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":"Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations: sampling for the 99%","authors":"R. Walker, Levi C. T. Pierce, Romelia Salomón-Ferrer","doi":"10.1145/2335755.2335810","DOIUrl":"https://doi.org/10.1145/2335755.2335810","url":null,"abstract":"This talk will cover recent developments in the acceleration of Molecular Dynamics Simulations using NVIDIA Graphics Processing units with the AMBER software package. In particular it will focus on recent algorithmic improvements aimed at accelerating the rate at which phase space is sampled. A recent success has been the reproduction and extension of key results from the DE Shaw 1 millisecond Anton MD simulation of BPTI (Science, Vol. 330 no. 6002 pp. 341-346) with just 2.5 days of dihedral boosted AMD sampling on a single GPU workstation, (Pierce L, Walker R. C. et al. JCTC, 2012 in review). These results show that with careful algorithm design it is possible to obtain sampling of rare biologically relevant events that occur on the millisecond timescale using just a single $500 GTX580 Graphics Card and a desktop workstation. Additional developments highlighted will include the acceleration of AMBER MD simulations using graphics processing units including Amazon EC2 and Microsoft Azure Cloud based automated ensemble calculations, a new precision model optimized for the upcoming Kepler architecture (Walker R. C. et al, JCP, 2012, in prep) as well as approaches for running large scale multi-dimensional GPU accelerated replica exchange calculations on Keeneland and BlueWaters.","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":"19 1","pages":"15:1"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87696802","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":"Conducting K-12 outreach to evoke early interest in IT, science, and advanced technology","authors":"Kristy A. Kallback-Rose, K. Seiffert, D. Antolovic, Theres Miller, Robert J. Ping, C. Stewart","doi":"10.1145/2335755.2335853","DOIUrl":"https://doi.org/10.1145/2335755.2335853","url":null,"abstract":"The Indiana University Pervasive Technology Institute has engaged for several years in K-12 Education, Outreach and Training (EOT) events related to technology in general and computing in particular. In each event we strive to positively influence children's perception of science and technology. We view K-12 EOT as a channel for technical professionals to engage young people in the pursuit of scientific and technical understanding. Our goal is for students to see these subjects as interesting, exciting and worth further pursuit. By providing opportunities for pre-college students to engage in science, technology, engineering and mathematics (STEM) activities first hand, we hope to influence their choices of careers and field-of-study later in life.\u0000 In this paper we give an account of our experiences with providing EOT: we describe several of our workshops and events; we provide details regarding techniques that we found to be successful in working with both students and instructors; we discuss program costs and logistics; and we describe our plans for the future.","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":"55:1-55:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83855886","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":"Excited states in lattice QCD using the stochastic LapH method","authors":"C. Morningstar, J. Bulava, J. Foley, K. Juge, C. H. Wong","doi":"10.1145/2335755.2335824","DOIUrl":"https://doi.org/10.1145/2335755.2335824","url":null,"abstract":"A new method for computing the mass spectrum of excited baryons and mesons from the temporal correlations of quantum-field operators in quantum chromodynamics is described. The correlations are determined using Markovchain Monte Carlo estimates of QCD path integrals formulated on an anisotropic space-time lattice. Access to the excited states of interest requires determinations of lower-lying multi-hadron state energies, necessitating the use of multi-hadron operators. Evaluating the correlations of such multi-hadron operators is difficult with standard methods. A new stochastic method of treating the low-lying modes of quark propagation which exploits a new procedure for spatially-smearing quark fields, known as Laplacian Heavi-side smearing, makes such calculations possible for the first time.","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":"112 1","pages":"28:1-28:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89347852","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 the XSEDE supercomputing and visualization resources to improve tornado prediction using data mining","authors":"Bradley Pirtle, Ross Kimes, Amy McGovern, Rodger A. Brown","doi":"10.1145/2335755.2335831","DOIUrl":"https://doi.org/10.1145/2335755.2335831","url":null,"abstract":"In this paper we introduce the use of XSEDE resources and mathematical models for the simulation of tornadoes, as well as novel techniques for analyzing the results of these simulations.","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":"21 1","pages":"35:1-35:2"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82001229","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":"Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations","authors":"Yuxing Peng, Christopher Knight, Philip D. Blood, Lonnie D. Crosby, G. Voth","doi":"10.1145/2335755.2335833","DOIUrl":"https://doi.org/10.1145/2335755.2335833","url":null,"abstract":"Conducting molecular dynamics (MD) simulations involving chemical reactions in large-scale condensed phase systems (liquids, proteins, fuel cells, etc...) is a computationally prohibitive task even though many new ab initio based methodologies (i.e., AIMD, QM/MM) have been developed. Chemical processes occur over a range of length scales and are coupled to slow (long time scale) system motions, which make adequate sampling a challenge. Multistate methodologies, such as the multistate empirical valence bond (MS-EVB) method, which are based on effective force fields, are more computationally efficient and enable the simulation of chemical reactions over the necessary time and length scales to properly converge statistical properties.\u0000 The typical parallel scaling bottleneck in both reactive and nonreactive all-atom MD simulations is the accurate treatment of long-range electrostatic interactions. Currently, Ewald-type algorithms rely on three-dimensional Fast Fourier Transform (3D-FFT) calculations. The parallel scaling of these 3D-FFT calculations can be severely degraded at higher processor counts due to necessary MPI all-to-all communication. This poses an even bigger problem in MS-EVB calculations, since the electrostatics, and hence the 3D-FFT, must be evaluated many times during a single time step.\u0000 Due to the limited scaling of the 3D-FFT in MD simulations, the traditional single-program-multiple-data (SPMD) parallelism model is only able to utilize several hundred CPU cores, even for very large systems. However, with a proper implementation of a multi-program (MP) model, large systems can scale to thousands of CPU cores. This paper will discuss recent efforts in collaboration with XSEDE advanced support to implement the MS-EVB model in the scalable LAMMPS MD code, and to further improve parallel scaling by implementing MP parallelization algorithms in LAMMPS. These algorithms improve parallel scaling in both the standard LAMMPS code and LAMMPS with MS-EVB, thus facilitating the efficient simulation of large-scale condensed phase systems, which include the ability to model chemical reactions.","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":"62 1","pages":"37:1-37:7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91306170","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 high throughput workflow environment for cosmological simulations","authors":"B. Erickson, Raminderjeet Singh, A. Evrard, M. Becker, M. Busha, A. Kravtsov, S. Marru, M. Pierce, R. Wechsler","doi":"10.1145/2335755.2335830","DOIUrl":"https://doi.org/10.1145/2335755.2335830","url":null,"abstract":"The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 1010-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manual management.","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":"24 1","pages":"34:1-34:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90514585","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 kerberized lustre over the WAN for high energy physics data","authors":"J. Palencia, R. Budden, Kathy Benninger, J. Rodriguez, J. Dilascio, D. Bourilkov, P. Avery, Mengxing Cheng, Yu Fu, Bockjoo Kim, D. Oliver, Daniel Majchrzak, D. Dykstra, N. Seenu, D. Shrum, J. Wilgenbusch","doi":"10.1145/2335755.2335803","DOIUrl":"https://doi.org/10.1145/2335755.2335803","url":null,"abstract":"This paper reports the design and implementation of a secure, wide area network, distributed filesystem by the ExTENCI project (Extending Science Through Enhanced National Cyber Infrastructure) based on lustre. The filesystem is used for remote access to analysis data from the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC), and from the Lattice Quantum ChromoDynamics (LQCD) project. Security is provided for by kerberos and reinforced with additional finegrained control using lustre ACLs and quotas. We show the impact of using kerberized lustre on the IO rates of CMS and LQCD applications on client nodes, both real and virtual. Pre-configured images of lustre virtual clients containing the complete software stack ease the difficulty of managing these 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":"48 1","pages":"12:1-12:7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78109752","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":"Multiscale modeling of high explosives for transportation accidents","authors":"Joseph R. Peterson, Jacqueline C. Beckvermit, T. Harman, M. Berzins, C. Wight","doi":"10.1145/2335755.2335828","DOIUrl":"https://doi.org/10.1145/2335755.2335828","url":null,"abstract":"The development of a reaction model to simulate the accidental detonation of a large array of seismic boosters in a semi-truck subject to fire is considered. To test this model large scale simulations of explosions and detonations were performed by leveraging the massively parallel capabilities of the Uintah Computational Framework and the XSEDE computational resources. Computed stress profiles in bulk-scale explosive materials were validated using compaction simulations of hundred micron scale particles and found to compare favorably with experimental data. A validation study of reaction models for deflagration and detonation showed that computational grid cell sizes up to 10 mm could be used without loss of fidelity. The Uintah Computational Framework shows linear scaling up to 180K cores which combined with coarse resolution and validated models will now enable simulations of semi-truck scale transportation accidents for the first time.","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":"136 1","pages":"32:1-32:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80506374","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":"WaterHUB: a resource for students and educators for learning hydrology","authors":"V. Merwade, W. Feng, Lan Zhao, Carol X. Song","doi":"10.1145/2335755.2335857","DOIUrl":"https://doi.org/10.1145/2335755.2335857","url":null,"abstract":"The study of surface water hydrology involves understanding the occurrence, distribution and movement of water on the surface of the earth. Because of human impacts in the form of landuse change, the hydrologic processes at one geographic location may be different than other locations under same or different climatic settings. As a result, a tool that educators and students can use to explore hydrology through observed data and computational simulations is needed. The objective of this paper is to present a prototype model sharing and data exploration tool that can be used for education as well as for research. A GIS-enabled model sharing platform for Soil Water Assessment Tool (SWAT), called SWATShare, is developed that enables students to not only run model simulations online, but also publish, share and visualize model results to study the impact of land use change on hydrology at watershed scale. SWATShare is developed as a part of the WaterHUB system that is built by combining Purdue's HUBzero technology and TeraGrid/XSEDE computation resources. Experience of developing and using SWATShare in a classroom will be presented and discussed. In addition, the development and implementation plan of another tool, called Hydrology Exploration Tool, will be presented.","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":"5 1","pages":"59:1-59:4"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80821155","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":"Monte Carlo strategies for first-principles simulations of elemental systems","authors":"L. Gelb","doi":"10.1145/2335755.2335821","DOIUrl":"https://doi.org/10.1145/2335755.2335821","url":null,"abstract":"We discuss the application of atomistic Monte Carlo simulation based on electronic structure calculations to elemental systems such as metals and alloys. As in prior work in this area, an approximate \"pre-sampling\" potential is used to generate large moves with a high probability of acceptance. Even with such a scheme, however, such simulations are extremely expensive and may benefit from algorithmic developments that improve acceptance rates and/or enable additional parallelization.\u0000 Here we consider several such developments. The first of these is a three-level hybrid algorithm in which two pre-sampling potentials are used. The lowest level is an empirical potential, and the \"middle\" level uses a low-quality density functional theory. The efficiency of the multistage algorithm is analyzed and an example application is given.\u0000 Two other schemes for reducing overall run-time are also considered. In the first, the Multiple-try Monte Carlo algorithm, a series of moves are attempted in parallel, with the choice of the next state in the chain made by using all the information gathered. This is found to be a poor choice for simulations of this type. In the second scheme, \"tree sampling,\" multiple trial moves are made in parallel such that if the first is rejected, the second is ready and can be considered immediately. Performance of this scheme is shown to be quite effective under certain reasonable run parameters.","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":"25:1-25:7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82955157","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}