing for analysis and reconstruction. Described at CHEP 2001, McRunjob converts core metadata into jobs submittable in a variety of environments. The powerful core metadata description language includes methods for converting the metadata into persistent forms, job descriptions, multi-step workflows, and data provenance information. The language features allow for structure in the metadata by including full expressions, namespaces, functional dependencies, site specific parameters in a grid environment, and ontological definitions. It also has simple control structures for parallelization of large jobs. McRunjob features a modular design which allows for easy expansion to new job description languages or new application level tasks.Comment: CHEP 2003 serial number TUCT00