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Mark L. Green

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Papers by Mark L. Green

Doing Your Science While You're in Orbit

Journal of physics, Nov 1, 2010

Large-scale neutron facilities such as the Spallation Neutron Source (SNS) located at Oak Ridge N... more 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 thinclient and its supporting Service Oriented Architecture (SOA) based services (available at ) 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 thickclient 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, thinand 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.

1 The Impact of Chicago on Lake Michigan: Results of the Lake Michigan Mass Balance Study A white paper prepared for the workshop on “Using Models to Develop Air Toxics Reduction Strategies: Lake Michigan as a Test Case.”

model for gas-phase persistent organic compounds over Lake Michigan has been constructed. Using a... more model for gas-phase persistent organic compounds over Lake Michigan has been constructed. Using air temperature, wind direction and atmospheric PCB concentration collected around and over the lake, the model predicts the concentration of PCB congeners (~100) and trans-nonachlor over the lake and gas exchange fluxes. The model shows that gas-phase PCB and trans-nonachlor concentrations over Lake Michigan vary considerably as a function of temperature, wind direction, and distance from the urban-industrial region of southwest Lake Michigan. The combined effects of southerly winds and high temperatures cause a large 'plume ' of gas-phase PCBs from Chicago. The Chicago urban air toxics plume can impact the whole lake when warm southerly winds are strong. In this paper, we examine the magnitude of the Chicago plume on gas deposition of these potentially toxic compounds to the lake. Findings-PCBs 1. The LMMB atmospheric modeling shows that Chicago is a source of gas-phase PCBs. ...

Large-Scale User Facility Imaging and Scattering Techniques to Facilitate Basic Medical Research

Medical Imaging, 2011

Challenges in Data Intensive Analysis at Scientific Experimental User Facilities

Handbook of Data Intensive Computing, 2011

The Operations Dashboard: A Collaborative Environment for Monitoring Virtual Organization-Specific Compute Element Operational Status

Parallel Processing Letters, 2006

Grid computing integrates heterogeneous, geographically distributed, Internet-ready resources tha... more 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.

Molecular structure determination on a computational and data grid

Parallel Computing, 2004

The focus of this paper is on the design and implementation of a critical program in structural b... more 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 several research institutions in Western New York. The second is Grid2003, the iVDGL grid established late in 2003 primarily for physics and astronomy applications. In this paper, we present an overview of the ACDC Grid and Grid2003, focusing on the implementation of several new ACDC computational and grid tools.

Shake-and-Bakeon the grid

Journal of Applied Crystallography, 2007

Computational and data grids represent an emerging technology that allows geographically and orga... more Computational and data grids represent an emerging technology that allows geographically and organizationally distributed resources (e.g.computing and storage resources) to be linked and accessed in a fashion that is transparent to the user, presenting an extension of the desktop for users whose computational, data and visualization needs extend beyond their local systems. The New York State Grid is an integrated computational and data grid that provides web-based access for users from around the world to computational, application and data storage resources. This grid is used in a ubiquitous fashion, where the users have virtual access to their data sets and applications, but do not need to be made aware of the details of the data storage or computational devices that are specifically employed. Two of the applications that users worldwide have access to on a variety of grids, including the New York State Grid, are theSnBandBnPprograms, which implement theShake-and-Bakemethod of mol...

The Impact of an Urban-Industrial Region on the Magnitude and Variability of Persistent Organic Pollutant Deposition to Lake Michigan

AMBIO: A Journal of the Human Environment, 2003

Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears... more Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. Allen Press and Royal Swedish Academy of Sciences are collaborating with JSTOR to digitize, preserve and extend access to Ambio.

Evolutionary Aseismic Design and Retrofit of Passively Damped Irregular Structures

In this paper, we develop a parallel genetic algorithm-based approach for discrete optimal design... more In this paper, we develop a parallel genetic algorithm-based approach for discrete optimal design of passively damped structural systems within an uncertain seismic environment. The primary structure may contain metallic yielding dampers, viscous fluid dampers or viscoelastic solid dampers of various sizes, distributed throughout the building. For each candidate design, a series of nonlinear transient dynamic analyses are conducted within a spatially-distributed seismic environment consistent with the USGS Gutenberg-Richter model for eastern North America. A graphical user interface also is created to enable visual display of evolving designs and to interactively interrogate the design database. Several examples are considered to elucidate the methodology and to assess the potential benefits of the evolutionary approach for seismic design and retrofit. While this methodology is sufficiently general to consider a broad range of structural systems, here the emphasis is placed on steel frame buildings with structural irregularities.

Evolutionary Aseismic Design and Retrofit of Buildings

Over the past decade, passive energy dissipation systems have provided an increasingly attractive... more Over the past decade, passive energy dissipation systems have provided an increasingly attractive approach for the seismic retrofit of existing structures, as well as, for the design of new seismically resistant structures. Many different types of passive devices have been developed and general design guidelines have been prepared. However, the choice between the device types for a specific application often is not clear, particularly when consideration must be given to the performance of non-structural components. For example, in general, are rate-independent devices and rate-dependent devices equally beneficial, or are there circumstances in which one of these two categories is preferable? Furthermore, regardless of device type selection, the designer also is faced with the complex issue of effective device distribution. In this paper, we present a genetic algorithm based methodology to address these aspects of aseismic design within the context of steel frame buildings. The primary structure is represented in terms of a nonlinear two-surface plasticity lumped parameter model. Meanwhile, the available passive device types include rate-independent metallic plate dampers, along with rate-dependent viscous fluid dampers and solid viscoelastic dampers. In order to capture more accurately the dynamic response, these devices are also represented by nonlinear models. The seismic environment is characterized either in terms of a fixed set of specified ground motions or by utilizing synthetic signals generated from geophysical models that simulate the actual uncertain seismicity of the site. Within the overall algorithm, passively damped structural designs evolve toward configurations that satisfy constraints on inter-story drift and absolute acceleration, while attempting to limit damper cost. For adjacent buildings, a separation constraint also may be included to alleviate structural pounding. Besides providing an overview of the simulation algorithm, the paper includes a number of illustrative examples to highlight the benefits of the proposed computational design approach.

The impact of Chicago on Lake Michigan: Results of the Lake Michigan mass balance study

As part of the U.S. EPA's Lake Michigan Mass Balance Study, a predictive model for gas-phase pers... more As part of the U.S. EPA's Lake Michigan Mass Balance Study, a predictive model for gas-phase persistent organic compounds over Lake Michigan has been constructed. Using air temperature, wind direction and atmospheric PCB concentration collected around and over the lake, the model predicts the concentration of PCB congeners (~100) and trans-nonachlor over the lake and gas exchange fluxes. The model shows that gas-phase PCB and trans-nonachlor concentrations over Lake Michigan vary considerably as a function of temperature, wind direction, and distance from the urban-industrial region of southwest Lake Michigan. The combined effects of southerly winds and high temperatures cause a large 'plume' of gas-phase PCBs from Chicago. The Chicago urban air toxics plume can impact the whole lake when warm southerly winds are strong. In this paper, we examine the magnitude of the Chicago plume on gas deposition of these potentially toxic compounds to the lake. Findings-PCBs 1. The LMMB atmospheric modeling shows that Chicago is a source of gas-phase PCBs. The Chicago region contributes 2 to 20% of the total deposition of PCB to the lake, depending on the congener and time of year. For an annual year the total gas-phase depositon of ΣPCBs is ~3200 kg and the Chicago contribution is ~330 kg. 2. The Chicago source behaves like a non-point release by volatilization from contaminated sites open to the atmosphere and subject to the same temperature fluctuations as the air temperature. Recommendations -PCBs 1. Reduce the deposition of PCBs to Lake Michigan by: a. Covering land surfaces contaminated with PCBs b. Removing structures contaminated with PCBs c. Conduct remediation activities in cool weather Findings -trans-nonachlor 1. The Chicago source of trans-nonachlor is most important in the winter. During the summertime, the source of trans-nonchlor is more diffuse. 2. The trans-nonachlor signal is not consistent with current use of the pesticide or of seasonal application. 3. Sources of trans-nonachlor are associated with high temperatures and southern winds. This model cannot identify the range of transport. Recommendations -trans-nonachlor 1.Reduce the deposition of trans-nonachlor to Lake Michigan: a. Prevent new application of trans-nonachlor inside and outside the Great Lakes basin b. Conduct remediation activities in cool weather.

GRID2003 Monitoring, Metrics, and Grid Cataloging System

Grid computing involves the close coordination of many different sites which offer distinct compu... more Grid computing involves the close coordination of many different sites which offer distinct computational and storage resources to the Grid user community. The resources at each site need to be monitored continuously. Static and dynamic site information needs to be presented to the user community in a simple and efficient manner. This paper will present both the design and implementation of the Grid3 monitoring infrastructure and the design details and the functionalities of a new application called the GridCat. The Grid3 monitoring architecture follows a useroriented design that specifies standard metrics and utilizes underlying monitoring tools to collect them into a diversified framework. Then existing tools can be integrated, their functionality extended and new tools developed. The primary tools used include the ACDC Job Monitoring system from University at Buffalo, Ganglia, a preliminary version of GridCat, Globus MDS, the University of Chicago Grid telemetry MDViewer, and US ...

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

Journal of physics, Jul 1, 2009

The primary mission of user facilities operated by Basic Energy Sciences under the Department of ... more 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

The grid2003 production grid: principles and practice

Proceedings. 13th IEEE International Symposium on High performance Distributed Computing, 2004.

The Grid2003 Project has deployed a multi-virtual organization, application-driven grid laborator... more The Grid2003 Project has deployed a multi-virtual organization, application-driven grid laboratory ("Grid3") that has sustained for several months the production-level services required by physics experiments of the Large Hadron Collider at CERN (ATLAS and CMS), the Sloan Digital Sky Survey project, the gravitational wave search experiment LIGO, the BTeV experiment at Fermilab, as well as applications in molecular structure analysis and genome analysis, and computer science research projects in such areas as job and data scheduling. The deployed infrastructure has been operating since November 2003 with 27 sites, a peak of 2800 processors, work loads from 10 different applications exceeding 1300 simultaneous jobs, and data transfers among sites of greater than 2 TB/day. We describe the principles that have guided the development of this unique infrastructure and the practical experiences that have resulted from its creation and use. We discuss application requirements for grid services deployment and configuration, monitoring infrastructure, application performance, metrics, and operational experiences. We also summarize lessons learned.

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

2010 Gateway Computing Environments Workshop (GCE), 2010

Gateway computing environments face several challenges in providing robust, scalable, and sustain... more 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 SNS/HFIR Web Portal System for SANS

Journal of Physics: Conference Series, 2010

The new generation of neutron scattering instruments being built are higher resolution and produc... more The new generation of neutron scattering instruments being built are higher resolution and produce one or more orders of magnitude larger data than the previous generation of instruments. For instance, we have grown out of being able to perform some important tasks with our laptops. The data sizes are too big and the computational time would be too long. These large datasets can be problematic as facility users now begin to struggle with many of the same issues faced by more established computing communities. These issues include data access, management, and movement, data format standards, distributed computing, and collaboration with others. The Neutron Science Portal has been designed, and implemented to provide users with an easy-to-use interface for managing and processing data, while also keeping an eye on meeting modern computer security requirements that are currently being imposed on institutions. Users can browse or search for data which they are allowed to see, run data reduction and analysis applications, perform sample activation calculations and perform McStas simulations. Collaboration is facilitated by providing users a read/writeable common area, shared across all experiment team members. The portal currently has over 370 registered users; almost 7TB of experiment and user data, approximately 1,000,000 files cataloged, and had almost 10,000 unique visits last year. Future directions for enhancing portal robustness include examining how to mirror data and portal services, better facilitation of collaborations via virtual organizations, enhancing disconnected service via "thick client" applications, and better inter-facility connectivity to support cross-cutting research.

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

Journal of Physics: Conference Series, 2009

The primary mission of user facilities operated by Basic Energy Sciences under the Department of ... more 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

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

Journal of Great Lakes Research, 2007

A particle tracking model (PTM) is linked with a hydrodynamic model to evaluate mean seasonal cir... more 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.

Evolutionary methodologies for decision support

The decision support sys tems under de vel op ment in this effort will incorporate the seismic re... more

Grid computing in Buffalo, New York

A computational and data grid developed at the Center for Comput ational Research in Buffalo, New... more A computational and data grid developed at the Center for Comput ational Research in Buffalo, New York, will provide a heterogeneous platform to enable scientific and engineering applications to run in a Buffalo-centric grid-based setting. A proof-ofconcept heterogeneous grid has been developed using a critical scientific application in the field of structural biology. The design and functionality of the prototype grid web portal is described, along with plans for a production level grid system based on Globus. Several projects covering a collaborative expansion of this system are also summarized with respect to the core research being investigated. This expansion involves researchers located across the United States who are interested in analyzing and grid-enabling existing software applications and grid technology. increased memory and disk storage devices, a number of parallel languages, including P4, Express, and LINDA, began to appear [1,7]. See Table 1. During the early 1990s, desktop workstations began to be incorporated into distributed computing systems. Further, the capabilities of CPUs, memory, and disk storage increased rapidly during this period. Asynchronous Transfer Mode (ATM) used for Wide Area Networks (WAN) allowed networks to efficiently carry services of the future. Network and computer performance increased by 1000 times and standards such as Message Passing Interface (MPI), High Performance Fortran (HPF), and Distributed Computing Environment (DCE) began to emerge [8]. PVM. Parallel Virtual Machine (PVM) is a software package that permits a heterogeneous collection of Unix and/or Windows computers connected together by a network to be used as a single parallel computer. The first version of PVM was written during the summer of 1989 at Oak Ridge National Laboratory. This initial version of PVM was used internally and not released publicly. Based on the internal success of PVM, Version 2 of the code was redesigned and written from scratch during February 1991 at the lab's sister institution, the University of Tennessee, Knoxville. Version 2 of the code was publicly released in March of 1991. This version was intended to clean up and stabilize the system so that external users could reap the benefits of this parallel computing middleware. PVM Version 3 was redesigned from scratch, and a complete rewrite started in September 1992, with first release of the software in March 1993. While similar in spirit to version 2, version 3 includes features that did not fit the old framework, including fault tolerance, better portability and scalability. Three subsequent versions of PVM were released over the next 9 years. The current version of the system is entitled PVM Version 3.4.4, which was released in September of 2001. Concurrent development of XPVM provided a graphical interface to the PVM console commands and information, along with several animated views to monitor the execution of PVM programs. These views provide information about the interactions among tasks in a PVM program in order to assist in debugging and performance tuning. XPVM Version 1.0 was released in November of 1996 and the latest XPVM Version is 1.2.5, released April 1998 [2]. MPI. The specification of the Message Passing Interface (MPI) standard 1.0 [3] was completed in April of 1994. This was the result of a community effort to try and define both the syntax and semantics of a core message-passing library that would be useful to a wide range of users and implemented on a wide range of Massively Parallel Processor (MPP) platforms. Clarifications were made and released in June 1995, where the major goals were portability, high performance, "common practice", features process model, point-to-point communication, collective operations, and mechanisms for writing safe libraries. All major computer vendors supported the MPI standard and work began on MPI-2, where new functionality, dynamic process management, one-sided communication, cooperative I/O, C++ bindings, Fortran 90 additions, extended collective operations, and miscellaneous other functionality were added to the MPI-1 standard [4]. MPI-1.2 and MPI-2 were released at the same time in July of 1997. The main advantage of establishing a message-passing standard is portability. One of the goals of developing MPI is to provide MPP vendors with a clearly defined base set of routines that they can implement efficiently or, in some cases, improve scalability by providing hardware support. Local Area Multi-computer (LAM) development followed as an MPI programming environment and development system for heterogeneous computers on a network. LAM-MPI 6.1 was released in June 1998 and further development of a graphical user interface continued as XMPI 1.0 was released in January 1999. With LAM-MPI, a dedicated cluster or an existing network computing infrastructure can act as one parallel computer solving one problem and be monitored with a graphical user interface [5]. Development of Grid Computing Integrating computational resources into parallel and distributed systems has become common practice since the early 1990s. A (computational) grid can be defined as a computing system in which computational resources, including computing, storage, databases, devices, sensors, and tools, are organized into a cohesive distributed system that spans multiple geographic and administrative domains. In this section, we provide a very brief history of grid computing, focusing on the capabilities of several toolkits and software packages that are critical to the Center for Computational Research Grid (CCR-Grid) that is the subject of this paper. In order to provide a framework for the discussion that follows in this section, it is important to know that the CCR-Grid system will leverage many of the communication, authentication, concurrency, security, system monitoring, and error handling capabilities available in Globus, a critical public domain grid software package that has become the de facto standard in academic (and many industrial) settings. Globus. The Globus project was established in 1996. It focuses on enabling the application of various grid concepts, predominantly in the domain of computational science and engineering. The Globus project is centered at Argonne National Laboratory,