Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery最新文献_第5页

Scaling a code in the human dimension 在人的维度上扩展代码

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484782

M. Turk

引用次数: 16

An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulations 纠错码对gpu加速分子动力学模拟影响的研究

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484774

R. Walker, Robin M. Betz

{"title":"An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulations","authors":"R. Walker, Robin M. Betz","doi":"10.1145/2484762.2484774","DOIUrl":"https://doi.org/10.1145/2484762.2484774","url":null,"abstract":"Molecular dynamics (MD) simulations rely on the accurate evaluation and integration of Newton's equations of motion to propagate the positions of atoms in proteins during a simulation. As such, one can expect them to be sensitive to any form of numerical error that may occur during a simulation. Increasingly graphics processing units (GPUs) are being used to accelerate MD simulations. Current GPU architectures designed for HPC applications support error correcting codes (ECC) that detect and correct single bit-flip error events in GPU memory; however, this error checking carries a penalty in terms of simulation speed. ECC is also a major distinguishing feature between HPC NVIDIA Tesla cards and the considerably more cost-effective NVIDIA GeForce gaming cards. An argument often put forward for not using GeForce cards is that the results are unreliable due to the lack of ECC. In an initial attempt to quantify these concerns, an investigation of the effects of ECC on GPU-accelerated MD simulations using the AMBER software was conducted on 720 GPUs of the XSEDE supercomputer Keeneland with and without ECC. While the data collected are insufficient to make solid conclusions and more extensive testing is needed to provide quantitative statistics, the absence of ECC events and lack of any silent errors in all the simulations conducted to date suggest that these errors are exceedingly rare and as such the time and memory penalty of ECC may outweigh the utility of error checking functionality. This is particularly true in the case of large scale HPC runs where simulation is more likely to be interrupted by a node or storage failure and thus reducing the simulation wall clock time by turning ECC off may actually reduce the overall simulation failure rate.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"102 4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125970250","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: 5

A sustainable national gateway for biological computation 一个可持续发展的国家生物计算门户

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484817

James Taylor, A. Nekrutenko, Nate Coraor, Philip D. Blood, A. Ropelewski, Zhihui Zhang, J. Palencia, S. Sanielevici, J. Yanovich, R. Budden

引用次数: 1

The institute for cyber-enabled research: regional organization to promote computation in science 网络研究协会:促进科学计算的区域组织

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484798

D. Colbry, B. Punch, Wolfgang Bauer

引用次数: 2

Using Gordon to accelerate LHC science 利用戈登来加速LHC的研究

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484834

R. Wagner, M. Tatineni, Eva Hocks, K. Yoshimoto, Scott Sakai, M. Norman, B. Bockelman, I. Sfiligoi, M. Tadel, J. Letts, F. Würthwein, L. Bauerdick

引用次数: 3

Scalable spectral transforms at petascale 千兆级的可伸缩光谱变换

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484810

D. Pekurovsky

引用次数: 0

Hadoop deployment and performance on Gordon data intensive supercomputer Hadoop在Gordon数据密集型超级计算机上的部署和性能

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484831

M. Tatineni, J. Greenberg, R. Wagner, Eva Hocks, Christopher Irving

引用次数: 4

SocialMapExplorer: visualizing social networks of massively multiplayer online games in temporal-geographic space SocialMapExplorer:在时间地理空间中可视化大型多人在线游戏的社交网络

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484805

Y. D. Cai, Channing Brown, Iftekhar Ahmed, Yannick Atouba Ada, Andrew Pilny, M. S. Poole

{"title":"SocialMapExplorer: visualizing social networks of massively multiplayer online games in temporal-geographic space","authors":"Y. D. Cai, Channing Brown, Iftekhar Ahmed, Yannick Atouba Ada, Andrew Pilny, M. S. Poole","doi":"10.1145/2484762.2484805","DOIUrl":"https://doi.org/10.1145/2484762.2484805","url":null,"abstract":"Massively Multiplayer Online Games (MMOGs) provide unique opportunities to investigate large social networks, such as player (working-group), trading, and communication (chat) networks. This paper presents a visualization tool -- SocialMapExplorer - that allows users to explore these networks over temporal-geographic space. Implemented on the GoogleMap framework, this web-based interactive tool applies visual features, including color, size, shape, weight and font, to represent various network features. Unlike other similar tools, SocialMapExplorer visualizes data on a real map and couples time and spatial information with other attributes. To meet the challenge of intensive computation, this tool runs on high performance computers. Three modules have been implemented: (1) NetViewer that analyzes network dynamics by visualizing social networks in time series; (2) GroupDetector that investigates group assembly and evolution by tracing groups in visualized data flow; and (3) CorrelationFinder that studies the correlation between selected census variables (such as age, gender, race, population, income, education, occupation, and marital status) and game-play variables (such as play time, play frequency, achievement, and loss) by overlapping the measurements of census data and game log data. We performed this study on EverQuestII (EQII) game logs. This demonstration of the tool shows how it can help us discover events that trigger a group to emerge, shrink, and expand, and explore the relationship between census data and game data. This paper presents the design of this visualization tool, demonstrates its functions on real game data, and discusses its applications to virtual social network analysis associated with temporal-geographic space.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"05 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130482883","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: 3

Embedding CIPRES science gateway capabilities in phylogenetics software environments 在系统发育软件环境中嵌入CIPRES科学网关功能

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484806

Mark A. Miller, Terri Schwartz, W. Pfeiffer

{"title":"Embedding CIPRES science gateway capabilities in phylogenetics software environments","authors":"Mark A. Miller, Terri Schwartz, W. Pfeiffer","doi":"10.1145/2484762.2484806","DOIUrl":"https://doi.org/10.1145/2484762.2484806","url":null,"abstract":"The explosive growth in DNA sequence data over the past decade makes it possible to clarify evolutionary relationships among all living things at an unprecedented level of resolution. Phylogenetic inference codes are computationally intensive, so turning this wealth of DNA sequence data into new insights about evolution requires access to high performance computing (HPC) resources. The CIPRES Science Gateway (CSG) was designed to meet this need by providing browser-based access to phylogenetic codes run on XSEDE compute resources. The CSG has lowered the barrier for access to HPC resources for biologists worldwide, supporting more than 6,100 users and enabling more than 600 publications over the past three years. Here we describe plans to create a new set of public CSG web services that can be accessed by any developer through a programmatic interface. These services will allow us to embed access to XSEDE resources within well-established phylogenetics software packages, thus leveraging the investments by developers in creating these rich work environments and by users in learning to use them. The services will also allow any developer with modest scripting skills to access and use CSG capabilities outside of the current browser interface. Our goal in creating these services is to allow scientists to conduct analyses without leaving their preferred work environment, whether that is a complex desktop application, a set of ad hoc scripted workflows, or the existing CSG browser interface. This paper describes the architectural design of the CSG web services, identifies potential issues that will be addressed in exposing programmatic access to HPC resources, and describes plans to embed the CSG web services in eight popular community applications.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125837740","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: 2

The influence of an applied heat flux on the violence of reaction of an explosive device 施加的热流对爆炸装置反应强度的影响

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484786

Monica Hall, Jacqueline C. Beckvermit, C. Wight, T. Harman, M. Berzins

引用次数: 3