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Application level scheduling of gene sequence comparison on metacomputers

Neil Spring, Rich Wolski
1998 Proceedings of the 12th international conference on Supercomputing - ICS '98  
Distribution of execution performance. Shown on the left is a histogram of average execution performance for one of the Sun HPC servers, measured in sequence pairs compared per millisecond.  ...  Conceptual view of expected and dependable performance. Sequences are placed based on the dependable performance of a processor.  ... 
doi:10.1145/277830.277860 dblp:conf/ics/SpringW98 fatcat:yruswpmktrf45fb7t3twhc755q

Application level scheduling of gene sequence comparison on metacomputers

Neil Spring, Rich Wolski
2014 25th Anniversary International Conference on Supercomputing Anniversary Volume -  
Distribution of execution performance. Shown on the left is a histogram of average execution performance for one of the Sun HPC servers, measured in sequence pairs compared per millisecond.  ...  Conceptual view of expected and dependable performance. Sequences are placed based on the dependable performance of a processor.  ... 
doi:10.1145/2591635.2667176 fatcat:zfkloa7wkrfdnmao6zq3l7l2ma

Metacomputing in practice: a distributed compute server for pharmaceutical industry

Robert Bywater, Jörn Gehring, Alexander Reinefeld, Friedrich Rippmann, Anke Weber
1999 Future generations computer systems  
They range from the automatic functional annotation of protein sequences to three-dimensional protein structure prediction tools and protein comparison applications.  ...  We describe a distributed high-performance compute server that has been implemented for running compute-intensive applications on a mixture of HPC systems interconnected by I n ter-and Intranet.  ...  This may yield more homology information than protein sequences alignments since sequence comparison has an inherent limit of 20 to 25 identity whereas structure comparison allows comparison of the folded  ... 
doi:10.1016/s0167-739x(99)00026-6 fatcat:uuyij365o5gznbssgvmgugfdfu

A taxonomy and survey of grid resource management systems for distributed computing

Klaus Krauter, Rajkumar Buyya, Muthucumaru Maheswaran
2002 Software, Practice & Experience  
Depending on the application, the job may specify quality of service (QoS) requirements or accept best-effort service levels.  ...  Our taxonomy provides classification of resource models and examines scheduling and state estimation at a finer level.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge all developers of the Grid systems described in the paper.  ... 
doi:10.1002/spe.432 fatcat:35mud2v6fnbzlldnczvg3peeqa

Cluster Computing [chapter]

Mark Baker, John Brooke, Ken Hawick, Rajkumar Buyya
2001 Lecture Notes in Computer Science  
Typically, there are three types of "owner": • Ones who use their workstations for sending and receiving mail or preparing papers, such as administrative staff, librarian, theoreticians, etc. • Ones involved  ...  This ownership often brings problems when attempting to form a cluster of workstations.  ...  , distributed simulation, gene sequencing, and speech recognition, on heterogeneous networks of workstations.  ... 
doi:10.1007/3-540-44681-8_100 fatcat:cr6rpynstjgufacwbmciciriha

Performance engineering in data Grids

Erwin Laure, Heinz Stockinger, Kurt Stockinger
2005 Concurrency and Computation  
These techniques are applicable at different layers of a Grid architecture and we discuss the tools required at each of these layers to implement them.  ...  In this paper we present performance engineering techniques that aim to facilitate an efficient use of Grid systems, in particular systems that deal with the management of large scale data sets in the  ...  The recent explosion of data, acquired by automated gene sequencers and other experimental techniques, requires vast amounts of computing power to analyze the biological functions of genes.  ... 
doi:10.1002/cpe.923 fatcat:7pry35r3cfh6zaejtterofhalm

Distributed, on-demand, data-intensive and collaborative simulation analysis

Arthurine Breckenridge, Lyndon Pierson, Sergiu Sanielevici, Joel Welling, Rainer Keller, Uwe Woessner, Juergen Schulze
2003 Future generations computer systems  
Distributed, on-demand, data-intensive, and collaborative simulation analysis tools are being developed by an international team to solve real problems such as bioinformatics applications.  ...  Computers in North America, Asia, and Europe are working on a common simulation programs.  ...  This work done by HLRS has been funded by the DAMIEN project (IST-2000-25406) and by the collaborative research centers (SFB) 374 and 382 of the German Research Council (DFG). The  ... 
doi:10.1016/s0167-739x(03)00065-7 fatcat:423uagcld5dkjdoebnhueto2wm

Using SCTP to hide latency in MPI programs

H. Kamal, B. Penoff, M. Tsai, E. Vong, A. Wagner
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
SCTP is a recently standardized transport level protocol that has a number of features that make it well-suited to MPI and our goal is to reduce the effect of latency on MPI programs in wide area networks  ...  larger than parallel programs executing on dedicated systems.  ...  Streams are multiplexed on an association and sequenced.  ... 
doi:10.1109/ipdps.2006.1639391 dblp:conf/ipps/KamalPTVW06 fatcat:pfmuswfct5a4jnd43sbiy6sl7a

The Web Service Discovery Architecture

W. Hoschek
2002 ACM/IEEE SC 2002 Conference (SC'02)  
At runtime, Grid applications can use this architecture to discover and adapt to remote services.  ...  WSDA promotes an interoperable web service discovery layer by defining appropriate services, interfaces, operations and protocol bindings, based on industry standards.  ...  We would like to thank Peter Kunszt for an early high-level analysis. Ben Segal supported this work with great enthusiasm, encouragement and proof-reading.  ... 
doi:10.1109/sc.2002.10033 dblp:conf/sc/Hoschek02 fatcat:uxrbzqpzajdfxhrzaytr3c7ucy

Soft Computing in Optimizing Assembly Lines Balancing

2010 Journal of Computer Science  
As part of manufacturing systems, the assembly line has become one of the most valuable researches to accomplish the real world problems related to them.  ...  Problem statement: Since it was published by Salveson in 1955, some methods and techniques have been developed based on mathematical modeling.  ...  The wide variety of applications benefiting from optimization include: Production planning and scheduling, raw material blending, yield and revenue management, crew scheduling, financial portfolio management  ... 
doi:10.3844/jcssp.2010.141.162 fatcat:rdv3e6wewzealnrlcmh5mcaa2a

Novel mediator architectures for Grid information systems

Alexander Wöhrer, Peter Brezany, A. Min Tjoa
2005 Future generations computer systems  
The alternative of forcing each grid application to interface directly to a set of databases and resolve federation problems internally would lead to application complexity, and duplication of effort.  ...  This technical report presents a data integration system based on the wrapper-mediator approach, namely the Grid Data Mediation Service.  ...  As an example, it should be possible to compare predicted gene sequences in a local database against those defined in a centralized repository. 3.  ... 
doi:10.1016/j.future.2004.09.018 fatcat:awe7tjxqpzbcpojgly256mw3lq

A Global Grid for Analysis of Arthropod Evolution

C.A. Stewart, R. Keller, R. Repasky, M. Hess, D. Hart, M. Muller, R. Sheppard, U. Wossner, M. Aumuller, Huian Li, D.K. Berry, J. Colbourne
Fifth IEEE/ACM International Workshop on Grid Computing  
This work was done as part of the SC03 HPC Challenge, and this project was given an HPC Challenge award for the "Most Distributed Application."  ...  Maximum likelihood analysis is a powerful technique for inferring evolutionary histories from genetic sequence data.  ...  Hacker for helpful comments about earlier versions of this paper. This paper is dedicated to the memory of our friend and colleague, David Moffett.  ... 
doi:10.1109/grid.2004.1 dblp:conf/grid/StewartKRHHMSWALBC04 fatcat:pixglgsgonemrdciom6jtrjwkm

The Single Row Routing Problem Revisited: A Solution Based on Genetic Algorithms

Albert Y. Zomaya, Roger Karpin, Stephan Olariu
2002 VLSI design (Print)  
As the complexity of ICs grows, the time and money spent on designing the circuits become more important.  ...  With the advent of VLSI technology, circuits with more than one million transistors have been integrated onto a single chip.  ...  The second problem is a classical problem in Computer Aided Design, applicable to all levels of scale.  ... 
doi:10.1080/10655140290010051 fatcat:nlha64jdsvdkjdpymv5rr222la

The AAAS Annual Meeting

1991 Science  
Ethnogenesis in the South Plains, Nancy Parrott Hickerson; Nationalism, colonialism, and the masculinization of Puerto Rico, Arlene Torres; Naming patterns as an indicator of Black Seminole ethnogenesis  ...  1492-1992: Nationalism, ethnic-bloc formation, and ideologies of racial cultures, Norman Whitten, Jr.; Ethnogenesis in the Guianas and Jamaica: Two maroon cases, Kenneth Bilby; Jumano to Kiowa?  ...  Taxis are located on the lower level of each terminal at O'Hare (approximate time to hotels: 1-2 hours, depending on time of day).  ... 
doi:10.1126/science.254.5034.1029 pmid:17731525 fatcat:hsmxd5iuzbfdtou2buwstrosla

Economic-based distributed resource management and scheduling for grid computing

Buyya, Rajkumar, 1970-
The concept of AppLeS has been applied to many application areas including Magnetohydrodynamics [44], Gene Sequence Comparison, and Tomography [127] .  ...  AppLeS: A Network Enabled Scheduler The AppLeS [28] (Application Level Scheduling) project at the University of California, San Diego primarily focuses on developing scheduling agents for individual  ...  One application scheduled computations needed for a drug design application that screened molecules, he said.  ... 
doi:10.4225/03/59ca0edcbb78e fatcat:26jzgqvl4feohm6y3duowmv3aa
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