Parallelization of nonuniform loops in supercomputers with distributed memory
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A template algorithm for parallel execution of independent iterations of the repetitive loop on a multiprocessor computer with distributed memory is constructed. Regardless of the number of processors, the algorithm must provide efficient utilization of computing capacity under essentially different complexities of iterations and/or performance of processors. The interprocessor data communication and control of parallel computations are assumed to be implemented using a standard message-passing interface (MPI), which is widely used in such systems. Existing methods for the loop parallelization are analyzed and the corresponding efficiencies are empirically estimated for various models of iteration nonuniformity.
Keywordshigh-performance computing parallelization distributed memory MPI nonuniform loops
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- 1.The OpenMP API specification for parallel programming http://openmp.org/wp/
- 2.Message-passing Interface Forum. MPI Documents http://www.mpi-forum.org/docs/docs.html
- 3.CENTAUR Software Tools for Hybrid Supercomputing http://centaur.botik.ru/home
- 4.Joint Supercomputer Center of Russian Academy Science. Computing Systems http://www.jscc.ru/scomputers.shtml
- 5.O. A. Zverkov, A. V. Seliverstov, and V. A. Lyubetskii, “Albuminous families typical of plastoms of small taxonomic groups of algas and protozoa,” Molekulyar. Biologiya 46, 799–809 (2012).Google Scholar
- 6.V. A. Lyubetsky, L. I. Rubanov, and A. V. Seliverstov, “Lack of conservation of bacterial type promoters in plastids of Streptophyta,” Biology Direct 5(34) (2010).Google Scholar
- 7.V. A. Lyubetsky, O. A. Zverkov, L. I. Rubanov, and A. V. Seliverstov, “Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level,” Biology Direct 6(3) (2011).Google Scholar
- 8.V. A. Lyubetsky, O. A. Zverkov, S. A. Pirogov, L. I. Rubanov, and A. V. Seliverstov, “Modeling RNA polymerase interaction in mitochondria of chordates,” Biology Direct 7(26) (2012).Google Scholar
- 9.V. A. Lyubetsky, L. I. Rubanov, L. Yu. Rusin, and K. Yu. Gorbunov, “Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios,” Biology Direct 7(48) (2012).Google Scholar