Introduction to Sequencing and Scheduling, 1974. ,
Flow and stretch metrics for scheduling continuous job streams, ACM- SIAM Symposium on Discrete Algorithms, pp.270-279, 1998. ,
A Generic Strategy for Multi-stage Stencils, 20th International Conference on Parallel Processing, pp.584-595, 2014. ,
DOI : 10.1007/978-3-319-09873-9_49
On contiguous and non-contiguous parallel task scheduling, Journal of Scheduling, vol.16, issue.2, 2013. ,
DOI : 10.1016/0167-8191(90)90056-F
An exact parallel algorithm to compare very long biological sequences in clusters of workstations, Cluster Computing, vol.64, issue.1, pp.187-202, 2007. ,
DOI : 10.1007/978-3-540-45209-6_74
Algorithms for minimizing weighted flow time, Proceedings of the thirty-third annual ACM symposium on Theory of computing , STOC '01, pp.84-93, 2001. ,
DOI : 10.1145/380752.380778
An adaptive grid implementation of DNA sequence alignment, Future Generation Computer Systems, vol.21, issue.7, pp.988-1003, 2005. ,
DOI : 10.1016/j.future.2005.03.001
Performance Bounds for Level-Oriented Two-Dimensional Packing Algorithms, SIAM Journal on Computing, vol.9, issue.4, pp.808-826, 1980. ,
DOI : 10.1137/0209062
Smith-waterman alignment of huge sequences with gpu in linear space, Parallel & Distributed Processing Symposium (IPDPS), pp.1199-1211, 2011. ,
The International Exascale Software Project roadmap, The International Journal of High Performance Computing Applications, vol.25, issue.1, pp.3-60, 2011. ,
DOI : 10.1088/1742-6596/180/1/012045
Scheduling for Parallel Processing Computer Communications and Networks, 2009. ,
Online Non-preemptive Scheduling to Optimize Max Stretch on a Single Machine, International Conference on Computing and Combinatorics (COCOON), pp.483-495, 2016. ,
DOI : 10.1016/j.orl.2003.11.008
URL : https://hal.archives-ouvertes.fr/hal-01309052
Striped Smith-Waterman speeds database searches six times over other SIMD implementations, Bioinformatics, vol.23, issue.2, pp.156-161, 2007. ,
DOI : 10.1093/bioinformatics/btl582
URL : https://academic.oup.com/bioinformatics/article-pdf/23/2/156/536640/btl582.pdf
Improved utilization and responsiveness with gang scheduling, International Workshop on Job Scheduling Strategies for Parallel Processing (IPPS), volume 1291 of LNCS, pp.238-261, 1997. ,
DOI : 10.2172/490476
URL : https://digital.library.unt.edu/ark:/67531/metadc675997/m2/1/high_res_d/490476.pdf
Metrics for parallel job scheduling and their convergence, Job Scheduling Strategies for Parallel Processing, pp.188-206, 2001. ,
A historical application profiler for use by parallel schedulers, International Workshop on Job Scheduling Strategies for Parallel Processing (IPPS), pp.58-77, 1997. ,
DOI : 10.1007/3-540-63574-2_16
An improved algorithm for matching biological sequences, Journal of Molecular Biology, vol.162, issue.3, pp.705-708, 1982. ,
DOI : 10.1016/0022-2836(82)90398-9
Bounds on Multiprocessing Timing Anomalies, SIAM Journal on Applied Mathematics, vol.17, issue.2, pp.416-429, 1969. ,
DOI : 10.1137/0117039
Using dual approximation algorithms for scheduling problems theoretical and practical results, J. ACM, vol.34, issue.1, pp.144-162, 1987. ,
Workload evolution on the Cornell Theory Center IBM SP2, International Workshop on Job Scheduling Strategies for Parallel Processing (IPPS), pp.27-40, 1996. ,
DOI : 10.1007/BFb0022285
Core Algorithms of the Maui Scheduler, 7th International Workshop on Job Scheduling Strategies for Parallel Processing, pp.87-102, 2001. ,
DOI : 10.1007/3-540-45540-X_6
François Tessier, and Gengbin Zheng. Communication and Topology-aware Load Balancing in Charm++ with TreeMatch, 2013. ,
A reconfigurable accelerator for smith?waterman algorithm. Circuits and Systems II: Express Briefs, IEEE Transactions on, vol.54, issue.12, pp.1077-1081, 2007. ,
DOI : 10.1109/tcsii.2007.909857
Scheduling for parallel supercomputing: A historical perspective of achievable utilization, Workshop on Job Scheduling Strategies for Parallel Processing, pp.1-16, 1999. ,
Approximation Algorithms for the Weighted Independent Set Problem, International Workshop on Graph-Theoretic Concepts in Computer Science, pp.341-350, 2005. ,
DOI : 10.1007/11604686_30
URL : http://www.hi.is/~mmh/papers/WIS_WG.pdf
Scheduling Independent Tasks on Multi-cores with GPU Accelerators, 11th HeteroPar 2013, International Workshop on Algorithms , Models and Tools for Parallel Computing on Heterogeneous Platforms, in conjuction with the Euro-Par 2013 conference, 2013. ,
DOI : 10.1007/978-3-642-54420-0_23
URL : https://hal.archives-ouvertes.fr/hal-00921357
Approximability and Nonapproximability Results for Minimizing Total Flow Time on a Single Machine, SIAM Journal on Computing, vol.28, issue.4, pp.1155-1166, 1999. ,
DOI : 10.1137/S0097539796305778
Minimizing the stretch when scheduling flows of divisible requests, Journal of Scheduling, vol.3, issue.1, pp.381-404, 2008. ,
DOI : 10.1145/322092.322101
URL : https://hal.archives-ouvertes.fr/hal-00789419
Approximating total flow time on parallel machines, Journal of Computer and System Sciences, vol.73, issue.6, pp.875-891, 2007. ,
DOI : 10.1016/j.jcss.2006.10.018
Task mapping stencil computations for non- 112 contiguous allocations, ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), pp.377-378, 2014. ,
DOI : 10.1145/2692916.2555277
The ANL/IBM SP scheduling system, International Workshop on Job Scheduling Strategies for Parallel Processing (IPPS), pp.295-303, 1995. ,
DOI : 10.1007/3-540-60153-8_35
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions, BMC Research Notes, vol.3, issue.1, p.93, 2010. ,
DOI : 10.1186/1756-0500-3-93
A new online method for scheduling independent tasks, IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01527746
Contiguity and Locality in Backfilling Scheduling, 2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 2015. ,
DOI : 10.1109/CCGrid.2015.143
URL : https://hal.archives-ouvertes.fr/hal-01230294
Online non-preemptive scheduling in a resource augmentation model based on duality, European Symposium on Algorithms (ESA) Schloss Dagstuhl -Leibniz- Zentrum fuer Informatik, pp.1-63, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01334219
Knapsack Problems: Algorithms and Computer Implementations, Series in Discrete Mathematics and Optimization, 1990. ,
A high-performance heterogeneous computing platform for biological sequence analysis. Parallel and Distributed Systems, IEEE Transactions on, vol.21, issue.9, pp.1267-1280, 2010. ,
Sequence and genome analysis, Bioinformatics, issue.2, 2004. ,
Utilization, predictability, workloads, and user runtime estimates in scheduling the ibm sp2 with backfilling, IEEE Transactions on Parallel and Distributed Systems, vol.12, issue.6, pp.529-543, 2001. ,
Online Scheduling to Minimize Average Stretch, SIAM Journal on Computing, vol.34, issue.2, pp.433-452, 2004. ,
DOI : 10.1137/S0097539701387544
Effects of topologyaware allocation policies on scheduling performance, 14th International Workshop on Job Scheduling Strategies for Parallel Processing, pp.138-156, 2009. ,
Rapid and sensitive sequence comparison with fastp and fasta, Methods in enzymology, vol.183, pp.63-98, 1990. ,
Space and time optimal parallel sequence alignments. Parallel and Distributed Systems, IEEE Transactions on, vol.15, issue.12, pp.1070-1081, 2004. ,
DOI : 10.1109/tpds.2004.86
Resource constrained scheduling on multiple machines, Information Processing Letters, vol.91, issue.4, pp.177-182, 2004. ,
DOI : 10.1016/j.ipl.2004.04.009
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation, BMC Bioinformatics, vol.12, issue.1, p.221, 2011. ,
DOI : 10.1016/j.ygeno.2010.03.001
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-221?site=bmcbioinformatics.biomedcentral.com
Maximizing Throughput of Overprovisioned HPC Data Centers Under a Strict Power Budget, SC14: International Conference for High Performance Computing, Networking, Storage and Analysis, pp.807-818, 2014. ,
DOI : 10.1109/SC.2014.71
A Hybrid Computational Grid Architecture for Comparative Genomics, IEEE Transactions on Information Technology in Biomedicine, vol.12, issue.2, pp.218-225, 2008. ,
DOI : 10.1109/TITB.2007.908462
Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems, 2011 5th International Conference on Bioinformatics and Biomedical Engineering, pp.1-4, 2011. ,
DOI : 10.1109/icbbe.2011.5780005
The EASY ??? LoadLeveler API project, International Workshop on Job Scheduling Strategies for Parallel Processing (IPPS), pp.41-47, 1996. ,
DOI : 10.1007/BFb0022286
Identification of common molecular subsequences, Journal of molecular biology, vol.147, issue.1, pp.195-197, 1981. ,
Various optimizers for single-stage production, Naval Research Logistics Quarterly, vol.2, issue.1-2, pp.59-66, 1956. ,
DOI : 10.1002/nav.3800030106
SWPS3 ??? fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ??86/SSE2, BMC Research Notes, vol.1, issue.1, p.107, 2008. ,
DOI : 10.1186/1756-0500-1-107
URL : https://doi.org/10.1186/1756-0500-1-107
WSPT's Competitive Performance for Minimizing the Total Weighted Flow Time: From Single to Parallel Machines, Mathematical Problems in Engineering, vol.2013, 1155. ,
DOI : 10.1137/S089548019936223X
SLURM: Simple Linux Utility for Resource Management, 9th International Workshop on Job Scheduling Strategies for Parallel Processing, pp.44-60, 2003. ,
DOI : 10.1007/10968987_3
URL : http://www.cs.huji.ac.il/~feit/parsched/p-03-3.ps.gz