Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery最新文献_第7页

The condo of condos 公寓中的公寓

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484775

James B. Bottum, R. Marinshaw, Henry Neeman, James Pepin, J. V. Oehsen

{"title":"The condo of condos","authors":"James B. Bottum, R. Marinshaw, Henry Neeman, James Pepin, J. V. Oehsen","doi":"10.1145/2484762.2484775","DOIUrl":"https://doi.org/10.1145/2484762.2484775","url":null,"abstract":"University-located computational and data storage resources are increasingly being aggregated into shared university-level systems that are dubbed \"condominium clusters.\" This session will describe the \"Condo of Condos,\" a \"consortium of the willing\" that is working together to extend this condominium model both locally and across the consortium. By aggregating resources and expertise at the institutional level it will be possible to create distributed technical and support operations that provide faculty and students with methods to leverage a much larger and robust set of resources. Partnering with Internet2, the consortium will use the Innovation Platform to connect campuses and allow high performance interconnections through Science DMZs that can be built and broken down in ad-hoc ways using SDN. The ability to develop these network connections, coupled with the project's community building characteristics, will be a model for \"team science\" that can be extended and replicated nationally. By leveraging existing local and national computing resources (XSEDE and Open Science Grid), we will enable science and education deployments that are not possible today, making complex collaborations with computational needs routine. This project will be transformative for campus IT and will create a community of practitioners that shares resources, experience, and expertise to facilitate new knowledge and discovery.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"25 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":"129909165","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

New atomic resolution insights into dynamic protein-carbohydrate interactions enabled by high-performance computing 新的原子分辨率洞察动态蛋白质-碳水化合物的相互作用，使高性能计算

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484770

Olgun Guvench

{"title":"New atomic resolution insights into dynamic protein-carbohydrate interactions enabled by high-performance computing","authors":"Olgun Guvench","doi":"10.1145/2484762.2484770","DOIUrl":"https://doi.org/10.1145/2484762.2484770","url":null,"abstract":"Protein-carbohydrate interactions are a critical component of cellular structure and function. However, the inherent flexibility of biological carbohydrate polymers and the microheterogeneity resulting from their non-template-based biosynthesis complicate their study using experimental methods. Therefore, simulation approaches, and all-atom explicit-solvent molecular dynamics (MD) simulations in particular, provide an enabling technology for advancing the understanding of protein-carbohydrate interactions at the atomic level of resolution. Here, we detail our recent MD studies on the CD44 receptor performed using the highly-parallel NAMD MD engine with the CHARMM all-atom force field on the Kraken supercomputer. With these technologies, simulation time lengths of hundreds of nanoseconds are routinely reached. Combining both regular unbiased MD and advanced MD methods that bias sampling to important degrees of freedom, new insights are obtained into the function of CD44, which is both a receptor for large carbohydrate molecules in the extracellular matrix and whose own function is modulated by covalent attachment of branched carbohydrates to make CD44 a glycoprotein. In particular, the simulations explain, for the first time, the molecular mechanism of the experimentally-observed order-to-disorder transition in CD44 that is known to enhance its carbohydrate binding affinity. Additionally, the simulations explain, again for the first time, the molecular mechanism through which particular monosaccharides in branched carbohydrates covalently attached to CD44 have been experimentally observed to block CD44 binding to extracellular matrix carbohydrates. These insights expand the understanding of how CD44 performs its biological functions, which include cell adhesion, migration, and vascular trafficking. Importantly, these new insights enabled by leading-edge simulation and computing technologies have not been accessible by existing experimental methods.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"62 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":"130098087","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: 0

A high-level framework for parallelizing legacy applications for multiple platforms 为多个平台并行处理遗留应用程序的高级框架

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484829

R. Arora, Ejenio Capetillo, P. Bangalore, M. Mernik

{"title":"A high-level framework for parallelizing legacy applications for multiple platforms","authors":"R. Arora, Ejenio Capetillo, P. Bangalore, M. Mernik","doi":"10.1145/2484762.2484829","DOIUrl":"https://doi.org/10.1145/2484762.2484829","url":null,"abstract":"The tremendous growth and diversification in the area of computer architectures has contributed towards an upsurge in the number of parallel programing paradigms, languages, and environments. However, it is often difficult for domain-experts to develop expertise in multiple programming paradigms and languages in order to write performance-oriented parallel applications. Several active research projects aim at reducing the burden on programmers by raising the level of abstraction of parallel programming. However, a majority of such research projects either entail manual invasive reengineering of existing code to insert new directives for parallelization or force conformance to specific interfaces. Some systems require that the programmers rewrite their entire application in a new parallel programing language or a domain-specific language. Moreover, only a few research projects are addressing the need of a single framework for generating parallel applications for multiple hardware platforms or doing hybrid programming. This paper presents a high-level framework for parallelizing existing serial applications for multiple target platforms. The framework, currently in its prototype stage, can semi-automatically generate parallel applications for systems with both distributed-memory architectures and shared-memory architectures through MPI, OpenMP, and hybrid programming. For all the test cases considered so far, the performance of the generated parallel applications is comparable to that of the manually written parallel versions of the applications. Our approach enhances the productivity of the end-users as they are not required to learn any low-level parallel programming, shortens the parallel application development cycle for multiple platforms, and preserves the existing version of serial applications.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"74 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":"132944245","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

Referee consensus: a platform technology for nonlinear optimization 裁判共识:一种非线性优化平台技术

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484789

D. Krieger, M. McNeil, Jinyin Zhang, W. Schneider, Xin Li, D. Okonkwo

{"title":"Referee consensus: a platform technology for nonlinear optimization","authors":"D. Krieger, M. McNeil, Jinyin Zhang, W. Schneider, Xin Li, D. Okonkwo","doi":"10.1145/2484762.2484789","DOIUrl":"https://doi.org/10.1145/2484762.2484789","url":null,"abstract":"Electrical current flow within populations of neurons is a fundamental constituent of brain function. The resulting fluctuating magnetic fields may be sampled noninvasively with an array of magnetic field detectors positioned outside the head. This is magnetoencephalography (MEG). Each source may be characterized by 5-6 parameters, the xyz location and the xyz direction. The magnetic field measurements are nonlinear in the location parameters; hence the source location is identifiable only via search of the brain volume. When there is one or a very few sources, this may be practical; solutions for the general problem have poor resolution and are readily defeated. Referee consensus is a novel cost function which enables identification of a source at one location at a time regardless of the number and location of other sources. This \"independence\" enables solution of the general problem and insures suitability to grid computing. The computation scales linearly with the number of nonlinear parameters. Since the method is not readily disrupted by noise or the presence of multiple unknown source, it is applicable to single trial data. MEG recordings were obtained from 26 volunteers while they performed a cognitive task The single trial recordings were processed on the Open Science Grid (≈300 CPU hours/sec of data) On average 500+ active sources were found throughout. Statistical analyses demonstrated 1-2 mm resolving power and high confidence findings (p < 0.0001) when testing for task specific information in the extracted virtual recordings. Referee consensus is applicable to a variety of systems in addition to MEG, e.g. the connectivity problem, the blurred image, both passive and active SONAR, and seismic tomography. Applicability requires (1) that the measurements be linear in at least one of the source parameters and (2) that a sequence of measurements in time be obtained.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"8 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":"115636259","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: 6

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery 极端科学与工程发现环境:探索之门会议论文集

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762

Nancy Wilkins-Diehr

引用次数: 23

Supercomputer assisted generation of machine learning agents for the calibration of building energy models 超级计算机辅助生成机器学习代理，用于校准建筑能源模型

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484818

J. Sanyal, J. New, Richard E. Edwards

{"title":"Supercomputer assisted generation of machine learning agents for the calibration of building energy models","authors":"J. Sanyal, J. New, Richard E. Edwards","doi":"10.1145/2484762.2484818","DOIUrl":"https://doi.org/10.1145/2484762.2484818","url":null,"abstract":"Building Energy Modeling (BEM) is an approach to model the energy usage in buildings for design and retrofit purposes. EnergyPlus is the flagship Department of Energy software that performs BEM for different types of buildings. The input to EnergyPlus can often extend in the order of a few thousand parameters which have to be calibrated manually by an expert for realistic energy modeling. This makes it challenging and expensive thereby making building energy modeling unfeasible for smaller projects. In this paper, we describe the \"Autotune\" research which employs machine learning algorithms to generate agents for the different kinds of standard reference buildings in the U.S. building stock. The parametric space and the variety of building locations and types make this a challenging computational problem necessitating the use of supercomputers. Millions of EnergyPlus simulations are run on supercomputers which are subsequently used to train machine learning algorithms to generate agents. These agents, once created, can then run in a fraction of the time thereby allowing cost-effective calibration of building models.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"13 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":"124896381","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: 15

Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures UltraScan科学网关的改进，使计算工作能够在大规模和基于开放标准的网络基础设施上进行

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484800

M. S. Memon, N. Attig, Gary Gorbet, Lahiru Gunathilake, M. Riedel, T. Lippert, S. Marru, A. Grimshaw, F. Janetzko, B. Demeler, Raminderjeet Singh

{"title":"Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures","authors":"M. S. Memon, N. Attig, Gary Gorbet, Lahiru Gunathilake, M. Riedel, T. Lippert, S. Marru, A. Grimshaw, F. Janetzko, B. Demeler, Raminderjeet Singh","doi":"10.1145/2484762.2484800","DOIUrl":"https://doi.org/10.1145/2484762.2484800","url":null,"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 (AUC) experiments. Since 2006, the UltraScan scientific gateway has been used with ordinary Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. Unlike other applications, UltraScan is implemented on a gateway architecture and leverages the power of supercomputing to extract very high resolution information from the experimental data. In this contribution, we will focus on several improvements of the UltraScan scientific gateway that enable a standardized job submission and management to computational resources while retaining its lightweight design in order to not disturb the established workflows of its end-users. This paper further presents a walkthrough of the architectural design including one real installation deployment of UltraScan in Europe. The aim is to provide evidence for the added value of open standards and resulting interoperability enabling not only UltraScan application submissions to resources offered in the US cyber infrastructure Extreme Science and Engineering Discovery Environment (XSEDE), but also submissions to similar infrastructures in Europe and around the world. The use of the Apache Airavata framework for scientific gateways within our approach bears the potential to have an impact on several other scientific gateways too.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"11 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":"128089224","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: 6

NCAR storage accounting and analysis possibilities NCAR存储核算和分析的可能性

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI: 10.1145/2484762.2484802

David L. Hart, P. Gillman, Erich Thanhardt

引用次数: 4

Alleviating the scaling problem of cosmological hydrodynamic simulations with HECA 用HECA缓解宇宙流体力学模拟的标度问题

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2012-07-15 DOI: 10.1145/2484762.2484776

L. Oser, M. Gajbe, K. Nagamine, G. Bryan, J. Ostriker, R. Cen

引用次数: 0