High-performance parallel computing with cloud and cloud technologies

Cloud Computing and Software Services: Theory and Techniques

Volumn , Issue , 2010, Pages 275-308

  Ekanayake, Jaliya ^a,b   Qiu, Xiaohong ^a   Gunarathne, Thilina ^a,b   Beason, Scott ^a   Fox, Geoffrey ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FILE ORGANIZATION; PLATFORM AS A SERVICE (PAAS);

CLOUD TECHNOLOGIES; COMMUNICATION FRAMEWORK; HADOOP DISTRIBUTED FILE SYSTEM (HDFS); HIGH PERFORMANCE PARALLEL COMPUTING; INFRASTRUCTURE SERVICES; MAP-REDUCE; RUNTIMES;

INFRASTRUCTURE AS A SERVICE (IAAS);

EID: 85015814074     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/EBK1439803158     Document Type: Chapter

References (44)

1. Amazon.com, Inc. 2009. Simple Storage Service (S3). http://aws.amazon.com/s3
2. ASF. 2009a. Apache Hadoop Core. http://hadoop.apache.org/core
3. ASF. 2009b. Apache Hadoop Pig. http://hadoop.apache.org/pig/
4. Barham, P., B. Dragovic et al. 2003. Xen and the art of virtualization. Proceedings of the 19th ACM Symposium on Operating Systems Principles, Bolton Landing, NY.
5. Batzer, M.A. and P.L. Deininger. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3(5): 370-379.
6. Condor Team. 2009. Condor DAGMan. http://www.cs.wisc.edu/condor/dagman/
7. Dean, J. and S. Ghemawat. 2008. MapReduce: Simplified data processing on large clusters. Commun. ACM 51(1): 107-113.
8. Dongarra, J., C.A. Geist et al. 1993. Integrated PVM framework supports heterogeneous network computing. Comput. Phys. 7(2): 166-175.
9. Ekanayake, J., S. Pallickara et al. 2008. MapReduce for data intensive scientific analyses. IEEE Fourth International Conference on eScience '08, Indianapolis, IN.
10. ElasticHosts Ltd. 2009. Cloud Hosting. http://www.elastichosts.com/
11. Ericsson 2009. Erlang programming language. http://www.erlang.org/
12. Evangelinos, C. and C. Hill. 2008. Cloud computing for parallel scientific HPC applications: Feasibility of running coupled atmosphere-ocean climate models on Amazon’s EC2. The First Workshop on Cloud Computing and its Applications (CCA’08), Chicago, IL.
13. Forum, MPI. MPI (Message Passing Interface). http://www.mcs.anl.gov/research/projects/mpi/
14. Foster, I. 2001. The anatomy of the grid: Enabling scalable virtual organizations. Int. J. Supercomput. Appl. 15: 200-222.
15. Fox, G.C., A. Hey, and S. Otto. 1987. Matrix algorithms on the hypercube I: Matrix multiplication. Parallel Comput. 4: 17.
16. Fox, G., S. Bae et al. 2008. Parallel data mining from multicore to cloudy grids. Proceedings of the International Advanced Research Workshop on High Performance Computing and Grids (HPC2008), Cetraro, Italy.
17. Gabriel, E., G.E. Fagg et al. 2004. Open MPI: Goals, concept, and design of a next generation MPI implementation. Proceedings of the 11th European PVM/MPI Users’ Group Meeting. Budapest, Hungary.
18. Gavrilovska, A., S. Kumar et al. March 2007. Abstract high-performance hypervisor architectures: Virtualization in HPC systems. Proceedings of the HPCVirt 2007, Lisbon, Portugal.
19. Ghemawat, S., H. Gobioff et al. 2003. The Google file system. SIGOPS Oper. Syst. Rev. 37(5): 29-43.
20. Gotoh, O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162: 705-708.
21. Gu, Y. and R.L. Grossman. 2009. Sector and sphere: The design and implementation of a high-performance data cloud. Philos. Trans. A: Math Phys. Eng. Sci. 367(1897): 2429-2445.
22. Huang, X. and A. Madan. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9(9): 868-877.
23. Hull, D., K. Wolstencroft et al. 2006. Taverna: A tool for building and running workflows of services. Nucleic Acids Res. 34(Web Server issue): W729-32.
24. Isard, M., M. Budiu et al. 2007. Dryad: Distributed data-parallel programs from sequential building blocks. SIGOPS Oper. Syst. Rev. 41(3): 59-72.
25. Johnsson, S.L., T. Harris et al. 1989. Matrix multiplication on the connection machine. Proceedings of the 1989 ACM/IEEE Conference on Supercomputing, Reno, NV. ACM, New York.
26. Jurka, J. 2000. Repbase update: A database and an electronic journal of repetitive elements. Trends Genet. 9:418-420.
27. Keahey, K., I. Foster et al. 2005. Virtual workspaces: Achieving quality of service and quality of life in the Grid. Sci. Program. 13(4): 265-275.
28. Ludscher, B., I. Altintas et al. 2006. Scientific workflow management and the Kepler system [research articles]. Concurr. Comput. Pract. Exp. 18(10): 1039-1065.
29. Macqueen, J. 1967. Some methods for classification and analysis of multivariate observations. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Vol. 1: Statistics, Berkeley, CA, pp. 281-297.
30. Moretti, C., H. Bui et al. 2009. All-pairs: An abstraction for data intensive computing on campus grids. IEEE Trans. Parallel Distrib. Syst. 21(1): 33-46.
31. Nokia. 2009. Disco project. http://discoproject.org/
32. Nurmi, D., R. Wolski et al. 2009. The eucalyptus open-source cloud-computing system. Proceedings of the Ninth IEEE/ACM International Symposium on Cluster Computing and the Grid, Shanghai, China.
33. Pallickara, S. and G. Fox. 2003. NaradaBrokering: A distributed middleware framework and architecture for enabling durable peer-to-peer grids. Proceedings of the ACM/IFIP/USENIX 2003 International Conference on Middleware, Rio de Janeiro, Brazil. Springer-Verlag, New York.
34. Pallickara, S. L. and M. Pierce. 2008. SWARM: Scheduling large-scale jobs over the looselycoupled HPC clusters. Proceedings of the IEEE Fourth International Conference on eScience '08 (eScience, 2008), Indianapolis, IN.
35. Pike, R., S. Dorward et al. 2005. Interpreting the data: Parallel analysis with Sawzall. Sci. Program. 13(4): 277-298.
36. Raicu, I., Y. Zhao et al. 2007. Falkon: A fast and light-weight tasK executiON framework. Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, Reno, NV. ACM, New York.
37. ServePath. 2009. GoGrid Cloud Hosting. http://www.gogrid.com/
38. Smith, T.F. and M.S. Waterman. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
39. Smith, A.F.A., R. Hubley, and P. Green. 2004. Repeatmasker. http://www.repeatmasker.org
40. Smith Waterman Software. http://jaligner.sourceforge.net/naligner/
41. Vermorel, J. 2005. NAligner (Smith Waterman software with Gotoh enhancement). http://jaligner.sourceforge.net/naligner/
42. Walker, E. 2008. Benchmarking Amazon EC2 for high-performance scientific computing. http://www.usenix.org/publications/login/2008-10/openpdfs/walker.pdf.
43. Youseff, L., R. Wolski et al. 2006. Evaluating the performance impact of Xen on MPI and process execution for HPC systems. Proceedings of the First International Workshop on Virtualization Technology in Distributed Computing, Tampa, FL.
44. Yu, Y., M. Isard et al. 2008. DryadLINQ: A system for general-purpose distributed dataparallel computing using a high-level language. Proceedings of the Symposium on Operating System Design and Implementation (OSDI), San Diego, CA.