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":"A distributed memory out-of-core method on HPC clusters and its application to quantum chemistry applications","authors":"Chris Simmons, K. Schulz","doi":"10.1145/2335755.2335785","DOIUrl":"https://doi.org/10.1145/2335755.2335785","url":null,"abstract":"Out-of-core methods, which repeatedly offload data to disk in order to overcome local on-node memory constraints are encountered in a range of scientific computing disciplines, including quantum chemistry. Unfortunately, these methods do not often map nicely onto global parallel file systems employed on modern HPC clusters and can overwhelm even the most capable of file systems causing unacceptably low application performance (while also degrading I/O performance for all system users). To address this bottleneck and explore more efficient use of HPC clusters for a quantum chemistry application, CFOUR, a new MPI-based utility has been developed to support out-of-core methods on distributed memory systems. This MPI Ocore utility leverages the high-speed interconnect available on HPC clusters to offload and retrieve out-of-core records to one or more remote memory storage pools, avoiding excessive I/O transactions on local or global file systems. In this paper, we present an overview of the Ocore implementation, it's direct application within a large quantum chemistry application, and micro-benchmark and application performance results from an HPC cluster interconnected with InfiniBand.","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":"9 1","pages":"1:1-1:7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73048659","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 systematic process for efficient execution on Intel's heterogeneous computation nodes","authors":"A. Rane, J. Browne, L. Koesterke","doi":"10.1145/2335755.2335797","DOIUrl":"https://doi.org/10.1145/2335755.2335797","url":null,"abstract":"Heterogeneous architectures (mainstream CPUs with accelerators/co-processors) are expected to become more prevalent in high performance computing clusters. This paper deals specifically with attaining efficient execution on nodes which combine Intel's multicore Sandy Bridge chips with MIC manycore chips. The architecture and software stack for Intel's heterogeneous computation nodes attempt to make migration from the now common multicore chips to the many-core chips straightforward. However, specific execution characteristics are favored by these manycore chips such as making use of the wider vector instructions, minimal inter-thread conflicts, etc. Additionally manycore chips have lower clock speed and no unified last-level cache. As a result, and as we demonstrate in this paper, it will commonly be the case that not all parts of an application will execute more efficiently on the manycore chip than on the multicore chip. This paper presents a process, based on measurements of execution on Westmere-based multicore chips, which can accurately predict which code segments will execute efficiently on the manycore chips and illustrates and evaluates its application to three substantial full programs -- HOMME, MOIL and MILC. The effectiveness of the process is validated by verifying scalability of the specific functions and loops that were recommended for MIC execution on a Knights Ferry computation node.","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":"7 1","pages":"8:1-8:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80088306","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":"Multiple concurrent queries on demand: large scale video analysis in a flash memory environment as a case for humanities supercomputing","authors":"Virginia Kuhn, Alan B. Craig, R. Arora","doi":"10.1145/2335755.2335825","DOIUrl":"https://doi.org/10.1145/2335755.2335825","url":null,"abstract":"In this paper, we present an overview of our efforts in facilitating humanities research in a supercomputing environment. We discuss some of the challenges related to adapting a humanities research workflow on High Performance Computing (HPC) resources and also present an overview of the design of Large Scale Video Analytics (LSVA) project that will be deployed on Gordon supercomputer at the San Diego Supercomputing Center (SDSC).","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":"195 1","pages":"29:1-29:2"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75881533","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 made easy via Globus services","authors":"Ian T Foster, R. Kettimuthu, Stuart Martin, S. Tuecke, Daniel J. Milroy, B. Palen, T. Hauser, Jazcek Braden","doi":"10.1145/2335755.2335847","DOIUrl":"https://doi.org/10.1145/2335755.2335847","url":null,"abstract":"As science becomes more computation and data intensive, computing needs often exceed campus capacity. Thus we see a desire to scale from the local environment to other campuses, to national cyberinfrastructure providers such as XSEDE, and/or to cloud providers---in other words, to \"bridge\" to the wider world. But given the realities of limited resources, time, and expertise, campus bridging methods must be exceedingly easy to use: as easy, for example, as are Netflix and Amazon movie streaming services. We report here on experiences with a service called Globus Online, which seeks to do for campus bridging what Netflix and Amazon do for movies: that is, use powerful cloud-hosted services and simple, intuitive web interfaces to make it \"so easy that your grandparent can do it.\" Specifically, we describe Globus Transfer, which addresses the important campus bridging use case of moving or synchronizing data across institutional boundaries. We describe how Globus Transfer achieves both ease of use for researchers and ease of administration for campus IT staff. We provide technical details on the Globus solution; quantitative data on usage by more than 25 early adopter campuses; and experience reports from two early adopters, the University of Michigan and the University of Colorado Boulder.","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":"13 1","pages":"50:1-50:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73935842","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 Eclipse parallel tools platform: toward an integrated development environment for XSEDE resources","authors":"Jay Alameda, Wyatt Spear, J. Overbey, K. Huck, G. R. Watson, Beth Tibbitts","doi":"10.1145/2335755.2335845","DOIUrl":"https://doi.org/10.1145/2335755.2335845","url":null,"abstract":"Eclipse [1] is a widely used, open source integrated development environment that includes support for C, C++, Fortran, and Python. The Parallel Tools Platform (PTP) [2] extends Eclipse to support development on high performance computers. PTP allows the user to run Eclipse on her laptop, while the code is compiled, run, debugged, and profiled on a remote HPC system. PTP provides development assistance for MPI, OpenMP, and UPC; it allows users to submit jobs to the remote batch system and monitor the job queue. It also provides a visual parallel debugger.\u0000 The XSEDE community comprises a large part of PTP's user base, and we are actively working to make PTP a productive, easy-to-use development environment for the full breadth of XSEDE resources. In this paper, we will describe capabilities we have recently added to PTP to better support XSEDE resources. These capabilities include submission and monitoring of jobs on systems running Sun/Oracle Grid Engine, support for GSI authentication and MyProxy logon, support for environment modules, and integration with compilers from Cray and PGI. We will describe ongoing work and directions for future collaboration, including OpenACC support and parallel debugger integration.","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":"148 1","pages":"48:1-48:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76441663","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":"Quantum algorithms for predicting the properties of complex materials","authors":"G. Schofield, Y. Saad, J. Chelikowsky","doi":"10.1145/2335755.2335820","DOIUrl":"https://doi.org/10.1145/2335755.2335820","url":null,"abstract":"A central goal in computational materials science is to find efficient methods for solving the Kohn-Sham equation. The realization of this goal would allow one to predict properties such as phase stability, structure and optical and dielectric properties for a wide variety of materials. Typically, a solution of the Kohn-Sham equation requires computing a set of low-lying eigenpairs. Standard methods for computing such eigenpairs require two procedures: (a) maintaining the orthogonality of an approximation space, and (b) forming approximate eigenpairs with the Rayleigh-Ritz method. These two procedures scale cubically with the number of desired eigenpairs. Recently, we presented a method, applicable to any large Hermitian eigenproblem, by which the spectrum is partitioned among distinct groups of processors. This \"divide and conquer\" approach serves as a parallelization scheme at the level of the solver, making it compatible with existing schemes that parallelize at a physical level and at the level of primitive operations, e.g., matrix-vector multiplication. In addition, among all processor sets, the size of any approximation subspace is reduced, thereby reducing the cost of orthogonalization and the Rayleigh-Ritz method. We will address the key aspects of the algorithm, its implementation in real space, and demonstrate the nature of the algorithm by computing the electronic structure of a metal-semiconductor interface.","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":"17 1","pages":"24:1-24:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80853516","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":"Longitudinal user and usage patterns in the XSEDE user community","authors":"David L. Hart","doi":"10.1145/2335755.2335851","DOIUrl":"https://doi.org/10.1145/2335755.2335851","url":null,"abstract":"The XSEDE user community is often assumed to be dominated by a (mostly) fixed set of users in a largely static pecking order. This assumption is based primarily on anecdotal experience but often the only quantitative data are the consistent patterns of overall resource consumption observed at many time scales. The XSEDE accounting system offers a unique opportunity to study consumption patterns over time by project teams and individuals. This analysis shows some tendency for larger-scale consumers to remain among the larger-scale consumers; however, the XSEDE user community is much more dynamic than often assumed. In addition, small-scale user behavior over time differs distinctly from large-scale user behavior, with the \"long tail\" more often comprised of short-lived projects. We define a number of metrics for describing these patterns and consider their implications for the outreach activities and user support within XSEDE and other HPC environments.","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":"104 1","pages":"53:1-53:7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88975028","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 simulations of Langmuir cells and submesoscale eddies using XSEDE resources","authors":"L. V. Roekel, P. Hamlington, B. Fox‐Kemper","doi":"10.1145/2335755.2335816","DOIUrl":"https://doi.org/10.1145/2335755.2335816","url":null,"abstract":"A proper treatment of upper ocean mixing is an essential part of accurate climate modeling. This problem is difficult because the upper ocean is home to many competing processes. Vertical turbulent mixing acts to unstratify the water column, while lateral submesoscale eddies attempt to stratify the column. Langmuir turbulence, which often dominates the vertical mixing, is driven by an interaction of the wind stress and surface wave (Stokes) drift, while the submesoscale eddies are driven by lateral density and velocity changes. Taken together, these processes span a large range of spatial and temporal scales. They have been studied separately via theory and modeling. It has been demonstrated that the way these scales are represented in climate models has a nontrivial impact on the global climate system. The largest impact is on upper ocean processes, which filter air-sea interactions. This interaction is especially interesting, because it is the interface between nonhydrostatic and hydrostatic, quasigeostrophic and ageostrophic, and small-scale and large-scale ocean dynamics. Previous studies have resulted in parameterizations for Langmuir turbulence and submesoscale fluxes, but these parameterizations assume that there is no interaction between these important processes. In this work we have utilized a large XSEDE allocation (9 million SUs) to perform multi-scale simulations that encompass the Langmuir scale (O(10-100m)) and submesoscale eddies (O(1-10km)). One simulation includes a Stokes drift, and hence Langmuir turbulence, while the other does not.\u0000 To adequately represent such disparate spatial scales is a challenge in numerous regards. Numerical prediction algorithms must balance efficiency, scalability, and accuracy. These simulations also present a large challenge for data storage and transfer. However, the results of these simulations will influence climate modeling for decades.","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":"63 ","pages":"20:1-20:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91550353","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":"Membrane protein simulations under asymmetric ionic concentrations","authors":"Fatemeh Khalili-Araghi, B. Ziervogel, B. Roux, J. Gumbart","doi":"10.1145/2335755.2335812","DOIUrl":"https://doi.org/10.1145/2335755.2335812","url":null,"abstract":"Important cellular processes, such as cell-cell recognition, signal transduction, and transport of electrical signals are controlled by membrane proteins. Membrane proteins act as gatekeepers of the cellular environment by allowing passage of ions, small molecules, or nascent proteins under specific environmental signals such as transmembrane voltage, changes in ionic concentration, or binding of a ligand. Molecular dynamics simulations of membrane proteins, performed in a lipid bilayer environment, mimic the cellular environment by representing the solvent, lipids, and the protein in full atomistic detail. These simulations employ periodic boundary conditions in three dimensions to avoid artifacts associated with the finite size of the system. Under these conditions, the membrane protein system is surrounded by ionic solutions on either side of the membrane whose properties cannot be changed independently. We have developed a computational method that allows simulations of membrane proteins under periodic boundary condition while controlling the two ionic solutions properties independently. In this method, an energy barrier is introduced between the two adjacent unit cells and separates the two ionic solutions. The height of the barrier affects the chemical potential of the ions on each side of the barrier, and thus allows for individual control over ionic properties. During the course of the simulation, the height of the barrier is adjusted dynamically to reach the proper ionic concentration on each side. This method has been implemented in the Tcl interface of the molecular dynamics program NAMD.\u0000 We have applied this method to simulate the voltage-gated potassium channel Kv1.2 under physiological conditions, in which the extracellular solution is made of 10mM KCl and 100mM of NaCl solution, while the intracellular solution has an ionic concentration of 100mM KCl and 10mM NaCl. The simulations maintain a 1:10 and 10:1 ratio between ionic concentrations on each side. The simulations are performed under a voltage bias of 100mV and provide the first simulation of potassium channels under the exact physiological condition.\u0000 The method has also been applied to simulate ionic currents passing through OmpF, an outer membrane porin, under membrane potentials. Here we were able to accurately calculate the reversal potential of the OmpF channel in a tenfold salt gradient of 0.1 intracellular to 1M extracellular KCl. Our results agree with experimental ion conductance measurements and reproduce key features of ion permeation and selectivity of the OmpF channel. Specifically, the I-V plots obtained under asymmetric ionic solutions revealed the natural asymmetry in the channel caused by increased conductance rates observed at positive potentials, as well as the inherent cation-selectivity of the OmpF pore. Therefore, we have developed a method that directly relates molecular dynamics simulations of ionic currents to electrophysiological measurements in ion","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":"141 1","pages":"16:1"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89840141","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 framework for federated two-factor authentication enabling cost-effective secure access to distributed cyberinfrastructure","authors":"M. Ezell, Gary L. Rogers, G. D. Peterson","doi":"10.1145/2335755.2335796","DOIUrl":"https://doi.org/10.1145/2335755.2335796","url":null,"abstract":"As cyber attacks become increasingly sophisticated, the security measures used to mitigate the risks must also increase in sophistication. One time password (OTP) systems provide strong authentication because security credentials are not reusable, thus thwarting credential replay attacks. The credential changes regularly, making brute-force attacks significantly more difficult. In high performance computing, end users may require access to resources housed at several different service provider locations. The ability to share a strong token between multiple computing resources reduces cost and complexity. The National Science Foundation (NSF) Extreme Science and Engineering Discovery Environment (XSEDE) provides access to digital resources, including supercomputers, data resources, and software tools. XSEDE will offer centralized strong authentication for services amongst service providers that leverage their own user databases and security profiles. This work implements a scalable framework built on standards to provide federated secure access to distributed cyberinfrastructure.","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":"7:1-7:8"},"PeriodicalIF":0.0,"publicationDate":"2012-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86353383","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}