Q. Snell, M. Whiting, M. Clement, David McLaughlin
{"title":"Parallel Phylogenetic Inference","authors":"Q. Snell, M. Whiting, M. Clement, David McLaughlin","doi":"10.1109/SC.2000.10062","DOIUrl":"https://doi.org/10.1109/SC.2000.10062","url":null,"abstract":"Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably sized data set. Some parallel algorithms have been developed but the biological research community does not use them because they don’t trust the results from newly developed parallel software. This paper presents a new phylogenetic algorithm that allows existing, trusted phylogenetic software packages to be executed in parallel using the DOGMA parallel processing system. The results presented here indicate that data sets that currently take as much as 11 months to search using current algorithms, can be searched in as little as 2 hours using as few as 8 processors. This reduction in the time necessary to complete a phylogenetic search allows new research questions to be explored in many of the biological sciences.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127091842","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 Hardware Performance Monitors to Isolate Memory Bottlenecks","authors":"B. Buck, J. Hollingsworth","doi":"10.5555/370049.370420","DOIUrl":"https://doi.org/10.5555/370049.370420","url":null,"abstract":"In this paper, we present and evaluate two techniques that use different styles of hardware support to provide data structure specific processor cache information. In one approach, hardware performance counter overflow interrupts are used to sample cache misses. In the other, cache misses within regions of memory are counted to perform an n-way search for the areas in which the most misses are occurring. We present a simulation-based study and comparison of the two techniques. We find that both techniques can provide accurate information, and describe the relative advantages and disadvantages of each.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128182153","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 1.349 Tflops simulation of black holes in a galactic center on GRAPE-6","authors":"J. Makino, T. Fukushige, Masaki Koga","doi":"10.1109/SC.2000.10042","DOIUrl":"https://doi.org/10.1109/SC.2000.10042","url":null,"abstract":"As an entry for the 2000 Gordon Bell performance prize, we report the performance achieved on a prototype GRAPE-6 system. GRAPE-6 is a special-purpose computer for as-trophysical N-body calculations. The present configuration has 96 custom pipeline processors, each containing six pipeline processors for the calculation of gravitational interactions between particles. Its theoretical peak performance is 2.889 Tflops. The complete GRAPE-6 system will consist of 3072 pipeline chips and will achieve a peak speed of 100 Tflops. The actual performance obtained on the present 96-chip system was 1.349 Tflops, for a simulation of massive black holes embedded in the core of a galaxy with 786,432 stars. For a short benchmark run with 1,400,000 particles, the average speed was 1.640 Tflops.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127189828","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":"Expressing and Enforcing Distributed Resource Sharing Agreements","authors":"Tao Zhao, V. Karamcheti","doi":"10.1109/SC.2000.10054","DOIUrl":"https://doi.org/10.1109/SC.2000.10054","url":null,"abstract":"Advances in computing and networking technology, and an explosion in information sources has resulted in a growing number of distributed systems getting constructed out of resources contributed by multiple sources. Use of such resources is typically governed by sharing agreements between owning principals, which limit both who can access a resource and in what quantity. Despite their increasing importance, existing resource management infrastructures offer only limited support for the expression and enforcement of sharing agreements, typically restricting themselves to identifying compatible resources. In this paper, we present a novel approach building on the concepts of tickets and currencies to express resource sharing agreements in an abstract, dynamic, and uniform fashion. We also formulate the allocation problem of enforcing these agreements as a linear-programming model, automatically factoring the transitive availability of resources via chained agreements. A case study modeling resource sharing among ISP-level web proxies shows the benefits of enforcing transitive agreements: worst-case waiting times of clients accessing these proxies improves by up to two orders of magnitude.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122301023","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":"Realizing Fault Resilience in Web-Server Cluster","authors":"Chu-Sing Yang, Mon-Yen Luo","doi":"10.1109/SC.2000.10012","DOIUrl":"https://doi.org/10.1109/SC.2000.10012","url":null,"abstract":"Today, a successful Internet service is absolutely critical to be up 100 percent of the time. Server clustering is the most promising approach to meet this requirement. However, the existing Web server-clustering solutions merely can provide high availability derived from its redundancy nature, but offer no guarantee about fault resilience for the service. In this paper, we address this problem by implementing an innovative mechanism that enables a Web request to be smoothly migrated and recovered on another working node in the presence of server failure. We will show that the request migration and recovery could be efficiently achieved in the manner of user transparency. The achieved capability of fault resilience is important and essential for a variety of critical services (e.g., E-commerce), which are increasingly widespread used. Our approach takes an important step toward providing a highly reliable Web service.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127706340","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}
K. B. Theobald, G. Agrawal, Rishi Kumar, G. Heber, G. Gao, Paul V. Stodghill, K. Pingali
{"title":"Landing CG on EARTH: A Case Study of Fine-Grained Multithreading on an Evolutionary Path","authors":"K. B. Theobald, G. Agrawal, Rishi Kumar, G. Heber, G. Gao, Paul V. Stodghill, K. Pingali","doi":"10.1109/SC.2000.10011","DOIUrl":"https://doi.org/10.1109/SC.2000.10011","url":null,"abstract":"We report on our work in developing a fine-grained multithreaded solution for the communication-intensive Conjugate Gradient (CG) problem. In our recent work, we developed a simple yet efficient program for sparse matrix-vector multiply on a multi-threaded system. This paper presents an effective mechanism for the reduction-broadcast phase, which is integrated with the sparse MVM, resulting in a scalable implementation of the complete CG application. Three major observations from our experiments on the EARTH multithreaded testbed are: (1) The scalability of our CG implementation is impressive, e.g., absolute speedup is 90 on 120 processors for the NAS CG class B input. (2) Our dataflow-style reduction-broadcast network based on fine-grain multithreading is twice as fast as a serial reduction scheme on the same system. (3) By slowing down the network by a factor of 2, no notable degradation of overall CG performance was observed.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133430434","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 Unified Algorithm for Load-balancing Adaptive Scientific Simulations","authors":"K. Schloegel, G. Karypis, Vipin Kumar","doi":"10.1109/SC.2000.10035","DOIUrl":"https://doi.org/10.1109/SC.2000.10035","url":null,"abstract":"Adaptive scientific simulations require that periodic repartitioning occur dynamically throughout the course of the computation. The repartitionings should be computed so as to minimize both the inter-processor communications incurred during the iterative mesh-based computation and the data redistribution costs required to balance the load. Recently developed schemes for computing repartitionings provide the user with only a limited control of the tradeoffs among these objectives. This paper describes a new Unified Repartitioning Algorithm that can tradeoff one objective for the other dependent upon a user-defined parameter describing the relative costs of these objectives. We show that the Unified Repartitioning Algorithm is able to reduce the precise overheads associated with repartitioning as well as or better than other repartitioning schemes for a variety of problems, regardless of the relative costs of performing inter-processor communication and data redistribution. Our experimental results show that this scheme is extremely fast and scalable to large problems.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131592890","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":"Single sided MPI implementations for SUN MPI","authors":"S. Booth, F. Mourão","doi":"10.1109/SC.2000.10022","DOIUrl":"https://doi.org/10.1109/SC.2000.10022","url":null,"abstract":"This paper describes an implementation of generic MPI-2 single sided communications for SUN-MPI. Our implementation is layered on top of point-to-point MPI communications and therefore can be adapted to other MPI implementations. The code is designed to co-exist with other MPI-2 single sided implementations (for example direct use of shared memory) providing a generic fall-back implementation for those communication paths where an optimised single-sided implementation is not available. MPI-2 single sided communications require the transfer of data-type information as well as user data. We describe a type packing and caching mechanism used to optimise the transfer of data-type information. The performance of this implementation is measured in comparison to equivalent point to point operations and the shared memory implementation provided by SUN.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130044393","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}
W. Johnston, Dennis Gannon, B. Nitzberg, Leigh Ann Tanner, Bill Thigpen, Alex Woo
{"title":"Computing and Data Grids for Science and Engineering","authors":"W. Johnston, Dennis Gannon, B. Nitzberg, Leigh Ann Tanner, Bill Thigpen, Alex Woo","doi":"10.1109/SC.2000.10007","DOIUrl":"https://doi.org/10.1109/SC.2000.10007","url":null,"abstract":"We use the term \"Grid\" to refer to a software system that provides uniform and location independent access to geographically and organizationally dispersed, heterogeneous resources that are persistent and supported. While, in general, Grids will provide the infrastructure to support a wide range of services in the scientific environment (e.g. collaboration and remote instrument control) in this paper we focus on services for high performance computing and data handling. We describe the services and architecture of NASA’s Information Power Grid (\"IPG\") - an early example of a large-scale Grid - and some of the issues that have come up in its implementation.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130092327","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":"Integrating Parallel File I/O and Database Support for High-Performance Scientific Data Management","authors":"Jaechun No, R. Thakur, A. Choudhary","doi":"10.1109/SC.2000.10048","DOIUrl":"https://doi.org/10.1109/SC.2000.10048","url":null,"abstract":"Many scientific applications have large I/O requirements, in terms of both the size of data and the number of files or data sets. Management, storage, efficient access, and analysis of this data present an extremely challenging task. Traditionally, two different solutions are used for this problem: file I/O or databases. File I/O can provide high performance but is tedious to use with large numbers of files and large and complex data sets. Databases can be convenient, flexible, and powerful but do not perform and scale well for parallel supercomputing applications. We have developed a software system, called Scientific Data Manager (SDM), that aims to combine the good features of both file I/O and databases. SDM provides a high-level API to the user and, internally, uses a parallel file system to store real data and a database to store application-related metadata. SDM takes advantage of various I/O optimizations available in MPI-IO, such as collective I/O and noncontiguous requests, in a manner that is transparent to the user. As a result, users can write and retrieve data with the performance of parallel file I/O, without having to bother with the details of actually performing file I/O. In this paper, we describe the design and implementation of SDM. With the help of two parallel application templates, ASTRO3D and an Euler solver, we illustrate how some of the design criteria affect performance.","PeriodicalId":228250,"journal":{"name":"ACM/IEEE SC 2000 Conference (SC'00)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116246842","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}
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