Two-Level Parallelism to Accelerate Multiple Genome Comparisons

• Published in: Euro-Par 2016: Parallel Processing Workshops Vol. 10104; pp. 445 - 456
• Main Authors: Torreno, Oscar, Trelles, Oswaldo
• Format: Book Chapter
• Language: English
• Published: Switzerland Springer International Publishing AG 2017; Springer International Publishing
• Series: Lecture Notes in Computer Science
• Subjects: Execution Time; Genome Comparison; Input Sequence; Parallelization Level; Parallelization Strategy
• ISBN: 9783319589428; 3319589423
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-319-58943-5_36

We present a two-level parallel strategy focused in the enhancement of GECKO software for multiple and pairwise genome comparisons. GECKO was developed to break the computational barriers on search space and memory demands faced by equivalent software. However, although being faster than equivalent software for comparing long sequences, its execution time attracted our interest to develop a parallel strategy. Additionally, the execution time is even higher in multiple genome comparisons where several independent pairwise comparisons are typically performed sequentially. After a careful study of the internal data dependencies of the GECKO modules, we noticed that most of them were subject to an easy and efficient parallelization. The result is a two-level parallel approach to accelerate multiple genome comparisons. The first level is aimed at parallelizing each independent pairwise genome comparison of a multiple comparison study to a different core. This level is application-independent, we are using GECKO but any other equivalent software can be used. The second level consists on the internal parallelization of GECKO modules with evident enhancements in performance while results remain invariant. After solving the problems of combining the big amount of I/O operations overlapped with computation, the obtained speedups reflect the good efficiency of the devised strategy.