Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1–10% of the total execution time

HydroShare – A Case Study of the Application of Modern Software Engineering to a Large Distributed Federally-Funded Scientific Software Development Project

HydroShare is an online collaborative system under development to support the open sharing of hydrologic data, analytical tools, and computer models. With HydroShare, scientists can easily discover, access, and analyze hydrologic data and thereby enhance the production and reproducibility of hydrologic scientific results. HydroShare also takes advantage of emerging social media functionality to enable users to enhance information about and collaboration around hydrologic data and models. HydroShare is being developed by an interdisciplinary collaborative team of domain scientists, university software developers, and professional software engineers from ten institutions located across the United States. While the combination of non–co-located, diverse stakeholders presents communication and management challenges, the interdisciplinary nature of the team is integral to the project’s goal of improving scientific software development and capabilities in academia. This chapter describes the challenges faced and lessons learned with the development of HydroShare, as well as the approach to software development that the HydroShare team adopted on the basis of the lessons learned. The chapter closes with recommendations for the application of modern software engineering techniques to large, collaborative, scientific software development projects, similar to the National Science Foundation (NSF)–funded HydroShare, in order to promote the successful application of the approach described herein by other teams for other projects

XSEDE: eXtreme Science and Engineering Discovery Environment Third Quarter 2012 Report

The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated digital resources and services in the world. It is an integrated cyberinfrastructure ecosystem with singular interfaces for allocations, support, and other key services that researchers can use to interactively share computing resources, data, and expertise.This a report of project activities and highlights from the third quarter of 2012.National Science Foundation, OCI-105357