检索结果-内蒙古大学图书馆

2000 ACM/IEEE Conference on Supercomputing, SC 2000

作者： No, Jaechun Thakur, Rajeev Choudhary, Alok Math. and Computer Science Division Argonne National Laboratory ArgonneIL60439 United States Dept. of Electrical and Computer Eng Northwestern University EvanstonIL60208 United States

ISBN: (纸本)0780398025

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. © 2000 IEEE.

关键词： Database systems

来源：评论

学校读者我要写书评

暂无评论

Improving the performance of MPI derived datatypes by optimizing memory-access cost

Improving the performance of MPI derived datatypes by optimi...

引用

IEEE International Conference on Cluster Computing, CLUSTER 2003

作者： Byna, Surendra Gropp, William Sun, Xian-He Thakur, Rajeev Department of Computer Science Illinois Institute of Technology ChicagoIL60616 United States Math. and Comp. Science Division Argonne National Laboratory ArgonneIL60439 United States

ISBN: (纸本)0769520669

The MPI Standard supports derived datatypes, which allow users to describe noncontiguous memory layout and communicate noncontiguous data with a single communication function. This feature enables an MPI implementation to optimize the transfer of noncontiguous data. In practice, however, few MPI implementations implement derived datatypes in a way that performs better than what the user can achieve by manually packing data into a contiguous buffer and then calling an MPI function. In this paper, we present a technique for improving the performance of derived datatypes by automatically using packing algorithms that are optimized for memory-access cost. The packing algorithms use memory-optimization techniques that the user cannot apply easily without advanced knowledge of the memory architecture. We present performance results for a matrix-transpose example that demonstrate that our implementation of derived datatypes significantly outperforms both manual packing by the user and the existing derived-datatype code in the MPI implementation (MPICH). © 2003 IEEE.

关键词： Memory architecture

来源：评论

学校读者我要写书评

暂无评论

A scientific data management system for irregular applications 15

A scientific data management system for irregular applicatio...

引用

15th International Parallel and Distributed Processing Symposium, IPDPS 2001

作者： No, Jaechun Thakur, R. Kaushik, D. Freitag, L. Choudhary, A. Math. and Computer Science Division Argonne National Laboratory ArgonneIL60439 United States Dept. of Elec. and Computer Eng. Northwestern University EvanstonIL60208 United States

ISBN: (纸本)0769509908

Many scientific applications are I/O intensive and generate large data sets, spanning hundreds or thousands of "files." Management, storage, efficient access, and analysis of this data present an extremely challenging task. We have developed a software system, called Scientific Data Manager (SDM), that uses a combination of parallel file I/O and database support for high-performance scientific data management. 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. In this paper, we describe how we designed and implemented SDM to support irregular applications. SDM can efficiently handle the reading and writing of data in an irregular mesh, as well as the distribution of index values. We describe the SDM user interface and how we have implemented it to achieve high performance. SDM makes extensive use of MPI-IO's noncontiguous collective I/O functions. SDM also uses the concept of a history file to optimize the cost of the index distribution using the metadata stored in database. We present performance results with two irregular applications, a CFD code called FUN3D and a Rayleigh-Taylor instability code, on the SGI Origin2000 at Argonne National Laboratory. © 2001 IEEE.

关键词： Metadata

来源：评论

学校读者我要写书评

暂无评论

Genome-scale expression of proteins from Bacillus subtilis

引用

Journal of Structural and Functional Genomics 2004年第1-2期5卷 103-109页

作者： Moy, S. Dieckman, L. Schiffer, M. Maltsev, N. Yu, G.-X. Collart, F.R. Biosciences Argonne IL 60439 United States Math. and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States Oak Ridge National Laboratory Oak Ridge TN 37831 United States

We have applied high throughput methods for cloning and expression of more than 850 genes from the Bacillus subtilis genome. The process uses 96-well plates and is automated from the level of primer design to the detection of soluble protein by a tag detection screen. This process was applied to a set of cytoplasmic targets from Bacillus subtilis to produce clones expressing soluble protein for incorporation into the structure determination pipeline of the Midwest Center for Structural Genomics. We also evaluated the feasibility of these plate-based methods for domain-based cloning and expression of secretory proteins and putative soluble domains of membrane proteins. This approach shows promise for implementation in a high throughput format and could provide additional target resources for structure determination. The continued development of new technologies that can be implemented in an automated format will be essential for continued success in the structural genomic programs.

关键词： Bacillus subtilis High-throughput Protein expression Structural genomics

来源：评论

学校读者我要写书评

暂无评论

CLARM: An integrative approach for functional modules discovery

CLARM: An integrative approach for functional modules discov...

引用

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Salem, Saeed Alroobi, Rami Banitaan, Shadi Seridi, Loqmane Brewer, James Aljarah, Ibrahim Department of Computer Science North Dakota State University Fargo ND 58102 United States Math. and Comp. Sci. and Eng. Division KAUST 23955-6900 Saudi Arabia

ISBN: (纸本)9781450307963

Functional module discovery aims to find well-connected subnetworks which can serve as candidate protein complexes. Advances in High-throughput proteomic technologies have enabled the collection of large amount of interaction data as well as gene expression data. We propose, CLARM, a clustering algorithm that integrates gene expression profiles and protein protein interaction network for biological modules discovery. The main premise is that by enriching the interaction network by adding interactions between genes which are highly co-expressed over a wide range of biological and environmental conditions, we can improve the quality of the discovered modules. Protein protein interactions, known protein complexes, and gene expression profiles for diverse environmental conditions from the yeast Saccharomyces cerevisiae were used for evaluate the biological significance of the reported modules. Our experiments show that the CLARM approach is competitive to wellestablished module discovery methods. Copyright © 2011 ACM.

关键词： Clustering algorithms

来源：评论

学校读者我要写书评

暂无评论

Algorithmic Learning Theory 1

引用

丛书名： Lecture Notes in computer science

1000年

作者： Yoav Freund László Györfi György Turán Thomas Zeugmann

ISBN: (数字)9783540879879

ISBN: (纸本)9783540879862

This volume contains papers presented at the 19th International Conference on Algorithmic Learning Theory (ALT 2008), which was held in Budapest, Hungary during October 13–16, 2008. The conference was co-located with the 11th - ternational Conference on Discovery science (DS 2008). The technical program of ALT 2008 contained 31 papers selected from 46 submissions, and 5 invited talks. The invited talks were presented in joint sessions of both conferences. ALT 2008 was the 19th in the ALT conference series, established in Japan in 1990. The series Analogical and Inductive Inference is a predecessor of this series: it was held in 1986, 1989 and 1992, co-located with ALT in 1994, and s- sequently merged with ALT. ALT maintains its strong connections to Japan, but has also been held in other countries, such as Australia, Germany, Italy, Sin- pore, Spain and the USA. The ALT conference series is supervised by its Steering Committee: Naoki Abe (IBM T. J.

关键词： Data Mining and Knowledge Discovery Artificial Intelligence Natural Language Processing (NLP) computer Appl. in Arts and Humanities

来源：评论

学校读者我要写书评

暂无评论

An evaluation of Java's I/O capabilities for high-performance computing

An evaluation of Java's I/O capabilities for high-performanc...

引用

ACM 2000 Java Grande Conference

作者： Dickens, Phillip M. Thakur, Rajeev Illinois Institute of Technology 10 West 31st Street Chicago IL 60616 United States Math. and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States

ISBN: (纸本)1581132883

Java is quickly becoming the preferred language for writing distributed applications because of its inherent support for programming on distributed platforms. In particular, Java provides compile-time and run-time security, automatic garbage collection, inherent support for multithreading, support for persistent objects and object migration, and portability. Given these significant advantages of Java, there is a growing interest in using Java for high-performance computing applications. To be successful in the high-performance computing domain, however, Java must have the capability to efficiently handle the significant I/O requirements commonly found in high-performance computing applications. While there has been significant research in high-performance I/O using languages such as C, C++, and Fortran, there has been relatively little research into the I/O capabilities of Java. In this paper, we evaluate the I/O capabilities of Java for high-performance computing. We examine several approaches that attempt to provide high-performance I/O - many of which are not obvious at first glance - and investigate their performance in both parallel and multithreaded environments. We also provide suggestions for expanding the I/O capabilities of Java to better support the needs of high-performance computing applications.

关键词： Java programming language

来源：评论

学校读者我要写书评

暂无评论

Curve-sensitive cuttings

Curve-sensitive cuttings

引用

Nineteenth Annual Symposium on Computational Geometry

作者： Koltun, Vladlen Sharir, Micha Computer Science Division University of California Berkeley CA 94720-1776 United States School of Computer Science Tel Aviv University Tel-Aviv 69978 Israel Courant Inst. of Math. Sciences New York University New York NY 10012 United States

We introduce (1/r)-cuttings for collections of surfaces in 3-space that are sensitive to an additional collection of curves. Specifically, let S be a set of n surfaces in 3 of constant description complexity, and let C be a set of m curves in 3 of constant description complexity. Let 1 ≤ r ≤ min{m, n} be a given parameter. We show the existence of a (1/r)-cutting Ξ of S of size O(r3+Ε), for any Ε > 0, such that the number of crossings between the curves of C and the cells of Ξ is O(m1+Εr). The latter bound improves, by roughly a factor of r, the bound that can be obtained for cuttings based on vertical decompositions. We view curve-sensitive cuttings as a powerful tool that is potentially useful in various scenarios that involve curves and surfaces in three dimensions. As a preliminary application, we use the construction to obtain a bound of O(m1/2+Εn2+Ε), for any Ε > 0, on the complexity of the multiple zone of m curves in the arrangement of n surfaces in 3-space.

关键词： Boolean algebra

来源：评论

学校读者我要写书评

暂无评论

Parallelizing a global atmospheric chemical tracer model

Parallelizing a global atmospheric chemical tracer model

引用

Scalable High Performance Computing Conference

作者： J. Demmel S. Smith Computer Science Division & Math. Department University of California Berkeley CA USA Computer Science Division University of California Berkeley CA USA

We describe the design of a parallel global atmospheric chemical tracer model. This is part of a larger Earth Systems Model (ESM) for atmospheric dynamics and physics, and ocean physics. The ESM will be used for global warming and ozone depletion studies, among others. The goal is to parallelize the chemistry model to run efficiently on current and future parallel architectures, including the Sequoia archival database. We describe the preliminary design, especially the detailed timing model, and some initial validations. We have found a timing modeling very valuable for designing for a large range of architectures.< >

关键词： Chemicals Atmospheric modeling Physics Timing Earth Oceans Global warming Chemistry Parallel architectures Databases

来源：评论

学校读者我要写书评

暂无评论

Tuning the Interpolation Basis in a Multigrid Decomposition for Local Error Control

Tuning the Interpolation Basis in a Multigrid Decomposition ...

引用

IEEE International Conference on Big Data

作者： Nicolas Vidal Qian Gong Viktor Reshniak Rick Archibald Scott Klasky Computer Science and Math. Division Oak Ridge National Laboratory Oak Ridge TN USA

ISBN: (数字)9798350362480

ISBN: (纸本)9798350362497

In the compression of scientific data, error-controlled compressors enable to considerably decrease the size of the dataset while maintaining adequate levels of accuracy. In this paper, we note that multi-level refactoring scheme such as MGARD i) rely on an approximation of the data based on the interpolation of coefficients, ii) estimate the resulting error with global metrics on the dataset. To improve on these two aspects, we propose a method that aims to divide the original dataset into blocks based on their smoothness and refactors each block separately with the most relevant interpolation order. We show the relevance of such a method on tailored datasets and the benefits and challenges when applying it to large scientific data.

关键词： Measurement Interpolation Codes Production Big Data Benchmark testing Compressors Entropy Error correction Tuning

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：