TeraGrid Conference最新文献

{"title":"The development of Mellanox/NVIDIA GPUDirect over InfiniBand: a new model for GPU to GPU communications","authors":"G. Shainer, Pak Lui, Tong Liu","doi":"10.1145/2016741.2016769","DOIUrl":"https://doi.org/10.1145/2016741.2016769","url":null,"abstract":"The usage and adoption of General Purpose GPUs (GPGPU) in HPC systems is increasing due to the unparalleled performance advantage of the GPUs and the ability to fulfill the ever-increasing demands for floating points operations. While the GPU can offload many of the application parallel computations, the system architecture of a GPU-CPU-InfiniBand server does require the CPU to initiate and manage memory transfers between remote GPUs via the high speed InfiniBand network. In this paper we introduce for the first time a new innovative technology - GPUDirect that enables Tesla GPUs to transfer data via InfiniBand without the involvement of the CPU or buffer copies, hence dramatically reducing the GPU communication time and increasing overall system performance and efficiency. We also explore for the first time the performance benefits of GPUDirect using Amber and LAMMPS applications.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131022517","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 TeraGrid to teach scientific computing","authors":"F. Löffler, Gabrielle Allen, W. Benger, A. Hutanu, S. Jha, E. Schnetter","doi":"10.1145/2016741.2016800","DOIUrl":"https://doi.org/10.1145/2016741.2016800","url":null,"abstract":"We describe how a new graduate course in scientific computing, taught during Fall 2010 at Louisiana State University, utilized TeraGrid resources to familiarize students with some of the real world issues that computational scientists regularly deal with in their work. The course was designed to provide a broad and practical introduction to scientific computing, creating the basic skills and experience to very quickly get involved in research projects involving modern cyberinfrastructure and complex real world scientific problems. As an integral part of the course, students had to utilize various TeraGrid resources, e.g., by deploying, using and extending scientific software within the national cyberinfrastructure.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"281 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116078550","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 hybrid parallelism to improve memory use in the Uintah framework","authors":"Qingyu Meng, M. Berzins, John A. Schmidt","doi":"10.1145/2016741.2016767","DOIUrl":"https://doi.org/10.1145/2016741.2016767","url":null,"abstract":"The Uintah Software framework was developed to provide an environment for solving fluid-structure interaction problems on structured adaptive grids on large-scale, long-running, data-intensive problems. Uintah uses a combination of fluid-flow solvers and particle-based methods for solids together with a novel asynchronous task-based approach with fully automated load balancing. Uintah's memory use associated with ghost cells and global meta-data has become a barrier to scalability beyond O(100K) cores. A hybrid memory approach that addresses this issue is described and evaluated. The new approach based on a combination of Pthreads and MPI is shown to greatly reduce memory usage as predicted by a simple theoretical model, with comparable CPU performance.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"102 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122030174","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":"Data-intensive CyberShake computations on an opportunistic cyberinfrastructure","authors":"Allan Espinosa, D. Katz, M. Wilde, K. Maheshwari, Ian T Foster, S. Callaghan, P. Maechling","doi":"10.1145/2016741.2016757","DOIUrl":"https://doi.org/10.1145/2016741.2016757","url":null,"abstract":"This abstract describes the aggregation of TeraGrid and Open Science Grid to run the SCEC CyberShake application faster than on TeraGrid alone. Because the resources are distributed and data movement is required to use more than one resource, a careful analysis of the cost of data movement vs. the benefits of distributed computation has been done in order to best distribute the work across the resources.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"230 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122807565","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":"Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences","authors":"O. Kenway, D. Wright, H. Heller, André Merzky, G. Pringle, Jules Wolfrat, P. Coveney, S. Jha","doi":"10.1145/2016741.2016746","DOIUrl":"https://doi.org/10.1145/2016741.2016746","url":null,"abstract":"The rapid acquisition of mutations conferring resistance to particular drugs remains a significant cause of anti-HIV treatment failure. Informatics based techniques give resistance scores to individual mutations which can be combined additively to assess the resistance levels of complete sequences. It is likely however, that the full picture is more complicated, with non-linear epistatic effects between combinations of mutations playing an important role in determining the level of viral resistance [1, 2]. Molecular dynamics is one simulation technique which offers the ability to derive quantitative (as well as qualitative) insight into the interplay of resistance-causing mutations. The dynamics of sequence specific models can be simulated and the free energy change associated with the drug binding calculated. The free energy change (or binding affinity) is the thermodynamic quantity which determines how tightly a drug will bind to its target. Hence, comparing values for mutant and wildtype systems allows the level of resistance of a particular sequence to be estimated. Validating such an approach is computationally demanding and the management of large numbers of simulations is a considerable administrative challenge. Here we present the use of tools based on the Simple API for Grid Applications (SAGA) to tackle this computational problem. This allows us to utilise high-end infrastructure, such as TeraGrid/XD, to provide extreme scales of throughput for highperformance simulations. This paper presents initial results and experience of using the TeraGrid in conjunction with DEISA, the European analogue of the US TeraGrid. High-throughput (high-performance) calculations are one of the few classes of computational problems that can easily exploit the computational power of widely distributed computing resources, thereby amassing more computational power than any of the individual resources could offer. In addition to the resource utilization rationale the need for cross-Grid capabilities in this case arises from shared and complementary scientific and technical skills found in this intercontinental collaboration.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"113 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128281583","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 multi-cultural success story for achieving diversity in multi-core/many-core internships","authors":"Jennifer Houchins, Jeffrey D. Krause, Scott A. Lathrop, R. Panoff","doi":"10.1145/2016741.2016796","DOIUrl":"https://doi.org/10.1145/2016741.2016796","url":null,"abstract":"One of the foremost challenges in high performance computing (HPC) is promoting involvement of historically underrepresented undergraduate students. The Blue Waters Undergraduate Petascale Education Program, funded by the National Science Foundation Office of CyberInfrastructure, has been facing this challenge head-on while supporting undergraduate internship experiences that involve the application of HPC to problems in the sciences, engineering, or mathematics. This paper describes an evolving approach to the recruitment efforts for undergraduate interns and mentors that demonstrates the importance of formative assessment supporting proactive program changes leading to success in generating a large, diverse applicant pool including substantial numbers of qualified women and minority candidates.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130524691","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":"Towards generic FutureGrid image management","authors":"G. von Laszewski, Javier Diaz, Fugang Wang, A. Younge, Archit Kulshrestha, Geoffrey Fox","doi":"10.1145/2016741.2016758","DOIUrl":"https://doi.org/10.1145/2016741.2016758","url":null,"abstract":"In this paper, we briefly outline the current design of a generic image management service for FutureGrid. The service is intended to generate, store, and verify images while interfacing with different localized cloud IaaS image. Additionally, we will also use the service to generate images for traditional bare-metal deployments.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133787903","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":"Reducing the barrier to entry using portable apps","authors":"D. Colbry","doi":"10.1145/2016741.2016792","DOIUrl":"https://doi.org/10.1145/2016741.2016792","url":null,"abstract":"An increasing number of turnkey, domain specific software packages are available to help users take advantage of advanced cyber-infrastructure and resources such as TeraGrid. However, novice users of cyber-infrastructure are often overwhelmed by the complexities of using cyber-infrastructure. For instance, the user may need to install multiple software tools just to connect with advanced hardware, and successfully installing and navigating this software frequently requires the use of Command Line Interfaces (CLI) that are unfamiliar to novice users. Even when applications provide a Graphical User Interface (GUI), special software (such as an X11 server) may be required to use the interface. Installing, configuring and running this software is generally a multi-step process that can be overly confusing to novice users and presents a barrier to entry, particularly in research domains not traditionally associated with advanced computation.\u0000 Scientific gateways (such as the TeraGrid Portal [1]) are one possible solution to this problem. However, not all research projects or High Performance Computing (HPC) centers have the resources necessary to provide scientific gateways. We have developed an alternative solution: a \"plug and play\" HPC system portal stored on a USB thumb drive. The thumb drive contains all the software necessary to connect to traditional cyber-infrastructure and all programs run directly from the thumb drive -- no installation or setup is required. To access the software from a Windows-based machine, the user simply connects the thumb drive and runs the desired programs. The current thumb drive includes all the typical software necessary to connect to an HPC resource, such as X11 [2], ssh [3], and scp [4]. Since the software is pre-installed on the drive, it can also be preconfigured with the necessary preferences required to immediately connect to the resource.\u0000 This presentation will describe the development process for the \"Portable Apps\" [5] HPC thumb drive, including lessons learned and suggestions for adapting the paradigm for other systems. The Portable Apps drive has been successfully distributed to both expert and novice HPC users at Michigan State University (MSU) and has proved to be a popular and easy-to-use tool for accessing local and national cyber-infrastructure resources, including TeraGrid [6]. This presentation will offer specific suggestions for adapting the Portable Apps idea (such as procedures for site specific applications [7]) and developing similar outreach and educational tools for other institutions and resources.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128246617","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":"Transitioning BioVLab cloud workbench to a science gateway","authors":"S. Marru, Heejoon Chae, Patanachai Tangchaisin, S. Kim, M. Pierce, K. Nephew","doi":"10.1145/2016741.2016784","DOIUrl":"https://doi.org/10.1145/2016741.2016784","url":null,"abstract":"BioVLab gateway is built upon Open Gateway Computing Environments and is currently used as reconfigurable cloud computing workbench. In this talk, we will discuss the new directions towards a TeraGrid Science Gateway and experiences and technical challenges in migrating a Cloud workbench Grid based science gateway.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"95 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133902359","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":"Visualization of multiscale simulation data: brain blood flow","authors":"J. Insley, Leopold Grinberg, M. Papka","doi":"10.1145/2016741.2016761","DOIUrl":"https://doi.org/10.1145/2016741.2016761","url":null,"abstract":"Accurately modeling many physical and biological systems requires simulating at multiple scales. This results in large heterogeneous data sets on vastly differing scales, both physical and temporal. To address the challenges in multi-scale data analysis and visualization we have developed and successfully applied a set of tools, which we described in this paper.","PeriodicalId":257555,"journal":{"name":"TeraGrid Conference","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125727890","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}