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Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures
Abstract
The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation experiments. Since 2006, the UltraScan scientific gateway has been used with Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. UltraScan supports its users with a scientific gateway in order to leverage the power of supercomputing. In this contribution, we will focus on several advancements of the UltraScan scientific gateway architecture with a standardized job management while retaining its lightweight design and end user interaction experience. This paper also presents insights into a production deployment of UltraScan in Europe. The approach is based on open standards with respect to job management and submissions to the Extreme Science and Engineering Discovery Environment in the USA and to similar infrastructures in Europe such as the European Grid Infrastructure or the Partnership for Advanced Computing in Europe (PRACE). Our implementation takes advantage of the Apache Airavata framework for scientific gateways that lays the foundation for easy integration into several other scientific gateways. Copyright © 2014 John Wiley & Sons, Ltd.
... It also has features designed to measure the rotor stretch function of any rotor, as a function of speed, and to measure radial position errors resulting from chromatic aberration as a function of wavelength. This work was recently described in [12], and has been implemented in the latest version of UltraScan [13,14], which associates a unique stretch profile with each rotor entered into the LIMS database [15] which provides an automatic stretch corrections during data analysis, and appropriate chromatic aberration corrections during data import for Optima AUC instruments. ...
... This avenue offers maximum flexibility and fosters development of new and interesting tools that can explore novel features like multi-wavelength experiments [19,20,21,22,23,24] and GMP capable data acquisition software, discussed here. Using the network-capable Linux tools provided with the Optima, our laboratory has extended the UltraScan-III AUC analysis software [13,14] and the UltraScan Laboratory Information Management Systems (UltraScan-LIMS) framework [15] to interface directly with the Optima for experimental design, data acquisition, and remote experiment monitoring. The goal for this software is to greatly simplify operation of the analytical ultracentrifuge and to automate all steps in the data acquisition and data analysis process without sacrificing flexibility. ...
Recent advances in instrumentation have moved analytical ultracentrifugation (AUC) closer to a possible validation in a Good Manufacturing Practices (GMP) environment. In order for AUC to be validated for a GMP environment, stringent requirements need to be satisfied; analysis procedures must be evaluated for consistency and reproducibility, and GMP capable data acquisition software needs to be developed and validated. These requirements extend to multiple regulatory aspects, covering documentation of instrument hardware functionality, data handling and software for data acquisition and data analysis, process control, audit trails and automation. Here we review the requirements for GMP validation of data acquisition software and illustrate software solutions based on UltraScan that address these requirements as far as they relate to the operation and data handling in conjunction with the latest analytical ultracentrifuge, the Optima AUC by Beckman Coulter. The software targets the needs of regulatory agencies, where AUC plays a critical role in the solutionbased characterization of biopolymers and macromolecular assemblies. Biopharmaceutical and regulatory agencies rely heavily on this technique for characterizations of pharmaceutical formulations, biosimilars, injectables, nanoparticles, and other soluble therapeutics. Because of its resolving power, AUC is a favorite application, despite the current lack of GMP validation. We believe that recent advances in standards, hardware, and software presented in this work manage to bridge this gap and allow AUC to be routinely used in a GMP environment. AUC has great potential to provide more detailed information, at higher resolution, and with greater confidence than other analytical techniques, and our software satisfies an urgent need for AUC operation in the GMP environment. The software, including documentation, are publicly available for free download from Github. The multi-platform software is licensed by the LGPL v.3 open source license and supports Windows, Mac and Linux platforms. Installation instructions and a mailing list are available from ultrascan.aucsolutions.com.
... Our implementation is deployed and currently used in production by the Ultrascan science gateway [27] community that spans the US and Europe. As one of the compute sites is the , it demonstrates the enormous capabilities of the XSEDE architecture to enable interoperability. ...
... As one of the compute sites is the , it demonstrates the enormous capabilities of the XSEDE architecture to enable interoperability. In [27] we described more details on our implementation and demonstrated it using a production JURECA cluster located at Juelich Supercomputing Centre with real usage numbers. ...
The XSEDE project seeks to provide “a single virtual system that scientists can use to interactively share computing resources, data and experience.” The potential compute resources in XSEDE are diverse in many dimensions, node architectures, interconnects, memory, local queue management systems, and authentication policies to name a few. The diversity is particularly rich when one considers the NSF funded service providers and the many campuses that wish to participate via campus bridging activities. Resource diversity presents challenges to both application developers and application platform developers (e.g., developers of gateways, portals, and workflow engines). The XSEDE Execution Management Services (EMS) architecture is an instance of the Open Grid Services Architecture EMS and is used by higher level services such as gateways and workflow engines to provide end users with execution services that meet their needs. The contribution of this paper is to provide a concise explanation and concrete examples of how the EMS
works, how it can be used to support scientific gateways and workflow engines, and how the XSEDE EMS and other OGSA EMS architectures can be used by applications developers to securely access heterogeneous distributed computing and data resources.
... Our research methodology is 'design science research' (Hevner and Chatterjee, 2010): gaining knowledge through designing and building tangible artifacts. In earlier research it was proven that high-resolution nD-SFCs (Space Filling Curves) in combination with parallel processing by employing and adapting solutions driven by High Performance/ High Throughput Computing (HPC/HTC) environments (Guan and Wu, 2010;Gentzsch et al., 2011;Memon et al., 2014) have the potential to cluster points close in reality (Fig. 2). Oosterom et al. (2015) and Liu et al. (2020a) developed an Index-Organized Table (IOT) approach to address nD window queries on massive point clouds. ...
Point clouds contain high detail and high accuracy geometry representation of the scanned Earth surface parts. To manage the huge amount of data, the point clouds are traditionally organized on location and map-scale; e.g. in an octree structure, where top-levels of the tree contain few points suitable for small scale overviews and lower levels of the tree contain more points suitable for large scale detailed views. The drawback of this solution is that it is based on discrete levels, causing visual artifacts in the form of data density shocks when creating the commonly used perspective views. This paper presents a method based on an optimized distribution of points over continuous levels, avoiding the visualization shocks. The traditional distribution ratio’s of data amounts over discrete levels of raster or vector data is considered the reference. How to convert this to point clouds with continuous levels (still benefiting from the proven advantages of the data distribution in discrete levels for efficient access at a wide range of scales)? In our solution, for each point a cLoD (continuous Level of Detail) value is computed and added as dimension to the point. A SFC (Space Filling Curve)-based nD data clustering technique can be used to organize the points, so that they can be efficiently queried. It should be noted that also other multi-dimensional indexing and clustering techniques could be applied to realize continuous levels based on the cLoD value. Besides the mathematical foundation of the approach also several implementations are described, varying from a 3D web-browser based solution to an augmented reality point cloud app in a mobile phone. The cLoD enables interactive real-time visualization using perspective views without data density shocks, while supporting continuous zoom-in/out and progressive data streaming between server and client. The described cLoD based approach is generic and supports different types of point clouds: from airborne, terrestrial, mobile and indoor laser scanning, but also from dense matching optical imagery or multi-beam echo soundings.
... Additional performance gains are realized from streamlined and automated workflows available through the networked science gateway and offered by the Extreme Science and Discovery Environment (XSEDE, funded by the National Science Foundation in the USA) and from the Partnership for Advanced Computing in Europe (PRACE). These workflows are accessed through efficient grid middleware implementations that allow investigators to distribute jobs to multiple supercomputer clusters simultaneously (Memon et al. 2014). US3 aims to provide a comprehensive and robust analysis environment for all hydrodynamic analysis. ...
The current status of the UltraScan-III (US3) data analysis software suite is described. An overview of the US3 concepts, software layout, the data workflows and US3 components is presented, followed by a discussion of the analysis methods and their applications. Also described are visualization modules for analysis results, US3’s utilities and simulation tools, as well as the collaboration environments for online data and result exchange.
... The client side API is useful for scientific communities which are not necessarily using the UNICORE's povided interface, but instead their own clients such as their application specific science portals or gateways (e.g. UltraScan Scientific Gateway [33]. Hence, all important functionality of the middleware services can be invoked through the direct client API interaction. ...
Emerging challenges for scientific communities are to efficiently process big data obtained by experimentation and computational simulations. Supercomputing architectures are available to support scalable and high performant processing environment, but many of the existing algorithm implementations are still unable to cope with its architectural complexity. One approach is to have innovative technologies that effectively use these resources and also deal with geographically dispersed large datasets. Those technologies should be accessible in a way that data scientists who are running data intensive computations do not have to deal with technical intricacies of the underling execution system. Our work primarily focuses on providing data scientists with transparent access to these resources in order to easily analyze data. Impact of our work is given by describing how we enabled access to multiple high performance computing resources through an open standards-based middleware that takes advantage of a unified data management provided by the the Global Federated File System. Our architectural design and its associated implementation is validated by a usecase that requires massivley parallel DBSCAN outlier detection on a 3D point clouds dataset.
... The Ultrascan science gateway [18] provides remote access to high speed ultracentrifuges and their associated analysis software and has been supporting analytical ultracentrifugation (AUC) experiments since 2006. Developments described in this paper include a standardized job management system and production deployment in Europe including on the European Grid Infrastructure (EGI) and the Partnership for Advanced Computing in Europe (PRACE) infrastructures using the Apache Airavata framework. ...
The 2014 Special Issue of Concurrency and Computation: Practice and Experience presents papers from the XSEDE13 conference held in San Diego, July 2013. The conference is an annual gathering of the extended community of those interested in advancing research cyber infrastructure (CI) and digital resources. One paper looked at ECC available on many of the modern graphics processing units (GPUs) used in HPC machines. It looks at the penalty involved in utilizing ECC and compares molecular dynamics simulation results regarding ECC events triggered during such simulations. Making Campus Bridging Work for Researchers proposes utilization of Campus Bridging experts to make this transition easier while requiring minimal investment from the organizing body. The paper on computational finance is looking into the impact of high frequency trading on the stock market. It discusses how the simulation, for this research, was speeded up by two orders of magnitude on XSEDE HPC resources.
A method for characterizing and quantifying peaks formed in an analytical buoyant density equilibrium (ABDE) experiment is presented. An algorithm is derived to calculate the concentration of the density forming gradient material at every point in the cell, provided the rotor speed, temperature, meniscus position, bottom of the cell position, and the loading concentration, molar mass, and partial specific volume of the density gradient-forming material are known. In addition, a new peak fitting algorithm has been developed which allows the user to automatically quantify the peaks formed in terms of density, apparent partial specific volume, and relative abundance. The method is suitable for both ionic and non-ionic density forming materials and can be used with data generated from the UV optical system as well as the AVIV fluorescence optical system. These methods have been programmed in a new UltraScan-III module (us_abde). Examples are shown that demonstrate the application of the new module to adeno-associated viral vector preparations and proteins.
Recent advances in multi-wavelength analytical ultracentrifugation (MWL-AUC) combine the power of an exquisitely sensitive hydrodynamic-based separation technique with the added dimension of spectral separation. This added dimension has opened up new doors to much improved characterization of multiple, interacting species in solution. When applied to structural investigations of RNA, MWL-AUC can precisely report on the hydrodynamic radius and the overall shape of an RNA molecule by enabling precise measurements of its sedimentation and diffusion coefficients and identify the stoichiometry of interacting components based on spectral decomposition. Information provided in this chapter will allow an investigator to design experiments for probing ion and/or protein-induced global conformational changes of an RNA molecule and exploit spectral differences between proteins and RNA to characterize their interactions in a physiological solution environment.
We describe important advances in methodologies for the analysis of multiwavelength data. In contrast to the Beckman-Coulter XL-A/I ultraviolet–visible light detector, multiwavelength detection is able to simultaneously collect sedimentation data for a large wavelength range in a single experiment. The additional dimension increases the data density by orders of magnitude, posing new challenges for data analysis and management. The additional data not only improve the statistics of the measurement but also provide new information for spectral characterization, which complements the hydrodynamic information. New data analysis and management approaches were integrated into the UltraScan software to address these challenges. In this chapter, we describe the enhancements and benefits realized by multiwavelength analysis and compare the results to those obtained from the traditional single-wavelength detector. We illustrate the advances offered by the new instruments by comparing results from mixtures that contain different ratios of protein and DNA samples, representing analytes with distinct spectral and hydrodynamic properties. For the first time, we demonstrate that the spectral dimension not only adds valuable detail, but when spectral properties are known, individual components with distinct spectral properties measured in a mixture by the multiwavelength system can be clearly separated and decomposed into traditional datasets for each of the spectrally distinct components, even when their sedimentation coefficients are virtually identical.
A performance prediction model for the two-dimensional spectrum analysis algorithm of the UltraScan software was developed to aid in the prediction of calculation times on XSEDE supercomputer infrastructure. The efficiency profiles for various analysis types and analysis parameter combinations when used on Lonestar, Trestles and Stampede were determined by mining performance data from past analyses stored in the UltraScan LIMS database. The resulting model was validated against an analytical performance model. The model can be integrated into the existing UltraScan submission infrastructure to provide improved wall time estimates for the XSEDE supercomputer clusters to increase queuing efficiency.
Existing Distributed Resource Managers (DRMs) lack support for a standard submis- sion language and interoperable interface for describing and launching jobs. This paper presents a standards-based job submission system, GridSAM1, which utilises Web Services and the Job Submission Description Language (JSDL). GridSAM provides a transparent and ecient bridge between users and existing DRM systems, such as Condor. We demonstrate, through a set of performance results, the small overhead imposed by the GridSAM submission pipeline while im- proving the overall system throughput and availability. The performance results are gathered from a variety of deployment configurations to exercise the wide-ranging support of GridSAM in terms of launching mechanism, clustering set up and persistence choice.
Computational Grids connect resources and users in a complex way in order to deliver nontrivial qualities of services. According
to the current trend various communities build their own Grids and due to the lack of generally accepted standards these Grids
are usually not interoperable. As a result, large scale sharing of resources is prevented by the isolation of Grid systems.
Similarly, people are isolated, because the collaborative work of Grid users is not supported by current environments. Each
user accesses Grids as an individual person without having the possibility of organizing teams that could overcome the difficulties
of application development and execution more easily. The paper describes a new workflow-oriented portal concept that solves
both problems. It enables the interoperability of various Grids during the execution of workflow applications, and supports
users to develop and run their Grid workflows in a collaborative way. The paper also introduces a classification model that
can be used to identify workflow-oriented Grid portals based on two general features: Ability to access multiple Grids, and
support for collaborative problem solving. Using the approach the different potential portal types are introduced, their unique
features are discussed and the portals and Problem Solving Environments (PSE) of our days are classified. The P-GRADE Portal
as a Globus-based implementation for the classification model is also presented.
This document specifies the semantics and structure of the Job Submission Description Language (JSDL). JSDL is used to describe the requirements of computational jobs for submission to
resources, particularly in Grid environments, though not restricted to the latter. The document
includes the normative XML Schema for the JSDL, along with examples of JSDL documents
based on this schema.
In this paper, we introduce Apache Airavata, a software framework to compose, manage, execute, and monitor distributed applications and workflows on computational resources ranging from local resources to computational grids and clouds. Airavata builds on general concepts of service-oriented computing, distributed messaging, and workflow composition and orchestration. This paper discusses the architecture of Airavata and its modules, and illustrates how the software can be used as individual components or as an integrated solution to build science gateways or general-purpose distributed application and workflow management systems.
In the last three years activities in Grid computing have changed; in particular in Europe the focus moved from pure research-oriented work on concepts, architectures, interfaces, and protocols towards activities driven by the usage of Grid technologies in day-to-day operation of e-infrastructure and in applicationdriven use cases. This change is also reected in the UNICORE activities [1]. The basic components and services have been established, and now the focus is increasingly on enhancement with higher level services, integration of upcoming standards, deployment in e-infrastructures, setup of interoperability use cases and integration of applications. The development of UNICORE started back more than 10 years ago, when in 1996 users, supercomputer centres and vendors were discussing "what prevents the efficient use of distributed supercomputers?". The result of this discussion was a consensus which still guides UNICORE today: seamless, secure and intuitive access to distributed resources. Since the end of 2002 continuous development of UNICORE took place in several EU-funded projects, with the subsequent broadening of the UNICORE community to participants from across Europe. In 2004 the UNICORE software became open source and since then UNICORE is developed within the open source developer community. Publishing UNICORE as open source under BSD license has promoted a major uptake in the community with contributions from multiple organisations. Today the developer community includes developers from Germany, Poland, Italy, UK, Russia and other countries. The structure of the paper is as follows. In Section 2 the architecture of UNICORE 6 as well as implemented standards are described, while Section 3 focusses on its clients. Section 4 covers recent developments and advancements of UNICORE 6, while in section 5 an outlook on future planned developments is given. The paper closes with a conclusion.
SAGA is a high-level programming abstraction, which significantly facilitates the development and deployment of Grid-aware applications. The primary aim of this paper is to discuss how each of the three main components of the SAGA landscape - interface specification, specific implementation and the different adaptors for middleware distribution - facilitate application-level interoperability. We discuss SAGA in relation to the ongoing GIN Community Group efforts and show the consistency of the SAGA approach with the GIN Group efforts. We demonstrate how interoperability can be enabled by the use of SAGA, by discussing two simple, yet meaningful applications: in the first, SAGA enables applications to utilize interoperability and in the second example SAGA adaptors provide the basis for interoperability.
Frequently in the physical sciences experimental data are analyzed to determine model parameters using techniques known as parameter estimation. Eliminating the eects of noise from experimental data often involves Tikhonov or Maximum-Entropy regularization. These methods in- troduce a bias which smoothes the solution. In the prob- lems considered here, the exact answer is sharp, containing a sparse set of parameters. Therefore, it is desirable to nd the simplest set of model parameters for the data with an equivalent goodness-of-t. This paper explains how to bias the solution towards a parsimonious model with a careful application of Genetic Algorithms. A method of representa- tion, initialization and mutation is introduced to ecien tly nd this model. The results are compared with results from two other methods on simulated data with known content. Our method is shown to be the only one to achieve the desired results. Analysis of Analytical Ultracentrifugation sedimentation velocity experimental data is the primary ex- ample application.
Computational simulations and thus scientific computing is the third pillar alongside theory and experiment in todays science.
The term e-science evolved as a new research field that focuses on collaboration in key areas of science using next generation
computing infrastructures (i.e. co-called e-science infrastructures) to extend the potential of scientific computing. During
the past years, significant international and broader interdisciplinary research is increasingly carried out by global collaborations
that often share a single e-science infrastructure. More recently, increasing complexity of e-science applications that embrace
multiple physical models (i.e. multi-physics) and consider a larger range of scales (i.e. multi-scale) is creating a steadily
growing demand for world-wide interoperable infrastructures that allow for new innovative types of e-science by jointly using
different kinds of e-science infrastructures. But interoperable infrastructures are still not seamlessly provided today and
we argue that this is due to the absence of a realistically implementable infrastructure reference model. Therefore, the fundamental
goal of this paper is to provide insights into our proposed infrastructure reference model that represents a trimmed down
version of ogsa in terms of functionality and complexity, while on the other hand being more specific and thus easier to implement. The proposed
reference model is underpinned with experiences gained from e-science applications that achieve research advances by using
interoperable e-science infrastructures.
We report a model-independent analysis approach for fitting sedimentation velocity data which permits simultaneous determination of shape and molecular weight distributions for mono- and polydisperse solutions of macromolecules. Our approach allows for heterogeneity in the frictional domain, providing a more faithful description of the experimental data for cases where frictional ratios are not identical for all components. Because of increased accuracy in the frictional properties of each component, our method also provides more reliable molecular weight distributions in the general case. The method is based on a fine grained two-dimensional grid search over s and f/f
0, where the grid is a linear combination of whole boundary models represented by finite element solutions of the Lamm equation with sedimentation and diffusion parameters corresponding to the grid points. A Monte Carlo approach is used to characterize confidence limits for the determined solutes. Computational algorithms addressing the very large memory needs for a fine grained search are discussed. The method is suitable for globally fitting multi-speed experiments, and constraints based on prior knowledge about the experimental system can be imposed. Time- and radially invariant noise can be eliminated. Serial and parallel implementations of the method are presented. We demonstrate with simulated and experimental data of known composition that our method provides superior accuracy and lower variance fits to experimental data compared to other methods in use today, and show that it can be used to identify modes of aggregation and slow polymerization.
In preparation for first data at the LHC, a series of Data Challenges, of increasing scale and complexity, have been performed. Large quantities of simulated data have been produced on three different Grids, integrated into the ATLAS production system. During 2006, the emphasis moved towards providing stable continuous production, as is required in the immediate run-up to first data, and thereafter. Here, we discuss the experience of the production done on EGEE resources, using submission based on the gLite WMS, CondorG and a system using Condor Glide-ins. The overall walltime efficiency of around 90% is largely independent of the submission method, and the dominant source of wasted cpu comes from data handling issues. The efficiency of grid job submission is significantly worse than this, and the glide-in method benefits greatly from factorising this out.
SAGA is a high-level programming abstraction, which significantly facilitates the development and deployment of Grid-aware applications. The primary aim of this paper is to discuss how each of the three main components of the SAGA landscape - interface specification, specific implementation and the different adaptors for middleware distribution - facilitate application-level interoperability. We discuss SAGA in relation to the ongoing GIN Community Group efforts and show the consistency of the SAGA approach with the GIN Group efforts. We demonstrate how interoperability can be enabled by the use of SAGA, by discussing two simple, yet meaningful applications: in the first, SAGA enables applications to utilize interoperability and in the second example SAGA adaptors provide the basis for interoperability.
‘My admiration for our current teaching profession is unbounded. Fettered by unprecedented bureaucracy, government jargon, and lost discipline, they soldier on in a culture, which is so much more difficult than was the case in my own teaching days.’ T
OGSA–DAI provides a framework for sharing and managing distributed data. OGSA–DAI is highly customizable and can be used to manage, share and process distributed data (e.g. relational, XML, files and RDF triples). It does this by executing workflows that can encapsulate complex distributed data management scenarios in which data from one or more sources can be accessed, updated, combined and transformed. Moreover, the data processing capabilities provided by OGSA–DAI are further augmented by a powerful distributed query processor and relational views component that allow distributed data sources to be viewed and queried as if they were a single resource. OGSA–DAI allows researchers and business users to move away from logistical and technical concerns such as data locations, data models, data transfers and optimization strategies for data integration and instead focus on application-specific data analysis and processing.
The Ultrascan gateway provides a user friendly web interface for evaluation of experimental analytical ultracentrifuge data using the UltraScan modeling software. The analysis tasks are executed on the TeraGrid and campus computational resources. The gateway is highly successful in providing the service to end users and consistently listed among the top five gateway community account usage. This continued growth and challenges of sustainability needed additional support to revisit the job management architecture.
In this paper we describe the enhancements to the Ultrascan gateway middleware infrastructure provided through the TeraGrid Advanced User Support program. The advanced support efforts primarily focused on a) expanding the TeraGrid resources incorporate new machines; b) upgrading UltraScan's job management interfaces to use GRAM5 in place of the deprecated WS-GRAM; c) providing realistic usage scenarios to the GRAM5 and INCA resource testing and monitoring teams; d) creating general-purpose, resource-specific, and UltraScan-specific error handling and fault tolerance strategies; and e) providing forward and backward compatibility for the job management system between UltraScan's version 2 (currently in production) and version 3 (expected to be released mid-2011).
The Vine Toolkit is a modular, extensible Java library that offers developers an easy-to-use, high-level API for Grid-enabling
applications. It supports a wide-variety of application environments and Grid middleware platforms.
High resolution analysis approaches for sedimentation experiments have recently been developed that promise to provide a detailed
description of heterogeneous samples by identifying both shape and molecular weight distributions. In this study, we describe
the effect experimental noise has on the accuracy and precision of such determinations and offer a stochastic Monte Carlo
approach, which reliably quantifies the effect of noise by determining the confidence intervals for the parameters that describe
each solute. As a result, we can now predict reliable confidence intervals for determined parameters. We also explore the
effect of various experimental parameters on the confidence intervals and provide suggestions for improving the statistics
by applying a few practical rules for the design of sedimentation experiments.
In the past years, hype over Web services and their uses in emerging software applications has prompted the creation of many standards and proto-standards. The OGF has seen a number of standards making their way through design and edit pipelines. While this standards process progresses, it is important that implementations of these standards develop in parallel in order to validate the efforts of the standards authors while also providing feedback for further specification refinement. No specification exists in isolation but rather composes with others to form higher order products. These specifications will form the grid infrastructure of the future and an evaluation of this emerging work becomes increasingly relevant. Genesis II is a grid system implemented using these standards that serves both to provide the feedback described above as well as to function as a production level grid system for research at the University of Virginia.
SUMMARY After seven years of life the Open Grid Forum (OGF), previously the Global Grid Forum, is beginning to produce standards that meet the needs of the community and that are being adopted by commercial and open source software providers. Accessing computational resources, specifically high performance computing resources, is a usage scenario that predates the emergence of the Grid and is well understood within the community. Building on this consensus the HPC Profile Working Group was established within the OGF to standardize access to HPC resources. Its first specification, the HPC Basic Profile 1.0, has been developed and has established interoperability within the community. Alongside the development of this protocol, another group within the OGF, the Simple API Grid Applications (SAGA) Working Group has been defining a programmatic interface relevant to application developers that encompasses access to compute resources. This paper examines the relationship between the "standard" protocol of the HPC Basic Profile and the programmatic interface of SAGA to access compute resources and assesses how well these address the problems faced by the community of users and application developers.
This document specifies the syntax and semantics of the Parameter Sweep extension to the Job Submission Description Language (JSDL) 1.0 [JSDL]. The syntax and semantics defined in this document provide an alternative to explicitly submitting thousands of individual JSDL job submissions of the same base job template, except with a different set of parameters for each.
Analytical ultracentrifugation experiments can be accurately modeled with the Lamm equation to obtain sedimentation and diffusion coefficients of the solute. Existing finite element methods for such models can cause artifactual oscillations in the solution close to the endpoints of the concentration gradient, or fail altogether, especially for cases where somega(2)/D is large. Such failures can currently only be overcome by an increase in the density of the grid points throughout the solution at the expense of increased computational costs. In this article, we present a robust, highly accurate and computationally efficient solution of the Lamm equation based on an adaptive space-time finite element method (ASTFEM). Compared to the widely used finite element method by Claverie and the moving hat method by Schuck, our ASTFEM method is not only more accurate but also free from the oscillation around the cell bottom for any somega(2)/D without any increase in computational effort. This method is especially superior for cases where large molecules are sedimented at faster rotor speeds, during which sedimentation resolution is highest. We describe the derivation and grid generation for the ASTFEM method, and present a quantitative comparison between this method and the existing solutions.
Emerging high-performance applications require the ability to exploit diverse, geographically distributed resources. These applications use high-speed networks to integrate supercomputers, large databases, archival storage devices, advanced visualization devices, and/or scientific instruments to form networked virtual supercomputers or metacomputers. While the physical infrastructure to build such systems is becoming widespread, the heterogeneous and dynamic nature of the metacomputing environment poses new challenges for developers of system software, parallel tools, and applications. In this article, we introduce Globus, a system that we are developing to address these challenges. The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and network. A low-level toolkit provides basic mechanisms such as communication, authentication, network information, and data access. These mechanisms are used to construct various higher-leve...
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