[show abstract][hide abstract] ABSTRACT: SCIRun is a general purpose problem solving environment that seeks to integrate the steps of preparing, executing, and visualizing simulations of physical and biological systems. The implementation of SCIRun is by means of an interactive dataflow network consisting of modules and data pipes exposed as a visual programming language. SCIRun also contains specific modules for bioelectric field simulations and visualizations and the combination of SCIRun with this package is known as BioPSE (www.sci.utah.edu/software/biopse). This software has been in the public domain since 2000 and in that time we have developed strategies for software development, engineering, testing, documentation, and training. We have also continued to expand the scope of the SCIRun/BioPSE package not only through our own codes but by constructing bridges to other systems, both open source and proprietary. We have also created a repository for relevant sample networks and datasets with the aim of allowing diverse groups to test and evaluate algorithms using identical data and to share their results with the community for comparison of performance and accuracy. We present here a summary of the software system and describe specific experiences and conclusions with regard to creating and managing a large open source software project carried out within a university setting.
Biomedical Imaging: Nano to Macro, 2004. IEEE International Symposium on; 05/2004
[show abstract][hide abstract] ABSTRACT: Describes Uintah, a component-based visual problem-solving
environment (PSE) that is designed to specifically address the unique
problems of massively parallel computation on tera-scale computing
platforms. Uintah supports the entire life-cycle of scientific
applications by allowing scientific programmers to quickly and easily
develop new techniques, debug new implementations and apply known
algorithms to solve novel problems. Uintah is built on three principles:
(1) as much as possible, the complexities of parallel execution should
be handled for the scientist, (2) the software should be reusable at the
component level, and (3) scientists should be able to dynamically steer
and visualize their simulation results as the simulation executes. To
provide this functionality, Uintah builds upon the best features of the
SCIRun (Scientific Computing and Imaging Run-time) PSE and the DoE
(Department of Energy) Common Component Architecture (CCA)
High-Performance Distributed Computing, 2000. Proceedings. The Ninth International Symposium on; 02/2000
[show abstract][hide abstract] ABSTRACT: Building systems that alter program behavior during execution based on user-specified criteria (computational steering systems) has been a recent research topic, particularly among the high performance computing community. To enable a computational steering system with powerful visualization capabilities to run on distributed memory architectures, a distributed infrastructure (or runtime system) must first be built. This infrastructure would permit harnessing a variety of machines to collaborate on an interactive simulation. Building such an infrastructure requires strategies for coordinating execution across machines (concurrency control mechanisms), mechanisms for fast data transfer between machines, and mechanisms for user manipulation of remote execution. We are creating a distributed infrastructure for the SCIRun computational steering system. SCIRun, a scientific problem solving environment (PSE), provides the ability to interactively guide or steer a running computation. Initially designed for a shared memory multiprocessor, SCIRun is a tightly integrated, multi-threaded framework for composing scientific applications from existing or new components. High performance computing is needed to maintain interactivity for scientists and engineers running simulations. Extending such a performance-sensitive application toolkit to enable pieces of the computation to run on different machine architectures all within the same computation would prove very useful. Not only could many different machines execute this framework, but also several machines could be configured to work synergistically on computations
High Performance Distributed Computing, 1998. Proceedings. The Seventh International Symposium on; 08/1998
[show abstract][hide abstract] ABSTRACT: With today's large and complex applications, scientists have
increasing difficulty analyzing and visualizing vast amounts of data.
Computational steering is an emerging technology that addresses this
problem, providing a mechanism for integrating simulation, data
analysis, visualization, and postprocessing
IEEE Computational Science and Engineering 11/1997;
[show abstract][hide abstract] ABSTRACT: SCIRun is a problem solving environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. We review related systems and introduce a taxonomy that explores different computational steering solutions. Considering these approaches, we discuss why a tightly integrated problem solving environment, such as SCIRun, simplifies the design and debugging phases of computational science applications and how such an environment aids in the scientific discovery process.
[show abstract][hide abstract] ABSTRACT: We present the design, implementation and application of SCIRun, a scientific programming environment that allows the interactive construction, debugging and steering of large scale scientific computations. Using this "computational workbench," a scientist can design and modify simulations interactively via a dataflow programming model. SCIRun enables scientists to design and modify models and automatically change parameters and boundary conditions as well as the mesh discretization level needed for an accurate numerical solution. As opposed to the typical "off-line" simulation mode - in which the scientist manually sets input parameters, computes results, visualizes the results via a separate visualization package, then starts again at the beginning - SCIRun "closes the loop" and allows interactive steering of the design and computation phases of the simulation. To make the dataflow programming paradigm applicable to large scientific problems, we have identified ways to avoid the excessive memory use inherent in standard dataflow implementations, and have implemented fine-grained dataflow in order to further promote computational efficiency. In this paper, we describe applications of the SCIRun system to several problems in computational medicine. In addition, an we have included an interactive demo program in the form of an application of SCIRun system to a small electrostatic field problem.
Supercomputing, 1995. Proceedings of the IEEE/ACM SC95 Conference; 02/1995
[show abstract][hide abstract] ABSTRACT: We describe a computational steering model which allows users to interactively change boundary conditions, model geometry, and computational parameters via a graphical user interface. To replace the typical simulation mode-in which the researcher manually sets input parameters, computes results, stores data off to disk, visualizes the results via a separate visualization package, then starts again at the beginning-we have designed software to “close the loop” and allow the visualization to help guide (steer) the design and computation phases of the simulation. We have applied the computational steering model to problems in medicine, specifically to applications in bioelectric field phenomena and biomedical device design