Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)最新文献

{"title":"Exploiting HPC resources for the 3D-time series analysis of caries lesion activity","authors":"Hui Zhang, Huian Li, M. Boyles, R. Henschel, E. K. Kohara, M. Ando","doi":"10.1145/2335755.2335815","DOIUrl":"https://doi.org/10.1145/2335755.2335815","url":null,"abstract":"We present a research framework to analyze 3D-time series caries lesion activity based on collections of SkyScan® μ-CT images taken at different times during the dynamic caries process. Analyzing caries progression (or reversal) is data-driven and computationally demanding. It involves segmenting high-resolution μ-CT images, constructing 3D models suitable for interactive visualization, and analyzing 3D and 4D (3D + time) dental images. Our development exploits XSEDE's supercomputing, storage, and visualization resources to facilitate the knowledge discovery process. In this paper, we describe the required image processing algorithms and then discuss the parallelization of these methods to utilize XSEDE's high performance computing resources. We then present a workflow for visualization and analysis using ParaView. This workflow enables quantitative analysis as well as three-dimensional comparison of multiple temporal datasets from the longitudinal dental research studies. Such quantitative assessment and visualization can help us to understand and evaluate the underlying processes that arise from dental treatment, and therefore can have significant impact in the clinical decision-making process and caries diagnosis.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"51 1","pages":"19:1-19:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82791577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources","authors":"Mark A. Miller, W. Pfeiffer, Terri Schwartz","doi":"10.1145/2335755.2335836","DOIUrl":"https://doi.org/10.1145/2335755.2335836","url":null,"abstract":"The CIPRES Science Gateway (CSG) provides browser-based access to computationally demanding phylogenetic codes run on large HPC resources. Since its release in December 2009, there has been a sustained, near-linear growth in the rate of CSG use, both in terms of number of users submitting jobs each month and number of jobs submitted. The average amount of computational time used per month by CSG increased more than 5-fold since its initial release. As of April 2012, more than 4,000 unique users have run parallel tree inference jobs on TeraGrid/XSEDE resources using the CSG. The steady growth in resource use suggests that the CSG is meeting an important need for computational resources in the Systematics/Evolutionary Biology community.\u0000 To ensure that XSEDE resources accessed through the CSG are used effectively, policies for resource consumption were developed, and an advanced set of management tools was implemented. Studies of usage trends show that these new management tools helped in distributing XSEDE resources across a large user population that has low-to-moderate computational needs.\u0000 In the first quarter of 2012, 30% of all active XSEDE users accessed computational resources through the CSG, while the analyses conducted by these users accounted for 0.7% of all allocable XSEDE computational resources. User survey results showed that the easy access to XSEDE/TeraGrid resources through the CSG had a critical and measurable scientific impact: at least 300 scholarly publications spanning all major groups within the Tree of Life have been enabled by the CSG since 2009. The same users reported that 82% of these publications would not have been possible without access to computational resources available through the CSG. The results indicate that the CSG is a critical and cost-effective enabler of science for phylogenetic researchers with limited resources.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"109 1","pages":"39:1-39:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80869479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Prickly Pear Archive: a portable hypermedia for scholarly publication","authors":"Dennis G. Castleberry, Steven R. Brandt, F. Löffler, H. Krishnan","doi":"10.1145/2335755.2335840","DOIUrl":"https://doi.org/10.1145/2335755.2335840","url":null,"abstract":"An executable paper is a hypermedia for publishing, reviewing, and reading scholarly papers which include a complete HPC software development or scientific code. A hypermedia is an integrated interface to multimedia including text, figures, video, and executables, on a subject of interest. Results within the executable paper include numeric output, graphs, charts, tables, equations and the underlying codes which generated such results. These results are dynamically regenerated and included in the paper upon recompilation and re-execution of the code. This enables a scientifically enriched environment which functions not only as a journal but as a laboratory in itself, in which readers and reviewers may interact with and validate the results.\u0000 The Prickly Pear Archive (PPA) is such a system [2]. One distinguishing feature of the PPA is the inclusion of an underlying component-based simulation framework, Cactus [8], which simplifies the process of composing, compiling, and executing simulation codes. Code creation is simplified using common bits of infrastructure; each paper augments to the functionality of the framework. New distinguishing features include the (1) portability and (2) reproducibility of the archive, which allow researchers to move and re-create the software environment in which the simulation code was created. Further, the (3) Piraha parser is now used to match complex multi-line expressions inside parameter and LaTEX files. Finally, (4) an altogether new web interface has been created. The new interface options closely mirror the directory structure within the paper itself, which gives the reader a transparent view of the paper. Thus, once accustomed to reading from the archive, assembling a paper package becomes a straightforward and intuitive process.\u0000 A PPA production system hosted on HPC resources (e.g. an XSEDE machine) unifies the computational scientific process with the publication process. A researcher may use the production archive to test simulations; and upon arriving at a scientifically meaningful result, the user may then incorporate the result in an executable paper on the very same resource the simulation was conducted. Housed within a virtual machine, the PPA allows multiple accounts within the same production archive, enabling users across campuses to bridge their efforts in developing scientific codes.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"22 1","pages":"43:1-43:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87646085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A tale of two systems: flexibility of usage of Kraken and Nautilus at the National Institute for Computational Sciences","authors":"A. Szczepanski, Jian Huang, Sean Ahern, M. Fahey","doi":"10.1145/2335755.2335794","DOIUrl":"https://doi.org/10.1145/2335755.2335794","url":null,"abstract":"The National Institute for Computational Sciences (NICS) at the University of Tennessee currently operates two computational resources for the eXtreme Science and Engineering Discovery Environment (XSEDE), Kraken, a 112,896-core Cray XT5 for general purpose computation, and Nautilus, a 1,024-core SGI Altix UV 1000 for data analysis and visualization. We analyze a year's worth of accounting logs for Kraken and Nautilus to understand how users take advantage of these two systems and how analysis jobs differ from general HPC computation We find that researchers take advantage of the flexibility offered by these systems, running a wide variety of jobs at many scales and using the full range of core counts and available memory for their jobs. The jobs on Nautilus tend to use less walltime and more memory per core than the jobs run on Kraken. Additionally, researchers are more likely to run interactive jobs on Nautilus than on Kraken. Small jobs experience a good quality of service on both systems. This information can be used for the management and allocation of time on existing HPC and analysis systems as well as for planning for deploying future HPC and analysis systems.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"30 1","pages":"6:1-6:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73064808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The data supercell","authors":"P. Nowoczynski, J. Sommerfield, J. Yanovich, J. R. Scott, Zhihui Zhang, Michael J. Levine","doi":"10.1145/2335755.2335805","DOIUrl":"https://doi.org/10.1145/2335755.2335805","url":null,"abstract":"The Data SuperCell (DSC) is a new, disk-based data archive deployed and in production at the Pittsburgh Supercomputing Center (PSC). It specifically deals with the archival demands of large data processing in an economic way. DSC incorporates PSCs SLASH2, layered filesystem technology, with commodity hardware and open software, to provide superior functionality, flexibility, manageability, reliability, performance and cost. Below, we describe DSC functionality goals; SLASH2 architecture, capabilities and suitability for archival applications; ZFS as an underlying file system; DSC architecture, structure and capabilities; followed by discussion of our experience with DSC, some performance measurements and plans for further development.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"34 1","pages":"13:1-13:11"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77884568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Building a partnership for computer science education","authors":"Diane A. Baxter, B. Simon","doi":"10.1145/2335755.2335862","DOIUrl":"https://doi.org/10.1145/2335755.2335862","url":null,"abstract":"The University of California San Diego (UCSD) piloted a new undergraduate introduction to computer science (CS) principles in fall 2010. The course was contextual, conceptual, and constructivist in its approach to programming; building interest and enthusiasm for the \"magic\" of computing; and designed to become a new high school AP Computer Science Principles course (to precede AP CS A)[2].\u0000 This paper describes a set of activities that set the stage to introduce the new CS Principles course into San Diego area high schools -- a region with many districts and a highly diverse student population -- truly a significant challenge. This exploratory project conducted by the San Diego Supercomputer Center (SDSC) at UCSD identified essential decision makers and stakeholders, and built and/or strengthened the strategic collaborative networks necessary to support sustainable change in the region's K-12 computer science education programs.\u0000 SDSC identified core leadership partners from UCSD, from San Diego State University (with the largest teacher preparation program in the region), the San Diego County Office of Education, and the San Diego Computer Science Teachers Association.\u0000 With guidance and introductions from these core leadership partners, project PIs met with district administrators, technology specialists, and high school teachers who shared the project goals. In turn, these contacts provided introductions and opportunities for project PIs to present the case for the course to elected officials and key district decision-makers. Guided by input from these meetings, the core leadership partnership developed and achieved an agenda of objectives to build the collaborative networks needed for sustainable regional implementation of the course. Those strategic objectives included:\u0000 • Identify protocols, processes, and decision criteria in each school and district; outline strategies for their effective use;\u0000 • Gain endorsements needed for district-wide implementation;\u0000 • Identify leaders within each district (teachers, professional development specialists, technology specialists, and administrators) willing to become advocates/ambassadors for the new (and not-yet AP) CS Principles course; and\u0000 • Recruit and train a Teacher Leadership Team to pilot test the \"Computer Science Principles\" course content and pedagogy in their own high school classrooms, and provide formative feedback to guide wider professional development and course implementation.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"150 1","pages":"64:1-64:5"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75762608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using stereoscopic 3D videos to inform the public about the benefits of computational science","authors":"M. Boyles, A. William, C. Frend, Chris Eller","doi":"10.1145/2335755.2335856","DOIUrl":"https://doi.org/10.1145/2335755.2335856","url":null,"abstract":"This paper describes an effort to create and disseminate a series of stereoscopic 3D videos that raise awareness about the value of computational science. While the videos target the general population, including the K-12 community, the audience for this paper includes scientific or technical peers who may be interested in sharing or demonstrating their own work more broadly. After outlining the motivation and goals of the project, the authors describe the visual content and computational science behind each of the videos. We then discuss our highly collaborative production workflow that has evolved over the past decade, as well as our distribution mechanisms. We include a summary of the most relevant and appropriate stereoscopic display technologies for the intended audience. Lastly, we analyze and compare this work to other forms of engagement, summarize best practices, and describe potential improvements to future stereoscopic 3D video production.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"139 1","pages":"58:1-58:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73260136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FutureGrid education: using case studies to develop a curriculum for communicating parallel and distributed computing concepts","authors":"J. Mitchell, J. Qiu, Massimo Canonio, S. Jha, Linda Hayden, B. O'Leary, R. Figueiredo, Geoffrey Fox","doi":"10.1145/2335755.2335859","DOIUrl":"https://doi.org/10.1145/2335755.2335859","url":null,"abstract":"The shift to parallel computing -- including multi-core computer architectures, cloud distributed computing, and generalpurpose GPU programming -- leads to fundamental changes in the design of software and systems. As a result, learning parallel, distributed, and cloud techniques in order to allow software to take advantage of the shift toward parallelism is of important significance. To this end, FutureGrid, an experimental testbed for cloud, grids, and high performance computing, provides a resource for anyone to find, share, and discuss modular teaching materials and computational platform supports.\u0000 This paper presents a series of case studies for experiences in parallel and distributed education using the FutureGrid testbed. Building on previous experiences from courses, workshops, and summer schools associated with FutureGrid, we present a viable solution to developing a curriculum by leveraging collaboration with organizations. Our approach to developing a successful guide stems from the idea of anyone interested in learning parallel and distributing computing can do so with minimum assistance from a domain expert, and it addresses the educational goals and objectives to help meet many challenges, which lie ahead in the discipline.\u0000 We validate our approach to developing a community driven curriculum by providing use cases and their experiences with the teaching modules. Examples of some use cases include the following: hosting a workshop for faulty members of historically black colleges and universities, courses in distributed and cloud computing at universities, such as Indiana University, Louisiana State University, and the University of Piemonte Orientale.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"1 1","pages":"61:1-61:5"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83401679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Campus bridging pilot project reports: XSEDE12 panel","authors":"R. Knepper, G. Almes, Thorbjörn Axelsson, P. Muzio, Joel P. Zysman","doi":"10.1145/2335755.2335865","DOIUrl":"https://doi.org/10.1145/2335755.2335865","url":null,"abstract":"The mission of XSEDE Campus Bridging Program is to improve access to national cyberinfrastructure and ease the transition of researchers from campus cyberinfrastructure to national resources. As described in the 2011 ACCI Task Force Report on Campus Bridging, the critical task for campus bridging is the seamless integration of cyberinfrastructure between scientists' desktops and local campus, regional, and national cyberinfrastructure. Bridging the gap between researcher ancyberinfrastructure requires an integrated approach to security, software, and system layouts to allow consistent access to systems across multiple levels.\u0000 In order to facilitate the use of XSEDE resources by campus researchers, the XSEDE Campus Bridging team has started a pilot program to test the Genesis II software. The Genesis II Global Federated File System allows for a global name space that spans from clients at the campus level across regional and national cyberinfrastructure resources. Working with the Genesis II Execution Management Service, users can access and share files across the wide area network, and use the file system as an abstraction layer for accessing job submission queues and databases as well as files.\u0000 Each of the pilot project sites proposed ambitious plans for making use of the Genesis II software. The pilot projects sites will present their use cases for the software, detailing their plans for integrating campus systems with XSEDE resources and partners at other campuses. Panel members will also discuss the use cases developed by the Campus Bridging team with the Architecture and Design team.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"10 1","pages":"67:1"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77764821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What is campus bridging and what is XSEDE doing about it?","authors":"C. Stewart, R. Knepper, J. Ferguson, Felix Bachmann, Ian T Foster, A. Grimshaw, Victor Hazlewood, D. Lifka","doi":"10.1145/2335755.2335844","DOIUrl":"https://doi.org/10.1145/2335755.2335844","url":null,"abstract":"The term \"campus bridging\" was first used in the charge given to an NSF Advisory Committee for Cyberinfrastructure task force. That task force developed this description of campus bridging:\u0000 \"Campus bridging is the seamlessly integrated use of cyberinfrastructure operated by a scientist or engineer with other cyberinfrastructure on the scientist's campus, at other campuses, and at the regional, national, and international levels as if they were proximate to the scientist, and when working within the context of a Virtual Organization (VO) make the 'virtual' aspect of the organization irrelevant (or helpful) to the work of the VO.\"\u0000 Campus bridging is more a viewpoint and a set of approaches to usability, software, and information concerns than a particular set of tools or software. We outline here several specific use cases that have been identified as priorities for XSEDE in the next four years. These priorities include documentation, deployment of software used entirely outside of XSEDE, and software that helps bridge from individual researcher to campus to XSEDE cyberinfrastructure. We also describe early pilot tests and means by which the user community may stay informed of campus bridging activities and participate in the implementation of Campus Bridging tools created by XSEDE. Metrics are still being developed, and will include (1) the number of campuses that adopt and use Campus Bridging tools developed by XSEDE and (2) the number of and extent to which XSEDE-developed Campus Bridging tools are adopted among other CI projects.","PeriodicalId":93364,"journal":{"name":"Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)","volume":"28 1","pages":"47:1-47:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88046151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}