Allocating Independent Subtasks on Parallel Processors
IEEE Transactions on Software Engineering
Combinatorial optimization: algorithms and complexity
Combinatorial optimization: algorithms and complexity
Guided self-scheduling: A practical scheduling scheme for parallel supercomputers
IEEE Transactions on Computers
Communications of the ACM
Factoring: a method for scheduling parallel loops
Communications of the ACM
Load-sharing in heterogeneous systems via weighted factoring
Proceedings of the eighth annual ACM symposium on Parallel algorithms and architectures
Distributed and parallel computing
Distributed and parallel computing
The grid: blueprint for a new computing infrastructure
The grid: blueprint for a new computing infrastructure
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
Trapezoid Self-Scheduling: A Practical Scheduling Scheme for Parallel Compilers
IEEE Transactions on Parallel and Distributed Systems
Performance of Scheduling Scientific Applications with Adaptive Weighted Factoring
IPDPS '01 Proceedings of the 15th International Parallel & Distributed Processing Symposium
BLAST++: a tool for BLASTing queries in batches
APBC '03 Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19
Adaptive scheduling of master/worker applications on distributed computational resources
Adaptive scheduling of master/worker applications on distributed computational resources
BLAST
Grid resource management: state of the art and future trends
Grid resource management: state of the art and future trends
GBTK: A Toolkit for Grid Implementation of BLAST
HPCASIA '04 Proceedings of the High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference
Parallel Computing for Bioinformatics and Computational Biology (Wiley Series on Parallel and Distributed Computing)
IEEE Transactions on Parallel and Distributed Systems
Scaling up Genome Similarity Search Services through Content Distribution
ICPP '07 Proceedings of the 2007 International Conference on Parallel Processing
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In the last decade, we have observed an unprecedented development in molecular biology. An extremely high number of organisms have been sequenced in genome projects and included in genomic databases, for further analysis. These databases present an exponential growth rate and they are intensively accessed daily, all over the world. Once a sequence is obtained, its function and/or structure must be determined. Direct experimentation is considered to be the most reliable method to do that. However, the experiments that must be conducted are very complex and time consuming. For this reason, it is far more productive to use computational methods to infer biological information from a sequence. This is usually done by comparing the new sequence with sequences that already had their characteristics determined. BLAST is the most widely used heuristic tool for sequence comparison. Thousands of BLAST searches are made daily, all over the world. In order to further reduce the BLAST execution time, cluster and grid environments can be effectively used. This paper proposes and evaluates an adaptive task allocation framework to perform BLAST searches in a grid environment. The framework, called PackageBLAST, provides an infrastructure that executes distributed BLAST genomic database comparisons. In addition, it is flexible since the user can choose or incorporate new task allocation strategies. Furthermore, we propose a mechanism to compute grid nodes' execution weight, adapting the chosen allocation policy to the observed computational power and local load of the nodes. Our results present very good speedups. For instance, in a 16-machine heterogeneous grid testbed, a speedup of 14.59 was achieved, reducing the BLAST execution time from 30.88 min to 2.11 min. Also, we show that the adaptive task allocation strategy was able to handle successfully the complexity of a grid environment.