Bertram Ludaescher

A framework for the design and reuse of grid workflows

Grid workflows can be seen as special scientific workflows involving high performance and/or high throughput computational tasks. Much work in grid workflows has focused on improving application performance through schedulers that optimize the use of computational resources and bandwidth. As high-end computing resources are becoming more of a commodity that is available to new scientific communities, there is an increasing need to also improve the design and reusability “performance” of scientific workflow systems. To this end, we are developing a framework that supports the design and reuse of grid workflows. Individual workflow components (e.g., for data movement, database querying, job scheduling, remote execution etc.) are abstracted into a set of generic, reusable tasks. Instantiations of these common tasks can be functionally equivalent atomic components (called actors) or composite components (so-called composite actors or subworkflows). In this way, a grid workflow designer does not have to commit to a particular Grid technology when developing a scientific workflow; instead different technologies (e.g. GridFTP, SRB, and scp) can be used interchangeably and in concert. We illustrate the application of our framework using two real-world Grid workflows from different scientific domains, i.e., cheminformatics and bioinformatics, respectively.

The GEON portal: accelerating knowledge discovery in the geosciences

Geoscience studies produce data from various observations, experiments, and simulations at an enormous rate. With proliferation of applications and data formats, the geoscience research community faces many challenges in effectively managing and sharing resources and in efficiently integrating and analyzing the data. In this paper, we discuss how this challenge is being addressed by the GEON Portal, a Web based distributed resource management system that provides integrated access to data and tools needed for knowledge discovery in the geosciences. Unlike previous data management efforts that were either data-driven or application-driven, the GEON Portal provides facilities for efficient sharing, discovery and integration of both data and services that use geoscience data. We identify the challenges involved in managing geoscientific resources and provide solutions that exploit the syntactic, semantic, temporal and spatial metadata associated with the resources. One of our goals is to provide some insight into the challenges involved in providing a comprehensive scientific data management solution based on our experiences with geoscientific data.

Workflow automation for processing plasma fusion simulation data

The Center for Plasma Edge Simulation project aims to automate the tedious tasks of monitoring the simulation, archiving and post-processing the output. This paper describes the tasks and requirements, the several components developed within the Kepler workflow system to provide the required functionality and the automated workflow solution. Besides functionality, the focus is on the robust execution of the workflow. A user-level checkpoint/restart model has been developed that allows the workflow to restart, moreover, it also performs operations that failed during the previous run.

Simulation of Fusion Plasmas: Current Status and Future Direction

I. Introduction (Z. Lin, G. Y. Fu, J. Q. Dong) II. Role of theory and simulation in fusion sciences 1. The Impact of theory and simulation on tokomak experiments (H. R. Wilson, T.S. Hahm and F. Zonca) 2. Tokomak Transport Physics for the Era of ITER: Issues for Simulations (P.H. Diamond and T.S. Hahm) III. Status of fusion simulation and modeling 1. Nonlinear Governing Equations for Plasma Simulations (T. S. Hahm) 2. Equilibrium and stability (L.L. Lao, J. Manickam) 3. Transport modeling (R.E. Waltz) 4. Nonlinear MHD (G.Y. Fu) 5. Turbulence (Z. Lin and R.E. Waltz) 6. RF heating and current drive (D.A. Batchelor) 7. Edge physics Simulations (X.Q. Xu and C.S. Chang) 8. Energetic particle physics (F. Zonca, G.Y. Fu and S.J. Wang) 9. Time-dependent Integrated Modeling (R.V. Budny) 10. Validation and verification (J. Manickam) IV. Major initiatives on fusion simulation 1. US Scientific Discovery through Advanced Computing (SciDAC) Program & Fusion Energy Science (W. Tang) 2. EU Integrated Tokamak Modelling (ITM) Task Force (A. Becoulet) 3. Fusion Simulations Activities in Japan (A. Fukuyama, N. Nakajima, Y. Kishimoto, T. Ozeki, and M. Yagi) V. Cross-disciplinary research in fusion simulation 1. Applied mathematics: Models, Discretizations, and Solvers (D.E. Keyes) 2. Computational Science (K. Li) 3. Scientific Data and Workflow Management (S. Klasky, M. Beck, B. Ludaescher, N. Podhorszki, M.A. Vouk) 4. Collaborative tools (J. Manickam)

A Web service composition and deployment framework for scientific workflows

The article presents the Web services framework in the Kepler scientific workflow system and illustrates them with a real-world example.

Introduction to scientific workflow management and the Kepler system

A scientific workflow combines data and processes into a configurable, structured set of steps that implement semi-automated computational solutions of a scientific data management or analysis problem. Scientific workflow systems provide graphical user interfaces to combine different technologies along with efficient methods for using them with the goal to increase the efficiency of the scientists. This tutorial provides an introduction to scientific workflow construction and management (Part I) and includes a detailed hands-on session (Part II) using the Kepler system. It is intended for an audience with a computational science background. It will cover principles and foundations of scientific workflows, Kepler environment installation, workflow construction using Kepler library components, and workflow execution management that uses Kepler facilities to provide process and data monitoring and provenance information, as well as high speed data movement solutions. This tutorial also incorporates hands-on exercises and application examples from different scientific disciplines.

The Center for Plasma Edge Simulation Workflow Requirements

The Center for Plasma Edge Simulation (CPES) is a recently funded prototype Fusion Simulation Project, which is part of the DOE SciDAC program. Our center is developing a novel integrated predictive plasma edge simulation framework, which is applicable to existing magnetic fusion facilities (D3D, NSTX, CMOD) and next generation burning plasma experiments, e.g. ITER. The success of this project will be in developing and understanding new models for the plasma edge in a kinetic regime with complex geometry. Because of the multi-scale nature of the problem, we will study the neoclassical physics time scale kinetically, and the fast and larger scale MHD modes via a fluid code. Our approach is to couple these codes via a scientific workflow system, Kepler-HPC. Kepler-HPC will enhance Kepler with capabilities such as code coupling and data redistribution, high volume data transfers and interactive (and autonomic) monitoring, steering and debugging, which will be necessary for scientific progress in this project.

Automation of Network-Based Scientific Workflows

Comprehensive, end-to-end, data and workflow management solutions are needed to handle the increasing complexity of processes and data volumes associated with modern distributed scientific problem solving, such as ultrascale simulations and high-throughput experiments. The key to the solution is an integrated network-based framework that is functional, dependable, faulttolerant, and supports data and process provenance. Such a framework needs to make development and use of application workflows dramatically easier so that scientists’ efforts can shift away from data management and utility software development to scientific research and discovery. An integrated view of these activities is provided by the notion of scientific workflows - a series of structured activities and computations that arise in scientific problem-solving. An information technology framework that supports scientific workflows is the Ptolemy II based environment called Kepler. This paper discusses the issues associated with practical automation of scientific processes and workflows and illustrates this with workflows developed using the Kepler framework and tools.

Scientific Data Management Integrated Software Infrastructure Center (SDM/ISIC): Scientific Process Automation (SPA), FINAL REPORT

This is the final report from SDSC and UC Davis on DE-FC02-01ER25486, Scientific Data Management Integrated Software Infrastructure Center (SDM/ISIC): Scientific Process Automation (SPA).

Merging Taxonomies under RCC-5 Algebraic Articulations

Taxonomies are widely used to classify information, and multiple (possibly competing) taxonomies often exist for the same domain. Given a set of correspondences between two taxonomies, it is often necessary to “merge” the taxonomies, thereby creating a unied taxonomy (e.g., that can then be used by data integration and discovery applications). We present an algorithm for merging taxonomies that have been related using articulations given as RCC-5 constraints. Two taxa N and M can be related using (disjunctions of) the ve base relations in RCC-5: N≡M; N ? M; N ?; N ? M (partial overlap of N and M); and N ! M (disjointness: N ∩ M = ?). RCC-5 is increasingly being adopted by scientists to specify mappings between large biological taxonomies. We discuss the properties of the proposed merge algorithm and evaluate our approach using real-world taxonomies.