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Accelerating science gateway development with Web 2.0 and Swift 用web2.0和Swift加速科学网关的开发
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838597
Wenjun Wu, T. Uram, M. Wilde, M. Hereld, M. Papka
{"title":"Accelerating science gateway development with Web 2.0 and Swift","authors":"Wenjun Wu, T. Uram, M. Wilde, M. Hereld, M. Papka","doi":"10.1145/1838574.1838597","DOIUrl":"https://doi.org/10.1145/1838574.1838597","url":null,"abstract":"A Science Gateway is a computational web portal that enables scientists to run scientific simulations, data analysis, and visualization through their web browsers. The major problem of building a science gateway on TeraGrid is how to deploy scientific applications rapidly on computational resources and expose these applications as web services to scientists. In this paper we propose a novel science application framework that can greatly accelerate the development cycle of science gateway systems. This framework enables science gateway developers to import their domain-specific scientific workflow scripts and generate Web 2.0 gadgets for running these application workflows and visualizing the output from workflow executions without writing any web related code. By assembling these application-specific gadgets and some common gadgets predefined in the framework for workflow management, developers can easily set up a customized computational science gateway to meet community requirements. We demonstrate the utility of the framework with an example from computational biochemistry.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"132 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132158838","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}
引用次数: 14
DASH-IO: an empirical study of flash-based IO for HPC DASH-IO:基于闪存的高性能计算IO的实证研究
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838584
J. He, Jeffrey Bennett, A. Snavely
{"title":"DASH-IO: an empirical study of flash-based IO for HPC","authors":"J. He, Jeffrey Bennett, A. Snavely","doi":"10.1145/1838574.1838584","DOIUrl":"https://doi.org/10.1145/1838574.1838584","url":null,"abstract":"HPC applications are becoming more and more data-intensive as a function of ever-growing simulation sizes and burgeoning data-acquisition. Unfortunately, the storage hierarchy of the existing HPC architecture has a 5-order-of-magnitude latency gap between main memory and spinning disks and cannot respond to the new data challenge well. Flash-based SSDs (Solid State Disks) are promising to fill the gap with their 2-order-of-magnitude lower latency. However, since all the existing hardware and software were designed without flash in mind, the question is how to integrate the new technology into existing architectures. DASH is a new Teragrid resource aggressively leveraging flash technology (and also distributed shared memory technology) to fill the latency gap. To explore the potentials and issues of integrating flash into today's HPC systems, we swept a large parameter space by fast and reliable measurements to investigate varying design options. We here provide some lessons we learned and also suggestions for future architecture design. Our results show that performance can be improved by 9x with appropriate existing technologies and probably further improved by future ones.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"57 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114013108","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}
引用次数: 26
Conjugating science gateways and grid portals into e-collaboration environments: the Liferay and GENIUS/EnginFrame use case 将科学网关和网格门户结合到电子协作环境中:Liferay和GENIUS/EnginFrame用例
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838575
R. Barbera, G. Rocca, R. Rotondo, A. Falzone, P. Maggi, N. Venuti
{"title":"Conjugating science gateways and grid portals into e-collaboration environments: the Liferay and GENIUS/EnginFrame use case","authors":"R. Barbera, G. Rocca, R. Rotondo, A. Falzone, P. Maggi, N. Venuti","doi":"10.1145/1838574.1838575","DOIUrl":"https://doi.org/10.1145/1838574.1838575","url":null,"abstract":"Nowadays, e-Science uses sophisticated high level tools that allow scientists separated by long distances and belonging to different administrative domains to work on the same project. Among them, Science Gateways and general purpose Grid Portals are becoming very popular. The first ones are generally customized for a given Virtual Research Community (VRC) while the second ones lack very often the possibility to be easily adapted to specific needs. In this paper we present a new e-Collaboration environment that merges the concepts of Science Gateway and Grid Portal. An implementation case using Liferay and GENIUS/Enginframe technologies will be shown.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121240374","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}
引用次数: 14
Uintah: a scalable framework for hazard analysis untah:可扩展的危害分析框架
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838577
M. Berzins, J. Luitjens, Qingyu Meng, T. Harman, C. Wight, Joseph R. Peterson
{"title":"Uintah: a scalable framework for hazard analysis","authors":"M. Berzins, J. Luitjens, Qingyu Meng, T. Harman, C. Wight, Joseph R. Peterson","doi":"10.1145/1838574.1838577","DOIUrl":"https://doi.org/10.1145/1838574.1838577","url":null,"abstract":"The Uintah Software system was developed to provide an environment for solving a fluid-structure interaction problems on structured adaptive grids on large-scale, long-running, data-intensive problems. Uintah uses a novel asynchronous task-based approach with fully automated load balancing. The application of Uintah to a petascale problem in hazard analysis arising from \"sympathetic\" explosions in which the collective interactions of a large ensemble of explosives results in dramatically increased explosion violence, is considered. The advances in scalability and combustion modeling needed to begin to solve this problem are discussed and illustrated by prototypical computational results.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124713322","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}
引用次数: 66
Petascale I/O using HDF-5 千兆级I/O使用HDF-5
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838585
Nicholas Malaya, K. Schulz, R. Moser
{"title":"Petascale I/O using HDF-5","authors":"Nicholas Malaya, K. Schulz, R. Moser","doi":"10.1145/1838574.1838585","DOIUrl":"https://doi.org/10.1145/1838574.1838585","url":null,"abstract":"Our work is focused on performing Petascale Direct Numerical Simulations (DNS) of turbulent flows. An essential performance component of these simulations are the restart files, as a single petascale simulation will write on the order of a petabyte. Petascale I/O requires both performance and dataset maintainability, for archival and post processing of the velocity fields for statistics. This paper presents benchmarks and comparisons between a single shared file written using the HDF-5 library and a POSIX compliant I/O library on several top-10 machines and filesystems. It is shown that a properly tuned HDF-5 routine provides strong I/O performance, which coupled with the metadata handling and portability available to the file format, indicates that the lower performance provides a worthy tradeoff. The benchmarks presented were provided from real turbulence simulations and required extensive tuning for different platforms, and in particular, between different file systems (GPFS and Lustre).","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"120 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132519195","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}
引用次数: 1
End-to-end framework for fault management for open source clusters: Ranger 用于开源集群故障管理的端到端框架:Ranger
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838583
John L. Hammond, T. Minyard, J. Browne
{"title":"End-to-end framework for fault management for open source clusters: Ranger","authors":"John L. Hammond, T. Minyard, J. Browne","doi":"10.1145/1838574.1838583","DOIUrl":"https://doi.org/10.1145/1838574.1838583","url":null,"abstract":"The scale and complexity of both hardware and software on large open source software systems such as Ranger make occurrence of faults and failures inevitable. What is not inevitable is that they should be allowed to go undetected, nor that diagnosis and recovery from failures should continue to be largely manual and effort intensive. This paper presents a framework for end-to-end fault management for open source clusters which is being developed on Ranger, but which targets general open source software based clusters. The elements of the framework are: a rationalized system logging stack for Linux, low overhead log and status monitoring, and a multilevel suite of diagnostic analyses. This paper describes this framework, presents the accomplishments to date, the results which have been obtained with the elements of the framework which are in place, and the plans for future development including a solicitation for collaboration on the project.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129228628","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}
引用次数: 23
Open grid computing environments: advanced gateway support activities 开放网格计算环境:高级网关支持活动
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838590
M. Pierce, S. Marru, Raminderjeet Singh, Archit Kulshrestha, K. Muthuraman
{"title":"Open grid computing environments: advanced gateway support activities","authors":"M. Pierce, S. Marru, Raminderjeet Singh, Archit Kulshrestha, K. Muthuraman","doi":"10.1145/1838574.1838590","DOIUrl":"https://doi.org/10.1145/1838574.1838590","url":null,"abstract":"We describe three case studies for providing advanced support for TeraGrid Science Gateways as part of our participation in the Advanced User Support (AUS) team. These case studies include providing workflow support, robust job management, and mass job submission to existing gateways targeting computational chemistry, biophysics, and bioinformatics, respectively. Selected tools from the Open Grid Computing Environments and other projects were used, demonstrating the need for flexibility when integrating tools from multiple software providers into specific gateways' software stacks.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123404785","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}
引用次数: 25
Modelling data-driven CO2 sequestration using distributed HPC cyberinfrastructure 利用分布式高性能计算网络基础设施对数据驱动的二氧化碳封存进行建模
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838580
Y. E. Khamra, S. Jha, C. White
{"title":"Modelling data-driven CO2 sequestration using distributed HPC cyberinfrastructure","authors":"Y. E. Khamra, S. Jha, C. White","doi":"10.1145/1838574.1838580","DOIUrl":"https://doi.org/10.1145/1838574.1838580","url":null,"abstract":"In this paper we lay out the computational challenges involved in effectively simulating complex phenomena such as sequestering CO2 in oil and gas reservoirs. The challenges arise at multiple levels: (i) the computational complexity of simulating the fundamental processes; (ii) the resource requirements of the computationally demanding simulations; (iii) the need for integrating real-time data (intensive) and computationally intensive simulations; (iv) and the need to implement all of these in a robust, scalable and extensible approach. We will outline the architecture and implementation of the solution we develop in response to these requirements, and discuss results to validate claims that our solution scales to effectively solve desired problem sizes and thus provides the capability to generate novel scientific insight.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132956618","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}
引用次数: 1
A compelling case for a centralized filesystem on the TeraGrid: enhancing an astrophysical workflow with the data capacitor WAN as a test case 在TeraGrid上集中式文件系统的一个引人注目的案例:用数据电容器WAN作为测试用例增强天体物理工作流
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838587
Scott Michael, Stephen C. Simms, W. B. Breckenridge, Roger M. Smith, Matthew R. Link
{"title":"A compelling case for a centralized filesystem on the TeraGrid: enhancing an astrophysical workflow with the data capacitor WAN as a test case","authors":"Scott Michael, Stephen C. Simms, W. B. Breckenridge, Roger M. Smith, Matthew R. Link","doi":"10.1145/1838574.1838587","DOIUrl":"https://doi.org/10.1145/1838574.1838587","url":null,"abstract":"In this article we explore the utility of a centralized filesystem provided by the TeraGrid to both TeraGrid and non-TeraGrid sites. We highlight several common cases in which such a filesystem would be useful in obtaining scientific insight. We present results from a test case using Indiana University's Data Capacitor over the wide area network as a central filesystem for simulation data generated at multiple TeraGrid sites and analyzed at Mississippi State University. Statistical analysis of the I/O patterns and rates, via detailed trace records generated with VampirTrace, for both the Data Capacitor and a local Lustre filesystem are provided. The benefits of a centralized filesystem and potential hurdles in adopting such a system for both TeraGrid and non-TeraGrid sites are discussed.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"175 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124963500","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}
引用次数: 4
Performance optimization of large non-negatively constrained least squares problems with an application in biophysics 大型非负约束最小二乘问题的性能优化及其在生物物理中的应用
TeraGrid Conference Pub Date : 2010-08-02 DOI: 10.1145/1838574.1838579
E. Brookes, B. Demeler
{"title":"Performance optimization of large non-negatively constrained least squares problems with an application in biophysics","authors":"E. Brookes, B. Demeler","doi":"10.1145/1838574.1838579","DOIUrl":"https://doi.org/10.1145/1838574.1838579","url":null,"abstract":"Solving large non-negatively constrained least squares systems is frequently used in the physical sciences to estimate model parameters which best fit experimental data. Analytical Ultracentrifugation (AUC) is an important hydrodynamic experimental technique used in biophysics to characterize macromolecules and to determine parameters such as molecular weight and shape. We previously developed a parallel divide and conquer method to facilitate solving the large systems obtained from AUC experiments. New AUC instruments equipped with multi-wavelength (MWL) detectors have recently increased the data sizes by three orders of magnitude. Analyzing the MWL data requires significant compute resources. To better utilize these resources, we introduce a procedure allowing the researcher to optimize the divide and conquer scheme along a continuum from minimum wall time to minimum compute service units. We achieve our results by implementing a preprocessing stage performed on a local workstation before job submission.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"298 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114849960","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}
引用次数: 4
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