Transparent runtime parallelization of the R scripting language

Journal of Parallel and Distributed Computing

Volumn 71, Issue 2, 2011, Pages 157-168

  Li, Jiangtian ^a   Ma, Xiaosong ^b,c   Yoginath, Srikanth ^c   Kora, Guruprasad ^c   Samatova, Nagiza F ^b,c  

^a MICROSOFT   (United States)

^b North Carolina State University   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Incremental analysis; Runtime parallelization; Scripting languages

Indexed keywords

CODE ANALYSIS; CODE MODIFICATIONS; DATA ANALYSIS; DATA PARALLELISM; DATA VOLUME; EVALUATION RESULTS; FILE ACCESS; INCREMENTAL ANALYSIS; NOVEL TECHNIQUES; PARALLELIZATIONS; PARALLELIZING COMPILER; PROGRAM DEPENDENCE; RUNTIMES; SCIENTIFIC DATA PROCESSING; SCIENTIFIC WORKFLOWS; SCRIPTING LANGUAGES; SEQUENTIAL DATA; SOURCE CODES; STATISTICAL COMPUTING; USE PATTERNS;

DATA FLOW ANALYSIS; PARALLEL ARCHITECTURES; PROGRAM COMPILERS;

DATA HANDLING;

EID: 78650418266     PISSN: 07437315     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jpdc.2010.08.013     Document Type: Article

References (44)

1. V. Adve, G. Jin, J. Mellor-Crummey, Q. Yi, High performance Fortran compilation techniques for parallelizing scientific codes, in: Supercomputing'98: Proceedings of the 1998 ACM/IEEE Conference on Supercomputing, CDROM, 1998.
2. G. Almasi, D. Padua, MaJIC: compiling MATLAB for speed and responsiveness, in: PLDI'02: Proceedings of the ACM SIGPLAN 2002 Conference on Programming Language Design and Implementation, 2002. (Pubitemid 34991527)
3. D.F. Bacon, S.L. Graham, and O.J. Sharp Compiler transformations for high-performance computing ACM Computing Surveys 1994
4. V. Balasundaram, K. Kennedy, A technique for summarizing data access and its use in parallelism enhancing transformations, in: PLDI'89: Proceedings of the ACM SIGPLAN 1989 Conference on Programming Language Design and Implementation, 1989, pp. 4153.
5. U. Banerjee, R. Eigenmann, A. Nicolau, and D.A. Padua Automatic program parallelization Proceedings of the IEEE 1993 (Pubitemid 23675613)
6. W. Blume, R. Eigenmann, K. Faigin, J. Grout, J. Hoeflinger, D. Padua, P. Petersen, B. Pottenger, L. Rauchwerger, P. Tu, S. Weatherford, Polaris: the next generation in parallelizing compilers, in: Proceedings of the Seventh Workshop on Languages and Compilers for Parallel Computing, 1994.
7. S. Chakrabarti, J. Demmel, and K.A. Yelick Models and scheduling algorithms for mixed data and task parallel programs Journal of Parallel and Distributed Computing 1997 (Pubitemid 127174399)
8. M.K. Chen, K. Olukotun, The jrpm system for dynamically parallelizing java programs, in: ISCA'03: Proceedings of the 30th Annual International Symposium on Computer Architecture, 2003.
9. D. Chen, J. Torrellas, P. Yew, An efficient algorithm for the run-time parallelization of DOACROSS loops, in: Supercomputing, 1994.
10. J. Choi, J. Dongarra, R. Pozo, D. Walker, Scalapack: a scalable linear algebra library for distributed memory concurrent computers, in: Proceedings of the 4th Symposium on the Frontiers of Massively Parallel Computation, 1992.
11. R. Choy, and A. Edelman Parallel MATLAB: doing it right Proceedings of the IEEE 93 2 2005 (Pubitemid 40851228)
12. R. Choy, A. Edelman, J.R. Gilbert, V. Shah, D. Cheng, Star-P: high productivity parallel computing, in: Proceedings of the Eighth Annual Workshop on High Performance Embedded Computing, HPEC 2004, 2004.
13. T. Cramer, R. Friedman, T. Miller, D. Seberger, R. Wilson, and M. Wolczko Compiling Java just in time IEEE Micro 17 3 1997 (Pubitemid 127563938)
14. C. Ding, Y. Zhong, Predicting whole-program locality through reuse distance analysis, in: PLDI'03: Proceedings of the ACM SIGPLAN 2003 Conference on Programming Language Design and Implementation, 2003, pp. 245257.
15. Z. Du, C. Lim, X. Li, C. Yang, Q. Zhao, T. Ngai, A cost-driven compilation framework for speculative parallelization of sequential programs, in: Proceedings of the ACM SIGPLAN 2004 Conference on Programming Language Design and Implementation, 2004.
16. J. Garvin, Rcc: a compiler for the R language for statistical computing, Master's Thesis, Rice University, Houston, TX, 2004.
17. B. Grant, M. Philipose, M. Mock, C. Chambers, S. Eggers, An evaluation of staged run-time optimizations in DyC, in: Proceedings of the ACM SIGPLAN 1999 Conference on Programming Language Design and Implementation, 1999. (Pubitemid 129686097)
18. M. Gupta, R. Nim, Techniques for speculative run-time parallelization of loops, in: Supercomputing'98: Proceedings of the 1998 ACM/IEEE Conference on Supercomputing, CDROM, 1998.
19. M. Haldar, A. Nayak, A. Kanhere, P.G. Joisha, N. Shenoy, A.N. Choudhary, P. Banerjee, Match virtual machine: an adaptive runtime system to execute MATLAB in parallel, in: International Conference on Parallel Processing, ICPP'00, 2000.
20. M.W. Hall, S.P. Amarasinghe, B.R. Murphy, S. Liao, and M.S. Lam Interprocedural parallelization analysis in SUIF ACM Transactions on Programming Languages and Systems 2005 (Pubitemid 43942503)
21. J. Li, X. Ma, K. Singh, M. Schulz, B.R. de Supinski, S.A. McKee, Machine learning based online performance prediction for runtime parallelization and task scheduling, in: IEEE International Symposium on Performance Analysis of Systems and Software, ISPASS, 2009.
22. J. Li, X. Ma, S. Yoginath, G. Kora, N. Samatova, Automatic, transparent runtime parallelization of the R scripting language, Tech. Rep. TR-2007-3, 2007.
23. X. Ma, J. Li, N.F. Samatova, Automatic parallelization of scripting languages: toward transparent desktop parallel computing, in: The Next Generation Software Workshop, NSFNGS, Held in Conjunction with IPDPS, 2007. (Pubitemid 47428595)
24. Matlab. http://www.mathworks.com/.
25. D.E. Maydan, J.L. Hennessy, M.S. Lam, Efficient and exact data dependence analysis, in: PLDI'91: Proceedings of the ACM SIGPLAN 1991 Conference on Programming Language Design and Implementation, 1991.
26. P. Miller, Parallel, distributed scripting with python, in: The Third LCI International Conference on Linux Clusters, 2002.
27. Message passing interface forum, in: MPI: Message-Passing Interface Standard, June 1995.
28. OpenMP. http://www.openmp.org/drupal/.
29. W. Pugh, Uniform techniques for loop optimization, in: ICS'91: Proceedings of the 5th International Conference on Supercomputing, 1991.
30. M.J. Quinn, A.G. Malishevsky, N. Seelam, Y. Zhao, Preliminary results from a parallel MATLAB compiler, in: Proceedings of the First Merged International Parallel Processing Symposium and Symposium on Parallel and Distributed Processing, 1998.
31. L. Rauchwerger Run-time parallelization: its time has come Parallel Computing 1998 (Pubitemid 128413650)
32. R Development Core Team, R: a language and environment for statistical computing, 2009, ISBN: 3-900051-07-0. http://www.R-project.org.
33. A. Rogers, and K. Pingali Compiling for distributed memory architectures IEEE Transactions on Parallel and Distributed Systems 5 3 1994 281 298
34. A. Rossini, L. Tierney, N. Li, Simple parallel statistical computing in R, UW Biostatistics Working Paper Series.
35. J.H. Saltz, R. Mirchandaney, and K. Crowley Run-time parallelization and scheduling of loops IEEE Transactions on Computers 1991 (Pubitemid 21675674)
36. N. Samatova High performance statistical computing with parallel R: applications to biology and climate modelling Journal of Physics: Conference Series 46 2006 (Pubitemid 44461040)
37. M. Schwartz, N. Delisle, V.S. Begwani, Incremental compilation in magpie, in: Proceedings of the 1984 SIGPLAN Symposium on Compiler Construction, 1984.
38. F.J. Seinstra, D. Koelma, J.M. Geusebroek, A software architecture for user transparent parallel image processing on MIMD computers, in: Proceedings of the International Conference on Parallel and Distributed Computing, Euro-Par 2001, 2001. (Pubitemid 33326607)
39. A. Silberstein, A. Gelfand, K. Munagala, G. Puggioni, J. Yang, Making sense of suppressions and failures in sensor data: a Bayesian approach, in: Proceedings of the 33rd International Conference on Very Large Data Bases, 2007.
40. taskPR: task-parallel R package. http://cran.r-project.org/src/contrib/ Descriptions/taskPR.html.
41. L. Tierney, Simple network of workstations for R. http://www.stat.uiowa. edu/luke/R/cluster/cluster.html.
42. R. Triolet, P. Feautrier, F. Irigoin, Automatic parallelization of FORTRAN programs in the presence of procedure calls, in: ESOP'86: Proceedings of the European Symposium on Programming, 1986. (Pubitemid 18668277)
43. T. Yang, and A. Gerasoulis Pyrros: static task scheduling and code generation for message passing multiprocessors ICS'92: Proceedings of the 6th International Conference on Supercomputing 1992 ACM Press New York, NY, USA 428 437 http://doi.acm.org/10.1145/143369.143446
44. S. Yoginath, N. Samatova, D. Bauer, G. Kora, G. Fann, A. Geist, RScaLAPACK: high performance parallel statistical computing with R and ScaLAPACK, in: Proceedings of the 18th International Conference on Parallel and Distributed Computing Systems, 2005.