Conrad Steenberg

NUPACK: Analysis and design of nucleic acid systems

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

Predicting the Resource Requirements of a Job Submission

Grid computing aims to provide an infrastructure for distributed problem solving in dynamic virtual organizations. It is gaining interest among many scientific disciplines as well as the industrial community. However, current grid solutions still require highly trained programmers with expertise in networking, high-performance computing, and operating systems. One of the big issues in full-scale usage of a grid is matching the resource requirements of job submission to the resources available on the grid. Resource brokers and job schedulers must make estimates of the resource usage of job submissions in order to ensure efficient use of grid resources. We prop ose a prediction engine that will operate as part of a grid scheduler. This prediction engine will provide estimates of the resources required by job submission based upon historical information. This paper presents the need for such a prediction engine and discusses two approaches for history based estimation.

Distributed computing grid experiences in CMS

The CMS experiment is currently developing a computing system capable of serving, processing and archiving the large number of events that will be generated when the CMS detector starts taking data. During 2004 CMS undertook a large scale data challenge to demonstrate the ability of the CMS computing system to cope with a sustained data-taking rate equivalent to 25% of startup rate. Its goals were: to run CMS event reconstruction at CERN for a sustained period at 25 Hz input rate; to distribute the data to several regional centers; and enable data access at those centers for analysis. Grid middleware was utilized to help complete all aspects of the challenge. To continue to provide scalable access from anywhere in the world to the data, CMS is developing a layer of software that uses Grid tools to gain access to data and resources, and that aims to provide physicists with a user friendly interface for submitting their analysis jobs. This paper describes the data challenge experience with Grid infrastructure and the current development of the CMS analysis system.

The Clarens Web service framework for distributed scientific analysis in grid projects

Large scientific collaborations are moving towards service oriented architectures for implementation and deployment of globally distributed systems. Clarens is a high performance, easy to deploy Web service framework that supports the construction of such globally distributed systems. This paper discusses some of the core functionality of Clarens that the authors believe is important for building distributed systems based on Web services that support scientific analysis.

Lambda Station: On-Demand Flow Based Routing for Data Intensive Grid Applications Over Multitopology Networks

Lambda Station is an ongoing project of Fermi National Accelerator Laboratory and the California Institute of Technology. The goal of this project is to design, develop and deploy network services for path selection, admission control and flow based forwarding of traffic among data- intensive Grid applications such as are used in High Energy Physics and other communities. Lambda Station deals with the last-mile problem in local area networks, connecting production clusters through a rich array of wide area networks. Selective forwarding of traffic is controlled dynamically at the demand of applications. This paper introduces the motivation of this project, design principles and current status. Integration of Lambda Station client API with the essential Grid middleware such as the dCache/SRM Storage Resource Manager is also described. Finally, the results of applying Lambda Station services to development and production clusters at Fermilab and Caltech over, advanced networks such as DOEs UltraScience Net and NSFs UltraLight is covered.

Resource management services for a grid analysis environment

Selecting optimal resources for submitting jobs on a computational grid or accessing data from a data grid is one of the most important tasks of any grid middleware. Most modern grid software today satisfies this responsibility and gives a best-effort performance to solve this problem. Almost all decisions regarding scheduling and data access are made by the software automatically, giving users little or no control over the entire process. To solve this problem, a more interactive set of services and middleware is desired that provides users more information about grid weather, and gives them more control over the decision making process. This paper presents a set of services that have been developed to provide more interactive resource management capabilities within the grid analysis environment (GAE) being developed collaboratively by Caltech, NUST and several other institutes. These include a steering service, a job monitoring service and an estimator service that have been designed and written using a common grid-enabled Web services framework named Clarens. The paper also presents a performance analysis of the developed services to show that they have indeed resulted in a more interactive and powerful system for user-centric grid-enabled physics analysis.

JClarens: a Java based interactive physics analysis environment for data intensive applications

In this paper we describe JClarens; a Java based implementation of the Clarens remote data server. JClarens provides Web services for an interactive analysis environment to dynamically access and analyze the tremendous amount of data scattered across various locations. Additionally this research is aimed to develop a service oriented grid enabled portal (GEP) that provides interface and access to several grid services to give a homogeneous and optimized view of the distributed and heterogeneous environment. Other than showing platform independent behavior provided by Java, the use of XML-RPC based Web services enabled JClarens to be a language neutral server and demonstrated interoperability with its Python variant. Extreme care has been taken in the usage and manipulation of various Java libraries to cater the needs of high performance computing. The overall exercise has yielded in a prototype with strong emphasis on security and virtual organization management (VOM). This shall provide a common platform to support development of larger, more flexible framework with future aims to integrate it with a loosely coupled, decentralized, and autonomous framework for grid enabled analysis environment (GAE).

The UltraLight Project: The Network as an Integrated and Managed Resource for Data-Intensive Science

Looks at the UltraLight project which treats the network interconnecting globally distributed data sets as a dynamic, configurable, and closely monitored resource to construct a next-generation system that can meet the high-energy physics communitys data-processing, distribution, access, and analysis needs.

Distributed Analysis and Load Balancing System for Grid Enabled Analysis on Hand-Held Devices Using Multi-agents Systems

Handheld devices, while growing rapidly, are inherently constrained and lack the capability of executing resource hungry applications. This paper presents the design and implementation of distributed analysis and load-balancing system for hand-held devices using multi-agents system. This system enables low resource mobile handheld devices to act as potential clients for Grid enabled applications and analysis environments. We propose a system, in which mobile agents will transport, schedule, execute and return results for heavy computational jobs submitted by handheld devices. Moreover, in this way, our system provides high throughput computing environment for hand-held devices.

Matchmaking, datasets and physics analysis

Grid enabled physics analysis requires a workload management system (WMS) that takes care of finding suitable computing resources to execute data intensive jobs. A typical example is the WMS available in the LCG2 (also referred to as EGEE-0) software system, used by several scientific experiments. Like many other current grid systems, LCG2 provides a file level granularity for accessing and analysing data. However, application scientists such as high energy physicists often require a higher abstraction level for accessing data, i.e. they prefer to use datasets rather than files in their physics analysis. We have improved the current WMS (in particular the Matchmaker) to allow physicists to express their analysis job requirements in terms of datasets. This required modifications to the WMS and its interface to potential data catalogues. As a result, we propose a simple data location interface that is based on a Web service approach and allows for interoperability of the WMS with new dataset and file catalogues. We took a particular high energy physics experiment as the source for our study and show that physics analysis can be improved by our modifications to the current grid system.