Mark L. Green

A Semi-Lagrangian Study of Circulation and Transport in Lake Ontario

ABSTRACT A particle tracking model (PTM) is linked with a hydrodynamic model to evaluate mean seasonal circulation patterns in Lake Ontario, and also to provide a basis for predicting movement of algal blooms. The PTM is based on a random walk algorithm that combines a deterministic advective component with a stochastic component associated with the turbulent diffusivity field to calculate trajectories of neutrally buoyant particles, where both the advective and diffusive velocities are obtained from the hydrodynamic model. Mean circulation is calculated using 30-year average meteorological forcing data collected from five stations around the lake. Seasonal variations in lake circulation are demonstrated, and a clockwise flow in the eastern basin during summer and early fall is identified, contrary to some previous observations that suggest counterclockwise flow. The impacts of Niagara and St. Lawrence river flows on general lake circulation are found to be small, except within approximately 10 km of the river mouth. Development and application of the PTM demonstrate its potential to provide calculations of (Lagrangian) movements as determined from the hydrodynamic output, and to serve as a first step toward development of an algal transport model. Particle tracking helps to visualize flow patterns and provides a means of evaluating the probability a bloom will reach a specified area, given an initial position and the predicted velocity and diffusivity fields. This capability, when set up for real-time applications, can provide an important tool to support management decisions that may be needed when a bloom is observed, for example in predicting potential impacts of the bloom on a beach or a water intake.

Grid-enabled virtual organization based dynamic firewall

The development of heterogeneous grid infrastructure is in its infancy and the potential impact of unauthorized network connections and/or potential system corruption is a serious concern. This project addresses the need for the integration of a dynamic firewall into a grid-enabled application environment. By its very nature, a grid-computing environment consists of a dynamic collection of applications, resources, and services that require access to network ports. The focus of this paper is on developing a dynamic iptables-based firewall that is capable of automatically identifying valid grid user/application network port connection requests and satisfying these requests based on a Globus proxy. The dynamic firewall (Dyna-Fire) service has been integrated into the Western New Yorks ACDC-Grid.

Molecular structure determination on a computational and data Grid

The focus of this paper is on the design and implementation of a critical program in structural biology onto two computational and data Grids. The first is the Buffalo-based ACDC Grid, which uses facilities at SUNY-Buffalo and several research institutions that are under distinct control. The second is Grid2003, the iVDGL Grid established late in 2003 primarily for physics and astronomy applications. In this paper, we prevent an overview of the ACDC Grid and Grid2003, focusing on the implementation of several new ACDC computational and Grid tools.

Evolutionary molecular structure determination using Grid-enabled data mining

A new computational framework is developed for the evolutionary determination of molecular crystal structures using the shake-and-bake methodology. Genetic algorithms are performed on the SnB results of known structures in order to optimize critical parameters of the program. The determination of efficient SnB input parameters can significantly reduce the time required to solve unknown molecular structures. Further, the Grid-enabled data mining approach that we introduce is able to exploit computational cycles that would otherwise go unused.

A client-server prototype for Grid-enabling application template design

A computational and data grid was developed at the Center for Computational Research in Buffalo, New York, in order to provide a platform to support scientific and engineering applications across a variety of computer and storage systems. This proof-of-concept grid has been deployed using a critical scientific application in the field of structural biology. The design and functionality of the prototype grid is described, along with plans for a production level grid system based on Globus.

Challenges in Data Intensive Analysis at Scientific Experimental User Facilities

Today’s scientific challenges such as routes to a sustainable energy future, materials by design or biological and chemical environmental remediation methods, are complex problems that require the integration of a wide range of complementary expertise to be addressed successfully. Experimental and computational science research methods can hereby offer fundamental insights for their solution.

Orbiter Commander: A flexible application framework for service-based scientific computing environments

Gateway computing environments face several challenges in providing robust, scalable, and sustainable capabilities to a wide range of users. Principles of encapsulation and cohesion have been applied in emerging trends of application framework development, where modular designs and abstraction layers allow these systems to remain flexible and agile as requirements evolve over time. Orbiter Commander is a modular and extensible application framework that leverages the Orbiter Federation Service Oriented Architecture to deliver fast and secure capabilities in an Eclipse RCP desktop application. Commander provides suites of modules that can be seamlessly delivered to end users on multiple platforms, enabling rapid component development through a flexible design and well-defined extension points. This paper presents our collaboration with the Spallation Neutron Source Neutron Experiment and Theory Hub (NExTHUB) and the Solenoidal Tracker at the at the RHIC (STAR) experiment, two suites of capabilities tailored to serve the needs of users at Oak Ridge National Laboratory and Brookhaven National Laboratory.

THE OPERATIONS DASHBOARD: A COLLABORATIVE ENVIRONMENT FOR MONITORING VIRTUAL ORGANIZATION-SPECIFIC COMPUTE ELEMENT OPERATIONAL STATUS

Grid computing integrates heterogeneous, geographically distributed, Internet-ready resources that are administered under multiple domains. A key challenge in grid computing is to provide a high quality of service to users in a transparent fashion, hiding issues that include ownership, administration, and geographic location of a wide variety of resources that provide compute cycles, data storage, rendering cycles, imaging devices, and sensors, to name a few. Ensuring the functionality of a wide variety of resources under multiple administrative policies requires tools for discovering, repairing, and publishing information on the services offered by individual sites within a given grid. In this paper, we present the ACDC Operations Dashboard, an interactive, collaborative environment for collecting, addressing, and publishing operational service information for resources across a computational grid.

Doing Your Science While You're in Orbit

Large-scale neutron facilities such as the Spallation Neutron Source (SNS) located at Oak Ridge National Laboratory need easy-to-use access to Department of Energy Leadership Computing Facilities and experiment repository data. The Orbiter thick- and thin-client and its supporting Service Oriented Architecture (SOA) based services (available at https://orbiter.sns.gov) consist of standards-based components that are reusable and extensible for accessing high performance computing, data and computational grid infrastructure, and cluster-based resources easily from a user configurable interface. The primary Orbiter system goals consist of (1) developing infrastructure for the creation and automation of virtual instrumentation experiment optimization, (2) developing user interfaces for thin- and thick-client access, (3) provide a prototype incorporating major instrument simulation packages, and (4) facilitate neutron science community access and collaboration. The secure Orbiter SOA authentication and authorization is achieved through the developed Virtual File System (VFS) services, which use Role-Based Access Control (RBAC) for data repository file access, thin-and thick-client functionality and application access, and computational job workflow management. The VFS Relational Database Management System (RDMS) consists of approximately 45 database tables describing 498 user accounts with 495 groups over 432,000 directories with 904,077 repository files. Over 59 million NeXus file metadata records are associated to the 12,800 unique NeXus file field/class names generated from the 52,824 repository NeXus files. Services that enable (a) summary dashboards of data repository status with Quality of Service (QoS) metrics, (b) data repository NeXus file field/class name full text search capabilities within a Google like interface, (c) fully functional RBAC browser for the read-only data repository and shared areas, (d) user/group defined and shared metadata for data repository files, (e) user, group, repository, and web 2.0 based global positioning with additional service capabilities are currently available. The SNS based Orbiter SOA integration progress with the Distributed Data Analysis for Neutron Scattering Experiments (DANSE) software development project is summarized with an emphasis on DANSE Central Services and the Virtual Neutron Facility (VNF). Additionally, the DANSE utilization of the Orbiter SOA authentication, authorization, and data transfer services best practice implementations are presented.

Data management and its role in delivering science at DOE BES user facilities – Past, Present, and Future

The primary mission of user facilities operated by Basic Energy Sciences under the Department of Energy is to produce data for users in support of open science and basic research [1]. We trace back almost 30 years of history across selected user facilities illustrating the evolution of facility data management practices and how these practices have related to performing scientific research. The facilities cover multiple techniques such as X-ray and neutron scattering, imaging and tomography sciences. Over time, detector and data acquisition technologies have dramatically increased the ability to produce prolific volumes of data challenging the traditional paradigm of users taking data home upon completion of their experiments to process and publish their results. During this time, computing capacity has also increased dramatically, though the size of the data has grown significantly faster than the capacity of ones laptop to manage and process this new facility produced data. Trends indicate that this will continue to be the case for yet some time. Thus users face a quandary for how to manage todays data complexity and size as these may exceed the computing resources users have available to themselves. This same quandary can also stifle collaboration and sharing. Realizing this, some facilities are already providing web portal access to data and computing thereby providing users access to resources they need [2]. Portal based computing is now driving researchers to think about how to use the data collected at multiple facilities in an integrated way to perform their research, and also how to collaborate and share data. In the future, inter-facility data management systems will enable next tier cross-instrument-cross facility scientific research fuelled by smart applications residing upon user computer resources. We can learn from the medical imaging community that has been working since the early 1990s to integrate data from across multiple modalities to achieve better diagnoses [3] – similarly, data fusion across BES facilities will lead to new scientific discoveries.