Approximate algorithms scheduling parallelizable tasks
SPAA '92 Proceedings of the fourth annual ACM symposium on Parallel algorithms and architectures
Linear-time approximation schemes for scheduling malleable parallel tasks
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Improved algorithms for stretch scheduling
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A parallel workload model and its implications for processor allocation
Cluster Computing
A Symbolic Approachto Modeling Cellular Behavior
HiPC '02 Proceedings of the 9th International Conference on High Performance Computing
Theory and Practice in Parallel Job Scheduling
IPPS '97 Proceedings of the Job Scheduling Strategies for Parallel Processing
Selective Reservation Strategies for Backfill Job Scheduling
JSSPP '02 Revised Papers from the 8th International Workshop on Job Scheduling Strategies for Parallel Processing
Online Scheduling to Minimize Average Stretch
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Minimizing the stretch when scheduling flows of biological requests
Proceedings of the eighteenth annual ACM symposium on Parallelism in algorithms and architectures
A $\frac32$-Approximation Algorithm for Scheduling Independent Monotonic Malleable Tasks
SIAM Journal on Computing
Bioinformatics
Parallel short sequence mapping for high throughput genome sequencing
IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
Moldable parallel job scheduling using job efficiency: an iterative approach
JSSPP'06 Proceedings of the 12th international conference on Job scheduling strategies for parallel processing
Optimizing the stretch of independent tasks on a cluster: From sequential tasks to moldable tasks
Journal of Parallel and Distributed Computing
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A crucial step in DNA sequence analysis is mapping short sequences generated by next-generation instruments to a reference genome. In this paper, we focus on efficient online scheduling of multi-user parallel short sequence mapping queries on a multiprocessor system. With the availability of parallel execution models, the problem at hand becomes a moldable task scheduling problem where the number of processors needed to execute a task is determined by the scheduler. We propose an online scheduling algorithm to minimize the stretch of the tasks in the system. This metric provides improved fairness to small tasks compared to flow time metric and suits well to the nature of the problem. Experimental evaluation on two workload scenarios indicate that the algorithm results in significantly smaller stretch compared to a recent algorithm and it is more fair to small sized tasks.